MON_LIB (CCP4: Library)

NAME

mon_lib - multi-purpose dictionary for macromolecules

Version 3.0.1 /31.05.00

CONTENTS

DESCRIPTION

Introduction

This dictionary can be use for several purposes: refinement, graphics, validation. The extended mmCIF format makes the dictionary self-explanatory, easy to adapt and to add new information.

The LIBCHECK program was developed to manage and check the information in the dictionary, and can also create new dictionary entries from different sources: PDB, CDS, CIF, SMILE.

Dictionary

MON_LIB defines:

  1. the chemical structure of the monomers (atom types, bond lengths, angles, chirality, planarity)
  2. the tree-like structure of each monomer
  3. the possible links between monomers (peptide bond, disulfide bridges, ...)
  4. the possible modifications of monomers (e.g. termini of polypeptide chains, ...)

All this information is constant, i.e. independent of the conformation of the molecule. A CIFile, describing a macromolecule, must contain the variable information (coordinates, occupancy, B-factors) and the list of modifications to and links between actual monomers.

The information about the names of chains and monomers, and the serial numbers of monomers for the links must be present in the CIFile or PDB file of coordinates.

The values for the amino acid bond lengths and angles have been taken from Engh and Huber, Acta Cryst. A47, 392-400 (1991).
The values for the purine and pyrimidine bond lengths and angles have been taken from O. Kennard & R. Taylor (1982), J. Am. Soc. Chem. vol. 104, pp. 3209-3212.
The values for the sugar-phosphate backbone bond lengths and bond angles have been taken from the W. Saenger's "Principles of Nucleic Acid Structure" (1983), Springer-Verlag, pp. 70,86.

Description of monomer

Definition:

A monomer is a set of atoms connected by bonds, or a single atom.

For example, it may be an amino acid, a polypeptide chain, or a polypeptide chain and a substrate connected by hydrogen bonds.

It is useful for some programs (dynamics, graphics and so on) to define a tree-like structure of the monomers. The specification for each atom of the monomer of a 'back atom' and a 'forward atom' defines the tree-like structure of the monomer. The 'back atom' of a given atom is its preceding atom in the tree. If an atom has some forward branches, their order is

  1. the first one is the shortest branch;
  2. the last one is the backbone branch or the longest branch.
The 'forward atom' of a given atom is an atom of the last branch. The first and the last atom of the tree must be a non-hydrogen atom.

The following categories describe the monomers:

_chem_comp.
list of the monomers with their general description (name, type, number of atoms):
_chem_comp.id
monomer identifier
_chem_comp.one_letter_code
one letter code of the monomer
_chem_comp.name
full name of the monomer
_chem_comp.type
type of the monomer:
  • "D-peptide"
  • "L-peptide"
  • "DNA"
  • "RNA"
  • "D-saccharide"
  • "L-saccharide"
  • "solvent"
  • "non-polymer"
_chem_comp.number_atoms_all
number of atoms in the monomer
_chem_comp.number_atoms_nh
number of non-hydrogen atoms in the monomer
_chem_comp_synonym.
for each monomer, the list of the synonyms of names of monomers and atoms
_chem_comp_synonym.comp_id
_chem_comp_synonym.comp_alternative_id
_chem_comp_synonym.mod_id
_chem_comp_synonym.atom_id
_chem_comp_synonym.atom_alternative_id
_chem_comp_atom.
for each monomer, the list of the atoms and their types
_chem_comp_atom.comp_id
monomer identifier
_chem_comp_atom.atom_id
atom name
_chem_comp_atom.type_symbol
element symbol
_chem_comp_atom.type_energy
the atom type; it is used in the energetic parameters library ener_lib
_chem_comp_atom.charge
charge assigned to atom
_chem_comp_tree.
for each monomer the definition of its tree-like structure
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
previous atom in the tree-like structure of the monomer; for the first atom the value is '.'
_chem_comp_tree.back_type
_chem_comp_tree.atom_forward
forward atom in the tree-like structure of the monomer; if the atom hasn't a forward atom the value is '.'; the value of the last atom of the tree must be 'END'
_chem_comp_tree.additional_connect_atom_id_1
_chem_comp_tree.additional_connect_atom_id_2
_chem_comp_tree.additional_connect_type
_chem_comp_bond.
for each monomer, the list of bonds and their standard value
_chem_comp_bond.comp_id
monomer identifier
_chem_comp_bond.atom_id_1, _chem_comp_bond.atom_id_2
the two atoms that form a bond
_chem_comp_bond.type
the chemical type of the bond: "coval", "disulf", "soltbr", "hydrog", "metal".
_chem_comp_bond.value_dist
standard bond length in angstroms
_chem_comp_bond.value_dist_esd
standard deviation of the bond length
_chem_comp_angle.
for each monomer, the list of the valence angles and their standard value
_chem_comp_angle.chem_id
monomer identifier
_chem_comp_angle.atom_id_1, _chem_comp_angle.atom_id_2, _chem_comp_angle.atom_id_3
the angles are designated by three atoms, with the second atom forming the vertex of the angle
_chem_comp_angle.value_angle
standard value of the angle in degrees
_chem_comp_angle.value_angle_esd
standard deviation of the angle value
_chem_comp_tor.
for each monomer, the list of torsion angles, their label and their standard value; an angle may be variable or constant; the label gives the standard name for variable angles, it is '.' for constant angles; the order of atoms must follow the tree-like structure.
_chem_comp_tor.comp_id
monomer identifier
_chem_comp_tor.label
torsion label, it must uniquely identify a torsion angle if it is variable; if the torsion angles is constant the value of label must be equal to '.'
_chem_comp_tor.atom_id_1, _chem_comp_tor.atom_id_2, _chem_comp_tor.atom_id_3, _chem_comp_tor.atom_id_4
the four atoms that form a torsion
_chem_comp_tor.value_angle
standard value of the angle in degrees; the value of variable angles is arbitrary and describes some conformation
_chem_comp_tor.value_angle_esd
standard deviation of the angle value
_chem_comp_tor.period
_chem_comp_chir.
the chirality of monomer atoms and the type of the chirality. Chirality:
         Let the vector direction atom_1 to atom_2 be v1, 
         the vector direction atom_1 to atom_3 be v2, 
         the vector direction atom_1 to atom_4 be v3;
         the chiral volume is the volume of the parallelepiped 
         formed by the three vectors: v1,v2,v3.
 
            VOLUME = v1 . [ v2 x v3 ]
The type is the sign of the chiral volume
_chem_comp_chir.comp_id
monomer identifier
_chem_comp_chir.atom_id_1, _chem_comp_chir.atom_id_2, _chem_comp_chir.atom_id_3, _chem_comp_chir.atom_id_4
the atom designated by_chem_comp_chir.atom_id_1 is the chiral atom; the atoms bonded to the chiral atom are specified by _chem_comp_chir.atom_id_2, _lib_mon_chiral_atom_id_3 and _chem_comp_chir.atom_id_4
_chem_comp_chir.volume_sign
the value of type must be equal 'positive' or 'negative'
_chem_comp_plane.
the list of the atoms lying in the same plane and their standard deviation from the plane
_chem_comp_plane.comp_id
monomer identifier
_chem_comp_plane.id
the label must uniquely identify a plane in a monomer
_chem_comp_plane.atom_id
an atom of the plane
_chem_comp_plane.esd
standard deviation of the atom distance to the plane

Description of links

Categories to describe the type of links between two atoms of different monomers. They describe only the type of the link, the atom names and the monomer flags. The information about the names of the chains and monomers, and the serial numbers of the monomers is given in the CIFile.

The monomer flag designates the first or the second monomer in the category _entity_link_ having its value given in the CIFile.

                        _entity_link_id
                        _entity_link_entity_id_1
                        _entity_link_mon_id_1
                        _entity_link_set_num_1
                        _entity_link_entity_id_2
                        _entity_link_mon_id_2
                        _entity_link_set_num_2
                        SS  Ach  CYS  20  Cch  CYS  40

The link "TRANS" is the default for polypeptide chain, "pd", the default for DNA, "pr", the default for RNA.

_chem_link.
_chem_link.link_id
_chem_link.one_letter_code
_chem_link.name
_chem_link.comp_id_1
_chem_link.type_comp_1
_chem_link.mod_id_1
_chem_link.comp_id_2
_chem_link.type_comp_2
_chem_link.mod_id_2
_chem_link_tree.
_chem_link_tree.link_id
_chem_link_tree.atom_comp_id
_chem_link_tree.atom_id
_chem_link_tree.atom_back_comp_id
_chem_link_tree.atom_back
_chem_link_tree.back_type
_chem_link_tree.atom_forward_comp_id
_chem_link_tree.atom_forward
_chem_link_tree.additional_connect_atom_1_comp_id
_chem_link_tree.additional_connect_atom_id_1
_chem_link_tree.additional_connect_atom_2_comp_id
_chem_link_tree.additional_connect_atom_id_2
_chem_link_tree.additional_connect_type
_chem_link_bond.
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
_chem_link_angle.
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
_chem_link_tor.
_chem_link_tor.link_id
_chem_link_tor.label
_chem_link_tor.atom_1_comp_id
_chem_link_tor.atom_id_1
_chem_link_tor.atom_2_comp_id
_chem_link_tor.atom_id_2
_chem_link_tor.atom_3_comp_id
_chem_link_tor.atom_id_3
_chem_link_tor.atom_4_comp_id
_chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
_chem_link_chir.
_chem_link_chir.link_id
_chem_link_chir.atom_1_comp_id
_chem_link_chir.atom_id_1
_chem_link_chir.atom_2_comp_id
_chem_link_chir.atom_id_2
_chem_link_chir.atom_3_comp_id
_chem_link_chir.atom_id_3
_chem_link_chir.atom_4_comp_id
_chem_link_chir.atom_id_4
_chem_link_chir.volume_sign
_chem_link_plane.
_chem_link_plane.link_id
_chem_link_plane.id
_chem_link_plane.atom_comp_id
_chem_link_plane.atom_id
_chem_link_plane.esd

Description of modifications

Categories to describe the possible modifications of monomers: the 'function' (add, delete, change), and the atoms, bonds, angles, chirality, planarity that will be modified. The information about the names and serial numbers of monomers is described in the CIFile. For example:

                        _entity_mod_id
                        _entity_mod_entity_id 
                        _entity_mod_mon_id 
                        _entity_mod_set_num
                        COO  Cchain  CYS  30

The modifications "NH3" and "COO" are the default for the polypeptide chain termini.
The modifications "d5*END" and "d3*END" are the default for DNA termini.
The modifications "r5*END" and "r3*END" are default for RNA termini.

_chem_mod.
_chem_mod.mod_id
identifier of the modification
_chem_mod.one_letter_code
_chem_mod.name
_chem_mod.sub_mod_id
_chem_mod.sub_mod_order
_chem_mod_atom.
_chem_mod_atom.mod_id
identifier of the modification
_chem_mod_atom.function
the function describing the type of modification: "add", "delete", "change"
_chem_mod_atom.atom_id
atom that will be modified
_chem_mod_atom.new_atom_id
new atom that will be added
_chem_mod_atom.new_type_energy
_chem_mod_atom.new_type_symbol
_chem_mod_atom.new_charge
_chem_mod_tree.
_chem_mod_tree.mod_id
_chem_mod_tree.function
_chem_mod_tree.atom_id
_chem_mod_tree.atom_back
_chem_mod_tree.back_type
_chem_mod_tree.atom_forward
_chem_mod_tree.additional_connect_atom_id_1
_chem_mod_tree.additional_connect_atom_id_2
_chem_mod_tree.additional_connect_type
_chem_mod_bond.
_chem_mod_bond.mod_id
_chem_mod_bond.function
_chem_mod_bond.atom_id_1
_chem_mod_bond.atom_id_2
_chem_mod_bond.new_type
_chem_mod_bond.new_value_dist
_chem_mod_bond.new_value_dist_esd
_chem_mod_angle.
_chem_mod_angle.mod_id
_chem_mod_angle.function
_chem_mod_angle.atom_id_1
_chem_mod_angle.atom_id_2
_chem_mod_angle.atom_id_3
_chem_mod_angle.new_value_angle
_chem_mod_angle.new_value_angle_esd
_chem_mod_tor.
_chem_mod_tor.mod_id
_chem_mod_tor.function
_chem_mod_tor.label
_chem_mod_tor.atom_id_1
_chem_mod_tor.atom_id_2
_chem_mod_tor.atom_id_3
_chem_mod_tor.atom_id_4
_chem_mod_tor.new_value_angle
_chem_mod_tor.new_value_angle_esd
_chem_mod_tor.new_period
_chem_mod_chir.
_chem_mod_chir.mod_id
_chem_mod_chir.function
_chem_mod_chir.atom_id_1
_chem_mod_chir.atom_id_2
_chem_mod_chir.atom_id_3
_chem_mod_chir.atom_id_4
_chem_mod_chir.new_volume_sign
_chem_mod_plane.
_chem_mod_plane.mod_id
_chem_mod_plane.function
_chem_mod_plane.id
_chem_mod_plane.atom_id
_chem_mod_plane.new_esd

EXAMPLES

Example of monomer description

 
  ---   LIST OF MONOMERS ---
 
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
. . . . 
CYS      CYS 'CYSTINE            ' L-peptide  10   6 
. . . .

 
  --- DESCRIPTION OF MONOMERS ---
 
data_comp_CYS
 
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
 CYS      N    N    NH1      -0.204
 CYS      H    H    HNH1      0.204
 CYS      CA   C    CH1       0.058
 CYS      HA   H    HCH1      0.046
 CYS      CB   C    CH2      -0.096
 CYS      HB1  H    HCH2      0.046
 CYS      HB2  H    HCH2      0.058
 CYS      SG   S    S         0.004
 CYS      C    C    C         0.318
 CYS      O    O    O        -0.422
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
 CYS      N    n/a          CA   START
 CYS      H    N            .    .
 CYS      CA   N            C    .
 CYS      HA   CA           .    .
 CYS      CB   CA           SG   .
 CYS      HB1  CB           .    .
 CYS      HB2  CB           .    .
 CYS      SG   CB           .    .
 CYS      C    CA           .    END
 CYS      O    C            .    .
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
 CYS        N    H       coval       0.860    0.020
 CYS        N    CA      coval       1.458    0.019
 CYS        CA   HA      coval       0.980    0.020
 CYS        CA   CB      coval       1.530    0.020
 CYS        CB   HB1     coval       0.970    0.020
 CYS        CB   HB2     coval       0.970    0.020
 CYS        CB   SG      coval       1.808    0.023
 CYS        CA   C       coval       1.525    0.021
 CYS        C    O       coval       1.231    0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 CYS        H    N    CA    114.000    3.000
 CYS        HA   CA   CB    109.000    3.000
 CYS        CB   CA   C     110.100    1.900
 CYS        HA   CA   C     109.000    3.000
 CYS        N    CA   HA    110.000    3.000
 CYS        N    CA   CB    110.500    1.700
 CYS        HB1  CB   HB2   110.000    3.000
 CYS        HB2  CB   SG    108.000    3.000
 CYS        HB1  CB   SG    108.000    3.000
 CYS        CA   CB   HB1   109.000    3.000
 CYS        CA   CB   HB2   109.000    3.000
 CYS        CA   CB   SG    114.400    2.300
 CYS        N    CA   C     111.200    2.800
 CYS        CA   C    O     120.800    1.700
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 CYS   chi1     N    CA   CB   SG    0.000   15.000   3
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 CYS chir_01  CA   N    CB   C       negativ

Example of modification

 
  ---   LIST OF MODIFICATIONS ---
 
data_mod_list
loop_
_chem_mod.id
_chem_mod.name
_chem_mod.comp_id
_chem_mod.group_id
. . . . 
COO      COO-terminus         .        peptide
. . . . 
 
  --- DESCRIPTION OF MODIFICATIONS ---
 
 
data_mod_COO
 
loop_
_chem_mod_atom.mod_id
_chem_mod_atom.function
_chem_mod_atom.atom_id
_chem_mod_atom.new_atom_id
_chem_mod_atom.new_type_symbol
_chem_mod_atom.new_type_energy
_chem_mod_atom.new_partial_charge
 COO      change   C    C    .    C       0.340
 COO      change   O    O    .    OC     -0.350
 COO      add      .    OXT  O    OC     -0.350
loop_
_chem_mod_tree.mod_id
_chem_mod_tree.function
_chem_mod_tree.atom_id
_chem_mod_tree.atom_back
_chem_mod_tree.atom_forward
_chem_mod_tree.connect_type
 COO      add      OXT  C          .      END
 COO      change   C    .          OXT    .
loop_
_chem_mod_bond.mod_id
_chem_mod_bond.function
_chem_mod_bond.atom_id_1
_chem_mod_bond.atom_id_2
_chem_mod_bond.new_type
_chem_mod_bond.new_value_dist
_chem_mod_bond.new_value_dist_esd
 COO      change   C     O       coval       1.231    0.020
 COO      add      C     OXT     coval       1.231    0.020
loop_
_chem_mod_angle.mod_id
_chem_mod_angle.function
_chem_mod_angle.atom_id_1
_chem_mod_angle.atom_id_2
_chem_mod_angle.atom_id_3
_chem_mod_angle.new_value_angle
_chem_mod_angle.new_value_angle_esd
 COO      change   CA    C     O     121.000    3.000
 COO      add      CA    C     OXT   121.000    3.000
loop_
_chem_mod_tor.mod_id
_chem_mod_tor.function
_chem_mod_tor.id
_chem_mod_tor.atom_id_1
_chem_mod_tor.atom_id_2
_chem_mod_tor.atom_id_3
_chem_mod_tor.atom_id_4
_chem_mod_tor.new_value_angle
_chem_mod_tor.new_value_angle_esd
_chem_mod_tor.new_period
 COO      add      psi      N    CA   C    OXT   160.00  30.0 2
loop_
_chem_mod_plane_atom.mod_id
_chem_mod_plane_atom.function
_chem_mod_plane_atom.plane_id
_chem_mod_plane_atom.atom_id
_chem_mod_plane_atom.new_dist_esd
 COO        add       oxt      C       0.020
 COO        add       oxt      CA      0.020
 COO        add       oxt      O       0.020
 COO        add       oxt      OXT     0.020

Example of link

 
  ---   LIST OF LINKS ---
 
data_link_list
loop_
_chem_link.id
_chem_link.name
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
. . . . 
SS       SS-bridge             CYS .  .        CYS .  .
TRANS    default-peptide-link  .   .  peptide  .   .  peptide
. . . .
 
  --- DESCRIPTION OF LINKS ---
 
 
data_link_SS
 
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
 SS       1 SG    2 SG      disulf      2.031    0.020
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
 SS       1 CB    1 SG    2 SG    110.000    3.000
 SS       1 SG    2 SG    2 CB    110.000    3.000
loop_
_chem_link_tor.link_id
_chem_link_tor.id
_chem_link_tor.atom_1_comp_id
_chem_link_tor.atom_id_1
_chem_link_tor.atom_2_comp_id
_chem_link_tor.atom_id_2
_chem_link_tor.atom_3_comp_id
_chem_link_tor.atom_id_3
_chem_link_tor.atom_4_comp_id
_chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
 SS    ss    1 CB   1 SG   2 SG   2 CB   90.00  10.0 2
 
data_link_TRANS
 
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
 TRANS    1 C     2 N       coval    1.329    0.014
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
 TRANS    1 O     1 C     2 N     123.000    1.600
 TRANS    1 CA    1 C     2 N     116.200    2.000
 TRANS    1 C     2 N     2 H     124.300    3.000
 TRANS    1 C     2 N     2 CA    121.700    1.800
loop_
_chem_link_tor.link_id
_chem_link_tor.id
_chem_link_tor.atom_1_comp_id
_chem_link_tor.atom_id_1
_chem_link_tor.atom_2_comp_id
_chem_link_tor.atom_id_2
_chem_link_tor.atom_3_comp_id
_chem_link_tor.atom_id_3
_chem_link_tor.atom_4_comp_id
_chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
 TRANS   psi    1 N    1 CA   1 C    2 N    160.00  30.0 2
 TRANS   omega  1 CA   1 C    2 N    2 CA   180.00  10.0 0
 TRANS   .      1 CA   1 C    2 N    2 H      0.00  10.0 0
 TRANS   phi    1 C    2 N    2 CA   2 C     60.00  20.0 3
loop_
_chem_link_plane.link_id
_chem_link_plane.plane_id
_chem_link_plane.atom_comp_id
_chem_link_plane.atom_id
_chem_link_plane.dist_esd
 TRANS   plane1    1 CA    0.02
 TRANS   plane1    1 C     0.02
 TRANS   plane1    1 O     0.02
 TRANS   plane1    2 N     0.02
 TRANS   plane2    1 C     0.02
 TRANS   plane2    2 N     0.02
 TRANS   plane2    2 CA    0.02
 TRANS   plane2    2 H     0.02

Energetic parameters

  ---------------------------------------------------
              ener_lib.cif              4-APR-95
  ---------------------------------------------------

Atom types

    -----------   Description of atom type --------     
 HEADER        C Carbon PI
 ATOMTYPE CSP  = with triple bond
 HEADER        C Carbon SP2
 ATOMTYPE C    = without hydrogen ( carbonyl C )
 ATOMTYPE C1   = connected to 1 hydrogen  
 ATOMTYPE C2   = connected to 2 hydrogens 
 ATOMTYPE CR1  = between two pyrrole units 
 ATOMTYPE CR1H = CR1 connected to 1 hydrogen ( CHA of HEME )
 ATOMTYPE CR15 = connected to 1 hydrogen in 5 atoms ring ( CE1 of HIS)
 ATOMTYPE CR16 = connected to 1 hydrogen in 6 atoms ring ( CE1 of PHE)
 ATOMTYPE CR6  = without hydrogen in 6 atoms ring 
 ATOMTYPE CR5  = without hydrogen in 5 atoms ring 
 ATOMTYPE CR56 = between two atoms in 5-6 rings ( CD2 CE2 of TRP )
 ATOMTYPE CR55 = between two atoms in 5-5 rings 
 ATOMTYPE CR66 = between two atoms in 6-6 rings 
 HEADER        C Carbon SP3
 ATOMTYPE CH1  = connected to 1 hydrogen  ( CA of most amono acids )
 ATOMTYPE CH2  = connected to 2 hydrogens ( CB of most amono acids)
 ATOMTYPE CH3  = connected to 3 hydrogens ( CD1 CD2 of LEUCINE)
 ATOMTYPE CT   = without hydrogen
 HEADER        H Hydrogen
 ATOMTYPE HCH  = hydrogen of aliphatic group
 ATOMTYPE HCR  = hydrogen of aromatic group
 ATOMTYPE HNC1 = hydrogen connected to NC1
 ATOMTYPE HNC2 = hydrogen connected to NC2
 ATOMTYPE HNC3 = hydrogen connected to NC3
 ATOMTYPE HNH1 = hydrogen connected to NH1
 ATOMTYPE HNH2 = hydrogen connected to NH2
 ATOMTYPE HNR5 = hydrogen connected to NR15
 ATOMTYPE HNR6 = hydrogen connected to NR16
 ATOMTYPE HOH1 = hydrogen connected to OH1
 ATOMTYPE HOH2 = hydrogen of water
 ATOMTYPE HSH1 = hydrogen of sulphur
 HEADER        N Nitrogen PI
 ATOMTYPE NS   = without hydrogen ( triple bond )
 ATOMTYPE NS1  = connected to 1 hydrogen
 HEADER        N Nitrogen SP2
 ATOMTYPE N    = without hydrogen ( N  of PRO )
 ATOMTYPE NC1  = connected to 1 hyd. in a charged group ( NE of ARG )
 ATOMTYPE NC2  = connected to 2 hyd. in a charged group ( NH2 of ARG )
 ATOMTYPE NH1  = connected to 1 hydrogen ( N of main chain )
 ATOMTYPE NH2  = connected to 2 hydrogen ( NE2 of GLU )
 ATOMTYPE NPA  = without hydrogen ( NA and NC of HEME )
 ATOMTYPE NPB  = without hydrogen ( NB and ND of HEME )
 ATOMTYPE NRD5 = without hydrogen but with electronic doublet in 5 atoms ring
 ATOMTYPE NRD6 = without hydrogen but with electronic doublet in 6 atoms ring 
 ATOMTYPE NR15 = connected to 1 hyd. in 5 atoms ring ( ND1 of HIS )
 ATOMTYPE NR16 = connected to 1 hyd. in 6  atoms ring 
 ATOMTYPE NR5  = connected to 3 atoms in 5 atoms ring ( N9 of ADE )
 ATOMTYPE NR6  = connected to 3 atoms in 6 atoms ring ( N1 of CYT )
 HEADER        N Nitrogen SP3
 ATOMTYPE NT   = without hydrogen
 ATOMTYPE NT1  = connected to 1 hydrogen
 ATOMTYPE NT2  = connected to 2 hydrogens
 ATOMTYPE NT3  = connected to 3 hydrogens
 HEADER        O Oxygen SP2
 ATOMTYPE O    = without  NET charge ( O of main chain )
 ATOMTYPE OC   = with a NET charge   ( OE1 OE2 of GLU )
 ATOMTYPE OP   = with a NET charge connected to P (O1P of phosphate group )
 ATOMTYPE OS   = with a NET charge connected to S ( O1 of sulphate group )
 ATOMTYPE OB   = with a NET charge connected to B
 HEADER        O Oxygen SP3
 ATOMTYPE O2   = connected to 2 atoms ( O4' of ribose )
 ATOMTYPE OC2  = with a NET charge connected to 2 ATOMS ( O3' of ribose )
 ATOMTYPE OH1  = oxygen of alcohol groups ( OG1 of THR )
 ATOMTYPE OH2  = oxygen of water
 ATOMTYPE OHA  = oxygen of water in MO6
 ATOMTYPE OHB  = oxygen of water in MO6
 ATOMTYPE OHC  = oxygen of water in MO6
 HEADER        S Sulphur 
 ATOMTYPE S    = sulphur without hydrogen 
 ATOMTYPE SH1  = sulphur with a hydrogen ( SG of CYS )
 HEADER        Fe
 ATOMTYPE FE   = iron
 HEADER        P
 ATOMTYPE P    = phosphorus
 HEADER        Zn
 ATOMTYPE ZN   = zinc
 END
 
 
  --- ATOM ---
 
loop_
_lib_atom.type
_lib_atom.weight
_lib_atom.hb_type
_lib_atom.vdw_radius
_lib_atom.vdwh_radius
_lib_atom.ion_radius
_lib_atom.element
_lib_atom.valency
 
   _type         atomic chemical type
   _weight       atomic weight
   _hb_type      donor/acceptor type:   
                      N=neither
                      D=donor
                      A=acceptor
                      B=both
                      H=hydrogen candidate to hydrogen bonding
    _vdw_radius  Van der Waals radius
    _vdwh_radius  Van der Waals radius for atom+H
   Ionic radii for most of the atoms without hydrogens are:
   WebElements
   
   or 
   Chemistry of the elements by Greenwood and Earnshaw
   VDW radii of carbon atoms with hydrogen have been taken from
    Li and Nussinov, Proteins, 32 111-127 (1998)
 
 CSP     12.01150  N     1.700     1.700     .     C   4
 C       12.01150  N     1.700     1.750     .     C   4
 C1      12.01150  N     1.700     1.820     .     C   4
 C2      12.01150  N     1.700     1.800     .     C   4
. . . . . 

Bond parameters

 
  ---  BONDS ---
 
loop_
_lib_bond.atom_type_1
_lib_bond.atom_type_2
_lib_bond.type
_lib_bond.const
_lib_bond.length
   
   _atom_type  atomic chemical type
   _const      constant KBOND
   _value     equilibrium length of this bond BOND0
               BOND - actual bond length 
 
               ENERGY = KBOND * ( BOND - BOND0 )**2
 
 
     Values for bond distances and sigmas are from (where it is possible):
    International tables for crystallography
     Volume C, 1992, 
     Edited by AJC Wilson
     Published for IUCr by Kluwer Academic Publishers, Dordrecht/Boston/London
     For carbon-carbon etc
     Section: Typical Interatomic distances: Organic compounds
     Authors: FH Allen, O Kennard, DG Watson, L Brammer, AG Orpen and R Taylor
     pages:   685-706
 
     For metal radii and distances.
     Section: Typical interatomic distances: Organometallic Compounds and 
              Coordination complexes of the d- and f-block metals
     Authors: AG Orpen, L Brammer, FH Allen, O Kennard, DG Watson and R Taylor
     pages:   707-791
 
 C    C    single    420.0      1.550  0.025
 C    C    double    420.0      1.330  0.020
. . . . . 

Angle parameters

  ---  ANGLES ---
 
loop_
_lib_angle.atom_type_1
_lib_angle.atom_type_2
_lib_angle.atom_type_3
_lib_angle.const
_lib_angle.value
 
  _atom_type atomic chemical type
  _const     constant KTHETA
  _value     equilibrium value for the angle THETA0
            THETA - actual angle    
 
            ENERGY = KTHETA * ( THETA - THETA0 )**2
 
 NS   CSP  CH3      .     180.000
 NS   CSP  SH1      .     180.000
. . . . . . . 

Torsion parameters



  ---  TORSIONS ---
 
loop_
_lib_tors.atom_type_1
_lib_tors.atom_type_2
_lib_tors.atom_type_3
_lib_tors.atom_type_4
_lib_tors.label
_lib_tors.const
_lib_tors.angle
_lib_tors.period
 
  _atom_type atomic chemical type
  _const     Constant KPHI
  _period    NPH number of minima in the function
  _angle     target angle DELTA
             PHI - actual angle 
 
           ENERGY = KPHI * ( 1 - COS( NPH * (PHI -   DELTA) ) )
 
 .    CH1  NH1  .    .           0.000    0.000     3     
 .    C    CH1  .    .           0.000  180.000     3   
. . . . . . .. 

VDW parameters


 
  ---  VDW contacts ---
 
loop_
_lib_vdw.atom_type_1
_lib_vdw.atom_type_2
_lib_vdw.energy_min
_lib_vdw.radius_min
_lib_vdw.H_flag
 
   _atom_type      atomic chemical type
   _energy_min     EPSij  minimum of energy parameter
   _radius_min     Rmin radius of the minimum of energy parameter
                   Rij - actual distance
   _H_flag         "h" - the parameters for atoms with hydrogens 
 
                       Lennard-Jones potential
 
              ENERGY =  EPSij * ( (Rmin/Rij)**12 - 2 * (Rmin/Rij)**6 )
 
 C    C       -0.19686     3.600   .
 C    C       -0.19686     3.600   h
. . . . .

H-bond parameters

 
  ---  H-BONDS ---
 
loop_
_lib_hbond.atom_type_1
_lib_hbond.atom_type_2
_lib_hbond.min
_lib_hbond.dist
 
   _atom_type     atomic chemical type
   _hbond_min     EPSHij  energy at minimum
   _hbond_dist    RHmin distance at minimum of energy
                  RHij - actual distance
 
              ENERGY =  EPSHij * ( (RHmin/RHij)**12 - 2 * (RHmin/RHij)**10 )
 
 NRD5 NH1    -1.500    2.850
 NRD5 NT3    -1.500    2.850
. . . . . .

Programs

LIBCHECK

AUTHOR


  Authors:
          A.Vagin and
          G.Murshudov, E.Dodson, K.Henrick,
          J.Richelle, S.Wodak.