# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 03:07:44 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: N-methyl-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](Cc1[nH]cnc1)C(O)=O
#
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
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 E9V  E9V  'N-methyl-L-histidine     '  L-peptide  22  12  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_E9V
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 E9V  N    N  NH1    0  -0.577  2.7367  -2.0186   2.5743
 E9V  CA   C  CH1    0  -0.246  3.8421  -2.6349   3.2919
 E9V  CB   C  CH2    0  -0.539  4.6766  -3.5514   2.4022
 E9V  CG   C  CR5    0   0.330  3.9082  -4.6553   1.7591
 E9V  ND1  N  NR15   0  -0.614  4.4929  -5.5362   0.8887
 E9V  CD2  C  CR15   0  -0.261  2.6166  -5.0986   1.8661
 E9V  CE1  C  CR15   0   0.069  3.5661  -6.4446   0.5183
 E9V  NE2  N  N      0  -0.445  2.4160  -6.2120   1.0934
 E9V  C    C  C      0   0.415  4.7320  -1.6204   4.0774
 E9V  O    O  O      0  -0.600  5.8626  -2.0124   4.4282
 E9V  CN2  C  CH3    0  -0.528  3.1284  -1.2778   1.3911
 E9V  H    H  HNH1   0   0.333  2.3139  -1.3626   3.2178
 E9V  HA   H  HCH1   0   0.227  3.3874  -3.2744   4.0630
 E9V  HB2  H  HCH2   0   0.257  5.4668  -3.9779   3.0223
 E9V  HB3  H  HCH2   0   0.239  5.1967  -2.9688   1.6341
 E9V  HD1  H  HNR5   0   0.410  5.4518  -5.5115   0.5782
 E9V  HD2  H  HCR5   0   0.236  1.8224  -4.6616   2.4496
 E9V  HE1  H  HCR5   0   0.267  3.7847  -7.2451  -0.1722
 E9V  3HN  H  HCH3   0   0.224  2.2816  -0.6815   1.0496
 E9V  H1   H  HCH3   0   0.189  3.9754  -0.5929   1.5339
 E9V  2HN  H  HCH3   0   0.214  3.3860  -1.9559   0.5751
 E9V  OXT  O  OC    -1  -0.601  4.2107  -0.5185   4.3403

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
_chem_comp_bond.value_dist_neutron
 E9V  CE1  ND1  aromatic  1.350  0.020  1.350
 E9V  CE1  NE2  aromatic  1.307  0.020  1.307
 E9V  ND1  CG   aromatic  1.370  0.020  1.370
 E9V  NE2  CD2  aromatic  1.370  0.020  1.370
 E9V  CN2  N    single    1.450  0.020  1.450
 E9V  CG   CD2  aromatic  1.370  0.020  1.370
 E9V  CG   CB   single    1.491  0.020  1.491
 E9V  N    CA   single    1.458  0.019  1.458
 E9V  CB   CA   single    1.530  0.020  1.530
 E9V  CA   C    single    1.525  0.021  1.525
 E9V  C    O    deloc     1.231  0.020  1.231
 E9V  N    H    single    0.860  0.020  0.860
 E9V  CA   HA   single    0.970  0.020  0.970
 E9V  CB   HB2  single    0.970  0.020  1.090
 E9V  CB   HB3  single    0.970  0.020  1.090
 E9V  ND1  HD1  single    0.860  0.020  1.020
 E9V  CD2  HD2  single    0.930  0.020  1.080
 E9V  CE1  HE1  single    0.930  0.020  1.080
 E9V  CN2  3HN  single    0.970  0.020  1.090
 E9V  CN2  H1   single    0.970  0.020  1.090
 E9V  CN2  2HN  single    0.970  0.020  1.090
 E9V  C    OXT  deloc     1.247  0.020  1.247

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
 E9V  H    N    CN2  107.50  3.000
 E9V  H    N    CA   114.00  3.000
 E9V  CN2  N    CA   114.44  3.000
 E9V  HA   CA   C    109.00  3.000
 E9V  HA   CA   CB   109.00  3.000
 E9V  C    CA   CB   110.10  1.900
 E9V  HA   CA   N    110.00  3.000
 E9V  C    CA   N    111.00  2.800
 E9V  CB   CA   N    110.50  1.700
 E9V  HB3  CB   HB2  105.22  3.000
 E9V  HB3  CB   CG   109.64  3.000
 E9V  HB2  CB   CG   109.20  3.000
 E9V  HB3  CB   CA   110.44  3.000
 E9V  HB2  CB   CA   107.43  3.000
 E9V  CG   CB   CA   114.48  3.000
 E9V  CD2  CG   ND1  104.13  3.000
 E9V  CD2  CG   CB   133.79  3.000
 E9V  ND1  CG   CB   122.03  3.000
 E9V  HD1  ND1  CE1  125.81  3.000
 E9V  HD1  ND1  CG   125.88  3.000
 E9V  CE1  ND1  CG   108.31  3.000
 E9V  HD2  CD2  NE2  121.80  3.000
 E9V  HD2  CD2  CG   127.28  3.000
 E9V  NE2  CD2  CG   110.92  3.000
 E9V  HE1  CE1  NE2  126.28  3.000
 E9V  HE1  CE1  ND1  122.38  3.000
 E9V  NE2  CE1  ND1  111.34  3.000
 E9V  CE1  NE2  CD2  105.31  3.000
 E9V  OXT  C    O    126.69  3.000
 E9V  OXT  C    CA   116.23  3.000
 E9V  O    C    CA   120.80  1.700
 E9V  2HN  CN2  H1   107.61  3.000
 E9V  2HN  CN2  3HN  106.78  3.000
 E9V  H1   CN2  3HN  107.37  3.000
 E9V  2HN  CN2  N    110.87  3.000
 E9V  H1   CN2  N    114.88  3.000
 E9V  3HN  CN2  N    108.97  3.000

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
 E9V  CONST_01  NE2  CE1  ND1  CG      0.00   0.0  0
 E9V  CONST_02  CE1  NE2  CD2  CG      0.00   0.0  0
 E9V  CONST_03  CD2  NE2  CE1  ND1     0.00   0.0  0
 E9V  CONST_04  NE2  CD2  CG   ND1     0.00   0.0  0
 E9V  CONST_05  CE1  ND1  CG   CD2     0.00   0.0  0
 E9V  CONST_06  CE1  ND1  CG   CB    180.00   0.0  0
 E9V  CONST_07  NE2  CD2  CG   CB    180.00   0.0  0
 E9V  CONST_08  HE1  CE1  ND1  CG    180.00   0.0  0
 E9V  CONST_09  HD2  CD2  CG   ND1   180.00   0.0  0
 E9V  CONST_10  HD1  ND1  CG   CD2   180.00   0.0  0
 E9V  Var_01    ND1  CG   CB   CA    177.37  30.0  3
 E9V  Var_02    3HN  CN2  N    CA   -167.82  30.0  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
 E9V  chir_01  CA  N  CB  C  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 E9V  plan-1  CB   0.020
 E9V  plan-1  CG   0.020
 E9V  plan-1  ND1  0.020
 E9V  plan-1  CD2  0.020
 E9V  plan-1  CE1  0.020
 E9V  plan-1  NE2  0.020
 E9V  plan-1  HD1  0.020
 E9V  plan-1  HD2  0.020
 E9V  plan-1  HE1  0.020
 E9V  plan-2  CA   0.020
 E9V  plan-2  C    0.020
 E9V  plan-2  O    0.020
 E9V  plan-2  OXT  0.020

