# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:38:05 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 1-methyl-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc(C[C@H](N)C(O)=O)c1
#
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
 NEM  NEM  '1-methyl-L-histidine     '  L-peptide  22  12  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NEM
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
 NEM  N    N  NH2    0  -0.802  -1.2350   1.1488  -1.1447
 NEM  CA   C  CH1    0  -0.193   0.0069   0.4622  -1.4471
 NEM  C    C  C      0   0.400   0.0568   0.0414  -2.9321
 NEM  O    O  O      0  -0.607  -1.0333  -0.1959  -3.4905
 NEM  CB   C  CH2    0  -0.530   0.2554  -0.7953  -0.5822
 NEM  CG   C  CR5    0   0.130   0.3385  -0.4759   0.8699
 NEM  ND1  N  N      0  -0.465   1.4454   0.1118   1.4214
 NEM  CD2  C  CR15   0  -0.135  -0.6230  -0.6277   1.8331
 NEM  CE1  C  CR15   0   0.079   1.1541   0.3016   2.6835
 NEM  NE2  N  NR5    0  -0.394  -0.0854  -0.1285   2.9877
 NEM  CM   C  CH3    0  -0.516  -0.7278  -0.0634   4.2796
 NEM  OXT  O  OC    -1  -0.618   1.1908  -0.0722  -3.4381
 NEM  H    H  HNH2   0   0.332  -1.3967   1.1529  -0.1439
 NEM  HN2  H  HNH2   0   0.326  -1.9943   0.6242  -1.5614
 NEM  HA   H  HCH1   0   0.203   0.8402   1.1486  -1.2614
 NEM  HB1  H  HCH2   0   0.230   1.1858  -1.2700  -0.9049
 NEM  HB2  H  HCH2   0   0.230  -0.5521  -1.5123  -0.7572
 NEM  HD2  H  HCR5   0   0.281  -1.6152  -1.0481   1.7965
 NEM  HE1  H  HCR5   0   0.274   1.8043   0.7410   3.4263
 NEM  HM1  H  HCH3   0   0.258  -1.6128   0.5691   4.2382
 NEM  HM2  H  HCH3   0   0.258  -1.0183  -1.0571   4.6145
 NEM  HM3  H  HCH3   0   0.261  -0.0326   0.3570   5.0014

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
 NEM  N    CA   single    1.458  0.019  1.458
 NEM  N    H    single    0.860  0.020  0.860
 NEM  N    HN2  single    0.890  0.020  1.040
 NEM  CA   C    single    1.525  0.021  1.525
 NEM  CA   CB   single    1.530  0.020  1.530
 NEM  CA   HA   single    0.970  0.020  0.970
 NEM  C    O    deloc     1.231  0.020  1.231
 NEM  C    OXT  deloc     1.247  0.020  1.247
 NEM  CB   CG   single    1.489  0.020  1.489
 NEM  CB   HB1  single    0.970  0.020  1.090
 NEM  CB   HB2  single    0.970  0.020  1.090
 NEM  CG   ND1  aromatic  1.369  0.020  1.369
 NEM  CG   CD2  aromatic  1.369  0.020  1.369
 NEM  ND1  CE1  aromatic  1.309  0.020  1.309
 NEM  CD2  NE2  aromatic  1.368  0.020  1.368
 NEM  CD2  HD2  single    0.930  0.020  1.080
 NEM  CE1  NE2  aromatic  1.347  0.020  1.347
 NEM  CE1  HE1  single    0.930  0.020  1.080
 NEM  NE2  CM   single    1.444  0.020  1.444
 NEM  CM   HM1  single    0.970  0.020  1.090
 NEM  CM   HM2  single    0.970  0.020  1.090
 NEM  CM   HM3  single    0.970  0.020  1.090

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
 NEM  HN2  N    H    106.78  3.000
 NEM  HN2  N    CA   108.12  3.000
 NEM  H    N    CA   114.00  3.000
 NEM  HA   CA   CB   109.00  3.000
 NEM  HA   CA   C    109.00  3.000
 NEM  CB   CA   C    110.10  1.900
 NEM  HA   CA   N    110.00  3.000
 NEM  CB   CA   N    110.50  1.700
 NEM  C    CA   N    111.00  2.800
 NEM  OXT  C    O    126.56  3.000
 NEM  OXT  C    CA   116.38  3.000
 NEM  O    C    CA   120.80  1.700
 NEM  HB2  CB   HB1  107.24  3.000
 NEM  HB2  CB   CG   109.74  3.000
 NEM  HB1  CB   CG   109.48  3.000
 NEM  HB2  CB   CA   108.96  3.000
 NEM  HB1  CB   CA   108.95  3.000
 NEM  CG   CB   CA   112.33  3.000
 NEM  CD2  CG   ND1  109.38  3.000
 NEM  CD2  CG   CB   128.53  3.000
 NEM  ND1  CG   CB   122.00  3.000
 NEM  CE1  ND1  CG   105.70  3.000
 NEM  HD2  CD2  NE2  122.19  3.000
 NEM  HD2  CD2  CG   131.72  3.000
 NEM  NE2  CD2  CG   106.10  3.000
 NEM  HE1  CE1  NE2  121.89  3.000
 NEM  HE1  CE1  ND1  126.01  3.000
 NEM  NE2  CE1  ND1  112.10  3.000
 NEM  CM   NE2  CE1  126.66  3.000
 NEM  CM   NE2  CD2  126.62  3.000
 NEM  CE1  NE2  CD2  106.72  3.000
 NEM  HM3  CM   HM2  108.64  3.000
 NEM  HM3  CM   HM1  108.69  3.000
 NEM  HM2  CM   HM1  108.99  3.000
 NEM  HM3  CM   NE2  109.08  3.000
 NEM  HM2  CM   NE2  110.67  3.000
 NEM  HM1  CM   NE2  110.72  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
 NEM  CONST_01  NE2  CE1  ND1  CG     0.00   0.0  0
 NEM  CONST_02  CE1  NE2  CD2  CG     0.00   0.0  0
 NEM  CONST_03  NE2  CD2  CG   ND1    0.00   0.0  0
 NEM  CONST_04  CD2  NE2  CE1  ND1    0.00   0.0  0
 NEM  CONST_05  CE1  ND1  CG   CD2    0.00   0.0  0
 NEM  CONST_06  CE1  ND1  CG   CB   180.00   0.0  0
 NEM  CONST_07  NE2  CD2  CG   CB   180.00   0.0  0
 NEM  CONST_08  CM   NE2  CD2  CG   180.00   0.0  0
 NEM  CONST_09  CM   NE2  CE1  ND1  180.00   0.0  0
 NEM  CONST_10  HE1  CE1  ND1  CG   180.00   0.0  0
 NEM  CONST_11  HD2  CD2  CG   ND1  180.00   0.0  0
 NEM  Var_01    ND1  CG   CB   CA   -75.59  30.0  2
 NEM  Var_02    HM1  CM   NE2  CD2  -62.16  30.0  2

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
 NEM  chir_01  CA  N  C  CB  positiv

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
 NEM  plan-1  CB   0.020
 NEM  plan-1  CG   0.020
 NEM  plan-1  ND1  0.020
 NEM  plan-1  CD2  0.020
 NEM  plan-1  CE1  0.020
 NEM  plan-1  NE2  0.020
 NEM  plan-1  CM   0.020
 NEM  plan-1  HD2  0.020
 NEM  plan-1  HE1  0.020
 NEM  plan-2  CA   0.020
 NEM  plan-2  C    0.020
 NEM  plan-2  O    0.020
 NEM  plan-2  OXT  0.020

