# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 20:55:00 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-{[4-({[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N[C@@H](CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CN2)C(=O)N1
#
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
 THG  THG  'N-{[4-({[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid'  ligand  53  32  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_THG
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
 THG  N3    N  NR16   0  -0.708   1.9459   1.2880   5.0918
 THG  C2    C  CR6    0   0.662   2.5687   0.1069   5.3086
 THG  N1    N  N      0  -0.522   1.9168  -1.0166   5.4094
 THG  C8A   C  CR66   0   0.497   0.5677  -0.9633   5.3012
 THG  C4A   C  CR66   0  -0.030  -0.1437   0.2057   5.0952
 THG  C4    C  CR6    0   0.469   0.5628   1.4194   4.9561
 THG  N8    N  NR16   0  -0.667  -0.0894  -2.1398   5.3767
 THG  C7    C  C      0  -0.265  -1.5315  -2.1913   5.3780
 THG  C6    C  CR16   0  -0.209  -2.0849  -1.0608   4.5156
 THG  N5    N  NR16   0  -0.642  -1.5556   0.1903   5.0294
 THG  C9    C  CH2    0  -0.240  -1.7789  -1.2900   3.0328
 THG  N10   N  NH1    0  -0.699  -2.4158  -0.2656   2.2426
 THG  C4'   C  CR6    0   0.393  -2.1074  -0.0110   0.9376
 THG  C3'   C  CR16   0  -0.342  -2.9484   0.8239   0.1788
 THG  C2'   C  CR16   0  -0.261  -2.6492   1.1349  -1.1288
 THG  C1'   C  CR6    0  -0.081  -1.5112   0.6242  -1.7591
 THG  C6'   C  CR16   0  -0.285  -0.6767  -0.1999  -1.0061
 THG  C5'   C  CR16   0  -0.341  -0.9609  -0.5208   0.3098
 THG  C11   C  C      0   0.538  -1.2434   1.0080  -3.1714
 THG  N     N  NH1    0  -0.640  -0.3444   0.2678  -3.8405
 THG  CA    C  CH1    0  -0.188  -0.0843   0.4639  -5.2480
 THG  C     C  C      0   0.408  -1.2374  -0.0511  -6.1467
 THG  OX2   O  OC    -1  -0.601  -2.0955  -0.7851  -5.6272
 THG  OX1   O  O      0  -0.620  -1.1779   0.3116  -7.3395
 THG  CB    C  CH2    0  -0.444   1.2402  -0.1997  -5.6287
 THG  CG    C  CH2    0  -0.577   2.4369   0.3888  -4.8984
 THG  CD    C  C      0   0.411   3.8142  -0.1540  -5.3177
 THG  OE1   O  O      0  -0.609   3.8522  -1.0362  -6.1979
 THG  OE2   O  OC    -1  -0.634   4.7976   0.3445  -4.7293
 THG  O11   O  O      0  -0.514  -1.8029   1.9774  -3.6786
 THG  O4    O  OC     0  -0.526   0.0707   2.5297   4.7391
 THG  N2    N  NH2    0  -0.830   3.9092   0.1272   5.4677
 THG  HN3   H  HNR6   0   0.417   2.4911   2.1365   5.0176
 THG  HN8   H  HNR6   0   0.390   0.4412  -2.9683   5.5867
 THG  HC71  H  H      0   0.249  -1.9376  -2.0981   6.3903
 THG  HC72  H  H      0   0.255  -1.8510  -3.1575   4.9879
 THG  HC6   H  HCR6   0   0.261  -3.1705  -1.0478   4.6509
 THG  HN5   H  HNR6   0   0.358  -1.8985   0.9832   4.5023
 THG  HC91  H  HCH2   0   0.240  -0.6993  -1.2414   2.8835
 THG  HC92  H  HCH2   0   0.231  -2.1010  -2.2965   2.7355
 THG  H10   H  HNH1   0   0.383  -3.3702  -0.0619   2.4990
 THG  HC3   H  HCR6   0   0.258  -3.8424   1.2325   0.6355
 THG  HC2   H  HCR6   0   0.250  -3.3178   1.7848  -1.6781
 THG  HC61  H  HCR6   0   0.247   0.2365  -0.6014  -1.4287
 THG  HC5   H  HCR6   0   0.264  -0.2776  -1.1671   0.8432
 THG  HN    H  HNH1   0   0.387  -0.0977  -0.6313  -3.4605
 THG  HCA   H  HCH1   0   0.225   0.0205   1.5386  -5.4230
 THG  HCB1  H  HCH2   0   0.209   1.1755  -1.2783  -5.4470
 THG  HCB2  H  HCH2   0   0.225   1.3687  -0.0829  -6.7048
 THG  HCG1  H  HCH2   0   0.218   2.4415   1.4772  -5.0326
 THG  HCG2  H  HCH2   0   0.221   2.3331   0.2419  -3.8184
 THG  HN21  H  HNH2   0   0.403   4.3752  -0.7634   5.4225
 THG  HN22  H  HNH2   0   0.406   4.4400   0.9046   5.1108

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
 THG  N3   C2    aromatic  1.353  0.020  1.353
 THG  N3   C4    aromatic  1.396  0.020  1.396
 THG  N3   HN3   single    0.860  0.020  1.020
 THG  C2   N1    aromatic  1.303  0.020  1.303
 THG  C2   N2    single    1.350  0.020  1.350
 THG  N1   C8A   aromatic  1.355  0.020  1.355
 THG  C8A  C4A   aromatic  1.384  0.020  1.384
 THG  C8A  N8    single    1.350  0.020  1.350
 THG  C4A  C4    aromatic  1.411  0.020  1.411
 THG  C4A  N5    single    1.414  0.020  1.414
 THG  C4   O4    double    1.234  0.020  1.234
 THG  N8   C7    single    1.443  0.020  1.443
 THG  N8   HN8   single    0.860  0.020  1.020
 THG  C7   C6    single    1.526  0.020  1.526
 THG  C7   HC71  single    0.970  0.020  1.090
 THG  C7   HC72  single    0.970  0.020  1.090
 THG  C6   N5    single    1.452  0.020  1.452
 THG  C6   C9    single    1.531  0.020  1.531
 THG  C6   HC6   single    0.970  0.020  1.090
 THG  N5   HN5   single    0.890  0.020  1.040
 THG  C9   N10   single    1.442  0.020  1.442
 THG  C9   HC91  single    0.970  0.020  1.090
 THG  C9   HC92  single    0.970  0.020  1.090
 THG  N10  C4'   single    1.365  0.020  1.365
 THG  N10  H10   single    0.890  0.020  1.040
 THG  C4'  C3'   aromatic  1.407  0.020  1.407
 THG  C4'  C5'   aromatic  1.403  0.020  1.403
 THG  C3'  C2'   aromatic  1.377  0.020  1.377
 THG  C3'  HC3   single    0.930  0.020  1.080
 THG  C2'  C1'   aromatic  1.398  0.020  1.398
 THG  C2'  HC2   single    0.930  0.020  1.080
 THG  C1'  C6'   aromatic  1.394  0.020  1.394
 THG  C1'  C11   single    1.488  0.020  1.488
 THG  C6'  C5'   aromatic  1.384  0.020  1.384
 THG  C6'  HC61  single    0.930  0.020  1.080
 THG  C5'  HC5   single    0.930  0.020  1.080
 THG  C11  N     single    1.343  0.020  1.343
 THG  C11  O11   double    1.229  0.020  1.229
 THG  N    CA    single    1.445  0.020  1.445
 THG  N    HN    single    0.890  0.020  1.040
 THG  CA   C     single    1.550  0.020  1.550
 THG  CA   CB    single    1.530  0.020  1.530
 THG  CA   HCA   single    0.970  0.020  1.090
 THG  C    OX2   deloc     1.243  0.020  1.243
 THG  C    OX1   deloc     1.248  0.020  1.248
 THG  CB   CG    single    1.520  0.020  1.520
 THG  CB   HCB1  single    0.970  0.020  1.090
 THG  CB   HCB2  single    0.970  0.020  1.090
 THG  CG   CD    single    1.539  0.020  1.539
 THG  CG   HCG1  single    0.970  0.020  1.090
 THG  CG   HCG2  single    0.970  0.020  1.090
 THG  CD   OE1   deloc     1.247  0.020  1.247
 THG  CD   OE2   deloc     1.250  0.020  1.250
 THG  N2   HN21  single    0.890  0.020  1.040
 THG  N2   HN22  single    0.890  0.020  1.040

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
 THG  HN3   N3   C4    116.62  3.000
 THG  HN3   N3   C2    119.74  3.000
 THG  C4    N3   C2    123.63  3.000
 THG  N2    C2   N1    120.04  3.000
 THG  N2    C2   N3    117.57  3.000
 THG  N1    C2   N3    122.35  3.000
 THG  C8A   N1   C2    117.27  3.000
 THG  N8    C8A  C4A   119.63  3.000
 THG  N8    C8A  N1    116.49  3.000
 THG  C4A   C8A  N1    123.86  3.000
 THG  N5    C4A  C4    120.32  3.000
 THG  N5    C4A  C8A   120.74  3.000
 THG  C4    C4A  C8A   118.94  3.000
 THG  O4    C4   C4A   126.28  3.000
 THG  O4    C4   N3    119.80  3.000
 THG  C4A   C4   N3    113.92  3.000
 THG  HN8   N8   C7    119.83  3.000
 THG  HN8   N8   C8A   118.22  3.000
 THG  C7    N8   C8A   121.18  3.000
 THG  HC72  C7   HC71  107.32  3.000
 THG  HC72  C7   C6    110.37  3.000
 THG  HC71  C7   C6    108.97  3.000
 THG  HC72  C7   N8    108.92  3.000
 THG  HC71  C7   N8    111.63  3.000
 THG  C6    C7   N8    109.60  3.000
 THG  HC6   C6   C9    108.65  3.000
 THG  HC6   C6   N5    107.92  3.000
 THG  C9    C6   N5    113.49  3.000
 THG  HC6   C6   C7    107.39  3.000
 THG  C9    C6   C7    111.35  3.000
 THG  N5    C6   C7    107.82  3.000
 THG  HN5   N5   C6    111.54  3.000
 THG  HN5   N5   C4A   110.74  3.000
 THG  C6    N5   C4A   112.95  3.000
 THG  HC92  C9   HC91  107.11  3.000
 THG  HC92  C9   N10   111.92  3.000
 THG  HC91  C9   N10   109.29  3.000
 THG  HC92  C9   C6    109.93  3.000
 THG  HC91  C9   C6    108.89  3.000
 THG  N10   C9   C6    109.64  3.000
 THG  H10   N10  C4'   114.78  3.000
 THG  H10   N10  C9    114.96  3.000
 THG  C4'   N10  C9    123.82  3.000
 THG  C5'   C4'  C3'   117.56  3.000
 THG  C5'   C4'  N10   123.01  3.000
 THG  C3'   C4'  N10   119.42  3.000
 THG  HC3   C3'  C2'   119.62  3.000
 THG  HC3   C3'  C4'   119.30  3.000
 THG  C2'   C3'  C4'   121.08  3.000
 THG  HC2   C2'  C1'   119.58  3.000
 THG  HC2   C2'  C3'   118.91  3.000
 THG  C1'   C2'  C3'   121.51  3.000
 THG  C11   C1'  C6'   123.89  3.000
 THG  C11   C1'  C2'   118.71  3.000
 THG  C6'   C1'  C2'   117.38  3.000
 THG  HC61  C6'  C5'   117.26  3.000
 THG  HC61  C6'  C1'   120.87  3.000
 THG  C5'   C6'  C1'   121.86  3.000
 THG  HC5   C5'  C6'   118.54  3.000
 THG  HC5   C5'  C4'   120.85  3.000
 THG  C6'   C5'  C4'   120.60  3.000
 THG  O11   C11  N     122.27  3.000
 THG  O11   C11  C1'   120.89  3.000
 THG  N     C11  C1'   116.82  3.000
 THG  HN    N    CA    116.41  3.000
 THG  HN    N    C11   117.92  3.000
 THG  CA    N    C11   122.08  3.000
 THG  HCA   CA   CB    107.67  3.000
 THG  HCA   CA   C     107.75  3.000
 THG  CB    CA   C     110.84  3.000
 THG  HCA   CA   N     107.85  3.000
 THG  CB    CA   N     109.85  3.000
 THG  C     CA   N     112.70  3.000
 THG  OX1   C    OX2   127.15  3.000
 THG  OX1   C    CA    114.97  3.000
 THG  OX2   C    CA    117.87  3.000
 THG  HCB2  CB   HCB1  106.03  3.000
 THG  HCB2  CB   CG    109.87  3.000
 THG  HCB1  CB   CG    110.35  3.000
 THG  HCB2  CB   CA    107.54  3.000
 THG  HCB1  CB   CA    109.56  3.000
 THG  CG    CB   CA    113.21  3.000
 THG  HCG2  CG   HCG1  104.73  3.000
 THG  HCG2  CG   CD    107.84  3.000
 THG  HCG1  CG   CD    108.25  3.000
 THG  HCG2  CG   CB    110.32  3.000
 THG  HCG1  CG   CB    109.19  3.000
 THG  CD    CG   CB    115.92  3.000
 THG  OE2   CD   OE1   126.20  3.000
 THG  OE2   CD   CG    115.81  3.000
 THG  OE1   CD   CG    117.99  3.000
 THG  HN22  N2   HN21  115.05  3.000
 THG  HN22  N2   C2    119.56  3.000
 THG  HN21  N2   C2    116.18  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
 THG  CONST_01  C8A   N1   C2   N3      0.00   0.0  0
 THG  CONST_02  C8A   C4A  C4   N3      0.00   0.0  0
 THG  CONST_03  C4A   C4   N3   C2      0.00   0.0  0
 THG  CONST_04  C4A   C8A  N1   C2      0.00   0.0  0
 THG  CONST_05  C4    N3   C2   N1      0.00   0.0  0
 THG  CONST_06  C4    C4A  C8A  N1      0.00   0.0  0
 THG  CONST_07  C1'   C2'  C3'  C4'     0.00   0.0  0
 THG  CONST_08  C1'   C6'  C5'  C4'     0.00   0.0  0
 THG  CONST_09  C6'   C5'  C4'  C3'     0.00   0.0  0
 THG  CONST_10  C6'   C1'  C2'  C3'     0.00   0.0  0
 THG  CONST_11  C5'   C4'  C3'  C2'     0.00   0.0  0
 THG  CONST_12  C5'   C6'  C1'  C2'     0.00   0.0  0
 THG  CONST_13  O4    C4   N3   C2    180.00   0.0  0
 THG  CONST_14  N2    C2   N1   C8A   180.00   0.0  0
 THG  CONST_15  O4    C4   C4A  C8A   180.00   0.0  0
 THG  CONST_16  N2    C2   N3   C4    180.00   0.0  0
 THG  CONST_17  O4    C4   C4A  N5      0.00   0.0  0
 THG  CONST_18  C2'   C3'  C4'  N10   180.00   0.0  0
 THG  CONST_19  C6'   C5'  C4'  N10   180.00   0.0  0
 THG  CONST_20  C11   C1'  C2'  C3'   180.00   0.0  0
 THG  CONST_21  C11   C1'  C6'  C5'   180.00   0.0  0
 THG  CONST_22  HN3   N3   C2   N1    180.00   0.0  0
 THG  CONST_23  HC2   C2'  C3'  C4'   180.00   0.0  0
 THG  CONST_24  HC61  C6'  C5'  C4'   180.00   0.0  0
 THG  CONST_25  HC5   C5'  C4'  C3'   180.00   0.0  0
 THG  CONST_26  HC3   C3'  C2'  C1'   180.00   0.0  0
 THG  CONST_27  C3'   C4'  N10  C9    180.00   0.0  0
 THG  CONST_28  C5'   C4'  N10  C9      0.00   0.0  0
 THG  CONST_29  HN21  N2   C2   N3    180.00   0.0  0
 THG  CONST_32  CA    N    C11  C1'   180.00   0.0  0
 THG  CONST_34  O11   C11  N    CA      0.00   0.0  0
 THG  Var_01    C7    N8   C8A  N1    175.14  30.0  1
 THG  Var_02    C6    N5   C4A  C8A   -29.77  30.0  1
 THG  Var_03    C6    C7   N8   C8A    33.17  30.0  1
 THG  Var_04    C4'   N10  C9   C6    165.07  30.0  3
 THG  Var_05    N     C11  C1'  C2'  -164.54  30.0  2
 THG  Var_06    CD    CG   CB   CA   -175.23  30.0  3
 THG  Var_07    OE1   CD   CG   CB     -0.96  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
 THG  chir_01  C6  C7  N5  C9  negativ
 THG  chir_02  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
 THG  plan-1  N10   0.020
 THG  plan-1  C4'   0.020
 THG  plan-1  C3'   0.020
 THG  plan-1  C2'   0.020
 THG  plan-1  C1'   0.020
 THG  plan-1  C6'   0.020
 THG  plan-1  C5'   0.020
 THG  plan-1  C11   0.020
 THG  plan-1  HC3   0.020
 THG  plan-1  HC2   0.020
 THG  plan-1  HC61  0.020
 THG  plan-1  HC5   0.020
 THG  plan-2  CA    0.020
 THG  plan-2  C     0.020
 THG  plan-2  OX2   0.020
 THG  plan-2  OX1   0.020
 THG  plan-3  CG    0.020
 THG  plan-3  CD    0.020
 THG  plan-3  OE1   0.020
 THG  plan-3  OE2   0.020
 THG  plan-4  C1'   0.020
 THG  plan-4  C11   0.020
 THG  plan-4  N     0.020
 THG  plan-4  CA    0.020
 THG  plan-4  O11   0.020
 THG  plan-4  HN    0.020
 THG  plan-5  C9    0.020
 THG  plan-5  N10   0.020
 THG  plan-5  C4'   0.020
 THG  plan-5  H10   0.020
 THG  plan-6  C2    0.020
 THG  plan-6  N2    0.020
 THG  plan-6  HN21  0.020
 THG  plan-6  HN22  0.020
 THG  plan-7  N3    0.020
 THG  plan-7  C2    0.020
 THG  plan-7  N1    0.020
 THG  plan-7  C8A   0.020
 THG  plan-7  C4A   0.020
 THG  plan-7  C4    0.020
 THG  plan-7  N8    0.020
 THG  plan-7  N5    0.020
 THG  plan-7  O4    0.020
 THG  plan-7  N2    0.020
 THG  plan-7  HN3   0.020

