# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:01:38 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: (2R,7E)-7-amino-2-[(1S,2S)-2-hydroxy-5-(3-methoxyphenyl)-2,3-dihydro-1H-inden-1-yl]-7-iminoheptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2ccc3[C@@H]([C@@H](O)Cc3c2)[C@@H](CCCCC(N)=N)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
 167  167  '(2R,7E)-7-amino-2-[(1S,2S)-2-hydroxy-5-(3-methoxyphenyl)-2,3-dihydro-1H-inden-1-yl]-7-iminoheptanoic acid'  ligand  56  29  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_167
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
 167  C1    C  CH2    0  -0.411   0.1023   0.4274  -2.7150
 167  C2    C  CH2    0  -0.417  -0.5662  -0.2208  -3.9227
 167  C3    C  CH2    0  -0.405  -2.0307   0.1789  -4.0606
 167  C4    C  CH2    0  -0.512  -2.6679  -0.4184  -5.3034
 167  C5    C  C      0   0.394  -4.1250  -0.0863  -5.5059
 167  N6    N  NH2    0  -0.817  -4.6219  -0.4993  -6.7096
 167  N7    N  N      0  -0.672  -4.7721   0.5594  -4.6143
 167  O8    O  O      0  -0.614   2.6928   1.1555  -4.0160
 167  O8A   O  OC    -1  -0.614   2.7205  -1.0597  -4.2382
 167  O9    O  OH1    0  -0.675   4.3088   0.9932  -0.2818
 167  C10   C  CH1    0  -0.340   2.1596   0.6081  -1.2271
 167  C11   C  CR6    0   0.108   1.9573  -0.5378   0.8532
 167  C12   C  CR6    0   0.141   1.3959   0.4643   0.0640
 167  C13   C  CH1    0   0.036   3.5168  -0.0238  -0.8607
 167  C14   C  CH2    0  -0.530   3.1634  -1.1109   0.1668
 167  C36   C  CR16   0  -0.318   0.2941   1.1649   0.5285
 167  C37   C  CR16   0  -0.317  -0.2444   0.8489   1.7706
 167  C38   C  CR6    0   0.079   0.3052  -0.1619   2.5622
 167  C39   C  CR16   0  -0.393   1.4221  -0.8575   2.0867
 167  C43   C  CR6    0   0.106  -0.2672  -0.4827   3.8861
 167  C44   C  CR16   0  -0.417  -0.7459   0.5297   4.7098
 167  C45   C  CR6    0   0.406  -1.2882   0.2428   5.9631
 167  C24   C  CR16   0  -0.397  -1.3521  -1.0771   6.4026
 167  C25   C  CR16   0  -0.227  -0.8708  -2.0872   5.5768
 167  C6    C  CR16   0  -0.337  -0.3330  -1.8064   4.3339
 167  O54   O  O2     0  -0.473  -1.7130   1.3027   6.6780
 167  C16   C  CH1    0  -0.312   1.4963  -0.1225  -2.4097
 167  C15   C  C      0   0.411   2.3875  -0.0035  -3.6644
 167  H12   H  HCH2   0   0.217  -0.5438   0.2866  -1.8436
 167  H11   H  HCH2   0   0.204   0.1657   1.5092  -2.8737
 167  H22   H  HCH2   0   0.213  -0.0294   0.0539  -4.8360
 167  H21   H  HCH2   0   0.206  -0.4917  -1.3108  -3.8420
 167  H32   H  HCH2   0   0.214  -2.5819  -0.1407  -3.1730
 167  H31   H  HCH2   0   0.212  -2.1150   1.2687  -4.0933
 167  H42   H  HCH2   0   0.247  -2.1175  -0.0979  -6.1945
 167  H41   H  HCH2   0   0.250  -2.5708  -1.5101  -5.2817
 167  H62   H  HNH2   0   0.383  -5.6211  -0.5338  -6.8312
 167  H61   H  HNH2   0   0.389  -4.1194  -1.2073  -7.2187
 167  HN7   H  H      0   0.310  -5.7400   0.6984  -4.8959
 167  H10   H  HCH1   0   0.240   2.2905   1.6550  -1.5150
 167  H13   H  HCH1   0   0.220   4.0195  -0.4581  -1.7323
 167  H142  H  HCH2   0   0.251   2.9117  -2.0481  -0.3391
 167  H141  H  HCH2   0   0.255   3.9898  -1.3361   0.8455
 167  H36   H  HCR6   0   0.247  -0.1486   1.9584  -0.0607
 167  H37   H  HCR6   0   0.247  -1.1142   1.3903   2.1222
 167  H39   H  HCR6   0   0.244   1.8860  -1.6203   2.7016
 167  H44   H  HCR6   0   0.257  -0.6816   1.5647   4.3957
 167  H24   H  HCR6   0   0.279  -1.7652  -1.3371   7.3672
 167  H25   H  HCR6   0   0.259  -0.9288  -3.1134   5.9162
 167  H6    H  HCR6   0   0.250   0.0159  -2.6134   3.7025
 167  H533  H  HCH3   0   0.259  -2.5097   2.0534   8.3678
 167  H532  H  HCH3   0   0.228  -3.1450   0.4566   7.9372
 167  H531  H  HCH3   0   0.228  -1.5171   0.6105   8.6351
 167  H16   H  HCH1   0   0.200   1.3892  -1.1836  -2.1545
 167  C53   C  CH3    0  -0.436  -2.2459   1.0776   7.9675
 167  H9    H  HOH1   0   0.446   5.1283   0.5969   0.0302

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
 167  C1   C2    single    1.525  0.020  1.525
 167  C1   C16   single    1.529  0.020  1.529
 167  C1   H12   single    0.970  0.020  1.090
 167  C1   H11   single    0.970  0.020  1.090
 167  C2   C3    single    1.524  0.020  1.524
 167  C2   H22   single    0.970  0.020  1.090
 167  C2   H21   single    0.970  0.020  1.090
 167  C3   C4    single    1.519  0.020  1.519
 167  C3   H32   single    0.970  0.020  1.090
 167  C3   H31   single    0.970  0.020  1.090
 167  C4   C5    single    1.508  0.020  1.508
 167  C4   H42   single    0.970  0.020  1.090
 167  C4   H41   single    0.970  0.020  1.090
 167  C5   N6    single    1.366  0.020  1.366
 167  C5   N7    double    1.277  0.020  1.277
 167  N6   H62   single    0.890  0.020  1.040
 167  N6   H61   single    0.890  0.020  1.040
 167  N7   HN7   single    0.890  0.020  1.040
 167  O8   C15   deloc     1.249  0.020  1.249
 167  O8A  C15   deloc     1.247  0.020  1.247
 167  O9   C13   single    1.413  0.020  1.413
 167  O9   H9    single    0.850  0.020  0.980
 167  C10  C12   single    1.507  0.020  1.507
 167  C10  C13   single    1.541  0.020  1.541
 167  C10  C16   single    1.540  0.020  1.540
 167  C10  H10   single    0.970  0.020  1.090
 167  C11  C12   aromatic  1.394  0.020  1.394
 167  C11  C14   single    1.501  0.020  1.501
 167  C11  C39   aromatic  1.382  0.020  1.382
 167  C12  C36   aromatic  1.386  0.020  1.386
 167  C13  C14   single    1.537  0.020  1.537
 167  C13  H13   single    0.970  0.020  1.090
 167  C14  H142  single    0.970  0.020  1.090
 167  C14  H141  single    0.970  0.020  1.090
 167  C36  C37   aromatic  1.390  0.020  1.390
 167  C36  H36   single    0.930  0.020  1.080
 167  C37  C38   aromatic  1.397  0.020  1.397
 167  C37  H37   single    0.930  0.020  1.080
 167  C38  C39   aromatic  1.399  0.020  1.399
 167  C38  C43   single    1.478  0.020  1.478
 167  C39  H39   single    0.930  0.020  1.080
 167  C43  C44   aromatic  1.390  0.020  1.390
 167  C43  C6    aromatic  1.399  0.020  1.399
 167  C44  C45   aromatic  1.395  0.020  1.395
 167  C44  H44   single    0.930  0.020  1.080
 167  C45  C24   aromatic  1.393  0.020  1.393
 167  C45  O54   single    1.347  0.020  1.347
 167  C24  C25   aromatic  1.391  0.020  1.391
 167  C24  H24   single    0.930  0.020  1.080
 167  C25  C6    aromatic  1.383  0.020  1.383
 167  C25  H25   single    0.930  0.020  1.080
 167  C6   H6    single    0.930  0.020  1.080
 167  C53  O54   single    1.413  0.020  1.413
 167  C53  H533  single    0.970  0.020  1.090
 167  C53  H532  single    0.970  0.020  1.090
 167  C53  H531  single    0.970  0.020  1.090
 167  C16  C15   single    1.544  0.020  1.544
 167  C16  H16   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
 167  H11   C1   H12   106.07  3.000
 167  H11   C1   C16   109.35  3.000
 167  H12   C1   C16   109.45  3.000
 167  H11   C1   C2    109.29  3.000
 167  H12   C1   C2    108.50  3.000
 167  C16   C1   C2    113.88  3.000
 167  H21   C2   H22   106.13  3.000
 167  H21   C2   C3    109.44  3.000
 167  H22   C2   C3    109.27  3.000
 167  H21   C2   C1    109.56  3.000
 167  H22   C2   C1    109.83  3.000
 167  C3    C2   C1    112.42  3.000
 167  H31   C3   H32   106.08  3.000
 167  H31   C3   C4    109.57  3.000
 167  H32   C3   C4    109.75  3.000
 167  H31   C3   C2    109.77  3.000
 167  H32   C3   C2    109.54  3.000
 167  C4    C3   C2    111.96  3.000
 167  H41   C4   H42   105.25  3.000
 167  H41   C4   C5    107.91  3.000
 167  H42   C4   C5    108.17  3.000
 167  H41   C4   C3    109.77  3.000
 167  H42   C4   C3    109.86  3.000
 167  C5    C4   C3    115.37  3.000
 167  N7    C5   N6    125.71  3.000
 167  N7    C5   C4    120.48  3.000
 167  N6    C5   C4    113.77  3.000
 167  H61   N6   H62   114.22  3.000
 167  H61   N6   C5    118.47  3.000
 167  H62   N6   C5    118.53  3.000
 167  HN7   N7   C5    110.97  3.000
 167  H9    O9   C13   108.29  3.000
 167  H10   C10  C16   107.67  3.000
 167  H10   C10  C13   110.46  3.000
 167  C16   C10  C13   111.55  3.000
 167  H10   C10  C12   112.18  3.000
 167  C16   C10  C12   113.23  3.000
 167  C13   C10  C12   101.74  3.000
 167  C39   C11  C14   129.11  3.000
 167  C39   C11  C12   121.05  3.000
 167  C14   C11  C12   109.83  3.000
 167  C36   C12  C11   119.60  3.000
 167  C36   C12  C10   129.93  3.000
 167  C11   C12  C10   110.46  3.000
 167  H13   C13  C14   110.91  3.000
 167  H13   C13  C10   112.17  3.000
 167  C14   C13  C10   104.27  3.000
 167  H13   C13  O9    110.73  3.000
 167  C14   C13  O9    111.34  3.000
 167  C10   C13  O9    107.21  3.000
 167  H141  C14  H142  106.53  3.000
 167  H141  C14  C13   112.77  3.000
 167  H142  C14  C13   110.46  3.000
 167  H141  C14  C11   113.71  3.000
 167  H142  C14  C11   110.70  3.000
 167  C13   C14  C11   102.73  3.000
 167  H36   C36  C37   119.63  3.000
 167  H36   C36  C12   120.87  3.000
 167  C37   C36  C12   119.50  3.000
 167  H37   C37  C38   119.60  3.000
 167  H37   C37  C36   119.17  3.000
 167  C38   C37  C36   121.23  3.000
 167  C43   C38  C39   120.38  3.000
 167  C43   C38  C37   120.83  3.000
 167  C39   C38  C37   118.78  3.000
 167  H39   C39  C38   119.92  3.000
 167  H39   C39  C11   120.21  3.000
 167  C38   C39  C11   119.83  3.000
 167  C6    C43  C44   118.90  3.000
 167  C6    C43  C38   120.70  3.000
 167  C44   C43  C38   120.41  3.000
 167  H44   C44  C45   118.67  3.000
 167  H44   C44  C43   120.23  3.000
 167  C45   C44  C43   121.08  3.000
 167  O54   C45  C24   124.32  3.000
 167  O54   C45  C44   115.94  3.000
 167  C24   C45  C44   119.74  3.000
 167  H24   C24  C25   119.17  3.000
 167  H24   C24  C45   121.81  3.000
 167  C25   C24  C45   119.03  3.000
 167  H25   C25  C6    119.68  3.000
 167  H25   C25  C24   118.94  3.000
 167  C6    C25  C24   121.38  3.000
 167  H6    C6   C25   119.88  3.000
 167  H6    C6   C43   120.24  3.000
 167  C25   C6   C43   119.87  3.000
 167  C53   O54  C45   118.54  3.000
 167  H16   C16  C15   108.67  3.000
 167  H16   C16  C10   108.81  3.000
 167  C15   C16  C10   109.81  3.000
 167  H16   C16  C1    107.78  3.000
 167  C15   C16  C1    109.65  3.000
 167  C10   C16  C1    112.04  3.000
 167  C16   C15  O8A   117.57  3.000
 167  C16   C15  O8    116.20  3.000
 167  O8A   C15  O8    126.22  3.000
 167  H531  C53  H532  108.81  3.000
 167  H531  C53  H533  108.69  3.000
 167  H532  C53  H533  108.69  3.000
 167  H531  C53  O54   111.96  3.000
 167  H532  C53  O54   112.04  3.000
 167  H533  C53  O54   106.53  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
 167  CONST_01  C37   C36  C12  C11    0.00   0.0  0
 167  CONST_02  C37   C38  C39  C11    0.00   0.0  0
 167  CONST_03  C43   C38  C39  C11  180.00   0.0  0
 167  CONST_04  C38   C39  C11  C12    0.00   0.0  0
 167  CONST_05  C38   C37  C36  C12    0.00   0.0  0
 167  CONST_06  C39   C11  C12  C36    0.00   0.0  0
 167  CONST_07  C39   C38  C37  C36    0.00   0.0  0
 167  CONST_08  C43   C38  C37  C36  180.00   0.0  0
 167  CONST_11  C45   C44  C43  C38  180.00   0.0  0
 167  CONST_12  C25   C6   C43  C38  180.00   0.0  0
 167  CONST_15  C24   C45  C44  C43    0.00   0.0  0
 167  CONST_16  C24   C25  C6   C43    0.00   0.0  0
 167  CONST_17  C25   C6   C43  C44    0.00   0.0  0
 167  CONST_18  C25   C24  C45  C44    0.00   0.0  0
 167  CONST_19  C6    C43  C44  C45    0.00   0.0  0
 167  CONST_20  C6    C25  C24  C45    0.00   0.0  0
 167  CONST_21  O54   C45  C44  C43  180.00   0.0  0
 167  CONST_22  O54   C45  C24  C25  180.00   0.0  0
 167  CONST_23  H36   C36  C12  C10    0.00   0.0  0
 167  CONST_24  H39   C39  C11  C12  180.00   0.0  0
 167  CONST_25  H37   C37  C36  C12  180.00   0.0  0
 167  CONST_26  H44   C44  C43  C38    0.00   0.0  0
 167  CONST_27  H6    C6   C43  C38    0.00   0.0  0
 167  CONST_28  H25   C25  C6   C43  180.00   0.0  0
 167  CONST_29  H24   C24  C45  C44  180.00   0.0  0
 167  CONST_32  HN7   N7   C5   C4   180.00   0.0  0
 167  Var_01    C13   C14  C11  C12   18.68  30.0  1
 167  Var_02    H533  C53  O54  C45  179.21  30.0  3
 167  Var_03    C4    C3   C2   C1   177.24  30.0  3
 167  Var_04    C5    C4   C3   C2   179.22  30.0  3
 167  Var_05    C16   C1   C2   C3   170.50  30.0  1
 167  Var_06    N6    C5   C4   C3   172.39  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
 167  chir_01  C10  C12  C13  C16  negativ
 167  chir_02  C13  O9   C10  C14  positiv
 167  chir_03  C16  C1   C10  C15  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
 167  plan-1  C38  0.020
 167  plan-1  C43  0.020
 167  plan-1  C44  0.020
 167  plan-1  C45  0.020
 167  plan-1  C24  0.020
 167  plan-1  C25  0.020
 167  plan-1  C6   0.020
 167  plan-1  O54  0.020
 167  plan-1  H44  0.020
 167  plan-1  H24  0.020
 167  plan-1  H25  0.020
 167  plan-1  H6   0.020
 167  plan-2  C10  0.020
 167  plan-2  C11  0.020
 167  plan-2  C12  0.020
 167  plan-2  C14  0.020
 167  plan-2  C36  0.020
 167  plan-2  C37  0.020
 167  plan-2  C38  0.020
 167  plan-2  C39  0.020
 167  plan-2  C43  0.020
 167  plan-2  H36  0.020
 167  plan-2  H37  0.020
 167  plan-2  H39  0.020
 167  plan-3  C4   0.020
 167  plan-3  C5   0.020
 167  plan-3  N6   0.020
 167  plan-3  N7   0.020
 167  plan-3  H62  0.020
 167  plan-3  H61  0.020
 167  plan-3  HN7  0.020
 167  plan-4  O8   0.020
 167  plan-4  O8A  0.020
 167  plan-4  C16  0.020
 167  plan-4  C15  0.020

