# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 07:24:21 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: ethyl (5S)-3-(3,4-difluorobenzene-1-carbonyl)-1,1-dimethyl-1,2,3,4,5,6-hexahydroazepino[4,5-b]indole-5-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)[C@H]1CN(CC(C)(C)c2c1[nH]c3ccccc23)C(=O)c4ccc(F)c(F)c4
#
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
 9M1  9M1  'ethyl (5S)-3-(3,4-difluorobenzene-1-carbonyl)-1,1-dimethyl-1,2,3,4,5,6-hexahydroazepino[4,5-b]indole-5-carboxylate'  ligand  55  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9M1
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
 9M1  N3   N  NT    0  -0.460   0.5635  -0.3406  -0.8504
 9M1  C4   C  CR5   0   0.066  -2.5318   0.2862  -0.4505
 9M1  C6   C  CH2   0  -0.294   0.3553   0.1098   0.5171
 9M1  C7   C  CT    0  -0.223  -1.7681   0.1543  -1.7468
 9M1  C8   C  C     0   0.546   1.8063  -0.6049  -1.3199
 9M1  C10  C  CR56  0   0.331  -4.1645   0.7093   1.1054
 9M1  C13  C  CR6   0  -0.087   2.9612   0.0262  -0.6069
 9M1  C15  C  CR6   0   0.413   4.1180   1.9694   0.1672
 9M1  C17  C  CR6   0   0.400   5.1929   1.1814   0.5452
 9M1  C20  C  CR16  0  -0.396   5.1650  -0.1827   0.3451
 9M1  C24  C  CH3   0  -0.651  -2.6678  -0.5017  -2.8065
 9M1  C26  C  CR16  0  -0.388  -4.7809   1.4839  -1.0952
 9M1  C28  C  CH2   0  -0.183   0.8023  -3.9680   1.0830
 9M1  C31  C  CH3   0  -0.693   2.2387  -4.1779   0.6728
 9M1  O22  O  O2    0  -0.445   0.5529  -2.5508   1.0945
 9M1  C11  C  C     0   0.636  -0.6879  -2.1310   1.2450
 9M1  O18  O  O     0  -0.438  -1.6390  -2.8526   1.4068
 9M1  C2   C  CH1   0  -0.568  -0.7811  -0.6146   1.2367
 9M1  C12  C  CH2   0  -0.295  -0.5734  -0.8075  -1.6247
 9M1  C25  C  CH3   0  -0.637  -1.2941   1.5216  -2.2476
 9M1  C1   C  CR5   0   0.353  -2.1199  -0.1230   0.7908
 9M1  N5   N  NR15  0  -0.743  -3.1007   0.1174   1.7130
 9M1  C27  C  CR16  0  -0.309  -5.3704   1.1458   1.6510
 9M1  C30  C  CR16  0  -0.288  -6.2724   1.7530   0.8006
 9M1  C29  C  CR16  0  -0.262  -5.9754   1.9257  -0.5604
 9M1  C9   C  CR56  0   0.058  -3.8455   0.8480  -0.2648
 9M1  O16  O  O     0  -0.476   2.0256  -1.2900  -2.3073
 9M1  C19  C  CR16  0  -0.264   4.0513  -0.7576  -0.2492
 9M1  F23  F  F     0  -0.300   6.2553   1.7630   1.1049
 9M1  F21  F  F     0  -0.302   4.1838   3.2895   0.3568
 9M1  C14  C  CR16  0  -0.401   2.9983   1.4031  -0.4003
 9M1  H1   H  HCH2  0   0.290   1.2686  -0.0328   1.0880
 9M1  H2   H  HCH2  0   0.267   0.1314   1.1792   0.5527
 9M1  H3   H  HCR6  0   0.299   6.0103  -0.7873   0.6461
 9M1  H4   H  HCH3  0   0.241  -3.5607   0.0825  -3.0157
 9M1  H5   H  HCH3  0   0.234  -2.1284  -0.6131  -3.7491
 9M1  H6   H  HCH3  0   0.233  -2.9944  -1.4923  -2.4848
 9M1  H7   H  HCR6  0   0.238  -4.5799   1.6507  -2.1449
 9M1  H8   H  HCH2  0   0.239   0.1242  -4.4534   0.3792
 9M1  H9   H  HCH2  0   0.242   0.6079  -4.3750   2.0769
 9M1  H10  H  HCH3  0   0.245   2.4576  -5.2453   0.6777
 9M1  H11  H  HCH3  0   0.236   2.4205  -3.8060  -0.3360
 9M1  H12  H  HCH3  0   0.237   2.9321  -3.6905   1.3587
 9M1  H13  H  HCH1  0   0.344  -0.6674  -0.3234   2.2896
 9M1  H14  H  HCH2  0   0.274  -0.2055  -1.0038  -2.6296
 9M1  H15  H  HCH2  0   0.249  -0.9327  -1.7742  -1.2529
 9M1  H16  H  HCH3  0   0.232  -0.6170   2.0013  -1.5396
 9M1  H17  H  HCH3  0   0.229  -0.7709   1.4250  -3.2017
 9M1  H18  H  HCH3  0   0.236  -2.1361   2.1979  -2.4016
 9M1  H19  H  HNR5  0   0.407  -3.0247  -0.0727   2.6987
 9M1  H20  H  HCR6  0   0.258  -5.5858   1.0205   2.7047
 9M1  H21  H  HCR6  0   0.249  -7.2173   2.1094   1.1895
 9M1  H22  H  HCR6  0   0.246  -6.6960   2.4182  -1.2007
 9M1  H23  H  HCR6  0   0.275   4.0356  -1.8253  -0.4196
 9M1  H24  H  HCR6  0   0.295   2.1708   2.0413  -0.6863

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
 9M1  C31  C28  single    1.508  0.020  1.508
 9M1  C28  O22  single    1.439  0.020  1.439
 9M1  O22  C11  single    1.319  0.020  1.319
 9M1  C12  N3   single    1.453  0.020  1.453
 9M1  C12  C7   single    1.539  0.020  1.539
 9M1  C25  C7   single    1.531  0.020  1.531
 9M1  N3   C6   single    1.455  0.020  1.455
 9M1  N3   C8   single    1.354  0.020  1.354
 9M1  C11  C2   single    1.519  0.020  1.519
 9M1  C11  O18  double    1.205  0.020  1.205
 9M1  C6   C2   single    1.528  0.020  1.528
 9M1  O16  C8   double    1.222  0.020  1.222
 9M1  F21  C15  single    1.335  0.020  1.335
 9M1  C2   C1   single    1.494  0.020  1.494
 9M1  C14  C15  aromatic  1.377  0.020  1.377
 9M1  C14  C13  aromatic  1.393  0.020  1.393
 9M1  C8   C13  single    1.497  0.020  1.497
 9M1  C7   C4   single    1.510  0.020  1.510
 9M1  C7   C24  single    1.537  0.020  1.537
 9M1  C15  C17  aromatic  1.385  0.020  1.385
 9M1  C13  C19  aromatic  1.390  0.020  1.390
 9M1  C1   C4   aromatic  1.370  0.020  1.370
 9M1  C1   N5   aromatic  1.367  0.020  1.367
 9M1  C4   C9   aromatic  1.441  0.020  1.441
 9M1  N5   C10  aromatic  1.361  0.020  1.361
 9M1  C17  F23  single    1.334  0.020  1.334
 9M1  C17  C20  aromatic  1.379  0.020  1.379
 9M1  C19  C20  aromatic  1.387  0.020  1.387
 9M1  C9   C10  aromatic  1.414  0.020  1.414
 9M1  C9   C26  aromatic  1.403  0.020  1.403
 9M1  C10  C27  aromatic  1.394  0.020  1.394
 9M1  C26  C29  aromatic  1.381  0.020  1.381
 9M1  C27  C30  aromatic  1.380  0.020  1.380
 9M1  C29  C30  aromatic  1.404  0.020  1.404
 9M1  C6   H1   single    0.970  0.020  1.090
 9M1  C6   H2   single    0.970  0.020  1.090
 9M1  C20  H3   single    0.930  0.020  1.080
 9M1  C24  H4   single    0.970  0.020  1.090
 9M1  C24  H5   single    0.970  0.020  1.090
 9M1  C24  H6   single    0.970  0.020  1.090
 9M1  C26  H7   single    0.930  0.020  1.080
 9M1  C28  H8   single    0.970  0.020  1.090
 9M1  C28  H9   single    0.970  0.020  1.090
 9M1  C31  H10  single    0.970  0.020  1.090
 9M1  C31  H11  single    0.970  0.020  1.090
 9M1  C31  H12  single    0.970  0.020  1.090
 9M1  C2   H13  single    0.970  0.020  1.090
 9M1  C12  H14  single    0.970  0.020  1.090
 9M1  C12  H15  single    0.970  0.020  1.090
 9M1  C25  H16  single    0.970  0.020  1.090
 9M1  C25  H17  single    0.970  0.020  1.090
 9M1  C25  H18  single    0.970  0.020  1.090
 9M1  N5   H19  single    0.860  0.020  1.020
 9M1  C27  H20  single    0.930  0.020  1.080
 9M1  C30  H21  single    0.930  0.020  1.080
 9M1  C29  H22  single    0.930  0.020  1.080
 9M1  C19  H23  single    0.930  0.020  1.080
 9M1  C14  H24  single    0.930  0.020  1.080

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
 9M1  C12  N3   C8   118.08  3.000
 9M1  C8   N3   C6   121.17  3.000
 9M1  C12  N3   C6   119.25  3.000
 9M1  C9   C4   C1   105.89  3.000
 9M1  C9   C4   C7   127.29  3.000
 9M1  C1   C4   C7   126.82  3.000
 9M1  H2   C6   H1   106.47  3.000
 9M1  H2   C6   C2   107.23  3.000
 9M1  H1   C6   C2   108.39  3.000
 9M1  H2   C6   N3   111.28  3.000
 9M1  H1   C6   N3   109.45  3.000
 9M1  C2   C6   N3   113.73  3.000
 9M1  C25  C7   C12  110.10  3.000
 9M1  C25  C7   C24  109.68  3.000
 9M1  C12  C7   C24  104.03  3.000
 9M1  C24  C7   C4   109.45  3.000
 9M1  C25  C7   C4   111.05  3.000
 9M1  C12  C7   C4   112.29  3.000
 9M1  O16  C8   C13  118.88  3.000
 9M1  C13  C8   N3   117.43  3.000
 9M1  O16  C8   N3   123.66  3.000
 9M1  C9   C10  C27  122.95  3.000
 9M1  C27  C10  N5   129.64  3.000
 9M1  C9   C10  N5   107.40  3.000
 9M1  C14  C13  C19  119.90  3.000
 9M1  C19  C13  C8   119.35  3.000
 9M1  C14  C13  C8   120.53  3.000
 9M1  C14  C15  F21  120.34  3.000
 9M1  C14  C15  C17  120.62  3.000
 9M1  F21  C15  C17  119.04  3.000
 9M1  F23  C17  C20  120.54  3.000
 9M1  C20  C17  C15  120.49  3.000
 9M1  F23  C17  C15  118.97  3.000
 9M1  H3   C20  C19  120.99  3.000
 9M1  H3   C20  C17  119.78  3.000
 9M1  C19  C20  C17  119.23  3.000
 9M1  H6   C24  H5   108.04  3.000
 9M1  H6   C24  H4   107.37  3.000
 9M1  H5   C24  H4   107.13  3.000
 9M1  H6   C24  C7   111.05  3.000
 9M1  H5   C24  C7   110.46  3.000
 9M1  H4   C24  C7   112.58  3.000
 9M1  H7   C26  C9   121.35  3.000
 9M1  H7   C26  C29  119.15  3.000
 9M1  C9   C26  C29  119.49  3.000
 9M1  H9   C28  H8   108.10  3.000
 9M1  H9   C28  O22  109.21  3.000
 9M1  H8   C28  O22  109.61  3.000
 9M1  H9   C28  C31  111.43  3.000
 9M1  H8   C28  C31  110.76  3.000
 9M1  O22  C28  C31  107.71  3.000
 9M1  H12  C31  H11  108.87  3.000
 9M1  H12  C31  H10  107.90  3.000
 9M1  H11  C31  H10  107.74  3.000
 9M1  H12  C31  C28  111.86  3.000
 9M1  H11  C31  C28  111.28  3.000
 9M1  H10  C31  C28  109.05  3.000
 9M1  C11  O22  C28  118.53  3.000
 9M1  C2   C11  O18  123.38  3.000
 9M1  O18  C11  O22  124.58  3.000
 9M1  C2   C11  O22  112.02  3.000
 9M1  H13  C2   C1   106.95  3.000
 9M1  H13  C2   C11  104.66  3.000
 9M1  C1   C2   C11  112.64  3.000
 9M1  H13  C2   C6   104.41  3.000
 9M1  C1   C2   C6   111.71  3.000
 9M1  C11  C2   C6   115.48  3.000
 9M1  H15  C12  H14  105.37  3.000
 9M1  H15  C12  C7   108.88  3.000
 9M1  H14  C12  C7   107.58  3.000
 9M1  H15  C12  N3   111.05  3.000
 9M1  H14  C12  N3   106.60  3.000
 9M1  C7   C12  N3   116.69  3.000
 9M1  H18  C25  H17  107.54  3.000
 9M1  H18  C25  H16  107.34  3.000
 9M1  H17  C25  H16  107.97  3.000
 9M1  H18  C25  C7   111.14  3.000
 9M1  H17  C25  C7   110.79  3.000
 9M1  H16  C25  C7   111.87  3.000
 9M1  N5   C1   C2   119.94  3.000
 9M1  N5   C1   C4   110.05  3.000
 9M1  C2   C1   C4   129.63  3.000
 9M1  H19  N5   C1   124.96  3.000
 9M1  H19  N5   C10  125.33  3.000
 9M1  C1   N5   C10  109.64  3.000
 9M1  H20  C27  C30  121.36  3.000
 9M1  H20  C27  C10  121.12  3.000
 9M1  C30  C27  C10  117.52  3.000
 9M1  H21  C30  C29  119.52  3.000
 9M1  H21  C30  C27  119.60  3.000
 9M1  C29  C30  C27  120.88  3.000
 9M1  H22  C29  C30  119.25  3.000
 9M1  H22  C29  C26  119.48  3.000
 9M1  C30  C29  C26  121.27  3.000
 9M1  C26  C9   C10  117.88  3.000
 9M1  C26  C9   C4   135.09  3.000
 9M1  C10  C9   C4   107.00  3.000
 9M1  H23  C19  C20  119.24  3.000
 9M1  H23  C19  C13  120.33  3.000
 9M1  C20  C19  C13  120.43  3.000
 9M1  H24  C14  C15  119.18  3.000
 9M1  H24  C14  C13  121.52  3.000
 9M1  C15  C14  C13  119.29  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
 9M1  CONST_01  N5   C10  C9   C4      0.00   0.0  0
 9M1  CONST_02  C27  C10  C9   C4    180.00   0.0  0
 9M1  CONST_03  C29  C26  C9   C4    180.00   0.0  0
 9M1  CONST_04  C29  C26  C9   C10     0.00   0.0  0
 9M1  CONST_05  C29  C30  C27  C10     0.00   0.0  0
 9M1  CONST_06  C17  C15  C14  C13     0.00   0.0  0
 9M1  CONST_07  C17  C20  C19  C13     0.00   0.0  0
 9M1  CONST_08  C19  C13  C14  C15     0.00   0.0  0
 9M1  CONST_09  C19  C20  C17  C15     0.00   0.0  0
 9M1  CONST_10  C14  C15  C17  C20     0.00   0.0  0
 9M1  CONST_11  C14  C13  C19  C20     0.00   0.0  0
 9M1  CONST_12  N5   C10  C9   C26   180.00   0.0  0
 9M1  CONST_13  C27  C10  C9   C26     0.00   0.0  0
 9M1  CONST_14  C27  C30  C29  C26     0.00   0.0  0
 9M1  CONST_15  C9   C10  N5   C1      0.00   0.0  0
 9M1  CONST_16  C27  C10  N5   C1    180.00   0.0  0
 9M1  CONST_17  C30  C27  C10  N5    180.00   0.0  0
 9M1  CONST_18  C9   C10  C27  C30     0.00   0.0  0
 9M1  CONST_19  C9   C26  C29  C30     0.00   0.0  0
 9M1  CONST_20  C15  C14  C13  C8    180.00   0.0  0
 9M1  CONST_21  C20  C19  C13  C8    180.00   0.0  0
 9M1  CONST_22  F21  C15  C14  C13   180.00   0.0  0
 9M1  CONST_23  F21  C15  C17  C20   180.00   0.0  0
 9M1  CONST_24  F23  C17  C20  C19   180.00   0.0  0
 9M1  CONST_25  C14  C15  C17  F23   180.00   0.0  0
 9M1  CONST_26  H7   C26  C9   C4      0.00   0.0  0
 9M1  CONST_27  H21  C30  C27  C10   180.00   0.0  0
 9M1  CONST_28  H3   C20  C19  C13   180.00   0.0  0
 9M1  CONST_29  H24  C14  C15  C17   180.00   0.0  0
 9M1  CONST_30  H23  C19  C20  C17   180.00   0.0  0
 9M1  CONST_31  H20  C27  C10  N5      0.00   0.0  0
 9M1  CONST_32  H19  N5   C10  C27     0.00   0.0  0
 9M1  CONST_33  H22  C29  C30  C27   180.00   0.0  0
 9M1  Var_01    C14  C13  C8   N3    -53.59  30.0  2
 9M1  Var_02    C2   C11  O22  C28   179.95  30.0  3
 9M1  Var_03    H16  C25  C7   C24  -177.56  30.0  3
 9M1  Var_04    H4   C24  C7   C25   -61.28  30.0  3
 9M1  Var_05    H10  C31  C28  O22   178.79  30.0  3
 9M1  Var_06    H8   C28  O22  C11    50.20  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
 9M1  chir_01  C2  C11  C6  C1  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
 9M1  plan-1  C8   0.020
 9M1  plan-1  C13  0.020
 9M1  plan-1  C15  0.020
 9M1  plan-1  C17  0.020
 9M1  plan-1  C20  0.020
 9M1  plan-1  C19  0.020
 9M1  plan-1  F23  0.020
 9M1  plan-1  F21  0.020
 9M1  plan-1  C14  0.020
 9M1  plan-1  H3   0.020
 9M1  plan-1  H23  0.020
 9M1  plan-1  H24  0.020
 9M1  plan-2  C4   0.020
 9M1  plan-2  C7   0.020
 9M1  plan-2  C10  0.020
 9M1  plan-2  C26  0.020
 9M1  plan-2  C2   0.020
 9M1  plan-2  C1   0.020
 9M1  plan-2  N5   0.020
 9M1  plan-2  C27  0.020
 9M1  plan-2  C30  0.020
 9M1  plan-2  C29  0.020
 9M1  plan-2  C9   0.020
 9M1  plan-2  H7   0.020
 9M1  plan-2  H19  0.020
 9M1  plan-2  H20  0.020
 9M1  plan-2  H21  0.020
 9M1  plan-2  H22  0.020
 9M1  plan-3  N3   0.020
 9M1  plan-3  C6   0.020
 9M1  plan-3  C8   0.020
 9M1  plan-3  C13  0.020
 9M1  plan-3  C12  0.020
 9M1  plan-3  O16  0.020
 9M1  plan-4  O22  0.020
 9M1  plan-4  C11  0.020
 9M1  plan-4  O18  0.020
 9M1  plan-4  C2   0.020

