# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 17:40:32 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@@H]2[C@H](CN1[S](=O)(=O)c3ccc4OCOc4c3)c5cnccc5N(C)C2=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
 7C6  7C6  (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one  ligand  47  28  .  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_7C6
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
 7C6  C11  C  CH3   0  -0.689   0.4755  -1.3327   2.2064
 7C6  C1   C  CH1   0  -0.019  -0.5973  -1.5632   1.1597
 7C6  C2   C  CH1   0  -0.409  -1.9043  -0.7645   1.2366
 7C6  C3   C  C     0   0.588  -1.7033   0.7348   1.3657
 7C6  O1   O  O     0  -0.442  -0.9179   1.2080   2.1598
 7C6  N2   N  NT    0  -0.587  -2.4753   1.5580   0.5747
 7C6  C12  C  CH3   0  -0.558  -2.2716   2.9951   0.6791
 7C6  C4   C  CR6   0   0.441  -3.5773   1.0925  -0.1369
 7C6  C5   C  CR16  0  -0.399  -4.6093   1.9350  -0.5432
 7C6  C6   C  CR16  0  -0.072  -5.6686   1.3888  -1.2503
 7C6  N3   N  N     0  -0.413  -5.7737   0.1038  -1.5612
 7C6  C7   C  CR16  0  -0.127  -4.7845  -0.6901  -1.1650
 7C6  C8   C  CR6   0   0.032  -3.6712  -0.2594  -0.4673
 7C6  C9   C  CH1   0  -0.374  -2.5554  -1.1621  -0.0839
 7C6  C10  C  CH2   0  -0.224  -1.3891  -1.1353  -1.0900
 7C6  N1   N  N     0  -0.634  -0.2008  -1.2659  -0.2300
 7C6  S1   S  S     0   1.387   1.1766  -1.8864  -0.8776
 7C6  O2   O  OS    0  -0.649   1.4468  -3.2319  -0.3865
 7C6  O3   O  OS    0  -0.658   1.0685  -1.6836  -2.3169
 7C6  C13  C  CR6   0  -0.199   2.4367  -0.8127  -0.2659
 7C6  C14  C  CR16  0  -0.303   2.2774   0.5654  -0.4806
 7C6  C15  C  CR56  0   0.313   3.2950   1.3600  -0.0321
 7C6  O4   O  O     0  -0.480   3.3971   2.7045  -0.0848
 7C6  C19  C  CH2   0   0.070   4.6795   3.0405   0.4308
 7C6  O5   O  O     0  -0.474   5.2489   1.8368   0.9385
 7C6  C16  C  CR56  0   0.323   4.4227   0.8346   0.5915
 7C6  C17  C  CR16  0  -0.335   4.5818  -0.5128   0.7960
 7C6  C18  C  CR16  0  -0.253   3.5530  -1.3480   0.3474
 7C6  H1   H  HCH3  0   0.251   0.0234  -1.4022   3.1953
 7C6  H2   H  HCH3  0   0.239   1.2333  -2.1125   2.1457
 7C6  H3   H  HCH3  0   0.248   0.9628  -0.3673   2.1200
 7C6  H4   H  HCH1  0   0.266  -0.8980  -2.6158   1.2381
 7C6  H5   H  HCH1  0   0.327  -2.4963  -1.0919   2.0964
 7C6  H6   H  HCH3  0   0.261  -2.4420   3.4544  -0.2913
 7C6  H7   H  HCH3  0   0.256  -2.9432   3.4482   1.4094
 7C6  H8   H  HCH3  0   0.276  -1.2489   3.1962   0.9763
 7C6  H9   H  HCR6  0   0.292  -4.6186   2.9908  -0.3152
 7C6  H10  H  HCR6  0   0.268  -6.4769   2.0358  -1.5727
 7C6  H11  H  HCR6  0   0.264  -4.8714  -1.7422  -1.4195
 7C6  H12  H  HCH1  0   0.302  -2.9209  -2.1869   0.0050
 7C6  H13  H  HCH2  0   0.271  -1.4969  -1.9478  -1.8073
 7C6  H14  H  HCH2  0   0.257  -1.3493  -0.1966  -1.6448
 7C6  H15  H  HCR6  0   0.293   1.3957   0.9804  -0.9497
 7C6  H16  H  HCH2  0   0.245   5.3104   3.4379  -0.3683
 7C6  H17  H  HCH2  0   0.251   4.5757   3.7665   1.2373
 7C6  H18  H  HCR6  0   0.288   5.4577  -0.9185   1.2821
 7C6  H19  H  HCR6  0   0.285   3.6393  -2.4145   0.4987

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
 7C6  O3   S1   double    1.458  0.020  1.458
 7C6  O2   S1   double    1.458  0.020  1.458
 7C6  S1   C13  single    1.765  0.020  1.765
 7C6  S1   N1   single    1.644  0.020  1.644
 7C6  C14  C13  aromatic  1.404  0.020  1.404
 7C6  C14  C15  aromatic  1.367  0.020  1.367
 7C6  C13  C18  aromatic  1.382  0.020  1.382
 7C6  C15  O4   single    1.349  0.020  1.349
 7C6  C15  C16  aromatic  1.392  0.020  1.392
 7C6  C18  C17  aromatic  1.399  0.020  1.399
 7C6  C19  O4   single    1.422  0.020  1.422
 7C6  C19  O5   single    1.425  0.020  1.425
 7C6  N1   C10  single    1.473  0.020  1.473
 7C6  N1   C1   single    1.475  0.020  1.475
 7C6  C16  C17  aromatic  1.372  0.020  1.372
 7C6  C16  O5   single    1.344  0.020  1.344
 7C6  C10  C9   single    1.540  0.020  1.540
 7C6  C1   C11  single    1.516  0.020  1.516
 7C6  C1   C2   single    1.534  0.020  1.534
 7C6  C7   N3   aromatic  1.329  0.020  1.329
 7C6  C7   C8   aromatic  1.383  0.020  1.383
 7C6  C9   C2   single    1.525  0.020  1.525
 7C6  C9   C8   single    1.485  0.020  1.485
 7C6  N3   C6   aromatic  1.326  0.020  1.326
 7C6  C2   C3   single    1.518  0.020  1.518
 7C6  C8   C4   aromatic  1.395  0.020  1.395
 7C6  C6   C5   aromatic  1.386  0.020  1.386
 7C6  C4   C5   aromatic  1.393  0.020  1.393
 7C6  C4   N2   single    1.392  0.020  1.392
 7C6  C3   N2   single    1.378  0.020  1.378
 7C6  C3   O1   double    1.213  0.020  1.213
 7C6  N2   C12  single    1.455  0.020  1.455
 7C6  C11  H1   single    0.970  0.020  1.090
 7C6  C11  H2   single    0.970  0.020  1.090
 7C6  C11  H3   single    0.970  0.020  1.090
 7C6  C1   H4   single    0.970  0.020  1.090
 7C6  C2   H5   single    0.970  0.020  1.090
 7C6  C12  H6   single    0.970  0.020  1.090
 7C6  C12  H7   single    0.970  0.020  1.090
 7C6  C12  H8   single    0.970  0.020  1.090
 7C6  C5   H9   single    0.930  0.020  1.080
 7C6  C6   H10  single    0.930  0.020  1.080
 7C6  C7   H11  single    0.930  0.020  1.080
 7C6  C9   H12  single    0.970  0.020  1.090
 7C6  C10  H13  single    0.970  0.020  1.090
 7C6  C10  H14  single    0.970  0.020  1.090
 7C6  C14  H15  single    0.930  0.020  1.080
 7C6  C19  H16  single    0.970  0.020  1.090
 7C6  C19  H17  single    0.970  0.020  1.090
 7C6  C17  H18  single    0.930  0.020  1.080
 7C6  C18  H19  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
 7C6  H3   C11  H2   108.68  3.000
 7C6  H3   C11  H1   108.38  3.000
 7C6  H2   C11  H1   107.08  3.000
 7C6  H3   C11  C1   113.46  3.000
 7C6  H2   C11  C1   110.18  3.000
 7C6  H1   C11  C1   108.86  3.000
 7C6  H4   C1   N1   109.52  3.000
 7C6  H4   C1   C2   105.21  3.000
 7C6  N1   C1   C2    99.87  3.000
 7C6  H4   C1   C11  106.87  3.000
 7C6  C2   C1   C11  119.28  3.000
 7C6  N1   C1   C11  115.43  3.000
 7C6  H5   C2   C9   111.81  3.000
 7C6  H5   C2   C3   107.48  3.000
 7C6  C9   C2   C3   112.80  3.000
 7C6  H5   C2   C1   110.16  3.000
 7C6  C3   C2   C1   113.93  3.000
 7C6  C9   C2   C1   100.64  3.000
 7C6  N2   C3   O1   120.36  3.000
 7C6  O1   C3   C2   121.78  3.000
 7C6  N2   C3   C2   117.83  3.000
 7C6  C4   N2   C12  118.54  3.000
 7C6  C12  N2   C3   118.06  3.000
 7C6  C4   N2   C3   122.48  3.000
 7C6  H8   C12  H7   108.68  3.000
 7C6  H8   C12  H6   108.32  3.000
 7C6  H7   C12  H6   109.01  3.000
 7C6  H8   C12  N2   109.57  3.000
 7C6  H7   C12  N2   111.85  3.000
 7C6  H6   C12  N2   109.35  3.000
 7C6  C8   C4   C5   117.86  3.000
 7C6  C5   C4   N2   122.23  3.000
 7C6  C8   C4   N2   119.91  3.000
 7C6  H9   C5   C6   119.10  3.000
 7C6  H9   C5   C4   122.42  3.000
 7C6  C6   C5   C4   118.48  3.000
 7C6  H10  C6   N3   116.70  3.000
 7C6  H10  C6   C5   119.10  3.000
 7C6  N3   C6   C5   124.19  3.000
 7C6  C7   N3   C6   116.74  3.000
 7C6  H11  C7   C8   118.97  3.000
 7C6  H11  C7   N3   116.71  3.000
 7C6  C8   C7   N3   124.32  3.000
 7C6  C9   C8   C7   123.08  3.000
 7C6  C9   C8   C4   118.51  3.000
 7C6  C7   C8   C4   118.40  3.000
 7C6  H12  C9   C10  108.84  3.000
 7C6  H12  C9   C8   109.88  3.000
 7C6  C10  C9   C8   112.93  3.000
 7C6  H12  C9   C2   108.49  3.000
 7C6  C8   C9   C2   112.69  3.000
 7C6  C10  C9   C2   103.75  3.000
 7C6  H14  C10  H13  108.09  3.000
 7C6  H14  C10  N1   110.11  3.000
 7C6  H13  C10  N1   113.47  3.000
 7C6  H14  C10  C9   112.00  3.000
 7C6  H13  C10  C9   110.01  3.000
 7C6  N1   C10  C9   103.18  3.000
 7C6  S1   N1   C10  118.66  3.000
 7C6  C10  N1   C1   110.55  3.000
 7C6  S1   N1   C1   121.35  3.000
 7C6  C13  S1   O3   108.09  3.000
 7C6  C13  S1   O2   108.21  3.000
 7C6  O3   S1   O2   118.35  3.000
 7C6  C13  S1   N1   103.42  3.000
 7C6  O2   S1   N1   111.79  3.000
 7C6  O3   S1   N1   105.93  3.000
 7C6  C18  C13  C14  122.68  3.000
 7C6  C18  C13  S1   119.67  3.000
 7C6  C14  C13  S1   117.60  3.000
 7C6  H15  C14  C15  121.75  3.000
 7C6  H15  C14  C13  122.38  3.000
 7C6  C15  C14  C13  115.86  3.000
 7C6  C16  C15  O4   109.41  3.000
 7C6  C16  C15  C14  122.06  3.000
 7C6  O4   C15  C14  128.52  3.000
 7C6  C19  O4   C15  106.83  3.000
 7C6  H17  C19  H16  110.71  3.000
 7C6  H17  C19  O5   109.70  3.000
 7C6  H16  C19  O5   109.69  3.000
 7C6  H17  C19  O4   109.85  3.000
 7C6  H16  C19  O4   109.96  3.000
 7C6  O5   C19  O4   106.85  3.000
 7C6  C16  O5   C19  106.99  3.000
 7C6  C17  C16  O5   128.49  3.000
 7C6  O5   C16  C15  109.40  3.000
 7C6  C17  C16  C15  122.11  3.000
 7C6  H18  C17  C18  121.07  3.000
 7C6  H18  C17  C16  121.98  3.000
 7C6  C18  C17  C16  116.95  3.000
 7C6  H19  C18  C17  119.05  3.000
 7C6  H19  C18  C13  120.60  3.000
 7C6  C17  C18  C13  120.35  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
 7C6  CONST_01  N3   C7   C8   C4     0.00   0.0  0
 7C6  CONST_02  N3   C6   C5   C4     0.00   0.0  0
 7C6  CONST_03  C7   N3   C6   C5     0.00   0.0  0
 7C6  CONST_04  C7   C8   C4   C5     0.00   0.0  0
 7C6  CONST_05  C8   C7   N3   C6     0.00   0.0  0
 7C6  CONST_06  C8   C4   C5   C6     0.00   0.0  0
 7C6  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 7C6  CONST_08  C16  C17  C18  C13    0.00   0.0  0
 7C6  CONST_09  C17  C18  C13  C14    0.00   0.0  0
 7C6  CONST_10  C17  C16  C15  C14    0.00   0.0  0
 7C6  CONST_11  C18  C13  C14  C15    0.00   0.0  0
 7C6  CONST_12  C18  C17  C16  C15    0.00   0.0  0
 7C6  CONST_13  C4   N2   C3   C2     0.00   0.0  0
 7C6  CONST_14  C15  C14  C13  S1   180.00   0.0  0
 7C6  CONST_15  C17  C18  C13  S1   180.00   0.0  0
 7C6  CONST_16  C12  N2   C3   C2   180.00   0.0  0
 7C6  CONST_17  C4   N2   C3   O1   180.00   0.0  0
 7C6  CONST_18  H9   C5   C4   N2     0.00   0.0  0
 7C6  CONST_19  H11  C7   C8   C4   180.00   0.0  0
 7C6  CONST_20  H10  C6   C5   C4   180.00   0.0  0
 7C6  CONST_21  H18  C17  C18  C13  180.00   0.0  0
 7C6  CONST_22  H19  C18  C13  C14  180.00   0.0  0
 7C6  CONST_23  H15  C14  C15  O4     0.00   0.0  0
 7C6  CONST_24  C12  N2   C3   O1     0.00   0.0  0
 7C6  Var_01    C9   C10  N1   C1     8.30  30.0  1
 7C6  Var_02    C8   C4   N2   C3   -23.01  30.0  1
 7C6  Var_03    O5   C19  O4   C15   -7.07  30.0  1
 7C6  Var_04    C16  C15  O4   C19    4.50  30.0  1
 7C6  Var_05    C17  C16  O5   C19  176.32  30.0  1
 7C6  Var_06    C13  S1   N1   C1   -80.81  30.0  1
 7C6  Var_07    C14  C13  S1   N1   -53.49  30.0  2
 7C6  Var_08    H6   C12  N2   C3   146.80  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
 7C6  chir_01  C1  N1  C11  C2   negativ
 7C6  chir_02  C2  C1  C9   C3   positiv
 7C6  chir_03  C9  C8  C2   C10  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
 7C6  plan-1  S1   0.020
 7C6  plan-1  C13  0.020
 7C6  plan-1  C14  0.020
 7C6  plan-1  C15  0.020
 7C6  plan-1  O4   0.020
 7C6  plan-1  O5   0.020
 7C6  plan-1  C16  0.020
 7C6  plan-1  C17  0.020
 7C6  plan-1  C18  0.020
 7C6  plan-1  H15  0.020
 7C6  plan-1  H18  0.020
 7C6  plan-1  H19  0.020
 7C6  plan-2  N2   0.020
 7C6  plan-2  C4   0.020
 7C6  plan-2  C5   0.020
 7C6  plan-2  C6   0.020
 7C6  plan-2  N3   0.020
 7C6  plan-2  C7   0.020
 7C6  plan-2  C8   0.020
 7C6  plan-2  C9   0.020
 7C6  plan-2  H9   0.020
 7C6  plan-2  H10  0.020
 7C6  plan-2  H11  0.020
 7C6  plan-3  C2   0.020
 7C6  plan-3  C3   0.020
 7C6  plan-3  O1   0.020
 7C6  plan-3  N2   0.020
 7C6  plan-3  C12  0.020
 7C6  plan-3  C4   0.020

