# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 04:30:33 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (3aS,8S,9aS)-10-methyl-4-oxo-1,4,6,8,9,9a-hexahydro-3a,8-epiminocyclohepta[1,2-c:4,5-c']dipyrrole-2(3H)-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@H]2C[C@H]3CN(C[C@@]13C(=O)c4c[nH]cc24)C=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
 RGV  RGV  (3aS,8S,9aS)-10-methyl-4-oxo-1,4,6,8,9,9a-hexahydro-3a,8-epiminocyclohepta[1,2-c:4,5-c']dipyrrole-2(3H)-carbaldehyde  ligand  33  18  .  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_RGV
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
 RGV  C10  C  C     0   0.376   0.5968  -1.1269   0.4387
 RGV  C13  C  CR15  0  -0.029   3.1493  -1.1746   0.7744
 RGV  C15  C  CR15  0  -0.104   3.5842   0.8436  -0.0955
 RGV  C01  C  CH3   0  -0.536   0.4864  -0.1079  -2.4228
 RGV  C03  C  CH1   0  -0.241   1.0966   1.5084  -0.6626
 RGV  C04  C  CH2   0  -0.411   0.3212   2.1160   0.5191
 RGV  C05  C  CR15  0  -0.268  -0.6579   1.0038   0.9220
 RGV  C06  C  CH2   0  -0.248  -2.1327   1.3507   0.7373
 RGV  C08  C  CH2   0  -0.255  -1.8100  -0.7485  -0.3808
 RGV  C09  C  CR5   0  -0.088  -0.4344  -0.1315  -0.1211
 RGV  C12  C  CR5   0  -0.139   1.9473  -0.6113   0.3850
 RGV  C16  C  CR5   0   0.058   2.2331   0.6717  -0.1652
 RGV  N02  N  NT    0  -0.404   0.0807   0.6367  -1.2515
 RGV  N07  N  NR5   0  -0.424  -2.7335   0.0899   0.3632
 RGV  N14  N  NR15  0  -0.570   4.1130  -0.2865   0.4792
 RGV  O11  O  O     0  -0.411   0.2889  -2.2079   0.9070
 RGV  O18  O  O     0  -0.503  -4.4743  -1.3609   0.3848
 RGV  H1   H  HCR5  0   0.291   3.3750  -2.1268   1.2251
 RGV  H2   H  HCR5  0   0.282   4.2169   1.6605  -0.4014
 RGV  H3   H  H     0   0.198  -4.4832   0.4443   1.3279
 RGV  H4   H  HCH3  0   0.241  -0.3632  -0.6593  -2.8273
 RGV  H5   H  HCH3  0   0.242   0.8105   0.5909  -3.1947
 RGV  H6   H  HCH3  0   0.209   1.3025  -0.8221  -2.2547
 RGV  H7   H  HCH1  0   0.255   1.4230   2.2636  -1.3802
 RGV  H8   H  HCH2  0   0.252   0.9808   2.4135   1.3323
 RGV  H9   H  HCH2  0   0.251  -0.2182   3.0067   0.1926
 RGV  H10  H  HCR5  0   0.279  -0.4912   0.6486   1.9407
 RGV  H11  H  HCH2  0   0.266  -2.5923   1.7504   1.6411
 RGV  H12  H  HCH2  0   0.242  -2.2536   2.0901  -0.0601
 RGV  H13  H  HCH2  0   0.255  -2.0462  -0.7443  -1.4473
 RGV  H14  H  HCH2  0   0.262  -1.8796  -1.7780  -0.0326
 RGV  H16  H  HNR5  0   0.421   5.0951  -0.4345   0.6474
 RGV  C17  C  C1    0   0.252  -3.9615  -0.2996   0.7059

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
 RGV  O18  C17  double    1.222  0.020  1.222
 RGV  C17  N07  single    1.333  0.020  1.333
 RGV  N07  C06  single    1.446  0.020  1.446
 RGV  N07  C08  single    1.452  0.020  1.452
 RGV  C06  C05  single    1.526  0.020  1.526
 RGV  C08  C09  single    1.530  0.020  1.530
 RGV  C05  C09  single    1.558  0.020  1.558
 RGV  C05  C04  single    1.536  0.020  1.536
 RGV  C09  N02  single    1.461  0.020  1.461
 RGV  C09  C10  single    1.539  0.020  1.539
 RGV  N02  C01  single    1.446  0.020  1.446
 RGV  N02  C03  single    1.462  0.020  1.462
 RGV  C04  C03  single    1.539  0.020  1.539
 RGV  C03  C16  single    1.496  0.020  1.496
 RGV  C10  O11  double    1.218  0.020  1.218
 RGV  C10  C12  single    1.447  0.020  1.447
 RGV  C16  C12  aromatic  1.425  0.020  1.425
 RGV  C16  C15  aromatic  1.364  0.020  1.364
 RGV  C12  C13  aromatic  1.383  0.020  1.383
 RGV  C15  N14  aromatic  1.374  0.020  1.374
 RGV  C13  N14  aromatic  1.343  0.020  1.343
 RGV  C13  H1   single    0.930  0.020  1.080
 RGV  C15  H2   single    0.930  0.020  1.080
 RGV  C17  H3   single    0.930  0.020  1.080
 RGV  C01  H4   single    0.970  0.020  1.090
 RGV  C01  H5   single    0.970  0.020  1.090
 RGV  C01  H6   single    0.970  0.020  1.090
 RGV  C03  H7   single    0.970  0.020  1.090
 RGV  C04  H8   single    0.970  0.020  1.090
 RGV  C04  H9   single    0.970  0.020  1.090
 RGV  C05  H10  single    0.970  0.020  1.090
 RGV  C06  H11  single    0.970  0.020  1.090
 RGV  C06  H12  single    0.970  0.020  1.090
 RGV  C08  H13  single    0.970  0.020  1.090
 RGV  C08  H14  single    0.970  0.020  1.090
 RGV  N14  H16  single    0.860  0.020  1.020

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
 RGV  O11  C10  C12  124.53  3.000
 RGV  C12  C10  C09  112.43  3.000
 RGV  O11  C10  C09  123.01  3.000
 RGV  H1   C13  N14  121.73  3.000
 RGV  H1   C13  C12  131.27  3.000
 RGV  N14  C13  C12  107.00  3.000
 RGV  H2   C15  N14  121.09  3.000
 RGV  H2   C15  C16  131.51  3.000
 RGV  N14  C15  C16  107.40  3.000
 RGV  H6   C01  H5   107.72  3.000
 RGV  H6   C01  H4   107.87  3.000
 RGV  H5   C01  H4   107.04  3.000
 RGV  H6   C01  N02  114.82  3.000
 RGV  H5   C01  N02  109.08  3.000
 RGV  H4   C01  N02  110.01  3.000
 RGV  H7   C03  N02  110.82  3.000
 RGV  H7   C03  C16  112.22  3.000
 RGV  N02  C03  C16  109.15  3.000
 RGV  H7   C03  C04  112.48  3.000
 RGV  C16  C03  C04  110.38  3.000
 RGV  N02  C03  C04  101.22  3.000
 RGV  H9   C04  H8   107.46  3.000
 RGV  H9   C04  C05  110.76  3.000
 RGV  H8   C04  C05  112.85  3.000
 RGV  H9   C04  C03  109.97  3.000
 RGV  H8   C04  C03  112.11  3.000
 RGV  C05  C04  C03  103.70  3.000
 RGV  H10  C05  C09  111.45  3.000
 RGV  H10  C05  C06  109.54  3.000
 RGV  C09  C05  C06  102.90  3.000
 RGV  H10  C05  C04  112.53  3.000
 RGV  C09  C05  C04  105.11  3.000
 RGV  C06  C05  C04  114.82  3.000
 RGV  H12  C06  H11  108.05  3.000
 RGV  H12  C06  N07  110.78  3.000
 RGV  H11  C06  N07  111.05  3.000
 RGV  H12  C06  C05  110.40  3.000
 RGV  H11  C06  C05  112.98  3.000
 RGV  N07  C06  C05  103.57  3.000
 RGV  H14  C08  H13  107.58  3.000
 RGV  H14  C08  N07  109.96  3.000
 RGV  H13  C08  N07  111.13  3.000
 RGV  H14  C08  C09  112.61  3.000
 RGV  H13  C08  C09  111.01  3.000
 RGV  N07  C08  C09  104.59  3.000
 RGV  N02  C09  C08  113.44  3.000
 RGV  N02  C09  C05  100.69  3.000
 RGV  C08  C09  C05  106.18  3.000
 RGV  N02  C09  C10  112.68  3.000
 RGV  C05  C09  C10  108.90  3.000
 RGV  C08  C09  C10  113.79  3.000
 RGV  C16  C12  C13  107.52  3.000
 RGV  C13  C12  C10  130.97  3.000
 RGV  C16  C12  C10  121.50  3.000
 RGV  C12  C16  C03  118.65  3.000
 RGV  C12  C16  C15  107.00  3.000
 RGV  C03  C16  C15  134.34  3.000
 RGV  C09  N02  C03  104.29  3.000
 RGV  C03  N02  C01  115.99  3.000
 RGV  C09  N02  C01  117.07  3.000
 RGV  C08  N07  C06  111.83  3.000
 RGV  C08  N07  C17  123.28  3.000
 RGV  C06  N07  C17  124.82  3.000
 RGV  H16  N14  C15  124.47  3.000
 RGV  H16  N14  C13  124.45  3.000
 RGV  C15  N14  C13  111.08  3.000
 RGV  H3   C17  O18  122.45  3.000
 RGV  H3   C17  N07  112.60  3.000
 RGV  O18  C17  N07  124.95  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
 RGV  CONST_01  C16  C15  N14  C13     0.00   0.0  0
 RGV  CONST_02  C12  C13  N14  C15     0.00   0.0  0
 RGV  CONST_03  H2   C15  N14  C13   180.00   0.0  0
 RGV  CONST_04  H1   C13  N14  C15   180.00   0.0  0
 RGV  CONST_05  H16  N14  C13  C12   180.00   0.0  0
 RGV  CONST_06  O18  C17  N07  C06   180.00   0.0  0
 RGV  CONST_07  O18  C17  N07  C08     0.00   0.0  0
 RGV  Var_01    C08  N07  C06  C05   -31.33  30.0  1
 RGV  Var_02    C09  C08  N07  C06    16.16  30.0  1
 RGV  Var_03    H4   C01  N02  C03  -175.41  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
 RGV  chir_01  C03  N02  C04  C16  negativ
 RGV  chir_02  C05  C06  C09  C04  negativ
 RGV  chir_03  C09  C10  C05  C08  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
 RGV  plan-1  C06  0.020
 RGV  plan-1  C08  0.020
 RGV  plan-1  N07  0.020
 RGV  plan-1  O18  0.020
 RGV  plan-1  H3   0.020
 RGV  plan-1  C17  0.020
 RGV  plan-2  C10  0.020
 RGV  plan-2  C13  0.020
 RGV  plan-2  C15  0.020
 RGV  plan-2  C03  0.020
 RGV  plan-2  C12  0.020
 RGV  plan-2  C16  0.020
 RGV  plan-2  N14  0.020
 RGV  plan-2  H1   0.020
 RGV  plan-2  H2   0.020
 RGV  plan-2  H16  0.020
 RGV  plan-3  C10  0.020
 RGV  plan-3  C09  0.020
 RGV  plan-3  C12  0.020
 RGV  plan-3  O11  0.020

