# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 05:36:02 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (3aS,8S,9aS)-2-acetyl-10-methyl-2,3,6,8,9,9a-hexahydro-3a,8-epiminocyclohepta[1,2-c:4,5-c']dipyrrol-4(1H)-one
#   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(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
 RGM  RGM  (3aS,8S,9aS)-2-acetyl-10-methyl-2,3,6,8,9,9a-hexahydro-3a,8-epiminocyclohepta[1,2-c:4,5-c']dipyrrol-4(1H)-one  ligand  36  19  .  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_RGM
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
 RGM  C10  C  C     0   0.381  -1.0281  -1.1525  -0.6588
 RGM  C13  C  CR15  0  -0.028  -3.5977  -0.9852  -0.7052
 RGM  C15  C  CR15  0  -0.105  -3.7654   1.0003   0.3197
 RGM  C01  C  CH3   0  -0.534  -0.5684  -0.3071   2.2596
 RGM  C03  C  CH1   0  -0.235  -1.1783   1.4296   0.6214
 RGM  C04  C  CH2   0  -0.422  -0.4893   2.0029  -0.6358
 RGM  C05  C  CR15  0  -0.278   0.4528   0.8727  -1.0803
 RGM  C06  C  CH2   0  -0.236   1.9319   1.1612  -0.8032
 RGM  C08  C  CH2   0  -0.234   1.4447  -1.0768  -0.0134
 RGM  C09  C  CR5   0  -0.105   0.1417  -0.3069  -0.1259
 RGM  C12  C  CR5   0  -0.136  -2.3177  -0.5427  -0.4223
 RGM  C16  C  CR5   0   0.053  -2.4345   0.7190   0.2282
 RGM  C18  C  CH3   0  -0.790   4.7161   0.8320  -0.1910
 RGM  N02  N  NT    0  -0.402  -0.1996   0.4434   1.0805
 RGM  N07  N  NR5   0  -0.455   2.4697  -0.0833  -0.2789
 RGM  N14  N  NR15  0  -0.570  -4.4462  -0.0468  -0.2539
 RGM  O11  O  O     0  -0.413  -0.8641  -2.2100  -1.2413
 RGM  O19  O  O     0  -0.517   4.1247  -1.3826   0.5021
 RGM  H1   H  HCR5  0   0.291  -3.9493  -1.8873  -1.1780
 RGM  H2   H  HCR5  0   0.282  -4.2896   1.8431   0.7389
 RGM  H3   H  HCH3  0   0.208  -1.4678  -0.9268   2.1517
 RGM  H4   H  HCH3  0   0.239   0.2521  -0.9584   2.5606
 RGM  H5   H  HCH3  0   0.242  -0.7419   0.3878   3.0822
 RGM  H6   H  HCH1  0   0.255  -1.3515   2.1870   1.3886
 RGM  H7   H  HCH2  0   0.255  -1.2172   2.2632  -1.4018
 RGM  H8   H  HCH2  0   0.253   0.0672   2.9092  -0.3945
 RGM  H9   H  HCR5  0   0.278   0.3155   0.5958  -2.1267
 RGM  H10  H  HCH2  0   0.254   2.4468   1.4670  -1.7153
 RGM  H11  H  HCH2  0   0.243   2.0429   1.9678  -0.0742
 RGM  H12  H  HCH2  0   0.253   1.5793  -1.5317   0.9686
 RGM  H13  H  HCH2  0   0.250   1.4840  -1.8812  -0.7505
 RGM  H14  H  HCH3  0   0.257   4.5630   1.3350  -1.1448
 RGM  H15  H  HCH3  0   0.268   4.5908   1.5814   0.5935
 RGM  H16  H  HCH3  0   0.265   5.7383   0.4641  -0.1500
 RGM  H18  H  HNR5  0   0.421  -5.4498  -0.1056  -0.3205
 RGM  C17  C  C     0   0.511   3.7561  -0.3097   0.0337

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
 RGM  C04  C05  single    1.537  0.020  1.537
 RGM  C04  C03  single    1.544  0.020  1.544
 RGM  C06  C05  single    1.532  0.020  1.532
 RGM  C06  N07  single    1.454  0.020  1.454
 RGM  C05  C09  single    1.549  0.020  1.549
 RGM  O19  C17  double    1.227  0.020  1.227
 RGM  C03  C16  single    1.496  0.020  1.496
 RGM  C03  N02  single    1.463  0.020  1.463
 RGM  C15  C16  aromatic  1.363  0.020  1.363
 RGM  C15  N14  aromatic  1.374  0.020  1.374
 RGM  C16  C12  aromatic  1.424  0.020  1.424
 RGM  N14  C13  aromatic  1.343  0.020  1.343
 RGM  N07  C17  single    1.343  0.020  1.343
 RGM  N07  C08  single    1.452  0.020  1.452
 RGM  C17  C18  single    1.509  0.020  1.509
 RGM  C12  C13  aromatic  1.384  0.020  1.384
 RGM  C12  C10  single    1.446  0.020  1.446
 RGM  C09  C10  single    1.539  0.020  1.539
 RGM  C09  N02  single    1.461  0.020  1.461
 RGM  C09  C08  single    1.518  0.020  1.518
 RGM  C10  O11  double    1.218  0.020  1.218
 RGM  N02  C01  single    1.446  0.020  1.446
 RGM  C13  H1   single    0.930  0.020  1.080
 RGM  C15  H2   single    0.930  0.020  1.080
 RGM  C01  H3   single    0.970  0.020  1.090
 RGM  C01  H4   single    0.970  0.020  1.090
 RGM  C01  H5   single    0.970  0.020  1.090
 RGM  C03  H6   single    0.970  0.020  1.090
 RGM  C04  H7   single    0.970  0.020  1.090
 RGM  C04  H8   single    0.970  0.020  1.090
 RGM  C05  H9   single    0.970  0.020  1.090
 RGM  C06  H10  single    0.970  0.020  1.090
 RGM  C06  H11  single    0.970  0.020  1.090
 RGM  C08  H12  single    0.970  0.020  1.090
 RGM  C08  H13  single    0.970  0.020  1.090
 RGM  C18  H14  single    0.970  0.020  1.090
 RGM  C18  H15  single    0.970  0.020  1.090
 RGM  C18  H16  single    0.970  0.020  1.090
 RGM  N14  H18  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
 RGM  O11  C10  C12  124.35  3.000
 RGM  O11  C10  C09  122.70  3.000
 RGM  C12  C10  C09  112.93  3.000
 RGM  H1   C13  N14  121.75  3.000
 RGM  H1   C13  C12  131.26  3.000
 RGM  N14  C13  C12  106.99  3.000
 RGM  H2   C15  N14  121.15  3.000
 RGM  H2   C15  C16  131.49  3.000
 RGM  N14  C15  C16  107.36  3.000
 RGM  H5   C01  H4   106.99  3.000
 RGM  H5   C01  H3   107.67  3.000
 RGM  H4   C01  H3   107.86  3.000
 RGM  H5   C01  N02  108.96  3.000
 RGM  H4   C01  N02  110.08  3.000
 RGM  H3   C01  N02  114.96  3.000
 RGM  H6   C03  N02  110.68  3.000
 RGM  H6   C03  C16  112.39  3.000
 RGM  N02  C03  C16  108.90  3.000
 RGM  H6   C03  C04  112.67  3.000
 RGM  N02  C03  C04  101.96  3.000
 RGM  C16  C03  C04  109.70  3.000
 RGM  H8   C04  H7   107.35  3.000
 RGM  H8   C04  C05  111.24  3.000
 RGM  H7   C04  C05  112.48  3.000
 RGM  H8   C04  C03  110.86  3.000
 RGM  H7   C04  C03  111.31  3.000
 RGM  C05  C04  C03  103.65  3.000
 RGM  H9   C05  C09  111.86  3.000
 RGM  H9   C05  C06  110.04  3.000
 RGM  C09  C05  C06  103.05  3.000
 RGM  H9   C05  C04  112.76  3.000
 RGM  C09  C05  C04  104.99  3.000
 RGM  C06  C05  C04  113.64  3.000
 RGM  H11  C06  H10  107.63  3.000
 RGM  H11  C06  N07  110.72  3.000
 RGM  H10  C06  N07  111.52  3.000
 RGM  H11  C06  C05  110.95  3.000
 RGM  H10  C06  C05  110.92  3.000
 RGM  N07  C06  C05  105.14  3.000
 RGM  H13  C08  H12  107.23  3.000
 RGM  H13  C08  N07  110.81  3.000
 RGM  H12  C08  N07  111.28  3.000
 RGM  H13  C08  C09  110.77  3.000
 RGM  H12  C08  C09  112.60  3.000
 RGM  N07  C08  C09  104.21  3.000
 RGM  N02  C09  C08  113.57  3.000
 RGM  C08  C09  C05  105.05  3.000
 RGM  N02  C09  C05   99.47  3.000
 RGM  C08  C09  C10  113.55  3.000
 RGM  N02  C09  C10  112.99  3.000
 RGM  C05  C09  C10  110.97  3.000
 RGM  C16  C12  C13  107.51  3.000
 RGM  C13  C12  C10  131.05  3.000
 RGM  C16  C12  C10  121.43  3.000
 RGM  C12  C16  C03  118.16  3.000
 RGM  C12  C16  C15  107.07  3.000
 RGM  C03  C16  C15  134.76  3.000
 RGM  H16  C18  H15  108.24  3.000
 RGM  H16  C18  H14  108.75  3.000
 RGM  H15  C18  H14  107.22  3.000
 RGM  H16  C18  C17  109.67  3.000
 RGM  H15  C18  C17  109.84  3.000
 RGM  H14  C18  C17  112.99  3.000
 RGM  C09  N02  C03  104.08  3.000
 RGM  C09  N02  C01  117.80  3.000
 RGM  C03  N02  C01  115.79  3.000
 RGM  C08  N07  C06  112.99  3.000
 RGM  C08  N07  C17  121.22  3.000
 RGM  C06  N07  C17  125.64  3.000
 RGM  H18  N14  C15  124.44  3.000
 RGM  H18  N14  C13  124.48  3.000
 RGM  C15  N14  C13  111.08  3.000
 RGM  O19  C17  N07  121.59  3.000
 RGM  N07  C17  C18  116.57  3.000
 RGM  O19  C17  C18  121.82  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
 RGM  CONST_01  C16  C15  N14  C13    0.00   0.0  0
 RGM  CONST_02  C12  C13  N14  C15    0.00   0.0  0
 RGM  CONST_03  H2   C15  N14  C13  180.00   0.0  0
 RGM  CONST_04  H1   C13  N14  C15  180.00   0.0  0
 RGM  CONST_05  H18  N14  C13  C12  180.00   0.0  0
 RGM  CONST_06  O19  C17  N07  C06  180.00   0.0  0
 RGM  CONST_07  C18  C17  N07  C06    0.00   0.0  0
 RGM  CONST_08  O19  C17  N07  C08    0.00   0.0  0
 RGM  CONST_09  C18  C17  N07  C08  180.00   0.0  0
 RGM  Var_01    C08  N07  C06  C05   -8.33  30.0  1
 RGM  Var_02    C09  C08  N07  C06  -11.46  30.0  1
 RGM  Var_03    H3   C01  N02  C03   62.09  30.0  3
 RGM  Var_04    H14  C18  C17  N07  -44.13  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
 RGM  chir_01  C03  C04  C16  N02  negativ
 RGM  chir_02  C05  C04  C06  C09  negativ
 RGM  chir_03  C09  C08  C10  C05  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
 RGM  plan-1  C06  0.020
 RGM  plan-1  C08  0.020
 RGM  plan-1  C18  0.020
 RGM  plan-1  N07  0.020
 RGM  plan-1  O19  0.020
 RGM  plan-1  C17  0.020
 RGM  plan-2  C10  0.020
 RGM  plan-2  C13  0.020
 RGM  plan-2  C15  0.020
 RGM  plan-2  C03  0.020
 RGM  plan-2  C12  0.020
 RGM  plan-2  C16  0.020
 RGM  plan-2  N14  0.020
 RGM  plan-2  H1   0.020
 RGM  plan-2  H2   0.020
 RGM  plan-2  H18  0.020
 RGM  plan-3  C10  0.020
 RGM  plan-3  C09  0.020
 RGM  plan-3  C12  0.020
 RGM  plan-3  O11  0.020

