# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 10:05:12 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2S,3aS,6R,7aS)-6-hydroxyoctahydro-1H-indole-2-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CC[C@H]2C[C@H](N[C@H]2C1)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
 RPH  RPH  (2S,3aS,6R,7aS)-6-hydroxyoctahydro-1H-indole-2-carbaldehyde  ligand  27  12  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RPH
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
 RPH  O2    O  O     0  -0.380   1.8536   0.6744  -2.3819
 RPH  OH2   O  OH1   0  -0.683   1.0498  -0.0954   3.3369
 RPH  N5    N  NH1   0  -0.605   0.3712  -1.1224  -0.8189
 RPH  C7    C  C1    0   0.174   0.7338   0.3957  -2.7266
 RPH  C8    C  CH1   0  -0.170  -0.1798  -0.5858  -2.0448
 RPH  C9    C  CH2   0  -0.488  -1.5288   0.0655  -1.6478
 RPH  C10   C  CH1   0  -0.248  -1.4707   0.1113  -0.1209
 RPH  C11   C  CH2   0  -0.432  -0.7841   1.3769   0.3925
 RPH  C12   C  CH2   0  -0.475  -0.3441   1.2461   1.8449
 RPH  C13   C  CH1   0   0.085   0.5980   0.0601   2.0042
 RPH  C14   C  CH2   0  -0.464  -0.1127  -1.2219   1.6062
 RPH  C15   C  CH1   0  -0.061  -0.6769  -1.1578   0.1937
 RPH  HN5   H  HNH1  0   0.350   0.8071  -2.0235  -0.9534
 RPH  H7    H  H     0   0.183   0.2875   0.8522  -3.6315
 RPH  H8    H  HCH1  0   0.264  -0.3752  -1.3538  -2.8090
 RPH  H91   H  HCH2  0   0.257  -2.3534  -0.5645  -1.9818
 RPH  H92   H  HCH2  0   0.249  -1.6806   1.0507  -2.0949
 RPH  H10   H  HCH1  0   0.240  -2.4720   0.0446   0.3125
 RPH  H111  H  HCH2  0   0.234  -1.4642   2.2244   0.2769
 RPH  H112  H  HCH2  0   0.221   0.0947   1.6073  -0.2182
 RPH  H121  H  HCH2  0   0.212  -1.2143   1.1089   2.4975
 RPH  H122  H  HCH2  0   0.230   0.1501   2.1687   2.1653
 RPH  H13   H  HCH1  0   0.191   1.4477   0.2059   1.3223
 RPH  H141  H  HCH2  0   0.234   0.5659  -2.0769   1.6913
 RPH  H142  H  HCH2  0   0.220  -0.9376  -1.4050   2.3039
 RPH  H15   H  HCH1  0   0.217  -1.3488  -2.0201   0.0575
 RPH  HO2   H  HOH1  0   0.444   1.5486   0.6920   3.5751

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
 RPH  O2   C7    double  1.204  0.020  1.204
 RPH  OH2  C13   single  1.416  0.020  1.416
 RPH  OH2  HO2   single  0.850  0.020  0.980
 RPH  N5   C8    single  1.447  0.020  1.447
 RPH  N5   C15   single  1.458  0.020  1.458
 RPH  N5   HN5   single  0.890  0.020  1.040
 RPH  C7   C8    single  1.504  0.020  1.504
 RPH  C7   H7    single  0.930  0.020  1.080
 RPH  C8   C9    single  1.550  0.020  1.550
 RPH  C8   H8    single  0.970  0.020  1.090
 RPH  C9   C10   single  1.529  0.020  1.529
 RPH  C9   H91   single  0.970  0.020  1.090
 RPH  C9   H92   single  0.970  0.020  1.090
 RPH  C10  C11   single  1.529  0.020  1.529
 RPH  C10  C15   single  1.530  0.020  1.530
 RPH  C10  H10   single  0.970  0.020  1.090
 RPH  C11  C12   single  1.523  0.020  1.523
 RPH  C11  H111  single  0.970  0.020  1.090
 RPH  C11  H112  single  0.970  0.020  1.090
 RPH  C12  C13   single  1.523  0.020  1.523
 RPH  C12  H121  single  0.970  0.020  1.090
 RPH  C12  H122  single  0.970  0.020  1.090
 RPH  C13  C14   single  1.519  0.020  1.519
 RPH  C13  H13   single  0.970  0.020  1.090
 RPH  C14  C15   single  1.522  0.020  1.522
 RPH  C14  H141  single  0.970  0.020  1.090
 RPH  C14  H142  single  0.970  0.020  1.090
 RPH  C15  H15   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
 RPH  HO2   OH2  C13   107.97  3.000
 RPH  HN5   N5   C15   112.40  3.000
 RPH  HN5   N5   C8    112.48  3.000
 RPH  C15   N5   C8    108.88  3.000
 RPH  H7    C7   C8    113.24  3.000
 RPH  H7    C7   O2    120.88  3.000
 RPH  C8    C7   O2    125.87  3.000
 RPH  H8    C8   C9    108.45  3.000
 RPH  H8    C8   C7    104.38  3.000
 RPH  C9    C8   C7    111.75  3.000
 RPH  H8    C8   N5    113.39  3.000
 RPH  C9    C8   N5    105.68  3.000
 RPH  C7    C8   N5    113.24  3.000
 RPH  H92   C9   H91   106.89  3.000
 RPH  H92   C9   C10   112.77  3.000
 RPH  H91   C9   C10   110.62  3.000
 RPH  H92   C9   C8    113.27  3.000
 RPH  H91   C9   C8    109.70  3.000
 RPH  C10   C9   C8    103.62  3.000
 RPH  H10   C10  C15   110.07  3.000
 RPH  H10   C10  C11   109.20  3.000
 RPH  C15   C10  C11   112.63  3.000
 RPH  H10   C10  C9    111.06  3.000
 RPH  C15   C10  C9    101.55  3.000
 RPH  C11   C10  C9    112.17  3.000
 RPH  H112  C11  H111  106.10  3.000
 RPH  H112  C11  C12   108.55  3.000
 RPH  H111  C11  C12   110.32  3.000
 RPH  H112  C11  C10   110.33  3.000
 RPH  H111  C11  C10   109.09  3.000
 RPH  C12   C11  C10   112.27  3.000
 RPH  H122  C12  H121  106.84  3.000
 RPH  H122  C12  C13   110.27  3.000
 RPH  H121  C12  C13   109.35  3.000
 RPH  H122  C12  C11   109.70  3.000
 RPH  H121  C12  C11   110.43  3.000
 RPH  C13   C12  C11   110.20  3.000
 RPH  H13   C13  C14   108.13  3.000
 RPH  H13   C13  C12   108.06  3.000
 RPH  C14   C13  C12   109.90  3.000
 RPH  H13   C13  OH2   110.60  3.000
 RPH  C14   C13  OH2   107.65  3.000
 RPH  C12   C13  OH2   112.42  3.000
 RPH  H142  C14  H141  106.65  3.000
 RPH  H142  C14  C15   108.59  3.000
 RPH  H141  C14  C15   109.56  3.000
 RPH  H142  C14  C13   109.05  3.000
 RPH  H141  C14  C13   110.41  3.000
 RPH  C15   C14  C13   112.40  3.000
 RPH  H15   C15  C14   107.93  3.000
 RPH  H15   C15  C10   107.91  3.000
 RPH  C14   C15  C10   114.71  3.000
 RPH  H15   C15  N5    111.82  3.000
 RPH  C14   C15  N5    112.27  3.000
 RPH  C10   C15  N5    102.13  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
 RPH  Var_01  C13  C12  C11  C10  57.82  30.0  1

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
 RPH  chir_01  C8   N5   C7   C9   positiv
 RPH  chir_02  C10  C15  C11  C9   negativ
 RPH  chir_03  C13  OH2  C12  C14  positiv
 RPH  chir_04  C15  N5   C10  C14  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
 RPH  plan-1  O2  0.020
 RPH  plan-1  C7  0.020
 RPH  plan-1  C8  0.020
 RPH  plan-1  H7  0.020

