# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 15:35:06 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: (1R,2R)-2,4,4-trimethyl-N-[(1H-pyrazol-3-yl)methyl]cyclopentan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC(C)(C)C[C@H]1NCc2cc[nH]n2
#
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
 8BI  8BI  "(1R,2R)-2,4,4-trimethyl-N-[(1H-pyrazol-3-yl)methyl]cyclopentan-1-amine"  ligand  36  15  .  2022-09-16  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8BI
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
 8BI  C10  C  CH2   0  -0.382   0.0635  4.9308  -11.6314
 8BI  C13  C  CR15  0   0.021   0.8427  1.4556  -12.5071
 8BI  C02  C  CH1   0  -0.259  -1.6351  5.2238   -8.2652
 8BI  C03  C  CH2   0  -0.405  -1.0524  4.6936   -6.9623
 8BI  C04  C  CT    0  -0.038  -0.4455  3.3200   -7.3104
 8BI  C05  C  CH3   0  -0.653  -1.4737  2.2140   -7.0748
 8BI  C06  C  CH3   0  -0.654   0.8004  3.0359   -6.4769
 8BI  C07  C  CH2   0  -0.425  -0.1166  3.4333   -8.8253
 8BI  C08  C  CH1   0  -0.018  -0.5471  4.8388   -9.2706
 8BI  N09  N  NH1   0  -0.607  -1.0053  4.9143  -10.6470
 8BI  C11  C  CR5   0   0.288   0.6001  3.5677  -11.9307
 8BI  C12  C  CR15  0  -0.498  -0.1136  2.4314  -12.3616
 8BI  N14  N  NR15  0  -0.430   2.0141  2.0236  -12.1750
 8BI  N15  N  N     0  -0.299   1.8900  3.2997  -11.8232
 8BI  H1   H  HCH2  0   0.209   0.9045  5.5762  -11.3355
 8BI  H2   H  HCH2  0   0.244  -0.3455  5.3558  -12.5518
 8BI  H3   H  HCR5  0   0.283   0.7758  0.4245  -12.8141
 8BI  H7   H  HCH1  0   0.217  -2.5398  4.6546   -8.5163
 8BI  H8   H  HCH2  0   0.212  -0.2625  5.3762   -6.6270
 8BI  H9   H  HCH2  0   0.226  -1.7853  4.6357   -6.1537
 8BI  H10  H  HCH3  0   0.217  -1.7277  2.1299   -6.0156
 8BI  H11  H  HCH3  0   0.223  -2.3982  2.4014   -7.6251
 8BI  H12  H  HCH3  0   0.220  -1.0885  1.2456   -7.4024
 8BI  H13  H  HCH3  0   0.217   0.5703  3.0380   -5.4087
 8BI  H14  H  HCH3  0   0.218   1.2256  2.0600   -6.7216
 8BI  H15  H  HCH3  0   0.219   1.5722  3.7884   -6.6519
 8BI  H16  H  HCH2  0   0.224  -0.6762  2.6907   -9.3994
 8BI  H17  H  HCH2  0   0.225   0.9409  3.2506   -9.0239
 8BI  H18  H  HCH1  0   0.182   0.3016  5.5292   -9.1064
 8BI  H19  H  HNH1  0   0.351  -1.5378  5.7675  -10.7615
 8BI  H21  H  HCR5  0   0.251  -1.1729  2.3425  -12.5355
 8BI  H22  H  HNR5  0   0.415   2.9219  1.5874  -12.1693
 8BI  C01  C  CH3   0  -0.662  -1.9746  6.7050   -8.2315
 8BI  H4   H  HCH3  0   0.229  -2.7086  6.9223   -7.4541
 8BI  H5   H  HCH3  0   0.214  -1.0827  7.3004   -8.0234
 8BI  H6   H  HCH3  0   0.223  -2.3974  7.0571   -9.1748

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
 8BI  C12  C13  aromatic  1.374  0.020  1.374
 8BI  C12  C11  aromatic  1.409  0.020  1.409
 8BI  C13  N14  aromatic  1.344  0.020  1.344
 8BI  C11  C10  single    1.495  0.020  1.495
 8BI  C11  N15  aromatic  1.322  0.020  1.322
 8BI  N14  N15  aromatic  1.329  0.020  1.329
 8BI  C10  N09  single    1.453  0.020  1.453
 8BI  N09  C08  single    1.453  0.020  1.453
 8BI  C08  C07  single    1.536  0.020  1.536
 8BI  C08  C02  single    1.531  0.020  1.531
 8BI  C07  C04  single    1.554  0.020  1.554
 8BI  C02  C01  single    1.520  0.020  1.520
 8BI  C02  C03  single    1.523  0.020  1.523
 8BI  C04  C05  single    1.528  0.020  1.528
 8BI  C04  C03  single    1.542  0.020  1.542
 8BI  C04  C06  single    1.526  0.020  1.526
 8BI  C10  H1   single    0.970  0.020  1.090
 8BI  C10  H2   single    0.970  0.020  1.090
 8BI  C13  H3   single    0.930  0.020  1.080
 8BI  C01  H4   single    0.970  0.020  1.090
 8BI  C01  H5   single    0.970  0.020  1.090
 8BI  C01  H6   single    0.970  0.020  1.090
 8BI  C02  H7   single    0.970  0.020  1.090
 8BI  C03  H8   single    0.970  0.020  1.090
 8BI  C03  H9   single    0.970  0.020  1.090
 8BI  C05  H10  single    0.970  0.020  1.090
 8BI  C05  H11  single    0.970  0.020  1.090
 8BI  C05  H12  single    0.970  0.020  1.090
 8BI  C06  H13  single    0.970  0.020  1.090
 8BI  C06  H14  single    0.970  0.020  1.090
 8BI  C06  H15  single    0.970  0.020  1.090
 8BI  C07  H16  single    0.970  0.020  1.090
 8BI  C07  H17  single    0.970  0.020  1.090
 8BI  C08  H18  single    0.970  0.020  1.090
 8BI  N09  H19  single    0.890  0.020  1.040
 8BI  C12  H21  single    0.930  0.020  1.080
 8BI  N14  H22  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
 8BI  H2   C10  H1   106.51  3.000
 8BI  H2   C10  C11  108.67  3.000
 8BI  H1   C10  C11  108.31  3.000
 8BI  H2   C10  N09  107.44  3.000
 8BI  H1   C10  N09  112.74  3.000
 8BI  C11  C10  N09  112.91  3.000
 8BI  H3   C13  N14  121.93  3.000
 8BI  H3   C13  C12  131.79  3.000
 8BI  N14  C13  C12  106.28  3.000
 8BI  H7   C02  C08  107.76  3.000
 8BI  H7   C02  C03  109.30  3.000
 8BI  C08  C02  C03  101.68  3.000
 8BI  H7   C02  C01  109.04  3.000
 8BI  C03  C02  C01  113.95  3.000
 8BI  C08  C02  C01  114.74  3.000
 8BI  H9   C03  H8   106.85  3.000
 8BI  H9   C03  C04  112.57  3.000
 8BI  H8   C03  C04  109.89  3.000
 8BI  H9   C03  C02  113.26  3.000
 8BI  H8   C03  C02  108.70  3.000
 8BI  C04  C03  C02  105.53  3.000
 8BI  C07  C04  C06  111.92  3.000
 8BI  C06  C04  C05  109.29  3.000
 8BI  C07  C04  C05  110.20  3.000
 8BI  C06  C04  C03  111.35  3.000
 8BI  C05  C04  C03  110.19  3.000
 8BI  C07  C04  C03  103.79  3.000
 8BI  H12  C05  H11  107.43  3.000
 8BI  H12  C05  H10  107.73  3.000
 8BI  H11  C05  H10  107.75  3.000
 8BI  H12  C05  C04  110.98  3.000
 8BI  H11  C05  C04  111.57  3.000
 8BI  H10  C05  C04  111.19  3.000
 8BI  H15  C06  H14  107.74  3.000
 8BI  H15  C06  H13  107.71  3.000
 8BI  H14  C06  H13  107.62  3.000
 8BI  H15  C06  C04  111.18  3.000
 8BI  H14  C06  C04  111.22  3.000
 8BI  H13  C06  C04  111.21  3.000
 8BI  H17  C07  H16  106.67  3.000
 8BI  H17  C07  C08  111.84  3.000
 8BI  H16  C07  C08  109.03  3.000
 8BI  H17  C07  C04  111.72  3.000
 8BI  H16  C07  C04  110.75  3.000
 8BI  C08  C07  C04  106.86  3.000
 8BI  H18  C08  N09  110.49  3.000
 8BI  H18  C08  C07  108.24  3.000
 8BI  N09  C08  C07  114.25  3.000
 8BI  H18  C08  C02  106.91  3.000
 8BI  C07  C08  C02  103.83  3.000
 8BI  N09  C08  C02  112.65  3.000
 8BI  H19  N09  C08  108.48  3.000
 8BI  H19  N09  C10  107.50  3.000
 8BI  C08  N09  C10  114.24  3.000
 8BI  N15  C11  C12  110.83  3.000
 8BI  N15  C11  C10  121.25  3.000
 8BI  C12  C11  C10  127.92  3.000
 8BI  H21  C12  C11  127.87  3.000
 8BI  H21  C12  C13  127.50  3.000
 8BI  C11  C12  C13  104.63  3.000
 8BI  H22  N14  N15  119.89  3.000
 8BI  H22  N14  C13  127.16  3.000
 8BI  N15  N14  C13  112.94  3.000
 8BI  N14  N15  C11  105.32  3.000
 8BI  H6   C01  H5   107.75  3.000
 8BI  H6   C01  H4   106.90  3.000
 8BI  H5   C01  H4   107.75  3.000
 8BI  H6   C01  C02  112.43  3.000
 8BI  H5   C01  C02  110.67  3.000
 8BI  H4   C01  C02  111.11  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
 8BI  CONST_01  N15  C11  C12  C13     0.00   0.0  0
 8BI  CONST_02  C11  N15  N14  C13     0.00   0.0  0
 8BI  CONST_03  N14  C13  C12  C11     0.00   0.0  0
 8BI  CONST_04  N15  N14  C13  C12     0.00   0.0  0
 8BI  CONST_05  N14  N15  C11  C12     0.00   0.0  0
 8BI  CONST_06  C13  C12  C11  C10   180.00   0.0  0
 8BI  CONST_07  N14  N15  C11  C10   180.00   0.0  0
 8BI  CONST_08  H3   C13  C12  C11   180.00   0.0  0
 8BI  CONST_09  H22  N14  N15  C11   180.00   0.0  0
 8BI  CONST_10  H22  N14  C13  C12   180.00   0.0  0
 8BI  CONST_11  H21  C12  C13  N14   180.00   0.0  0
 8BI  CONST_12  H21  C12  C11  N15   180.00   0.0  0
 8BI  CONST_13  H3   C13  N14  N15   180.00   0.0  0
 8BI  Var_01    C07  C04  C03  C02    25.83  30.0  1
 8BI  Var_02    C08  C07  C04  C03    -0.22  30.0  1
 8BI  Var_03    C05  C04  C03  C02   -92.15  30.0  1
 8BI  Var_04    C06  C04  C03  C02   146.40  30.0  1
 8BI  Var_05    C08  C07  C04  C05   117.75  30.0  1
 8BI  Var_06    C08  C07  C04  C06  -120.41  30.0  1
 8BI  Var_07    H16  C07  C04  C03  -118.84  30.0  1
 8BI  Var_08    H17  C07  C04  C03   122.40  30.0  1
 8BI  Var_09    H8   C03  C04  C07   -91.20  30.0  1
 8BI  Var_10    H9   C03  C04  C07   149.84  30.0  1
 8BI  Var_11    C11  C10  N09  C08    81.05  30.0  1
 8BI  Var_12    C12  C11  C10  N09    55.31  30.0  1
 8BI  Var_13    N15  C11  C10  N09  -125.60  30.0  1
 8BI  Var_14    H10  C05  C04  C03   -65.22  30.0  3
 8BI  Var_15    H11  C05  C04  C03    55.10  30.0  3
 8BI  Var_16    H12  C05  C04  C03   174.88  30.0  3
 8BI  Var_17    H13  C06  C04  C03    59.78  30.0  3
 8BI  Var_18    H14  C06  C04  C03   179.71  30.0  3
 8BI  Var_19    H15  C06  C04  C03   -60.24  30.0  3
 8BI  Var_20    H16  C07  C04  C05    -0.87  30.0  1
 8BI  Var_21    H17  C07  C04  C05  -119.62  30.0  1
 8BI  Var_22    H8   C03  C04  C05   150.82  30.0  1
 8BI  Var_23    H9   C03  C04  C05    31.86  30.0  1
 8BI  Var_24    H16  C07  C04  C06   120.97  30.0  1
 8BI  Var_25    H17  C07  C04  C06     2.21  30.0  1
 8BI  Var_26    H8   C03  C04  C06    29.37  30.0  1
 8BI  Var_27    H9   C03  C04  C06   -89.59  30.0  1
 8BI  Var_28    H10  C05  C04  C07  -179.18  30.0  3
 8BI  Var_29    H11  C05  C04  C07   -58.85  30.0  3
 8BI  Var_30    H12  C05  C04  C07    60.92  30.0  3
 8BI  Var_31    H13  C06  C04  C07   175.45  30.0  3
 8BI  Var_32    H14  C06  C04  C07   -64.62  30.0  3
 8BI  Var_33    H15  C06  C04  C07    55.43  30.0  3
 8BI  Var_34    H1   C10  C11  C12  -179.12  30.0  2
 8BI  Var_35    H2   C10  C11  C12   -63.79  30.0  2
 8BI  Var_36    H1   C10  C11  N15    -0.02  30.0  2
 8BI  Var_37    H2   C10  C11  N15   115.31  30.0  2
 8BI  Var_38    H13  C06  C04  C05   -62.20  30.0  3
 8BI  Var_39    H14  C06  C04  C05    57.74  30.0  3
 8BI  Var_40    H15  C06  C04  C05   177.79  30.0  3
 8BI  Var_41    H10  C05  C04  C06    57.44  30.0  3
 8BI  Var_42    H11  C05  C04  C06   177.77  30.0  3
 8BI  Var_43    H12  C05  C04  C06   -62.46  30.0  3
 8BI  Var_44    H1   C10  N09  C08   -42.11  30.0  1
 8BI  Var_45    H2   C10  N09  C08  -159.15  30.0  1
 8BI  Var_46    H19  N09  C10  C11  -158.53  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
 8BI  chir_01  C02  C08  C01  C03  positiv
 8BI  chir_02  C08  N09  C02  C07  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
 8BI  plan-1  C10  0.020
 8BI  plan-1  C13  0.020
 8BI  plan-1  C11  0.020
 8BI  plan-1  C12  0.020
 8BI  plan-1  N14  0.020
 8BI  plan-1  N15  0.020
 8BI  plan-1  H3   0.020
 8BI  plan-1  H21  0.020
 8BI  plan-1  H22  0.020

