# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:15:27 2021
#   Inital geometry file: a 59 line input string
#   Ligand name: 4-(1H-pyrazol-3-yl)piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC(CCN1)c2cc[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
 W6S  W6S  4-(1H-pyrazol-3-yl)piperidine  ligand  24  11  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W6S
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
 W6S  C01   C  CR15  0   0.017  -38.1804   1.5040  3.5293
 W6S  C02   C  CR15  0  -0.528  -39.1509   1.0171  4.3746
 W6S  C03   C  CR5   0   0.315  -39.1778  -0.3709  4.1317
 W6S  C04   C  CH1   0  -0.321  -40.0252  -1.3993  4.8122
 W6S  C05   C  CH2   0  -0.459  -39.2153  -2.2685  5.7756
 W6S  C06   C  CH2   0  -0.298  -40.1608  -3.1472  6.6133
 W6S  C08   C  CH2   0  -0.323  -41.1816  -3.6368  4.4867
 W6S  C09   C  CH2   0  -0.442  -40.7727  -2.3095  3.8221
 W6S  N07   N  NH1   0  -0.589  -41.3884  -3.5322  5.9204
 W6S  N10   N  N     0  -0.308  -38.2887  -0.6987  3.2075
 W6S  N11   N  NR15  0  -0.423  -37.7031   0.4430  2.8619
 W6S  H011  H  HCR5  0   0.286  -37.8080   2.5007  3.3587
 W6S  H021  H  HCR5  0   0.254  -39.7561   1.5760  5.0691
 W6S  H041  H  HCH1  0   0.239  -40.7646  -0.8506  5.4063
 W6S  H051  H  HCH2  0   0.224  -38.5202  -2.8862  5.1989
 W6S  H052  H  HCH2  0   0.239  -38.6052  -1.6508  6.4381
 W6S  H061  H  HCH2  0   0.216  -39.6263  -4.0472  6.9343
 W6S  H062  H  HCH2  0   0.229  -40.4452  -2.6160  7.5238
 W6S  H082  H  HCH2  0   0.235  -42.0880  -4.0263  4.0192
 W6S  H081  H  HCH2  0   0.222  -40.4068  -4.3905  4.3184
 W6S  H092  H  HCH2  0   0.226  -40.1397  -2.5183  2.9563
 W6S  H091  H  HCH2  0   0.229  -41.6536  -1.7839  3.4453
 W6S  H1    H  HNH1  0   0.341  -42.1063  -2.8414  6.0990
 W6S  H111  H  HNR5  0   0.417  -36.9818   0.4435  2.1595

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
 W6S  N11  N10   aromatic  1.329  0.020  1.329
 W6S  N11  C01   aromatic  1.341  0.020  1.341
 W6S  N10  C03   aromatic  1.324  0.020  1.324
 W6S  C01  C02   aromatic  1.376  0.020  1.376
 W6S  C09  C08   single    1.540  0.020  1.540
 W6S  C09  C04   single    1.539  0.020  1.539
 W6S  C03  C02   aromatic  1.409  0.020  1.409
 W6S  C03  C04   single    1.496  0.020  1.496
 W6S  C08  N07   single    1.452  0.020  1.452
 W6S  C04  C05   single    1.530  0.020  1.530
 W6S  C05  C06   single    1.539  0.020  1.539
 W6S  N07  C06   single    1.461  0.020  1.461
 W6S  C01  H011  single    0.930  0.020  1.080
 W6S  C02  H021  single    0.930  0.020  1.080
 W6S  C04  H041  single    0.970  0.020  1.090
 W6S  C05  H051  single    0.970  0.020  1.090
 W6S  C05  H052  single    0.970  0.020  1.090
 W6S  C06  H061  single    0.970  0.020  1.090
 W6S  C06  H062  single    0.970  0.020  1.090
 W6S  C08  H082  single    0.970  0.020  1.090
 W6S  C08  H081  single    0.970  0.020  1.090
 W6S  C09  H092  single    0.970  0.020  1.090
 W6S  C09  H091  single    0.970  0.020  1.090
 W6S  N07  H1    single    0.890  0.020  1.040
 W6S  N11  H111  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
 W6S  H011  C01  N11   122.00  3.000
 W6S  H011  C01  C02   131.93  3.000
 W6S  N11   C01  C02   106.07  3.000
 W6S  H021  C02  C03   127.67  3.000
 W6S  H021  C02  C01   127.49  3.000
 W6S  C03   C02  C01   104.84  3.000
 W6S  N10   C03  C04   121.85  3.000
 W6S  C04   C03  C02   127.55  3.000
 W6S  N10   C03  C02   110.57  3.000
 W6S  H041  C04  C09   108.50  3.000
 W6S  H041  C04  C05   107.48  3.000
 W6S  C09   C04  C05   109.05  3.000
 W6S  H041  C04  C03   106.53  3.000
 W6S  C05   C04  C03   112.16  3.000
 W6S  C09   C04  C03   112.90  3.000
 W6S  H052  C05  H051  106.51  3.000
 W6S  H052  C05  C06   109.63  3.000
 W6S  H051  C05  C06   110.79  3.000
 W6S  H052  C05  C04   110.88  3.000
 W6S  H051  C05  C04   108.98  3.000
 W6S  C06   C05  C04   110.00  3.000
 W6S  H062  C06  H061  106.41  3.000
 W6S  H062  C06  N07   107.74  3.000
 W6S  H061  C06  N07   109.42  3.000
 W6S  H062  C06  C05   109.65  3.000
 W6S  H061  C06  C05   109.21  3.000
 W6S  N07   C06  C05   114.11  3.000
 W6S  H081  C08  H082  106.05  3.000
 W6S  H081  C08  N07   107.60  3.000
 W6S  H082  C08  N07   109.28  3.000
 W6S  H081  C08  C09   109.84  3.000
 W6S  H082  C08  C09   110.08  3.000
 W6S  N07   C08  C09   113.69  3.000
 W6S  H091  C09  H092  106.59  3.000
 W6S  H091  C09  C08   110.45  3.000
 W6S  H092  C09  C08   109.34  3.000
 W6S  H091  C09  C04   109.20  3.000
 W6S  H092  C09  C04   109.97  3.000
 W6S  C08   C09  C04   111.18  3.000
 W6S  H1    N07  C08   108.93  3.000
 W6S  H1    N07  C06   109.41  3.000
 W6S  C08   N07  C06   111.56  3.000
 W6S  N11   N10  C03   105.36  3.000
 W6S  H111  N11  N10   119.84  3.000
 W6S  H111  N11  C01   127.00  3.000
 W6S  N10   N11  C01   113.16  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
 W6S  CONST_01  C03   N10  N11  C01    0.00   0.0  0
 W6S  CONST_02  N10   C03  C02  C01    0.00   0.0  0
 W6S  CONST_03  N10   N11  C01  C02    0.00   0.0  0
 W6S  CONST_04  N11   N10  C03  C02    0.00   0.0  0
 W6S  CONST_05  N11   C01  C02  C03    0.00   0.0  0
 W6S  CONST_06  C04   C03  C02  C01  180.00   0.0  0
 W6S  CONST_07  N11   N10  C03  C04  180.00   0.0  0
 W6S  CONST_08  H111  N11  C01  C02  180.00   0.0  0
 W6S  CONST_09  H011  C01  C02  C03  180.00   0.0  0
 W6S  CONST_10  H021  C02  C03  C04    0.00   0.0  0
 W6S  Var_01    N07   C08  C09  C04   28.02  30.0  1
 W6S  Var_02    N07   C06  C05  C04   31.22  30.0  1
 W6S  Var_03    C08   N07  C06  C05   30.17  30.0  1
 W6S  Var_04    C09   C08  N07  C06  -62.50  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
 W6S  chir_01  C04  C09  C03  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
 W6S  plan-1  C01   0.020
 W6S  plan-1  C02   0.020
 W6S  plan-1  C03   0.020
 W6S  plan-1  C04   0.020
 W6S  plan-1  N10   0.020
 W6S  plan-1  N11   0.020
 W6S  plan-1  H011  0.020
 W6S  plan-1  H021  0.020
 W6S  plan-1  H111  0.020

