# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:13:17 2021
#   Inital geometry file: a 55 line input string
#   Ligand name: [(3R,5R)-5-methylpiperidin-3-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CNC[C@H](CO)C1
#
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
 W2J  W2J  '[(3R,5R)-5-methylpiperidin-3-yl]methanol'  ligand  24  9  .  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_W2J
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
 W2J  C4   C  CH1   0  -0.236  6.7043  25.1951  17.4307
 W2J  C5   C  CH3   0  -0.667  7.7686  26.1691  16.9412
 W2J  C6   C  CH2   0  -0.432  7.3171  23.8902  17.9665
 W2J  C1   C  CH1   0  -0.301  7.4443  22.8507  16.8587
 W2J  C3   C  CH2   0  -0.308  5.6975  24.8735  16.3092
 W2J  N    N  NH1   0  -0.591  5.0629  23.5755  16.4519
 W2J  C2   C  CH2   0  -0.277  6.0362  22.4912  16.3387
 W2J  H1   H  HCH1  0   0.223  6.1578  25.6734  18.2502
 W2J  H2   H  HCH3  0   0.225  8.4129  26.4973  17.7586
 W2J  H3   H  HCH3  0   0.216  8.4044  25.7074  16.1813
 W2J  H4   H  HCH3  0   0.225  7.3194  27.0593  16.4956
 W2J  H5   H  HCH2  0   0.222  6.6959  23.4824  18.7711
 W2J  H6   H  HCH2  0   0.229  8.2925  24.0962  18.4170
 W2J  H7   H  HOH1  0   0.452  8.7471  19.9111  16.6155
 W2J  H10  H  HCH1  0   0.226  8.0257  23.2974  16.0416
 W2J  H11  H  HCH2  0   0.214  6.2070  24.8888  15.3389
 W2J  H12  H  HCH2  0   0.234  4.9316  25.6512  16.2605
 W2J  H13  H  HNH1  0   0.340  4.6177  23.5299  17.3601
 W2J  H15  H  HCH2  0   0.218  5.6458  21.6359  16.8969
 W2J  H16  H  HCH2  0   0.218  6.1013  22.1758  15.2932
 W2J  C    C  CH2   0  -0.134  8.1994  21.6268  17.3396
 W2J  H8   H  HCH2  0   0.183  7.6668  21.1964  18.2005
 W2J  O    O  OH1   0  -0.675  8.3036  20.6961  16.2826
 W2J  H9   H  HCH2  0   0.197  9.1913  21.9315  17.7005

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
 W2J  C3  N    single  1.452  0.020  1.452
 W2J  C3  C4   single  1.541  0.020  1.541
 W2J  O   C    single  1.412  0.020  1.412
 W2J  N   C2   single  1.461  0.020  1.461
 W2J  C2  C1   single  1.544  0.020  1.544
 W2J  C1  C    single  1.516  0.020  1.516
 W2J  C1  C6   single  1.525  0.020  1.525
 W2J  C5  C4   single  1.524  0.020  1.524
 W2J  C4  C6   single  1.538  0.020  1.538
 W2J  C4  H1   single  0.970  0.020  1.090
 W2J  C5  H2   single  0.970  0.020  1.090
 W2J  C5  H3   single  0.970  0.020  1.090
 W2J  C5  H4   single  0.970  0.020  1.090
 W2J  C6  H5   single  0.970  0.020  1.090
 W2J  C6  H6   single  0.970  0.020  1.090
 W2J  O   H7   single  0.850  0.020  0.980
 W2J  C   H8   single  0.970  0.020  1.090
 W2J  C   H9   single  0.970  0.020  1.090
 W2J  C1  H10  single  0.970  0.020  1.090
 W2J  C3  H11  single  0.970  0.020  1.090
 W2J  C3  H12  single  0.970  0.020  1.090
 W2J  N   H13  single  0.890  0.020  1.040
 W2J  C2  H15  single  0.970  0.020  1.090
 W2J  C2  H16  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
 W2J  H1   C4  C3   108.04  3.000
 W2J  H1   C4  C6   107.98  3.000
 W2J  C3   C4  C6   109.68  3.000
 W2J  H1   C4  C5   108.05  3.000
 W2J  C6   C4  C5   112.09  3.000
 W2J  C3   C4  C5   110.86  3.000
 W2J  H4   C5  H3   107.45  3.000
 W2J  H4   C5  H2   107.66  3.000
 W2J  H3   C5  H2   107.72  3.000
 W2J  H4   C5  C4   111.40  3.000
 W2J  H3   C5  C4   111.08  3.000
 W2J  H2   C5  C4   111.35  3.000
 W2J  H6   C6  H5   105.86  3.000
 W2J  H6   C6  C1   110.68  3.000
 W2J  H5   C6  C1   109.10  3.000
 W2J  H6   C6  C4   109.81  3.000
 W2J  H5   C6  C4   110.24  3.000
 W2J  C1   C6  C4   111.02  3.000
 W2J  H10  C1  C2   109.10  3.000
 W2J  H10  C1  C    107.50  3.000
 W2J  C2   C1  C    111.91  3.000
 W2J  H10  C1  C6   107.91  3.000
 W2J  C    C1  C6   111.19  3.000
 W2J  C2   C1  C6   109.11  3.000
 W2J  H12  C3  H11  106.05  3.000
 W2J  H12  C3  N    109.53  3.000
 W2J  H11  C3  N    107.62  3.000
 W2J  H12  C3  C4   109.98  3.000
 W2J  H11  C3  C4   109.73  3.000
 W2J  N    C3  C4   113.62  3.000
 W2J  H13  N   C2   109.20  3.000
 W2J  H13  N   C3   108.71  3.000
 W2J  C2   N   C3   111.38  3.000
 W2J  H16  C2  H15  106.48  3.000
 W2J  H16  C2  N    109.12  3.000
 W2J  H15  C2  N    107.64  3.000
 W2J  H16  C2  C1   109.56  3.000
 W2J  H15  C2  C1   109.62  3.000
 W2J  N    C2  C1   114.12  3.000
 W2J  H9   C   H8   106.78  3.000
 W2J  H9   C   C1   109.26  3.000
 W2J  H8   C   C1   108.84  3.000
 W2J  H9   C   O    111.22  3.000
 W2J  H8   C   O    111.32  3.000
 W2J  C1   C   O    109.34  3.000
 W2J  H7   O   C    108.24  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
 W2J  Var_01  C2  N  C3  C4  -64.31  30.0  1
 W2J  Var_02  C3  N  C2  C1   31.73  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
 W2J  chir_01  C4  C3  C5  C6  positiv
 W2J  chir_02  C1  C2  C   C6  positiv

