# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 05:24:00 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: (2R,3S,4S,5R)-2-[2-(methylsulfanyl)ethyl]piperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H]1NC[C@@H](O)[C@H](O)[C@H]1O
#
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
 P9V  P9V  (2R,3S,4S,5R)-2-[2-(methylsulfanyl)ethyl]piperidine-3,4,5-triol  ligand  30  13  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P9V
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
 P9V  C1   C  CH3   0  -0.777  -45.4319  40.7510  -4.0829
 P9V  C3   C  CH1   0  -0.140  -42.0445  40.0155  -5.2365
 P9V  C4   C  CH1   0   0.026  -41.9400  41.2920  -6.0827
 P9V  C5   C  CH1   0   0.020  -41.0045  41.1171  -7.2785
 P9V  C6   C  CH1   0   0.048  -39.6434  40.6316  -6.8126
 P9V  C7   C  CH2   0  -0.339  -39.8038  39.3906  -5.9410
 P9V  C16  C  CH2   0  -0.428  -42.7839  38.8412  -5.8962
 P9V  C17  C  CH2   0  -0.562  -44.3065  38.9035  -5.9184
 P9V  N2   N  NH1   0  -0.605  -40.6824  39.6954  -4.8283
 P9V  O10  O  OH1   0  -0.671  -38.8577  40.3728  -7.9530
 P9V  O12  O  OH1   0  -0.671  -43.1789  41.7280  -6.6031
 P9V  O8   O  OH1   0  -0.677  -40.8348  42.3342  -7.9668
 P9V  S18  S  S2    0  -0.052  -45.0981  38.9847  -4.2795
 P9V  H1   H  HCH3  0   0.279  -46.0897  40.8581  -3.2219
 P9V  H2   H  HCH3  0   0.250  -44.5279  41.3274  -3.8932
 P9V  H3   H  HCH3  0   0.264  -45.9460  41.1497  -4.9561
 P9V  H4   H  HCH1  0   0.236  -42.5835  40.2679  -4.3170
 P9V  H5   H  HCH1  0   0.224  -41.5037  42.0673  -5.4376
 P9V  H6   H  HCH1  0   0.200  -41.4314  40.3553  -7.9513
 P9V  H7   H  HCH1  0   0.200  -39.1933  41.4219  -6.1933
 P9V  H8   H  HCH2  0   0.203  -40.1450  38.5518  -6.5662
 P9V  H9   H  HCH2  0   0.243  -38.8270  39.1062  -5.5415
 P9V  H10  H  HCH2  0   0.236  -42.4929  37.9350  -5.3556
 P9V  H11  H  HCH2  0   0.234  -42.4506  38.6859  -6.9265
 P9V  H12  H  HCH2  0   0.272  -44.6751  39.7335  -6.5184
 P9V  H13  H  HCH2  0   0.274  -44.6856  37.9887  -6.3767
 P9V  H14  H  HNH1  0   0.357  -40.6917  38.9274  -4.1705
 P9V  H16  H  HOH1  0   0.451  -37.9650  40.1646  -7.6607
 P9V  H17  H  HOH1  0   0.459  -43.6590  42.1957  -5.9141
 P9V  H18  H  HOH1  0   0.445  -41.7125  42.6842  -8.1543

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
 P9V  O8   C5   single  1.408  0.020  1.408
 P9V  O10  C6   single  1.409  0.020  1.409
 P9V  C5   C6   single  1.518  0.020  1.518
 P9V  C5   C4   single  1.528  0.020  1.528
 P9V  O12  C4   single  1.413  0.020  1.413
 P9V  C6   C7   single  1.525  0.020  1.525
 P9V  C4   C3   single  1.535  0.020  1.535
 P9V  C17  C16  single  1.524  0.020  1.524
 P9V  C17  S18  single  1.822  0.020  1.822
 P9V  C16  C3   single  1.537  0.020  1.537
 P9V  C7   N2   single  1.450  0.020  1.450
 P9V  C3   N2   single  1.457  0.020  1.457
 P9V  S18  C1   single  1.808  0.020  1.808
 P9V  C1   H1   single  0.970  0.020  1.090
 P9V  C1   H2   single  0.970  0.020  1.090
 P9V  C1   H3   single  0.970  0.020  1.090
 P9V  C3   H4   single  0.970  0.020  1.090
 P9V  C4   H5   single  0.970  0.020  1.090
 P9V  C5   H6   single  0.970  0.020  1.090
 P9V  C6   H7   single  0.970  0.020  1.090
 P9V  C7   H8   single  0.970  0.020  1.090
 P9V  C7   H9   single  0.970  0.020  1.090
 P9V  C16  H10  single  0.970  0.020  1.090
 P9V  C16  H11  single  0.970  0.020  1.090
 P9V  C17  H12  single  0.970  0.020  1.090
 P9V  C17  H13  single  0.970  0.020  1.090
 P9V  N2   H14  single  0.890  0.020  1.040
 P9V  O10  H16  single  0.850  0.020  0.980
 P9V  O12  H17  single  0.850  0.020  0.980
 P9V  O8   H18  single  0.850  0.020  0.980

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
 P9V  H3   C1   H2   109.74  3.000
 P9V  H3   C1   H1   108.23  3.000
 P9V  H2   C1   H1   108.17  3.000
 P9V  H3   C1   S18  110.95  3.000
 P9V  H2   C1   S18  112.51  3.000
 P9V  H1   C1   S18  107.07  3.000
 P9V  H4   C3   N2   105.98  3.000
 P9V  H4   C3   C16  107.44  3.000
 P9V  N2   C3   C16  113.71  3.000
 P9V  H4   C3   C4   107.74  3.000
 P9V  N2   C3   C4   105.86  3.000
 P9V  C16  C3   C4   115.57  3.000
 P9V  H5   C4   O12  110.28  3.000
 P9V  H5   C4   C5   107.28  3.000
 P9V  O12  C4   C5   106.49  3.000
 P9V  H5   C4   C3   106.87  3.000
 P9V  O12  C4   C3   113.58  3.000
 P9V  C5   C4   C3   112.20  3.000
 P9V  H6   C5   O8   110.21  3.000
 P9V  H6   C5   C6   108.26  3.000
 P9V  O8   C5   C6   108.56  3.000
 P9V  H6   C5   C4   108.64  3.000
 P9V  C6   C5   C4   110.20  3.000
 P9V  O8   C5   C4   110.93  3.000
 P9V  H7   C6   O10  111.06  3.000
 P9V  H7   C6   C7   107.81  3.000
 P9V  O10  C6   C7   111.83  3.000
 P9V  H7   C6   C5   108.04  3.000
 P9V  C7   C6   C5   109.96  3.000
 P9V  O10  C6   C5   108.08  3.000
 P9V  H9   C7   H8   106.65  3.000
 P9V  H9   C7   N2   108.41  3.000
 P9V  H8   C7   N2   114.10  3.000
 P9V  H9   C7   C6   109.07  3.000
 P9V  H8   C7   C6   109.16  3.000
 P9V  N2   C7   C6   109.34  3.000
 P9V  H11  C16  H10  105.47  3.000
 P9V  H11  C16  C17  107.24  3.000
 P9V  H10  C16  C17  107.86  3.000
 P9V  H11  C16  C3   111.48  3.000
 P9V  H10  C16  C3   107.02  3.000
 P9V  C17  C16  C3   117.11  3.000
 P9V  H13  C17  H12  106.87  3.000
 P9V  H13  C17  S18  105.32  3.000
 P9V  H12  C17  S18  108.35  3.000
 P9V  H13  C17  C16  108.60  3.000
 P9V  H12  C17  C16  112.18  3.000
 P9V  S18  C17  C16  115.01  3.000
 P9V  H14  N2   C7   110.18  3.000
 P9V  H14  N2   C3   109.90  3.000
 P9V  C7   N2   C3   113.42  3.000
 P9V  H16  O10  C6   108.14  3.000
 P9V  H17  O12  C4   108.91  3.000
 P9V  H18  O8   C5   107.42  3.000
 P9V  C17  S18  C1   102.80  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
 P9V  Var_01  C6   C7   N2   C3    64.54  30.0  1
 P9V  Var_02  S18  C17  C16  C3   -59.95  30.0  1
 P9V  Var_03  C16  C17  S18  C1    98.40  30.0  1
 P9V  Var_04  H1   C1   S18  C17  168.42  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
 P9V  chir_01  C3  C4   C16  N2  negativ
 P9V  chir_02  C4  O12  C3   C5  negativ
 P9V  chir_03  C5  O8   C4   C6  positiv
 P9V  chir_04  C6  O10  C5   C7  negativ

