# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:03:00 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: 1-{(2S,4S)-4-fluoro-1-[(2-methyl-1,3-thiazol-4-yl)methyl]pyrrolidin-2-yl}methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1scc(CN2C[C@@H](F)C[C@H]2CN)n1
#
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
 WGD  WGD  1-{(2S,4S)-4-fluoro-1-[(2-methyl-1,3-thiazol-4-yl)methyl]pyrrolidin-2-yl}methanamine  ligand  31  15  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WGD
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
 WGD  N1   N  N     0  -0.376  28.6064  4.6359  -41.3934
 WGD  N3   N  NH2   0  -0.794  32.5399  4.1452  -41.0924
 WGD  C4   C  CH2   0  -0.352  29.8876  6.6909  -41.9084
 WGD  C5   C  CH2   0  -0.303  30.6388  7.2397  -39.6508
 WGD  C6   C  CH1   0   0.183  31.9151  7.0151  -38.8755
 WGD  C7   C  CH2   0  -0.555  32.9803  7.0406  -39.9583
 WGD  C8   C  CH1   0  -0.051  32.2648  6.6420  -41.2645
 WGD  C10  C  CR15  0  -0.556  27.4027  6.5948  -41.3878
 WGD  C1   C  CH3   0  -0.727  27.1077  2.7566  -40.8361
 WGD  C2   C  CR5   0   0.051  27.4334  4.1865  -41.0904
 WGD  C3   C  CR5   0   0.333  28.6073  5.9961  -41.5647
 WGD  N2   N  NT    0  -0.438  30.8674  6.5032  -40.8714
 WGD  C9   C  CH2   0  -0.315  32.7713  5.3366  -41.8858
 WGD  S1   S  S2    0   0.195  26.2169  5.4190  -40.9918
 WGD  H1   H  HNH2  0   0.336  33.0954  4.1824  -40.2462
 WGD  H2   H  HNH2  0   0.339  31.5737  4.1737  -40.7829
 WGD  H4   H  HCH2  0   0.255  30.2758  6.2643  -42.8373
 WGD  H5   H  HCH2  0   0.222  29.6857  7.7547  -42.1121
 WGD  H6   H  HCH2  0   0.202  30.5091  8.3229  -39.8171
 WGD  H7   H  HCH2  0   0.248  29.7523  6.8863  -39.1186
 WGD  H8   H  HCH1  0   0.225  32.0754  7.7525  -38.0886
 WGD  H9   H  HCH2  0   0.258  33.8237  6.3936  -39.7083
 WGD  H10  H  HCH2  0   0.258  33.3751  8.0538  -40.0409
 WGD  H11  H  HCH1  0   0.213  32.3979  7.4464  -42.0049
 WGD  H12  H  HCR5  0   0.299  27.1638  7.6441  -41.4626
 WGD  H13  H  HCH3  0   0.263  26.2919  2.4135  -41.4721
 WGD  H14  H  HCH3  0   0.264  27.9833  2.1427  -41.0349
 WGD  H15  H  HCH3  0   0.265  26.8046  2.5995  -39.8004
 WGD  H17  H  HCH2  0   0.218  32.2906  5.1997  -42.8601
 WGD  H18  H  HCH2  0   0.227  33.8401  5.4350  -42.0937
 WGD  F1   F  F     0  -0.387  31.8783  5.7584  -38.2602

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
 WGD  C4   C3   single    1.497  0.020  1.497
 WGD  C4   N2   single    1.439  0.020  1.439
 WGD  C9   C8   single    1.532  0.020  1.532
 WGD  C9   N3   single    1.450  0.020  1.450
 WGD  C10  C3   aromatic  1.357  0.020  1.357
 WGD  C10  S1   aromatic  1.716  0.020  1.716
 WGD  C3   N1   aromatic  1.371  0.020  1.371
 WGD  S1   C2   aromatic  1.735  0.020  1.735
 WGD  N1   C2   aromatic  1.292  0.020  1.292
 WGD  C8   N2   single    1.458  0.020  1.458
 WGD  C8   C7   single    1.542  0.020  1.542
 WGD  C2   C1   single    1.488  0.020  1.488
 WGD  N2   C5   single    1.444  0.020  1.444
 WGD  C7   C6   single    1.519  0.020  1.519
 WGD  C5   C6   single    1.510  0.020  1.510
 WGD  C6   F1   single    1.400  0.020  1.400
 WGD  N3   H1   single    0.890  0.020  1.040
 WGD  N3   H2   single    0.890  0.020  1.040
 WGD  C4   H4   single    0.970  0.020  1.090
 WGD  C4   H5   single    0.970  0.020  1.090
 WGD  C5   H6   single    0.970  0.020  1.090
 WGD  C5   H7   single    0.970  0.020  1.090
 WGD  C6   H8   single    0.970  0.020  1.090
 WGD  C7   H9   single    0.970  0.020  1.090
 WGD  C7   H10  single    0.970  0.020  1.090
 WGD  C8   H11  single    0.970  0.020  1.090
 WGD  C10  H12  single    0.930  0.020  1.080
 WGD  C1   H13  single    0.970  0.020  1.090
 WGD  C1   H14  single    0.970  0.020  1.090
 WGD  C1   H15  single    0.970  0.020  1.090
 WGD  C9   H17  single    0.970  0.020  1.090
 WGD  C9   H18  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
 WGD  C3   N1   C2   112.02  3.000
 WGD  H2   N3   H1   105.44  3.000
 WGD  H2   N3   C9   107.20  3.000
 WGD  H1   N3   C9   109.84  3.000
 WGD  H5   C4   H4   106.54  3.000
 WGD  H5   C4   N2   112.58  3.000
 WGD  H4   C4   N2   108.64  3.000
 WGD  H5   C4   C3   109.51  3.000
 WGD  H4   C4   C3   108.52  3.000
 WGD  N2   C4   C3   110.88  3.000
 WGD  H7   C5   H6   107.19  3.000
 WGD  H7   C5   N2   112.04  3.000
 WGD  H6   C5   N2   113.07  3.000
 WGD  H7   C5   C6   112.79  3.000
 WGD  H6   C5   C6   108.82  3.000
 WGD  N2   C5   C6   102.97  3.000
 WGD  H8   C6   F1   107.09  3.000
 WGD  H8   C6   C7   113.58  3.000
 WGD  F1   C6   C7   110.29  3.000
 WGD  H8   C6   C5   113.22  3.000
 WGD  F1   C6   C5   109.70  3.000
 WGD  C7   C6   C5   102.95  3.000
 WGD  H10  C7   H9   106.75  3.000
 WGD  H10  C7   C8   110.13  3.000
 WGD  H9   C7   C8   113.53  3.000
 WGD  H10  C7   C6   108.87  3.000
 WGD  H9   C7   C6   111.62  3.000
 WGD  C8   C7   C6   105.91  3.000
 WGD  H11  C8   C9   108.04  3.000
 WGD  H11  C8   N2   111.50  3.000
 WGD  C9   C8   N2   110.19  3.000
 WGD  H11  C8   C7   108.94  3.000
 WGD  N2   C8   C7   103.94  3.000
 WGD  C9   C8   C7   114.23  3.000
 WGD  H12  C10  S1   121.97  3.000
 WGD  H12  C10  C3   128.08  3.000
 WGD  S1   C10  C3   109.95  3.000
 WGD  H15  C1   H14  108.42  3.000
 WGD  H15  C1   H13  107.51  3.000
 WGD  H14  C1   H13  108.56  3.000
 WGD  H15  C1   C2   111.19  3.000
 WGD  H14  C1   C2   109.56  3.000
 WGD  H13  C1   C2   111.51  3.000
 WGD  S1   C2   C1   121.29  3.000
 WGD  C1   C2   N1   124.95  3.000
 WGD  S1   C2   N1   113.76  3.000
 WGD  C10  C3   C4   125.77  3.000
 WGD  C10  C3   N1   114.90  3.000
 WGD  C4   C3   N1   119.33  3.000
 WGD  C8   N2   C5   109.34  3.000
 WGD  C5   N2   C4   115.78  3.000
 WGD  C8   N2   C4   116.48  3.000
 WGD  H18  C9   H17  105.73  3.000
 WGD  H18  C9   C8   108.89  3.000
 WGD  H17  C9   C8   108.80  3.000
 WGD  H18  C9   N3   109.51  3.000
 WGD  H17  C9   N3   108.31  3.000
 WGD  C8   C9   N3   115.18  3.000
 WGD  C2   S1   C10   89.37  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
 WGD  CONST_01  S1   C10  C3  N1      0.00   0.0  0
 WGD  CONST_02  C10  S1   C2  N1      0.00   0.0  0
 WGD  CONST_03  C2   N1   C3  C10     0.00   0.0  0
 WGD  CONST_04  C3   C10  S1  C2      0.00   0.0  0
 WGD  CONST_05  S1   C2   N1  C3      0.00   0.0  0
 WGD  CONST_06  S1   C10  C3  C4    180.00   0.0  0
 WGD  CONST_07  C2   N1   C3  C4    180.00   0.0  0
 WGD  CONST_08  C1   C2   S1  C10   180.00   0.0  0
 WGD  CONST_09  C3   N1   C2  C1    180.00   0.0  0
 WGD  CONST_10  H12  C10  C3  N1    180.00   0.0  0
 WGD  Var_01    C8   N2   C5  C6    -37.28  30.0  1
 WGD  Var_02    N2   C4   C3  N1    -61.11  30.0  2
 WGD  Var_03    C3   C4   N2  C5    -72.87  30.0  1
 WGD  Var_04    H13  C1   C2  N1   -125.44  30.0  2
 WGD  Var_05    H1   N3   C9  C8    -66.96  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
 WGD  chir_01  C6  C7  C5  F1  negativ
 WGD  chir_02  C8  N2  C9  C7  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
 WGD  plan-1  N1   0.020
 WGD  plan-1  C4   0.020
 WGD  plan-1  C10  0.020
 WGD  plan-1  C1   0.020
 WGD  plan-1  C2   0.020
 WGD  plan-1  C3   0.020
 WGD  plan-1  S1   0.020
 WGD  plan-1  H12  0.020

