# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 20:43:58 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: [(3R)-3-hydroxypiperidin-1-yl](1-phenylcyclopropyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCCN(C1)C(=O)C2(CC2)c3ccccc3
#
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
 5GJ  5GJ  '[(3R)-3-hydroxypiperidin-1-yl](1-phenylcyclopropyl)methanone'  ligand  37  18  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5GJ
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
 5GJ  C4   C  CR16  0  -0.309   2.2008  -0.1274   1.3318
 5GJ  C5   C  CR16  0  -0.239   3.2242  -0.9672   1.7452
 5GJ  C6   C  CT    0  -0.214   0.9241   1.1125  -0.4189
 5GJ  C7   C  CH2   0  -0.482   0.7230   1.5275  -1.8527
 5GJ  C8   C  CH2   0  -0.460   1.3212   2.4871  -0.8821
 5GJ  C9   C  C     0   0.535  -0.3309   1.0325   0.4229
 5GJ  C10  C  CH2   0  -0.318  -0.8438  -1.1568  -0.6514
 5GJ  C11  C  CH2   0  -0.441  -1.9991  -1.1449  -1.6444
 5GJ  C12  C  CH2   0  -0.487  -3.3350  -1.2728  -0.9191
 5GJ  C13  C  CH1   0   0.074  -3.4645  -0.2147   0.1707
 5GJ  C14  C  CH2   0  -0.341  -2.2610  -0.2770   1.1068
 5GJ  O    O  O     0  -0.490  -0.6644   1.9595   1.1489
 5GJ  C3   C  CR6   0   0.160   2.0161   0.1693  -0.0195
 5GJ  C2   C  CR16  0  -0.324   2.8896  -0.3990  -0.9438
 5GJ  C1   C  CR16  0  -0.238   3.9194  -1.2346  -0.5312
 5GJ  C    C  CR16  0  -0.272   4.0908  -1.5254   0.8145
 5GJ  N    N  NT    0  -0.443  -1.0342  -0.1178   0.3489
 5GJ  O1   O  OH1   0  -0.672  -4.6131  -0.3933   0.9677
 5GJ  H1   H  HCR6  0   0.251   1.5487   0.3093   2.0786
 5GJ  H2   H  HCR6  0   0.256   3.3465  -1.1822   2.7990
 5GJ  H3   H  HCH2  0   0.267   1.3479   1.0895  -2.6202
 5GJ  H4   H  HCH2  0   0.268  -0.2973   1.7007  -2.1737
 5GJ  H5   H  HCH2  0   0.262   0.7311   3.3299  -0.5474
 5GJ  H6   H  HCH2  0   0.263   2.3834   2.6824  -0.9541
 5GJ  H8   H  HCH2  0   0.281   0.1057  -1.0360  -1.1625
 5GJ  H9   H  HCH2  0   0.228  -1.9673  -0.2166  -2.2237
 5GJ  H10  H  HCH2  0   0.247  -1.8739  -1.9648  -2.3540
 5GJ  H11  H  HCH2  0   0.245  -4.1634  -1.1874  -1.6276
 5GJ  H12  H  HCH2  0   0.224  -3.4052  -2.2643  -0.4582
 5GJ  H13  H  HCH1  0   0.199  -3.4665   0.7785  -0.3046
 5GJ  H14  H  HCH2  0   0.269  -2.3258   0.4934   1.8712
 5GJ  H15  H  HCH2  0   0.245  -2.2379  -1.2498   1.6107
 5GJ  H16  H  HCR6  0   0.251   2.7741  -0.1979  -2.0009
 5GJ  H17  H  HCR6  0   0.256   4.5862  -1.6630  -1.2685
 5GJ  H18  H  HCR6  0   0.255   4.8919  -2.1786   1.1352
 5GJ  H19  H  HOH1  0   0.452  -5.3866  -0.3580   0.3964
 5GJ  H7   H  HCH2  0   0.246  -0.8069  -2.1214  -0.1354

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
 5GJ  O1   C13  single    1.409  0.020  1.409
 5GJ  C12  C13  single    1.524  0.020  1.524
 5GJ  C12  C11  single    1.525  0.020  1.525
 5GJ  C13  C14  single    1.526  0.020  1.526
 5GJ  C11  C10  single    1.523  0.020  1.523
 5GJ  C14  N    single    1.451  0.020  1.451
 5GJ  C10  N    single    1.455  0.020  1.455
 5GJ  N    C9   single    1.350  0.020  1.350
 5GJ  C9   O    double    1.224  0.020  1.224
 5GJ  C9   C6   single    1.513  0.020  1.513
 5GJ  C4   C5   aromatic  1.387  0.020  1.387
 5GJ  C4   C3   aromatic  1.396  0.020  1.396
 5GJ  C5   C    aromatic  1.389  0.020  1.389
 5GJ  C6   C3   single    1.497  0.020  1.497
 5GJ  C6   C7   single    1.506  0.020  1.506
 5GJ  C6   C8   single    1.504  0.020  1.504
 5GJ  C3   C2   aromatic  1.393  0.020  1.393
 5GJ  C7   C8   single    1.490  0.020  1.490
 5GJ  C    C1   aromatic  1.387  0.020  1.387
 5GJ  C2   C1   aromatic  1.389  0.020  1.389
 5GJ  C4   H1   single    0.930  0.020  1.080
 5GJ  C5   H2   single    0.930  0.020  1.080
 5GJ  C7   H3   single    0.970  0.020  1.090
 5GJ  C7   H4   single    0.970  0.020  1.090
 5GJ  C8   H5   single    0.970  0.020  1.090
 5GJ  C8   H6   single    0.970  0.020  1.090
 5GJ  C10  H7   single    0.970  0.020  1.090
 5GJ  C10  H8   single    0.970  0.020  1.090
 5GJ  C11  H9   single    0.970  0.020  1.090
 5GJ  C11  H10  single    0.970  0.020  1.090
 5GJ  C12  H11  single    0.970  0.020  1.090
 5GJ  C12  H12  single    0.970  0.020  1.090
 5GJ  C13  H13  single    0.970  0.020  1.090
 5GJ  C14  H14  single    0.970  0.020  1.090
 5GJ  C14  H15  single    0.970  0.020  1.090
 5GJ  C2   H16  single    0.930  0.020  1.080
 5GJ  C1   H17  single    0.930  0.020  1.080
 5GJ  C    H18  single    0.930  0.020  1.080
 5GJ  O1   H19  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
 5GJ  H1   C4   C3   120.14  3.000
 5GJ  H1   C4   C5   118.86  3.000
 5GJ  C3   C4   C5   121.00  3.000
 5GJ  H2   C5   C    120.14  3.000
 5GJ  H2   C5   C4   119.59  3.000
 5GJ  C    C5   C4   120.26  3.000
 5GJ  C3   C6   C9   115.04  3.000
 5GJ  C3   C6   C8   117.74  3.000
 5GJ  C9   C6   C8   116.02  3.000
 5GJ  C8   C6   C7    59.35  3.000
 5GJ  C3   C6   C7   121.66  3.000
 5GJ  C9   C6   C7   115.68  3.000
 5GJ  H4   C7   H3   113.47  3.000
 5GJ  H4   C7   C8   117.91  3.000
 5GJ  H3   C7   C8   119.38  3.000
 5GJ  H4   C7   C6   116.86  3.000
 5GJ  H3   C7   C6   119.11  3.000
 5GJ  C8   C7   C6    60.25  3.000
 5GJ  H6   C8   H5   114.54  3.000
 5GJ  H6   C8   C7   117.83  3.000
 5GJ  H5   C8   C7   118.96  3.000
 5GJ  H6   C8   C6   116.39  3.000
 5GJ  H5   C8   C6   118.21  3.000
 5GJ  C7   C8   C6    60.40  3.000
 5GJ  N    C9   O    122.41  3.000
 5GJ  O    C9   C6   121.06  3.000
 5GJ  N    C9   C6   116.52  3.000
 5GJ  H8   C10  H7   106.90  3.000
 5GJ  H8   C10  N    111.03  3.000
 5GJ  H7   C10  N    108.04  3.000
 5GJ  H8   C10  C11  110.84  3.000
 5GJ  H7   C10  C11  109.86  3.000
 5GJ  N    C10  C11  110.08  3.000
 5GJ  H10  C11  H9   106.84  3.000
 5GJ  H10  C11  C12  110.28  3.000
 5GJ  H9   C11  C12  110.37  3.000
 5GJ  H10  C11  C10  109.32  3.000
 5GJ  H9   C11  C10  109.24  3.000
 5GJ  C12  C11  C10  110.70  3.000
 5GJ  H12  C12  H11  107.14  3.000
 5GJ  H12  C12  C13  108.78  3.000
 5GJ  H11  C12  C13  110.16  3.000
 5GJ  H12  C12  C11  109.39  3.000
 5GJ  H11  C12  C11  110.42  3.000
 5GJ  C13  C12  C11  110.86  3.000
 5GJ  H13  C13  O1   110.91  3.000
 5GJ  H13  C13  C14  107.64  3.000
 5GJ  O1   C13  C14  106.90  3.000
 5GJ  H13  C13  C12  108.52  3.000
 5GJ  C14  C13  C12  110.07  3.000
 5GJ  O1   C13  C12  112.68  3.000
 5GJ  H15  C14  H14  107.87  3.000
 5GJ  H15  C14  N    108.65  3.000
 5GJ  H14  C14  N    109.88  3.000
 5GJ  H15  C14  C13  109.57  3.000
 5GJ  H14  C14  C13  110.82  3.000
 5GJ  N    C14  C13  110.00  3.000
 5GJ  C2   C3   C6   122.51  3.000
 5GJ  C2   C3   C4   118.21  3.000
 5GJ  C6   C3   C4   119.25  3.000
 5GJ  H16  C2   C1   118.75  3.000
 5GJ  H16  C2   C3   120.36  3.000
 5GJ  C1   C2   C3   120.89  3.000
 5GJ  H17  C1   C    120.11  3.000
 5GJ  H17  C1   C2   119.51  3.000
 5GJ  C    C1   C2   120.38  3.000
 5GJ  H18  C    C1   120.35  3.000
 5GJ  H18  C    C5   120.39  3.000
 5GJ  C1   C    C5   119.26  3.000
 5GJ  C14  N    C10  113.05  3.000
 5GJ  C10  N    C9   125.31  3.000
 5GJ  C14  N    C9   120.34  3.000
 5GJ  H19  O1   C13  108.35  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
 5GJ  CONST_01  C1   C    C5   C4      0.00   0.0  0
 5GJ  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 5GJ  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 5GJ  CONST_04  C2   C1   C    C5      0.00   0.0  0
 5GJ  CONST_05  C    C5   C4   C3      0.00   0.0  0
 5GJ  CONST_06  C    C1   C2   C3      0.00   0.0  0
 5GJ  CONST_07  C6   C3   C4   C5    180.00   0.0  0
 5GJ  CONST_08  C1   C2   C3   C6    180.00   0.0  0
 5GJ  CONST_09  C14  N    C9   C6    180.00   0.0  0
 5GJ  CONST_10  C10  N    C9   C6      0.00   0.0  0
 5GJ  CONST_11  H18  C    C5   C4    180.00   0.0  0
 5GJ  CONST_12  H16  C2   C3   C4    180.00   0.0  0
 5GJ  CONST_13  H17  C1   C    C5    180.00   0.0  0
 5GJ  CONST_14  H1   C4   C3   C6      0.00   0.0  0
 5GJ  CONST_15  H2   C5   C4   C3    180.00   0.0  0
 5GJ  CONST_16  O    C9   N    C10   180.00   0.0  0
 5GJ  CONST_17  O    C9   N    C14     0.00   0.0  0
 5GJ  Var_01    C7   C6   C3   C4    176.70  30.0  3
 5GJ  Var_02    C3   C6   C8   C7    112.20  30.0  1
 5GJ  Var_03    C13  C12  C11  C10    53.33  30.0  1
 5GJ  Var_04    C13  C14  N    C10   -60.69  30.0  1
 5GJ  Var_05    C14  N    C10  C11    59.83  30.0  1
 5GJ  Var_06    N    C10  C11  C12   -55.07  30.0  1
 5GJ  Var_07    N    C9   C6   C7     84.27  30.0  3
 5GJ  Var_08    H5   C8   C7   C6   -107.88  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
 5GJ  chir_02  C13  O1  C12  C14  positiv
 5GJ  chir_03  C6   C3  C7   C8   both

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
 5GJ  plan-1  C4   0.020
 5GJ  plan-1  C5   0.020
 5GJ  plan-1  C6   0.020
 5GJ  plan-1  C3   0.020
 5GJ  plan-1  C2   0.020
 5GJ  plan-1  C1   0.020
 5GJ  plan-1  C    0.020
 5GJ  plan-1  H1   0.020
 5GJ  plan-1  H2   0.020
 5GJ  plan-1  H16  0.020
 5GJ  plan-1  H17  0.020
 5GJ  plan-1  H18  0.020
 5GJ  plan-2  C6   0.020
 5GJ  plan-2  C9   0.020
 5GJ  plan-2  C10  0.020
 5GJ  plan-2  C14  0.020
 5GJ  plan-2  O    0.020
 5GJ  plan-2  N    0.020

