# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 08:05:42 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-[(2R,3S,4R,5R)-1-[3-(4-fluorophenyl)propyl]-5-(hydroxymethyl)-3,4-bis(oxidanyl)pyrrolidin-2-yl]-N-methyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C[C@@H]1[C@H](O)[C@H](O)[C@@H](CO)N1CCCc2ccc(F)cc2
#
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
 V0N  V0N  2-[(2R,3S,4R,5R)-1-[3-(4-fluorophenyl)propyl]-5-(hydroxymethyl)-3,4-bis(oxidanyl)pyrrolidin-2-yl]-N-methyl-ethanamide  ligand  49  24  .  2021-08-24  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V0N
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
 V0N  C1    C  CH2   0  -0.300  -0.7289  -0.2098  -1.0133
 V0N  C2    C  CH2   0  -0.519   1.7385   0.2627  -1.2743
 V0N  N2    N  NT    0  -0.474  -1.8137  -0.5811  -0.1370
 V0N  C3    C  CH1   0  -0.054  -2.9894   0.2729  -0.0685
 V0N  C4    C  CH1   0  -0.013  -4.0565  -0.6145   0.5660
 V0N  C5    C  CH1   0  -0.011  -3.6837  -1.9870   0.0151
 V0N  C6    C  CH1   0  -0.043  -2.1568  -1.9802   0.0820
 V0N  O7    O  OH1   0  -0.669  -4.2086  -3.0612   0.7555
 V0N  O8    O  OH1   0  -0.676  -3.9490  -0.5958   1.9693
 V0N  C9    C  CH2   0  -0.211  -1.5197  -3.0002  -0.8450
 V0N  O10   O  OH1   0  -0.667  -1.9900  -2.8490  -2.1651
 V0N  C11   C  CH2   0  -0.548  -2.7664   1.5650   0.7235
 V0N  C12   C  C     0   0.532  -1.9642   2.6023  -0.0300
 V0N  N13   N  NH1   0  -0.618  -0.8446   3.0234   0.5743
 V0N  C14   C  CH3   0  -0.519   0.0376   4.0054  -0.0078
 V0N  O15   O  O     0  -0.509  -2.3257   3.0394  -1.1174
 V0N  C16   C  CH2   0  -0.416   0.6215  -0.1329  -0.3093
 V0N  C19   C  CR6   0   0.137   3.0733   0.3758  -0.5951
 V0N  C20   C  CR16  0  -0.292   3.8330  -0.7611  -0.3240
 V0N  C21   C  CR16  0  -0.395   5.0498  -0.6789   0.3377
 V0N  C22   C  CR6   0   0.504   5.5038   0.5654   0.7310
 V0N  C23   C  CR16  0  -0.395   4.7844   1.7171   0.4825
 V0N  C24   C  CR16  0  -0.301   3.5693   1.6090  -0.1813
 V0N  F25   F  F     0  -0.320   6.6833   0.6576   1.3713
 V0N  H1    H  HCH2  0   0.229  -0.6495  -0.8841  -1.8734
 V0N  H2    H  HCH2  0   0.242   1.7959  -0.4738  -2.0813
 V0N  H3    H  HCH1  0   0.219  -3.3515   0.5497  -1.0714
 V0N  H4    H  HCH1  0   0.225  -5.0589  -0.2989   0.2460
 V0N  H5    H  HCH1  0   0.231  -3.9994  -2.0334  -1.0335
 V0N  H6    H  HCH1  0   0.211  -1.8541  -2.2969   1.0929
 V0N  H9    H  HCH2  0   0.215  -0.4261  -2.9127  -0.7940
 V0N  HO10  H  HOH1  0   0.457  -1.5483  -3.5010  -2.7163
 V0N  H1A   H  HCH2  0   0.239  -0.9537   0.7659  -1.4501
 V0N  H11   H  HCH2  0   0.265  -3.7401   2.0211   0.9278
 V0N  H11A  H  HCH2  0   0.250  -2.3122   1.3273   1.6850
 V0N  HN13  H  HNH1  0   0.404  -0.5940   2.6268   1.4635
 V0N  H14   H  HCH3  0   0.250   0.8769   4.1554   0.6652
 V0N  H16   H  HCH2  0   0.218   0.5660   0.5912   0.5078
 V0N  H20   H  HCR6  0   0.257   3.4710  -1.7338  -0.6356
 V0N  H21   H  HCR6  0   0.276   5.6347  -1.5670   0.5392
 V0N  H2A   H  HCH2  0   0.238   1.4840   1.2162  -1.7462
 V0N  H23   H  HCR6  0   0.276   5.1633   2.6814   0.7952
 V0N  H24   H  HCR6  0   0.252   3.0028   2.5103  -0.3835
 V0N  H14A  H  HCH3  0   0.235   0.4275   3.6775  -0.9727
 V0N  H14B  H  HCH3  0   0.243  -0.4623   4.9636  -0.1518
 V0N  H16A  H  HCH2  0   0.223   0.8599  -1.0986   0.1478
 V0N  H9A   H  HCH2  0   0.221  -1.7677  -3.9915  -0.4445
 V0N  HO7   H  HOH1  0   0.460  -5.1164  -3.2140   0.4757
 V0N  HO8   H  HOH1  0   0.444  -4.2917  -1.4377   2.2928

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
 V0N  C1   N2    single    1.443  0.020  1.443
 V0N  C1   C16   single    1.525  0.020  1.525
 V0N  C1   H1    single    0.970  0.020  1.090
 V0N  C1   H1A   single    0.970  0.020  1.090
 V0N  C2   C16   single    1.528  0.020  1.528
 V0N  C2   C19   single    1.502  0.020  1.502
 V0N  C2   H2    single    0.970  0.020  1.090
 V0N  C2   H2A   single    0.970  0.020  1.090
 V0N  N2   C3    single    1.455  0.020  1.455
 V0N  N2   C6    single    1.457  0.020  1.457
 V0N  C3   C4    single    1.526  0.020  1.526
 V0N  C3   C11   single    1.532  0.020  1.532
 V0N  C3   H3    single    0.970  0.020  1.090
 V0N  C4   C5    single    1.525  0.020  1.525
 V0N  C4   O8    single    1.407  0.020  1.407
 V0N  C4   H4    single    0.970  0.020  1.090
 V0N  C5   C6    single    1.528  0.020  1.528
 V0N  C5   O7    single    1.406  0.020  1.406
 V0N  C5   H5    single    0.970  0.020  1.090
 V0N  C6   C9    single    1.518  0.020  1.518
 V0N  C6   H6    single    0.970  0.020  1.090
 V0N  O7   HO7   single    0.850  0.020  0.980
 V0N  O8   HO8   single    0.850  0.020  0.980
 V0N  C9   O10   single    1.410  0.020  1.410
 V0N  C9   H9    single    0.970  0.020  1.090
 V0N  C9   H9A   single    0.970  0.020  1.090
 V0N  O10  HO10  single    0.850  0.020  0.980
 V0N  C11  C12   single    1.512  0.020  1.512
 V0N  C11  H11   single    0.970  0.020  1.090
 V0N  C11  H11A  single    0.970  0.020  1.090
 V0N  C12  N13   single    1.340  0.020  1.340
 V0N  C12  O15   double    1.226  0.020  1.226
 V0N  N13  C14   single    1.443  0.020  1.443
 V0N  N13  HN13  single    0.860  0.020  1.020
 V0N  C14  H14   single    0.970  0.020  1.090
 V0N  C14  H14A  single    0.970  0.020  1.090
 V0N  C14  H14B  single    0.970  0.020  1.090
 V0N  C16  H16   single    0.970  0.020  1.090
 V0N  C16  H16A  single    0.970  0.020  1.090
 V0N  C19  C20   aromatic  1.394  0.020  1.394
 V0N  C19  C24   aromatic  1.392  0.020  1.392
 V0N  C20  C21   aromatic  1.388  0.020  1.388
 V0N  C20  H20   single    0.930  0.020  1.080
 V0N  C21  C22   aromatic  1.382  0.020  1.382
 V0N  C21  H21   single    0.930  0.020  1.080
 V0N  C22  C23   aromatic  1.380  0.020  1.380
 V0N  C22  F25   single    1.345  0.020  1.345
 V0N  C23  C24   aromatic  1.389  0.020  1.389
 V0N  C23  H23   single    0.930  0.020  1.080
 V0N  C24  H24   single    0.930  0.020  1.080

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
 V0N  H1A   C1   H1    104.51  3.000
 V0N  H1A   C1   C16   108.77  3.000
 V0N  H1    C1   C16   109.23  3.000
 V0N  H1A   C1   N2    108.53  3.000
 V0N  H1    C1   N2    111.89  3.000
 V0N  C16   C1   N2    113.48  3.000
 V0N  H2A   C2   H2    106.31  3.000
 V0N  H2A   C2   C19   109.65  3.000
 V0N  H2    C2   C19   109.74  3.000
 V0N  H2A   C2   C16   109.14  3.000
 V0N  H2    C2   C16   109.26  3.000
 V0N  C19   C2   C16   112.55  3.000
 V0N  C6    N2   C3    111.48  3.000
 V0N  C6    N2   C1    121.02  3.000
 V0N  C3    N2   C1    119.02  3.000
 V0N  H3    C3   C11   107.85  3.000
 V0N  H3    C3   C4    107.15  3.000
 V0N  C11   C3   C4    112.17  3.000
 V0N  H3    C3   N2    111.73  3.000
 V0N  C11   C3   N2    113.69  3.000
 V0N  C4    C3   N2    104.09  3.000
 V0N  H4    C4   O8    110.88  3.000
 V0N  H4    C4   C5    112.10  3.000
 V0N  O8    C4   C5    110.69  3.000
 V0N  H4    C4   C3    110.48  3.000
 V0N  O8    C4   C3    110.70  3.000
 V0N  C5    C4   C3    101.66  3.000
 V0N  H5    C5   O7    111.34  3.000
 V0N  H5    C5   C6    109.25  3.000
 V0N  O7    C5   C6    110.68  3.000
 V0N  H5    C5   C4    108.26  3.000
 V0N  O7    C5   C4    113.96  3.000
 V0N  C6    C5   C4    102.97  3.000
 V0N  H6    C6   C9    104.58  3.000
 V0N  H6    C6   C5    108.26  3.000
 V0N  C9    C6   C5    112.93  3.000
 V0N  H6    C6   N2    110.44  3.000
 V0N  C9    C6   N2    117.03  3.000
 V0N  C5    C6   N2    103.47  3.000
 V0N  HO7   O7   C5    108.68  3.000
 V0N  HO8   O8   C4    107.20  3.000
 V0N  H9A   C9   H9    106.26  3.000
 V0N  H9A   C9   O10   111.30  3.000
 V0N  H9    C9   O10   111.54  3.000
 V0N  H9A   C9   C6    106.81  3.000
 V0N  H9    C9   C6    109.63  3.000
 V0N  O10   C9   C6    111.08  3.000
 V0N  HO10  O10  C9    108.12  3.000
 V0N  H11A  C11  H11   107.28  3.000
 V0N  H11A  C11  C12   111.61  3.000
 V0N  H11   C11  C12   106.20  3.000
 V0N  H11A  C11  C3    109.44  3.000
 V0N  H11   C11  C3    108.57  3.000
 V0N  C12   C11  C3    113.46  3.000
 V0N  O15   C12  N13   122.28  3.000
 V0N  O15   C12  C11   122.00  3.000
 V0N  N13   C12  C11   115.72  3.000
 V0N  HN13  N13  C14   118.23  3.000
 V0N  HN13  N13  C12   118.88  3.000
 V0N  C14   N13  C12   122.88  3.000
 V0N  H14B  C14  H14A  108.12  3.000
 V0N  H14B  C14  H14   108.34  3.000
 V0N  H14A  C14  H14   108.26  3.000
 V0N  H14B  C14  N13   111.79  3.000
 V0N  H14A  C14  N13   111.76  3.000
 V0N  H14   C14  N13   108.45  3.000
 V0N  H16A  C16  H16   106.46  3.000
 V0N  H16A  C16  C2    109.44  3.000
 V0N  H16   C16  C2    109.73  3.000
 V0N  H16A  C16  C1    109.95  3.000
 V0N  H16   C16  C1    109.48  3.000
 V0N  C2    C16  C1    111.64  3.000
 V0N  C24   C19  C20   118.07  3.000
 V0N  C24   C19  C2    121.18  3.000
 V0N  C20   C19  C2    120.72  3.000
 V0N  H20   C20  C21   118.90  3.000
 V0N  H20   C20  C19   119.61  3.000
 V0N  C21   C20  C19   121.49  3.000
 V0N  H21   C21  C22   120.56  3.000
 V0N  H21   C21  C20   120.93  3.000
 V0N  C22   C21  C20   118.51  3.000
 V0N  F25   C22  C23   119.04  3.000
 V0N  F25   C22  C21   119.03  3.000
 V0N  C23   C22  C21   121.93  3.000
 V0N  H23   C23  C24   120.92  3.000
 V0N  H23   C23  C22   120.59  3.000
 V0N  C24   C23  C22   118.49  3.000
 V0N  H24   C24  C23   118.81  3.000
 V0N  H24   C24  C19   119.67  3.000
 V0N  C23   C24  C19   121.52  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
 V0N  CONST_01  C22   C21  C20  C19     0.00   0.0  0
 V0N  CONST_02  C22   C23  C24  C19     0.00   0.0  0
 V0N  CONST_03  C23   C24  C19  C20     0.00   0.0  0
 V0N  CONST_04  C23   C22  C21  C20     0.00   0.0  0
 V0N  CONST_05  C24   C19  C20  C21     0.00   0.0  0
 V0N  CONST_06  C24   C23  C22  C21     0.00   0.0  0
 V0N  CONST_07  C21   C20  C19  C2    180.00   0.0  0
 V0N  CONST_08  C23   C24  C19  C2    180.00   0.0  0
 V0N  CONST_09  F25   C22  C21  C20   180.00   0.0  0
 V0N  CONST_10  F25   C22  C23  C24   180.00   0.0  0
 V0N  CONST_11  H21   C21  C20  C19   180.00   0.0  0
 V0N  CONST_12  H23   C23  C24  C19   180.00   0.0  0
 V0N  CONST_13  H24   C24  C19  C20   180.00   0.0  0
 V0N  CONST_14  H20   C20  C21  C22   180.00   0.0  0
 V0N  CONST_15  C14   N13  C12  C11   180.00   0.0  0
 V0N  CONST_16  O15   C12  N13  C14     0.00   0.0  0
 V0N  CONST_17  HN13  N13  C12  C11     0.00   0.0  0
 V0N  Var_01    C16   C1   N2   C3    125.97  30.0  2
 V0N  Var_02    C20   C19  C2   C16    80.47  30.0  2
 V0N  Var_03    C19   C2   C16  C1    178.67  30.0  1
 V0N  Var_04    N2    C1   C16  C2    179.99  30.0  1
 V0N  Var_05    N13   C12  C11  C3   -122.74  30.0  3
 V0N  Var_06    H14   C14  N13  C12  -178.76  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
 V0N  chir_01  C3  N2  C4  C11  negativ
 V0N  chir_02  C4  O8  C3  C5   negativ
 V0N  chir_03  C5  O7  C4  C6   negativ
 V0N  chir_04  C6  N2  C5  C9   negativ

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
 V0N  plan-1  C2    0.020
 V0N  plan-1  C19   0.020
 V0N  plan-1  C20   0.020
 V0N  plan-1  C21   0.020
 V0N  plan-1  C22   0.020
 V0N  plan-1  C23   0.020
 V0N  plan-1  C24   0.020
 V0N  plan-1  F25   0.020
 V0N  plan-1  H20   0.020
 V0N  plan-1  H21   0.020
 V0N  plan-1  H23   0.020
 V0N  plan-1  H24   0.020
 V0N  plan-2  C11   0.020
 V0N  plan-2  C12   0.020
 V0N  plan-2  N13   0.020
 V0N  plan-2  C14   0.020
 V0N  plan-2  O15   0.020
 V0N  plan-2  HN13  0.020

