# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:36:27 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (3S)-N-methyl-N-phenylpyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C(=O)[C@H]1CCNC1)c2ccccc2
#
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
 O3A  O3A  (3S)-N-methyl-N-phenylpyrrolidine-3-carboxamide  ligand  31  15  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O3A
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
 O3A  N1   N  NT    0  -0.554   0.2865   0.2974  -0.7282
 O3A  C4   C  CH2   0  -0.444  -3.1548  -1.1945  -0.2156
 O3A  C5   C  CH2   0  -0.323  -3.8519  -0.5405   0.9793
 O3A  C6   C  CH2   0  -0.300  -2.6037   1.1649   0.0653
 O3A  C7   C  CR6   0   0.314   1.6011   0.1166  -0.2113
 O3A  C8   C  CR16  0  -0.273   2.4860  -0.7432  -0.8476
 O3A  C10  C  CR16  0  -0.253   4.1916  -0.1686   0.7506
 O3A  C1   C  CH3   0  -0.540   0.1245   1.4250  -1.6295
 O3A  C11  C  CR16  0  -0.259   3.3056   0.6936   1.3836
 O3A  C12  C  CR16  0  -0.267   2.0110   0.8368   0.9036
 O3A  C2   C  C     0   0.546  -0.7105  -0.4735  -0.2202
 O3A  C3   C  CH1   0  -0.443  -2.1239  -0.1450  -0.6519
 O3A  C9   C  CR16  0  -0.260   3.7798  -0.8866  -0.3648
 O3A  N2   N  NH1   0  -0.578  -3.8939   0.8834   0.6732
 O3A  O1   O  O     0  -0.482  -0.4626  -1.3573   0.5863
 O3A  H2   H  HCH2  0   0.235  -3.8792  -1.3436  -1.0188
 O3A  H3   H  HCH2  0   0.240  -4.8540  -0.9278   1.1642
 O3A  H4   H  HCH2  0   0.224  -3.2663  -0.6943   1.8906
 O3A  H5   H  HCH2  0   0.232  -1.8931   1.4469   0.8492
 O3A  H6   H  HCH2  0   0.248  -2.6731   2.0097  -0.6191
 O3A  H7   H  HCR6  0   0.260   2.1614  -1.2955  -1.7205
 O3A  H8   H  HCR6  0   0.260   5.2012  -0.2791   1.1240
 O3A  H9   H  HCH3  0   0.246   0.1311   2.3756  -1.0923
 O3A  H10  H  HCH3  0   0.263   0.9443   1.4330  -2.3463
 O3A  H11  H  HCH3  0   0.261  -0.8000   1.3569  -2.1944
 O3A  H12  H  HCR6  0   0.260   3.6216   1.2552   2.2531
 O3A  H13  H  HCR6  0   0.259   1.3177   1.5089   1.3941
 O3A  H14  H  HCH1  0   0.283  -2.1624  -0.0141  -1.7345
 O3A  H15  H  HCR6  0   0.260   4.4660  -1.5607  -0.8604
 O3A  H16  H  HNH1  0   0.346  -4.6174   1.0372  -0.0196
 O3A  H1   H  HCH2  0   0.242  -2.7150  -2.1628   0.0162

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
 O3A  C9   C8   aromatic  1.388  0.020  1.388
 O3A  C9   C10  aromatic  1.389  0.020  1.389
 O3A  C8   C7   aromatic  1.388  0.020  1.388
 O3A  O1   C2   double    1.222  0.020  1.222
 O3A  C10  C11  aromatic  1.389  0.020  1.389
 O3A  C7   N1   single    1.424  0.020  1.424
 O3A  C7   C12  aromatic  1.389  0.020  1.389
 O3A  C1   N1   single    1.453  0.020  1.453
 O3A  N1   C2   single    1.359  0.020  1.359
 O3A  C2   C3   single    1.514  0.020  1.514
 O3A  C11  C12  aromatic  1.388  0.020  1.388
 O3A  C3   C4   single    1.534  0.020  1.534
 O3A  C3   C6   single    1.569  0.020  1.569
 O3A  C4   C5   single    1.530  0.020  1.530
 O3A  C5   N2   single    1.457  0.020  1.457
 O3A  N2   C6   single    1.454  0.020  1.454
 O3A  C4   H1   single    0.970  0.020  1.090
 O3A  C4   H2   single    0.970  0.020  1.090
 O3A  C5   H3   single    0.970  0.020  1.090
 O3A  C5   H4   single    0.970  0.020  1.090
 O3A  C6   H5   single    0.970  0.020  1.090
 O3A  C6   H6   single    0.970  0.020  1.090
 O3A  C8   H7   single    0.930  0.020  1.080
 O3A  C10  H8   single    0.930  0.020  1.080
 O3A  C1   H9   single    0.970  0.020  1.090
 O3A  C1   H10  single    0.970  0.020  1.090
 O3A  C1   H11  single    0.970  0.020  1.090
 O3A  C11  H12  single    0.930  0.020  1.080
 O3A  C12  H13  single    0.930  0.020  1.080
 O3A  C3   H14  single    0.970  0.020  1.090
 O3A  C9   H15  single    0.930  0.020  1.080
 O3A  N2   H16  single    0.890  0.020  1.040

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
 O3A  C2   N1   C1   126.19  3.000
 O3A  C2   N1   C7   118.01  3.000
 O3A  C1   N1   C7   115.26  3.000
 O3A  H2   C4   H1   107.65  3.000
 O3A  H2   C4   C3   109.27  3.000
 O3A  H1   C4   C3   113.43  3.000
 O3A  H2   C4   C5   109.30  3.000
 O3A  H1   C4   C5   113.45  3.000
 O3A  C3   C4   C5   103.64  3.000
 O3A  H4   C5   H3   107.51  3.000
 O3A  H4   C5   N2   109.13  3.000
 O3A  H3   C5   N2   110.87  3.000
 O3A  H4   C5   C4   110.27  3.000
 O3A  H3   C5   C4   113.54  3.000
 O3A  N2   C5   C4   105.47  3.000
 O3A  H6   C6   H5   106.94  3.000
 O3A  H6   C6   N2   110.87  3.000
 O3A  H5   C6   N2   109.05  3.000
 O3A  H6   C6   C3   112.32  3.000
 O3A  H5   C6   C3   110.11  3.000
 O3A  N2   C6   C3   107.51  3.000
 O3A  C12  C7   C8   120.06  3.000
 O3A  C12  C7   N1   119.86  3.000
 O3A  C8   C7   N1   120.04  3.000
 O3A  H7   C8   C9   120.46  3.000
 O3A  H7   C8   C7   119.63  3.000
 O3A  C9   C8   C7   119.91  3.000
 O3A  H8   C10  C9   120.06  3.000
 O3A  H8   C10  C11  120.08  3.000
 O3A  C9   C10  C11  119.86  3.000
 O3A  H11  C1   H10  107.40  3.000
 O3A  H11  C1   H9   108.41  3.000
 O3A  H10  C1   H9   108.23  3.000
 O3A  H11  C1   N1   111.66  3.000
 O3A  H10  C1   N1   109.27  3.000
 O3A  H9   C1   N1   111.71  3.000
 O3A  H12  C11  C12  119.77  3.000
 O3A  H12  C11  C10  120.14  3.000
 O3A  C12  C11  C10  120.09  3.000
 O3A  H13  C12  C11  120.29  3.000
 O3A  H13  C12  C7   119.76  3.000
 O3A  C11  C12  C7   119.95  3.000
 O3A  O1   C2   C3   122.32  3.000
 O3A  C3   C2   N1   117.09  3.000
 O3A  O1   C2   N1   120.54  3.000
 O3A  H14  C3   C2   109.99  3.000
 O3A  H14  C3   C6   110.04  3.000
 O3A  C2   C3   C6   109.66  3.000
 O3A  H14  C3   C4   109.91  3.000
 O3A  C6   C3   C4   103.63  3.000
 O3A  C2   C3   C4   113.44  3.000
 O3A  H15  C9   C10  120.12  3.000
 O3A  H15  C9   C8   119.74  3.000
 O3A  C10  C9   C8   120.14  3.000
 O3A  H16  N2   C6   108.56  3.000
 O3A  H16  N2   C5   108.21  3.000
 O3A  C6   N2   C5   104.57  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
 O3A  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 O3A  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 O3A  CONST_03  C11  C10  C9   C8     0.00   0.0  0
 O3A  CONST_04  C11  C12  C7   C8     0.00   0.0  0
 O3A  CONST_05  C9   C8   C7   C12    0.00   0.0  0
 O3A  CONST_06  C9   C10  C11  C12    0.00   0.0  0
 O3A  CONST_07  C9   C8   C7   N1   180.00   0.0  0
 O3A  CONST_08  C11  C12  C7   N1   180.00   0.0  0
 O3A  CONST_09  H15  C9   C8   C7   180.00   0.0  0
 O3A  CONST_10  H12  C11  C12  C7   180.00   0.0  0
 O3A  CONST_11  H8   C10  C9   C8   180.00   0.0  0
 O3A  CONST_12  H13  C12  C7   C8   180.00   0.0  0
 O3A  CONST_13  H7   C8   C9   C10  180.00   0.0  0
 O3A  CONST_14  C3   C2   N1   C7   180.00   0.0  0
 O3A  CONST_19  O1   C2   N1   C7     0.00   0.0  0
 O3A  CONST_20  C3   C2   N1   C1     0.00   0.0  0
 O3A  CONST_21  O1   C2   N1   C1   180.00   0.0  0
 O3A  Var_01    C6   N2   C5   C4   -39.94  30.0  1
 O3A  Var_02    C3   C6   N2   C5    29.35  30.0  1
 O3A  Var_03    N2   C5   C4   C3    34.52  30.0  1
 O3A  Var_04    H9   C1   N1   C7   -74.00  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
 O3A  chir_01  C3  C2  C4  C6  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
 O3A  plan-1  N1   0.020
 O3A  plan-1  C7   0.020
 O3A  plan-1  C8   0.020
 O3A  plan-1  C10  0.020
 O3A  plan-1  C11  0.020
 O3A  plan-1  C12  0.020
 O3A  plan-1  C9   0.020
 O3A  plan-1  H7   0.020
 O3A  plan-1  H8   0.020
 O3A  plan-1  H12  0.020
 O3A  plan-1  H13  0.020
 O3A  plan-1  H15  0.020
 O3A  plan-2  N1   0.020
 O3A  plan-2  C7   0.020
 O3A  plan-2  C1   0.020
 O3A  plan-2  C2   0.020
 O3A  plan-2  C3   0.020
 O3A  plan-2  O1   0.020

