# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 17:29:36 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (2R)-2-phenylpyrrolidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN[C@H](C1)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
 96B  96B  '(2R)-2-phenylpyrrolidine '  ligand  24  11  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_96B
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
 96B  N    N  NH1   0  -0.610  -1.7285   0.6431  -0.9682
 96B  C3   C  CH2   0  -0.289  -2.9122   0.8707  -0.1365
 96B  C    C  CH2   0  -0.466  -3.0993  -0.4051   0.6792
 96B  C1   C  CH2   0  -0.460  -1.6533  -0.8126   0.9272
 96B  C2   C  CH1   0  -0.136  -0.9592  -0.4715  -0.4068
 96B  C4   C  CR6   0   0.145   0.5058  -0.1626  -0.2163
 96B  C9   C  CR16  0  -0.311   0.9497   1.1337   0.0300
 96B  C5   C  CR16  0  -0.316   1.4406  -1.1947  -0.2336
 96B  C6   C  CR16  0  -0.243   2.7872  -0.9429  -0.0032
 96B  C7   C  CR16  0  -0.275   3.2192   0.3528   0.2472
 96B  C8   C  CR16  0  -0.241   2.2943   1.3898   0.2628
 96B  H1   H  HNH1  0   0.352  -2.0069   0.4200  -1.9122
 96B  H3   H  HCH2  0   0.209  -2.7438   1.7175   0.5374
 96B  H4   H  HCH2  0   0.231  -3.7757   1.1207  -0.7542
 96B  H5   H  HCH2  0   0.235  -3.6676  -0.2497   1.5972
 96B  H6   H  HCH2  0   0.224  -3.6155  -1.1646   0.0859
 96B  H7   H  HCH2  0   0.230  -1.2283  -0.2138   1.7377
 96B  H8   H  HCH2  0   0.246  -1.5245  -1.8615   1.1949
 96B  H9   H  HCH1  0   0.235  -1.0320  -1.3469  -1.0625
 96B  H10  H  HCR6  0   0.245   0.2339   1.9458   0.0270
 96B  H11  H  HCR6  0   0.242   1.1138  -2.2087  -0.4370
 96B  H12  H  HCR6  0   0.251   3.4996  -1.7577  -0.0249
 96B  H13  H  HCR6  0   0.250   4.2684   0.5542   0.4214
 96B  H14  H  HCR6  0   0.249   2.6227   2.4041   0.4525

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
 96B  C   C3   single    1.526  0.020  1.526
 96B  C   C1   single    1.523  0.020  1.523
 96B  C3  N    single    1.464  0.020  1.464
 96B  C1  C2   single    1.542  0.020  1.542
 96B  N   C2   single    1.466  0.020  1.466
 96B  C2  C4   single    1.509  0.020  1.509
 96B  C4  C5   aromatic  1.393  0.020  1.393
 96B  C4  C9   aromatic  1.392  0.020  1.392
 96B  C5  C6   aromatic  1.389  0.020  1.389
 96B  C9  C8   aromatic  1.388  0.020  1.388
 96B  C6  C7   aromatic  1.389  0.020  1.389
 96B  C8  C7   aromatic  1.390  0.020  1.390
 96B  N   H1   single    0.890  0.020  1.040
 96B  C3  H3   single    0.970  0.020  1.090
 96B  C3  H4   single    0.970  0.020  1.090
 96B  C   H5   single    0.970  0.020  1.090
 96B  C   H6   single    0.970  0.020  1.090
 96B  C1  H7   single    0.970  0.020  1.090
 96B  C1  H8   single    0.970  0.020  1.090
 96B  C2  H9   single    0.970  0.020  1.090
 96B  C9  H10  single    0.930  0.020  1.080
 96B  C5  H11  single    0.930  0.020  1.080
 96B  C6  H12  single    0.930  0.020  1.080
 96B  C7  H13  single    0.930  0.020  1.080
 96B  C8  H14  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
 96B  H1   N   C2  109.56  3.000
 96B  H1   N   C3  110.04  3.000
 96B  C2   N   C3  108.95  3.000
 96B  H4   C3  H3  107.03  3.000
 96B  H4   C3  C   113.42  3.000
 96B  H3   C3  C   109.66  3.000
 96B  H4   C3  N   110.72  3.000
 96B  H3   C3  N   110.20  3.000
 96B  C    C3  N   105.83  3.000
 96B  H6   C   H5  108.04  3.000
 96B  H6   C   C1  110.54  3.000
 96B  H5   C   C1  113.32  3.000
 96B  H6   C   C3  110.40  3.000
 96B  H5   C   C3  113.25  3.000
 96B  C1   C   C3  101.21  3.000
 96B  H8   C1  H7  107.39  3.000
 96B  H8   C1  C2  111.84  3.000
 96B  H7   C1  C2  110.19  3.000
 96B  H8   C1  C   114.18  3.000
 96B  H7   C1  C   110.07  3.000
 96B  C2   C1  C   103.14  3.000
 96B  H9   C2  C4  107.66  3.000
 96B  H9   C2  C1  108.12  3.000
 96B  C4   C2  C1  111.90  3.000
 96B  H9   C2  N   110.08  3.000
 96B  C4   C2  N   113.71  3.000
 96B  C1   C2  N   105.26  3.000
 96B  C5   C4  C9  118.57  3.000
 96B  C9   C4  C2  121.49  3.000
 96B  C5   C4  C2  119.89  3.000
 96B  H10  C9  C8  120.16  3.000
 96B  H10  C9  C4  119.16  3.000
 96B  C8   C9  C4  120.68  3.000
 96B  H11  C5  C6  119.52  3.000
 96B  H11  C5  C4  119.53  3.000
 96B  C6   C5  C4  120.95  3.000
 96B  H12  C6  C7  120.08  3.000
 96B  H12  C6  C5  119.88  3.000
 96B  C7   C6  C5  120.04  3.000
 96B  H13  C7  C8  120.30  3.000
 96B  H13  C7  C6  120.28  3.000
 96B  C8   C7  C6  119.42  3.000
 96B  H14  C8  C7  119.94  3.000
 96B  H14  C8  C9  119.73  3.000
 96B  C7   C8  C9  120.33  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
 96B  CONST_01  C7   C6  C5  C4    0.00   0.0  0
 96B  CONST_02  C7   C8  C9  C4    0.00   0.0  0
 96B  CONST_03  C6   C5  C4  C9    0.00   0.0  0
 96B  CONST_04  C6   C7  C8  C9    0.00   0.0  0
 96B  CONST_05  C8   C9  C4  C5    0.00   0.0  0
 96B  CONST_06  C8   C7  C6  C5    0.00   0.0  0
 96B  CONST_07  C6   C5  C4  C2  180.00   0.0  0
 96B  CONST_08  C8   C9  C4  C2  180.00   0.0  0
 96B  CONST_09  H11  C5  C4  C2    0.00   0.0  0
 96B  CONST_10  H10  C9  C4  C2    0.00   0.0  0
 96B  CONST_11  H12  C6  C5  C4  180.00   0.0  0
 96B  CONST_12  H14  C8  C9  C4  180.00   0.0  0
 96B  CONST_13  H13  C7  C8  C9  180.00   0.0  0
 96B  Var_01    C1   C   C3  N    35.35  30.0  1
 96B  Var_02    C2   C1  C   C3  -38.57  30.0  1
 96B  Var_03    C2   N   C3  C   -18.14  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
 96B  chir_01  C2  C1  N  C4  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
 96B  plan-1  C2   0.020
 96B  plan-1  C4   0.020
 96B  plan-1  C9   0.020
 96B  plan-1  C5   0.020
 96B  plan-1  C6   0.020
 96B  plan-1  C7   0.020
 96B  plan-1  C8   0.020
 96B  plan-1  H10  0.020
 96B  plan-1  H11  0.020
 96B  plan-1  H12  0.020
 96B  plan-1  H13  0.020
 96B  plan-1  H14  0.020

