# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:04:28 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: (3R)-N-benzylpyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@H](CN1)NCc2ccccc2
#
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
 WP4  WP4  (3R)-N-benzylpyrrolidin-3-amine  ligand  29  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WP4
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
 WP4  C10  C  CR16  0  -0.241  -28.0741   -8.2171  -18.8023
 WP4  C13  C  CR16  0  -0.306  -28.5956   -8.4313  -21.5156
 WP4  C01  C  CH2   0  -0.388  -30.5440   -9.9805  -21.1093
 WP4  C03  C  CR15  0  -0.073  -32.2415   -8.2413  -20.8571
 WP4  C04  C  CH2   0  -0.487  -32.9717   -8.8304  -19.6458
 WP4  C05  C  CH2   0  -0.305  -34.1668   -7.8731  -19.4159
 WP4  C07  C  CH2   0  -0.324  -33.3642   -7.4694  -21.5540
 WP4  C08  C  CR6   0   0.111  -29.3922   -9.1348  -20.6127
 WP4  C09  C  CR16  0  -0.302  -29.1193   -9.0153  -19.2538
 WP4  C11  C  CR16  0  -0.272  -27.2882   -7.5226  -19.7108
 WP4  C12  C  CR16  0  -0.242  -27.5521   -7.6327  -21.0717
 WP4  N02  N  NH1   0  -0.591  -31.6434   -9.2455  -21.7138
 WP4  N06  N  NR15  0  -0.588  -34.1426   -6.8667  -20.4838
 WP4  H1   H  HCR6  0   0.253  -27.8750   -8.1385  -17.7411
 WP4  H2   H  HCR6  0   0.247  -28.7888   -8.5130  -22.5801
 WP4  H3   H  HCH2  0   0.241  -30.9360  -10.5747  -20.2803
 WP4  H4   H  HCH2  0   0.251  -30.1757  -10.6936  -21.8514
 WP4  H5   H  HCR5  0   0.204  -31.5030   -7.5068  -20.4982
 WP4  H7   H  HCH2  0   0.237  -32.3305   -8.9113  -18.7676
 WP4  H8   H  HCH2  0   0.231  -34.1313   -7.3829  -18.4428
 WP4  H9   H  HCH2  0   0.221  -35.1054   -8.4315  -19.4544
 WP4  H10  H  HCH2  0   0.239  -33.0034   -6.7105  -22.2504
 WP4  H11  H  HCH2  0   0.214  -33.9867   -8.1734  -22.1178
 WP4  H12  H  HCR6  0   0.246  -29.7258   -9.5588  -18.5380
 WP4  H13  H  HCR6  0   0.253  -26.4719   -6.9023  -19.3633
 WP4  H14  H  HCR6  0   0.253  -26.9400   -7.0968  -21.7861
 WP4  H15  H  HNH1  0   0.345  -31.3169   -8.8016  -22.5646
 WP4  H17  H  HNR5  0   0.344  -33.6379   -6.0553  -20.1493
 WP4  H6   H  HCH2  0   0.229  -33.3231   -9.8356  -19.8902

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
 WP4  C13  C12  aromatic  1.387  0.020  1.387
 WP4  C13  C08  aromatic  1.394  0.020  1.394
 WP4  N02  C01  single    1.454  0.020  1.454
 WP4  N02  C03  single    1.449  0.020  1.449
 WP4  C07  C03  single    1.530  0.020  1.530
 WP4  C07  N06  single    1.454  0.020  1.454
 WP4  C12  C11  aromatic  1.391  0.020  1.391
 WP4  C01  C08  single    1.513  0.020  1.513
 WP4  C03  C04  single    1.532  0.020  1.532
 WP4  N06  C05  single    1.468  0.020  1.468
 WP4  C08  C09  aromatic  1.391  0.020  1.391
 WP4  C11  C10  aromatic  1.388  0.020  1.388
 WP4  C04  C05  single    1.548  0.020  1.548
 WP4  C09  C10  aromatic  1.390  0.020  1.390
 WP4  C10  H1   single    0.930  0.020  1.080
 WP4  C13  H2   single    0.930  0.020  1.080
 WP4  C01  H3   single    0.970  0.020  1.090
 WP4  C01  H4   single    0.970  0.020  1.090
 WP4  C03  H5   single    0.970  0.020  1.090
 WP4  C04  H6   single    0.970  0.020  1.090
 WP4  C04  H7   single    0.970  0.020  1.090
 WP4  C05  H8   single    0.970  0.020  1.090
 WP4  C05  H9   single    0.970  0.020  1.090
 WP4  C07  H10  single    0.970  0.020  1.090
 WP4  C07  H11  single    0.970  0.020  1.090
 WP4  C09  H12  single    0.930  0.020  1.080
 WP4  C11  H13  single    0.930  0.020  1.080
 WP4  C12  H14  single    0.930  0.020  1.080
 WP4  N02  H15  single    0.890  0.020  1.040
 WP4  N06  H17  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
 WP4  H1   C10  C11  120.08  3.000
 WP4  H1   C10  C09  119.88  3.000
 WP4  C11  C10  C09  120.03  3.000
 WP4  H2   C13  C12  119.42  3.000
 WP4  H2   C13  C08  119.71  3.000
 WP4  C12  C13  C08  120.86  3.000
 WP4  H4   C01  H3   106.33  3.000
 WP4  H4   C01  N02  107.59  3.000
 WP4  H3   C01  N02  108.60  3.000
 WP4  H4   C01  C08  109.34  3.000
 WP4  H3   C01  C08  109.16  3.000
 WP4  N02  C01  C08  115.44  3.000
 WP4  H5   C03  N02  112.20  3.000
 WP4  H5   C03  C07  107.69  3.000
 WP4  N02  C03  C07  112.53  3.000
 WP4  H5   C03  C04  108.56  3.000
 WP4  C07  C03  C04  101.79  3.000
 WP4  N02  C03  C04  113.43  3.000
 WP4  H7   C04  H6   107.53  3.000
 WP4  H7   C04  C05  112.34  3.000
 WP4  H6   C04  C05  110.72  3.000
 WP4  H7   C04  C03  112.65  3.000
 WP4  H6   C04  C03  109.28  3.000
 WP4  C05  C04  C03  104.33  3.000
 WP4  H9   C05  H8   106.81  3.000
 WP4  H9   C05  N06  109.81  3.000
 WP4  H8   C05  N06  109.92  3.000
 WP4  H9   C05  C04  109.98  3.000
 WP4  H8   C05  C04  112.67  3.000
 WP4  N06  C05  C04  107.65  3.000
 WP4  H11  C07  H10  107.83  3.000
 WP4  H11  C07  N06  109.92  3.000
 WP4  H10  C07  N06  111.00  3.000
 WP4  H11  C07  C03  109.09  3.000
 WP4  H10  C07  C03  113.50  3.000
 WP4  N06  C07  C03  105.47  3.000
 WP4  C09  C08  C01  121.20  3.000
 WP4  C09  C08  C13  118.50  3.000
 WP4  C01  C08  C13  120.29  3.000
 WP4  H12  C09  C08  119.47  3.000
 WP4  H12  C09  C10  119.60  3.000
 WP4  C08  C09  C10  120.92  3.000
 WP4  H13  C11  C12  120.17  3.000
 WP4  H13  C11  C10  120.25  3.000
 WP4  C12  C11  C10  119.58  3.000
 WP4  H14  C12  C11  119.95  3.000
 WP4  H14  C12  C13  119.94  3.000
 WP4  C11  C12  C13  120.10  3.000
 WP4  H15  N02  C03  109.01  3.000
 WP4  H15  N02  C01  109.07  3.000
 WP4  C03  N02  C01  114.62  3.000
 WP4  H17  N06  C07  107.97  3.000
 WP4  H17  N06  C05  108.51  3.000
 WP4  C07  N06  C05  105.08  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
 WP4  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 WP4  CONST_02  C13  C08  C09  C10    0.00   0.0  0
 WP4  CONST_03  C11  C12  C13  C08    0.00   0.0  0
 WP4  CONST_04  C11  C10  C09  C08    0.00   0.0  0
 WP4  CONST_05  C12  C13  C08  C09    0.00   0.0  0
 WP4  CONST_06  C12  C11  C10  C09    0.00   0.0  0
 WP4  CONST_07  C01  C08  C09  C10  180.00   0.0  0
 WP4  CONST_08  C12  C13  C08  C01  180.00   0.0  0
 WP4  CONST_09  H14  C12  C11  C10  180.00   0.0  0
 WP4  CONST_10  H13  C11  C12  C13  180.00   0.0  0
 WP4  CONST_11  H12  C09  C08  C13  180.00   0.0  0
 WP4  CONST_12  H1   C10  C09  C08  180.00   0.0  0
 WP4  CONST_13  H2   C13  C08  C09  180.00   0.0  0
 WP4  Var_01    C05  N06  C07  C03  -37.88  30.0  1
 WP4  Var_02    N06  C05  C04  C03    3.19  30.0  1
 WP4  Var_03    C07  N06  C05  C04   21.25  30.0  1
 WP4  Var_04    N02  C01  C08  C13  -66.66  30.0  2
 WP4  Var_05    C08  C01  N02  C03  -57.08  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
 WP4  chir_01  C03  N02  C07  C04  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
 WP4  plan-1  C10  0.020
 WP4  plan-1  C13  0.020
 WP4  plan-1  C01  0.020
 WP4  plan-1  C08  0.020
 WP4  plan-1  C09  0.020
 WP4  plan-1  C11  0.020
 WP4  plan-1  C12  0.020
 WP4  plan-1  H1   0.020
 WP4  plan-1  H2   0.020
 WP4  plan-1  H12  0.020
 WP4  plan-1  H13  0.020
 WP4  plan-1  H14  0.020

