# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 08:52:16 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: benzyl (2S)-2-{[(2S)-2-formylpyrrolidin-1-yl]carbonyl}pyrrolidine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C[C@@H]1CCCN1C(=O)[C@@H]2CCCN2C(=O)OCc3ccccc3
#
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
 ZPR  ZPR  'benzyl (2S)-2-{[(2S)-2-formylpyrrolidin-1-yl]carbonyl}pyrrolidine-1-carboxylate'  peptide  46  24  .  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_ZPR
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
 ZPR  C20   C  CR16  0  -0.292   0.3561  -1.0988  -5.1391
 ZPR  C21   C  CR16  0  -0.243   0.4446  -0.5667  -6.4186
 ZPR  C22   C  CR16  0  -0.262  -0.3845   0.4825  -6.7931
 ZPR  C23   C  CR16  0  -0.242  -1.3027   0.9954  -5.8854
 ZPR  C24   C  CR16  0  -0.288  -1.3888   0.4601  -4.6079
 ZPR  C19   C  CR6   0   0.076  -0.5611  -0.5914  -4.2241
 ZPR  C18   C  CH2   0  -0.238  -0.6365  -1.1455  -2.8344
 ZPR  O17   O  O2    0  -0.475   0.2102  -0.3288  -2.0164
 ZPR  C15   C  C     0   0.773   0.3142  -0.6637  -0.7290
 ZPR  O16   O  O     0  -0.529  -0.2848  -1.5899  -0.2140
 ZPR  N14   N  NT    0  -0.511   1.1640   0.1367  -0.0671
 ZPR  C10   C  CH1   0  -0.164   1.3492  -0.0381   1.3557
 ZPR  C8    C  C     0   0.561   0.0472   0.1752   2.1118
 ZPR  O9    O  O     0  -0.490  -0.8354   0.9012   1.6718
 ZPR  C11   C  CH2   0  -0.478   2.3590   1.0653   1.7267
 ZPR  C12   C  CH2   0  -0.473   3.0755   1.3545   0.4115
 ZPR  C13   C  CH2   0  -0.266   1.9693   1.2141  -0.6245
 ZPR  C4    C  CH2   0  -0.486  -0.8034  -0.6523   5.5201
 ZPR  C5    C  CH2   0  -0.480   0.1257  -1.8101   5.1747
 ZPR  C1    C  C1    0   0.182  -1.5199   1.3491   4.2231
 ZPR  O2    O  O     0  -0.378  -2.6258   1.8076   4.3468
 ZPR  N7    N  NT    0  -0.501  -0.0541  -0.3919   3.3227
 ZPR  C6    C  CH2   0  -0.276   0.8982  -1.2982   3.9647
 ZPR  C3    C  CH1   0  -0.139  -1.2248  -0.1260   4.1423
 ZPR  H201  H  HCR6  0   0.255   1.0015  -1.9209  -4.8526
 ZPR  H211  H  HCR6  0   0.258   1.1589  -0.9733  -7.1226
 ZPR  H221  H  HCR6  0   0.259  -0.3189   0.8959  -7.7912
 ZPR  H231  H  HCR6  0   0.258  -1.9539   1.8105  -6.1737
 ZPR  H241  H  HCR6  0   0.255  -2.1098   0.8613  -3.9054
 ZPR  H181  H  HCH2  0   0.248  -0.2963  -2.1827  -2.8108
 ZPR  H182  H  HCH2  0   0.247  -1.6619  -1.1148  -2.4595
 ZPR  H101  H  HCH1  0   0.285   1.7683  -1.0254   1.5653
 ZPR  H111  H  HCH2  0   0.253   1.8380   1.9618   2.0690
 ZPR  H112  H  HCH2  0   0.268   3.0303   0.7474   2.5223
 ZPR  H121  H  HCH2  0   0.258   3.5399   2.3395   0.3943
 ZPR  H122  H  HCH2  0   0.246   3.8527   0.6099   0.2296
 ZPR  H131  H  HCH2  0   0.239   1.3866   2.1361  -0.7112
 ZPR  H132  H  HCH2  0   0.258   2.3507   0.9575  -1.6110
 ZPR  H42   H  HCH2  0   0.273  -1.6637  -0.9437   6.1197
 ZPR  H51   H  HCH2  0   0.264   0.7873  -2.0811   5.9959
 ZPR  H52   H  HCH2  0   0.251  -0.4558  -2.6931   4.9040
 ZPR  H11   H  H     0   0.192  -0.6162   1.9864   4.2581
 ZPR  H61   H  HCH2  0   0.253   1.8013  -0.7631   4.2682
 ZPR  H62   H  HCH2  0   0.265   1.1906  -2.1082   3.2969
 ZPR  H31   H  HCH1  0   0.280  -2.1062  -0.6585   3.7718
 ZPR  H41   H  HCH2  0   0.253  -0.2528   0.1175   6.0689

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
 ZPR  C1   O2    double    1.204  0.020  1.204
 ZPR  C1   C3    single    1.507  0.020  1.507
 ZPR  C1   H11   single    0.930  0.020  1.080
 ZPR  C3   C4    single    1.534  0.020  1.534
 ZPR  C3   N7    single    1.454  0.020  1.454
 ZPR  C3   H31   single    0.970  0.020  1.090
 ZPR  C4   C5    single    1.524  0.020  1.524
 ZPR  C4   H41   single    0.970  0.020  1.090
 ZPR  C4   H42   single    0.970  0.020  1.090
 ZPR  C5   C6    single    1.524  0.020  1.524
 ZPR  C5   H51   single    0.970  0.020  1.090
 ZPR  C5   H52   single    0.970  0.020  1.090
 ZPR  C6   N7    single    1.463  0.020  1.463
 ZPR  C6   H61   single    0.970  0.020  1.090
 ZPR  C6   H62   single    0.970  0.020  1.090
 ZPR  N7   C8    single    1.341  0.020  1.341
 ZPR  C8   O9    double    1.225  0.020  1.225
 ZPR  C8   C10   single    1.521  0.020  1.521
 ZPR  C10  C11   single    1.541  0.020  1.541
 ZPR  C10  N14   single    1.445  0.020  1.445
 ZPR  C10  H101  single    0.970  0.020  1.090
 ZPR  C11  C12   single    1.525  0.020  1.525
 ZPR  C11  H111  single    0.970  0.020  1.090
 ZPR  C11  H112  single    0.970  0.020  1.090
 ZPR  C12  C13   single    1.522  0.020  1.522
 ZPR  C12  H121  single    0.970  0.020  1.090
 ZPR  C12  H122  single    0.970  0.020  1.090
 ZPR  C13  N14   single    1.456  0.020  1.456
 ZPR  C13  H131  single    0.970  0.020  1.090
 ZPR  C13  H132  single    0.970  0.020  1.090
 ZPR  N14  C15   single    1.342  0.020  1.342
 ZPR  C15  O16   double    1.217  0.020  1.217
 ZPR  C15  O17   single    1.334  0.020  1.334
 ZPR  O17  C18   single    1.433  0.020  1.433
 ZPR  C18  C19   single    1.498  0.020  1.498
 ZPR  C18  H181  single    0.970  0.020  1.090
 ZPR  C18  H182  single    0.970  0.020  1.090
 ZPR  C19  C20   aromatic  1.391  0.020  1.391
 ZPR  C19  C24   aromatic  1.392  0.020  1.392
 ZPR  C20  C21   aromatic  1.389  0.020  1.389
 ZPR  C20  H201  single    0.930  0.020  1.080
 ZPR  C21  C22   aromatic  1.389  0.020  1.389
 ZPR  C21  H211  single    0.930  0.020  1.080
 ZPR  C22  C23   aromatic  1.389  0.020  1.389
 ZPR  C22  H221  single    0.930  0.020  1.080
 ZPR  C23  C24   aromatic  1.388  0.020  1.388
 ZPR  C23  H231  single    0.930  0.020  1.080
 ZPR  C24  H241  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
 ZPR  H201  C20  C19   119.70  3.000
 ZPR  H201  C20  C21   119.76  3.000
 ZPR  C19   C20  C21   120.54  3.000
 ZPR  H211  C21  C22   120.16  3.000
 ZPR  H211  C21  C20   119.84  3.000
 ZPR  C22   C21  C20   120.00  3.000
 ZPR  H221  C22  C23   120.10  3.000
 ZPR  H221  C22  C21   120.08  3.000
 ZPR  C23   C22  C21   119.82  3.000
 ZPR  H231  C23  C24   119.89  3.000
 ZPR  H231  C23  C22   120.11  3.000
 ZPR  C24   C23  C22   120.00  3.000
 ZPR  H241  C24  C19   119.77  3.000
 ZPR  H241  C24  C23   119.69  3.000
 ZPR  C19   C24  C23   120.55  3.000
 ZPR  C18   C19  C24   120.35  3.000
 ZPR  C24   C19  C20   119.09  3.000
 ZPR  C18   C19  C20   120.55  3.000
 ZPR  H182  C18  H181  108.17  3.000
 ZPR  H182  C18  O17   110.05  3.000
 ZPR  H181  C18  O17   110.19  3.000
 ZPR  H182  C18  C19   110.81  3.000
 ZPR  H181  C18  C19   110.84  3.000
 ZPR  O17   C18  C19   106.79  3.000
 ZPR  C15   O17  C18   116.98  3.000
 ZPR  N14   C15  O16   123.83  3.000
 ZPR  O16   C15  O17   124.11  3.000
 ZPR  N14   C15  O17   112.05  3.000
 ZPR  C13   N14  C10   113.29  3.000
 ZPR  C13   N14  C15   127.07  3.000
 ZPR  C10   N14  C15   119.63  3.000
 ZPR  H101  C10  C11   110.45  3.000
 ZPR  H101  C10  C8    111.08  3.000
 ZPR  C11   C10  C8    109.94  3.000
 ZPR  H101  C10  N14   110.31  3.000
 ZPR  C11   C10  N14   103.55  3.000
 ZPR  C8    C10  N14   111.27  3.000
 ZPR  N7    C8   O9    121.38  3.000
 ZPR  O9    C8   C10   121.44  3.000
 ZPR  N7    C8   C10   117.02  3.000
 ZPR  H112  C11  H111  107.76  3.000
 ZPR  H112  C11  C12   113.32  3.000
 ZPR  H111  C11  C12   109.80  3.000
 ZPR  H112  C11  C10   111.78  3.000
 ZPR  H111  C11  C10   110.53  3.000
 ZPR  C12   C11  C10   103.65  3.000
 ZPR  H122  C12  H121  108.09  3.000
 ZPR  H122  C12  C13   109.95  3.000
 ZPR  H121  C12  C13   112.50  3.000
 ZPR  H122  C12  C11   110.41  3.000
 ZPR  H121  C12  C11   112.66  3.000
 ZPR  C13   C12  C11   103.18  3.000
 ZPR  H132  C13  H131  108.27  3.000
 ZPR  H132  C13  C12   112.58  3.000
 ZPR  H131  C13  C12   111.30  3.000
 ZPR  H132  C13  N14   111.49  3.000
 ZPR  H131  C13  N14   111.06  3.000
 ZPR  C12   C13  N14   102.10  3.000
 ZPR  H42   C4   H41   108.05  3.000
 ZPR  H42   C4   C3    111.69  3.000
 ZPR  H41   C4   C3    110.33  3.000
 ZPR  H42   C4   C5    113.79  3.000
 ZPR  H41   C4   C5    109.96  3.000
 ZPR  C3    C4   C5    102.97  3.000
 ZPR  H52   C5   H51   108.02  3.000
 ZPR  H52   C5   C6    110.17  3.000
 ZPR  H51   C5   C6    111.99  3.000
 ZPR  H52   C5   C4    110.25  3.000
 ZPR  H51   C5   C4    112.87  3.000
 ZPR  C6    C5   C4    103.52  3.000
 ZPR  H11   C1   C3    113.93  3.000
 ZPR  H11   C1   O2    121.87  3.000
 ZPR  C3    C1   O2    123.95  3.000
 ZPR  C3    N7   C6    112.96  3.000
 ZPR  C6    N7   C8    127.53  3.000
 ZPR  C3    N7   C8    119.51  3.000
 ZPR  H62   C6   H61   108.21  3.000
 ZPR  H62   C6   N7    111.47  3.000
 ZPR  H61   C6   N7    110.88  3.000
 ZPR  H62   C6   C5    111.89  3.000
 ZPR  H61   C6   C5    111.28  3.000
 ZPR  N7    C6   C5    103.10  3.000
 ZPR  H31   C3   N7    111.64  3.000
 ZPR  H31   C3   C1    109.68  3.000
 ZPR  N7    C3   C1    111.54  3.000
 ZPR  H31   C3   C4    111.00  3.000
 ZPR  N7    C3   C4    102.85  3.000
 ZPR  C1    C3   C4    109.97  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
 ZPR  CONST_01  C23   C24  C19  C20    0.00   0.0  0
 ZPR  CONST_02  C23   C22  C21  C20    0.00   0.0  0
 ZPR  CONST_03  C24   C19  C20  C21    0.00   0.0  0
 ZPR  CONST_04  C24   C23  C22  C21    0.00   0.0  0
 ZPR  CONST_05  C19   C20  C21  C22    0.00   0.0  0
 ZPR  CONST_06  C19   C24  C23  C22    0.00   0.0  0
 ZPR  CONST_07  C18   C19  C20  C21  180.00   0.0  0
 ZPR  CONST_08  C18   C19  C24  C23  180.00   0.0  0
 ZPR  CONST_09  C3    N7   C8   C10  180.00   0.0  0
 ZPR  CONST_10  C6    N7   C8   C10    0.00   0.0  0
 ZPR  CONST_11  H241  C24  C19  C20  180.00   0.0  0
 ZPR  CONST_12  H221  C22  C21  C20  180.00   0.0  0
 ZPR  CONST_13  H231  C23  C22  C21  180.00   0.0  0
 ZPR  CONST_14  H201  C20  C21  C22  180.00   0.0  0
 ZPR  CONST_15  H211  C21  C22  C23  180.00   0.0  0
 ZPR  CONST_16  C3    N7   C8   O9     0.00   0.0  0
 ZPR  CONST_17  C6    N7   C8   O9   180.00   0.0  0
 ZPR  Var_01    C11   C12  C13  N14  -35.20  30.0  1
 ZPR  Var_02    C13   C12  C11  C10   36.57  30.0  1
 ZPR  Var_03    C12   C13  N14  C10   21.62  30.0  1
 ZPR  Var_04    N7    C6   C5   C4   -29.91  30.0  1
 ZPR  Var_05    C3    N7   C6   C5    10.16  30.0  1
 ZPR  Var_06    C3    C4   C5   C6    38.49  30.0  1
 ZPR  Var_07    O17   C18  C19  C20   93.26  30.0  2
 ZPR  Var_08    C10   N14  C15  O17  176.91  30.0  2
 ZPR  Var_09    N14   C15  O17  C18  177.89  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
 ZPR  chir_01  C10  C8  C11  N14  positiv
 ZPR  chir_02  C3   N7  C4   C1   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
 ZPR  plan-1  C10   0.020
 ZPR  plan-1  C8    0.020
 ZPR  plan-1  O9    0.020
 ZPR  plan-1  N7    0.020
 ZPR  plan-1  C6    0.020
 ZPR  plan-1  C3    0.020
 ZPR  plan-2  C20   0.020
 ZPR  plan-2  C21   0.020
 ZPR  plan-2  C22   0.020
 ZPR  plan-2  C23   0.020
 ZPR  plan-2  C24   0.020
 ZPR  plan-2  C19   0.020
 ZPR  plan-2  C18   0.020
 ZPR  plan-2  H201  0.020
 ZPR  plan-2  H211  0.020
 ZPR  plan-2  H221  0.020
 ZPR  plan-2  H231  0.020
 ZPR  plan-2  H241  0.020
 ZPR  plan-3  C1    0.020
 ZPR  plan-3  O2    0.020
 ZPR  plan-3  C3    0.020
 ZPR  plan-3  H11   0.020
 ZPR  plan-4  O17   0.020
 ZPR  plan-4  C15   0.020
 ZPR  plan-4  O16   0.020
 ZPR  plan-4  N14   0.020

