# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:43:12 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (2S)-N-benzyl-2-({(2S)-2-[(1R)-1,2-dihydroxyethyl]pyrrolidin-1-yl}carbonyl)pyrrolidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)[C@@H]1CCCN1C(=O)[C@@H]2CCCN2C(=O)NCc3ccccc3
#
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
 2P8  2P8  (2S)-N-benzyl-2-({(2S)-2-[(1R)-1,2-dihydroxyethyl]pyrrolidin-1-yl}carbonyl)pyrrolidine-1-carboxamide  ligand  53  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2P8
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
 2P8  C17   C  C     0   0.742   1.6127  -0.0841   1.9582
 2P8  O18   O  O     0  -0.546   1.4399  -1.2870   1.7798
 2P8  N19   N  NH1   0  -0.693   2.8526   0.4751   1.9758
 2P8  C20   C  CH2   0  -0.328   4.0203  -0.2812   1.6179
 2P8  C21   C  CR6   0   0.080   4.2681  -0.4303   0.1313
 2P8  C22   C  CR16  0  -0.289   5.4385  -1.0604  -0.2900
 2P8  C23   C  CR16  0  -0.245   5.7110  -1.2285  -1.6390
 2P8  C24   C  CR16  0  -0.271   4.8126  -0.7661  -2.5942
 2P8  C25   C  CR16  0  -0.243   3.6463  -0.1382  -2.1835
 2P8  C26   C  CR16  0  -0.311   3.3747   0.0286  -0.8295
 2P8  N16   N  NT    0  -0.494   0.5752   0.7601   2.1922
 2P8  C12   C  CH1   0  -0.226  -0.7736   0.2857   2.0264
 2P8  C10   C  C     0   0.572  -1.0744   0.0494   0.5432
 2P8  O11   O  O     0  -0.486  -0.3313   0.4975  -0.3199
 2P8  C13   C  CH2   0  -0.461  -1.6053   1.4506   2.5754
 2P8  C14   C  CH2   0  -0.487  -0.7930   2.6780   2.1705
 2P8  C15   C  CH2   0  -0.286   0.6612   2.2124   2.2677
 2P8  C1    C  CH1   0  -0.009  -2.9522   0.4112  -1.9433
 2P8  O2    O  OH1   0  -0.664  -3.3855   0.0521  -3.2368
 2P8  C3    C  CH2   0  -0.169  -3.9456   1.3074  -1.2204
 2P8  O4    O  OH1   0  -0.669  -4.1247   2.4783  -1.9822
 2P8  C5    C  CH1   0  -0.067  -2.5931  -0.8595  -1.1516
 2P8  C6    C  CH2   0  -0.518  -3.7484  -1.8665  -1.0336
 2P8  C7    C  CH2   0  -0.451  -3.5627  -2.4938   0.3424
 2P8  C8    C  CH2   0  -0.291  -3.0716  -1.3222   1.1762
 2P8  N9    N  NT    0  -0.491  -2.2080  -0.6073   0.2418
 2P8  HN19  H  HNH1  0   0.408   2.9532   1.4752   2.0166
 2P8  H20   H  HCH2  0   0.267   4.8823   0.2066   2.0759
 2P8  H20A  H  HCH2  0   0.260   3.9567  -1.2714   2.0714
 2P8  H22   H  HCR6  0   0.246   6.1466  -1.4214   0.4480
 2P8  H23   H  HCR6  0   0.253   6.6259  -1.7185  -1.9467
 2P8  H24   H  HCR6  0   0.253   5.0237  -0.8939  -3.6480
 2P8  H25   H  HCR6  0   0.252   2.9387   0.2247  -2.9185
 2P8  H26   H  HCR6  0   0.255   2.4569   0.5206  -0.5337
 2P8  H12   H  HCH1  0   0.286  -0.9338  -0.6220   2.6087
 2P8  H13   H  HCH2  0   0.260  -2.6263   1.4666   2.1938
 2P8  H13A  H  HCH2  0   0.261  -1.6631   1.3653   3.6617
 2P8  H14   H  HCH2  0   0.245  -1.0281   2.9731   1.1472
 2P8  H14A  H  HCH2  0   0.260  -0.9874   3.5368   2.8109
 2P8  H15   H  HCH2  0   0.247   1.1176   2.5213   3.2121
 2P8  H15A  H  HCH2  0   0.242   1.2623   2.6281   1.4542
 2P8  H1    H  HCH1  0   0.240  -2.0362   0.9852  -2.0934
 2P8  HO2   H  HOH1  0   0.449  -4.2510  -0.3665  -3.1749
 2P8  H3    H  HCH2  0   0.195  -4.8986   0.7804  -1.0697
 2P8  H3A   H  HCH2  0   0.201  -3.5520   1.5340  -0.2220
 2P8  HO4   H  HOH1  0   0.455  -4.7439   3.0445  -1.5134
 2P8  H5    H  HCH1  0   0.263  -1.7506  -1.3342  -1.6651
 2P8  H6    H  HCH2  0   0.239  -4.7196  -1.3667  -1.0706
 2P8  H6A   H  HCH2  0   0.266  -3.7265  -2.5982  -1.8393
 2P8  H7    H  HCH2  0   0.254  -4.4775  -2.9322   0.7389
 2P8  H7A   H  HCH2  0   0.242  -2.7977  -3.2723   0.3115
 2P8  H8    H  HCH2  0   0.242  -3.9090  -0.6948   1.4986
 2P8  H8A   H  HCH2  0   0.264  -2.5341  -1.6391   2.0667

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
 2P8  C1   O2    single    1.411  0.020  1.411
 2P8  C1   C3    single    1.521  0.020  1.521
 2P8  C1   C5    single    1.540  0.020  1.540
 2P8  C3   O4    single    1.408  0.020  1.408
 2P8  C5   C6    single    1.537  0.020  1.537
 2P8  C5   N9    single    1.467  0.020  1.467
 2P8  C6   C7    single    1.524  0.020  1.524
 2P8  C7   C8    single    1.520  0.020  1.520
 2P8  C8   N9    single    1.459  0.020  1.459
 2P8  N9   C10   single    1.344  0.020  1.344
 2P8  C10  O11   double    1.224  0.020  1.224
 2P8  C10  C12   single    1.532  0.020  1.532
 2P8  C12  C13   single    1.533  0.020  1.533
 2P8  C12  N16   single    1.439  0.020  1.439
 2P8  C13  C14   single    1.526  0.020  1.526
 2P8  C14  C15   single    1.530  0.020  1.530
 2P8  C15  N16   single    1.457  0.020  1.457
 2P8  N16  C17   single    1.358  0.020  1.358
 2P8  C17  O18   double    1.228  0.020  1.228
 2P8  C17  N19   single    1.360  0.020  1.360
 2P8  N19  C20   single    1.437  0.020  1.437
 2P8  C20  C21   single    1.515  0.020  1.515
 2P8  C21  C22   aromatic  1.394  0.020  1.394
 2P8  C21  C26   aromatic  1.390  0.020  1.390
 2P8  C22  C23   aromatic  1.386  0.020  1.386
 2P8  C23  C24   aromatic  1.390  0.020  1.390
 2P8  C24  C25   aromatic  1.387  0.020  1.387
 2P8  C25  C26   aromatic  1.391  0.020  1.391
 2P8  C1   H1    single    0.970  0.020  1.090
 2P8  O2   HO2   single    0.850  0.020  0.980
 2P8  C3   H3    single    0.970  0.020  1.090
 2P8  C3   H3A   single    0.970  0.020  1.090
 2P8  O4   HO4   single    0.850  0.020  0.980
 2P8  C5   H5    single    0.970  0.020  1.090
 2P8  C6   H6    single    0.970  0.020  1.090
 2P8  C6   H6A   single    0.970  0.020  1.090
 2P8  C7   H7    single    0.970  0.020  1.090
 2P8  C7   H7A   single    0.970  0.020  1.090
 2P8  C8   H8    single    0.970  0.020  1.090
 2P8  C8   H8A   single    0.970  0.020  1.090
 2P8  C12  H12   single    0.970  0.020  1.090
 2P8  C13  H13   single    0.970  0.020  1.090
 2P8  C13  H13A  single    0.970  0.020  1.090
 2P8  C14  H14   single    0.970  0.020  1.090
 2P8  C14  H14A  single    0.970  0.020  1.090
 2P8  C15  H15   single    0.970  0.020  1.090
 2P8  C15  H15A  single    0.970  0.020  1.090
 2P8  N19  HN19  single    0.860  0.020  1.020
 2P8  C20  H20   single    0.970  0.020  1.090
 2P8  C20  H20A  single    0.970  0.020  1.090
 2P8  C22  H22   single    0.930  0.020  1.080
 2P8  C23  H23   single    0.930  0.020  1.080
 2P8  C24  H24   single    0.930  0.020  1.080
 2P8  C25  H25   single    0.930  0.020  1.080
 2P8  C26  H26   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
 2P8  N16   C17  N19  116.02  3.000
 2P8  N19   C17  O18  122.19  3.000
 2P8  N16   C17  O18  121.76  3.000
 2P8  HN19  N19  C20  116.88  3.000
 2P8  HN19  N19  C17  120.03  3.000
 2P8  C20   N19  C17  121.42  3.000
 2P8  H20A  C20  H20  106.10  3.000
 2P8  H20A  C20  C21  109.16  3.000
 2P8  H20   C20  C21  109.07  3.000
 2P8  H20A  C20  N19  109.08  3.000
 2P8  H20   C20  N19  107.59  3.000
 2P8  C21   C20  N19  115.43  3.000
 2P8  C26   C21  C22  118.68  3.000
 2P8  C26   C21  C20  122.74  3.000
 2P8  C22   C21  C20  118.58  3.000
 2P8  H22   C22  C23  119.57  3.000
 2P8  H22   C22  C21  119.52  3.000
 2P8  C23   C22  C21  120.91  3.000
 2P8  H23   C23  C24  120.09  3.000
 2P8  H23   C23  C22  119.84  3.000
 2P8  C24   C23  C22  120.07  3.000
 2P8  H24   C24  C25  120.39  3.000
 2P8  H24   C24  C23  120.23  3.000
 2P8  C25   C24  C23  119.38  3.000
 2P8  H25   C25  C26  119.54  3.000
 2P8  H25   C25  C24  120.01  3.000
 2P8  C26   C25  C24  120.45  3.000
 2P8  H26   C26  C25  119.07  3.000
 2P8  H26   C26  C21  120.41  3.000
 2P8  C25   C26  C21  120.52  3.000
 2P8  C15   N16  C12  112.95  3.000
 2P8  C15   N16  C17  125.71  3.000
 2P8  C12   N16  C17  119.42  3.000
 2P8  H12   C12  C13  111.21  3.000
 2P8  H12   C12  C10  111.10  3.000
 2P8  C13   C12  C10  110.94  3.000
 2P8  H12   C12  N16  110.52  3.000
 2P8  C13   C12  N16  102.51  3.000
 2P8  C10   C12  N16  110.27  3.000
 2P8  N9    C10  O11  122.19  3.000
 2P8  O11   C10  C12  120.48  3.000
 2P8  N9    C10  C12  117.26  3.000
 2P8  H13A  C13  H13  107.46  3.000
 2P8  H13A  C13  C14  110.80  3.000
 2P8  H13   C13  C14  113.19  3.000
 2P8  H13A  C13  C12  109.02  3.000
 2P8  H13   C13  C12  113.20  3.000
 2P8  C14   C13  C12  103.14  3.000
 2P8  H14A  C14  H14  107.45  3.000
 2P8  H14A  C14  C15  111.86  3.000
 2P8  H14   C14  C15  110.29  3.000
 2P8  H14A  C14  C13  112.54  3.000
 2P8  H14   C14  C13  110.59  3.000
 2P8  C15   C14  C13  104.13  3.000
 2P8  H15A  C15  H15  107.80  3.000
 2P8  H15A  C15  C14  111.07  3.000
 2P8  H15   C15  C14  111.44  3.000
 2P8  H15A  C15  N16  111.89  3.000
 2P8  H15   C15  N16  110.55  3.000
 2P8  C14   C15  N16  104.12  3.000
 2P8  H1    C1   C5   108.00  3.000
 2P8  H1    C1   C3   107.68  3.000
 2P8  C5    C1   C3   113.23  3.000
 2P8  H1    C1   O2   105.40  3.000
 2P8  C5    C1   O2   109.46  3.000
 2P8  C3    C1   O2   112.66  3.000
 2P8  HO2   O2   C1   109.12  3.000
 2P8  H3A   C3   H3   106.57  3.000
 2P8  H3A   C3   O4   111.49  3.000
 2P8  H3    C3   O4   111.25  3.000
 2P8  H3A   C3   C1   108.66  3.000
 2P8  H3    C3   C1   110.42  3.000
 2P8  O4    C3   C1   108.42  3.000
 2P8  HO4   O4   C3   107.93  3.000
 2P8  H5    C5   N9   108.54  3.000
 2P8  H5    C5   C6   109.29  3.000
 2P8  N9    C5   C6   103.71  3.000
 2P8  H5    C5   C1   107.22  3.000
 2P8  N9    C5   C1   114.06  3.000
 2P8  C6    C5   C1   113.88  3.000
 2P8  H6A   C6   H6   107.47  3.000
 2P8  H6A   C6   C7   112.90  3.000
 2P8  H6    C6   C7   109.09  3.000
 2P8  H6A   C6   C5   111.62  3.000
 2P8  H6    C6   C5   111.46  3.000
 2P8  C7    C6   C5   104.33  3.000
 2P8  H7A   C7   H7   108.17  3.000
 2P8  H7A   C7   C8   109.80  3.000
 2P8  H7    C7   C8   112.46  3.000
 2P8  H7A   C7   C6   110.69  3.000
 2P8  H7    C7   C6   113.09  3.000
 2P8  C8    C7   C6   102.56  3.000
 2P8  H8A   C8   H8   107.69  3.000
 2P8  H8A   C8   N9   112.00  3.000
 2P8  H8    C8   N9   111.12  3.000
 2P8  H8A   C8   C7   112.61  3.000
 2P8  H8    C8   C7   110.87  3.000
 2P8  N9    C8   C7   102.57  3.000
 2P8  C8    N9   C5   111.62  3.000
 2P8  C8    N9   C10  126.49  3.000
 2P8  C5    N9   C10  121.21  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
 2P8  CONST_01  C24   C23  C22  C21    0.00   0.0  0
 2P8  CONST_02  C24   C25  C26  C21    0.00   0.0  0
 2P8  CONST_03  C25   C26  C21  C22    0.00   0.0  0
 2P8  CONST_04  C25   C24  C23  C22    0.00   0.0  0
 2P8  CONST_05  C26   C21  C22  C23    0.00   0.0  0
 2P8  CONST_06  C26   C25  C24  C23    0.00   0.0  0
 2P8  CONST_07  C23   C22  C21  C20  180.00   0.0  0
 2P8  CONST_08  C25   C26  C21  C20  180.00   0.0  0
 2P8  CONST_09  C5    N9   C10  C12  180.00   0.0  0
 2P8  CONST_10  C8    N9   C10  C12    0.00   0.0  0
 2P8  CONST_11  H23   C23  C22  C21  180.00   0.0  0
 2P8  CONST_12  H25   C25  C26  C21  180.00   0.0  0
 2P8  CONST_13  H26   C26  C21  C22  180.00   0.0  0
 2P8  CONST_14  H24   C24  C23  C22  180.00   0.0  0
 2P8  CONST_15  H22   C22  C23  C24  180.00   0.0  0
 2P8  CONST_16  C12   N16  C17  O18    0.00   0.0  0
 2P8  CONST_17  C15   N16  C17  O18  180.00   0.0  0
 2P8  CONST_18  C5    N9   C10  O11    0.00   0.0  0
 2P8  CONST_19  C8    N9   C10  O11  180.00   0.0  0
 2P8  CONST_20  C12   N16  C17  N19  180.00   0.0  0
 2P8  CONST_21  C15   N16  C17  N19    0.00   0.0  0
 2P8  CONST_22  N16   C17  N19  C20  180.00   0.0  0
 2P8  CONST_23  HN19  N19  C17  N16    0.00   0.0  0
 2P8  CONST_24  C20   N19  C17  O18    0.00   0.0  0
 2P8  Var_01    C13   C14  C15  N16   20.85  30.0  1
 2P8  Var_02    C15   C14  C13  C12  -34.35  30.0  1
 2P8  Var_03    C14   C15  N16  C12    1.42  30.0  1
 2P8  Var_04    C8    C7   C6   C5    36.55  30.0  1
 2P8  Var_05    C7    C8   N9   C5    25.56  30.0  1
 2P8  Var_06    N9    C8   C7   C6   -37.57  30.0  1
 2P8  Var_07    C22   C21  C20  N19  175.00  30.0  2
 2P8  Var_08    C21   C20  N19  C17   80.45  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
 2P8  chir_01  C12  C10  C13  N16  positiv
 2P8  chir_02  C1   O2   C3   C5   negativ
 2P8  chir_03  C5   N9   C6   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
 2P8  plan-1  C17   0.020
 2P8  plan-1  O18   0.020
 2P8  plan-1  N19   0.020
 2P8  plan-1  C20   0.020
 2P8  plan-1  N16   0.020
 2P8  plan-1  C12   0.020
 2P8  plan-1  C15   0.020
 2P8  plan-1  HN19  0.020
 2P8  plan-2  C20   0.020
 2P8  plan-2  C21   0.020
 2P8  plan-2  C22   0.020
 2P8  plan-2  C23   0.020
 2P8  plan-2  C24   0.020
 2P8  plan-2  C25   0.020
 2P8  plan-2  C26   0.020
 2P8  plan-2  H22   0.020
 2P8  plan-2  H23   0.020
 2P8  plan-2  H24   0.020
 2P8  plan-2  H25   0.020
 2P8  plan-2  H26   0.020
 2P8  plan-3  C12   0.020
 2P8  plan-3  C10   0.020
 2P8  plan-3  O11   0.020
 2P8  plan-3  C5    0.020
 2P8  plan-3  C8    0.020
 2P8  plan-3  N9    0.020

