# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 20:11:07 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (5R)-N-benzyl-5-({(2S)-2-[(1R)-1,2-dihydroxyethyl]pyrrolidin-1-yl}carbonyl)cyclopent-1-ene-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)[C@@H]1CCCN1C(=O)[C@@H]2CCC=C2C(=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
 2P4  2P4  (5R)-N-benzyl-5-({(2S)-2-[(1R)-1,2-dihydroxyethyl]pyrrolidin-1-yl}carbonyl)cyclopent-1-ene-1-carboxamide  ligand  52  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 OK
;

data_comp_2P4
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
 2P4  C10   C  C     0   0.572  -1.1261   0.3341  -0.0743
 2P4  O11   O  O     0  -0.484  -1.0460   0.4369  -1.2914
 2P4  C12   C  CR15  0  -0.498  -1.5251   1.5560   0.7393
 2P4  C13   C  CH2   0  -0.445  -3.0513   1.8036   0.6157
 2P4  C14   C  CH2   0  -0.471  -3.2093   3.3225   0.4317
 2P4  C15   C  CR15  0  -0.259  -1.8533   3.7632  -0.0157
 2P4  C16   C  CR5   0   0.057  -0.9351   2.8148   0.1530
 2P4  C1    C  CH1   0  -0.007  -1.8665  -2.8064  -0.7003
 2P4  O2    O  OH1   0  -0.659  -2.7808  -3.0438   0.3460
 2P4  C3    C  CH2   0  -0.160  -2.5372  -2.1611  -1.9009
 2P4  O4    O  OH1   0  -0.674  -3.4872  -3.0718  -2.4099
 2P4  C5    C  CH1   0  -0.083  -0.6211  -2.0627  -0.1955
 2P4  C6    C  CH2   0  -0.475   0.1735  -2.9231   0.8026
 2P4  C7    C  CH2   0  -0.453   0.5444  -1.9790   1.9375
 2P4  C8    C  CH2   0  -0.303  -0.6389  -1.0251   1.9777
 2P4  N9    N  NT    0  -0.488  -0.9555  -0.8450   0.5606
 2P4  C17   C  C     0   0.519   0.5024   2.9828  -0.1604
 2P4  O18   O  O     0  -0.490   0.8991   3.7788  -1.0017
 2P4  N19   N  NH1   0  -0.643   1.3246   2.1858   0.5516
 2P4  C20   C  CH2   0  -0.348   2.7519   2.0865   0.3535
 2P4  C21   C  CR6   0   0.091   3.1800   0.6461   0.2315
 2P4  C22   C  CR16  0  -0.280   2.6334  -0.1682  -0.7598
 2P4  C23   C  CR16  0  -0.241   3.0270  -1.4917  -0.8792
 2P4  C24   C  CR16  0  -0.265   3.9649  -2.0244  -0.0015
 2P4  C25   C  CR16  0  -0.240   4.5079  -1.2234   0.9917
 2P4  C26   C  CR16  0  -0.309   4.1163   0.1062   1.1051
 2P4  H12   H  HCR5  0   0.284  -1.2625   1.4633   1.7957
 2P4  H13   H  HCH2  0   0.255  -3.4408   1.2899  -0.2643
 2P4  H13A  H  HCH2  0   0.256  -3.5924   1.4247   1.4810
 2P4  H14   H  HCH2  0   0.253  -3.9912   3.5784  -0.2860
 2P4  H14A  H  HCH2  0   0.255  -3.4752   3.8225   1.3683
 2P4  H15   H  HCR5  0   0.260  -1.6486   4.7593  -0.3870
 2P4  H1    H  HCH1  0   0.239  -1.5167  -3.7948  -1.0207
 2P4  HO2   H  HOH1  0   0.441  -3.1312  -2.1938   0.6346
 2P4  H3    H  HCH2  0   0.195  -3.0125  -1.2154  -1.6101
 2P4  H3A   H  HCH2  0   0.198  -1.7697  -1.9185  -2.6452
 2P4  HO4   H  HOH1  0   0.454  -3.9367  -2.6488  -3.1465
 2P4  H5    H  HCH1  0   0.257   0.0041  -1.7901  -1.0491
 2P4  H6    H  HCH2  0   0.244  -0.4494  -3.7354   1.1817
 2P4  H6A   H  HCH2  0   0.251   1.0440  -3.3711   0.3263
 2P4  H7    H  HCH2  0   0.247   0.6960  -2.4898   2.8879
 2P4  H7A   H  HCH2  0   0.247   1.4571  -1.4296   1.6968
 2P4  H8    H  HCH2  0   0.247  -1.4838  -1.4679   2.5113
 2P4  H8A   H  HCH2  0   0.255  -0.3966  -0.0861   2.4680
 2P4  HN19  H  HNH1  0   0.403   0.9440   1.6521   1.3164
 2P4  H20   H  HCH2  0   0.269   3.0024   2.6367  -0.5531
 2P4  H20A  H  HCH2  0   0.261   3.2877   2.5670   1.1759
 2P4  H22   H  HCR6  0   0.250   1.8863   0.2321  -1.4352
 2P4  H23   H  HCR6  0   0.256   2.5953  -2.1142  -1.6529
 2P4  H24   H  HCR6  0   0.255   4.2659  -3.0600  -0.0923
 2P4  H25   H  HCR6  0   0.255   5.2352  -1.6312   1.6821
 2P4  H26   H  HCR6  0   0.253   4.5437   0.7279   1.8832

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
 2P4  C1   O2    single    1.410  0.020  1.410
 2P4  C1   C3    single    1.519  0.020  1.519
 2P4  C1   C5    single    1.536  0.020  1.536
 2P4  C3   O4    single    1.411  0.020  1.411
 2P4  C5   C6    single    1.539  0.020  1.539
 2P4  C5   N9    single    1.472  0.020  1.472
 2P4  C6   C7    single    1.522  0.020  1.522
 2P4  C7   C8    single    1.520  0.020  1.520
 2P4  C8   N9    single    1.463  0.020  1.463
 2P4  N9   C10   single    1.350  0.020  1.350
 2P4  C10  O11   double    1.224  0.020  1.224
 2P4  C10  C12   single    1.521  0.020  1.521
 2P4  C12  C13   single    1.551  0.020  1.551
 2P4  C12  C16   single    1.509  0.020  1.509
 2P4  C13  C14   single    1.538  0.020  1.538
 2P4  C14  C15   single    1.494  0.020  1.494
 2P4  C15  C16   double    1.331  0.020  1.331
 2P4  C16  C17   single    1.481  0.020  1.481
 2P4  C17  O18   double    1.224  0.020  1.224
 2P4  C17  N19   single    1.348  0.020  1.348
 2P4  N19  C20   single    1.444  0.020  1.444
 2P4  C20  C21   single    1.508  0.020  1.508
 2P4  C21  C22   aromatic  1.394  0.020  1.394
 2P4  C21  C26   aromatic  1.390  0.020  1.390
 2P4  C22  C23   aromatic  1.386  0.020  1.386
 2P4  C23  C24   aromatic  1.391  0.020  1.391
 2P4  C24  C25   aromatic  1.387  0.020  1.387
 2P4  C25  C26   aromatic  1.391  0.020  1.391
 2P4  C1   H1    single    0.970  0.020  1.090
 2P4  O2   HO2   single    0.850  0.020  0.980
 2P4  C3   H3    single    0.970  0.020  1.090
 2P4  C3   H3A   single    0.970  0.020  1.090
 2P4  O4   HO4   single    0.850  0.020  0.980
 2P4  C5   H5    single    0.970  0.020  1.090
 2P4  C6   H6    single    0.970  0.020  1.090
 2P4  C6   H6A   single    0.970  0.020  1.090
 2P4  C7   H7    single    0.970  0.020  1.090
 2P4  C7   H7A   single    0.970  0.020  1.090
 2P4  C8   H8    single    0.970  0.020  1.090
 2P4  C8   H8A   single    0.970  0.020  1.090
 2P4  C12  H12   single    0.970  0.020  1.090
 2P4  C13  H13   single    0.970  0.020  1.090
 2P4  C13  H13A  single    0.970  0.020  1.090
 2P4  C14  H14   single    0.970  0.020  1.090
 2P4  C14  H14A  single    0.970  0.020  1.090
 2P4  C15  H15   single    0.930  0.020  1.080
 2P4  N19  HN19  single    0.860  0.020  1.020
 2P4  C20  H20   single    0.970  0.020  1.090
 2P4  C20  H20A  single    0.970  0.020  1.090
 2P4  C22  H22   single    0.930  0.020  1.080
 2P4  C23  H23   single    0.930  0.020  1.080
 2P4  C24  H24   single    0.930  0.020  1.080
 2P4  C25  H25   single    0.930  0.020  1.080
 2P4  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
 2P4  N9    C10  C12  118.89  3.000
 2P4  C12   C10  O11  118.78  3.000
 2P4  N9    C10  O11  122.19  3.000
 2P4  H12   C12  C16  110.65  3.000
 2P4  H12   C12  C13  109.09  3.000
 2P4  C16   C12  C13  102.75  3.000
 2P4  H12   C12  C10  112.70  3.000
 2P4  C16   C12  C10  111.08  3.000
 2P4  C13   C12  C10  110.10  3.000
 2P4  H13A  C13  H13  107.45  3.000
 2P4  H13A  C13  C14  112.81  3.000
 2P4  H13   C13  C14  109.38  3.000
 2P4  H13A  C13  C12  111.73  3.000
 2P4  H13   C13  C12  109.91  3.000
 2P4  C14   C13  C12  105.56  3.000
 2P4  H14A  C14  H14  106.35  3.000
 2P4  H14A  C14  C15  109.99  3.000
 2P4  H14   C14  C15  112.57  3.000
 2P4  H14A  C14  C13  111.95  3.000
 2P4  H14   C14  C13  112.56  3.000
 2P4  C15   C14  C13  103.52  3.000
 2P4  H15   C15  C16  124.66  3.000
 2P4  H15   C15  C14  123.07  3.000
 2P4  C16   C15  C14  112.21  3.000
 2P4  C17   C16  C15  124.20  3.000
 2P4  C17   C16  C12  123.81  3.000
 2P4  C15   C16  C12  111.96  3.000
 2P4  H1    C1   C5   105.89  3.000
 2P4  H1    C1   C3   107.03  3.000
 2P4  C5    C1   C3   114.33  3.000
 2P4  H1    C1   O2   105.79  3.000
 2P4  C5    C1   O2   111.32  3.000
 2P4  C3    C1   O2   111.83  3.000
 2P4  HO2   O2   C1   108.03  3.000
 2P4  H3A   C3   H3   107.00  3.000
 2P4  H3A   C3   O4   111.67  3.000
 2P4  H3    C3   O4   111.10  3.000
 2P4  H3A   C3   C1   108.75  3.000
 2P4  H3    C3   C1   110.36  3.000
 2P4  O4    C3   C1   107.95  3.000
 2P4  HO4   O4   C3   107.90  3.000
 2P4  H5    C5   N9   108.96  3.000
 2P4  H5    C5   C6   110.53  3.000
 2P4  N9    C5   C6   104.28  3.000
 2P4  H5    C5   C1   109.15  3.000
 2P4  N9    C5   C1   112.66  3.000
 2P4  C6    C5   C1   111.17  3.000
 2P4  H6A   C6   H6   107.58  3.000
 2P4  H6A   C6   C7   112.75  3.000
 2P4  H6    C6   C7   109.98  3.000
 2P4  H6A   C6   C5   111.05  3.000
 2P4  H6    C6   C5   110.28  3.000
 2P4  C7    C6   C5   105.22  3.000
 2P4  H7A   C7   H7   108.16  3.000
 2P4  H7A   C7   C8   109.91  3.000
 2P4  H7    C7   C8   112.29  3.000
 2P4  H7A   C7   C6   110.57  3.000
 2P4  H7    C7   C6   113.17  3.000
 2P4  C8    C7   C6   102.67  3.000
 2P4  H8A   C8   H8   107.58  3.000
 2P4  H8A   C8   N9   112.27  3.000
 2P4  H8    C8   N9   110.82  3.000
 2P4  H8A   C8   C7   112.37  3.000
 2P4  H8    C8   C7   111.12  3.000
 2P4  N9    C8   C7   102.71  3.000
 2P4  C8    N9   C5   110.28  3.000
 2P4  C8    N9   C10  126.18  3.000
 2P4  C5    N9   C10  120.65  3.000
 2P4  N19   C17  O18  123.34  3.000
 2P4  N19   C17  C16  114.40  3.000
 2P4  O18   C17  C16  122.26  3.000
 2P4  HN19  N19  C20  116.17  3.000
 2P4  HN19  N19  C17  118.93  3.000
 2P4  C20   N19  C17  124.80  3.000
 2P4  H20A  C20  H20  106.94  3.000
 2P4  H20A  C20  C21  109.98  3.000
 2P4  H20   C20  C21  110.47  3.000
 2P4  H20A  C20  N19  110.55  3.000
 2P4  H20   C20  N19  107.85  3.000
 2P4  C21   C20  N19  110.94  3.000
 2P4  C26   C21  C22  118.96  3.000
 2P4  C26   C21  C20  120.77  3.000
 2P4  C22   C21  C20  120.27  3.000
 2P4  H22   C22  C23  119.65  3.000
 2P4  H22   C22  C21  119.84  3.000
 2P4  C23   C22  C21  120.50  3.000
 2P4  H23   C23  C24  119.97  3.000
 2P4  H23   C23  C22  119.83  3.000
 2P4  C24   C23  C22  120.20  3.000
 2P4  H24   C24  C25  120.26  3.000
 2P4  H24   C24  C23  120.08  3.000
 2P4  C25   C24  C23  119.66  3.000
 2P4  H25   C25  C26  119.83  3.000
 2P4  H25   C25  C24  120.15  3.000
 2P4  C26   C25  C24  120.03  3.000
 2P4  H26   C26  C25  119.73  3.000
 2P4  H26   C26  C21  119.62  3.000
 2P4  C25   C26  C21  120.66  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
 2P4  CONST_01  C24   C23  C22  C21     0.00   0.0  0
 2P4  CONST_02  C24   C25  C26  C21     0.00   0.0  0
 2P4  CONST_03  C25   C26  C21  C22     0.00   0.0  0
 2P4  CONST_04  C25   C24  C23  C22     0.00   0.0  0
 2P4  CONST_05  C26   C21  C22  C23     0.00   0.0  0
 2P4  CONST_06  C26   C25  C24  C23     0.00   0.0  0
 2P4  CONST_07  C23   C22  C21  C20   180.00   0.0  0
 2P4  CONST_08  C25   C26  C21  C20   180.00   0.0  0
 2P4  CONST_09  C5    N9   C10  C12   180.00   0.0  0
 2P4  CONST_11  H23   C23  C22  C21   180.00   0.0  0
 2P4  CONST_12  H25   C25  C26  C21   180.00   0.0  0
 2P4  CONST_13  H26   C26  C21  C22   180.00   0.0  0
 2P4  CONST_14  H24   C24  C23  C22   180.00   0.0  0
 2P4  CONST_15  H22   C22  C23  C24   180.00   0.0  0
 2P4  CONST_16  C5    N9   C10  O11     0.00   0.0  0
 2P4  CONST_19  C20   N19  C17  C16   180.00   0.0  0
 2P4  CONST_20  HN19  N19  C17  C16     0.00   0.0  0
 2P4  CONST_21  C20   N19  C17  O18     0.00   0.0  0
 2P4  Var_01    C15   C14  C13  C12    19.19  30.0  1
 2P4  Var_02    C14   C15  C16  C12     0.45  30.0  1
 2P4  Var_03    C16   C15  C14  C13   -12.69  30.0  1
 2P4  Var_04    C8    C7   C6   C5     32.60  30.0  1
 2P4  Var_05    C7    C8   N9   C5     30.83  30.0  1
 2P4  Var_06    N9    C8   C7   C6    -38.32  30.0  1
 2P4  Var_07    O18   C17  C16  C15   -26.32  30.0  2
 2P4  Var_08    C22   C21  C20  N19    57.80  30.0  2
 2P4  Var_09    C21   C20  N19  C17  -129.83  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
 2P4  chir_01  C12  C10  C13  C16  positiv
 2P4  chir_02  C1   O2   C3   C5   negativ
 2P4  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
 2P4  plan-1  C10   0.020
 2P4  plan-1  O11   0.020
 2P4  plan-1  C12   0.020
 2P4  plan-1  C5    0.020
 2P4  plan-1  C8    0.020
 2P4  plan-1  N9    0.020
 2P4  plan-2  C20   0.020
 2P4  plan-2  C21   0.020
 2P4  plan-2  C22   0.020
 2P4  plan-2  C23   0.020
 2P4  plan-2  C24   0.020
 2P4  plan-2  C25   0.020
 2P4  plan-2  C26   0.020
 2P4  plan-2  H22   0.020
 2P4  plan-2  H23   0.020
 2P4  plan-2  H24   0.020
 2P4  plan-2  H25   0.020
 2P4  plan-2  H26   0.020
 2P4  plan-3  C12   0.020
 2P4  plan-3  C16   0.020
 2P4  plan-3  C17   0.020
 2P4  plan-3  O18   0.020
 2P4  plan-3  N19   0.020
 2P4  plan-3  C20   0.020
 2P4  plan-3  HN19  0.020

