# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 13:55:52 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-[(2-{(2S,4S)-2-[(R)-(5-tert-butyl-1,3,4-oxadiazol-2-yl)(hydroxy)methyl]-4-fluoropyrrolidin-1-yl}-2-oxoethyl)amino]-2-methylpropan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1oc(nn1)[C@H](O)[C@@H]2C[C@H](F)CN2C(=O)CNC(C)(C)CO
#
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
 13Z  13Z  2-[(2-{(2S,4S)-2-[(R)-(5-tert-butyl-1,3,4-oxadiazol-2-yl)(hydroxy)methyl]-4-fluoropyrrolidin-1-yl}-2-oxoethyl)amino]-2-methylpropan-1-ol  ligand  55  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_13Z
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
 13Z  C1    C  CH1   0  -0.089   1.5974   2.3717  -0.7230
 13Z  C2    C  CH2   0  -0.578   2.6463   2.7198   0.3371
 13Z  C3    C  CH1   0   0.210   1.8316   2.8778   1.6057
 13Z  C4    C  CH2   0  -0.352   0.7669   1.8009   1.4809
 13Z  C6    C  CH2   0  -0.406  -1.7425   0.8872   0.3861
 13Z  C7    C  CH1   0  -0.060   2.1214   1.3749  -1.7844
 13Z  N1    N  NT    0  -0.508   0.4803   1.8413   0.0588
 13Z  N2    N  N     0  -0.312   3.4337  -0.5836  -0.9395
 13Z  N3    N  N     0  -0.314   3.1022  -1.8072  -0.4069
 13Z  N4    N  NH1   0  -0.604  -2.6334   0.0695  -0.3976
 13Z  C8    C  CR5   0   0.429   2.3291   0.0116  -1.2040
 13Z  F1    F  F     0  -0.364   2.5967   2.7024   2.7459
 13Z  O1    O  O     0  -0.489  -0.8990   1.6894  -1.7065
 13Z  O2    O  OH1   0  -0.641   3.2867   1.8500  -2.3880
 13Z  C9    C  CR5   0   0.537   1.8188  -1.8686  -0.3802
 13Z  O3    O  O     0  -0.409   1.2716  -0.7446  -0.8799
 13Z  C12   C  CH3   0  -0.647   0.4770  -2.4990   1.5718
 13Z  C14   C  CH3   0  -0.656  -0.3073  -3.1004  -0.7334
 13Z  C16   C  CH3   0  -0.635   1.6991  -4.2451   0.2523
 13Z  C11   C  CT    0   0.059  -3.8038  -0.4795   0.2895
 13Z  C13   C  CH3   0  -0.653  -4.8146   0.6048   0.6786
 13Z  C15   C  CH2   0  -0.133  -4.4189  -1.4403  -0.7322
 13Z  C17   C  CH3   0  -0.678  -3.3690  -1.2606   1.5262
 13Z  O4    O  OH1   0  -0.670  -5.6029  -2.0024  -0.2194
 13Z  H1    H  HCH1  0   0.292   1.2813   3.2707  -1.2585
 13Z  H2    H  HCH2  0   0.256   3.3531   1.8974   0.4890
 13Z  H2A   H  HCH2  0   0.292   3.2129   3.6125   0.0804
 13Z  H3    H  HCH1  0   0.236   1.3701   3.8660   1.6614
 13Z  H4    H  HCH2  0   0.252   1.1717   0.8321   1.7967
 13Z  H4A   H  HCH2  0   0.285  -0.1147   2.0211   2.0806
 13Z  H6    H  HCH2  0   0.261  -1.2633   0.2718   1.1478
 13Z  H6A   H  HCH2  0   0.248  -2.2300   1.7138   0.9311
 13Z  H7    H  HCH1  0   0.296   1.3726   1.2932  -2.5740
 13Z  HN4   H  HNH1  0   0.344  -2.9396   0.5976  -1.2065
 13Z  HO2   H  HOH1  0   0.461   4.0226   1.8032  -1.7670
 13Z  H12   H  HCH3  0   0.236  -0.0746  -1.5575   1.5482
 13Z  H12A  H  HCH3  0   0.248  -0.1838  -3.2552   1.9981
 13Z  H12B  H  HCH3  0   0.247   1.3280  -2.3793   2.2434
 13Z  H14   H  HCH3  0   0.241  -0.0251  -3.3342  -1.7610
 13Z  H14A  H  HCH3  0   0.240  -0.9092  -3.9285  -0.3577
 13Z  H14B  H  HCH3  0   0.248  -0.9383  -2.2094  -0.7380
 13Z  H16   H  HCH3  0   0.239   2.5789  -4.1550   0.8896
 13Z  H16A  H  HCH3  0   0.240   1.0561  -5.0166   0.6772
 13Z  H16B  H  HCH3  0   0.239   2.0251  -4.5818  -0.7321
 13Z  H13   H  HCH3  0   0.220  -5.1848   1.1260  -0.2080
 13Z  H13A  H  HCH3  0   0.231  -5.6733   0.1899   1.2058
 13Z  H13B  H  HCH3  0   0.226  -4.3619   1.3479   1.3378
 13Z  H15   H  HCH2  0   0.192  -4.6156  -0.8853  -1.6620
 13Z  H15A  H  HCH2  0   0.203  -3.6724  -2.2101  -0.9674
 13Z  H17   H  HCH3  0   0.231  -2.9609  -0.6081   2.3000
 13Z  H17A  H  HCH3  0   0.241  -4.2187  -1.7821   1.9645
 13Z  H17B  H  HCH3  0   0.233  -2.6069  -2.0025   1.2753
 13Z  HO4   H  HOH1  0   0.456  -5.9299  -2.6406  -0.8590
 13Z  C5    C  C     0   0.567  -0.6908   1.5040  -0.5165
 13Z  C10   C  CT    0  -0.238   0.9222  -2.9322   0.1666

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
 13Z  C1   C2    single    1.531  0.020  1.531
 13Z  C1   C7    single    1.548  0.020  1.548
 13Z  C1   N1    single    1.463  0.020  1.463
 13Z  C2   C3    single    1.516  0.020  1.516
 13Z  C3   C4    single    1.520  0.020  1.520
 13Z  C3   F1    single    1.384  0.020  1.384
 13Z  C4   N1    single    1.451  0.020  1.451
 13Z  C5   C6    single    1.517  0.020  1.517
 13Z  C5   N1    single    1.348  0.020  1.348
 13Z  C5   O1    double    1.222  0.020  1.222
 13Z  C6   N4    single    1.441  0.020  1.441
 13Z  C7   C8    single    1.496  0.020  1.496
 13Z  C7   O2    single    1.396  0.020  1.396
 13Z  N2   N3    aromatic  1.375  0.020  1.375
 13Z  N2   C8    aromatic  1.282  0.020  1.282
 13Z  N3   C9    aromatic  1.285  0.020  1.285
 13Z  N4   C11   single    1.464  0.020  1.464
 13Z  C8   O3    aromatic  1.340  0.020  1.340
 13Z  C10  C9    single    1.495  0.020  1.495
 13Z  C10  C12   single    1.536  0.020  1.536
 13Z  C10  C14   single    1.533  0.020  1.533
 13Z  C10  C16   single    1.528  0.020  1.528
 13Z  C9   O3    aromatic  1.346  0.020  1.346
 13Z  C11  C13   single    1.533  0.020  1.533
 13Z  C11  C15   single    1.532  0.020  1.532
 13Z  C11  C17   single    1.526  0.020  1.526
 13Z  C15  O4    single    1.407  0.020  1.407
 13Z  C1   H1    single    0.970  0.020  1.090
 13Z  C2   H2    single    0.970  0.020  1.090
 13Z  C2   H2A   single    0.970  0.020  1.090
 13Z  C3   H3    single    0.970  0.020  1.090
 13Z  C4   H4    single    0.970  0.020  1.090
 13Z  C4   H4A   single    0.970  0.020  1.090
 13Z  C6   H6    single    0.970  0.020  1.090
 13Z  C6   H6A   single    0.970  0.020  1.090
 13Z  C7   H7    single    0.970  0.020  1.090
 13Z  N4   HN4   single    0.890  0.020  1.040
 13Z  O2   HO2   single    0.850  0.020  0.980
 13Z  C12  H12   single    0.970  0.020  1.090
 13Z  C12  H12A  single    0.970  0.020  1.090
 13Z  C12  H12B  single    0.970  0.020  1.090
 13Z  C14  H14   single    0.970  0.020  1.090
 13Z  C14  H14A  single    0.970  0.020  1.090
 13Z  C14  H14B  single    0.970  0.020  1.090
 13Z  C16  H16   single    0.970  0.020  1.090
 13Z  C16  H16A  single    0.970  0.020  1.090
 13Z  C16  H16B  single    0.970  0.020  1.090
 13Z  C13  H13   single    0.970  0.020  1.090
 13Z  C13  H13A  single    0.970  0.020  1.090
 13Z  C13  H13B  single    0.970  0.020  1.090
 13Z  C15  H15   single    0.970  0.020  1.090
 13Z  C15  H15A  single    0.970  0.020  1.090
 13Z  C17  H17   single    0.970  0.020  1.090
 13Z  C17  H17A  single    0.970  0.020  1.090
 13Z  C17  H17B  single    0.970  0.020  1.090
 13Z  O4   HO4   single    0.850  0.020  0.980

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
 13Z  H1    C1   N1    109.83  3.000
 13Z  H1    C1   C7    106.96  3.000
 13Z  N1    C1   C7    113.05  3.000
 13Z  H1    C1   C2    110.50  3.000
 13Z  N1    C1   C2    103.62  3.000
 13Z  C7    C1   C2    112.91  3.000
 13Z  H2A   C2   H2    108.23  3.000
 13Z  H2A   C2   C3    113.07  3.000
 13Z  H2    C2   C3    108.01  3.000
 13Z  H2A   C2   C1    112.32  3.000
 13Z  H2    C2   C1    111.56  3.000
 13Z  C3    C2   C1    103.59  3.000
 13Z  H3    C3   F1    107.83  3.000
 13Z  H3    C3   C4    110.45  3.000
 13Z  F1    C3   C4    111.41  3.000
 13Z  H3    C3   C2    111.36  3.000
 13Z  F1    C3   C2    112.27  3.000
 13Z  C4    C3   C2    103.53  3.000
 13Z  H4A   C4   H4    108.60  3.000
 13Z  H4A   C4   N1    111.98  3.000
 13Z  H4    C4   N1    112.32  3.000
 13Z  H4A   C4   C3    112.26  3.000
 13Z  H4    C4   C3    110.11  3.000
 13Z  N1    C4   C3    101.49  3.000
 13Z  H6A   C6   H6    105.78  3.000
 13Z  H6A   C6   N4    114.87  3.000
 13Z  H6    C6   N4    109.35  3.000
 13Z  H6A   C6   C5    107.19  3.000
 13Z  H6    C6   C5    109.90  3.000
 13Z  N4    C6   C5    109.62  3.000
 13Z  H7    C7   O2    106.58  3.000
 13Z  H7    C7   C8    107.93  3.000
 13Z  O2    C7   C8    111.23  3.000
 13Z  H7    C7   C1    108.19  3.000
 13Z  O2    C7   C1    111.10  3.000
 13Z  C8    C7   C1    111.59  3.000
 13Z  C5    N1   C4    125.66  3.000
 13Z  C5    N1   C1    121.74  3.000
 13Z  C4    N1   C1    112.51  3.000
 13Z  C8    N2   N3    106.58  3.000
 13Z  C9    N3   N2    106.93  3.000
 13Z  HN4   N4   C11   109.17  3.000
 13Z  HN4   N4   C6    108.98  3.000
 13Z  C11   N4   C6    116.86  3.000
 13Z  O3    C8   N2    111.59  3.000
 13Z  O3    C8   C7    119.90  3.000
 13Z  N2    C8   C7    128.50  3.000
 13Z  HO2   O2   C7    110.01  3.000
 13Z  O3    C9   C10   119.08  3.000
 13Z  O3    C9   N3    111.00  3.000
 13Z  C10   C9   N3    129.84  3.000
 13Z  C9    O3   C8    103.89  3.000
 13Z  H12B  C12  H12A  107.94  3.000
 13Z  H12B  C12  H12   108.24  3.000
 13Z  H12A  C12  H12   107.47  3.000
 13Z  H12B  C12  C10   111.59  3.000
 13Z  H12A  C12  C10   109.73  3.000
 13Z  H12   C12  C10   111.71  3.000
 13Z  H14B  C14  H14A  107.59  3.000
 13Z  H14B  C14  H14   108.69  3.000
 13Z  H14A  C14  H14   107.73  3.000
 13Z  H14B  C14  C10   112.11  3.000
 13Z  H14A  C14  C10   108.89  3.000
 13Z  H14   C14  C10   111.65  3.000
 13Z  H16B  C16  H16A  108.03  3.000
 13Z  H16B  C16  H16   108.19  3.000
 13Z  H16A  C16  H16   107.85  3.000
 13Z  H16B  C16  C10   111.51  3.000
 13Z  H16A  C16  C10   109.26  3.000
 13Z  H16   C16  C10   111.85  3.000
 13Z  C17   C11  C15   109.51  3.000
 13Z  C17   C11  C13   110.14  3.000
 13Z  C15   C11  C13   110.39  3.000
 13Z  C17   C11  N4    110.15  3.000
 13Z  C15   C11  N4    104.08  3.000
 13Z  C13   C11  N4    112.40  3.000
 13Z  H13B  C13  H13A  107.08  3.000
 13Z  H13B  C13  H13   107.80  3.000
 13Z  H13A  C13  H13   107.89  3.000
 13Z  H13B  C13  C11   111.19  3.000
 13Z  H13A  C13  C11   111.91  3.000
 13Z  H13   C13  C11   110.78  3.000
 13Z  H15A  C15  H15   107.11  3.000
 13Z  H15A  C15  O4    111.72  3.000
 13Z  H15   C15  O4    111.03  3.000
 13Z  H15A  C15  C11   108.04  3.000
 13Z  H15   C15  C11   108.60  3.000
 13Z  O4    C15  C11   110.20  3.000
 13Z  H17B  C17  H17A  108.14  3.000
 13Z  H17B  C17  H17   107.94  3.000
 13Z  H17A  C17  H17   107.02  3.000
 13Z  H17B  C17  C11   111.11  3.000
 13Z  H17A  C17  C11   110.42  3.000
 13Z  H17   C17  C11   112.03  3.000
 13Z  HO4   O4   C15   107.99  3.000
 13Z  O1    C5   N1    121.72  3.000
 13Z  O1    C5   C6    121.52  3.000
 13Z  N1    C5   C6    116.76  3.000
 13Z  C16   C10  C14   110.27  3.000
 13Z  C16   C10  C12   109.77  3.000
 13Z  C14   C10  C12   109.60  3.000
 13Z  C16   C10  C9    109.08  3.000
 13Z  C14   C10  C9    110.15  3.000
 13Z  C12   C10  C9    107.93  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
 13Z  CONST_01  O3   C9   N3   N2     0.00   0.0  0
 13Z  CONST_02  C9   O3   C8   N2     0.00   0.0  0
 13Z  CONST_03  O3   C8   N2   N3     0.00   0.0  0
 13Z  CONST_04  C8   O3   C9   N3     0.00   0.0  0
 13Z  CONST_05  C9   N3   N2   C8     0.00   0.0  0
 13Z  CONST_06  N3   N2   C8   C7   180.00   0.0  0
 13Z  CONST_07  C9   O3   C8   C7   180.00   0.0  0
 13Z  CONST_08  C10  C9   N3   N2   180.00   0.0  0
 13Z  CONST_09  C10  C9   O3   C8   180.00   0.0  0
 13Z  CONST_10  C6   C5   N1   C1   180.00   0.0  0
 13Z  CONST_11  O1   C5   N1   C1     0.00   0.0  0
 13Z  CONST_12  C6   C5   N1   C4     0.00   0.0  0
 13Z  CONST_13  O1   C5   N1   C4   180.00   0.0  0
 13Z  Var_01    C3   C4   N1   C1    24.42  30.0  1
 13Z  Var_02    C12  C10  C9   N3    97.68  30.0  3
 13Z  Var_03    N4   C6   C5   N1  -154.68  30.0  3
 13Z  Var_04    H12  C12  C10  C9    60.71  30.0  3
 13Z  Var_05    H14  C14  C10  C9    57.07  30.0  3
 13Z  Var_06    H16  C16  C10  C9    59.08  30.0  3
 13Z  Var_07    C11  N4   C6   C5  -173.11  30.0  3
 13Z  Var_08    C13  C11  N4   C6    68.37  30.0  3
 13Z  Var_09    O4   C15  C11  N4  -177.36  30.0  3
 13Z  Var_10    H13  C13  C11  N4    60.63  30.0  3
 13Z  Var_11    H17  C17  C11  N4    68.46  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
 13Z  chir_01  C1  C2  C7  N1  negativ
 13Z  chir_02  C3  F1  C4  C2  positiv
 13Z  chir_03  C7  O2  C8  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
 13Z  plan-1  C7   0.020
 13Z  plan-1  N2   0.020
 13Z  plan-1  N3   0.020
 13Z  plan-1  C8   0.020
 13Z  plan-1  C9   0.020
 13Z  plan-1  O3   0.020
 13Z  plan-1  C10  0.020
 13Z  plan-2  C1   0.020
 13Z  plan-2  C4   0.020
 13Z  plan-2  C6   0.020
 13Z  plan-2  N1   0.020
 13Z  plan-2  O1   0.020
 13Z  plan-2  C5   0.020

