# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 09:54:04 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-[1-(aminomethyl)cyclopropyl]-3-(morpholin-4-ylsulfonyl)-N~2~-[(1S)-2,2,2-trifluoro-1-(4-fluorophenyl)ethyl]-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1(CC1)NC(=O)[C@H](C[S](=O)(=O)N2CCOCC2)N[C@@H](c3ccc(F)cc3)C(F)(F)F
#
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
 C28  C28  N-[1-(aminomethyl)cyclopropyl]-3-(morpholin-4-ylsulfonyl)-N~2~-[(1S)-2,2,2-trifluoro-1-(4-fluorophenyl)ethyl]-L-alaninamide  ligand  58  32  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_C28
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
 C28  C2    C  CR6   0   0.523   5.5921   1.6069  -1.3342
 C28  C4    C  CR16  0  -0.280   4.5611   0.1524   0.2388
 C28  C5    C  CR6   0   0.082   3.3809   0.8823   0.1552
 C28  C6    C  CR16  0  -0.279   3.3317   1.9891  -0.6901
 C28  C1    C  CR16  0  -0.397   4.4360   2.3556  -1.4445
 C28  C3    C  CR16  0  -0.398   5.6774   0.5075  -0.5036
 C28  C8    C  CH1   0  -0.358   2.1860   0.4681   0.9793
 C28  F7    F  F     0  -0.312   6.6645   1.9567  -2.0603
 C28  N9    N  NH1   0  -0.588   0.9489   0.5517   0.2310
 C28  C10   C  CT    0   1.034   2.0788   1.3566   2.2148
 C28  C11   C  CH1   0  -0.235   0.0091  -0.5116   0.4522
 C28  C12   C  C     0   0.539   0.4915  -1.8891  -0.0278
 C28  C13   C  CH2   0  -0.671  -1.2714  -0.2495  -0.3385
 C28  S14   S  S     0   1.391  -2.1247   1.2375   0.1971
 C28  N15   N  N     0  -0.578  -3.6648   1.0834  -0.3945
 C28  N16   N  NH1   0  -0.635  -0.0725  -2.9234   0.6228
 C28  O17   O  O     0  -0.462   1.2630  -1.9959  -0.9636
 C28  C18   C  CT    0   0.155  -0.2262  -4.2117   0.0183
 C28  C19   C  CH2   0  -0.477   0.9629  -5.1113  -0.0379
 C28  C20   C  CH2   0  -0.503  -0.1356  -5.3863   0.9444
 C28  O21   O  OS    0  -0.661  -2.2225   1.1989   1.6481
 C28  F22   F  F     0  -0.307   1.0612   0.9914   3.0066
 C28  F23   F  F     0  -0.307   3.1934   1.2857   2.9569
 C28  F24   F  F     0  -0.300   1.8899   2.6431   1.9108
 C28  O25   O  OS    0  -0.651  -1.5413   2.3981  -0.4518
 C28  C26   C  CH2   0  -0.331  -4.5197   0.0515   0.1919
 C28  C27   C  CH2   0  -0.182  -5.9605   0.3675  -0.1686
 C28  O28   O  O2    0  -0.479  -6.1400   0.4646  -1.5621
 C28  C29   C  CH2   0  -0.183  -5.3206   1.4709  -2.1097
 C28  C30   C  CH2   0  -0.326  -3.8507   1.2033  -1.8415
 C28  N32   N  NH2   0  -0.787  -2.5042  -3.6806  -0.6725
 C28  C31   C  CH2   0  -0.296  -1.2357  -4.2406  -1.1091
 C28  H4    H  HCR6  0   0.271   4.6155  -0.7129   0.8873
 C28  H6    H  HCR6  0   0.276   2.4275   2.5780  -0.7779
 C28  H1    H  HCR6  0   0.285   4.3969   3.2124  -2.1040
 C28  H3    H  HCR6  0   0.284   6.5933  -0.0644  -0.4374
 C28  H8    H  HCH1  0   0.294   2.3781  -0.5469   1.3549
 C28  HN9   H  HNH1  0   0.373   1.1427   0.6335  -0.7583
 C28  H11   H  HCH1  0   0.296  -0.2443  -0.5675   1.5129
 C28  H131  H  HCH2  0   0.314  -1.0601  -0.1327  -1.4038
 C28  H132  H  HCH2  0   0.325  -1.9636  -1.0898  -0.2280
 C28  HN16  H  HNH1  0   0.398  -0.7521  -2.6975   1.3340
 C28  H191  H  HCH2  0   0.254   1.0594  -5.7614  -0.8988
 C28  H192  H  HCH2  0   0.261   1.9014  -4.7313   0.3426
 C28  H201  H  HCH2  0   0.261   0.0584  -5.1954   1.9924
 C28  H202  H  HCH2  0   0.257  -0.7991  -6.2213   0.7559
 C28  H261  H  HCH2  0   0.235  -4.2541  -0.9485  -0.1772
 C28  H262  H  HCH2  0   0.280  -4.4195   0.0518   1.2755
 C28  H271  H  HCH2  0   0.252  -6.6075  -0.4325   0.1925
 C28  H272  H  HCH2  0   0.216  -6.2587   1.3004   0.3280
 C28  H291  H  HCH2  0   0.252  -5.4947   1.4896  -3.1859
 C28  H292  H  HCH2  0   0.216  -5.5882   2.4546  -1.7011
 C28  H301  H  HCH2  0   0.279  -3.2634   2.0339  -2.2280
 C28  H302  H  HCH2  0   0.241  -3.5367   0.2887  -2.3607
 C28  H321  H  HNH2  0   0.355  -3.1198  -3.5713  -1.4669
 C28  H322  H  HNH2  0   0.344  -2.9669  -4.3247  -0.0428
 C28  H311  H  HCH2  0   0.206  -1.3043  -5.2698  -1.4869
 C28  H312  H  HCH2  0   0.234  -0.8628  -3.6341  -1.9383

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
 C28  C2   C1    aromatic  1.382  0.020  1.382
 C28  C2   C3    aromatic  1.381  0.020  1.381
 C28  C2   F7    single    1.341  0.020  1.341
 C28  C4   C5    aromatic  1.390  0.020  1.390
 C28  C4   C3    aromatic  1.387  0.020  1.387
 C28  C4   H4    single    0.930  0.020  1.080
 C28  C5   C6    aromatic  1.394  0.020  1.394
 C28  C5   C8    single    1.509  0.020  1.509
 C28  C6   C1    aromatic  1.387  0.020  1.387
 C28  C6   H6    single    0.930  0.020  1.080
 C28  C1   H1    single    0.930  0.020  1.080
 C28  C3   H3    single    0.930  0.020  1.080
 C28  C8   N9    single    1.448  0.020  1.448
 C28  C8   C10   single    1.526  0.020  1.526
 C28  C8   H8    single    0.970  0.020  1.090
 C28  N9   C11   single    1.436  0.020  1.436
 C28  N9   HN9   single    0.890  0.020  1.040
 C28  C10  F22   single    1.340  0.020  1.340
 C28  C10  F23   single    1.341  0.020  1.341
 C28  C10  F24   single    1.335  0.020  1.335
 C28  C11  C12   single    1.536  0.020  1.536
 C28  C11  C13   single    1.528  0.020  1.528
 C28  C11  H11   single    0.970  0.020  1.090
 C28  C12  N16   single    1.346  0.020  1.346
 C28  C12  O17   double    1.217  0.020  1.217
 C28  C13  S14   single    1.796  0.020  1.796
 C28  C13  H131  single    0.970  0.020  1.090
 C28  C13  H132  single    0.970  0.020  1.090
 C28  S14  N15   single    1.657  0.020  1.657
 C28  S14  O21   double    1.455  0.020  1.455
 C28  S14  O25   double    1.452  0.020  1.452
 C28  N15  C26   single    1.463  0.020  1.463
 C28  N15  C30   single    1.464  0.020  1.464
 C28  N16  C18   single    1.431  0.020  1.431
 C28  N16  HN16  single    0.890  0.020  1.040
 C28  C18  C19   single    1.492  0.020  1.492
 C28  C18  C20   single    1.498  0.020  1.498
 C28  C18  C31   single    1.514  0.020  1.514
 C28  C19  C20   single    1.499  0.020  1.499
 C28  C19  H191  single    0.970  0.020  1.090
 C28  C19  H192  single    0.970  0.020  1.090
 C28  C20  H201  single    0.970  0.020  1.090
 C28  C20  H202  single    0.970  0.020  1.090
 C28  C26  C27   single    1.519  0.020  1.519
 C28  C26  H261  single    0.970  0.020  1.090
 C28  C26  H262  single    0.970  0.020  1.090
 C28  C27  O28   single    1.408  0.020  1.408
 C28  C27  H271  single    0.970  0.020  1.090
 C28  C27  H272  single    0.970  0.020  1.090
 C28  O28  C29   single    1.409  0.020  1.409
 C28  C29  C30   single    1.518  0.020  1.518
 C28  C29  H291  single    0.970  0.020  1.090
 C28  C29  H292  single    0.970  0.020  1.090
 C28  C30  H301  single    0.970  0.020  1.090
 C28  C30  H302  single    0.970  0.020  1.090
 C28  N32  C31   single    1.454  0.020  1.454
 C28  N32  H321  single    0.890  0.020  1.040
 C28  N32  H322  single    0.890  0.020  1.040
 C28  C31  H311  single    0.970  0.020  1.090
 C28  C31  H312  single    0.970  0.020  1.090

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
 C28  F7    C2   C3    118.94  3.000
 C28  F7    C2   C1    118.97  3.000
 C28  C3    C2   C1    122.09  3.000
 C28  H4    C4   C3    119.00  3.000
 C28  H4    C4   C5    119.89  3.000
 C28  C3    C4   C5    121.11  3.000
 C28  C8    C5   C6    121.41  3.000
 C28  C8    C5   C4    119.68  3.000
 C28  C6    C5   C4    118.91  3.000
 C28  H6    C6   C1    118.51  3.000
 C28  H6    C6   C5    120.71  3.000
 C28  C1    C6   C5    120.78  3.000
 C28  H1    C1   C6    120.80  3.000
 C28  H1    C1   C2    120.53  3.000
 C28  C6    C1   C2    118.67  3.000
 C28  H3    C3   C4    120.89  3.000
 C28  H3    C3   C2    120.67  3.000
 C28  C4    C3   C2    118.44  3.000
 C28  H8    C8   C10   105.86  3.000
 C28  H8    C8   N9    112.29  3.000
 C28  C10   C8   N9    108.96  3.000
 C28  H8    C8   C5    107.55  3.000
 C28  C10   C8   C5    109.75  3.000
 C28  N9    C8   C5    112.23  3.000
 C28  HN9   N9   C11   109.63  3.000
 C28  HN9   N9   C8    110.27  3.000
 C28  C11   N9   C8    115.89  3.000
 C28  F24   C10  F23   107.13  3.000
 C28  F24   C10  F22   106.83  3.000
 C28  F23   C10  F22   106.84  3.000
 C28  F24   C10  C8    112.75  3.000
 C28  F23   C10  C8    111.04  3.000
 C28  F22   C10  C8    111.91  3.000
 C28  H11   C11  C13   108.49  3.000
 C28  H11   C11  C12   109.29  3.000
 C28  C13   C11  C12   104.79  3.000
 C28  H11   C11  N9    109.84  3.000
 C28  C13   C11  N9    109.98  3.000
 C28  C12   C11  N9    114.22  3.000
 C28  O17   C12  N16   124.73  3.000
 C28  O17   C12  C11   121.18  3.000
 C28  N16   C12  C11   113.98  3.000
 C28  H132  C13  H131  107.63  3.000
 C28  H132  C13  S14   107.76  3.000
 C28  H131  C13  S14   107.10  3.000
 C28  H132  C13  C11   110.26  3.000
 C28  H131  C13  C11   111.16  3.000
 C28  S14   C13  C11   112.70  3.000
 C28  O25   S14  O21   119.60  3.000
 C28  O25   S14  N15   106.75  3.000
 C28  O21   S14  N15   106.93  3.000
 C28  O25   S14  C13   109.73  3.000
 C28  O21   S14  C13   107.90  3.000
 C28  N15   S14  C13   104.96  3.000
 C28  C30   N15  C26   112.32  3.000
 C28  C30   N15  S14   117.60  3.000
 C28  C26   N15  S14   117.76  3.000
 C28  HN16  N16  C18   115.26  3.000
 C28  HN16  N16  C12   116.80  3.000
 C28  C18   N16  C12   122.18  3.000
 C28  C31   C18  C20   119.06  3.000
 C28  C31   C18  C19   119.47  3.000
 C28  C20   C18  C19    60.17  3.000
 C28  C31   C18  N16   113.79  3.000
 C28  C20   C18  N16   115.98  3.000
 C28  C19   C18  N16   118.22  3.000
 C28  H192  C19  H191  114.41  3.000
 C28  H192  C19  C20   118.01  3.000
 C28  H191  C19  C20   118.42  3.000
 C28  H192  C19  C18   117.80  3.000
 C28  H191  C19  C18   117.57  3.000
 C28  C20   C19  C18    60.12  3.000
 C28  H202  C20  H201  114.47  3.000
 C28  H202  C20  C19   118.44  3.000
 C28  H201  C20  C19   118.07  3.000
 C28  H202  C20  C18   117.37  3.000
 C28  H201  C20  C18   118.09  3.000
 C28  C19   C20  C18    59.71  3.000
 C28  H262  C26  H261  108.21  3.000
 C28  H262  C26  C27   108.89  3.000
 C28  H261  C26  C27   109.82  3.000
 C28  H262  C26  N15   110.19  3.000
 C28  H261  C26  N15   111.49  3.000
 C28  C27   C26  N15   108.21  3.000
 C28  H272  C27  H271  108.20  3.000
 C28  H272  C27  O28   110.75  3.000
 C28  H271  C27  O28   107.62  3.000
 C28  H272  C27  C26   109.09  3.000
 C28  H271  C27  C26   109.37  3.000
 C28  O28   C27  C26   111.73  3.000
 C28  C29   O28  C27   111.09  3.000
 C28  H292  C29  H291  108.24  3.000
 C28  H292  C29  C30   109.15  3.000
 C28  H291  C29  C30   109.39  3.000
 C28  H292  C29  O28   110.70  3.000
 C28  H291  C29  O28   107.65  3.000
 C28  C30   C29  O28   111.63  3.000
 C28  H302  C30  H301  108.28  3.000
 C28  H302  C30  C29   109.90  3.000
 C28  H301  C30  C29   108.98  3.000
 C28  H302  C30  N15   111.29  3.000
 C28  H301  C30  N15   110.19  3.000
 C28  C29   C30  N15   108.18  3.000
 C28  H322  N32  H321  106.21  3.000
 C28  H322  N32  C31   109.90  3.000
 C28  H321  N32  C31   109.70  3.000
 C28  H312  C31  H311  106.28  3.000
 C28  H312  C31  N32   108.17  3.000
 C28  H311  C31  N32   114.18  3.000
 C28  H312  C31  C18   109.09  3.000
 C28  H311  C31  C18   108.40  3.000
 C28  N32   C31  C18   110.54  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
 C28  CONST_01  C5    C6   C1   C2      0.00   0.0  0
 C28  CONST_02  C5    C4   C3   C2      0.00   0.0  0
 C28  CONST_03  C1    C6   C5   C4      0.00   0.0  0
 C28  CONST_04  C1    C2   C3   C4      0.00   0.0  0
 C28  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 C28  CONST_06  C3    C2   C1   C6      0.00   0.0  0
 C28  CONST_07  F7    C2   C3   C4    180.00   0.0  0
 C28  CONST_08  F7    C2   C1   C6    180.00   0.0  0
 C28  CONST_09  C8    C5   C6   C1    180.00   0.0  0
 C28  CONST_10  C8    C5   C4   C3    180.00   0.0  0
 C28  CONST_11  H6    C6   C1   C2    180.00   0.0  0
 C28  CONST_12  H4    C4   C3   C2    180.00   0.0  0
 C28  CONST_13  H3    C3   C4   C5    180.00   0.0  0
 C28  CONST_14  H1    C1   C6   C5    180.00   0.0  0
 C28  CONST_17  HN16  N16  C12  C11     0.00   0.0  0
 C28  Var_01    O28   C27  C26  N15    56.54  30.0  1
 C28  Var_02    O28   C29  C30  N15   -56.77  30.0  1
 C28  Var_03    C29   C30  N15  C26    56.17  30.0  1
 C28  Var_04    C30   N15  C26  C27   -56.04  30.0  1
 C28  Var_05    C30   C29  O28  C27    59.28  30.0  1
 C28  Var_06    C20   C19  C18  N16   105.39  30.0  1
 C28  Var_07    H201  C20  C19  C18  -107.84  30.0  1
 C28  Var_08    C19   C18  N16  C12    79.12  30.0  3
 C28  Var_09    C26   N15  S14  C13    68.95  30.0  3
 C28  Var_10    N32   C31  C18  C19   160.05  30.0  3
 C28  Var_11    N15   S14  C13  C11  -162.14  30.0  3
 C28  Var_12    H321  N32  C31  C18   171.15  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
 C28  chir_01  C8   C5   N9   C10  positiv
 C28  chir_02  C11  N9   C12  C13  positiv
 C28  chir_03  C18  C19  C20  C31  both

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
 C28  plan-1  C2    0.020
 C28  plan-1  C4    0.020
 C28  plan-1  C5    0.020
 C28  plan-1  C6    0.020
 C28  plan-1  C1    0.020
 C28  plan-1  C3    0.020
 C28  plan-1  C8    0.020
 C28  plan-1  F7    0.020
 C28  plan-1  H4    0.020
 C28  plan-1  H6    0.020
 C28  plan-1  H1    0.020
 C28  plan-1  H3    0.020
 C28  plan-2  C11   0.020
 C28  plan-2  C12   0.020
 C28  plan-2  N16   0.020
 C28  plan-2  O17   0.020
 C28  plan-2  C18   0.020
 C28  plan-2  HN16  0.020

