# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 05:57:02 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (3R)-4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-3-(2,2,2-trifluoroethyl)-1,4-diazepan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)N1CCCNC(=O)[C@H]1CC(F)(F)F)Cc2cc(F)c(F)cc2F
#
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
 872  872  (3R)-4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-3-(2,2,2-trifluoroethyl)-1,4-diazepan-2-one  ligand  47  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_872
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
 872  C1    C  CR16  0  -0.551  2.9552   1.0836  -4.6177
 872  C2    C  CR6   0   0.523  3.0616   2.2924  -3.9539
 872  C3    C  CR6   0  -0.078  4.2628   2.8024  -3.4864
 872  C4    C  CR16  0  -0.438  5.4022   2.0318  -3.7148
 872  C5    C  CR6   0   0.406  5.3243   0.8245  -4.3729
 872  C6    C  CR6   0   0.401  4.1040   0.3515  -4.8236
 872  F9    F  F     0  -0.306  6.4262   0.0984  -4.5890
 872  F10   F  F     0  -0.307  1.9332   2.9897  -3.7513
 872  C11   C  CH2   0  -0.505  4.3662   4.1058  -2.7483
 872  C12   C  CH1   0  -0.080  4.4716   3.9487  -1.2235
 872  C15   C  CH2   0  -0.605  3.2595   3.1979  -0.6678
 872  C16   C  C     0   0.602  3.3830   2.8490   0.7999
 872  N19   N  NT    0  -0.465  2.2972   2.2855   1.3949
 872  N20   N  NH2   0  -0.792  4.6809   5.2693  -0.6554
 872  O22   O  O     0  -0.481  4.4048   3.0686   1.4318
 872  C25   C  CH2   0  -0.365  1.2741   1.5913   0.6248
 872  C26   C  CH2   0  -0.428  1.6982   0.1676   0.2931
 872  C27   C  CH2   0  -0.321  2.0384  -0.6661   1.5221
 872  N28   N  NH1   0  -0.625  3.2554  -0.2844   2.2283
 872  C29   C  C     0   0.577  3.4374   0.8043   3.0005
 872  C30   C  CH1   0  -0.268  2.3936   1.9065   2.7976
 872  C37   C  CH2   0  -0.664  2.6065   3.0623   3.7716
 872  O39   O  O     0  -0.475  4.3541   0.9039   3.7982
 872  F41   F  F     0  -0.301  4.0473  -0.8193  -5.4611
 872  C42   C  CT    0   1.015  1.6226   4.1873   3.5914
 872  F45   F  F     0  -0.306  1.8376   4.9119   2.4837
 872  F46   F  F     0  -0.312  1.6834   5.0485   4.6201
 872  F47   F  F     0  -0.315  0.3509   3.7577   3.5254
 872  H1    H  HCR6  0   0.314  1.9974   0.7198  -4.9661
 872  H4    H  HCR6  0   0.297  6.3685   2.3856  -3.3769
 872  H111  H  HCH2  0   0.253  3.5187   4.7527  -2.9861
 872  H112  H  HCH2  0   0.268  5.2607   4.6312  -3.0875
 872  H12   H  HCH1  0   0.236  5.3681   3.3597  -1.0104
 872  H151  H  HCH2  0   0.274  2.3546   3.7930  -0.8291
 872  H152  H  HCH2  0   0.265  3.1137   2.2664  -1.2231
 872  H201  H  HNH2  0   0.350  4.8612   5.1867   0.3363
 872  H202  H  HNH2  0   0.337  3.8354   5.8216  -0.7471
 872  H251  H  HCH2  0   0.280  1.0391   2.1467  -0.2804
 872  H252  H  HCH2  0   0.270  0.3555   1.5814   1.2148
 872  H261  H  HCH2  0   0.237  2.5531   0.1712  -0.3890
 872  H262  H  HCH2  0   0.255  0.8776  -0.3274  -0.2311
 872  H271  H  HCH2  0   0.246  1.1856  -0.6756   2.2088
 872  H272  H  HCH2  0   0.280  2.1884  -1.6975   1.2103
 872  HN28  H  HNH1  0   0.399  3.9327  -1.0195   2.3671
 872  H30   H  HCH1  0   0.309  1.4269   1.4601   3.0499
 872  H371  H  HCH2  0   0.297  3.6143   3.4677   3.7121
 872  H372  H  HCH2  0   0.297  2.4760   2.6735   4.7835

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
 872  C1   C2    aromatic  1.383  0.020  1.383
 872  C1   C6    aromatic  1.378  0.020  1.378
 872  C1   H1    single    0.930  0.020  1.080
 872  C2   F10   single    1.342  0.020  1.342
 872  C2   C3    aromatic  1.386  0.020  1.386
 872  C3   C11   single    1.501  0.020  1.501
 872  C3   C4    aromatic  1.394  0.020  1.394
 872  C4   C5    aromatic  1.377  0.020  1.377
 872  C4   H4    single    0.930  0.020  1.080
 872  C5   C6    aromatic  1.384  0.020  1.384
 872  C5   F9    single    1.337  0.020  1.337
 872  C6   F41   single    1.334  0.020  1.334
 872  C11  C12   single    1.536  0.020  1.536
 872  C11  H111  single    0.970  0.020  1.090
 872  C11  H112  single    0.970  0.020  1.090
 872  C12  C15   single    1.530  0.020  1.530
 872  C12  N20   single    1.453  0.020  1.453
 872  C12  H12   single    0.970  0.020  1.090
 872  C15  C16   single    1.514  0.020  1.514
 872  C15  H151  single    0.970  0.020  1.090
 872  C15  H152  single    0.970  0.020  1.090
 872  C16  N19   single    1.360  0.020  1.360
 872  C16  O22   double    1.221  0.020  1.221
 872  N19  C25   single    1.457  0.020  1.457
 872  N19  C30   single    1.456  0.020  1.456
 872  N20  H201  single    0.890  0.020  1.040
 872  N20  H202  single    0.890  0.020  1.040
 872  C25  C26   single    1.522  0.020  1.522
 872  C25  H251  single    0.970  0.020  1.090
 872  C25  H252  single    0.970  0.020  1.090
 872  C26  C27   single    1.524  0.020  1.524
 872  C26  H261  single    0.970  0.020  1.090
 872  C26  H262  single    0.970  0.020  1.090
 872  C27  N28   single    1.458  0.020  1.458
 872  C27  H271  single    0.970  0.020  1.090
 872  C27  H272  single    0.970  0.020  1.090
 872  N28  C29   single    1.347  0.020  1.347
 872  N28  HN28  single    0.860  0.020  1.020
 872  C29  C30   single    1.532  0.020  1.532
 872  C29  O39   double    1.219  0.020  1.219
 872  C30  C37   single    1.526  0.020  1.526
 872  C30  H30   single    0.970  0.020  1.090
 872  C37  C42   single    1.505  0.020  1.505
 872  C37  H371  single    0.970  0.020  1.090
 872  C37  H372  single    0.970  0.020  1.090
 872  C42  F47   single    1.344  0.020  1.344
 872  C42  F45   single    1.341  0.020  1.341
 872  C42  F46   single    1.343  0.020  1.343

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
 872  H1    C1   C6    120.75  3.000
 872  H1    C1   C2    121.09  3.000
 872  C6    C1   C2    118.16  3.000
 872  F10   C2   C3    119.12  3.000
 872  C3    C2   C1    123.37  3.000
 872  F10   C2   C1    117.51  3.000
 872  C11   C3   C4    120.27  3.000
 872  C4    C3   C2    116.71  3.000
 872  C11   C3   C2    123.01  3.000
 872  H4    C4   C5    119.07  3.000
 872  H4    C4   C3    119.83  3.000
 872  C5    C4   C3    121.10  3.000
 872  F9    C5   C6    119.23  3.000
 872  F9    C5   C4    120.44  3.000
 872  C6    C5   C4    120.33  3.000
 872  F41   C6   C5    119.53  3.000
 872  F41   C6   C1    120.15  3.000
 872  C5    C6   C1    120.32  3.000
 872  H112  C11  H111  106.44  3.000
 872  H112  C11  C12   107.54  3.000
 872  H111  C11  C12   109.25  3.000
 872  H112  C11  C3    108.76  3.000
 872  H111  C11  C3    110.71  3.000
 872  C12   C11  C3    113.82  3.000
 872  H12   C12  N20   107.17  3.000
 872  H12   C12  C15   108.32  3.000
 872  N20   C12  C15   114.71  3.000
 872  H12   C12  C11   107.74  3.000
 872  N20   C12  C11   107.76  3.000
 872  C15   C12  C11   110.87  3.000
 872  H152  C15  H151  106.13  3.000
 872  H152  C15  C16   107.86  3.000
 872  H151  C15  C16   109.61  3.000
 872  H152  C15  C12   109.81  3.000
 872  H151  C15  C12   109.54  3.000
 872  C16   C15  C12   113.62  3.000
 872  O22   C16  N19   121.06  3.000
 872  O22   C16  C15   121.91  3.000
 872  N19   C16  C15   117.03  3.000
 872  C30   N19  C25   115.58  3.000
 872  C30   N19  C16   118.45  3.000
 872  C25   N19  C16   121.79  3.000
 872  H202  N20  H201  106.37  3.000
 872  H202  N20  C12   109.85  3.000
 872  H201  N20  C12   109.56  3.000
 872  H252  C25  H251  105.82  3.000
 872  H252  C25  C26   110.11  3.000
 872  H251  C25  C26   110.88  3.000
 872  H252  C25  N19   108.03  3.000
 872  H251  C25  N19   110.39  3.000
 872  C26   C25  N19   111.43  3.000
 872  H262  C26  H261  106.83  3.000
 872  H262  C26  C27   107.87  3.000
 872  H261  C26  C27   109.29  3.000
 872  H262  C26  C25   108.61  3.000
 872  H261  C26  C25   110.53  3.000
 872  C27   C26  C25   113.47  3.000
 872  H272  C27  H271  106.19  3.000
 872  H272  C27  N28   105.78  3.000
 872  H271  C27  N28   110.40  3.000
 872  H272  C27  C26   108.57  3.000
 872  H271  C27  C26   109.68  3.000
 872  N28   C27  C26   115.71  3.000
 872  HN28  N28  C29   114.78  3.000
 872  HN28  N28  C27   115.86  3.000
 872  C29   N28  C27   127.02  3.000
 872  O39   C29  C30   122.70  3.000
 872  O39   C29  N28   122.87  3.000
 872  C30   C29  N28   114.43  3.000
 872  H30   C30  C37   106.56  3.000
 872  H30   C30  C29   106.14  3.000
 872  C37   C30  C29   111.42  3.000
 872  H30   C30  N19   105.65  3.000
 872  C37   C30  N19   115.27  3.000
 872  C29   C30  N19   111.10  3.000
 872  H372  C37  H371  107.10  3.000
 872  H372  C37  C42   107.40  3.000
 872  H371  C37  C42   108.69  3.000
 872  H372  C37  C30   107.76  3.000
 872  H371  C37  C30   112.12  3.000
 872  C42   C37  C30   113.47  3.000
 872  F47   C42  F46   106.59  3.000
 872  F46   C42  F45   106.20  3.000
 872  F47   C42  F45   106.49  3.000
 872  F46   C42  C37   110.97  3.000
 872  F45   C42  C37   113.45  3.000
 872  F47   C42  C37   112.67  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
 872  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 872  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 872  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 872  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 872  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 872  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 872  CONST_07  C11  C3   C2   C1   180.00   0.0  0
 872  CONST_08  F9   C5   C6   C1   180.00   0.0  0
 872  CONST_09  F41  C6   C1   C2   180.00   0.0  0
 872  CONST_10  F9   C5   C4   C3   180.00   0.0  0
 872  CONST_11  F10  C2   C3   C4   180.00   0.0  0
 872  CONST_12  F41  C6   C5   C4   180.00   0.0  0
 872  CONST_13  C11  C3   C4   C5   180.00   0.0  0
 872  CONST_14  F10  C2   C1   C6   180.00   0.0  0
 872  CONST_15  H4   C4   C3   C2   180.00   0.0  0
 872  CONST_16  H1   C1   C2   C3   180.00   0.0  0
 872  Var_01    C12  C11  C3   C2   100.25  30.0  2
 872  Var_02    N19  C16  C15  C12  174.39  30.0  3
 872  Var_03    F47  C42  C37  C30   48.67  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
 872  chir_01  C12  C11  C15  N20  positiv
 872  chir_02  C30  N19  C29  C37  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
 872  plan-1  C1    0.020
 872  plan-1  C2    0.020
 872  plan-1  C3    0.020
 872  plan-1  C4    0.020
 872  plan-1  C5    0.020
 872  plan-1  C6    0.020
 872  plan-1  F9    0.020
 872  plan-1  F10   0.020
 872  plan-1  C11   0.020
 872  plan-1  F41   0.020
 872  plan-1  H1    0.020
 872  plan-1  H4    0.020
 872  plan-2  C15   0.020
 872  plan-2  C16   0.020
 872  plan-2  N19   0.020
 872  plan-2  O22   0.020
 872  plan-2  C25   0.020
 872  plan-2  C30   0.020
 872  plan-3  C27   0.020
 872  plan-3  N28   0.020
 872  plan-3  C29   0.020
 872  plan-3  C30   0.020
 872  plan-3  O39   0.020
 872  plan-3  HN28  0.020

