# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 21:21:34 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (3R)-4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-3-methyl-1,4-diazepan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N(CCCNC1=O)C(=O)C[C@H](N)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
 565  565  (3R)-4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-3-methyl-1,4-diazepan-2-one  ligand  44  24  .  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_565
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
 565  C1    C  CR16  0  -0.554   8.5685   0.6725  -0.7655
 565  C2    C  CR6   0   0.524   7.2647   0.9791  -0.4198
 565  C3    C  CR6   0  -0.027   6.2389   1.0990  -1.3443
 565  C4    C  CR16  0  -0.443   6.5741   0.9032  -2.6818
 565  C5    C  CR6   0   0.399   7.8644   0.5953  -3.0536
 565  C6    C  CR6   0   0.397   8.8591   0.4802  -2.0989
 565  F9    F  F     0  -0.309   8.1697   0.4014  -4.3426
 565  F10   F  F     0  -0.304   6.9925   1.1650   0.8803
 565  C11   C  CH2   0  -0.527   4.8378   1.4419  -0.9355
 565  C12   C  CH1   0  -0.069   4.5995   2.9518  -0.8045
 565  C15   C  CH2   0  -0.603   3.1945   3.2164  -0.2419
 565  C16   C  C     0   0.570   3.0476   2.7897   1.2061
 565  N19   N  NT    0  -0.456   1.8464   2.3286   1.6444
 565  N20   N  NH2   0  -0.777   4.8208   3.5825  -2.0930
 565  O22   O  O     0  -0.483   3.9956   2.9055   1.9683
 565  C25   C  CH2   0  -0.371   0.8211   1.8292   0.7367
 565  C26   C  CH2   0  -0.427   1.1380   0.4169   0.2671
 565  C27   C  CH2   0  -0.319   1.3516  -0.5675   1.4118
 565  N28   N  NH1   0  -0.621   2.5409  -0.3506   2.2278
 565  C29   C  C     0   0.550   2.7022   0.6105   3.1665
 565  C30   C  CH1   0  -0.232   1.7696   1.8115   3.0111
 565  C37   C  CH3   0  -0.652   1.9317   2.8565   4.1016
 565  O42   O  O     0  -0.475   3.5227   0.5214   4.0632
 565  F44   F  F     0  -0.303  10.1031   0.1758  -2.4771
 565  H1    H  HCR6  0   0.310   9.3401   0.5825  -0.0123
 565  H4    H  HCR6  0   0.288   5.8119   0.9841  -3.4459
 565  H111  H  HCH2  0   0.263   4.5863   0.9452   0.0032
 565  H112  H  HCH2  0   0.250   4.1471   1.0454  -1.6863
 565  H12   H  HCH1  0   0.244   5.3340   3.3625  -0.1090
 565  H151  H  HCH2  0   0.287   2.9967   4.2937  -0.2736
 565  H152  H  HCH2  0   0.252   2.4633   2.7553  -0.9064
 565  H201  H  HNH2  0   0.349   4.7181   4.5861  -2.0048
 565  H202  H  HNH2  0   0.336   4.1076   3.2872  -2.7506
 565  H251  H  HCH2  0   0.275   0.6914   2.5071  -0.1035
 565  H252  H  HCH2  0   0.268  -0.1283   1.8397   1.2748
 565  H261  H  HCH2  0   0.238   2.0195   0.4212  -0.3793
 565  H262  H  HCH2  0   0.249   0.3051   0.0498  -0.3368
 565  H271  H  HCH2  0   0.242   0.4550  -0.5954   2.0402
 565  H272  H  HCH2  0   0.275   1.4574  -1.5659   0.9920
 565  HN28  H  HNH1  0   0.392   3.1389  -1.1551   2.3438
 565  H30   H  HCH1  0   0.285   0.7509   1.4251   3.1165
 565  H371  H  HCH3  0   0.242   2.9446   3.2369   4.1805
 565  H372  H  HCH3  0   0.234   1.2575   3.6894   3.9041
 565  H373  H  HCH3  0   0.233   1.6501   2.4286   5.0634

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
 565  C1   C2    aromatic  1.383  0.020  1.383
 565  C1   C6    aromatic  1.378  0.020  1.378
 565  C1   H1    single    0.930  0.020  1.080
 565  C2   F10   single    1.341  0.020  1.341
 565  C2   C3    aromatic  1.386  0.020  1.386
 565  C3   C11   single    1.499  0.020  1.499
 565  C3   C4    aromatic  1.393  0.020  1.393
 565  C4   C5    aromatic  1.378  0.020  1.378
 565  C4   H4    single    0.930  0.020  1.080
 565  C5   C6    aromatic  1.383  0.020  1.383
 565  C5   F9    single    1.339  0.020  1.339
 565  C6   F44   single    1.335  0.020  1.335
 565  C11  C12   single    1.534  0.020  1.534
 565  C11  H111  single    0.970  0.020  1.090
 565  C11  H112  single    0.970  0.020  1.090
 565  C12  N20   single    1.452  0.020  1.452
 565  C12  C15   single    1.536  0.020  1.536
 565  C12  H12   single    0.970  0.020  1.090
 565  C15  C16   single    1.517  0.020  1.517
 565  C15  H151  single    0.970  0.020  1.090
 565  C15  H152  single    0.970  0.020  1.090
 565  C16  N19   single    1.359  0.020  1.359
 565  C16  O22   double    1.222  0.020  1.222
 565  N19  C25   single    1.458  0.020  1.458
 565  N19  C30   single    1.463  0.020  1.463
 565  N20  H201  single    0.890  0.020  1.040
 565  N20  H202  single    0.890  0.020  1.040
 565  C25  C26   single    1.522  0.020  1.522
 565  C25  H251  single    0.970  0.020  1.090
 565  C25  H252  single    0.970  0.020  1.090
 565  C26  C27   single    1.525  0.020  1.525
 565  C26  H261  single    0.970  0.020  1.090
 565  C26  H262  single    0.970  0.020  1.090
 565  C27  N28   single    1.459  0.020  1.459
 565  C27  H271  single    0.970  0.020  1.090
 565  C27  H272  single    0.970  0.020  1.090
 565  N28  C29   single    1.353  0.020  1.353
 565  N28  HN28  single    0.890  0.020  1.040
 565  C29  O42   double    1.219  0.020  1.219
 565  C29  C30   single    1.529  0.020  1.529
 565  C30  C37   single    1.519  0.020  1.519
 565  C30  H30   single    0.970  0.020  1.090
 565  C37  H371  single    0.970  0.020  1.090
 565  C37  H372  single    0.970  0.020  1.090
 565  C37  H373  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
 565  H1    C1   C6    120.77  3.000
 565  H1    C1   C2    121.10  3.000
 565  C6    C1   C2    118.13  3.000
 565  F10   C2   C3    118.97  3.000
 565  C3    C2   C1    123.37  3.000
 565  F10   C2   C1    117.66  3.000
 565  C11   C3   C4    121.26  3.000
 565  C4    C3   C2    116.76  3.000
 565  C11   C3   C2    121.98  3.000
 565  H4    C4   C5    119.06  3.000
 565  H4    C4   C3    119.87  3.000
 565  C5    C4   C3    121.06  3.000
 565  F9    C5   C6    119.24  3.000
 565  F9    C5   C4    120.38  3.000
 565  C6    C5   C4    120.38  3.000
 565  F44   C6   C5    119.55  3.000
 565  F44   C6   C1    120.15  3.000
 565  C5    C6   C1    120.29  3.000
 565  H112  C11  H111  106.25  3.000
 565  H112  C11  C12   108.49  3.000
 565  H111  C11  C12   109.79  3.000
 565  H112  C11  C3    108.66  3.000
 565  H111  C11  C3    110.23  3.000
 565  C12   C11  C3    113.17  3.000
 565  H12   C12  N20   107.42  3.000
 565  H12   C12  C15   108.49  3.000
 565  N20   C12  C15   112.93  3.000
 565  H12   C12  C11   108.67  3.000
 565  C15   C12  C11   110.05  3.000
 565  N20   C12  C11   109.16  3.000
 565  H152  C15  H151  106.08  3.000
 565  H152  C15  C16   113.44  3.000
 565  H151  C15  C16   106.66  3.000
 565  H152  C15  C12   108.50  3.000
 565  H151  C15  C12   108.89  3.000
 565  C16   C15  C12   112.94  3.000
 565  O22   C16  N19   121.10  3.000
 565  O22   C16  C15   119.58  3.000
 565  N19   C16  C15   119.27  3.000
 565  C30   N19  C25   115.07  3.000
 565  C30   N19  C16   117.87  3.000
 565  C25   N19  C16   122.48  3.000
 565  H202  N20  H201  105.88  3.000
 565  H202  N20  C12   109.99  3.000
 565  H201  N20  C12   109.75  3.000
 565  H252  C25  H251  105.74  3.000
 565  H252  C25  C26   110.01  3.000
 565  H251  C25  C26   111.41  3.000
 565  H252  C25  N19   107.55  3.000
 565  H251  C25  N19   110.58  3.000
 565  C26   C25  N19   111.33  3.000
 565  H262  C26  H261  106.81  3.000
 565  H262  C26  C27   107.76  3.000
 565  H261  C26  C27   109.48  3.000
 565  H262  C26  C25   108.89  3.000
 565  H261  C26  C25   110.29  3.000
 565  C27   C26  C25   113.37  3.000
 565  H272  C27  H271  106.11  3.000
 565  H272  C27  N28   105.84  3.000
 565  H271  C27  N28   110.50  3.000
 565  H272  C27  C26   108.44  3.000
 565  H271  C27  C26   109.43  3.000
 565  N28   C27  C26   115.99  3.000
 565  HN28  N28  C29   114.58  3.000
 565  HN28  N28  C27   115.40  3.000
 565  C29   N28  C27   126.22  3.000
 565  O42   C29  C30   122.89  3.000
 565  C30   C29  N28   114.51  3.000
 565  O42   C29  N28   122.60  3.000
 565  H30   C30  C37   105.84  3.000
 565  H30   C30  C29   106.29  3.000
 565  C37   C30  C29   113.73  3.000
 565  H30   C30  N19   105.28  3.000
 565  C37   C30  N19   114.95  3.000
 565  C29   C30  N19   109.91  3.000
 565  H373  C37  H372  107.47  3.000
 565  H373  C37  H371  108.35  3.000
 565  H372  C37  H371  108.84  3.000
 565  H373  C37  C30   109.63  3.000
 565  H372  C37  C30   109.25  3.000
 565  H371  C37  C30   113.15  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
 565  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 565  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 565  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 565  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 565  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 565  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 565  CONST_07  C11  C3   C2   C1    180.00   0.0  0
 565  CONST_08  F9   C5   C6   C1    180.00   0.0  0
 565  CONST_09  F44  C6   C1   C2    180.00   0.0  0
 565  CONST_10  F9   C5   C4   C3    180.00   0.0  0
 565  CONST_11  F10  C2   C3   C4    180.00   0.0  0
 565  CONST_12  F44  C6   C5   C4    180.00   0.0  0
 565  CONST_13  C11  C3   C4   C5    180.00   0.0  0
 565  CONST_14  F10  C2   C1   C6    180.00   0.0  0
 565  CONST_15  H4   C4   C3   C2    180.00   0.0  0
 565  CONST_16  H1   C1   C2   C3    180.00   0.0  0
 565  Var_01    C12  C11  C3   C2     85.20  30.0  2
 565  Var_02    N19  C16  C15  C12  -147.46  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
 565  chir_01  C12  C11  N20  C15  negativ
 565  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
 565  plan-1  C1    0.020
 565  plan-1  C2    0.020
 565  plan-1  C3    0.020
 565  plan-1  C4    0.020
 565  plan-1  C5    0.020
 565  plan-1  C6    0.020
 565  plan-1  F9    0.020
 565  plan-1  F10   0.020
 565  plan-1  C11   0.020
 565  plan-1  F44   0.020
 565  plan-1  H1    0.020
 565  plan-1  H4    0.020
 565  plan-2  C15   0.020
 565  plan-2  C16   0.020
 565  plan-2  N19   0.020
 565  plan-2  O22   0.020
 565  plan-2  C25   0.020
 565  plan-2  C30   0.020
 565  plan-3  C27   0.020
 565  plan-3  N28   0.020
 565  plan-3  C29   0.020
 565  plan-3  C30   0.020
 565  plan-3  O42   0.020
 565  plan-3  HN28  0.020

