# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 06:06:27 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: N~2~-[(3,5-difluorophenyl)acetyl]-N-[(3S,7R)-1-methyl-2-oxo-7-phenyl-2,3,4,7-tetrahydro-1H-azepin-3-yl]-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)Cc1cc(F)cc(F)c1)C(=O)N[C@H]2CC=C[C@@H](N(C)C2=O)c3ccccc3
#
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
 4L9  4L9  N~2~-[(3,5-difluorophenyl)acetyl]-N-[(3S,7R)-1-methyl-2-oxo-7-phenyl-2,3,4,7-tetrahydro-1H-azepin-3-yl]-L-alaninamide  ligand  57  32  .  2022-07-23  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_4L9
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
 4L9  C1   C  CH3   0  -0.642  -0.9279   2.2943   0.8329
 4L9  C2   C  CH1   0  -0.213  -0.7009   1.1294  -0.1347
 4L9  O5   O  O     0  -0.474   1.1366  -0.2341   0.6091
 4L9  N6   N  NH1   0  -0.644   1.5930   1.4515  -0.8158
 4L9  C7   C  CH1   0  -0.179   3.0200   1.3521  -0.6651
 4L9  C9   C  CH2   0  -0.514   3.6957   2.2204  -1.7221
 4L9  C10  C  C1    0  -0.200   5.1839   2.1149  -1.7759
 4L9  C11  C  C1    0  -0.233   5.9947   1.4757  -0.9402
 4L9  C12  C  CH1   0  -0.208   5.6297   0.7443   0.3297
 4L9  C15  C  C     0   0.563   3.4315   1.8113   0.7353
 4L9  C19  C  CR16  0  -0.283   5.6512  -1.4082  -1.0269
 4L9  C20  C  CR16  0  -0.245   5.3917  -2.7663  -1.1641
 4L9  C21  C  CR16  0  -0.267   4.7611  -3.4642  -0.1445
 4L9  C22  C  CR16  0  -0.242   4.3932  -2.7929   1.0144
 4L9  C27  C  CH2   0  -0.689  -3.4444  -1.4592   0.1721
 4L9  C30  C  CR6   0   0.557  -7.0529  -0.7819   0.9925
 4L9  C31  C  CR16  0  -0.570  -7.7249  -1.1762  -0.1486
 4L9  C32  C  CR6   0   0.555  -6.9522  -1.6748  -1.1793
 4L9  C33  C  CR16  0  -0.473  -5.5778  -1.7840  -1.1017
 4L9  C4   C  C     0   0.565   0.7601   0.7018  -0.0773
 4L9  N14  N  NT    0  -0.462   4.6564   1.4477   1.1623
 4L9  O16  O  O     0  -0.483   2.6835   2.5013   1.4093
 4L9  C17  C  CH3   0  -0.534   5.0880   1.9207   2.4672
 4L9  C18  C  CR6   0   0.089   5.2872  -0.7291   0.1321
 4L9  C23  C  CR16  0  -0.262   4.6552  -1.4378   1.1512
 4L9  N24  N  NH1   0  -0.637  -1.5238  -0.0100   0.1854
 4L9  C25  C  C     0   0.571  -2.7758  -0.1649  -0.2700
 4L9  O26  O  O     0  -0.484  -3.3302   0.6399  -1.0011
 4L9  C28  C  CR6   0   0.179  -4.9362  -1.3785   0.0630
 4L9  C29  C  CR16  0  -0.463  -5.6814  -0.8715   1.1230
 4L9  F35  F  F     0  -0.310  -7.7689  -0.2926   2.0138
 4L9  H1   H  HCH3  0   0.237  -0.3228   3.1574   0.5578
 4L9  H2   H  HCH3  0   0.248  -1.9741   2.5951   0.8097
 4L9  H3   H  HCH3  0   0.235  -0.6694   2.0075   1.8521
 4L9  H4   H  HCH1  0   0.279  -0.9402   1.4579  -1.1484
 4L9  H5   H  HNH1  0   0.406   1.2241   2.2696  -1.2757
 4L9  H6   H  HCH1  0   0.297   3.3116   0.3115  -0.8192
 4L9  H7   H  HCH2  0   0.278   3.3016   1.9342  -2.7018
 4L9  H8   H  HCH2  0   0.265   3.4097   3.2693  -1.5822
 4L9  H9   H  H     0   0.258   5.6370   2.6171  -2.6235
 4L9  H10  H  H     0   0.266   7.0533   1.4740  -1.1723
 4L9  H11  H  HCH1  0   0.300   6.5449   0.7464   0.9257
 4L9  H12  H  HCR6  0   0.251   6.1321  -0.8788  -1.8392
 4L9  H13  H  HCR6  0   0.255   5.6803  -3.2755  -2.0747
 4L9  H14  H  HCR6  0   0.255   4.5536  -4.5209  -0.2531
 4L9  H15  H  HCR6  0   0.254   3.8962  -3.3242   1.8159
 4L9  H16  H  HCH2  0   0.307  -3.0590  -2.2621  -0.4626
 4L9  H17  H  HCH2  0   0.290  -3.1479  -1.7051   1.1938
 4L9  H18  H  HCR6  0   0.302  -8.8011  -1.1015  -0.2294
 4L9  H19  H  HCR6  0   0.279  -5.0173  -2.1861  -1.9356
 4L9  H20  H  HCH3  0   0.253   4.2900   1.8184   3.1987
 4L9  H21  H  HCH3  0   0.251   5.9303   1.3213   2.8019
 4L9  H22  H  HCH3  0   0.245   5.3996   2.9668   2.4397
 4L9  H23  H  HCR6  0   0.250   4.3527  -0.9315   2.0590
 4L9  H24  H  HNH1  0   0.401  -1.1335  -0.6955   0.8144
 4L9  H25  H  HCR6  0   0.280  -5.1999  -0.5502   2.0379
 4L9  F34  F  F     0  -0.310  -7.5695  -2.0684  -2.3016

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
 4L9  F34  C32  single    1.340  0.020  1.340
 4L9  C32  C31  aromatic  1.381  0.020  1.381
 4L9  C32  C33  aromatic  1.381  0.020  1.381
 4L9  C31  C30  aromatic  1.382  0.020  1.382
 4L9  C33  C28  aromatic  1.390  0.020  1.390
 4L9  C30  F35  single    1.340  0.020  1.340
 4L9  C30  C29  aromatic  1.381  0.020  1.381
 4L9  C28  C29  aromatic  1.391  0.020  1.391
 4L9  C28  C27  single    1.498  0.020  1.498
 4L9  C27  C25  single    1.522  0.020  1.522
 4L9  C21  C20  aromatic  1.387  0.020  1.387
 4L9  C21  C22  aromatic  1.389  0.020  1.389
 4L9  C20  C19  aromatic  1.389  0.020  1.389
 4L9  C22  C23  aromatic  1.387  0.020  1.387
 4L9  N24  C25  single    1.341  0.020  1.341
 4L9  N24  C2   single    1.442  0.020  1.442
 4L9  C25  O26  double    1.220  0.020  1.220
 4L9  O5   C4   double    1.220  0.020  1.220
 4L9  C1   C2   single    1.531  0.020  1.531
 4L9  C19  C18  aromatic  1.392  0.020  1.392
 4L9  C2   C4   single    1.523  0.020  1.523
 4L9  C23  C18  aromatic  1.393  0.020  1.393
 4L9  C4   N6   single    1.342  0.020  1.342
 4L9  C18  C12  single    1.526  0.020  1.526
 4L9  N6   C7   single    1.438  0.020  1.438
 4L9  O16  C15  double    1.221  0.020  1.221
 4L9  C17  N14  single    1.454  0.020  1.454
 4L9  C15  N14  single    1.347  0.020  1.347
 4L9  C15  C7   single    1.530  0.020  1.530
 4L9  N14  C12  single    1.461  0.020  1.461
 4L9  C7   C9   single    1.526  0.020  1.526
 4L9  C12  C11  single    1.510  0.020  1.510
 4L9  C11  C10  double    1.328  0.020  1.328
 4L9  C9   C10  single    1.493  0.020  1.493
 4L9  C1   H1   single    0.970  0.020  1.090
 4L9  C1   H2   single    0.970  0.020  1.090
 4L9  C1   H3   single    0.970  0.020  1.090
 4L9  C2   H4   single    0.970  0.020  1.090
 4L9  N6   H5   single    0.860  0.020  1.020
 4L9  C7   H6   single    0.970  0.020  1.090
 4L9  C9   H7   single    0.970  0.020  1.090
 4L9  C9   H8   single    0.970  0.020  1.090
 4L9  C10  H9   single    0.930  0.020  1.080
 4L9  C11  H10  single    0.930  0.020  1.080
 4L9  C12  H11  single    0.970  0.020  1.090
 4L9  C19  H12  single    0.930  0.020  1.080
 4L9  C20  H13  single    0.930  0.020  1.080
 4L9  C21  H14  single    0.930  0.020  1.080
 4L9  C22  H15  single    0.930  0.020  1.080
 4L9  C27  H16  single    0.970  0.020  1.090
 4L9  C27  H17  single    0.970  0.020  1.090
 4L9  C31  H18  single    0.930  0.020  1.080
 4L9  C33  H19  single    0.930  0.020  1.080
 4L9  C17  H20  single    0.970  0.020  1.090
 4L9  C17  H21  single    0.970  0.020  1.090
 4L9  C17  H22  single    0.970  0.020  1.090
 4L9  C23  H23  single    0.930  0.020  1.080
 4L9  N24  H24  single    0.860  0.020  1.020
 4L9  C29  H25  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
 4L9  H3   C1   H2   108.69  3.000
 4L9  H3   C1   H1   108.23  3.000
 4L9  H2   C1   H1   108.03  3.000
 4L9  H3   C1   C2   110.83  3.000
 4L9  H2   C1   C2   109.83  3.000
 4L9  H1   C1   C2   111.15  3.000
 4L9  H4   C2   N24  108.59  3.000
 4L9  H4   C2   C4   109.25  3.000
 4L9  N24  C2   C4   108.50  3.000
 4L9  H4   C2   C1   108.98  3.000
 4L9  C4   C2   C1   109.39  3.000
 4L9  N24  C2   C1   112.11  3.000
 4L9  H5   N6   C4   118.50  3.000
 4L9  H5   N6   C7   117.82  3.000
 4L9  C4   N6   C7   121.30  3.000
 4L9  H6   C7   C15  110.08  3.000
 4L9  H6   C7   C9   109.05  3.000
 4L9  C15  C7   C9   110.13  3.000
 4L9  H6   C7   N6   108.43  3.000
 4L9  C9   C7   N6   109.12  3.000
 4L9  C15  C7   N6   109.99  3.000
 4L9  H8   C9   H7   105.69  3.000
 4L9  H8   C9   C10  109.41  3.000
 4L9  H7   C9   C10  107.96  3.000
 4L9  H8   C9   C7   109.91  3.000
 4L9  H7   C9   C7   108.18  3.000
 4L9  C10  C9   C7   115.23  3.000
 4L9  H9   C10  C11  117.36  3.000
 4L9  H9   C10  C9   114.33  3.000
 4L9  C11  C10  C9   128.30  3.000
 4L9  H10  C11  C12  114.54  3.000
 4L9  H10  C11  C10  117.54  3.000
 4L9  C12  C11  C10  127.92  3.000
 4L9  H11  C12  C18  105.11  3.000
 4L9  H11  C12  N14  104.26  3.000
 4L9  C18  C12  N14  112.90  3.000
 4L9  H11  C12  C11  104.80  3.000
 4L9  N14  C12  C11  114.01  3.000
 4L9  C18  C12  C11  114.40  3.000
 4L9  O16  C15  N14  122.32  3.000
 4L9  N14  C15  C7   116.97  3.000
 4L9  O16  C15  C7   120.68  3.000
 4L9  H12  C19  C18  120.17  3.000
 4L9  H12  C19  C20  119.15  3.000
 4L9  C18  C19  C20  120.68  3.000
 4L9  H13  C20  C21  120.19  3.000
 4L9  H13  C20  C19  119.54  3.000
 4L9  C21  C20  C19  120.27  3.000
 4L9  H14  C21  C22  120.32  3.000
 4L9  H14  C21  C20  120.31  3.000
 4L9  C22  C21  C20  119.37  3.000
 4L9  H15  C22  C23  119.56  3.000
 4L9  H15  C22  C21  120.15  3.000
 4L9  C23  C22  C21  120.30  3.000
 4L9  H17  C27  H16  106.38  3.000
 4L9  H17  C27  C28  110.53  3.000
 4L9  H16  C27  C28  110.38  3.000
 4L9  H17  C27  C25  110.12  3.000
 4L9  H16  C27  C25  107.51  3.000
 4L9  C28  C27  C25  111.74  3.000
 4L9  F35  C30  C29  118.85  3.000
 4L9  C29  C30  C31  122.87  3.000
 4L9  F35  C30  C31  118.28  3.000
 4L9  H18  C31  C32  121.71  3.000
 4L9  H18  C31  C30  121.72  3.000
 4L9  C32  C31  C30  116.56  3.000
 4L9  F34  C32  C33  118.84  3.000
 4L9  C33  C32  C31  122.91  3.000
 4L9  F34  C32  C31  118.25  3.000
 4L9  H19  C33  C28  121.00  3.000
 4L9  H19  C33  C32  120.10  3.000
 4L9  C28  C33  C32  118.90  3.000
 4L9  N6   C4   O5   123.13  3.000
 4L9  N6   C4   C2   114.69  3.000
 4L9  O5   C4   C2   122.17  3.000
 4L9  C17  N14  C15  117.82  3.000
 4L9  C15  N14  C12  123.71  3.000
 4L9  C17  N14  C12  118.05  3.000
 4L9  H22  C17  H21  108.36  3.000
 4L9  H22  C17  H20  108.45  3.000
 4L9  H21  C17  H20  108.04  3.000
 4L9  H22  C17  N14  111.96  3.000
 4L9  H21  C17  N14  109.10  3.000
 4L9  H20  C17  N14  110.82  3.000
 4L9  C23  C18  C19  118.67  3.000
 4L9  C23  C18  C12  119.90  3.000
 4L9  C19  C18  C12  121.36  3.000
 4L9  H23  C23  C18  120.16  3.000
 4L9  H23  C23  C22  119.13  3.000
 4L9  C18  C23  C22  120.70  3.000
 4L9  H24  N24  C25  119.63  3.000
 4L9  H24  N24  C2   117.04  3.000
 4L9  C25  N24  C2   123.28  3.000
 4L9  O26  C25  N24  123.46  3.000
 4L9  O26  C25  C27  122.35  3.000
 4L9  N24  C25  C27  114.18  3.000
 4L9  C29  C28  C33  119.83  3.000
 4L9  C29  C28  C27  119.84  3.000
 4L9  C33  C28  C27  120.32  3.000
 4L9  H25  C29  C28  120.91  3.000
 4L9  H25  C29  C30  120.16  3.000
 4L9  C28  C29  C30  118.93  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
 4L9  CONST_01  C22  C21  C20  C19    0.00   0.0  0
 4L9  CONST_02  C22  C23  C18  C19    0.00   0.0  0
 4L9  CONST_03  C23  C22  C21  C20    0.00   0.0  0
 4L9  CONST_04  C23  C18  C19  C20    0.00   0.0  0
 4L9  CONST_05  C18  C19  C20  C21    0.00   0.0  0
 4L9  CONST_06  C18  C23  C22  C21    0.00   0.0  0
 4L9  CONST_07  C33  C32  C31  C30    0.00   0.0  0
 4L9  CONST_08  C33  C28  C29  C30    0.00   0.0  0
 4L9  CONST_09  C28  C33  C32  C31    0.00   0.0  0
 4L9  CONST_10  C28  C29  C30  C31    0.00   0.0  0
 4L9  CONST_11  C29  C30  C31  C32    0.00   0.0  0
 4L9  CONST_12  C29  C28  C33  C32    0.00   0.0  0
 4L9  CONST_13  C20  C19  C18  C12  180.00   0.0  0
 4L9  CONST_14  C22  C23  C18  C12  180.00   0.0  0
 4L9  CONST_15  C32  C33  C28  C27  180.00   0.0  0
 4L9  CONST_16  C30  C29  C28  C27  180.00   0.0  0
 4L9  CONST_17  F34  C32  C31  C30  180.00   0.0  0
 4L9  CONST_18  F35  C30  C31  C32  180.00   0.0  0
 4L9  CONST_19  F34  C32  C33  C28  180.00   0.0  0
 4L9  CONST_20  F35  C30  C29  C28  180.00   0.0  0
 4L9  CONST_21  H12  C19  C18  C12    0.00   0.0  0
 4L9  CONST_22  H23  C23  C18  C12    0.00   0.0  0
 4L9  CONST_23  H14  C21  C20  C19  180.00   0.0  0
 4L9  CONST_24  H15  C22  C21  C20  180.00   0.0  0
 4L9  CONST_25  H13  C20  C21  C22  180.00   0.0  0
 4L9  CONST_26  H19  C33  C32  C31  180.00   0.0  0
 4L9  CONST_27  H25  C29  C30  C31  180.00   0.0  0
 4L9  CONST_28  H18  C31  C32  C33  180.00   0.0  0
 4L9  CONST_29  C7   N6   C4   C2   180.00   0.0  0
 4L9  CONST_30  C7   N6   C4   O5     0.00   0.0  0
 4L9  CONST_31  C27  C25  N24  C2   180.00   0.0  0
 4L9  CONST_32  O26  C25  N24  C2     0.00   0.0  0
 4L9  CONST_33  H5   N6   C4   C2     0.00   0.0  0
 4L9  CONST_34  H24  N24  C25  C27    0.00   0.0  0
 4L9  Var_01    C25  C27  C28  C33   91.45  30.0  2
 4L9  Var_02    C28  C27  C25  N24  160.03  30.0  2

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
 4L9  chir_01  C2   N24  C1   C4   negativ
 4L9  chir_02  C7   N6   C15  C9   positiv
 4L9  chir_03  C12  N14  C11  C18  positiv

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
 4L9  plan-1  C12  0.020
 4L9  plan-1  C19  0.020
 4L9  plan-1  C20  0.020
 4L9  plan-1  C21  0.020
 4L9  plan-1  C22  0.020
 4L9  plan-1  C18  0.020
 4L9  plan-1  C23  0.020
 4L9  plan-1  H12  0.020
 4L9  plan-1  H13  0.020
 4L9  plan-1  H14  0.020
 4L9  plan-1  H15  0.020
 4L9  plan-1  H23  0.020
 4L9  plan-2  C27  0.020
 4L9  plan-2  C30  0.020
 4L9  plan-2  C31  0.020
 4L9  plan-2  C32  0.020
 4L9  plan-2  C33  0.020
 4L9  plan-2  C28  0.020
 4L9  plan-2  C29  0.020
 4L9  plan-2  F35  0.020
 4L9  plan-2  H18  0.020
 4L9  plan-2  H19  0.020
 4L9  plan-2  H25  0.020
 4L9  plan-2  F34  0.020
 4L9  plan-3  C7   0.020
 4L9  plan-3  C12  0.020
 4L9  plan-3  C15  0.020
 4L9  plan-3  N14  0.020
 4L9  plan-3  O16  0.020
 4L9  plan-3  C17  0.020
 4L9  plan-4  C2   0.020
 4L9  plan-4  O5   0.020
 4L9  plan-4  N6   0.020
 4L9  plan-4  C7   0.020
 4L9  plan-4  C4   0.020
 4L9  plan-4  H5   0.020
 4L9  plan-5  C2   0.020
 4L9  plan-5  C27  0.020
 4L9  plan-5  N24  0.020
 4L9  plan-5  C25  0.020
 4L9  plan-5  O26  0.020
 4L9  plan-5  H24  0.020

