# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 22:54:32 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (3S)-5-(cyclobutylmethyl)-3-(2,4-dichlorophenyl)-2,3,4,5-tetrahydro-1,5-benzoxazepine-7-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2OC[C@H](CN(CC3CCC3)c2c1)c4ccc(Cl)cc4Cl
#
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
 LOJ  LOJ  '(3S)-5-(cyclobutylmethyl)-3-(2,4-dichlorophenyl)-2,3,4,5-tetrahydro-1,5-benzoxazepine-7-carboxylic acid'  ligand  47  27  .  2022-07-25  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_LOJ
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
 LOJ  C1   C   CR16   0  -0.144   4.6252   0.1436   0.0163
 LOJ  C2   C   CR6    0  -0.069   4.8414  -1.0572  -0.6358
 LOJ  C3   C   CR16   0  -0.181   3.7974  -1.9334  -0.8789
 LOJ  C7   C   CR16   0  -0.390  -3.4714  -0.5450  -0.5497
 LOJ  C8   C   CR6    0  -0.097  -4.4111  -1.4800  -0.1266
 LOJ  C9   C   CR16   0  -0.316  -4.1499  -2.2131   1.0255
 LOJ  C10  C   CR16   0  -0.338  -2.9737  -2.0074   1.7307
 LOJ  C11  C   CH2    0  -0.155   0.3070  -1.1619   1.5632
 LOJ  C12  C   CH2    0  -0.286  -0.0378   0.1453  -0.5839
 LOJ  C13  C   CR6    0   0.295  -2.2888  -0.3062   0.1502
 LOJ  C14  C   CR6    0   0.305  -2.0532  -1.0570   1.3134
 LOJ  C15  C   CH1    0  -0.367   0.8493  -0.0711   0.6461
 LOJ  C19  C   CH1    0  -0.248  -0.9780   3.0014  -0.8805
 LOJ  C20  C   CH2    0  -0.431  -1.5609   4.3534  -1.3405
 LOJ  C21  C   CH2    0  -0.455  -0.9313   4.9964  -0.0892
 LOJ  N1   N   NT     0  -0.498  -1.3539   0.6560  -0.2481
 LOJ  O1   O   O2     0  -0.495  -0.9630  -0.8293   2.0975
 LOJ  O2   O   O      0  -0.594  -5.8394  -1.0076  -1.9494
 LOJ  O3   O   OC    -1  -0.597  -6.4740  -2.5675  -0.4925
 LOJ  C17  C   CH2    0  -0.299  -1.8302   1.7621  -1.0600
 LOJ  C18  C   CH2    0  -0.425  -0.8293   3.5897   0.5332
 LOJ  C4   C   CR16   0  -0.337   2.5269  -1.5900  -0.4503
 LOJ  C5   C   CR6    0   0.261   2.2563  -0.3957   0.2192
 LOJ  C6   C   CR6    0  -0.156   3.3387   0.4575   0.4312
 LOJ  CL1  CL  CL     0  -0.117   3.1289   1.9824   1.2331
 LOJ  CL2  CL  CL     0  -0.116   6.4419  -1.4609  -1.1524
 LOJ  H1   H   HCR6   0   0.300   5.4427   0.8269   0.2004
 LOJ  H2   H   HCR6   0   0.286   3.9659  -2.8686  -1.3945
 LOJ  H3   H   HCR6   0   0.256  -3.6745   0.0063  -1.4586
 LOJ  H4   H   HCR6   0   0.239  -4.8637  -2.9470   1.3741
 LOJ  H5   H   HCR6   0   0.252  -2.7728  -2.5673   2.6363
 LOJ  H6   H   HCH2   0   0.217   0.2552  -2.1237   1.0404
 LOJ  H7   H   HCH2   0   0.252   0.9725  -1.2856   2.4185
 LOJ  H8   H   HCH2   0   0.259   0.4592   0.8645  -1.2345
 LOJ  H9   H   HCH2   0   0.232  -0.1076  -0.7874  -1.1613
 LOJ  H10  H   HCH1   0   0.264   0.8458   0.8606   1.2140
 LOJ  H11  H   HCH1   0   0.237   0.0116   2.8682  -1.3280
 LOJ  H12  H   HCH2   0   0.228  -1.2629   4.7322  -2.3185
 LOJ  H13  H   HCH2   0   0.219  -2.6522   4.3549  -1.2852
 LOJ  H14  H   HCH2   0   0.224   0.0524   5.4173  -0.3028
 LOJ  H15  H   HCH2   0   0.226  -1.5193   5.7446   0.4426
 LOJ  H17  H   HCH2   0   0.234  -2.8448   1.9982  -0.7303
 LOJ  H18  H   HCH2   0   0.213  -1.8973   1.5087  -2.1296
 LOJ  H19  H   HCH2   0   0.218  -1.6965   3.3580   1.1555
 LOJ  H20  H   HCH2   0   0.222   0.0742   3.3401   1.0902
 LOJ  H21  H   HCR6   0   0.276   1.7192  -2.2823  -0.6520
 LOJ  C16  C   C      0   0.396  -5.6867  -1.7036  -0.9263

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
 LOJ  CL2  C2   single    1.730  0.020  1.730
 LOJ  C3   C2   aromatic  1.384  0.020  1.384
 LOJ  C3   C4   aromatic  1.384  0.020  1.384
 LOJ  C2   C1   aromatic  1.383  0.020  1.383
 LOJ  C4   C5   aromatic  1.396  0.020  1.396
 LOJ  C1   C6   aromatic  1.388  0.020  1.388
 LOJ  O1   C11  single    1.417  0.020  1.417
 LOJ  O1   C14  single    1.362  0.020  1.362
 LOJ  C5   C6   aromatic  1.394  0.020  1.394
 LOJ  C5   C15  single    1.506  0.020  1.506
 LOJ  C6   CL1  single    1.736  0.020  1.736
 LOJ  C11  C15  single    1.525  0.020  1.525
 LOJ  C10  C14  aromatic  1.387  0.020  1.387
 LOJ  C10  C9   aromatic  1.387  0.020  1.387
 LOJ  C14  C13  aromatic  1.404  0.020  1.404
 LOJ  C15  C12  single    1.532  0.020  1.532
 LOJ  C9   C8   aromatic  1.390  0.020  1.390
 LOJ  C12  N1   single    1.451  0.020  1.451
 LOJ  C13  N1   single    1.399  0.020  1.399
 LOJ  C13  C7   aromatic  1.395  0.020  1.395
 LOJ  N1   C17  single    1.452  0.020  1.452
 LOJ  C8   C7   aromatic  1.392  0.020  1.392
 LOJ  C8   C16  single    1.522  0.020  1.522
 LOJ  O2   C16  deloc     1.247  0.020  1.247
 LOJ  C16  O3   deloc     1.247  0.020  1.247
 LOJ  C18  C19  single    1.538  0.020  1.538
 LOJ  C18  C21  single    1.542  0.020  1.542
 LOJ  C17  C19  single    1.515  0.020  1.515
 LOJ  C19  C20  single    1.542  0.020  1.542
 LOJ  C21  C20  single    1.541  0.020  1.541
 LOJ  C1   H1   single    0.930  0.020  1.080
 LOJ  C3   H2   single    0.930  0.020  1.080
 LOJ  C7   H3   single    0.930  0.020  1.080
 LOJ  C9   H4   single    0.930  0.020  1.080
 LOJ  C10  H5   single    0.930  0.020  1.080
 LOJ  C11  H6   single    0.970  0.020  1.090
 LOJ  C11  H7   single    0.970  0.020  1.090
 LOJ  C12  H8   single    0.970  0.020  1.090
 LOJ  C12  H9   single    0.970  0.020  1.090
 LOJ  C15  H10  single    0.970  0.020  1.090
 LOJ  C19  H11  single    0.970  0.020  1.090
 LOJ  C20  H12  single    0.970  0.020  1.090
 LOJ  C20  H13  single    0.970  0.020  1.090
 LOJ  C21  H14  single    0.970  0.020  1.090
 LOJ  C21  H15  single    0.970  0.020  1.090
 LOJ  C17  H17  single    0.970  0.020  1.090
 LOJ  C17  H18  single    0.970  0.020  1.090
 LOJ  C18  H19  single    0.970  0.020  1.090
 LOJ  C18  H20  single    0.970  0.020  1.090
 LOJ  C4   H21  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
 LOJ  H1   C1   C6   120.47  3.000
 LOJ  H1   C1   C2   120.71  3.000
 LOJ  C6   C1   C2   118.82  3.000
 LOJ  CL2  C2   C3   119.84  3.000
 LOJ  C3   C2   C1   120.95  3.000
 LOJ  CL2  C2   C1   119.21  3.000
 LOJ  H2   C3   C4   120.35  3.000
 LOJ  H2   C3   C2   120.91  3.000
 LOJ  C4   C3   C2   118.74  3.000
 LOJ  H3   C7   C13  119.56  3.000
 LOJ  H3   C7   C8   118.10  3.000
 LOJ  C13  C7   C8   122.34  3.000
 LOJ  C16  C8   C9   121.02  3.000
 LOJ  C16  C8   C7   120.32  3.000
 LOJ  C9   C8   C7   118.65  3.000
 LOJ  H4   C9   C10  119.77  3.000
 LOJ  H4   C9   C8   120.06  3.000
 LOJ  C10  C9   C8   120.17  3.000
 LOJ  H5   C10  C14  118.84  3.000
 LOJ  H5   C10  C9   120.38  3.000
 LOJ  C14  C10  C9   120.76  3.000
 LOJ  H7   C11  H6   107.66  3.000
 LOJ  H7   C11  O1   106.13  3.000
 LOJ  H6   C11  O1   110.09  3.000
 LOJ  H7   C11  C15  109.62  3.000
 LOJ  H6   C11  C15  110.95  3.000
 LOJ  O1   C11  C15  112.19  3.000
 LOJ  H9   C12  H8   105.99  3.000
 LOJ  H9   C12  N1   111.26  3.000
 LOJ  H8   C12  N1   108.64  3.000
 LOJ  H9   C12  C15  109.80  3.000
 LOJ  H8   C12  C15  107.96  3.000
 LOJ  N1   C12  C15  112.90  3.000
 LOJ  N1   C13  C14  119.42  3.000
 LOJ  N1   C13  C7   122.77  3.000
 LOJ  C14  C13  C7   117.80  3.000
 LOJ  O1   C14  C13  121.45  3.000
 LOJ  C13  C14  C10  120.27  3.000
 LOJ  O1   C14  C10  118.20  3.000
 LOJ  H10  C15  C5   109.55  3.000
 LOJ  H10  C15  C12  107.18  3.000
 LOJ  C5   C15  C12  110.12  3.000
 LOJ  H10  C15  C11  107.26  3.000
 LOJ  C12  C15  C11  112.21  3.000
 LOJ  C5   C15  C11  110.41  3.000
 LOJ  H11  C19  C18  109.57  3.000
 LOJ  H11  C19  C17  111.14  3.000
 LOJ  C18  C19  C17  118.43  3.000
 LOJ  H11  C19  C20  109.06  3.000
 LOJ  C17  C19  C20  117.98  3.000
 LOJ  C18  C19  C20   88.59  3.000
 LOJ  H13  C20  H12  108.53  3.000
 LOJ  H13  C20  C21  111.49  3.000
 LOJ  H12  C20  C21  118.14  3.000
 LOJ  H13  C20  C19  111.32  3.000
 LOJ  H12  C20  C19  117.95  3.000
 LOJ  C21  C20  C19   88.23  3.000
 LOJ  H15  C21  H14  108.48  3.000
 LOJ  H15  C21  C18  117.71  3.000
 LOJ  H14  C21  C18  111.81  3.000
 LOJ  H15  C21  C20  117.52  3.000
 LOJ  H14  C21  C20  111.73  3.000
 LOJ  C18  C21  C20   88.52  3.000
 LOJ  C17  N1   C13  117.63  3.000
 LOJ  C17  N1   C12  115.85  3.000
 LOJ  C13  N1   C12  115.45  3.000
 LOJ  C14  O1   C11  117.45  3.000
 LOJ  H18  C17  H17  106.63  3.000
 LOJ  H18  C17  N1   112.81  3.000
 LOJ  H17  C17  N1   107.48  3.000
 LOJ  H18  C17  C19  109.74  3.000
 LOJ  H17  C17  C19  108.06  3.000
 LOJ  N1   C17  C19  111.87  3.000
 LOJ  H20  C18  H19  108.56  3.000
 LOJ  H20  C18  C21  118.03  3.000
 LOJ  H19  C18  C21  111.78  3.000
 LOJ  H20  C18  C19  117.51  3.000
 LOJ  H19  C18  C19  111.45  3.000
 LOJ  C21  C18  C19   88.37  3.000
 LOJ  H21  C4   C5   119.47  3.000
 LOJ  H21  C4   C3   117.93  3.000
 LOJ  C5   C4   C3   122.60  3.000
 LOJ  C6   C5   C4   116.49  3.000
 LOJ  C6   C5   C15  123.39  3.000
 LOJ  C4   C5   C15  120.10  3.000
 LOJ  CL1  C6   C5   120.92  3.000
 LOJ  CL1  C6   C1   116.68  3.000
 LOJ  C5   C6   C1   122.40  3.000
 LOJ  O3   C16  O2   126.51  3.000
 LOJ  O3   C16  C8   116.63  3.000
 LOJ  O2   C16  C8   116.86  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
 LOJ  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 LOJ  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 LOJ  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 LOJ  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 LOJ  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 LOJ  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 LOJ  CONST_07  C10  C9   C8   C7     0.00   0.0  0
 LOJ  CONST_08  C14  C10  C9   C8     0.00   0.0  0
 LOJ  CONST_09  C13  C7   C8   C9     0.00   0.0  0
 LOJ  CONST_10  C15  C5   C6   C1   180.00   0.0  0
 LOJ  CONST_11  C15  C5   C4   C3   180.00   0.0  0
 LOJ  CONST_12  CL1  C6   C1   C2   180.00   0.0  0
 LOJ  CONST_13  C16  C8   C9   C10  180.00   0.0  0
 LOJ  CONST_14  C16  C8   C7   C13  180.00   0.0  0
 LOJ  CONST_15  CL1  C6   C5   C15    0.00   0.0  0
 LOJ  CONST_16  CL2  C2   C3   C4   180.00   0.0  0
 LOJ  CONST_17  CL1  C6   C5   C4   180.00   0.0  0
 LOJ  CONST_18  CL2  C2   C1   C6   180.00   0.0  0
 LOJ  CONST_19  H2   C3   C2   C1   180.00   0.0  0
 LOJ  CONST_20  H21  C4   C3   C2   180.00   0.0  0
 LOJ  CONST_21  H1   C1   C2   C3   180.00   0.0  0
 LOJ  CONST_22  H4   C9   C8   C7   180.00   0.0  0
 LOJ  CONST_23  H5   C10  C9   C8   180.00   0.0  0
 LOJ  CONST_24  H3   C7   C8   C9   180.00   0.0  0
 LOJ  Var_01    C20  C21  C18  C19   18.83  30.0  1
 LOJ  Var_02    O2   C16  C8   C7    -0.61  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
 LOJ  chir_01  C15  C5   C11  C12  positiv
 LOJ  chir_02  C19  C20  C17  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
 LOJ  plan-1  C1   0.020
 LOJ  plan-1  C2   0.020
 LOJ  plan-1  C3   0.020
 LOJ  plan-1  C15  0.020
 LOJ  plan-1  C4   0.020
 LOJ  plan-1  C5   0.020
 LOJ  plan-1  C6   0.020
 LOJ  plan-1  CL1  0.020
 LOJ  plan-1  CL2  0.020
 LOJ  plan-1  H1   0.020
 LOJ  plan-1  H2   0.020
 LOJ  plan-1  H21  0.020
 LOJ  plan-2  C7   0.020
 LOJ  plan-2  C8   0.020
 LOJ  plan-2  C9   0.020
 LOJ  plan-2  C10  0.020
 LOJ  plan-2  C13  0.020
 LOJ  plan-2  C14  0.020
 LOJ  plan-2  N1   0.020
 LOJ  plan-2  O1   0.020
 LOJ  plan-2  H3   0.020
 LOJ  plan-2  H4   0.020
 LOJ  plan-2  H5   0.020
 LOJ  plan-2  C16  0.020
 LOJ  plan-3  C8   0.020
 LOJ  plan-3  O2   0.020
 LOJ  plan-3  O3   0.020
 LOJ  plan-3  C16  0.020

