# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:40:08 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: 2,3-dihydro-1-benzoxepine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=CCCOc2ccccc12
#
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
 SR4  SR4  '2,3-dihydro-1-benzoxepine-5-carboxylic acid'  ligand  24  14  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SR4
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
 SR4  C4   C  CH2   0  -0.162  48.7525  115.9075  32.2132
 SR4  C5   C  CR6   0   0.313  51.1331  115.8586  32.1794
 SR4  C6   C  CR16  0  -0.326  51.9316  116.6075  33.0353
 SR4  C7   C  CR16  0  -0.260  53.1535  117.0921  32.5947
 SR4  C8   C  CR16  0  -0.256  53.5735  116.8394  31.2947
 SR4  C10  C  CR6   0   0.006  51.5456  115.5877  30.8687
 SR4  O    O  O     0  -0.444  50.5150  113.1746  28.2628
 SR4  C1   C  C     0  -0.063  50.6470  114.8317  29.9738
 SR4  C2   C  C1    0  -0.191  49.3430  115.1324  29.9107
 SR4  C3   C  CH2   0  -0.580  48.7513  116.2363  30.7223
 SR4  C9   C  CR16  0  -0.289  52.7750  116.0924  30.4436
 SR4  O1   O  OH1   0  -0.589  52.3613  113.3090  29.5030
 SR4  O2   O  O2    0  -0.493  49.9747  115.3255  32.6525
 SR4  H1   H  HCH2  0   0.233  48.5308  116.8145  32.7858
 SR4  H2   H  HCH2  0   0.243  47.9849  115.1680  32.4407
 SR4  H3   H  HCR6  0   0.265  51.5962  116.7958  34.0476
 SR4  H4   H  HCR6  0   0.261  53.7735  117.6730  33.2648
 SR4  H5   H  HCR6  0   0.258  54.5224  117.2232  30.9448
 SR4  H6   H  H     0   0.276  48.6911  114.5593  29.2629
 SR4  H7   H  HCH2  0   0.272  49.3177  117.1570  30.5506
 SR4  H8   H  HCH2  0   0.282  47.7230  116.4364  30.4222
 SR4  H9   H  HCR6  0   0.254  53.1066  115.9100  29.4296
 SR4  H10  H  HOH1  0   0.485  52.6446  112.5725  28.9404
 SR4  C    C  C     0   0.505  51.1459  113.7028  29.1481

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
 SR4  O    C    double    1.209  0.020  1.209
 SR4  C    O1   single    1.326  0.020  1.326
 SR4  C    C1   single    1.485  0.020  1.485
 SR4  C2   C1   double    1.340  0.020  1.340
 SR4  C2   C3   single    1.492  0.020  1.492
 SR4  C1   C10  single    1.476  0.020  1.476
 SR4  C9   C10  aromatic  1.395  0.020  1.395
 SR4  C9   C8   aromatic  1.386  0.020  1.386
 SR4  C3   C4   single    1.527  0.020  1.527
 SR4  C10  C5   aromatic  1.401  0.020  1.401
 SR4  C8   C7   aromatic  1.389  0.020  1.389
 SR4  C4   O2   single    1.423  0.020  1.423
 SR4  C5   O2   single    1.360  0.020  1.360
 SR4  C5   C6   aromatic  1.390  0.020  1.390
 SR4  C7   C6   aromatic  1.386  0.020  1.386
 SR4  C4   H1   single    0.970  0.020  1.090
 SR4  C4   H2   single    0.970  0.020  1.090
 SR4  C6   H3   single    0.930  0.020  1.080
 SR4  C7   H4   single    0.930  0.020  1.080
 SR4  C8   H5   single    0.930  0.020  1.080
 SR4  C2   H6   single    0.930  0.020  1.080
 SR4  C3   H7   single    0.970  0.020  1.090
 SR4  C3   H8   single    0.970  0.020  1.090
 SR4  C9   H9   single    0.930  0.020  1.080
 SR4  O1   H10  single    0.850  0.020  0.980

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
 SR4  H2   C4   H1   108.07  3.000
 SR4  H2   C4   O2   105.25  3.000
 SR4  H1   C4   O2   110.55  3.000
 SR4  H2   C4   C3   110.46  3.000
 SR4  H1   C4   C3   109.39  3.000
 SR4  O2   C4   C3   112.96  3.000
 SR4  O2   C5   C10  120.04  3.000
 SR4  O2   C5   C6   119.10  3.000
 SR4  C10  C5   C6   120.76  3.000
 SR4  H3   C6   C7   120.62  3.000
 SR4  H3   C6   C5   119.44  3.000
 SR4  C7   C6   C5   119.94  3.000
 SR4  H4   C7   C8   120.26  3.000
 SR4  H4   C7   C6   119.73  3.000
 SR4  C8   C7   C6   120.01  3.000
 SR4  H5   C8   C9   119.88  3.000
 SR4  H5   C8   C7   120.22  3.000
 SR4  C9   C8   C7   119.91  3.000
 SR4  C9   C10  C1   122.47  3.000
 SR4  C9   C10  C5   118.34  3.000
 SR4  C1   C10  C5   119.14  3.000
 SR4  C2   C1   C    118.13  3.000
 SR4  C2   C1   C10  120.40  3.000
 SR4  C    C1   C10  121.46  3.000
 SR4  H6   C2   C3   118.56  3.000
 SR4  H6   C2   C1   119.68  3.000
 SR4  C3   C2   C1   121.76  3.000
 SR4  H8   C3   H7   106.90  3.000
 SR4  H8   C3   C2   111.11  3.000
 SR4  H7   C3   C2   109.38  3.000
 SR4  H8   C3   C4   108.01  3.000
 SR4  H7   C3   C4   109.51  3.000
 SR4  C2   C3   C4   111.80  3.000
 SR4  H9   C9   C10  119.63  3.000
 SR4  H9   C9   C8   119.32  3.000
 SR4  C10  C9   C8   121.04  3.000
 SR4  H10  O1   C    109.77  3.000
 SR4  C5   O2   C4   117.63  3.000
 SR4  O1   C    C1   112.64  3.000
 SR4  C1   C    O    124.35  3.000
 SR4  O1   C    O    123.00  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
 SR4  CONST_01  C8   C7  C6  C5    0.00  0.0  0
 SR4  CONST_02  C9   C8  C7  C6    0.00  0.0  0
 SR4  CONST_03  C10  C9  C8  C7    0.00  0.0  0
 SR4  CONST_04  H4   C7  C6  C5  180.00  0.0  0
 SR4  CONST_05  H5   C8  C7  C6  180.00  0.0  0
 SR4  CONST_06  H9   C9  C8  C7  180.00  0.0  0
 SR4  CONST_07  H3   C6  C7  C8  180.00  0.0  0
 SR4  CONST_08  H10  O1  C   C1  180.00  0.0  0

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
 SR4  plan-1  O    0.020
 SR4  plan-1  C1   0.020
 SR4  plan-1  O1   0.020
 SR4  plan-1  H10  0.020
 SR4  plan-1  C    0.020
 SR4  plan-2  C5   0.020
 SR4  plan-2  C6   0.020
 SR4  plan-2  C7   0.020
 SR4  plan-2  C8   0.020
 SR4  plan-2  C10  0.020
 SR4  plan-2  C1   0.020
 SR4  plan-2  C9   0.020
 SR4  plan-2  O2   0.020
 SR4  plan-2  H3   0.020
 SR4  plan-2  H4   0.020
 SR4  plan-2  H5   0.020
 SR4  plan-2  H9   0.020

