# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:30:12 2021
#   Inital geometry file: a 83 line input string
#   Ligand name: 4-(3,4-dihydro-2H-1,5-benzodioxepin-7-yl)-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)c1ccc2OCCCOc2c1
#
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
 RKY  RKY  '4-(3,4-dihydro-2H-1,5-benzodioxepin-7-yl)-4-oxobutanoic acid'  ligand  32  18  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RKY
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
 RKY  C10  C  CR16  0  -0.346  10.6716   6.5103  28.6692
 RKY  C13  C  CH2   0  -0.216   7.4299   5.9939  27.2600
 RKY  C15  C  CH2   0  -0.216   7.9748   7.8897  25.7092
 RKY  C17  C  CR6   0   0.333   9.2670   8.1974  27.6687
 RKY  O01  O  OH1   0  -0.595  14.8880  12.7878  30.1660
 RKY  C02  C  C     0   0.553  14.5671  11.5520  29.7995
 RKY  O03  O  O     0  -0.450  14.7790  11.1168  28.6947
 RKY  C04  C  CH2   0  -0.580  13.9655  10.7642  30.9307
 RKY  C05  C  CH2   0  -0.590  13.1901   9.5548  30.4511
 RKY  O07  O  O     0  -0.403  11.6924  11.0920  29.4406
 RKY  C08  C  CR6   0  -0.015  11.1680   8.8362  29.0352
 RKY  C09  C  CR16  0  -0.297  11.4717   7.4894  29.2268
 RKY  C11  C  CR6   0   0.333   9.5603   6.8394  27.8980
 RKY  O12  O  O2    0  -0.482   8.8408   5.8156  27.3994
 RKY  C14  C  CH2   0  -0.480   7.0718   6.6933  25.9620
 RKY  O16  O  O2    0  -0.491   8.2266   8.6199  26.9078
 RKY  C18  C  CR16  0  -0.384  10.0680   9.1675  28.2450
 RKY  H1   H  HCR6  0   0.274  10.8959   5.4643  28.8339
 RKY  H2   H  HCH2  0   0.240   7.0404   6.5406  28.1229
 RKY  H3   H  HCH2  0   0.266   6.9997   4.9937  27.2901
 RKY  H4   H  HCH2  0   0.236   8.9211   7.5804  25.2553
 RKY  H5   H  HCH2  0   0.263   7.5017   8.5885  25.0197
 RKY  H6   H  HOH1  0   0.478  15.3068  13.2535  29.4267
 RKY  H7   H  HCH2  0   0.303  14.7902  10.4315  31.5685
 RKY  H8   H  HCH2  0   0.278  13.3484  11.4160  31.5498
 RKY  H9   H  HCH2  0   0.295  12.8488   8.9784  31.3158
 RKY  H10  H  HCH2  0   0.280  13.8337   8.8794  29.8829
 RKY  H11  H  HCR6  0   0.265  12.3214   7.1837  29.8217
 RKY  H12  H  HCH2  0   0.251   6.0252   6.9994  26.0214
 RKY  H13  H  HCH2  0   0.251   7.1569   6.0098  25.1148
 RKY  H14  H  HCR6  0   0.269   9.8258  10.2064  28.0592
 RKY  C06  C  C     0   0.380  11.9862   9.9269  29.6183

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
 RKY  C15  C14  single    1.520  0.020  1.520
 RKY  C15  O16  single    1.426  0.020  1.426
 RKY  C14  C13  single    1.517  0.020  1.517
 RKY  O16  C17  single    1.356  0.020  1.356
 RKY  C13  O12  single    1.429  0.020  1.429
 RKY  O12  C11  single    1.347  0.020  1.347
 RKY  C17  C11  aromatic  1.408  0.020  1.408
 RKY  C17  C18  aromatic  1.384  0.020  1.384
 RKY  C11  C10  aromatic  1.392  0.020  1.392
 RKY  C18  C08  aromatic  1.394  0.020  1.394
 RKY  O03  C02  double    1.206  0.020  1.206
 RKY  C10  C09  aromatic  1.382  0.020  1.382
 RKY  C08  C09  aromatic  1.394  0.020  1.394
 RKY  C08  C06  single    1.483  0.020  1.483
 RKY  O01  C02  single    1.328  0.020  1.328
 RKY  C02  C04  single    1.504  0.020  1.504
 RKY  O07  C06  double    1.215  0.020  1.215
 RKY  C06  C05  single    1.510  0.020  1.510
 RKY  C05  C04  single    1.515  0.020  1.515
 RKY  C10  H1   single    0.930  0.020  1.080
 RKY  C13  H2   single    0.970  0.020  1.090
 RKY  C13  H3   single    0.970  0.020  1.090
 RKY  C15  H4   single    0.970  0.020  1.090
 RKY  C15  H5   single    0.970  0.020  1.090
 RKY  O01  H6   single    0.850  0.020  0.980
 RKY  C04  H7   single    0.970  0.020  1.090
 RKY  C04  H8   single    0.970  0.020  1.090
 RKY  C05  H9   single    0.970  0.020  1.090
 RKY  C05  H10  single    0.970  0.020  1.090
 RKY  C09  H11  single    0.930  0.020  1.080
 RKY  C14  H12  single    0.970  0.020  1.090
 RKY  C14  H13  single    0.970  0.020  1.090
 RKY  C18  H14  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
 RKY  H1   C10  C11  118.57  3.000
 RKY  H1   C10  C09  120.22  3.000
 RKY  C11  C10  C09  121.21  3.000
 RKY  H3   C13  H2   107.26  3.000
 RKY  H3   C13  C14  110.71  3.000
 RKY  H2   C13  C14  111.14  3.000
 RKY  H3   C13  O12  105.82  3.000
 RKY  H2   C13  O12  109.71  3.000
 RKY  C14  C13  O12  111.96  3.000
 RKY  H5   C15  H4   107.12  3.000
 RKY  H5   C15  O16  106.26  3.000
 RKY  H4   C15  O16  109.92  3.000
 RKY  H5   C15  C14  110.61  3.000
 RKY  H4   C15  C14  111.12  3.000
 RKY  O16  C15  C14  111.60  3.000
 RKY  C18  C17  O16  117.34  3.000
 RKY  C18  C17  C11  119.19  3.000
 RKY  O16  C17  C11  123.48  3.000
 RKY  H6   O01  C02  109.94  3.000
 RKY  C04  C02  O03  124.76  3.000
 RKY  C04  C02  O01  112.11  3.000
 RKY  O03  C02  O01  123.09  3.000
 RKY  H8   C04  H7   106.10  3.000
 RKY  H8   C04  C05  111.55  3.000
 RKY  H7   C04  C05  109.13  3.000
 RKY  H8   C04  C02  109.90  3.000
 RKY  H7   C04  C02  107.23  3.000
 RKY  C05  C04  C02  112.64  3.000
 RKY  H10  C05  H9   105.62  3.000
 RKY  H10  C05  C06  109.58  3.000
 RKY  H9   C05  C06  108.48  3.000
 RKY  H10  C05  C04  110.90  3.000
 RKY  H9   C05  C04  109.28  3.000
 RKY  C06  C05  C04  112.70  3.000
 RKY  C18  C08  C09  118.64  3.000
 RKY  C09  C08  C06  122.44  3.000
 RKY  C18  C08  C06  118.91  3.000
 RKY  H11  C09  C08  121.33  3.000
 RKY  H11  C09  C10  118.46  3.000
 RKY  C08  C09  C10  120.20  3.000
 RKY  O12  C11  C17  124.16  3.000
 RKY  C17  C11  C10  118.98  3.000
 RKY  O12  C11  C10  116.86  3.000
 RKY  C11  O12  C13  117.95  3.000
 RKY  H13  C14  H12  107.00  3.000
 RKY  H13  C14  C15  108.51  3.000
 RKY  H12  C14  C15  110.96  3.000
 RKY  H13  C14  C13  110.90  3.000
 RKY  H12  C14  C13  107.99  3.000
 RKY  C15  C14  C13  111.40  3.000
 RKY  C17  O16  C15  116.58  3.000
 RKY  H14  C18  C08  120.12  3.000
 RKY  H14  C18  C17  118.14  3.000
 RKY  C08  C18  C17  121.74  3.000
 RKY  C08  C06  O07  120.96  3.000
 RKY  O07  C06  C05  120.65  3.000
 RKY  C08  C06  C05  118.38  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
 RKY  CONST_01  C18  C08  C09  C10     0.00   0.0  0
 RKY  CONST_02  C09  C08  C18  C17     0.00   0.0  0
 RKY  CONST_03  C11  C10  C09  C08     0.00   0.0  0
 RKY  CONST_04  C06  C08  C09  C10   180.00   0.0  0
 RKY  CONST_05  C06  C08  C18  C17   180.00   0.0  0
 RKY  CONST_06  H1   C10  C09  C08   180.00   0.0  0
 RKY  CONST_07  H14  C18  C08  C09   180.00   0.0  0
 RKY  CONST_08  H11  C09  C10  C11   180.00   0.0  0
 RKY  CONST_09  H6   O01  C02  O03     0.00   0.0  0
 RKY  Var_01    C18  C08  C06  C05  -178.87  30.0  2
 RKY  Var_02    C08  C06  C05  C04   177.46  30.0  1
 RKY  Var_03    C05  C04  C02  O01   161.11  30.0  3
 RKY  Var_04    C06  C05  C04  C02   -63.99  30.0  1

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
 RKY  plan-1  C05  0.020
 RKY  plan-1  O07  0.020
 RKY  plan-1  C08  0.020
 RKY  plan-1  C06  0.020
 RKY  plan-2  C10  0.020
 RKY  plan-2  C17  0.020
 RKY  plan-2  C08  0.020
 RKY  plan-2  C09  0.020
 RKY  plan-2  C11  0.020
 RKY  plan-2  O12  0.020
 RKY  plan-2  O16  0.020
 RKY  plan-2  C18  0.020
 RKY  plan-2  H1   0.020
 RKY  plan-2  H11  0.020
 RKY  plan-2  H14  0.020
 RKY  plan-2  C06  0.020
 RKY  plan-3  O01  0.020
 RKY  plan-3  C02  0.020
 RKY  plan-3  O03  0.020
 RKY  plan-3  C04  0.020
 RKY  plan-3  H6   0.020

