# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 02:58:07 2022
#   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  31  18  .  2022-03-23  2022-03-23
;
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  -0.345  10.7540   6.5537  28.6248
 RKY  C13  C  CH2    0  -0.215   7.5600   5.9515  27.1738
 RKY  C15  C  CH2    0  -0.215   8.0043   7.9484  25.7240
 RKY  C17  C  CR6    0   0.337   9.2785   8.2223  27.7035
 RKY  O01  O  OC    -1  -0.620  15.2061  12.4982  29.8204
 RKY  C02  C  C      0   0.418  14.5500  11.4493  29.6631
 RKY  O03  O  O      0  -0.601  14.3497  10.8437  28.5910
 RKY  C04  C  CH2    0  -0.582  13.9434  10.8346  30.9410
 RKY  C05  C  CH2    0  -0.565  13.0563   9.6360  30.6741
 RKY  O07  O  O      0  -0.410  11.3865  11.1039  29.8305
 RKY  C08  C  CR6    0  -0.022  11.1111   8.8742  29.1589
 RKY  C09  C  CR16   0  -0.300  11.4883   7.5368  29.2622
 RKY  C11  C  CR6    0   0.323   9.6401   6.8708  27.8539
 RKY  O12  O  O2     0  -0.480   8.9786   5.8434  27.2809
 RKY  C14  C  CH2    0  -0.479   7.1436   6.7135  25.9285
 RKY  O16  O  O2     0  -0.487   8.2328   8.6402  26.9476
 RKY  C18  C  CR16   0  -0.389  10.0095   9.1938  28.3664
 RKY  H1   H  HCR6   0   0.268  11.0307   5.5122  28.7296
 RKY  H2   H  HCH2   0   0.237   7.1537   6.4178  28.0758
 RKY  H3   H  HCH2   0   0.262   7.1826   4.9298  27.1427
 RKY  H4   H  HCH2   0   0.235   8.9589   7.6876  25.2574
 RKY  H5   H  HCH2   0   0.260   7.5064   8.6564  25.0616
 RKY  H7   H  HCH2   0   0.234  14.7628  10.5267  31.5986
 RKY  H8   H  HCH2   0   0.223  13.4026  11.6073  31.4927
 RKY  H9   H  HCH2   0   0.263  12.7010   9.1979  31.6155
 RKY  H10  H  HCH2   0   0.245  13.6296   8.8506  30.1823
 RKY  H11  H  HCR6   0   0.259  12.3383   7.2393  29.8598
 RKY  H12  H  HCH2   0   0.248   6.0899   6.9829  26.0297
 RKY  H13  H  HCH2   0   0.248   7.2272   6.0839  25.0402
 RKY  H14  H  HCR6   0   0.264   9.7092  10.2276  28.2493
 RKY  C06  C  C      0   0.386  11.8285   9.9730  29.8657

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    1.519  0.020  1.519
 RKY  C15  O16  single    1.424  0.020  1.424
 RKY  C14  C13  single    1.518  0.020  1.518
 RKY  O16  C17  single    1.356  0.020  1.356
 RKY  C13  O12  single    1.427  0.020  1.427
 RKY  O12  C11  single    1.350  0.020  1.350
 RKY  C17  C11  aromatic  1.407  0.020  1.407
 RKY  C17  C18  aromatic  1.385  0.020  1.385
 RKY  C11  C10  aromatic  1.391  0.020  1.391
 RKY  C18  C08  aromatic  1.394  0.020  1.394
 RKY  O03  C02  deloc     1.248  0.020  1.248
 RKY  C10  C09  aromatic  1.383  0.020  1.383
 RKY  C08  C09  aromatic  1.393  0.020  1.393
 RKY  C08  C06  single    1.490  0.020  1.490
 RKY  O01  C02  deloc     1.247  0.020  1.247
 RKY  C02  C04  single    1.542  0.020  1.542
 RKY  O07  C06  double    1.215  0.020  1.215
 RKY  C06  C05  single    1.508  0.020  1.508
 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  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  118.52  3.000
 RKY  H1   C10  C09  120.23  3.000
 RKY  C11  C10  C09  121.24  3.000
 RKY  H3   C13  H2   107.13  3.000
 RKY  H3   C13  C14  110.62  3.000
 RKY  H2   C13  C14  111.14  3.000
 RKY  H3   C13  O12  105.99  3.000
 RKY  H2   C13  O12  109.86  3.000
 RKY  C14  C13  O12  111.86  3.000
 RKY  H5   C15  H4   107.11  3.000
 RKY  H5   C15  O16  106.25  3.000
 RKY  H4   C15  O16  110.01  3.000
 RKY  H5   C15  C14  110.55  3.000
 RKY  H4   C15  C14  110.98  3.000
 RKY  O16  C15  C14  111.73  3.000
 RKY  C18  C17  O16  117.23  3.000
 RKY  C18  C17  C11  119.15  3.000
 RKY  O16  C17  C11  123.62  3.000
 RKY  C04  C02  O03  117.09  3.000
 RKY  C04  C02  O01  115.95  3.000
 RKY  O03  C02  O01  126.95  3.000
 RKY  H8   C04  H7   105.43  3.000
 RKY  H8   C04  C05  111.02  3.000
 RKY  H7   C04  C05  108.76  3.000
 RKY  H8   C04  C02  109.33  3.000
 RKY  H7   C04  C02  108.38  3.000
 RKY  C05  C04  C02  113.56  3.000
 RKY  H10  C05  H9   105.65  3.000
 RKY  H10  C05  C06  110.33  3.000
 RKY  H9   C05  C06  106.59  3.000
 RKY  H10  C05  C04  109.98  3.000
 RKY  H9   C05  C04  110.75  3.000
 RKY  C06  C05  C04  113.23  3.000
 RKY  C18  C08  C09  118.42  3.000
 RKY  C09  C08  C06  122.83  3.000
 RKY  C18  C08  C06  118.75  3.000
 RKY  H11  C09  C08  121.20  3.000
 RKY  H11  C09  C10  118.48  3.000
 RKY  C08  C09  C10  120.30  3.000
 RKY  O12  C11  C17  124.05  3.000
 RKY  C17  C11  C10  118.94  3.000
 RKY  O12  C11  C10  117.01  3.000
 RKY  C11  O12  C13  117.49  3.000
 RKY  H13  C14  H12  106.95  3.000
 RKY  H13  C14  C15  108.41  3.000
 RKY  H12  C14  C15  111.01  3.000
 RKY  H13  C14  C13  110.91  3.000
 RKY  H12  C14  C13  108.20  3.000
 RKY  C15  C14  C13  111.29  3.000
 RKY  C17  O16  C15  116.93  3.000
 RKY  H14  C18  C08  119.96  3.000
 RKY  H14  C18  C17  118.14  3.000
 RKY  C08  C18  C17  121.90  3.000
 RKY  C08  C06  O07  119.83  3.000
 RKY  O07  C06  C05  121.32  3.000
 RKY  C08  C06  C05  118.77  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  Var_01    C18  C08  C06  C05  -177.34  30.0  2
 RKY  Var_02    C08  C06  C05  C04   160.41  30.0  1
 RKY  Var_03    C05  C04  C02  O01   174.80  30.0  3
 RKY  Var_04    C06  C05  C04  C02   -63.90  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

