# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:37:43 2022
#   Inital geometry file: a 166 line input string
#   Ligand name: (2Z,6E,10E)-13-[(2R)-6-hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl]-2,6,10-trimethyltrideca-2,6,10-trienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C(CC\C=C(\C)C(O)=O)=C/CC\C(C)=C\CC[C@]1(C)CCc2cc(O)cc(C)c2O1
#
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
 NQD  NQD  '(2Z,6E,10E)-13-[(2R)-6-hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl]-2,6,10-trimethyltrideca-2,6,10-trienoic acid'  ligand  68  31  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NQD
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
 NQD  C12  C  CH2    0  -0.493   -2.2045   0.4149   1.2873
 NQD  C11  C  C1     0  -0.282   -3.6838   0.3073   1.5046
 NQD  C01  C  CH3    0  -0.736   -3.9127  -2.0894   0.8231
 NQD  C02  C  C      0   0.129   -4.4468  -0.7700   1.3016
 NQD  C03  C  CH2    0  -0.486   -5.9339  -0.7127   1.5220
 NQD  C04  C  CH2    0  -0.485   -6.7478  -0.8981   0.2316
 NQD  C05  C  C1     0  -0.245   -8.2167  -0.9204   0.5177
 NQD  C06  C  C      0  -0.055   -9.1251   0.0263   0.2636
 NQD  C07  C  CH3    0  -0.707  -10.5495  -0.1444   0.7122
 NQD  C08  C  C      0   0.361   -8.8118   1.3519  -0.4128
 NQD  C13  C  CH2    0  -0.480   -1.8661   0.8608  -0.1453
 NQD  C14  C  C      0   0.109   -0.3887   1.0323  -0.3833
 NQD  C15  C  CH3    0  -0.728    0.2362   2.2157   0.2968
 NQD  C16  C  C1     0  -0.262    0.2756   0.1611  -1.1477
 NQD  C17  C  CH2    0  -0.506    1.7395   0.1423  -1.4620
 NQD  C18  C  CH2    0  -0.419    2.4255  -1.0522  -0.7927
 NQD  C19  C  CT     0   0.195    3.9433  -1.1240  -0.9550
 NQD  C20  C  CH3    0  -0.680    4.3558  -1.2220  -2.4212
 NQD  C21  C  CH2    0  -0.449    4.4923  -2.2977  -0.1450
 NQD  C22  C  CH2    0  -0.500    6.0138  -2.3152  -0.1577
 NQD  C23  C  CR6    0   0.023    6.5676  -0.9398   0.0912
 NQD  C24  C  CR16   0  -0.413    7.8949  -0.7654   0.4748
 NQD  C25  C  CR6    0   0.357    8.4041   0.5010   0.7139
 NQD  C26  C  CR16   0  -0.438    7.5726   1.6091   0.5681
 NQD  C27  C  CR6    0  -0.005    6.2475   1.4645   0.1814
 NQD  C28  C  CR6    0   0.321    5.7499   0.1780  -0.0567
 NQD  C30  C  CH3    0  -0.713    5.3535   2.6587   0.0243
 NQD  O09  O  O      0  -0.610   -9.3240   2.3556   0.1251
 NQD  O10  O  OC    -1  -0.600   -8.1006   1.3454  -1.4371
 NQD  O29  O  O2     0  -0.492    4.4422   0.0995  -0.4018
 NQD  O31  O  OH1    0  -0.648    9.7026   0.6096   1.0888
 NQD  H1   H  HCH2   0   0.233   -1.7929   1.1322   2.0016
 NQD  H2   H  HCH2   0   0.234   -1.7020  -0.5357   1.4839
 NQD  H3   H  H      0   0.220   -4.1777   1.2217   1.8245
 NQD  H4   H  HCH3   0   0.234   -4.3752  -2.9162   1.3666
 NQD  H5   H  HCH3   0   0.240   -4.1395  -2.2474  -0.2341
 NQD  H6   H  HCH3   0   0.240   -2.8330  -2.1762   0.9349
 NQD  H7   H  HCH2   0   0.221   -6.2222  -1.4911   2.2387
 NQD  H8   H  HCH2   0   0.230   -6.2088   0.2444   1.9721
 NQD  H9   H  HCH2   0   0.243   -6.5024  -0.1063  -0.4731
 NQD  H10  H  HCH2   0   0.223   -6.4652  -1.8467  -0.2359
 NQD  H11  H  H      0   0.214   -8.5564  -1.8046   1.0566
 NQD  H12  H  HCH3   0   0.228  -10.8176   0.5938   1.4694
 NQD  H13  H  HCH3   0   0.224  -11.2498  -0.0080  -0.1155
 NQD  H14  H  HCH3   0   0.223  -10.7218  -1.1359   1.1316
 NQD  H15  H  HCH2   0   0.235   -2.2738   0.1225  -0.8403
 NQD  H16  H  HCH2   0   0.226   -2.3845   1.8036  -0.3536
 NQD  H17  H  HCH3   0   0.237    0.1029   2.1664   1.3797
 NQD  H18  H  HCH3   0   0.236    1.3036   2.3095   0.1081
 NQD  H19  H  HCH3   0   0.235   -0.2419   3.1419  -0.0318
 NQD  H20  H  H      0   0.219   -0.2956  -0.6586  -1.5800
 NQD  H21  H  HCH2   0   0.231    1.8669   0.0806  -2.5469
 NQD  H22  H  HCH2   0   0.241    2.2216   1.0676  -1.1476
 NQD  H23  H  HCH2   0   0.232    2.1937  -1.0351   0.2770
 NQD  H24  H  HCH2   0   0.227    1.9986  -1.9817  -1.1820
 NQD  H25  H  HCH3   0   0.245    3.9646  -0.3880  -3.0035
 NQD  H26  H  HCH3   0   0.241    5.4397  -1.2232  -2.5428
 NQD  H27  H  HCH3   0   0.232    3.9754  -2.1467  -2.8586
 NQD  H28  H  HCH2   0   0.240    4.1328  -2.2120   0.8848
 NQD  H29  H  HCH2   0   0.245    4.0941  -3.2328  -0.5428
 NQD  H30  H  HCH2   0   0.259    6.3867  -3.0081   0.5994
 NQD  H31  H  HCH2   0   0.251    6.3822  -2.6936  -1.1160
 NQD  H32  H  HCR6   0   0.251    8.5324  -1.6348   0.5930
 NQD  H33  H  HCR6   0   0.258    7.9592   2.6052   0.7589
 NQD  H34  H  HCH3   0   0.243    4.9243   2.7094  -0.9775
 NQD  H35  H  HCH3   0   0.240    4.5146   2.6288   0.7226
 NQD  H36  H  HCH3   0   0.239    5.9016   3.5828   0.2025
 NQD  H38  H  HOH1   0   0.470    9.9301   1.5347   1.2294

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
 NQD  C05  C04  single    1.497  0.020  1.497
 NQD  C05  C06  double    1.336  0.020  1.336
 NQD  C07  C06  single    1.503  0.020  1.503
 NQD  C03  C04  single    1.537  0.020  1.537
 NQD  C03  C02  single    1.504  0.020  1.504
 NQD  C06  C08  single    1.521  0.020  1.521
 NQD  C02  C11  double    1.336  0.020  1.336
 NQD  C02  C01  single    1.502  0.020  1.502
 NQD  C11  C12  single    1.499  0.020  1.499
 NQD  C08  O09  deloc     1.249  0.020  1.249
 NQD  C08  O10  deloc     1.247  0.020  1.247
 NQD  C12  C13  single    1.538  0.020  1.538
 NQD  C13  C14  single    1.506  0.020  1.506
 NQD  C15  C14  single    1.501  0.020  1.501
 NQD  C14  C16  double    1.336  0.020  1.336
 NQD  O31  C25  single    1.356  0.020  1.356
 NQD  C26  C25  aromatic  1.393  0.020  1.393
 NQD  C26  C27  aromatic  1.388  0.020  1.388
 NQD  C25  C24  aromatic  1.386  0.020  1.386
 NQD  C30  C27  single    1.500  0.020  1.500
 NQD  C27  C28  aromatic  1.400  0.020  1.400
 NQD  C16  C17  single    1.497  0.020  1.497
 NQD  C24  C23  aromatic  1.393  0.020  1.393
 NQD  C28  C23  aromatic  1.393  0.020  1.393
 NQD  C28  O29  single    1.355  0.020  1.355
 NQD  C17  C18  single    1.531  0.020  1.531
 NQD  C23  C22  single    1.503  0.020  1.503
 NQD  O29  C19  single    1.432  0.020  1.432
 NQD  C22  C21  single    1.522  0.020  1.522
 NQD  C18  C19  single    1.528  0.020  1.528
 NQD  C21  C19  single    1.528  0.020  1.528
 NQD  C19  C20  single    1.526  0.020  1.526
 NQD  C12  H1   single    0.970  0.020  1.090
 NQD  C12  H2   single    0.970  0.020  1.090
 NQD  C11  H3   single    0.930  0.020  1.080
 NQD  C01  H4   single    0.970  0.020  1.090
 NQD  C01  H5   single    0.970  0.020  1.090
 NQD  C01  H6   single    0.970  0.020  1.090
 NQD  C03  H7   single    0.970  0.020  1.090
 NQD  C03  H8   single    0.970  0.020  1.090
 NQD  C04  H9   single    0.970  0.020  1.090
 NQD  C04  H10  single    0.970  0.020  1.090
 NQD  C05  H11  single    0.930  0.020  1.080
 NQD  C07  H12  single    0.970  0.020  1.090
 NQD  C07  H13  single    0.970  0.020  1.090
 NQD  C07  H14  single    0.970  0.020  1.090
 NQD  C13  H15  single    0.970  0.020  1.090
 NQD  C13  H16  single    0.970  0.020  1.090
 NQD  C15  H17  single    0.970  0.020  1.090
 NQD  C15  H18  single    0.970  0.020  1.090
 NQD  C15  H19  single    0.970  0.020  1.090
 NQD  C16  H20  single    0.930  0.020  1.080
 NQD  C17  H21  single    0.970  0.020  1.090
 NQD  C17  H22  single    0.970  0.020  1.090
 NQD  C18  H23  single    0.970  0.020  1.090
 NQD  C18  H24  single    0.970  0.020  1.090
 NQD  C20  H25  single    0.970  0.020  1.090
 NQD  C20  H26  single    0.970  0.020  1.090
 NQD  C20  H27  single    0.970  0.020  1.090
 NQD  C21  H28  single    0.970  0.020  1.090
 NQD  C21  H29  single    0.970  0.020  1.090
 NQD  C22  H30  single    0.970  0.020  1.090
 NQD  C22  H31  single    0.970  0.020  1.090
 NQD  C24  H32  single    0.930  0.020  1.080
 NQD  C26  H33  single    0.930  0.020  1.080
 NQD  C30  H34  single    0.970  0.020  1.090
 NQD  C30  H35  single    0.970  0.020  1.090
 NQD  C30  H36  single    0.970  0.020  1.090
 NQD  O31  H38  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
 NQD  H2   C12  H1   106.27  3.000
 NQD  H2   C12  C13  108.57  3.000
 NQD  H1   C12  C13  109.62  3.000
 NQD  H2   C12  C11  111.42  3.000
 NQD  H1   C12  C11  108.91  3.000
 NQD  C13  C12  C11  111.90  3.000
 NQD  H3   C11  C02  117.62  3.000
 NQD  H3   C11  C12  115.49  3.000
 NQD  C02  C11  C12  126.85  3.000
 NQD  H6   C01  H5   107.08  3.000
 NQD  H6   C01  H4   107.97  3.000
 NQD  H5   C01  H4   106.50  3.000
 NQD  H6   C01  C02  112.95  3.000
 NQD  H5   C01  C02  111.19  3.000
 NQD  H4   C01  C02  110.85  3.000
 NQD  C03  C02  C01  115.58  3.000
 NQD  C01  C02  C11  123.63  3.000
 NQD  C03  C02  C11  120.77  3.000
 NQD  H8   C03  H7   106.65  3.000
 NQD  H8   C03  C04  108.56  3.000
 NQD  H7   C03  C04  108.90  3.000
 NQD  H8   C03  C02  110.02  3.000
 NQD  H7   C03  C02  109.18  3.000
 NQD  C04  C03  C02  113.32  3.000
 NQD  H10  C04  H9   107.20  3.000
 NQD  H10  C04  C05  108.79  3.000
 NQD  H9   C04  C05  110.85  3.000
 NQD  H10  C04  C03  109.06  3.000
 NQD  H9   C04  C03  109.68  3.000
 NQD  C05  C04  C03  111.16  3.000
 NQD  H11  C05  C06  117.19  3.000
 NQD  H11  C05  C04  114.37  3.000
 NQD  C06  C05  C04  128.33  3.000
 NQD  C08  C06  C07  115.28  3.000
 NQD  C08  C06  C05  124.19  3.000
 NQD  C07  C06  C05  120.46  3.000
 NQD  H14  C07  H13  107.67  3.000
 NQD  H14  C07  H12  108.03  3.000
 NQD  H13  C07  H12  106.49  3.000
 NQD  H14  C07  C06  111.58  3.000
 NQD  H13  C07  C06  111.53  3.000
 NQD  H12  C07  C06  111.30  3.000
 NQD  O10  C08  O09  126.30  3.000
 NQD  O10  C08  C06  118.57  3.000
 NQD  O09  C08  C06  115.12  3.000
 NQD  H16  C13  H15  106.48  3.000
 NQD  H16  C13  C14  109.63  3.000
 NQD  H15  C13  C14  110.02  3.000
 NQD  H16  C13  C12  108.80  3.000
 NQD  H15  C13  C12  108.33  3.000
 NQD  C14  C13  C12  113.33  3.000
 NQD  C16  C14  C15  124.50  3.000
 NQD  C16  C14  C13  120.26  3.000
 NQD  C15  C14  C13  115.24  3.000
 NQD  H19  C15  H18  107.69  3.000
 NQD  H19  C15  H17  106.44  3.000
 NQD  H18  C15  H17  107.19  3.000
 NQD  H19  C15  C14  110.47  3.000
 NQD  H18  C15  C14  113.44  3.000
 NQD  H17  C15  C14  111.27  3.000
 NQD  H20  C16  C17  114.85  3.000
 NQD  H20  C16  C14  117.22  3.000
 NQD  C17  C16  C14  127.91  3.000
 NQD  H22  C17  H21  106.41  3.000
 NQD  H22  C17  C18  109.76  3.000
 NQD  H21  C17  C18  109.71  3.000
 NQD  H22  C17  C16  111.18  3.000
 NQD  H21  C17  C16  108.82  3.000
 NQD  C18  C17  C16  110.85  3.000
 NQD  H24  C18  H23  106.16  3.000
 NQD  H24  C18  C19  108.04  3.000
 NQD  H23  C18  C19  108.35  3.000
 NQD  H24  C18  C17  109.41  3.000
 NQD  H23  C18  C17  108.67  3.000
 NQD  C19  C18  C17  115.79  3.000
 NQD  O29  C19  C21  109.04  3.000
 NQD  C21  C19  C20  111.27  3.000
 NQD  O29  C19  C20  109.37  3.000
 NQD  C20  C19  C18  111.93  3.000
 NQD  C21  C19  C18  109.67  3.000
 NQD  O29  C19  C18  105.36  3.000
 NQD  H27  C20  H26  107.51  3.000
 NQD  H27  C20  H25  108.01  3.000
 NQD  H26  C20  H25  107.34  3.000
 NQD  H27  C20  C19  110.19  3.000
 NQD  H26  C20  C19  112.07  3.000
 NQD  H25  C20  C19  111.54  3.000
 NQD  H29  C21  H28  106.87  3.000
 NQD  H29  C21  C22  110.61  3.000
 NQD  H28  C21  C22  109.72  3.000
 NQD  H29  C21  C19  109.50  3.000
 NQD  H28  C21  C19  108.70  3.000
 NQD  C22  C21  C19  111.32  3.000
 NQD  H31  C22  H30  105.83  3.000
 NQD  H31  C22  C23  109.72  3.000
 NQD  H30  C22  C23  109.87  3.000
 NQD  H31  C22  C21  110.36  3.000
 NQD  H30  C22  C21  110.06  3.000
 NQD  C23  C22  C21  110.88  3.000
 NQD  C28  C23  C24  119.23  3.000
 NQD  C28  C23  C22  120.02  3.000
 NQD  C24  C23  C22  120.75  3.000
 NQD  H32  C24  C25  119.85  3.000
 NQD  H32  C24  C23  119.33  3.000
 NQD  C25  C24  C23  120.81  3.000
 NQD  O31  C25  C26  122.47  3.000
 NQD  C26  C25  C24  119.31  3.000
 NQD  O31  C25  C24  118.22  3.000
 NQD  H33  C26  C27  118.99  3.000
 NQD  H33  C26  C25  119.93  3.000
 NQD  C27  C26  C25  121.07  3.000
 NQD  C30  C27  C28  120.14  3.000
 NQD  C28  C27  C26  118.85  3.000
 NQD  C30  C27  C26  121.01  3.000
 NQD  O29  C28  C27  116.08  3.000
 NQD  O29  C28  C23  123.18  3.000
 NQD  C27  C28  C23  120.72  3.000
 NQD  H36  C30  H35  107.78  3.000
 NQD  H36  C30  H34  107.99  3.000
 NQD  H35  C30  H34  106.64  3.000
 NQD  H36  C30  C27  111.00  3.000
 NQD  H35  C30  C27  111.66  3.000
 NQD  H34  C30  C27  111.56  3.000
 NQD  C28  O29  C19  118.95  3.000
 NQD  H38  O31  C25  110.10  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
 NQD  CONST_01  C26  C25  C24  C23     0.00   0.0  0
 NQD  CONST_02  C26  C27  C28  C23     0.00   0.0  0
 NQD  CONST_03  C27  C26  C25  C24     0.00   0.0  0
 NQD  CONST_04  C27  C28  C23  C24     0.00   0.0  0
 NQD  CONST_05  C28  C27  C26  C25     0.00   0.0  0
 NQD  CONST_06  C28  C23  C24  C25     0.00   0.0  0
 NQD  CONST_07  O31  C25  C24  C23   180.00   0.0  0
 NQD  CONST_08  C30  C27  C28  C23   180.00   0.0  0
 NQD  CONST_09  C30  C27  C26  C25   180.00   0.0  0
 NQD  CONST_10  O31  C25  C26  C27   180.00   0.0  0
 NQD  CONST_11  O29  C28  C27  C30     0.00   0.0  0
 NQD  CONST_12  H32  C24  C23  C22     0.00   0.0  0
 NQD  CONST_13  H33  C26  C25  C24   180.00   0.0  0
 NQD  Var_01    C27  C28  O29  C19   165.74  30.0  1
 NQD  Var_02    C23  C22  C21  C19    45.30  30.0  1
 NQD  Var_03    C24  C23  C22  C21   162.79  30.0  1
 NQD  Var_04    H34  C30  C27  C26   123.26  30.0  2
 NQD  Var_05    C19  C18  C17  C16  -175.69  30.0  3
 NQD  Var_06    C03  C02  C11  C12  -177.95   0.0  2
 NQD  Var_07    C07  C06  C05  C04  -175.84   0.0  2
 NQD  Var_08    C17  C16  C14  C13  -177.95   0.0  2
 NQD  Var_09    C15  C14  C13  C12   -70.97  30.0  3
 NQD  Var_10    C04  C03  C02  C11   114.32  30.0  3
 NQD  Var_11    C14  C13  C12  C11   177.72  30.0  3
 NQD  Var_12    C05  C04  C03  C02   176.37  30.0  3
 NQD  Var_13    C13  C12  C11  C02    89.56  30.0  3
 NQD  Var_14    C06  C05  C04  C03   106.70  30.0  2
 NQD  Var_15    O09  C08  C06  C05  -134.81  30.0  2
 NQD  Var_16    C18  C17  C16  C14   110.87  30.0  3
 NQD  Var_17    H4   C01  C02  C11   138.17  30.0  3
 NQD  Var_18    H12  C07  C06  C05   114.29  30.0  3
 NQD  Var_19    H17  C15  C14  C13    58.83  30.0  3

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
 NQD  chir_01  C19  O29  C21  C20  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
 NQD  plan-1  C06  0.020
 NQD  plan-1  C08  0.020
 NQD  plan-1  O09  0.020
 NQD  plan-1  O10  0.020
 NQD  plan-2  C22  0.020
 NQD  plan-2  C23  0.020
 NQD  plan-2  C24  0.020
 NQD  plan-2  C25  0.020
 NQD  plan-2  C26  0.020
 NQD  plan-2  C27  0.020
 NQD  plan-2  C28  0.020
 NQD  plan-2  C30  0.020
 NQD  plan-2  O29  0.020
 NQD  plan-2  O31  0.020
 NQD  plan-2  H32  0.020
 NQD  plan-2  H33  0.020
 NQD  plan-3  C04  0.020
 NQD  plan-3  C05  0.020
 NQD  plan-3  C06  0.020
 NQD  plan-3  C07  0.020
 NQD  plan-3  C08  0.020
 NQD  plan-3  H11  0.020
 NQD  plan-4  C12  0.020
 NQD  plan-4  C11  0.020
 NQD  plan-4  C01  0.020
 NQD  plan-4  C02  0.020
 NQD  plan-4  C03  0.020
 NQD  plan-4  H3   0.020
 NQD  plan-5  C13  0.020
 NQD  plan-5  C14  0.020
 NQD  plan-5  C15  0.020
 NQD  plan-5  C16  0.020
 NQD  plan-5  C17  0.020
 NQD  plan-5  H20  0.020

