# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 10:24:38 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: (2S)-2-(4-{2-[3-(fluoromethyl)azetidin-1-yl]ethoxy}phenyl)-3-(3-hydroxyphenyl)-4-methyl-2H-1-benzopyran-8-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C([C@@H](Oc2c(O)cccc12)c3ccc(OCCN4CC(CF)C4)cc3)c5cccc(O)c5
#
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
 ODY  ODY  (2S)-2-(4-{2-[3-(fluoromethyl)azetidin-1-yl]ethoxy}phenyl)-3-(3-hydroxyphenyl)-4-methyl-2H-1-benzopyran-8-ol  ligand  62  34  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ODY
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
 ODY  C4   C  CH1   0  -0.124  -2.5207  -0.0814   0.8825
 ODY  C14  C  CR6   0   0.110  -1.0337  -0.3150   0.7588
 ODY  C11  C  CR16  0  -0.367  -3.7122  -4.4488  -0.4032
 ODY  C7   C  CR6   0   0.226  -3.4375  -2.1624   0.2666
 ODY  C8   C  CR6   0   0.024  -3.7412  -1.7208  -1.0178
 ODY  C9   C  CR16  0  -0.364  -4.0393  -2.6687  -1.9977
 ODY  C10  C  CR16  0  -0.248  -4.0224  -4.0194  -1.6869
 ODY  C12  C  CR6   0   0.288  -3.4132  -3.5191   0.5850
 ODY  C3   C  C     0  -0.047  -3.1281   0.5167  -0.3608
 ODY  C2   C  C     0   0.111  -3.7268  -0.2742  -1.2666
 ODY  O6   O  O2    0  -0.491  -3.1959  -1.2820   1.2670
 ODY  O13  O  OH1   0  -0.632  -3.1135  -3.9448   1.8289
 ODY  C15  C  CR16  0  -0.255  -0.4358  -0.6929  -0.4428
 ODY  C16  C  CR16  0  -0.338   0.9182  -0.9571  -0.5137
 ODY  C17  C  CR6   0   0.386   1.7203  -0.8437   0.6246
 ODY  C18  C  CR16  0  -0.377   1.1385  -0.4584   1.8311
 ODY  C19  C  CR16  0  -0.299  -0.2256  -0.2020   1.8822
 ODY  O20  O  O2    0  -0.464   3.0251  -1.1167   0.4612
 ODY  C21  C  CH2   0  -0.204   3.9009  -0.9865   1.5670
 ODY  C22  C  CH2   0  -0.310   5.2994  -1.3301   1.1097
 ODY  N23  N  N     0  -0.411   5.7753  -0.4254   0.0986
 ODY  C24  C  C     0  -0.258   7.1434  -0.6016  -0.3900
 ODY  C25  C  C     0  -0.364   7.2825   0.9281  -0.4590
 ODY  C26  C  C     0  -0.263   6.0652   0.9599   0.4792
 ODY  C27  C  CH2   0   0.003   8.5763   1.5120   0.0261
 ODY  F28  F  F     0  -0.383   8.4683   2.9021   0.0973
 ODY  C29  C  CR6   0   0.083  -2.9325   1.9724  -0.5180
 ODY  C30  C  CR16  0  -0.318  -2.2288   2.4802  -1.6109
 ODY  C31  C  CR16  0  -0.228  -2.0308   3.8473  -1.7278
 ODY  C32  C  CR16  0  -0.391  -2.5194   4.7232  -0.7699
 ODY  C33  C  CR6   0   0.373  -3.2166   4.2210   0.3260
 ODY  C34  C  CR16  0  -0.398  -3.4146   2.8486   0.4509
 ODY  O35  O  OH1   0  -0.633  -3.7211   5.0138   1.2923
 ODY  H5   H  HCH1  0   0.272  -2.6917   0.5942   1.7237
 ODY  H41  H  HCR6  0   0.266  -3.6923  -5.5046  -0.1629
 ODY  H39  H  HCR6  0   0.254  -4.2809  -2.3525  -3.0034
 ODY  H40  H  HCR6  0   0.256  -4.2498  -4.7511  -2.4508
 ODY  H38  H  HCH3  0   0.250  -5.3789  -0.1975  -2.6259
 ODY  H37  H  HCH3  0   0.261  -4.4724   1.3111  -2.5232
 ODY  H36  H  HCH3  0   0.248  -3.8156  -0.0611  -3.4070
 ODY  H42  H  HOH1  0   0.469  -2.8792  -3.1921   2.3858
 ODY  H43  H  HCR6  0   0.259  -1.0317  -0.7733  -1.3435
 ODY  H44  H  HCR6  0   0.261   1.3688  -1.2483  -1.4543
 ODY  H45  H  HCR6  0   0.280   1.7256  -0.3518   2.7332
 ODY  H46  H  HCR6  0   0.258  -0.6598   0.0982   2.8289
 ODY  H48  H  HCH2  0   0.230   3.8672   0.0349   1.9655
 ODY  H47  H  HCH2  0   0.239   3.6099  -1.6637   2.3774
 ODY  H50  H  HCH2  0   0.205   5.9435  -1.3331   2.0058
 ODY  H49  H  HCH2  0   0.245   5.3147  -2.3485   0.7111
 ODY  H51  H  H     0   0.205   7.8181  -1.0386   0.3611
 ODY  H52  H  H     0   0.235   7.2440  -1.1714  -1.3161
 ODY  H53  H  H     0   0.262   7.0391   1.3086  -1.4529
 ODY  H55  H  H     0   0.234   5.2730   1.6819   0.2704
 ODY  H54  H  H     0   0.204   6.3660   1.0688   1.5325
 ODY  H57  H  HCH2  0   0.199   8.8251   1.1431   1.0234
 ODY  H56  H  HCH2  0   0.214   9.3976   1.2691  -0.6515
 ODY  H58  H  HCR6  0   0.249  -1.8265   1.8087  -2.3581
 ODY  H59  H  HCR6  0   0.261  -1.4828   4.2411  -2.5739
 ODY  H60  H  HCR6  0   0.272  -2.3546   5.7895  -0.8743
 ODY  H61  H  HCR6  0   0.264  -3.9672   2.4729   1.3046
 ODY  H62  H  HOH1  0   0.475  -3.5328   5.9393   1.1010
 ODY  C1   C  CH3   0  -0.758  -4.3795   0.2281  -2.5174

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
 ODY  C26  C25  single    1.537  0.020  1.537
 ODY  C26  N23  single    1.466  0.020  1.466
 ODY  C27  C25  single    1.500  0.020  1.500
 ODY  C27  F28  single    1.396  0.020  1.396
 ODY  C25  C24  single    1.538  0.020  1.538
 ODY  N23  C22  single    1.438  0.020  1.438
 ODY  N23  C24  single    1.463  0.020  1.463
 ODY  C22  C21  single    1.511  0.020  1.511
 ODY  O20  C21  single    1.417  0.020  1.417
 ODY  O20  C17  single    1.343  0.020  1.343
 ODY  C10  C11  aromatic  1.389  0.020  1.389
 ODY  C10  C9   aromatic  1.386  0.020  1.386
 ODY  C16  C17  aromatic  1.397  0.020  1.397
 ODY  C16  C15  aromatic  1.381  0.020  1.381
 ODY  C11  C12  aromatic  1.389  0.020  1.389
 ODY  C9   C8   aromatic  1.396  0.020  1.396
 ODY  C17  C18  aromatic  1.394  0.020  1.394
 ODY  C15  C14  aromatic  1.394  0.020  1.394
 ODY  C12  O13  single    1.348  0.020  1.348
 ODY  C12  C7   aromatic  1.394  0.020  1.394
 ODY  C8   C7   aromatic  1.392  0.020  1.392
 ODY  C8   C2   single    1.468  0.020  1.468
 ODY  C1   C2   single    1.498  0.020  1.498
 ODY  C7   O6   single    1.354  0.020  1.354
 ODY  C2   C3   double    1.343  0.020  1.343
 ODY  C18  C19  aromatic  1.389  0.020  1.389
 ODY  C14  C19  aromatic  1.389  0.020  1.389
 ODY  C14  C4   single    1.510  0.020  1.510
 ODY  C30  C31  aromatic  1.386  0.020  1.386
 ODY  C30  C29  aromatic  1.395  0.020  1.395
 ODY  C3   C4   single    1.507  0.020  1.507
 ODY  C3   C29  single    1.477  0.020  1.477
 ODY  O6   C4   single    1.430  0.020  1.430
 ODY  C31  C32  aromatic  1.387  0.020  1.387
 ODY  C29  C34  aromatic  1.393  0.020  1.393
 ODY  C32  C33  aromatic  1.393  0.020  1.393
 ODY  C34  C33  aromatic  1.392  0.020  1.392
 ODY  C33  O35  single    1.348  0.020  1.348
 ODY  C4   H5   single    0.970  0.020  1.090
 ODY  C11  H41  single    0.930  0.020  1.080
 ODY  C9   H39  single    0.930  0.020  1.080
 ODY  C10  H40  single    0.930  0.020  1.080
 ODY  C1   H38  single    0.970  0.020  1.090
 ODY  C1   H37  single    0.970  0.020  1.090
 ODY  C1   H36  single    0.970  0.020  1.090
 ODY  O13  H42  single    0.850  0.020  0.980
 ODY  C15  H43  single    0.930  0.020  1.080
 ODY  C16  H44  single    0.930  0.020  1.080
 ODY  C18  H45  single    0.930  0.020  1.080
 ODY  C19  H46  single    0.930  0.020  1.080
 ODY  C21  H48  single    0.970  0.020  1.090
 ODY  C21  H47  single    0.970  0.020  1.090
 ODY  C22  H50  single    0.970  0.020  1.090
 ODY  C22  H49  single    0.970  0.020  1.090
 ODY  C24  H51  single    0.970  0.020  1.090
 ODY  C24  H52  single    0.970  0.020  1.090
 ODY  C25  H53  single    0.970  0.020  1.090
 ODY  C26  H55  single    0.970  0.020  1.090
 ODY  C26  H54  single    0.970  0.020  1.090
 ODY  C27  H57  single    0.970  0.020  1.090
 ODY  C27  H56  single    0.970  0.020  1.090
 ODY  C30  H58  single    0.930  0.020  1.080
 ODY  C31  H59  single    0.930  0.020  1.080
 ODY  C32  H60  single    0.930  0.020  1.080
 ODY  C34  H61  single    0.930  0.020  1.080
 ODY  O35  H62  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
 ODY  H5   C4   O6   103.79  3.000
 ODY  H5   C4   C3   109.07  3.000
 ODY  O6   C4   C3   111.39  3.000
 ODY  H5   C4   C14  108.23  3.000
 ODY  O6   C4   C14  110.92  3.000
 ODY  C3   C4   C14  112.98  3.000
 ODY  C19  C14  C15  118.02  3.000
 ODY  C19  C14  C4   119.62  3.000
 ODY  C15  C14  C4   122.32  3.000
 ODY  H41  C11  C12  119.38  3.000
 ODY  H41  C11  C10  120.71  3.000
 ODY  C12  C11  C10  119.91  3.000
 ODY  O6   C7   C12  117.45  3.000
 ODY  O6   C7   C8   120.95  3.000
 ODY  C12  C7   C8   121.56  3.000
 ODY  C2   C8   C9   123.54  3.000
 ODY  C2   C8   C7   117.84  3.000
 ODY  C9   C8   C7   118.63  3.000
 ODY  H39  C9   C10  119.74  3.000
 ODY  H39  C9   C8   120.14  3.000
 ODY  C10  C9   C8   120.13  3.000
 ODY  H40  C10  C9   119.88  3.000
 ODY  H40  C10  C11  119.37  3.000
 ODY  C9   C10  C11  120.75  3.000
 ODY  O13  C12  C7   121.46  3.000
 ODY  C7   C12  C11  119.03  3.000
 ODY  O13  C12  C11  119.52  3.000
 ODY  C29  C3   C2   124.57  3.000
 ODY  C29  C3   C4   115.18  3.000
 ODY  C2   C3   C4   120.14  3.000
 ODY  C1   C2   C3   124.06  3.000
 ODY  C3   C2   C8   118.05  3.000
 ODY  C1   C2   C8   117.89  3.000
 ODY  C7   O6   C4   115.56  3.000
 ODY  H42  O13  C12  109.87  3.000
 ODY  H43  C15  C16  118.85  3.000
 ODY  H43  C15  C14  120.06  3.000
 ODY  C16  C15  C14  121.09  3.000
 ODY  H44  C16  C17  119.38  3.000
 ODY  H44  C16  C15  120.26  3.000
 ODY  C17  C16  C15  120.36  3.000
 ODY  O20  C17  C18  124.54  3.000
 ODY  C18  C17  C16  119.22  3.000
 ODY  O20  C17  C16  116.24  3.000
 ODY  H45  C18  C19  118.96  3.000
 ODY  H45  C18  C17  121.51  3.000
 ODY  C19  C18  C17  119.53  3.000
 ODY  H46  C19  C18  118.47  3.000
 ODY  H46  C19  C14  119.74  3.000
 ODY  C18  C19  C14  121.79  3.000
 ODY  C21  O20  C17  119.14  3.000
 ODY  H47  C21  H48  107.38  3.000
 ODY  H47  C21  C22  109.22  3.000
 ODY  H48  C21  C22  110.50  3.000
 ODY  H47  C21  O20  110.88  3.000
 ODY  H48  C21  O20  110.50  3.000
 ODY  C22  C21  O20  108.36  3.000
 ODY  H49  C22  H50  106.58  3.000
 ODY  H49  C22  N23  108.96  3.000
 ODY  H50  C22  N23  112.31  3.000
 ODY  H49  C22  C21  109.57  3.000
 ODY  H50  C22  C21  107.16  3.000
 ODY  N23  C22  C21  112.09  3.000
 ODY  C26  N23  C24   90.89  3.000
 ODY  C24  N23  C22  117.94  3.000
 ODY  C26  N23  C22  118.53  3.000
 ODY  H52  C24  H51  108.37  3.000
 ODY  H52  C24  C25  118.22  3.000
 ODY  H51  C24  C25  111.74  3.000
 ODY  H52  C24  N23  115.60  3.000
 ODY  H51  C24  N23  113.15  3.000
 ODY  C25  C24  N23   88.84  3.000
 ODY  H53  C25  C27  110.55  3.000
 ODY  H53  C25  C26  111.83  3.000
 ODY  C27  C25  C26  118.53  3.000
 ODY  H53  C25  C24  111.55  3.000
 ODY  C27  C25  C24  116.79  3.000
 ODY  C26  C25  C24   85.50  3.000
 ODY  H54  C26  H55  108.40  3.000
 ODY  H54  C26  C25  111.69  3.000
 ODY  H55  C26  C25  118.13  3.000
 ODY  H54  C26  N23  113.33  3.000
 ODY  H55  C26  N23  115.58  3.000
 ODY  C25  C26  N23   88.78  3.000
 ODY  H56  C27  H57  108.67  3.000
 ODY  H56  C27  F28  108.14  3.000
 ODY  H57  C27  F28  107.90  3.000
 ODY  H56  C27  C25  111.19  3.000
 ODY  H57  C27  C25  111.12  3.000
 ODY  F28  C27  C25  109.71  3.000
 ODY  C34  C29  C30  119.38  3.000
 ODY  C34  C29  C3   120.01  3.000
 ODY  C30  C29  C3   120.58  3.000
 ODY  H58  C30  C31  120.04  3.000
 ODY  H58  C30  C29  120.16  3.000
 ODY  C31  C30  C29  119.80  3.000
 ODY  H59  C31  C32  119.24  3.000
 ODY  H59  C31  C30  119.81  3.000
 ODY  C32  C31  C30  120.94  3.000
 ODY  H60  C32  C33  120.44  3.000
 ODY  H60  C32  C31  120.07  3.000
 ODY  C33  C32  C31  119.48  3.000
 ODY  O35  C33  C34  117.53  3.000
 ODY  O35  C33  C32  122.64  3.000
 ODY  C34  C33  C32  119.82  3.000
 ODY  H61  C34  C33  118.99  3.000
 ODY  H61  C34  C29  120.42  3.000
 ODY  C33  C34  C29  120.57  3.000
 ODY  H62  O35  C33  110.46  3.000
 ODY  H36  C1   H37  107.67  3.000
 ODY  H36  C1   H38  106.77  3.000
 ODY  H37  C1   H38  108.04  3.000
 ODY  H36  C1   C2   111.50  3.000
 ODY  H37  C1   C2   112.08  3.000
 ODY  H38  C1   C2   110.57  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
 ODY  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 ODY  CONST_02  C17  C18  C19  C14     0.00   0.0  0
 ODY  CONST_03  C8   C9   C10  C11     0.00   0.0  0
 ODY  CONST_04  C8   C7   C12  C11     0.00   0.0  0
 ODY  CONST_05  C10  C11  C12  C7      0.00   0.0  0
 ODY  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 ODY  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 ODY  CONST_08  C12  C7   C8   C9      0.00   0.0  0
 ODY  CONST_09  C18  C17  C16  C15     0.00   0.0  0
 ODY  CONST_10  C18  C19  C14  C15     0.00   0.0  0
 ODY  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 ODY  CONST_12  C19  C14  C15  C16     0.00   0.0  0
 ODY  CONST_13  C32  C31  C30  C29     0.00   0.0  0
 ODY  CONST_14  C32  C33  C34  C29     0.00   0.0  0
 ODY  CONST_15  C33  C32  C31  C30     0.00   0.0  0
 ODY  CONST_16  C33  C34  C29  C30     0.00   0.0  0
 ODY  CONST_17  C34  C29  C30  C31     0.00   0.0  0
 ODY  CONST_18  C34  C33  C32  C31     0.00   0.0  0
 ODY  CONST_19  C16  C15  C14  C4    180.00   0.0  0
 ODY  CONST_20  C18  C19  C14  C4    180.00   0.0  0
 ODY  CONST_21  C31  C30  C29  C3    180.00   0.0  0
 ODY  CONST_22  C33  C34  C29  C3    180.00   0.0  0
 ODY  CONST_23  O13  C12  C7   C8    180.00   0.0  0
 ODY  CONST_24  O13  C12  C11  C10   180.00   0.0  0
 ODY  CONST_25  O13  C12  C7   O6      0.00   0.0  0
 ODY  CONST_26  O20  C17  C16  C15   180.00   0.0  0
 ODY  CONST_27  O20  C17  C18  C19   180.00   0.0  0
 ODY  CONST_28  O35  C33  C34  C29   180.00   0.0  0
 ODY  CONST_29  O35  C33  C32  C31   180.00   0.0  0
 ODY  CONST_30  H43  C15  C14  C4      0.00   0.0  0
 ODY  CONST_31  H46  C19  C14  C4      0.00   0.0  0
 ODY  CONST_32  H44  C16  C15  C14   180.00   0.0  0
 ODY  CONST_33  H45  C18  C19  C14   180.00   0.0  0
 ODY  CONST_34  H39  C9   C10  C11   180.00   0.0  0
 ODY  CONST_35  H41  C11  C12  C7    180.00   0.0  0
 ODY  CONST_36  H40  C10  C9   C8    180.00   0.0  0
 ODY  CONST_37  H58  C30  C29  C3      0.00   0.0  0
 ODY  CONST_38  H61  C34  C29  C3      0.00   0.0  0
 ODY  CONST_39  H59  C31  C30  C29   180.00   0.0  0
 ODY  CONST_40  H60  C32  C31  C30   180.00   0.0  0
 ODY  Var_01    C8   C2   C3   C4     -1.27  30.0  1
 ODY  Var_02    C30  C29  C3   C4    118.41  30.0  2
 ODY  Var_03    C12  C7   O6   C4    147.02  30.0  1
 ODY  Var_04    C3   C2   C8   C7     15.39  30.0  1
 ODY  Var_05    C25  C26  N23  C24    18.81  30.0  1
 ODY  Var_06    H38  C1   C2   C8     49.20  30.0  3
 ODY  Var_07    C22  C21  O20  C17  -179.17  30.0  3
 ODY  Var_08    N23  C22  C21  O20    62.58  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
 ODY  chir_01  C4   C14  C3   O6   negativ
 ODY  chir_02  C25  C26  C27  C24  negativ

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
 ODY  plan-1  C4   0.020
 ODY  plan-1  C14  0.020
 ODY  plan-1  C15  0.020
 ODY  plan-1  C16  0.020
 ODY  plan-1  C17  0.020
 ODY  plan-1  C18  0.020
 ODY  plan-1  C19  0.020
 ODY  plan-1  O20  0.020
 ODY  plan-1  H43  0.020
 ODY  plan-1  H44  0.020
 ODY  plan-1  H45  0.020
 ODY  plan-1  H46  0.020
 ODY  plan-2  C11  0.020
 ODY  plan-2  C7   0.020
 ODY  plan-2  C8   0.020
 ODY  plan-2  C9   0.020
 ODY  plan-2  C10  0.020
 ODY  plan-2  C12  0.020
 ODY  plan-2  C2   0.020
 ODY  plan-2  O6   0.020
 ODY  plan-2  O13  0.020
 ODY  plan-2  H41  0.020
 ODY  plan-2  H39  0.020
 ODY  plan-2  H40  0.020
 ODY  plan-3  C3   0.020
 ODY  plan-3  C29  0.020
 ODY  plan-3  C30  0.020
 ODY  plan-3  C31  0.020
 ODY  plan-3  C32  0.020
 ODY  plan-3  C33  0.020
 ODY  plan-3  C34  0.020
 ODY  plan-3  O35  0.020
 ODY  plan-3  H58  0.020
 ODY  plan-3  H59  0.020
 ODY  plan-3  H60  0.020
 ODY  plan-3  H61  0.020

