# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:47:11 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 3-[6-[(1~{S},6~{R})-3-oxabicyclo[4.1.0]heptan-6-yl]pyridin-2-yl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(c1)c2cccc(n2)[C@]34CCOC[C@H]3C4
#
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
 G62  G62  3-[6-[(1~{S},6~{R})-3-oxabicyclo[4.1.0]heptan-6-yl]pyridin-2-yl]phenol  ligand  37  20  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_G62
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
 G62  C10  C  CR16  0  -0.141   0.0062   2.9473   0.3572
 G62  C15  C  CH2   0  -0.469  -2.5527  -0.8157  -1.3172
 G62  C17  C  CH2   0  -0.168  -3.7861  -1.8761   0.7341
 G62  C20  C  CH2   0  -0.484  -3.8234   0.9775   0.0571
 G62  C11  C  CR16  0  -0.353  -1.2272   2.3278   0.2351
 G62  C16  C  CH1   0  -0.276  -2.5480  -1.2571   0.1063
 G62  N13  N  N     0  -0.465  -0.1421   0.2586  -0.1753
 G62  C09  C  CR16  0  -0.350   1.1646   2.2051   0.2114
 G62  C06  C  CR6   0   0.085   2.2289  -0.0277  -0.2492
 G62  O18  O  O2    0  -0.478  -4.7423  -0.9415   1.1795
 G62  C12  C  CR6   0   0.302  -1.2613   0.9608  -0.0378
 G62  C04  C  CR16  0  -0.228   3.2232  -2.0129  -1.1770
 G62  C19  C  CH2   0  -0.202  -5.0133   0.0443   0.2110
 G62  C03  C  CR16  0  -0.347   4.4589  -1.6650  -0.6551
 G62  C05  C  CR16  0  -0.320   2.1096  -1.2107  -0.9772
 G62  C14  C  CT    0  -0.091  -2.5422   0.2191  -0.2205
 G62  C02  C  CR6   0   0.392   4.5810  -0.4899   0.0829
 G62  C07  C  CR16  0  -0.470   3.4697   0.3227   0.2824
 G62  C08  C  CR6   0   0.223   1.0450   0.8416  -0.0546
 G62  H1   H  HCR6  0   0.271   0.0629   4.0098   0.5544
 G62  H2   H  HCH2  0   0.261  -1.6415  -0.9355  -1.8891
 G62  H3   H  HCH2  0   0.254  -3.4642  -0.9287  -1.8942
 G62  H4   H  HCH2  0   0.204  -4.2481  -2.5745   0.0224
 G62  H5   H  HCH2  0   0.236  -3.4927  -2.4554   1.6107
 G62  H6   H  HCH2  0   0.240  -4.0258   1.7048  -0.7340
 G62  H7   H  HCH2  0   0.235  -3.7219   1.5398   0.9896
 G62  H8   H  HCR6  0   0.269  -2.1336   2.9063   0.3392
 G62  H9   H  HCH1  0   0.270  -1.6070  -1.6533   0.4694
 G62  H10  H  HCR6  0   0.266   2.1307   2.6845   0.2824
 G62  H11  H  HCR6  0   0.258   3.1297  -2.9254  -1.7517
 G62  H12  H  HCH2  0   0.245  -5.8820   0.6072   0.5554
 G62  H13  H  HCH2  0   0.204  -5.2873  -0.4135  -0.7509
 G62  H14  H  HCR6  0   0.265   5.3246  -2.2962  -0.8125
 G62  H15  H  HCR6  0   0.255   1.1510  -1.4930  -1.3891
 G62  H16  H  HOH1  0   0.475   5.7598   0.6415   1.0760
 G62  H17  H  HCR6  0   0.266   3.5762   1.2250   0.8748
 G62  O01  O  OH1   0  -0.634   5.7945  -0.1877   0.5860

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
 G62  C04  C05  aromatic  1.387  0.020  1.387
 G62  C04  C03  aromatic  1.386  0.020  1.386
 G62  C05  C06  aromatic  1.394  0.020  1.394
 G62  C09  C10  aromatic  1.383  0.020  1.383
 G62  C09  C08  aromatic  1.394  0.020  1.394
 G62  C10  C11  aromatic  1.386  0.020  1.386
 G62  C11  C12  aromatic  1.394  0.020  1.394
 G62  C03  C02  aromatic  1.393  0.020  1.393
 G62  C08  C06  single    1.482  0.020  1.482
 G62  C08  N13  aromatic  1.328  0.020  1.328
 G62  C06  C07  aromatic  1.395  0.020  1.395
 G62  N13  C12  aromatic  1.328  0.020  1.328
 G62  C12  C14  single    1.491  0.020  1.491
 G62  C02  C07  aromatic  1.391  0.020  1.391
 G62  C02  O01  single    1.348  0.020  1.348
 G62  C15  C14  single    1.508  0.020  1.508
 G62  C15  C16  single    1.490  0.020  1.490
 G62  C14  C20  single    1.514  0.020  1.514
 G62  C14  C16  single    1.512  0.020  1.512
 G62  C20  C19  single    1.520  0.020  1.520
 G62  C16  C17  single    1.520  0.020  1.520
 G62  C19  O18  single    1.408  0.020  1.408
 G62  O18  C17  single    1.409  0.020  1.409
 G62  C10  H1   single    0.930  0.020  1.080
 G62  C15  H2   single    0.970  0.020  1.090
 G62  C15  H3   single    0.970  0.020  1.090
 G62  C17  H4   single    0.970  0.020  1.090
 G62  C17  H5   single    0.970  0.020  1.090
 G62  C20  H6   single    0.970  0.020  1.090
 G62  C20  H7   single    0.970  0.020  1.090
 G62  C11  H8   single    0.930  0.020  1.080
 G62  C16  H9   single    0.970  0.020  1.090
 G62  C09  H10  single    0.930  0.020  1.080
 G62  C04  H11  single    0.930  0.020  1.080
 G62  C19  H12  single    0.970  0.020  1.090
 G62  C19  H13  single    0.970  0.020  1.090
 G62  C03  H14  single    0.930  0.020  1.080
 G62  C05  H15  single    0.930  0.020  1.080
 G62  O01  H16  single    0.850  0.020  0.980
 G62  C07  H17  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
 G62  H1   C10  C09  120.13  3.000
 G62  H1   C10  C11  120.11  3.000
 G62  C09  C10  C11  119.75  3.000
 G62  H3   C15  H2   114.51  3.000
 G62  H3   C15  C14  117.66  3.000
 G62  H2   C15  C14  117.02  3.000
 G62  H3   C15  C16  118.68  3.000
 G62  H2   C15  C16  117.98  3.000
 G62  C14  C15  C16   60.57  3.000
 G62  H5   C17  H4   107.21  3.000
 G62  H5   C17  O18  106.30  3.000
 G62  H4   C17  O18  109.93  3.000
 G62  H5   C17  C16  109.21  3.000
 G62  H4   C17  C16  109.50  3.000
 G62  O18  C17  C16  114.40  3.000
 G62  H7   C20  H6   106.98  3.000
 G62  H7   C20  C14  109.59  3.000
 G62  H6   C20  C14  110.92  3.000
 G62  H7   C20  C19  107.58  3.000
 G62  H6   C20  C19  109.67  3.000
 G62  C14  C20  C19  111.93  3.000
 G62  H8   C11  C12  121.56  3.000
 G62  H8   C11  C10  119.93  3.000
 G62  C12  C11  C10  118.51  3.000
 G62  H9   C16  C14  115.21  3.000
 G62  H9   C16  C17  114.84  3.000
 G62  C14  C16  C17  119.34  3.000
 G62  H9   C16  C15  115.53  3.000
 G62  C17  C16  C15  120.83  3.000
 G62  C14  C16  C15   60.29  3.000
 G62  C08  N13  C12  120.77  3.000
 G62  H10  C09  C08  121.53  3.000
 G62  H10  C09  C10  120.24  3.000
 G62  C08  C09  C10  118.22  3.000
 G62  C08  C06  C07  120.89  3.000
 G62  C07  C06  C05  119.24  3.000
 G62  C08  C06  C05  119.87  3.000
 G62  C19  O18  C17  112.17  3.000
 G62  C14  C12  N13  116.62  3.000
 G62  C14  C12  C11  122.18  3.000
 G62  N13  C12  C11  121.19  3.000
 G62  H11  C04  C05  119.65  3.000
 G62  H11  C04  C03  119.25  3.000
 G62  C05  C04  C03  121.10  3.000
 G62  H13  C19  H12  107.01  3.000
 G62  H13  C19  O18  110.98  3.000
 G62  H12  C19  O18  107.29  3.000
 G62  H13  C19  C20  111.22  3.000
 G62  H12  C19  C20  109.79  3.000
 G62  O18  C19  C20  110.41  3.000
 G62  H14  C03  C02  119.91  3.000
 G62  H14  C03  C04  120.78  3.000
 G62  C02  C03  C04  119.30  3.000
 G62  H15  C05  C04  120.41  3.000
 G62  H15  C05  C06  119.77  3.000
 G62  C04  C05  C06  119.82  3.000
 G62  C12  C14  C16  117.54  3.000
 G62  C16  C14  C20  116.49  3.000
 G62  C12  C14  C20  117.07  3.000
 G62  C16  C14  C15   59.14  3.000
 G62  C20  C14  C15  118.10  3.000
 G62  C12  C14  C15  115.87  3.000
 G62  C07  C02  O01  122.32  3.000
 G62  O01  C02  C03  117.76  3.000
 G62  C07  C02  C03  119.92  3.000
 G62  H17  C07  C02  119.07  3.000
 G62  H17  C07  C06  120.30  3.000
 G62  C02  C07  C06  120.61  3.000
 G62  C06  C08  C09  122.02  3.000
 G62  C06  C08  N13  116.41  3.000
 G62  C09  C08  N13  121.55  3.000
 G62  H16  O01  C02  110.50  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
 G62  CONST_01  C06  C08  C09  C10   180.00   0.0  0
 G62  CONST_02  N13  C08  C09  C10     0.00   0.0  0
 G62  CONST_03  N13  C12  C11  C10     0.00   0.0  0
 G62  CONST_04  C08  C09  C10  C11     0.00   0.0  0
 G62  CONST_05  C08  N13  C12  C11     0.00   0.0  0
 G62  CONST_08  C12  C11  C10  C09     0.00   0.0  0
 G62  CONST_11  C12  N13  C08  C09     0.00   0.0  0
 G62  CONST_12  C03  C04  C05  C06     0.00   0.0  0
 G62  CONST_13  C12  N13  C08  C06   180.00   0.0  0
 G62  CONST_14  C03  C02  C07  C06     0.00   0.0  0
 G62  CONST_15  C08  C06  C05  C04   180.00   0.0  0
 G62  CONST_16  C07  C06  C05  C04     0.00   0.0  0
 G62  CONST_17  C07  C02  C03  C04     0.00   0.0  0
 G62  CONST_18  C02  C03  C04  C05     0.00   0.0  0
 G62  CONST_19  C02  C07  C06  C05     0.00   0.0  0
 G62  CONST_20  C08  C06  C07  C02   180.00   0.0  0
 G62  CONST_21  C14  C12  C11  C10   180.00   0.0  0
 G62  CONST_22  C08  N13  C12  C14   180.00   0.0  0
 G62  CONST_23  O01  C02  C07  C06   180.00   0.0  0
 G62  CONST_24  O01  C02  C03  C04   180.00   0.0  0
 G62  CONST_25  H10  C09  C10  C11   180.00   0.0  0
 G62  CONST_26  H8   C11  C12  N13   180.00   0.0  0
 G62  CONST_27  H11  C04  C05  C06   180.00   0.0  0
 G62  CONST_28  H1   C10  C11  C12   180.00   0.0  0
 G62  CONST_29  H15  C05  C04  C03   180.00   0.0  0
 G62  CONST_30  H17  C07  C02  C03   180.00   0.0  0
 G62  CONST_31  H14  C03  C04  C05   180.00   0.0  0
 G62  Var_01    C11  C12  C14  C15   139.95  30.0  2
 G62  Var_02    C19  C20  C14  C15    49.72  30.0  1
 G62  Var_03    C17  C16  C14  C15  -110.87  30.0  1
 G62  Var_04    O18  C17  C16  C15   -82.03  30.0  1
 G62  Var_05    C20  C19  O18  C17   -70.65  30.0  1
 G62  Var_06    C14  C20  C19  O18    53.47  30.0  1

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
 G62  chir_01  C16  C15  C14  C17  both

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
 G62  plan-1  C10  0.020
 G62  plan-1  C11  0.020
 G62  plan-1  N13  0.020
 G62  plan-1  C09  0.020
 G62  plan-1  C06  0.020
 G62  plan-1  C12  0.020
 G62  plan-1  C14  0.020
 G62  plan-1  C08  0.020
 G62  plan-1  H1   0.020
 G62  plan-1  H8   0.020
 G62  plan-1  H10  0.020
 G62  plan-2  C06  0.020
 G62  plan-2  C04  0.020
 G62  plan-2  C03  0.020
 G62  plan-2  C05  0.020
 G62  plan-2  C02  0.020
 G62  plan-2  C07  0.020
 G62  plan-2  C08  0.020
 G62  plan-2  H11  0.020
 G62  plan-2  H14  0.020
 G62  plan-2  H15  0.020
 G62  plan-2  H17  0.020
 G62  plan-2  O01  0.020

