# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 16:22:10 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: (3~{R},4~{R})-4-[(3,4-dimethoxyphenyl)methyl]-3-[(3-methoxy-4-oxidanyl-phenyl)methyl]oxolan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(C[C@@H]2[C@H](COC2=O)Cc3ccc(OC)c(OC)c3)ccc1O
#
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
 EQC  EQC  (3~{R},4~{R})-4-[(3,4-dimethoxyphenyl)methyl]-3-[(3-methoxy-4-oxidanyl-phenyl)methyl]oxolan-2-one  ligand  51  27  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EQC
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
 EQC  C4   C  CR5   0   0.591  24.6051  80.1629  29.2805
 EQC  C14  C  CR16  0  -0.321  25.9745  75.7950  28.1870
 EQC  C5   C  CH2   0  -0.532  23.1293  77.7784  26.8572
 EQC  C6   C  CH2   0  -0.507  25.3115  77.7755  29.5853
 EQC  C11  C  CR6   0   0.294  23.5377  77.2928  22.5925
 EQC  C7   C  CR6   0   0.116  25.1329  76.3542  29.1338
 EQC  C8   C  CR6   0   0.139  23.2391  77.6183  25.3661
 EQC  C9   C  CR16  0  -0.444  24.1083  76.6508  24.8491
 EQC  C10  C  CR6   0   0.324  24.2642  76.4764  23.4857
 EQC  C12  C  CR16  0  -0.368  22.6775  78.2493  23.1036
 EQC  C13  C  CR16  0  -0.335  22.5283  78.4084  24.4826
 EQC  C3   C  CR15  0  -0.431  24.2785  78.7218  28.9597
 EQC  C1   C  CH2   0  -0.153  23.9501  80.1748  27.0929
 EQC  C15  C  CR16  0  -0.336  25.7579  74.5034  27.7128
 EQC  C16  C  CR6   0   0.265  24.6929  73.7559  28.1781
 EQC  C17  C  CR6   0   0.310  23.8387  74.3099  29.1492
 EQC  C18  C  CR16  0  -0.422  24.0646  75.5930  29.6177
 EQC  C2   C  CR15  0  -0.278  24.2023  78.7037  27.4326
 EQC  C20  C  CH3   0  -0.434  23.0291  77.8318  20.3464
 EQC  C21  C  CH3   0  -0.430  21.8744  73.9948  30.4491
 EQC  O1   O  O     0  -0.437  24.4465  80.9308  28.2046
 EQC  O2   O  O2    0  -0.462  25.0695  75.5589  22.9173
 EQC  O4   O  O2    0  -0.487  22.8376  73.4947  29.5448
 EQC  O5   O  OH1   0  -0.629  24.4940  72.5103  27.6991
 EQC  O6   O  O     0  -0.430  24.9760  80.6171  30.3288
 EQC  H1   H  HCR6  0   0.246  26.8097  76.3659  27.8001
 EQC  H2   H  HCH2  0   0.250  22.1444  78.1718  27.1257
 EQC  H3   H  HCH2  0   0.269  23.2122  76.7989  27.3297
 EQC  H4   H  HCH2  0   0.255  26.3137  78.1162  29.3138
 EQC  H5   H  HCH2  0   0.259  25.2376  77.8453  30.6728
 EQC  H6   H  HCR6  0   0.286  24.6565  76.0277  25.5460
 EQC  H7   H  HCR6  0   0.276  22.1045  78.8838  22.4409
 EQC  H8   H  HCR6  0   0.243  21.8417  79.1589  24.8552
 EQC  H9   H  HCR5  0   0.302  23.2894  78.5098  29.3869
 EQC  H10  H  HCH2  0   0.255  24.4666  80.5115  26.1959
 EQC  H11  H  HCH2  0   0.238  22.8837  80.3873  26.9809
 EQC  H12  H  HCR6  0   0.262  26.4187  74.0757  26.9686
 EQC  H13  H  HCR6  0   0.277  23.4066  76.0297  30.3596
 EQC  H14  H  HCH3  0   0.258  26.3760  74.0419  23.1191
 EQC  H15  H  HCH3  0   0.225  26.4937  75.2518  24.4102
 EQC  H16  H  HCH3  0   0.225  25.1484  74.0927  24.3978
 EQC  H17  H  HCR5  0   0.275  25.1798  78.4096  27.0349
 EQC  H18  H  HCH3  0   0.257  23.3357  77.4906  19.3604
 EQC  H19  H  HCH3  0   0.225  21.9484  77.6962  20.4449
 EQC  H20  H  HCH3  0   0.225  23.2567  78.8978  20.4355
 EQC  H21  H  HCH3  0   0.261  21.1475  73.2008  30.6002
 EQC  H22  H  HCH3  0   0.230  22.3188  74.2546  31.4132
 EQC  H23  H  HCH3  0   0.230  21.3620  74.8733  30.0482
 EQC  H24  H  HOH1  0   0.469  23.7160  72.1177  28.1137
 EQC  O3   O  O2    0  -0.462  23.7470  77.0566  21.2817
 EQC  C19  C  CH3   0  -0.438  25.8021  74.7010  23.7661

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
 EQC  C20  O3   single    1.411  0.020  1.411
 EQC  O3   C11  single    1.348  0.020  1.348
 EQC  C11  C12  aromatic  1.384  0.020  1.384
 EQC  C11  C10  aromatic  1.411  0.020  1.411
 EQC  O2   C10  single    1.347  0.020  1.347
 EQC  O2   C19  single    1.412  0.020  1.412
 EQC  C12  C13  aromatic  1.396  0.020  1.396
 EQC  C10  C9   aromatic  1.383  0.020  1.383
 EQC  C13  C8   aromatic  1.382  0.020  1.382
 EQC  C9   C8   aromatic  1.400  0.020  1.400
 EQC  C8   C5   single    1.504  0.020  1.504
 EQC  C5   C2   single    1.529  0.020  1.529
 EQC  C1   C2   single    1.531  0.020  1.531
 EQC  C1   O1   single    1.433  0.020  1.433
 EQC  C2   C3   single    1.529  0.020  1.529
 EQC  C15  C14  aromatic  1.393  0.020  1.393
 EQC  C15  C16  aromatic  1.382  0.020  1.382
 EQC  O1   C4   single    1.331  0.020  1.331
 EQC  O5   C16  single    1.349  0.020  1.349
 EQC  C14  C7   aromatic  1.385  0.020  1.385
 EQC  C16  C17  aromatic  1.407  0.020  1.407
 EQC  C3   C4   single    1.512  0.020  1.512
 EQC  C3   C6   single    1.534  0.020  1.534
 EQC  C7   C6   single    1.502  0.020  1.502
 EQC  C7   C18  aromatic  1.398  0.020  1.398
 EQC  C4   O6   double    1.201  0.020  1.201
 EQC  C17  C18  aromatic  1.384  0.020  1.384
 EQC  C17  O4   single    1.350  0.020  1.350
 EQC  O4   C21  single    1.413  0.020  1.413
 EQC  C14  H1   single    0.930  0.020  1.080
 EQC  C5   H2   single    0.970  0.020  1.090
 EQC  C5   H3   single    0.970  0.020  1.090
 EQC  C6   H4   single    0.970  0.020  1.090
 EQC  C6   H5   single    0.970  0.020  1.090
 EQC  C9   H6   single    0.930  0.020  1.080
 EQC  C12  H7   single    0.930  0.020  1.080
 EQC  C13  H8   single    0.930  0.020  1.080
 EQC  C3   H9   single    0.970  0.020  1.090
 EQC  C1   H10  single    0.970  0.020  1.090
 EQC  C1   H11  single    0.970  0.020  1.090
 EQC  C15  H12  single    0.930  0.020  1.080
 EQC  C18  H13  single    0.930  0.020  1.080
 EQC  C19  H14  single    0.970  0.020  1.090
 EQC  C19  H15  single    0.970  0.020  1.090
 EQC  C19  H16  single    0.970  0.020  1.090
 EQC  C2   H17  single    0.970  0.020  1.090
 EQC  C20  H18  single    0.970  0.020  1.090
 EQC  C20  H19  single    0.970  0.020  1.090
 EQC  C20  H20  single    0.970  0.020  1.090
 EQC  C21  H21  single    0.970  0.020  1.090
 EQC  C21  H22  single    0.970  0.020  1.090
 EQC  C21  H23  single    0.970  0.020  1.090
 EQC  O5   H24  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
 EQC  O6   C4   O1   121.60  3.000
 EQC  O6   C4   C3   127.75  3.000
 EQC  O1   C4   C3   110.64  3.000
 EQC  H1   C14  C15  119.15  3.000
 EQC  H1   C14  C7   120.00  3.000
 EQC  C15  C14  C7   120.84  3.000
 EQC  H3   C5   H2   106.56  3.000
 EQC  H3   C5   C2   109.09  3.000
 EQC  H2   C5   C2   108.77  3.000
 EQC  H3   C5   C8   109.17  3.000
 EQC  H2   C5   C8   110.33  3.000
 EQC  C2   C5   C8   112.73  3.000
 EQC  H5   C6   H4   106.83  3.000
 EQC  H5   C6   C3   108.72  3.000
 EQC  H4   C6   C3   108.89  3.000
 EQC  H5   C6   C7   110.60  3.000
 EQC  H4   C6   C7   109.23  3.000
 EQC  C3   C6   C7   112.40  3.000
 EQC  O3   C11  C12  125.21  3.000
 EQC  C12  C11  C10  119.07  3.000
 EQC  O3   C11  C10  115.73  3.000
 EQC  C18  C7   C6   120.13  3.000
 EQC  C18  C7   C14  118.77  3.000
 EQC  C6   C7   C14  121.03  3.000
 EQC  C13  C8   C9   118.59  3.000
 EQC  C9   C8   C5   119.03  3.000
 EQC  C13  C8   C5   122.38  3.000
 EQC  H6   C9   C10  120.29  3.000
 EQC  H6   C9   C8   118.30  3.000
 EQC  C10  C9   C8   121.41  3.000
 EQC  O2   C10  C9   124.70  3.000
 EQC  C9   C10  C11  119.53  3.000
 EQC  O2   C10  C11  115.77  3.000
 EQC  H7   C12  C13  118.79  3.000
 EQC  H7   C12  C11  120.55  3.000
 EQC  C13  C12  C11  120.66  3.000
 EQC  H8   C13  C12  119.10  3.000
 EQC  H8   C13  C8   120.15  3.000
 EQC  C12  C13  C8   120.75  3.000
 EQC  H9   C3   C2   109.96  3.000
 EQC  H9   C3   C6   109.19  3.000
 EQC  C2   C3   C6   115.69  3.000
 EQC  H9   C3   C4   107.22  3.000
 EQC  C6   C3   C4   110.85  3.000
 EQC  C2   C3   C4   103.53  3.000
 EQC  H11  C1   H10  108.56  3.000
 EQC  H11  C1   O1   108.35  3.000
 EQC  H10  C1   O1   108.16  3.000
 EQC  H11  C1   C2   111.73  3.000
 EQC  H10  C1   C2   113.70  3.000
 EQC  O1   C1   C2   106.13  3.000
 EQC  H12  C15  C16  119.20  3.000
 EQC  H12  C15  C14  120.34  3.000
 EQC  C16  C15  C14  120.45  3.000
 EQC  O5   C16  C17  121.27  3.000
 EQC  C17  C16  C15  119.17  3.000
 EQC  O5   C16  C15  119.57  3.000
 EQC  O4   C17  C18  125.55  3.000
 EQC  O4   C17  C16  114.49  3.000
 EQC  C18  C17  C16  119.96  3.000
 EQC  H13  C18  C17  120.40  3.000
 EQC  H13  C18  C7   118.79  3.000
 EQC  C17  C18  C7   120.80  3.000
 EQC  H17  C2   C1   108.93  3.000
 EQC  H17  C2   C3   108.74  3.000
 EQC  C1   C2   C3   102.62  3.000
 EQC  H17  C2   C5   109.09  3.000
 EQC  C3   C2   C5   114.70  3.000
 EQC  C1   C2   C5   112.48  3.000
 EQC  H20  C20  H19  108.61  3.000
 EQC  H20  C20  H18  108.72  3.000
 EQC  H19  C20  H18  108.75  3.000
 EQC  H20  C20  O3   112.06  3.000
 EQC  H19  C20  O3   112.02  3.000
 EQC  H18  C20  O3   106.57  3.000
 EQC  H23  C21  H22  108.84  3.000
 EQC  H23  C21  H21  108.94  3.000
 EQC  H22  C21  H21  108.84  3.000
 EQC  H23  C21  O4   111.67  3.000
 EQC  H22  C21  O4   111.82  3.000
 EQC  H21  C21  O4   106.64  3.000
 EQC  C1   O1   C4   111.34  3.000
 EQC  C19  O2   C10  118.07  3.000
 EQC  C21  O4   C17  118.64  3.000
 EQC  H24  O5   C16  109.99  3.000
 EQC  C20  O3   C11  117.98  3.000
 EQC  H16  C19  H15  108.53  3.000
 EQC  H16  C19  H14  108.79  3.000
 EQC  H15  C19  H14  108.77  3.000
 EQC  H16  C19  O2   112.03  3.000
 EQC  H15  C19  O2   112.09  3.000
 EQC  H14  C19  O2   106.53  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
 EQC  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 EQC  CONST_02  C17  C18  C7   C14     0.00   0.0  0
 EQC  CONST_03  C8   C13  C12  C11     0.00   0.0  0
 EQC  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 EQC  CONST_05  C16  C15  C14  C7      0.00   0.0  0
 EQC  CONST_06  C16  C17  C18  C7      0.00   0.0  0
 EQC  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 EQC  CONST_08  C12  C13  C8   C9      0.00   0.0  0
 EQC  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 EQC  CONST_10  C13  C8   C9   C10     0.00   0.0  0
 EQC  CONST_11  C18  C7   C14  C15     0.00   0.0  0
 EQC  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 EQC  CONST_13  O5   C16  C15  C14   180.00   0.0  0
 EQC  CONST_14  C12  C13  C8   C5    180.00   0.0  0
 EQC  CONST_15  C10  C9   C8   C5    180.00   0.0  0
 EQC  CONST_16  C15  C14  C7   C6    180.00   0.0  0
 EQC  CONST_17  C17  C18  C7   C6    180.00   0.0  0
 EQC  CONST_18  O4   C17  C18  C7    180.00   0.0  0
 EQC  CONST_19  O2   C10  C9   C8    180.00   0.0  0
 EQC  CONST_20  O3   C11  C10  C9    180.00   0.0  0
 EQC  CONST_21  O2   C10  C11  C12   180.00   0.0  0
 EQC  CONST_22  O3   C11  C12  C13   180.00   0.0  0
 EQC  CONST_23  O4   C17  C16  C15   180.00   0.0  0
 EQC  CONST_24  O5   C16  C17  C18   180.00   0.0  0
 EQC  CONST_25  H13  C18  C7   C14   180.00   0.0  0
 EQC  CONST_26  H8   C13  C12  C11   180.00   0.0  0
 EQC  CONST_27  H6   C9   C10  C11   180.00   0.0  0
 EQC  CONST_28  H12  C15  C14  C7    180.00   0.0  0
 EQC  CONST_29  H7   C12  C13  C8    180.00   0.0  0
 EQC  CONST_30  H1   C14  C15  C16   180.00   0.0  0
 EQC  Var_01    C2   C1   O1   C4    -17.29  30.0  1
 EQC  Var_02    C3   C6   C7   C14   103.36  30.0  2
 EQC  Var_03    C2   C5   C8   C9     85.30  30.0  2
 EQC  Var_04    O6   C4   O1   C1   -177.80  30.0  1
 EQC  Var_05    H18  C20  O3   C11  -179.96  30.0  3
 EQC  Var_06    H14  C19  O2   C10   179.67  30.0  3
 EQC  Var_07    H21  C21  O4   C17   177.73  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
 EQC  chir_01  C3  C2  C4  C6  positiv
 EQC  chir_02  C2  C3  C1  C5  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
 EQC  plan-1  C5   0.020
 EQC  plan-1  C11  0.020
 EQC  plan-1  C8   0.020
 EQC  plan-1  C9   0.020
 EQC  plan-1  C10  0.020
 EQC  plan-1  C12  0.020
 EQC  plan-1  C13  0.020
 EQC  plan-1  O2   0.020
 EQC  plan-1  H6   0.020
 EQC  plan-1  H7   0.020
 EQC  plan-1  H8   0.020
 EQC  plan-1  O3   0.020
 EQC  plan-2  C14  0.020
 EQC  plan-2  C6   0.020
 EQC  plan-2  C7   0.020
 EQC  plan-2  C15  0.020
 EQC  plan-2  C16  0.020
 EQC  plan-2  C17  0.020
 EQC  plan-2  C18  0.020
 EQC  plan-2  O4   0.020
 EQC  plan-2  O5   0.020
 EQC  plan-2  H1   0.020
 EQC  plan-2  H12  0.020
 EQC  plan-2  H13  0.020
 EQC  plan-3  C4   0.020
 EQC  plan-3  C3   0.020
 EQC  plan-3  O1   0.020
 EQC  plan-3  O6   0.020

