# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 04:32:19 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-[[(3~{S},4~{S},5~{R})-4-(hydroxymethyl)-5-(3-methoxy-4-oxidanyl-phenyl)oxolan-3-yl]methyl]-2-methoxy-phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(C[C@@H]2CO[C@H]([C@@H]2CO)c3ccc(O)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
 GFR  GFR  4-[[(3~{S},4~{S},5~{R})-4-(hydroxymethyl)-5-(3-methoxy-4-oxidanyl-phenyl)oxolan-3-yl]methyl]-2-methoxy-phenol  ligand  50  26  .  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_GFR
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
 GFR  CAY  C  CH3   0  -0.435  -150.6463  24.5912  14.3294
 GFR  OAX  O  O2    0  -0.465  -150.7335  23.4876  15.2046
 GFR  CAV  C  CR6   0   0.339  -151.8305  22.7072  15.1365
 GFR  CAW  C  CR16  0  -0.452  -152.8836  22.8914  14.2522
 GFR  CAU  C  CR6   0   0.256  -151.8790  21.6413  16.0497
 GFR  OAZ  O  OH1   0  -0.624  -150.8280  21.4995  16.8840
 GFR  CAT  C  CR16  0  -0.361  -152.9821  20.8030  16.0529
 GFR  CAS  C  CR16  0  -0.329  -154.0303  20.9950  15.1596
 GFR  CAR  C  CR6   0   0.131  -153.9855  22.0362  14.2468
 GFR  CAN  C  CH1   0   0.016  -155.0634  22.2340  13.2164
 GFR  CAO  C  CH1   0  -0.317  -155.0006  21.2271  12.0606
 GFR  CAP  C  CH2   0  -0.148  -153.9562  21.5836  11.0255
 GFR  OAQ  O  OH1   0  -0.666  -153.9983  20.6222   9.9954
 GFR  OAM  O  O2    0  -0.503  -156.3547  22.0839  13.7791
 GFR  CAL  C  CH2   0  -0.146  -157.1582  21.2490  12.9537
 GFR  CAK  C  CH1   0  -0.293  -156.4632  21.1811  11.5992
 GFR  CAJ  C  CH2   0  -0.535  -156.8498  22.3291  10.6556
 GFR  CAE  C  CR6   0   0.140  -158.3019  22.3065  10.2638
 GFR  CAD  C  CR16  0  -0.440  -159.1994  23.2357  10.7934
 GFR  CAF  C  CR16  0  -0.324  -158.7829  21.3567   9.3734
 GFR  CAG  C  CR16  0  -0.327  -160.1264  21.3267   9.0178
 GFR  CAH  C  CR6   0   0.262  -161.0149  22.2497   9.5421
 GFR  OAI  O  OH1   0  -0.632  -162.3138  22.2021   9.1742
 GFR  CAC  C  CR6   0   0.309  -160.5411  23.2176  10.4411
 GFR  OAB  O  O2    0  -0.488  -161.4790  24.0806  10.8931
 GFR  CAA  C  CH3   0  -0.429  -161.0924  25.0780  11.8149
 GFR  H1   H  HCH3  0   0.258  -149.7030  25.0860  14.5479
 GFR  H2   H  HCH3  0   0.225  -150.6467  24.2847  13.2795
 GFR  H3   H  HCH3  0   0.226  -151.4610  25.3039  14.4864
 GFR  H4   H  HCR6  0   0.275  -152.8614  23.7149  13.5487
 GFR  H5   H  HOH1  0   0.472  -150.9719  20.7470  17.4686
 GFR  H6   H  HCR6  0   0.267  -153.0260  19.9838  16.7626
 GFR  H7   H  HCR6  0   0.247  -154.8758  20.3193  15.1843
 GFR  H8   H  HCH1  0   0.224  -154.9643  23.2532  12.8113
 GFR  H9   H  HCH1  0   0.254  -154.7496  20.2437  12.4772
 GFR  H10  H  HCH2  0   0.195  -154.1391  22.5966  10.6432
 GFR  H11  H  HCH2  0   0.214  -152.9704  21.6086  11.5100
 GFR  H12  H  HOH1  0   0.452  -153.3436  20.8617   9.3330
 GFR  H13  H  HCH2  0   0.211  -157.2340  20.2473  13.3935
 GFR  H14  H  HCH2  0   0.226  -158.1675  21.6638  12.8995
 GFR  H15  H  HCH1  0   0.257  -156.6889  20.2322  11.1075
 GFR  H16  H  HCH2  0   0.249  -156.6091  23.2943  11.1101
 GFR  H17  H  HCH2  0   0.255  -156.2397  22.2567   9.7522
 GFR  H18  H  HCR6  0   0.274  -158.8272  23.9823  11.4843
 GFR  H19  H  HCR6  0   0.241  -158.1065  20.6290   8.9405
 GFR  H20  H  HCR6  0   0.257  -160.4914  20.5834   8.3195
 GFR  H21  H  HOH1  0   0.468  -162.8104  22.8967   9.6235
 GFR  H22  H  HCH3  0   0.260  -161.9878  25.6487  12.0484
 GFR  H23  H  HCH3  0   0.229  -160.6978  24.6466  12.7385
 GFR  H24  H  HCH3  0   0.229  -160.3435  25.7527  11.3922

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
 GFR  CAY  OAX  single    1.411  0.020  1.411
 GFR  OAX  CAV  single    1.348  0.020  1.348
 GFR  CAV  CAW  aromatic  1.387  0.020  1.387
 GFR  CAV  CAU  aromatic  1.405  0.020  1.405
 GFR  CAW  CAR  aromatic  1.395  0.020  1.395
 GFR  CAU  OAZ  single    1.349  0.020  1.349
 GFR  CAU  CAT  aromatic  1.385  0.020  1.385
 GFR  CAT  CAS  aromatic  1.391  0.020  1.391
 GFR  CAS  CAR  aromatic  1.385  0.020  1.385
 GFR  CAR  CAN  single    1.504  0.020  1.504
 GFR  CAN  CAO  single    1.534  0.020  1.534
 GFR  CAN  OAM  single    1.417  0.020  1.417
 GFR  CAO  CAP  single    1.513  0.020  1.513
 GFR  CAO  CAK  single    1.534  0.020  1.534
 GFR  CAP  OAQ  single    1.410  0.020  1.410
 GFR  OAM  CAL  single    1.423  0.020  1.423
 GFR  CAL  CAK  single    1.524  0.020  1.524
 GFR  CAK  CAJ  single    1.535  0.020  1.535
 GFR  CAJ  CAE  single    1.504  0.020  1.504
 GFR  CAE  CAD  aromatic  1.396  0.020  1.396
 GFR  CAE  CAF  aromatic  1.388  0.020  1.388
 GFR  CAD  CAC  aromatic  1.387  0.020  1.387
 GFR  CAF  CAG  aromatic  1.390  0.020  1.390
 GFR  CAG  CAH  aromatic  1.384  0.020  1.384
 GFR  CAH  OAI  single    1.351  0.020  1.351
 GFR  CAH  CAC  aromatic  1.403  0.020  1.403
 GFR  CAC  OAB  single    1.352  0.020  1.352
 GFR  OAB  CAA  single    1.412  0.020  1.412
 GFR  CAY  H1   single    0.970  0.020  1.090
 GFR  CAY  H2   single    0.970  0.020  1.090
 GFR  CAY  H3   single    0.970  0.020  1.090
 GFR  CAW  H4   single    0.930  0.020  1.080
 GFR  OAZ  H5   single    0.850  0.020  0.980
 GFR  CAT  H6   single    0.930  0.020  1.080
 GFR  CAS  H7   single    0.930  0.020  1.080
 GFR  CAN  H8   single    0.970  0.020  1.090
 GFR  CAO  H9   single    0.970  0.020  1.090
 GFR  CAP  H10  single    0.970  0.020  1.090
 GFR  CAP  H11  single    0.970  0.020  1.090
 GFR  OAQ  H12  single    0.850  0.020  0.980
 GFR  CAL  H13  single    0.970  0.020  1.090
 GFR  CAL  H14  single    0.970  0.020  1.090
 GFR  CAK  H15  single    0.970  0.020  1.090
 GFR  CAJ  H16  single    0.970  0.020  1.090
 GFR  CAJ  H17  single    0.970  0.020  1.090
 GFR  CAD  H18  single    0.930  0.020  1.080
 GFR  CAF  H19  single    0.930  0.020  1.080
 GFR  CAG  H20  single    0.930  0.020  1.080
 GFR  OAI  H21  single    0.850  0.020  0.980
 GFR  CAA  H22  single    0.970  0.020  1.090
 GFR  CAA  H23  single    0.970  0.020  1.090
 GFR  CAA  H24  single    0.970  0.020  1.090

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
 GFR  H3   CAY  H2   108.67  3.000
 GFR  H3   CAY  H1   108.71  3.000
 GFR  H2   CAY  H1   108.71  3.000
 GFR  H3   CAY  OAX  111.99  3.000
 GFR  H2   CAY  OAX  112.10  3.000
 GFR  H1   CAY  OAX  106.55  3.000
 GFR  CAV  OAX  CAY  118.14  3.000
 GFR  CAU  CAV  CAW  119.28  3.000
 GFR  CAU  CAV  OAX  115.75  3.000
 GFR  CAW  CAV  OAX  124.97  3.000
 GFR  H4   CAW  CAR  118.67  3.000
 GFR  H4   CAW  CAV  119.96  3.000
 GFR  CAR  CAW  CAV  121.38  3.000
 GFR  CAT  CAU  OAZ  123.72  3.000
 GFR  CAT  CAU  CAV  119.22  3.000
 GFR  OAZ  CAU  CAV  117.06  3.000
 GFR  H5   OAZ  CAU  109.92  3.000
 GFR  H6   CAT  CAS  119.61  3.000
 GFR  H6   CAT  CAU  119.39  3.000
 GFR  CAS  CAT  CAU  121.01  3.000
 GFR  H7   CAS  CAR  120.61  3.000
 GFR  H7   CAS  CAT  119.21  3.000
 GFR  CAR  CAS  CAT  120.18  3.000
 GFR  CAN  CAR  CAS  121.80  3.000
 GFR  CAN  CAR  CAW  119.22  3.000
 GFR  CAS  CAR  CAW  118.93  3.000
 GFR  H8   CAN  OAM  109.04  3.000
 GFR  H8   CAN  CAO  109.06  3.000
 GFR  OAM  CAN  CAO  105.49  3.000
 GFR  H8   CAN  CAR  108.01  3.000
 GFR  OAM  CAN  CAR  111.54  3.000
 GFR  CAO  CAN  CAR  113.61  3.000
 GFR  H9   CAO  CAK  107.79  3.000
 GFR  H9   CAO  CAP  108.24  3.000
 GFR  CAK  CAO  CAP  117.35  3.000
 GFR  H9   CAO  CAN  108.15  3.000
 GFR  CAK  CAO  CAN  101.96  3.000
 GFR  CAP  CAO  CAN  112.89  3.000
 GFR  H11  CAP  H10  106.38  3.000
 GFR  H11  CAP  OAQ  111.38  3.000
 GFR  H10  CAP  OAQ  111.70  3.000
 GFR  H11  CAP  CAO  108.85  3.000
 GFR  H10  CAP  CAO  109.91  3.000
 GFR  OAQ  CAP  CAO  108.58  3.000
 GFR  H12  OAQ  CAP  108.25  3.000
 GFR  CAL  OAM  CAN  110.27  3.000
 GFR  H14  CAL  H13  107.63  3.000
 GFR  H14  CAL  CAK  113.21  3.000
 GFR  H13  CAL  CAK  110.32  3.000
 GFR  H14  CAL  OAM  109.13  3.000
 GFR  H13  CAL  OAM  110.02  3.000
 GFR  CAK  CAL  OAM  106.51  3.000
 GFR  H15  CAK  CAJ  108.71  3.000
 GFR  H15  CAK  CAL  110.15  3.000
 GFR  CAJ  CAK  CAL  113.46  3.000
 GFR  H15  CAK  CAO  111.00  3.000
 GFR  CAJ  CAK  CAO  113.73  3.000
 GFR  CAL  CAK  CAO   99.56  3.000
 GFR  H17  CAJ  H16  106.21  3.000
 GFR  H17  CAJ  CAE  108.83  3.000
 GFR  H16  CAJ  CAE  109.50  3.000
 GFR  H17  CAJ  CAK  108.55  3.000
 GFR  H16  CAJ  CAK  110.43  3.000
 GFR  CAE  CAJ  CAK  113.08  3.000
 GFR  CAF  CAE  CAD  118.42  3.000
 GFR  CAF  CAE  CAJ  120.79  3.000
 GFR  CAD  CAE  CAJ  120.78  3.000
 GFR  H18  CAD  CAC  120.22  3.000
 GFR  H18  CAD  CAE  118.67  3.000
 GFR  CAC  CAD  CAE  121.11  3.000
 GFR  H19  CAF  CAG  119.11  3.000
 GFR  H19  CAF  CAE  119.97  3.000
 GFR  CAG  CAF  CAE  120.92  3.000
 GFR  H20  CAG  CAH  119.04  3.000
 GFR  H20  CAG  CAF  120.36  3.000
 GFR  CAH  CAG  CAF  120.60  3.000
 GFR  CAC  CAH  OAI  121.56  3.000
 GFR  CAC  CAH  CAG  119.06  3.000
 GFR  OAI  CAH  CAG  119.38  3.000
 GFR  H21  OAI  CAH  110.05  3.000
 GFR  OAB  CAC  CAH  114.84  3.000
 GFR  OAB  CAC  CAD  125.28  3.000
 GFR  CAH  CAC  CAD  119.88  3.000
 GFR  CAA  OAB  CAC  118.63  3.000
 GFR  H24  CAA  H23  108.84  3.000
 GFR  H24  CAA  H22  108.86  3.000
 GFR  H23  CAA  H22  108.84  3.000
 GFR  H24  CAA  OAB  111.79  3.000
 GFR  H23  CAA  OAB  111.82  3.000
 GFR  H22  CAA  OAB  106.59  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
 GFR  CONST_01  CAS  CAR  CAW  CAV     0.00   0.0  0
 GFR  CONST_02  CAS  CAT  CAU  CAV     0.00   0.0  0
 GFR  CONST_03  CAT  CAU  CAV  CAW     0.00   0.0  0
 GFR  CONST_04  CAT  CAS  CAR  CAW     0.00   0.0  0
 GFR  CONST_05  CAR  CAW  CAV  CAU     0.00   0.0  0
 GFR  CONST_06  CAR  CAS  CAT  CAU     0.00   0.0  0
 GFR  CONST_07  CAH  CAC  CAD  CAE     0.00   0.0  0
 GFR  CONST_08  CAH  CAG  CAF  CAE     0.00   0.0  0
 GFR  CONST_09  CAG  CAF  CAE  CAD     0.00   0.0  0
 GFR  CONST_10  CAG  CAH  CAC  CAD     0.00   0.0  0
 GFR  CONST_11  CAC  CAD  CAE  CAF     0.00   0.0  0
 GFR  CONST_12  CAC  CAH  CAG  CAF     0.00   0.0  0
 GFR  CONST_13  CAN  CAR  CAW  CAV   180.00   0.0  0
 GFR  CONST_14  CAN  CAR  CAS  CAT   180.00   0.0  0
 GFR  CONST_15  CAR  CAW  CAV  OAX   180.00   0.0  0
 GFR  CONST_16  CAT  CAU  CAV  OAX   180.00   0.0  0
 GFR  CONST_17  OAZ  CAU  CAV  CAW   180.00   0.0  0
 GFR  CONST_18  CAS  CAT  CAU  OAZ   180.00   0.0  0
 GFR  CONST_19  CAC  CAD  CAE  CAJ   180.00   0.0  0
 GFR  CONST_20  CAG  CAF  CAE  CAJ   180.00   0.0  0
 GFR  CONST_21  OAB  CAC  CAD  CAE   180.00   0.0  0
 GFR  CONST_22  OAI  CAH  CAC  CAD   180.00   0.0  0
 GFR  CONST_23  OAI  CAH  CAG  CAF   180.00   0.0  0
 GFR  CONST_24  OAB  CAC  CAH  CAG   180.00   0.0  0
 GFR  CONST_25  H6   CAT  CAU  CAV   180.00   0.0  0
 GFR  CONST_26  H7   CAS  CAR  CAW   180.00   0.0  0
 GFR  CONST_27  H4   CAW  CAV  CAU   180.00   0.0  0
 GFR  CONST_28  H20  CAG  CAF  CAE   180.00   0.0  0
 GFR  CONST_29  H19  CAF  CAE  CAD   180.00   0.0  0
 GFR  CONST_30  H18  CAD  CAE  CAF   180.00   0.0  0
 GFR  Var_01    CAK  CAL  OAM  CAN   -16.43  30.0  1
 GFR  Var_02    CAD  CAE  CAJ  CAK   106.59  30.0  2
 GFR  Var_03    CAW  CAV  OAX  CAY     1.02  30.0  2
 GFR  Var_04    H1   CAY  OAX  CAV   179.59  30.0  3
 GFR  Var_05    H22  CAA  OAB  CAC  -179.61  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
 GFR  chir_01  CAN  CAR  CAO  OAM  negativ
 GFR  chir_02  CAO  CAK  CAP  CAN  negativ
 GFR  chir_03  CAK  CAO  CAL  CAJ  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
 GFR  plan-1  OAX  0.020
 GFR  plan-1  CAV  0.020
 GFR  plan-1  CAW  0.020
 GFR  plan-1  CAU  0.020
 GFR  plan-1  OAZ  0.020
 GFR  plan-1  CAT  0.020
 GFR  plan-1  CAS  0.020
 GFR  plan-1  CAR  0.020
 GFR  plan-1  CAN  0.020
 GFR  plan-1  H4   0.020
 GFR  plan-1  H6   0.020
 GFR  plan-1  H7   0.020
 GFR  plan-2  CAJ  0.020
 GFR  plan-2  CAE  0.020
 GFR  plan-2  CAD  0.020
 GFR  plan-2  CAF  0.020
 GFR  plan-2  CAG  0.020
 GFR  plan-2  CAH  0.020
 GFR  plan-2  OAI  0.020
 GFR  plan-2  CAC  0.020
 GFR  plan-2  OAB  0.020
 GFR  plan-2  H18  0.020
 GFR  plan-2  H19  0.020
 GFR  plan-2  H20  0.020

