# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 15:21:33 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (3aS,4R,9bR)-2,2-difluoro-4-(4-hydroxyphenyl)-6-(methoxymethyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCc1cc(O)cc2[C@@H]3CC(F)(F)C[C@@H]3[C@@H](Oc12)c4ccc(O)cc4
#
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
 3AS  3AS  (3aS,4R,9bR)-2,2-difluoro-4-(4-hydroxyphenyl)-6-(methoxymethyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol  ligand  46  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3AS
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
 3AS  C1    C  CR6   0   0.377  -4.0369   0.1112   0.8594
 3AS  C2    C  CR16  0  -0.459  -3.6732  -1.1320   0.3444
 3AS  C3    C  CR6   0  -0.075  -2.3429  -1.4222   0.0873
 3AS  C4    C  CR6   0   0.301  -1.3760  -0.4447   0.3334
 3AS  O5    O  O2    0  -0.497  -0.0839  -0.7770   0.0642
 3AS  C6    C  CH1   0   0.002   0.8791  -0.1201   0.8679
 3AS  C8    C  CR6   0   0.060   2.2450  -0.6114   0.4769
 3AS  C9    C  CR16  0  -0.287   3.2650  -0.6068   1.4210
 3AS  C10   C  CR16  0  -0.371   4.5563  -0.9898   1.0922
 3AS  C11   C  CR6   0   0.343   4.8490  -1.3959  -0.2066
 3AS  O12   O  OH1   0  -0.632   6.0829  -1.7814  -0.5897
 3AS  C13   C  CR16  0  -0.325   3.8334  -1.4155  -1.1599
 3AS  C14   C  CR16  0  -0.290   2.5489  -1.0247  -0.8176
 3AS  C15   C  CH1   0  -0.306   0.7498   1.3907   0.7361
 3AS  C17   C  CH1   0  -0.293  -0.6917   1.8820   1.0334
 3AS  C19   C  CR6   0   0.057  -1.7253   0.8050   0.8274
 3AS  C20   C  CR16  0  -0.400  -3.0652   1.0690   1.1003
 3AS  C21   C  CH2   0  -0.556  -0.9213   3.0817   0.0785
 3AS  C22   C  CT    0   0.754   0.4191   3.3076  -0.5903
 3AS  F23   F  F     0  -0.344   0.3099   3.9069  -1.8100
 3AS  F24   F  F     0  -0.358   1.1828   4.1676   0.1627
 3AS  C25   C  CH2   0  -0.551   1.0862   1.9559  -0.6420
 3AS  C26   C  CH2   0  -0.134  -1.9028  -2.7587  -0.4431
 3AS  O27   O  O2    0  -0.488  -3.0093  -3.5963  -0.6196
 3AS  C28   C  CH3   0  -0.394  -2.6470  -4.8716  -1.0859
 3AS  O29   O  OH1   0  -0.643  -5.3225   0.4268   1.1401
 3AS  H2    H  HCR6  0   0.268  -4.4339  -1.8802   0.1583
 3AS  H6    H  HCH1  0   0.251   0.6977  -0.3794   1.9211
 3AS  H9    H  HCR6  0   0.255   3.0545  -0.3024   2.4398
 3AS  H10   H  HCR6  0   0.271   5.3307  -0.9774   1.8507
 3AS  H12   H  HOH1  0   0.474   6.6991  -1.7167   0.1485
 3AS  H13   H  HCR6  0   0.263   4.0533  -1.7360  -2.1707
 3AS  H14   H  HCR6  0   0.253   1.7804  -1.0489  -1.5788
 3AS  H15   H  HCH1  0   0.280   1.4263   1.8311   1.4729
 3AS  H17   H  HCH1  0   0.285  -0.7540   2.2202   2.0695
 3AS  H20   H  HCR6  0   0.258  -3.3543   2.0374   1.4933
 3AS  H211  H  HCH2  0   0.270  -1.6571   2.8337  -0.6877
 3AS  H212  H  HCH2  0   0.277  -1.2771   3.9737   0.5942
 3AS  H251  H  HCH2  0   0.279   2.1552   2.0167  -0.8469
 3AS  H252  H  HCH2  0   0.262   0.6191   1.3669  -1.4363
 3AS  H261  H  HCH2  0   0.220  -1.3634  -2.6240  -1.3928
 3AS  H262  H  HCH2  0   0.220  -1.1796  -3.2081   0.2546
 3AS  H281  H  HCH3  0   0.207  -2.1399  -4.8251  -2.0568
 3AS  H282  H  HCH3  0   0.207  -1.9842  -5.3908  -0.3840
 3AS  H283  H  HCH3  0   0.237  -3.5577  -5.4577  -1.2002
 3AS  H29   H  HOH1  0   0.472  -5.9010  -0.3137   0.9286

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
 3AS  C21  C22   single    1.515  0.020  1.515
 3AS  C21  C17   single    1.550  0.020  1.550
 3AS  F24  C22   single    1.375  0.020  1.375
 3AS  C22  F23   single    1.363  0.020  1.363
 3AS  C22  C25   single    1.508  0.020  1.508
 3AS  O29  C1    single    1.353  0.020  1.353
 3AS  C20  C1    aromatic  1.385  0.020  1.385
 3AS  C20  C19   aromatic  1.393  0.020  1.393
 3AS  C17  C19   single    1.507  0.020  1.507
 3AS  C17  C15   single    1.552  0.020  1.552
 3AS  C1   C2    aromatic  1.394  0.020  1.394
 3AS  C19  C4    aromatic  1.388  0.020  1.388
 3AS  C15  C25   single    1.527  0.020  1.527
 3AS  C15  C6    single    1.522  0.020  1.522
 3AS  C2   C3    aromatic  1.386  0.020  1.386
 3AS  C4   C3    aromatic  1.397  0.020  1.397
 3AS  C4   O5    single    1.361  0.020  1.361
 3AS  C6   O5    single    1.416  0.020  1.416
 3AS  C6   C8    single    1.503  0.020  1.503
 3AS  C3   C26   single    1.504  0.020  1.504
 3AS  C14  C8    aromatic  1.392  0.020  1.392
 3AS  C14  C13   aromatic  1.386  0.020  1.386
 3AS  C8   C9    aromatic  1.390  0.020  1.390
 3AS  C13  C11   aromatic  1.393  0.020  1.393
 3AS  C26  O27   single    1.399  0.020  1.399
 3AS  C9   C10   aromatic  1.386  0.020  1.386
 3AS  O27  C28   single    1.405  0.020  1.405
 3AS  C11  C10   aromatic  1.392  0.020  1.392
 3AS  C11  O12   single    1.348  0.020  1.348
 3AS  C2   H2    single    0.930  0.020  1.080
 3AS  C6   H6    single    0.970  0.020  1.090
 3AS  C9   H9    single    0.930  0.020  1.080
 3AS  C10  H10   single    0.930  0.020  1.080
 3AS  O12  H12   single    0.850  0.020  0.980
 3AS  C13  H13   single    0.930  0.020  1.080
 3AS  C14  H14   single    0.930  0.020  1.080
 3AS  C15  H15   single    0.970  0.020  1.090
 3AS  C17  H17   single    0.970  0.020  1.090
 3AS  C20  H20   single    0.930  0.020  1.080
 3AS  C21  H211  single    0.970  0.020  1.090
 3AS  C21  H212  single    0.970  0.020  1.090
 3AS  C25  H251  single    0.970  0.020  1.090
 3AS  C25  H252  single    0.970  0.020  1.090
 3AS  C26  H261  single    0.970  0.020  1.090
 3AS  C26  H262  single    0.970  0.020  1.090
 3AS  C28  H281  single    0.970  0.020  1.090
 3AS  C28  H282  single    0.970  0.020  1.090
 3AS  C28  H283  single    0.970  0.020  1.090
 3AS  O29  H29   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
 3AS  O29   C1   C20   117.98  3.000
 3AS  C20   C1   C2    119.85  3.000
 3AS  O29   C1   C2    122.17  3.000
 3AS  H2    C2   C3    119.85  3.000
 3AS  H2    C2   C1    119.76  3.000
 3AS  C3    C2   C1    120.39  3.000
 3AS  C26   C3   C4    118.79  3.000
 3AS  C26   C3   C2    122.18  3.000
 3AS  C4    C3   C2    119.03  3.000
 3AS  C19   C4   O5    121.94  3.000
 3AS  O5    C4   C3    116.84  3.000
 3AS  C19   C4   C3    121.23  3.000
 3AS  C6    O5   C4    114.84  3.000
 3AS  H6    C6   C15   107.64  3.000
 3AS  H6    C6   C8    108.78  3.000
 3AS  C15   C6   C8    112.27  3.000
 3AS  H6    C6   O5    108.78  3.000
 3AS  C8    C6   O5    108.58  3.000
 3AS  C15   C6   O5    110.71  3.000
 3AS  C14   C8   C9    118.18  3.000
 3AS  C9    C8   C6    119.28  3.000
 3AS  C14   C8   C6    122.49  3.000
 3AS  H9    C9   C10   118.77  3.000
 3AS  H9    C9   C8    119.79  3.000
 3AS  C10   C9   C8    121.44  3.000
 3AS  H10   C10  C11   120.40  3.000
 3AS  H10   C10  C9    119.75  3.000
 3AS  C11   C10  C9    119.85  3.000
 3AS  C13   C11  O12   117.96  3.000
 3AS  O12   C11  C10   122.75  3.000
 3AS  C13   C11  C10   119.30  3.000
 3AS  H12   O12  C11   110.39  3.000
 3AS  H13   C13  C14   120.15  3.000
 3AS  H13   C13  C11   119.66  3.000
 3AS  C14   C13  C11   120.19  3.000
 3AS  H14   C14  C13   118.58  3.000
 3AS  H14   C14  C8    120.38  3.000
 3AS  C13   C14  C8    121.05  3.000
 3AS  H15   C15  C25   108.84  3.000
 3AS  H15   C15  C17   108.56  3.000
 3AS  C25   C15  C17   105.09  3.000
 3AS  H15   C15  C6    106.80  3.000
 3AS  C25   C15  C6    115.27  3.000
 3AS  C17   C15  C6    112.12  3.000
 3AS  H17   C17  C21   109.65  3.000
 3AS  H17   C17  C19   108.18  3.000
 3AS  C21   C17  C19   111.55  3.000
 3AS  H17   C17  C15   109.45  3.000
 3AS  C19   C17  C15   112.63  3.000
 3AS  C21   C17  C15   105.34  3.000
 3AS  C20   C19  C17   119.85  3.000
 3AS  C17   C19  C4    121.29  3.000
 3AS  C20   C19  C4    118.84  3.000
 3AS  H20   C20  C19   119.79  3.000
 3AS  H20   C20  C1    119.56  3.000
 3AS  C19   C20  C1    120.65  3.000
 3AS  H212  C21  H211  107.35  3.000
 3AS  H212  C21  C22   112.06  3.000
 3AS  H211  C21  C22   108.70  3.000
 3AS  H212  C21  C17   112.96  3.000
 3AS  H211  C21  C17   110.89  3.000
 3AS  C22   C21  C17   104.85  3.000
 3AS  C25   C22  F24   109.49  3.000
 3AS  C25   C22  F23   113.50  3.000
 3AS  F24   C22  F23   105.04  3.000
 3AS  C25   C22  C21   105.84  3.000
 3AS  F23   C22  C21   112.93  3.000
 3AS  F24   C22  C21   110.06  3.000
 3AS  H252  C25  H251  108.20  3.000
 3AS  H252  C25  C22   108.58  3.000
 3AS  H251  C25  C22   112.97  3.000
 3AS  H252  C25  C15   111.23  3.000
 3AS  H251  C25  C15   113.97  3.000
 3AS  C22   C25  C15   101.73  3.000
 3AS  H262  C26  H261  105.96  3.000
 3AS  H262  C26  O27   110.81  3.000
 3AS  H261  C26  O27   110.61  3.000
 3AS  H262  C26  C3    109.37  3.000
 3AS  H261  C26  C3    109.82  3.000
 3AS  O27   C26  C3    110.19  3.000
 3AS  C28   O27  C26   112.42  3.000
 3AS  H283  C28  H282  108.54  3.000
 3AS  H283  C28  H281  108.46  3.000
 3AS  H282  C28  H281  107.90  3.000
 3AS  H283  C28  O27   107.92  3.000
 3AS  H282  C28  O27   111.92  3.000
 3AS  H281  C28  O27   112.00  3.000
 3AS  H29   O29  C1    110.23  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
 3AS  CONST_01  C4    C19  C20  C1     0.00   0.0  0
 3AS  CONST_02  C4    C3   C2   C1     0.00   0.0  0
 3AS  CONST_03  C19   C20  C1   C2     0.00   0.0  0
 3AS  CONST_04  C19   C4   C3   C2     0.00   0.0  0
 3AS  CONST_05  C20   C1   C2   C3     0.00   0.0  0
 3AS  CONST_06  C20   C19  C4   C3     0.00   0.0  0
 3AS  CONST_07  C11   C13  C14  C8     0.00   0.0  0
 3AS  CONST_08  C11   C10  C9   C8     0.00   0.0  0
 3AS  CONST_09  C13   C14  C8   C9     0.00   0.0  0
 3AS  CONST_10  C13   C11  C10  C9     0.00   0.0  0
 3AS  CONST_11  C14   C8   C9   C10    0.00   0.0  0
 3AS  CONST_12  C14   C13  C11  C10    0.00   0.0  0
 3AS  CONST_13  C13   C14  C8   C6   180.00   0.0  0
 3AS  CONST_14  C10   C9   C8   C6   180.00   0.0  0
 3AS  CONST_15  C26   C3   C2   C1   180.00   0.0  0
 3AS  CONST_16  O29   C1   C2   C3   180.00   0.0  0
 3AS  CONST_17  C26   C3   C4   O5     0.00   0.0  0
 3AS  CONST_18  O12   C11  C10  C9   180.00   0.0  0
 3AS  CONST_19  C14   C13  C11  O12  180.00   0.0  0
 3AS  CONST_20  O29   C1   C20  C19  180.00   0.0  0
 3AS  CONST_21  C26   C3   C4   C19  180.00   0.0  0
 3AS  CONST_22  H20   C20  C1   C2   180.00   0.0  0
 3AS  CONST_23  H2    C2   C3   C4   180.00   0.0  0
 3AS  CONST_24  H14   C14  C8   C6     0.00   0.0  0
 3AS  CONST_25  H9    C9   C8   C6     0.00   0.0  0
 3AS  CONST_26  H13   C13  C14  C8   180.00   0.0  0
 3AS  CONST_27  H10   C10  C9   C8   180.00   0.0  0
 3AS  Var_01    C19   C4   O5   C6    29.44  30.0  1
 3AS  Var_02    C21   C22  C25  C15  -41.63  30.0  1
 3AS  Var_03    C25   C22  C21  C17   29.70  30.0  1
 3AS  Var_04    O27   C26  C3   C2     0.13  30.0  2
 3AS  Var_05    H281  C28  O27  C26  -60.48  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
 3AS  chir_01  C6   C15  O5   C8   negativ
 3AS  chir_02  C15  C6   C25  C17  negativ
 3AS  chir_03  C17  C15  C19  C21  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
 3AS  plan-1  C6   0.020
 3AS  plan-1  C8   0.020
 3AS  plan-1  C9   0.020
 3AS  plan-1  C10  0.020
 3AS  plan-1  C11  0.020
 3AS  plan-1  O12  0.020
 3AS  plan-1  C13  0.020
 3AS  plan-1  C14  0.020
 3AS  plan-1  H9   0.020
 3AS  plan-1  H10  0.020
 3AS  plan-1  H13  0.020
 3AS  plan-1  H14  0.020
 3AS  plan-2  C1   0.020
 3AS  plan-2  C2   0.020
 3AS  plan-2  C3   0.020
 3AS  plan-2  C4   0.020
 3AS  plan-2  O5   0.020
 3AS  plan-2  C17  0.020
 3AS  plan-2  C19  0.020
 3AS  plan-2  C20  0.020
 3AS  plan-2  C26  0.020
 3AS  plan-2  O29  0.020
 3AS  plan-2  H2   0.020
 3AS  plan-2  H20  0.020

