# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 15:46:51 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (6aR,9R,9aR)-9-hydroxy-4-methoxy-2,3,6a,8,9,9a-hexahydrocyclopenta[c]furo[3',2':4,5]furo[2,3-h]chromene-1,11-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2O[C@H]3OC[C@H](O)[C@H]3c2c4OC(=O)C5=C(CCC5=O)c14
#
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
 AFN  AFN  (6aR,9R,9aR)-9-hydroxy-4-methoxy-2,3,6a,8,9,9a-hexahydrocyclopenta[c]furo[3',2':4,5]furo[2,3-h]chromene-1,11-dione  ligand  38  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AFN
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
 AFN  C8A   C  CH2   0  -0.232  -0.8097  -1.3964  -3.7602
 AFN  C9    C  CH1   0   0.047  -1.7507  -0.5327  -2.9324
 AFN  O9    O  OH1   0  -0.667  -2.8144  -0.0130  -3.6902
 AFN  C9A   C  CR15  0  -0.431  -0.8346   0.6416  -2.5732
 AFN  C9B   C  CR56  0  -0.124   0.0475   0.4076  -1.3925
 AFN  O7    O  O2    0  -0.473  -0.0364  -0.4612  -4.5085
 AFN  C6A   C  CR15  0   0.289   0.1983   0.6510  -3.7304
 AFN  O6A   O  O     0  -0.487   1.5041   0.5644  -3.1179
 AFN  C5A   C  CR56  0   0.467   1.3689   0.3774  -1.8045
 AFN  C5B   C  CR16  0  -0.524   2.4423   0.1895  -0.9451
 AFN  C4B   C  CR6   0   0.367   2.1583   0.0287   0.4035
 AFN  O4    O  O2    0  -0.451   3.0970  -0.1598   1.3232
 AFN  CM    C  CH3   0  -0.444   4.4616  -0.1896   0.9330
 AFN  C4A   C  CR66  0  -0.162   0.8184   0.0614   0.8830
 AFN  C10   C  CR66  0   0.363  -0.2196   0.2603  -0.0533
 AFN  O10   O  O     0  -0.470  -1.5125   0.3173   0.3182
 AFN  C11   C  CR6   0   0.548  -1.9477   0.1871   1.6088
 AFN  O11   O  OC    0  -0.403  -3.1322   0.2603   1.7964
 AFN  C12   C  CR56  0  -0.341  -0.9075  -0.0232   2.5754
 AFN  C3A   C  CR56  0   0.274   0.4179  -0.0844   2.2383
 AFN  C3    C  CH2   0  -0.510   1.2668  -0.3121   3.4534
 AFN  C2A   C  CH2   0  -0.585   0.2769  -0.3911   4.6159
 AFN  C1    C  CR5   0   0.352  -1.0986  -0.1977   4.0120
 AFN  O1    O  O     0  -0.406  -2.1467  -0.1926   4.6197
 AFN  H8A2  H  HCH2  0   0.233  -0.1758  -2.0117  -3.1122
 AFN  H8A   H  HCH2  0   0.263  -1.3239  -2.0579  -4.4584
 AFN  H9    H  HCH1  0   0.249  -2.1044  -1.0703  -2.0467
 AFN  HO9   H  HOH1  0   0.458  -3.3851  -0.7405  -3.9577
 AFN  H9A   H  HCR5  0   0.311  -1.3954   1.5753  -2.4972
 AFN  H6A   H  HCR5  0   0.269   0.2086   1.5382  -4.3615
 AFN  H5B   H  HCR6  0   0.306   3.4516   0.1761  -1.3303
 AFN  HM1   H  HCH3  0   0.273   5.0318  -0.3564   1.8419
 AFN  HM2   H  HCH3  0   0.242   4.6587  -1.0026   0.2319
 AFN  HM3   H  HCH3  0   0.243   4.7682   0.7569   0.4841
 AFN  H31   H  HCH2  0   0.288   1.9838   0.5008   3.5724
 AFN  H32   H  HCH2  0   0.288   1.8522  -1.2253   3.3440
 AFN  H2A1  H  HCH2  0   0.289   0.4570   0.3772   5.3694
 AFN  H2A2  H  HCH2  0   0.289   0.3152  -1.3537   5.1291

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
 AFN  C8A  C9    single    1.522  0.020  1.522
 AFN  C8A  O7    single    1.426  0.020  1.426
 AFN  C8A  H8A2  single    0.970  0.020  1.090
 AFN  C8A  H8A   single    0.970  0.020  1.090
 AFN  C9   O9    single    1.406  0.020  1.406
 AFN  C9   C9A   single    1.532  0.020  1.532
 AFN  C9   H9    single    0.970  0.020  1.090
 AFN  O9   HO9   single    0.850  0.020  0.980
 AFN  C9A  C9B   single    1.492  0.020  1.492
 AFN  C9A  C6A   single    1.551  0.020  1.551
 AFN  C9A  H9A   single    0.970  0.020  1.090
 AFN  C9B  C5A   aromatic  1.384  0.020  1.384
 AFN  C9B  C10   aromatic  1.374  0.020  1.374
 AFN  O7   C6A   single    1.378  0.020  1.378
 AFN  C6A  O6A   single    1.445  0.020  1.445
 AFN  C6A  H6A   single    0.970  0.020  1.090
 AFN  O6A  C5A   single    1.333  0.020  1.333
 AFN  C5A  C5B   aromatic  1.388  0.020  1.388
 AFN  C5B  C4B   aromatic  1.388  0.020  1.388
 AFN  C5B  H5B   single    0.930  0.020  1.080
 AFN  C4B  O4    single    1.328  0.020  1.328
 AFN  C4B  C4A   aromatic  1.423  0.020  1.423
 AFN  O4   CM    single    1.420  0.020  1.420
 AFN  CM   HM1   single    0.970  0.020  1.090
 AFN  CM   HM2   single    0.970  0.020  1.090
 AFN  CM   HM3   single    0.970  0.020  1.090
 AFN  C4A  C10   aromatic  1.412  0.020  1.412
 AFN  C4A  C3A   aromatic  1.421  0.020  1.421
 AFN  C10  O10   aromatic  1.346  0.020  1.346
 AFN  O10  C11   aromatic  1.368  0.020  1.368
 AFN  C11  O11   double    1.202  0.020  1.202
 AFN  C11  C12   aromatic  1.435  0.020  1.435
 AFN  C12  C3A   aromatic  1.369  0.020  1.369
 AFN  C12  C1    single    1.460  0.020  1.460
 AFN  C3A  C3    single    1.500  0.020  1.500
 AFN  C3   C2A   single    1.529  0.020  1.529
 AFN  C3   H31   single    0.970  0.020  1.090
 AFN  C3   H32   single    0.970  0.020  1.090
 AFN  C2A  C1    single    1.515  0.020  1.515
 AFN  C2A  H2A1  single    0.970  0.020  1.090
 AFN  C2A  H2A2  single    0.970  0.020  1.090
 AFN  C1   O1    double    1.212  0.020  1.212

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
 AFN  H8A   C8A  H8A2  108.11  3.000
 AFN  H8A   C8A  O7    108.52  3.000
 AFN  H8A2  C8A  O7    111.41  3.000
 AFN  H8A   C8A  C9    113.63  3.000
 AFN  H8A2  C8A  C9    110.78  3.000
 AFN  O7    C8A  C9    104.39  3.000
 AFN  H9    C9   C9A   112.32  3.000
 AFN  H9    C9   O9    111.91  3.000
 AFN  C9A   C9   O9    107.19  3.000
 AFN  H9    C9   C8A   111.17  3.000
 AFN  C9A   C9   C8A   101.12  3.000
 AFN  O9    C9   C8A   112.61  3.000
 AFN  HO9   O9   C9    108.60  3.000
 AFN  H9A   C9A  C6A   112.88  3.000
 AFN  H9A   C9A  C9B   112.50  3.000
 AFN  C6A   C9A  C9B   101.40  3.000
 AFN  H9A   C9A  C9    111.38  3.000
 AFN  C6A   C9A  C9    103.17  3.000
 AFN  C9B   C9A  C9    114.76  3.000
 AFN  C10   C9B  C5A   118.26  3.000
 AFN  C10   C9B  C9A   132.32  3.000
 AFN  C5A   C9B  C9A   109.40  3.000
 AFN  C6A   O7   C8A   109.00  3.000
 AFN  H6A   C6A  O6A   106.62  3.000
 AFN  H6A   C6A  O7    109.40  3.000
 AFN  O6A   C6A  O7    110.18  3.000
 AFN  H6A   C6A  C9A   116.34  3.000
 AFN  O6A   C6A  C9A   106.57  3.000
 AFN  O7    C6A  C9A   107.64  3.000
 AFN  C5A   O6A  C6A   109.53  3.000
 AFN  C5B   C5A  O6A   123.40  3.000
 AFN  C5B   C5A  C9B   123.84  3.000
 AFN  O6A   C5A  C9B   112.76  3.000
 AFN  H5B   C5B  C4B   122.43  3.000
 AFN  H5B   C5B  C5A   120.23  3.000
 AFN  C4B   C5B  C5A   117.34  3.000
 AFN  C4A   C4B  O4    115.82  3.000
 AFN  C4A   C4B  C5B   121.16  3.000
 AFN  O4    C4B  C5B   123.03  3.000
 AFN  CM    O4   C4B   119.49  3.000
 AFN  HM3   CM   HM2   109.33  3.000
 AFN  HM3   CM   HM1   109.26  3.000
 AFN  HM2   CM   HM1   109.17  3.000
 AFN  HM3   CM   O4    111.40  3.000
 AFN  HM2   CM   O4    111.46  3.000
 AFN  HM1   CM   O4    106.13  3.000
 AFN  C3A   C4A  C10   116.09  3.000
 AFN  C3A   C4A  C4B   125.75  3.000
 AFN  C10   C4A  C4B   118.15  3.000
 AFN  O10   C10  C4A   121.93  3.000
 AFN  O10   C10  C9B   116.82  3.000
 AFN  C4A   C10  C9B   121.25  3.000
 AFN  C11   O10  C10   124.17  3.000
 AFN  C12   C11  O11   128.19  3.000
 AFN  C12   C11  O10   114.75  3.000
 AFN  O11   C11  O10   117.06  3.000
 AFN  C1    C12  C3A   111.33  3.000
 AFN  C1    C12  C11   125.82  3.000
 AFN  C3A   C12  C11   122.84  3.000
 AFN  C3    C3A  C12   110.81  3.000
 AFN  C3    C3A  C4A   128.97  3.000
 AFN  C12   C3A  C4A   120.22  3.000
 AFN  H32   C3   H31   106.40  3.000
 AFN  H32   C3   C2A   112.38  3.000
 AFN  H31   C3   C2A   112.42  3.000
 AFN  H32   C3   C3A   110.48  3.000
 AFN  H31   C3   C3A   110.33  3.000
 AFN  C2A   C3   C3A   104.91  3.000
 AFN  H2A2  C2A  H2A1  106.89  3.000
 AFN  H2A2  C2A  C1    109.39  3.000
 AFN  H2A1  C2A  C1    109.59  3.000
 AFN  H2A2  C2A  C3    112.35  3.000
 AFN  H2A1  C2A  C3    112.44  3.000
 AFN  C1    C2A  C3    106.16  3.000
 AFN  O1    C1   C2A   125.88  3.000
 AFN  O1    C1   C12   127.34  3.000
 AFN  C2A   C1   C12   106.78  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
 AFN  CONST_01  C4B   C5B  C5A  C9B     0.00   0.0  0
 AFN  CONST_02  C4B   C4A  C10  C9B     0.00   0.0  0
 AFN  CONST_03  C3A   C4A  C10  C9B   180.00   0.0  0
 AFN  CONST_04  C11   O10  C10  C9B   180.00   0.0  0
 AFN  CONST_05  C4A   C10  C9B  C5A     0.00   0.0  0
 AFN  CONST_06  O10   C10  C9B  C5A   180.00   0.0  0
 AFN  CONST_07  C4A   C4B  C5B  C5A     0.00   0.0  0
 AFN  CONST_08  C10   C9B  C5A  C5B     0.00   0.0  0
 AFN  CONST_09  C10   C4A  C4B  C5B     0.00   0.0  0
 AFN  CONST_10  C3A   C4A  C4B  C5B   180.00   0.0  0
 AFN  CONST_11  O10   C10  C4A  C4B   180.00   0.0  0
 AFN  CONST_12  C12   C3A  C4A  C4B   180.00   0.0  0
 AFN  CONST_13  C11   O10  C10  C4A     0.00   0.0  0
 AFN  CONST_14  C11   C12  C3A  C4A     0.00   0.0  0
 AFN  CONST_15  C12   C3A  C4A  C10     0.00   0.0  0
 AFN  CONST_16  C12   C11  O10  C10     0.00   0.0  0
 AFN  CONST_17  C3A   C4A  C10  O10     0.00   0.0  0
 AFN  CONST_18  C3A   C12  C11  O10     0.00   0.0  0
 AFN  CONST_19  O4    C4B  C5B  C5A   180.00   0.0  0
 AFN  CONST_20  C10   C4A  C4B  O4    180.00   0.0  0
 AFN  CONST_21  C3A   C4A  C4B  O4      0.00   0.0  0
 AFN  CONST_22  O11   C11  O10  C10   180.00   0.0  0
 AFN  CONST_23  C3A   C12  C11  O11   180.00   0.0  0
 AFN  CONST_24  C1    C12  C11  O11     0.00   0.0  0
 AFN  CONST_25  H5B   C5B  C5A  C9B   180.00   0.0  0
 AFN  Var_01    C5B   C5A  O6A  C6A   176.77  30.0  1
 AFN  Var_02    C2A   C3   C3A  C4A  -179.77  30.0  1
 AFN  Var_03    C2A   C1   C12  C11   179.83  30.0  1
 AFN  Var_04    C3    C2A  C1   C12     0.26  30.0  1
 AFN  Var_05    C1    C2A  C3   C3A    -0.27  30.0  1
 AFN  Var_06    H8A2  C8A  O7   C6A   -83.61  30.0  1
 AFN  Var_07    C4A   C4B  O4   CM   -179.25  30.0  1
 AFN  Var_08    HM1   CM   O4   C4B  -179.85  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
 AFN  chir_01  C9   C8A  O9   C9A  positiv
 AFN  chir_02  C9A  C9   C9B  C6A  negativ
 AFN  chir_03  C6A  O6A  O7   C9A  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
 AFN  plan-1  C12  0.020
 AFN  plan-1  C2A  0.020
 AFN  plan-1  C1   0.020
 AFN  plan-1  O1   0.020
 AFN  plan-2  C9A  0.020
 AFN  plan-2  C9B  0.020
 AFN  plan-2  O6A  0.020
 AFN  plan-2  C5A  0.020
 AFN  plan-2  C5B  0.020
 AFN  plan-2  C4B  0.020
 AFN  plan-2  O4   0.020
 AFN  plan-2  C4A  0.020
 AFN  plan-2  C10  0.020
 AFN  plan-2  O10  0.020
 AFN  plan-2  C3A  0.020
 AFN  plan-2  H5B  0.020
 AFN  plan-3  O10  0.020
 AFN  plan-3  C11  0.020
 AFN  plan-3  O11  0.020
 AFN  plan-3  C12  0.020

