# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 16:04:19 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: (6aR,12aR)-3-(hydroxymethyl)-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromen-6a(12aH)-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccc2[C@H]3Oc4cc5OCOc5cc4[C@@]3(O)COc2c1
#
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
 P1S  P1S  (6aR,12aR)-3-(hydroxymethyl)-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromen-6a(12aH)-ol  ligand  37  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P1S
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
 P1S  C1    C  CH2   0  -0.211   0.2323   1.4959   0.9483
 P1S  O1    O  O2    0  -0.475   1.6284   1.7162   0.8938
 P1S  C2    C  CR6   0   0.384   2.3575   0.6677   0.4537
 P1S  C3    C  CR6   0  -0.059   1.8148  -0.3354  -0.3447
 P1S  C4    C  CR15  0   0.013   0.4026  -0.2528  -0.8236
 P1S  C5    C  CR5   0   0.101  -0.3184   1.0388  -0.3991
 P1S  C6    C  CR16  0  -0.412   3.7052   0.6335   0.8116
 P1S  C7    C  CR6   0   0.083   4.5173  -0.4102   0.4038
 P1S  C8    C  CR16  0  -0.295   3.9745  -1.4295  -0.3833
 P1S  C9    C  CR16  0  -0.272   2.6458  -1.3783  -0.7543
 P1S  O2    O  O     0  -0.484  -0.3880  -1.3323  -0.2954
 P1S  C10   C  CR56  0   0.392  -1.6512  -0.8575  -0.1547
 P1S  C11   C  CR56  0  -0.032  -1.7209   0.5214  -0.2285
 P1S  C12   C  CR16  0  -0.438  -2.7667  -1.6697   0.0343
 P1S  C13   C  CR56  0   0.306  -3.9525  -0.9786   0.1561
 P1S  C14   C  CR56  0   0.284  -4.0368   0.4065   0.0879
 P1S  C15   C  CR16  0  -0.402  -2.9308   1.2011  -0.1026
 P1S  O3    O  O     0  -0.483  -5.1872  -1.4915   0.3609
 P1S  C16   C  CH2   0   0.066  -6.0934  -0.4105   0.1692
 P1S  O4    O  O     0  -0.490  -5.3333   0.7822   0.2630
 P1S  O5    O  OH1   0  -0.655  -0.1232   1.9931  -1.4021
 P1S  C17   C  CH2   0  -0.214   5.9589  -0.4604   0.8266
 P1S  O6    O  OH1   0  -0.667   6.7636  -0.7109  -0.3030
 P1S  H11   H  HCH2  0   0.273  -0.2244   2.4381   1.2567
 P1S  H12A  H  HCH2  0   0.244   0.0039   0.7449   1.7135
 P1S  H4    H  HCR5  0   0.274   0.3726  -0.3201  -1.9186
 P1S  H6    H  HCR6  0   0.262   4.1096   1.4383   1.4148
 P1S  H8    H  HCR6  0   0.251   4.5911  -2.2549  -0.7138
 P1S  H9    H  HCR6  0   0.260   2.2373  -2.1601  -1.3841
 P1S  H12   H  HCR6  0   0.285  -2.7079  -2.7485   0.0810
 P1S  H15   H  HCR6  0   0.276  -3.0016   2.2803  -0.1514
 P1S  H161  H  HCH2  0   0.232  -6.5524  -0.4889  -0.8231
 P1S  H162  H  HCH2  0   0.248  -6.8552  -0.4274   0.9469
 P1S  HO5   H  HOH1  0   0.460  -0.4490   2.8480  -1.1002
 P1S  H171  H  HCH2  0   0.221   6.0761  -1.2501   1.5793
 P1S  H172  H  HCH2  0   0.214   6.2271   0.4831   1.3180
 P1S  HO6   H  HOH1  0   0.458   7.6421  -0.9516   0.0053

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
 P1S  C1   O1    single    1.415  0.020  1.415
 P1S  C1   C5    single    1.526  0.020  1.526
 P1S  C1   H11   single    0.970  0.020  1.090
 P1S  C1   H12A  single    0.970  0.020  1.090
 P1S  O1   C2    single    1.351  0.020  1.351
 P1S  C2   C3    aromatic  1.392  0.020  1.392
 P1S  C2   C6    aromatic  1.395  0.020  1.395
 P1S  C3   C4    single    1.493  0.020  1.493
 P1S  C3   C9    aromatic  1.395  0.020  1.395
 P1S  C4   C5    single    1.539  0.020  1.539
 P1S  C4   O2    single    1.439  0.020  1.439
 P1S  C4   H4    single    0.970  0.020  1.090
 P1S  C5   C11   single    1.505  0.020  1.505
 P1S  C5   O5    single    1.398  0.020  1.398
 P1S  C6   C7    aromatic  1.384  0.020  1.384
 P1S  C6   H6    single    0.930  0.020  1.080
 P1S  C7   C8    aromatic  1.398  0.020  1.398
 P1S  C7   C17   single    1.503  0.020  1.503
 P1S  C8   C9    aromatic  1.380  0.020  1.380
 P1S  C8   H8    single    0.930  0.020  1.080
 P1S  C9   H9    single    0.930  0.020  1.080
 P1S  O2   C10   single    1.357  0.020  1.357
 P1S  C10  C11   aromatic  1.383  0.020  1.383
 P1S  C10  C12   aromatic  1.393  0.020  1.393
 P1S  C11  C15   aromatic  1.393  0.020  1.393
 P1S  C12  C13   aromatic  1.378  0.020  1.378
 P1S  C12  H12   single    0.930  0.020  1.080
 P1S  C13  C14   aromatic  1.389  0.020  1.389
 P1S  C13  O3    single    1.352  0.020  1.352
 P1S  C14  C15   aromatic  1.375  0.020  1.375
 P1S  C14  O4    single    1.361  0.020  1.361
 P1S  C15  H15   single    0.930  0.020  1.080
 P1S  O3   C16   single    1.424  0.020  1.424
 P1S  C16  O4    single    1.417  0.020  1.417
 P1S  C16  H161  single    0.970  0.020  1.090
 P1S  C16  H162  single    0.970  0.020  1.090
 P1S  O5   HO5   single    0.850  0.020  0.980
 P1S  C17  O6    single    1.409  0.020  1.409
 P1S  C17  H171  single    0.970  0.020  1.090
 P1S  C17  H172  single    0.970  0.020  1.090
 P1S  O6   HO6   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
 P1S  H12A  C1   H11   107.88  3.000
 P1S  H12A  C1   C5    109.64  3.000
 P1S  H11   C1   C5    110.92  3.000
 P1S  H12A  C1   O1    109.83  3.000
 P1S  H11   C1   O1    106.82  3.000
 P1S  C5    C1   O1    111.64  3.000
 P1S  C2    O1   C1    115.11  3.000
 P1S  C6    C2   C3    120.41  3.000
 P1S  C6    C2   O1    117.19  3.000
 P1S  C3    C2   O1    122.39  3.000
 P1S  C9    C3   C4    120.70  3.000
 P1S  C9    C3   C2    118.35  3.000
 P1S  C4    C3   C2    120.84  3.000
 P1S  H4    C4   O2    107.77  3.000
 P1S  H4    C4   C5    108.29  3.000
 P1S  O2    C4   C5    105.73  3.000
 P1S  H4    C4   C3    110.02  3.000
 P1S  O2    C4   C3    111.13  3.000
 P1S  C5    C4   C3    113.64  3.000
 P1S  O5    C5   C11   116.50  3.000
 P1S  O5    C5   C4    108.03  3.000
 P1S  C11   C5   C4    100.33  3.000
 P1S  O5    C5   C1    112.25  3.000
 P1S  C11   C5   C1    109.84  3.000
 P1S  C4    C5   C1    109.02  3.000
 P1S  H6    C6   C7    120.33  3.000
 P1S  H6    C6   C2    119.02  3.000
 P1S  C7    C6   C2    120.65  3.000
 P1S  C17   C7   C8    120.44  3.000
 P1S  C17   C7   C6    120.33  3.000
 P1S  C8    C7   C6    119.22  3.000
 P1S  H8    C8   C9    119.65  3.000
 P1S  H8    C8   C7    120.47  3.000
 P1S  C9    C8   C7    119.88  3.000
 P1S  H9    C9   C8    119.48  3.000
 P1S  H9    C9   C3    119.04  3.000
 P1S  C8    C9   C3    121.48  3.000
 P1S  C10   O2   C4    106.69  3.000
 P1S  C12   C10  C11   123.26  3.000
 P1S  C12   C10  O2    123.76  3.000
 P1S  C11   C10  O2    112.98  3.000
 P1S  C15   C11  C10   121.70  3.000
 P1S  C15   C11  C5    130.68  3.000
 P1S  C10   C11  C5    107.58  3.000
 P1S  H12   C12  C13   122.91  3.000
 P1S  H12   C12  C10   122.96  3.000
 P1S  C13   C12  C10   114.13  3.000
 P1S  O3    C13  C14   109.28  3.000
 P1S  O3    C13  C12   127.50  3.000
 P1S  C14   C13  C12   123.22  3.000
 P1S  O4    C14  C15   128.64  3.000
 P1S  O4    C14  C13   109.06  3.000
 P1S  C15   C14  C13   122.28  3.000
 P1S  H15   C15  C14   121.98  3.000
 P1S  H15   C15  C11   122.61  3.000
 P1S  C14   C15  C11   115.40  3.000
 P1S  C16   O3   C13   105.83  3.000
 P1S  H162  C16  H161  110.65  3.000
 P1S  H162  C16  O4    109.93  3.000
 P1S  H161  C16  O4    110.16  3.000
 P1S  H162  C16  O3    109.72  3.000
 P1S  H161  C16  O3    109.52  3.000
 P1S  O4    C16  O3    106.78  3.000
 P1S  C16   O4   C14   105.66  3.000
 P1S  HO5   O5   C5    109.49  3.000
 P1S  H172  C17  H171  106.60  3.000
 P1S  H172  C17  O6    111.85  3.000
 P1S  H171  C17  O6    111.15  3.000
 P1S  H172  C17  C7    109.38  3.000
 P1S  H171  C17  C7    108.63  3.000
 P1S  O6    C17  C7    109.15  3.000
 P1S  HO6   O6   C17   108.00  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
 P1S  CONST_01  C8   C9   C3   C2      0.00   0.0  0
 P1S  CONST_02  C8   C7   C6   C2      0.00   0.0  0
 P1S  CONST_03  C7   C6   C2   C3      0.00   0.0  0
 P1S  CONST_04  C7   C8   C9   C3      0.00   0.0  0
 P1S  CONST_05  C9   C3   C2   C6      0.00   0.0  0
 P1S  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 P1S  CONST_07  C14  C15  C11  C10     0.00   0.0  0
 P1S  CONST_08  C14  C13  C12  C10     0.00   0.0  0
 P1S  CONST_09  C13  C12  C10  C11     0.00   0.0  0
 P1S  CONST_10  C13  C14  C15  C11     0.00   0.0  0
 P1S  CONST_11  C15  C11  C10  C12     0.00   0.0  0
 P1S  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 P1S  CONST_13  C17  C7   C6   C2    180.00   0.0  0
 P1S  CONST_14  C17  C7   C8   C9    180.00   0.0  0
 P1S  CONST_15  H6   C6   C2   O1      0.00   0.0  0
 P1S  CONST_16  H9   C9   C3   C2    180.00   0.0  0
 P1S  CONST_17  H8   C8   C9   C3    180.00   0.0  0
 P1S  CONST_18  H15  C15  C11  C5      0.00   0.0  0
 P1S  CONST_19  H12  C12  C10  O2      0.00   0.0  0
 P1S  Var_01    C3   C2   O1   C1     23.29  30.0  1
 P1S  Var_02    C5   C1   O1   C2    -55.06  30.0  1
 P1S  Var_03    C11  C10  O2   C4    -14.86  30.0  1
 P1S  Var_04    O4   C16  O3   C13   -17.74  30.0  1
 P1S  Var_05    O3   C16  O4   C14    18.03  30.0  1
 P1S  Var_06    O6   C17  C7   C6   -131.44  30.0  2

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
 P1S  chir_01  C4  C3  C5  O2   positiv
 P1S  chir_02  C5  C1  C4  C11  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
 P1S  plan-1  O1   0.020
 P1S  plan-1  C2   0.020
 P1S  plan-1  C3   0.020
 P1S  plan-1  C4   0.020
 P1S  plan-1  C6   0.020
 P1S  plan-1  C7   0.020
 P1S  plan-1  C8   0.020
 P1S  plan-1  C9   0.020
 P1S  plan-1  C17  0.020
 P1S  plan-1  H6   0.020
 P1S  plan-1  H8   0.020
 P1S  plan-1  H9   0.020
 P1S  plan-2  C5   0.020
 P1S  plan-2  O2   0.020
 P1S  plan-2  C10  0.020
 P1S  plan-2  C11  0.020
 P1S  plan-2  C12  0.020
 P1S  plan-2  C13  0.020
 P1S  plan-2  C14  0.020
 P1S  plan-2  C15  0.020
 P1S  plan-2  O3   0.020
 P1S  plan-2  O4   0.020
 P1S  plan-2  H12  0.020
 P1S  plan-2  H15  0.020

