# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 18:36:41 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (5~{S},5~{a}~{R},8~{a}~{R},9~{R})-9-(3,5-dimethoxy-4-oxidanyl-phenyl)-5-oxidanyl-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[6,5-f][1,3]benzodioxol-8-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1O)[C@H]2[C@@H]3[C@H](COC3=O)[C@H](O)c4cc5OCOc5cc24
#
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
 89O  89O  (5~{S},5~{a}~{R},8~{a}~{R},9~{R})-9-(3,5-dimethoxy-4-oxidanyl-phenyl)-5-oxidanyl-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[6,5-f][1,3]benzodioxol-8-one  ligand  49  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_89O
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
 89O  C10   C  CR16  0  -0.369  -1.9211  -0.7714   1.3289
 89O  C15   C  CR16  0  -0.462   0.7962  -0.8609  -0.7953
 89O  C17   C  CR6   0   0.169   2.9226  -1.9871  -0.6091
 89O  C24   C  CH3   0  -0.438   0.4434  -2.1974  -3.2383
 89O  C28   C  CH2   0  -0.146   0.4464   3.6880  -1.2936
 89O  C01   C  CH1   0  -0.032  -1.7474   2.2812  -1.0100
 89O  C02   C  CR15  0  -0.338  -0.2433   2.3856  -0.9227
 89O  C03   C  CR15  0  -0.452   0.2069   2.1986   0.5114
 89O  C04   C  CH1   0  -0.383   0.0072   0.7654   0.9882
 89O  C05   C  CR6   0   0.115  -1.4201   0.3595   0.6592
 89O  C06   C  CR6   0   0.026  -2.1979   1.0146  -0.2966
 89O  C07   C  CR16  0  -0.401  -3.4919   0.5482  -0.6020
 89O  C08   C  CR56  0   0.305  -3.9553  -0.5507   0.0662
 89O  C09   C  CR56  0   0.310  -3.1826  -1.1975   1.0194
 89O  O11   O  O     0  -0.486  -3.8823  -2.2344   1.5366
 89O  C12   C  CH2   0   0.068  -5.0568  -2.3557   0.7437
 89O  O13   O  O     0  -0.486  -5.1555  -1.1701  -0.0353
 89O  C14   C  CR6   0   0.165   1.0147  -0.2160   0.4180
 89O  C16   C  CR6   0   0.337   1.7433  -1.7401  -1.3124
 89O  C18   C  CR6   0   0.326   3.1324  -1.3461   0.6124
 89O  C19   C  CR16  0  -0.451   2.1830  -0.4711   1.1252
 89O  O20   O  O2    0  -0.493   4.3019  -1.6583   1.2141
 89O  O23   O  O2    0  -0.469   1.6139  -2.4073  -2.4772
 89O  C25   C  CR5   0   0.612   1.5779   2.8170   0.5077
 89O  O26   O  O     0  -0.422   2.4798   2.6832   1.2880
 89O  O27   O  O     0  -0.450   1.6712   3.6542  -0.5314
 89O  O29   O  OH1   0  -0.659  -2.3101   3.4303  -0.4098
 89O  H101  H  HCR6  0   0.268  -1.3152  -1.2844   2.0654
 89O  H151  H  HCR6  0   0.263  -0.1310  -0.6908  -1.3258
 89O  H213  H  HCH3  0   0.263   5.6255  -1.3559   2.7012
 89O  H211  H  HCH3  0   0.229   4.6701   0.0828   2.2963
 89O  H212  H  HCH3  0   0.230   3.9350  -1.2455   3.2227
 89O  H242  H  HCH3  0   0.262   0.5385  -2.8151  -4.1280
 89O  H243  H  HCH3  0   0.225  -0.4579  -2.4991  -2.6975
 89O  H241  H  HCH3  0   0.226   0.3366  -1.1537  -3.5468
 89O  H281  H  HCH2  0   0.260   0.7089   3.7645  -2.3467
 89O  H282  H  HCH2  0   0.249  -0.1236   4.5709  -1.0014
 89O  H011  H  HCH1  0   0.240  -2.0523   2.2138  -2.0626
 89O  H021  H  HCR5  0   0.287   0.1827   1.5871  -1.5394
 89O  H031  H  HCR5  0   0.318  -0.3997   2.8479   1.1595
 89O  H041  H  HCH1  0   0.282   0.1174   0.7499   2.0764
 89O  H071  H  HCR6  0   0.275  -4.0967   1.0406  -1.3544
 89O  H121  H  HCH2  0   0.236  -4.9718  -3.2269   0.0860
 89O  H122  H  HCH2  0   0.247  -5.9300  -2.4465   1.3894
 89O  H191  H  HCR6  0   0.272   2.3482   0.0203   2.0736
 89O  H221  H  HOH1  0   0.471   4.5743  -2.9315  -0.5397
 89O  H291  H  HOH1  0   0.457  -3.2692   3.3522  -0.4306
 89O  O22   O  OH1   0  -0.626   3.8190  -2.8503  -1.1344
 89O  C21   C  CH3   0  -0.431   4.6367  -1.0027   2.4208

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
 89O  O13  C12   single    1.422  0.020  1.422
 89O  O13  C08   single    1.354  0.020  1.354
 89O  C12  O11   single    1.422  0.020  1.422
 89O  C07  C08   aromatic  1.367  0.020  1.367
 89O  C07  C06   aromatic  1.409  0.020  1.409
 89O  C08  C09   aromatic  1.387  0.020  1.387
 89O  O29  C01   single    1.413  0.020  1.413
 89O  C01  C06   single    1.522  0.020  1.522
 89O  C01  C02   single    1.510  0.020  1.510
 89O  O11  C09   single    1.354  0.020  1.354
 89O  C06  C05   aromatic  1.396  0.020  1.396
 89O  C09  C10   aromatic  1.367  0.020  1.367
 89O  C02  C28   single    1.520  0.020  1.520
 89O  C02  C03   single    1.515  0.020  1.515
 89O  C28  O27   single    1.443  0.020  1.443
 89O  C05  C10   aromatic  1.407  0.020  1.407
 89O  C05  C04   single    1.520  0.020  1.520
 89O  C21  O20   single    1.413  0.020  1.413
 89O  C03  C04   single    1.524  0.020  1.524
 89O  C03  C25   single    1.504  0.020  1.504
 89O  C04  C14   single    1.518  0.020  1.518
 89O  O27  C25   single    1.338  0.020  1.338
 89O  C19  C14   aromatic  1.389  0.020  1.389
 89O  C19  C18   aromatic  1.389  0.020  1.389
 89O  O20  C18   single    1.352  0.020  1.352
 89O  C25  O26   double    1.200  0.020  1.200
 89O  C14  C15   aromatic  1.391  0.020  1.391
 89O  C18  C17   aromatic  1.395  0.020  1.395
 89O  C15  C16   aromatic  1.392  0.020  1.392
 89O  C17  C16   aromatic  1.395  0.020  1.395
 89O  C17  O22   single    1.351  0.020  1.351
 89O  C16  O23   single    1.349  0.020  1.349
 89O  O23  C24   single    1.412  0.020  1.412
 89O  C10  H101  single    0.930  0.020  1.080
 89O  C15  H151  single    0.930  0.020  1.080
 89O  C21  H213  single    0.970  0.020  1.090
 89O  C21  H211  single    0.970  0.020  1.090
 89O  C21  H212  single    0.970  0.020  1.090
 89O  C24  H242  single    0.970  0.020  1.090
 89O  C24  H243  single    0.970  0.020  1.090
 89O  C24  H241  single    0.970  0.020  1.090
 89O  C28  H281  single    0.970  0.020  1.090
 89O  C28  H282  single    0.970  0.020  1.090
 89O  C01  H011  single    0.970  0.020  1.090
 89O  C02  H021  single    0.970  0.020  1.090
 89O  C03  H031  single    0.970  0.020  1.090
 89O  C04  H041  single    0.970  0.020  1.090
 89O  C07  H071  single    0.930  0.020  1.080
 89O  C12  H121  single    0.970  0.020  1.090
 89O  C12  H122  single    0.970  0.020  1.090
 89O  C19  H191  single    0.930  0.020  1.080
 89O  O22  H221  single    0.850  0.020  0.980
 89O  O29  H291  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
 89O  H101  C10  C09   121.51  3.000
 89O  H101  C10  C05   120.36  3.000
 89O  C09   C10  C05   118.14  3.000
 89O  H151  C15  C16   120.02  3.000
 89O  H151  C15  C14   119.30  3.000
 89O  C16   C15  C14   120.66  3.000
 89O  O22   C17  C18   122.29  3.000
 89O  O22   C17  C16   118.56  3.000
 89O  C18   C17  C16   119.15  3.000
 89O  H241  C24  H243  108.80  3.000
 89O  H241  C24  H242  108.66  3.000
 89O  H243  C24  H242  108.67  3.000
 89O  H241  C24  O23   112.02  3.000
 89O  H243  C24  O23   112.07  3.000
 89O  H242  C24  O23   106.51  3.000
 89O  H282  C28  H281  109.18  3.000
 89O  H282  C28  O27   108.72  3.000
 89O  H281  C28  O27   107.95  3.000
 89O  H282  C28  C02   113.02  3.000
 89O  H281  C28  C02   113.95  3.000
 89O  O27   C28  C02   103.67  3.000
 89O  H011  C01  O29   110.27  3.000
 89O  H011  C01  C06   108.43  3.000
 89O  O29   C01  C06   111.09  3.000
 89O  H011  C01  C02   109.64  3.000
 89O  C06   C01  C02   108.98  3.000
 89O  O29   C01  C02   108.41  3.000
 89O  H021  C02  C03   109.12  3.000
 89O  H021  C02  C01   107.72  3.000
 89O  C03   C02  C01   110.01  3.000
 89O  H021  C02  C28   108.11  3.000
 89O  C03   C02  C28   101.65  3.000
 89O  C01   C02  C28   119.81  3.000
 89O  H031  C03  C25   105.16  3.000
 89O  H031  C03  C04   107.38  3.000
 89O  C25   C03  C04   120.46  3.000
 89O  H031  C03  C02   108.73  3.000
 89O  C25   C03  C02   102.58  3.000
 89O  C04   C03  C02   111.93  3.000
 89O  H041  C04  C14   107.31  3.000
 89O  H041  C04  C05   107.83  3.000
 89O  C14   C04  C05   111.68  3.000
 89O  H041  C04  C03   108.15  3.000
 89O  C14   C04  C03   113.81  3.000
 89O  C05   C04  C03   107.85  3.000
 89O  C06   C05  C04   123.11  3.000
 89O  C04   C05  C10   116.50  3.000
 89O  C06   C05  C10   120.33  3.000
 89O  C07   C06  C05   120.33  3.000
 89O  C05   C06  C01   123.14  3.000
 89O  C07   C06  C01   116.47  3.000
 89O  H071  C07  C08   121.03  3.000
 89O  H071  C07  C06   120.84  3.000
 89O  C08   C07  C06   118.13  3.000
 89O  O13   C08  C09   109.38  3.000
 89O  C09   C08  C07   121.46  3.000
 89O  O13   C08  C07   129.15  3.000
 89O  O11   C09  C08   109.38  3.000
 89O  O11   C09  C10   129.00  3.000
 89O  C08   C09  C10   121.62  3.000
 89O  C12   O11  C09   106.21  3.000
 89O  H122  C12  H121  110.60  3.000
 89O  H122  C12  O13   109.78  3.000
 89O  H121  C12  O13   109.86  3.000
 89O  H122  C12  O11   109.78  3.000
 89O  H121  C12  O11   109.79  3.000
 89O  O13   C12  O11   106.95  3.000
 89O  C12   O13  C08   106.19  3.000
 89O  C19   C14  C04   119.06  3.000
 89O  C19   C14  C15   119.40  3.000
 89O  C04   C14  C15   121.54  3.000
 89O  O23   C16  C17   115.39  3.000
 89O  O23   C16  C15   124.62  3.000
 89O  C17   C16  C15   119.98  3.000
 89O  O20   C18  C19   124.91  3.000
 89O  O20   C18  C17   114.44  3.000
 89O  C19   C18  C17   120.65  3.000
 89O  H191  C19  C18   120.39  3.000
 89O  H191  C19  C14   119.45  3.000
 89O  C18   C19  C14   120.16  3.000
 89O  C18   O20  C21   118.54  3.000
 89O  C16   O23  C24   118.13  3.000
 89O  O27   C25  O26   121.50  3.000
 89O  O26   C25  C03   129.62  3.000
 89O  O27   C25  C03   108.83  3.000
 89O  C25   O27  C28   111.46  3.000
 89O  H291  O29  C01   108.76  3.000
 89O  H221  O22  C17   109.49  3.000
 89O  H212  C21  H211  108.90  3.000
 89O  H212  C21  H213  108.82  3.000
 89O  H211  C21  H213  108.92  3.000
 89O  H212  C21  O20   111.80  3.000
 89O  H211  C21  O20   111.75  3.000
 89O  H213  C21  O20   106.56  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
 89O  CONST_01  C07   C08  C09  C10     0.00   0.0  0
 89O  CONST_02  C07   C06  C05  C10     0.00   0.0  0
 89O  CONST_03  C18   C19  C14  C15     0.00   0.0  0
 89O  CONST_04  C18   C17  C16  C15     0.00   0.0  0
 89O  CONST_05  C14   C19  C18  C17     0.00   0.0  0
 89O  CONST_06  C14   C15  C16  C17     0.00   0.0  0
 89O  CONST_07  C08   C07  C06  C05     0.00   0.0  0
 89O  CONST_08  C08   C09  C10  C05     0.00   0.0  0
 89O  CONST_09  C09   C08  C07  C06     0.00   0.0  0
 89O  CONST_10  C09   C10  C05  C06     0.00   0.0  0
 89O  CONST_11  C19   C14  C15  C16     0.00   0.0  0
 89O  CONST_12  C19   C18  C17  C16     0.00   0.0  0
 89O  CONST_13  C18   C19  C14  C04   180.00   0.0  0
 89O  CONST_14  C16   C15  C14  C04   180.00   0.0  0
 89O  CONST_15  O22   C17  C16  C15   180.00   0.0  0
 89O  CONST_16  O20   C18  C19  C14   180.00   0.0  0
 89O  CONST_17  O23   C16  C15  C14   180.00   0.0  0
 89O  CONST_18  O20   C18  C17  C16   180.00   0.0  0
 89O  CONST_19  O23   C16  C17  C18   180.00   0.0  0
 89O  CONST_20  O22   C17  C18  C19   180.00   0.0  0
 89O  CONST_21  H191  C19  C14  C15   180.00   0.0  0
 89O  CONST_22  H151  C15  C16  C17   180.00   0.0  0
 89O  CONST_23  H071  C07  C06  C01     0.00   0.0  0
 89O  CONST_24  H101  C10  C05  C04     0.00   0.0  0
 89O  Var_01    C03   C25  O27  C28     0.00  30.0  1
 89O  Var_02    O11   C12  O13  C08    13.35  30.0  1
 89O  Var_03    O13   C12  O11  C09   -13.40  30.0  1
 89O  Var_04    H281  C28  O27  C25  -142.24  30.0  1
 89O  Var_05    C19   C18  O20  C21    -3.61  30.0  2
 89O  Var_06    H242  C24  O23  C16   179.70  30.0  3
 89O  Var_07    H213  C21  O20  C18  -177.02  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
 89O  chir_01  C01  O29  C06  C02  positiv
 89O  chir_02  C02  C01  C28  C03  negativ
 89O  chir_03  C03  C02  C04  C25  negativ
 89O  chir_04  C04  C14  C03  C05  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
 89O  plan-1  C15   0.020
 89O  plan-1  C17   0.020
 89O  plan-1  C04   0.020
 89O  plan-1  C14   0.020
 89O  plan-1  C16   0.020
 89O  plan-1  C18   0.020
 89O  plan-1  C19   0.020
 89O  plan-1  O20   0.020
 89O  plan-1  O23   0.020
 89O  plan-1  H151  0.020
 89O  plan-1  H191  0.020
 89O  plan-1  O22   0.020
 89O  plan-2  C10   0.020
 89O  plan-2  C01   0.020
 89O  plan-2  C04   0.020
 89O  plan-2  C05   0.020
 89O  plan-2  C06   0.020
 89O  plan-2  C07   0.020
 89O  plan-2  C08   0.020
 89O  plan-2  C09   0.020
 89O  plan-2  O11   0.020
 89O  plan-2  O13   0.020
 89O  plan-2  H101  0.020
 89O  plan-2  H071  0.020
 89O  plan-3  C03   0.020
 89O  plan-3  C25   0.020
 89O  plan-3  O26   0.020
 89O  plan-3  O27   0.020

