# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 18:58:06 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: 3-chloro-4,6-dihydroxy-5-[(2Z,6Z,8E)-11-hydroxy-3,7,11-trimethyl-10-oxododeca-2,6,8-trien-1-yl]-2-methylbenzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(/CC\C=C(C)/C=C/C(=O)C(C)(C)O)=C/Cc1c(O)c(Cl)c(C)c(C=O)c1O
#
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
 9BX  9BX  3-chloro-4,6-dihydroxy-5-[(2Z,6Z,8E)-11-hydroxy-3,7,11-trimethyl-10-oxododeca-2,6,8-trien-1-yl]-2-methylbenzaldehyde  ligand  58  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_9BX
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
 9BX  CAU  C   CH3   0  -0.672  -3.4463   3.5132   0.6496
 9BX  CAT  C   CT    0   0.099  -3.5324   2.1040   1.2255
 9BX  CAW  C   CH3   0  -0.659  -2.4769   1.9036   2.3118
 9BX  OAV  O   OH1   0  -0.661  -4.7879   1.8848   1.8374
 9BX  CAS  C   C     0   0.363  -3.2586   1.0469   0.1452
 9BX  OAX  O   O     0  -0.410  -2.5777   1.3187  -0.8244
 9BX  CAR  C   C1    0  -0.376  -3.8036  -0.3043   0.3730
 9BX  CAQ  C   C1    0  -0.213  -3.4002  -1.3335  -0.3890
 9BX  CAO  C   C     0   0.115  -3.8045  -2.7203  -0.2399
 9BX  CAP  C   CH3   0  -0.737  -4.9621  -3.0361   0.6610
 9BX  CAN  C   C1    0  -0.242  -3.1217  -3.6919  -0.8740
 9BX  CAM  C   CH2   0  -0.514  -1.8976  -3.5071  -1.7176
 9BX  CAL  C   CH2   0  -0.529  -0.6321  -3.3965  -0.8445
 9BX  CAJ  C   C     0   0.114   0.6187  -3.1987  -1.6595
 9BX  CAK  C   CH3   0  -0.718   1.3243  -4.4570  -2.0718
 9BX  CAI  C   C1    0  -0.250   1.0719  -1.9979  -2.0273
 9BX  CAH  C   CH2   0  -0.576   0.4377  -0.6673  -1.7309
 9BX  CAG  C   CR6   0  -0.085   1.3167   0.2274  -0.8944
 9BX  CAY  C   CR6   0   0.385   1.1362   0.3392   0.4841
 9BX  OAZ  O   OH1   0  -0.612   0.1673  -0.3708   1.0440
 9BX  CBA  C   CR6   0  -0.235   1.9566   1.1865   1.2678
 9BX  CBB  C   C1    0   0.145   1.7142   1.2755   2.6883
 9BX  OBC  O   O     0  -0.458   0.8269   0.6589   3.2759
 9BX  CAB  C   CR6   0   0.160   2.9962   1.9338   0.6670
 9BX  CAA  C   CH3   0  -0.757   3.8671   2.8303   1.4999
 9BX  CAC  C   CR6   0  -0.270   3.1663   1.8047  -0.6935
 9BX  CLA  CL  CL    0  -0.118   4.4093   2.6757  -1.5465
 9BX  CAE  C   CR6   0   0.442   2.3433   0.9626  -1.4728
 9BX  OAF  O   OH1   0  -0.591   2.5124   0.8368  -2.7864
 9BX  H1   H   HCH3  0   0.235  -2.4605   3.7206   0.2377
 9BX  H2   H   HCH3  0   0.236  -4.1807   3.6705  -0.1433
 9BX  H3   H   HCH3  0   0.238  -3.6388   4.2414   1.4387
 9BX  H4   H   HCH3  0   0.246  -2.6264   2.6291   3.1131
 9BX  H5   H   HCH3  0   0.242  -2.5235   0.9029   2.7436
 9BX  H6   H   HCH3  0   0.233  -1.4779   2.0514   1.9045
 9BX  H7   H   HOH1  0   0.451  -5.4834   2.0881   1.2023
 9BX  H8   H   H     0   0.265  -4.4919  -0.4480   1.1944
 9BX  H10  H   H     0   0.252  -2.6895  -1.1158  -1.1785
 9BX  H11  H   HCH3  0   0.241  -5.8643  -2.5074   0.3473
 9BX  H12  H   HCH3  0   0.249  -5.1801  -4.1030   0.6635
 9BX  H13  H   HCH3  0   0.241  -4.7603  -2.7358   1.6913
 9BX  H14  H   H     0   0.248  -3.4354  -4.7181  -0.7071
 9BX  H16  H   HCH2  0   0.256  -1.7973  -4.3522  -2.4017
 9BX  H17  H   HCH2  0   0.252  -1.9726  -2.6157  -2.3443
 9BX  H18  H   HCH2  0   0.258  -0.7624  -2.5794  -0.1339
 9BX  H19  H   HCH2  0   0.247  -0.5375  -4.3058  -0.2438
 9BX  H21  H   HCH3  0   0.233   0.6448  -5.1318  -2.5994
 9BX  H22  H   HCH3  0   0.237   2.1732  -4.2592  -2.7257
 9BX  H23  H   HCH3  0   0.236   1.6871  -5.0058  -1.1990
 9BX  H24  H   H     0   0.231   1.9790  -1.9575  -2.6245
 9BX  H26  H   HCH2  0   0.263   0.2109  -0.1649  -2.6749
 9BX  H27  H   HCH2  0   0.273  -0.5182  -0.7914  -1.2280
 9BX  H28  H   HOH1  0   0.478   0.1605  -0.1707   2.0111
 9BX  H29  H   H     0   0.238   2.3663   1.9385   3.2686
 9BX  H30  H   HCH3  0   0.267   4.3392   2.2775   2.3118
 9BX  H31  H   HCH3  0   0.267   4.6593   3.2886   0.9171
 9BX  H32  H   HCH3  0   0.270   3.2834   3.6360   1.9465
 9BX  H33  H   HOH1  0   0.476   3.2481   1.3773  -3.1055

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
 9BX  CAU  CAT  single    1.525  0.020  1.525
 9BX  OBC  CBB  double    1.230  0.020  1.230
 9BX  CBB  CBA  single    1.444  0.020  1.444
 9BX  OAX  CAS  double    1.216  0.020  1.216
 9BX  CAT  CAW  single    1.528  0.020  1.528
 9BX  CAT  CAS  single    1.536  0.020  1.536
 9BX  CAT  OAV  single    1.414  0.020  1.414
 9BX  CAS  CAR  single    1.475  0.020  1.475
 9BX  OAZ  CAY  single    1.325  0.020  1.325
 9BX  CBA  CAY  aromatic  1.416  0.020  1.416
 9BX  CBA  CAB  aromatic  1.414  0.020  1.414
 9BX  CAA  CAB  single    1.502  0.020  1.502
 9BX  CAY  CAG  aromatic  1.395  0.020  1.395
 9BX  CAR  CAQ  double    1.343  0.020  1.343
 9BX  CAB  CAC  aromatic  1.377  0.020  1.377
 9BX  CAQ  CAO  single    1.452  0.020  1.452
 9BX  CAG  CAH  single    1.508  0.020  1.508
 9BX  CAG  CAE  aromatic  1.389  0.020  1.389
 9BX  CAC  CAE  aromatic  1.412  0.020  1.412
 9BX  CAC  CLA  single    1.741  0.020  1.741
 9BX  CAH  CAI  single    1.504  0.020  1.504
 9BX  CAO  CAP  single    1.500  0.020  1.500
 9BX  CAO  CAN  double    1.346  0.020  1.346
 9BX  CAM  CAL  single    1.541  0.020  1.541
 9BX  CAM  CAN  single    1.498  0.020  1.498
 9BX  CAE  OAF  single    1.330  0.020  1.330
 9BX  CAL  CAJ  single    1.506  0.020  1.506
 9BX  CAI  CAJ  double    1.335  0.020  1.335
 9BX  CAJ  CAK  single    1.500  0.020  1.500
 9BX  CAU  H1   single    0.970  0.020  1.090
 9BX  CAU  H2   single    0.970  0.020  1.090
 9BX  CAU  H3   single    0.970  0.020  1.090
 9BX  CAW  H4   single    0.970  0.020  1.090
 9BX  CAW  H5   single    0.970  0.020  1.090
 9BX  CAW  H6   single    0.970  0.020  1.090
 9BX  OAV  H7   single    0.850  0.020  0.980
 9BX  CAR  H8   single    0.930  0.020  1.080
 9BX  CAQ  H10  single    0.930  0.020  1.080
 9BX  CAP  H11  single    0.970  0.020  1.090
 9BX  CAP  H12  single    0.970  0.020  1.090
 9BX  CAP  H13  single    0.970  0.020  1.090
 9BX  CAN  H14  single    0.930  0.020  1.080
 9BX  CAM  H16  single    0.970  0.020  1.090
 9BX  CAM  H17  single    0.970  0.020  1.090
 9BX  CAL  H18  single    0.970  0.020  1.090
 9BX  CAL  H19  single    0.970  0.020  1.090
 9BX  CAK  H21  single    0.970  0.020  1.090
 9BX  CAK  H22  single    0.970  0.020  1.090
 9BX  CAK  H23  single    0.970  0.020  1.090
 9BX  CAI  H24  single    0.930  0.020  1.080
 9BX  CAH  H26  single    0.970  0.020  1.090
 9BX  CAH  H27  single    0.970  0.020  1.090
 9BX  OAZ  H28  single    0.850  0.020  0.980
 9BX  CBB  H29  single    0.930  0.020  1.080
 9BX  CAA  H30  single    0.970  0.020  1.090
 9BX  CAA  H31  single    0.970  0.020  1.090
 9BX  CAA  H32  single    0.970  0.020  1.090
 9BX  OAF  H33  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
 9BX  H3   CAU  H2   108.08  3.000
 9BX  H3   CAU  H1   107.85  3.000
 9BX  H2   CAU  H1   107.87  3.000
 9BX  H3   CAU  CAT  109.50  3.000
 9BX  H2   CAU  CAT  111.68  3.000
 9BX  H1   CAU  CAT  111.72  3.000
 9BX  CAS  CAT  OAV  110.85  3.000
 9BX  OAV  CAT  CAW  106.58  3.000
 9BX  CAS  CAT  CAW  106.66  3.000
 9BX  OAV  CAT  CAU  110.91  3.000
 9BX  CAS  CAT  CAU  111.13  3.000
 9BX  CAW  CAT  CAU  110.53  3.000
 9BX  H6   CAW  H5   108.16  3.000
 9BX  H6   CAW  H4   108.07  3.000
 9BX  H5   CAW  H4   108.26  3.000
 9BX  H6   CAW  CAT  110.49  3.000
 9BX  H5   CAW  CAT  111.86  3.000
 9BX  H4   CAW  CAT  109.90  3.000
 9BX  H7   OAV  CAT  108.84  3.000
 9BX  CAR  CAS  OAX  122.35  3.000
 9BX  CAR  CAS  CAT  117.13  3.000
 9BX  OAX  CAS  CAT  120.46  3.000
 9BX  H8   CAR  CAQ  121.37  3.000
 9BX  H8   CAR  CAS  118.32  3.000
 9BX  CAQ  CAR  CAS  120.24  3.000
 9BX  H10  CAQ  CAO  116.68  3.000
 9BX  H10  CAQ  CAR  117.15  3.000
 9BX  CAO  CAQ  CAR  126.16  3.000
 9BX  CAN  CAO  CAP  121.48  3.000
 9BX  CAN  CAO  CAQ  119.97  3.000
 9BX  CAP  CAO  CAQ  118.52  3.000
 9BX  H13  CAP  H12  107.71  3.000
 9BX  H13  CAP  H11  106.90  3.000
 9BX  H12  CAP  H11  108.04  3.000
 9BX  H13  CAP  CAO  111.47  3.000
 9BX  H12  CAP  CAO  111.22  3.000
 9BX  H11  CAP  CAO  111.29  3.000
 9BX  H14  CAN  CAM  116.04  3.000
 9BX  H14  CAN  CAO  117.59  3.000
 9BX  CAM  CAN  CAO  126.21  3.000
 9BX  H17  CAM  H16  106.17  3.000
 9BX  H17  CAM  CAL  108.83  3.000
 9BX  H16  CAM  CAL  109.57  3.000
 9BX  H17  CAM  CAN  111.57  3.000
 9BX  H16  CAM  CAN  109.42  3.000
 9BX  CAL  CAM  CAN  111.15  3.000
 9BX  H19  CAL  H18  105.98  3.000
 9BX  H19  CAL  CAJ  109.54  3.000
 9BX  H18  CAL  CAJ  110.70  3.000
 9BX  H19  CAL  CAM  108.80  3.000
 9BX  H18  CAL  CAM  108.95  3.000
 9BX  CAJ  CAL  CAM  112.63  3.000
 9BX  CAI  CAJ  CAK  121.26  3.000
 9BX  CAK  CAJ  CAL  115.42  3.000
 9BX  CAI  CAJ  CAL  123.31  3.000
 9BX  H23  CAK  H22  108.16  3.000
 9BX  H23  CAK  H21  106.36  3.000
 9BX  H22  CAK  H21  107.86  3.000
 9BX  H23  CAK  CAJ  110.96  3.000
 9BX  H22  CAK  CAJ  112.27  3.000
 9BX  H21  CAK  CAJ  110.97  3.000
 9BX  H24  CAI  CAH  115.31  3.000
 9BX  H24  CAI  CAJ  117.92  3.000
 9BX  CAH  CAI  CAJ  126.76  3.000
 9BX  H27  CAH  H26  105.64  3.000
 9BX  H27  CAH  CAG  108.88  3.000
 9BX  H26  CAH  CAG  109.11  3.000
 9BX  H27  CAH  CAI  111.17  3.000
 9BX  H26  CAH  CAI  108.91  3.000
 9BX  CAG  CAH  CAI  112.87  3.000
 9BX  CAE  CAG  CAY  117.70  3.000
 9BX  CAE  CAG  CAH  120.93  3.000
 9BX  CAY  CAG  CAH  121.37  3.000
 9BX  CBA  CAY  OAZ  120.68  3.000
 9BX  CBA  CAY  CAG  121.33  3.000
 9BX  OAZ  CAY  CAG  117.98  3.000
 9BX  H28  OAZ  CAY  108.07  3.000
 9BX  CAB  CBA  CBB  120.59  3.000
 9BX  CAB  CBA  CAY  120.46  3.000
 9BX  CBB  CBA  CAY  118.96  3.000
 9BX  H29  CBB  OBC  118.66  3.000
 9BX  H29  CBB  CBA  117.27  3.000
 9BX  OBC  CBB  CBA  124.08  3.000
 9BX  CAC  CAB  CAA  122.16  3.000
 9BX  CAC  CAB  CBA  117.44  3.000
 9BX  CAA  CAB  CBA  120.40  3.000
 9BX  H32  CAA  H31  107.38  3.000
 9BX  H32  CAA  H30  107.56  3.000
 9BX  H31  CAA  H30  107.35  3.000
 9BX  H32  CAA  CAB  110.96  3.000
 9BX  H31  CAA  CAB  112.18  3.000
 9BX  H30  CAA  CAB  111.19  3.000
 9BX  CAE  CAC  CLA  116.36  3.000
 9BX  CLA  CAC  CAB  121.68  3.000
 9BX  CAE  CAC  CAB  121.95  3.000
 9BX  OAF  CAE  CAC  121.82  3.000
 9BX  OAF  CAE  CAG  117.08  3.000
 9BX  CAC  CAE  CAG  121.11  3.000
 9BX  H33  OAF  CAE  111.70  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
 9BX  CONST_01  CAB  CBA  CAY  CAG     0.00   0.0  0
 9BX  CONST_02  CAB  CAC  CAE  CAG     0.00   0.0  0
 9BX  CONST_03  CAC  CAB  CBA  CAY     0.00   0.0  0
 9BX  CONST_04  CAC  CAE  CAG  CAY     0.00   0.0  0
 9BX  CONST_05  CAE  CAG  CAY  CBA     0.00   0.0  0
 9BX  CONST_06  CAE  CAC  CAB  CBA     0.00   0.0  0
 9BX  CONST_07  CBA  CAY  CAG  CAH   180.00   0.0  0
 9BX  CONST_08  CAC  CAE  CAG  CAH   180.00   0.0  0
 9BX  CONST_09  CBB  CBA  CAY  CAG   180.00   0.0  0
 9BX  CONST_10  CLA  CAC  CAE  CAG   180.00   0.0  0
 9BX  CONST_11  CAA  CAB  CBA  CAY   180.00   0.0  0
 9BX  CONST_12  OAF  CAE  CAG  CAY   180.00   0.0  0
 9BX  CONST_13  CAB  CBA  CAY  OAZ   180.00   0.0  0
 9BX  CONST_14  CAE  CAG  CAY  OAZ   180.00   0.0  0
 9BX  CONST_15  CLA  CAC  CAB  CBA   180.00   0.0  0
 9BX  CONST_16  CAC  CAB  CBA  CBB   180.00   0.0  0
 9BX  CONST_17  OAF  CAE  CAC  CAB   180.00   0.0  0
 9BX  CONST_18  CAE  CAC  CAB  CAA   180.00   0.0  0
 9BX  Var_01    CAY  CAG  CAH  CAI   -98.63  30.0  3
 9BX  Var_02    OBC  CBB  CBA  CAY    -0.21  30.0  2
 9BX  Var_03    H30  CAA  CAB  CBA    56.06  30.0  2
 9BX  Var_04    CAG  CAH  CAI  CAJ   117.97  30.0  2
 9BX  Var_05    CAO  CAQ  CAR  CAS   177.07   0.0  2
 9BX  Var_06    CAM  CAN  CAO  CAQ     2.66   0.0  2
 9BX  Var_07    CAH  CAI  CAJ  CAL    -1.00   0.0  2
 9BX  Var_08    OAX  CAS  CAT  CAU    26.08  30.0  3
 9BX  Var_09    CAQ  CAR  CAS  CAT  -167.48  30.0  2
 9BX  Var_10    CAP  CAO  CAQ  CAR    12.35  30.0  2
 9BX  Var_11    CAL  CAM  CAN  CAO    81.19  30.0  1
 9BX  Var_12    CAJ  CAL  CAM  CAN  -179.55  30.0  3
 9BX  Var_13    CAI  CAJ  CAL  CAM    88.21  30.0  3
 9BX  Var_14    H4   CAW  CAT  CAU    59.36  30.0  3
 9BX  Var_15    H1   CAU  CAT  CAW    57.97  30.0  3
 9BX  Var_16    H11  CAP  CAO  CAQ    57.89  30.0  3
 9BX  Var_17    H21  CAK  CAJ  CAL    54.50  30.0  3

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
 9BX  plan-1  CAH  0.020
 9BX  plan-1  CAG  0.020
 9BX  plan-1  CAY  0.020
 9BX  plan-1  OAZ  0.020
 9BX  plan-1  CBA  0.020
 9BX  plan-1  CBB  0.020
 9BX  plan-1  CAB  0.020
 9BX  plan-1  CAA  0.020
 9BX  plan-1  CAC  0.020
 9BX  plan-1  CLA  0.020
 9BX  plan-1  CAE  0.020
 9BX  plan-1  OAF  0.020
 9BX  plan-2  CAT  0.020
 9BX  plan-2  CAS  0.020
 9BX  plan-2  OAX  0.020
 9BX  plan-2  CAR  0.020
 9BX  plan-3  CBA  0.020
 9BX  plan-3  CBB  0.020
 9BX  plan-3  OBC  0.020
 9BX  plan-3  H29  0.020
 9BX  plan-4  CAS  0.020
 9BX  plan-4  CAR  0.020
 9BX  plan-4  CAQ  0.020
 9BX  plan-4  CAO  0.020
 9BX  plan-4  H8   0.020
 9BX  plan-4  H10  0.020
 9BX  plan-5  CAQ  0.020
 9BX  plan-5  CAO  0.020
 9BX  plan-5  CAP  0.020
 9BX  plan-5  CAN  0.020
 9BX  plan-5  CAM  0.020
 9BX  plan-5  H14  0.020
 9BX  plan-6  CAL  0.020
 9BX  plan-6  CAJ  0.020
 9BX  plan-6  CAK  0.020
 9BX  plan-6  CAI  0.020
 9BX  plan-6  CAH  0.020
 9BX  plan-6  H24  0.020

