# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:24:21 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 4-formyl-3-hydroxy-8-methoxy-1,9-dimethyl-11-oxo-11H-dibenzo[b,e][1,4]dioxepine-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(C(O)=O)c2Oc3c(C=O)c(O)cc(C)c3C(=O)Oc2c1C
#
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
 PJA  PJA  '4-formyl-3-hydroxy-8-methoxy-1,9-dimethyl-11-oxo-11H-dibenzo[b,e][1,4]dioxepine-6-carboxylic acid'  ligand  39  26  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PJA
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
 PJA  O    O  O      0  -0.445  -3.0197   3.2628  -0.1882
 PJA  CAN  C  C1     0   0.155  -2.2312   2.4050  -0.5706
 PJA  CBB  C  CR6    0  -0.281  -2.3616   1.0073  -0.1929
 PJA  CBF  C  CR6    0   0.407  -1.4534   0.0357  -0.6299
 PJA  OAS  O  O2     0  -0.509  -0.3985   0.4459  -1.3839
 PJA  CBE  C  CR6    0   0.242   0.8259   0.2025  -0.7859
 PJA  CBA  C  CR6    0  -0.132   1.6055   1.2206  -0.2694
 PJA  CAU  C  C      0   0.392   1.2771   2.7039  -0.4159
 PJA  OAH  O  O      0  -0.582   0.8519   3.0666  -1.5274
 PJA  OAE  O  OC    -1  -0.581   1.5053   3.4095   0.5801
 PJA  CAL  C  CR16   0  -0.451   2.7949   0.8681   0.3686
 PJA  CAZ  C  CR6    0   0.375   3.1998  -0.4552   0.4678
 PJA  OAQ  O  O2     0  -0.465   4.3447  -0.8473   1.0558
 PJA  CAA  C  CH3    0  -0.438   5.1948   0.1353   1.6127
 PJA  CAY  C  CR6    0  -0.112   2.4112  -1.4933  -0.0545
 PJA  CAD  C  CH3    0  -0.708   2.8611  -2.9185   0.0600
 PJA  CBD  C  CR6    0   0.358   1.2291  -1.1228  -0.6721
 PJA  OAR  O  O2     0  -0.469   0.4882  -2.1076  -1.2780
 PJA  CBC  C  C      0   0.569  -0.8177  -2.3295  -1.0491
 PJA  OAG  O  O      0  -0.396  -1.2754  -3.3545  -1.4756
 PJA  CBG  C  CR6    0  -0.274  -1.6237  -1.3126  -0.3423
 PJA  CAW  C  CR6    0   0.119  -2.7058  -1.7081   0.4804
 PJA  CAC  C  CH3    0  -0.730  -2.9358  -3.1352   0.8789
 PJA  CAK  C  CR16   0  -0.408  -3.5758  -0.7516   0.9621
 PJA  CAX  C  CR6    0   0.413  -3.4424   0.5922   0.6142
 PJA  OAJ  O  OH1    0  -0.606  -4.3356   1.4510   1.0686
 PJA  H2   H  H      0   0.261  -1.3967   2.6797  -1.2236
 PJA  H5   H  HCR6   0   0.282   3.3980   1.6641   0.7836
 PJA  H6   H  HCH3   0   0.261   6.0445  -0.3963   2.0335
 PJA  H7   H  HCH3   0   0.230   5.5567   0.8370   0.8568
 PJA  H8   H  HCH3   0   0.230   4.7011   0.6984   2.4087
 PJA  H9   H  HCH3   0   0.250   3.1104  -3.1656   1.0920
 PJA  H10  H  HCH3   0   0.251   2.0995  -3.6181  -0.2732
 PJA  H11  H  HCH3   0   0.252   3.7570  -3.0969  -0.5374
 PJA  H12  H  HCH3   0   0.255  -2.0129  -3.6352   1.1695
 PJA  H13  H  HCH3   0   0.257  -3.6230  -3.1802   1.7213
 PJA  H14  H  HCH3   0   0.268  -3.3717  -3.7060   0.0600
 PJA  H15  H  HCR6   0   0.277  -4.3954  -1.0426   1.6068
 PJA  H16  H  HOH1   0   0.481  -4.0939   2.3498   0.7400

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
 PJA  CAA  OAQ  single    1.414  0.020  1.414
 PJA  OAQ  CAZ  single    1.346  0.020  1.346
 PJA  CAD  CAY  single    1.499  0.020  1.499
 PJA  CAZ  CAY  aromatic  1.404  0.020  1.404
 PJA  CAZ  CAL  aromatic  1.387  0.020  1.387
 PJA  CAY  CBD  aromatic  1.384  0.020  1.384
 PJA  CAL  CBA  aromatic  1.395  0.020  1.395
 PJA  CBD  OAR  single    1.373  0.020  1.373
 PJA  CBD  CBE  aromatic  1.390  0.020  1.390
 PJA  OAR  CBC  single    1.344  0.020  1.344
 PJA  CBA  CBE  aromatic  1.382  0.020  1.382
 PJA  CBA  CAU  single    1.526  0.020  1.526
 PJA  CBE  OAS  single    1.384  0.020  1.384
 PJA  OAH  CAU  deloc     1.244  0.020  1.244
 PJA  OAG  CBC  double    1.201  0.020  1.201
 PJA  CBC  CBG  single    1.478  0.020  1.478
 PJA  CAU  OAE  deloc     1.242  0.020  1.242
 PJA  OAS  CBF  single    1.360  0.020  1.360
 PJA  CBG  CBF  aromatic  1.389  0.020  1.389
 PJA  CBG  CAW  aromatic  1.416  0.020  1.416
 PJA  CBF  CBB  aromatic  1.400  0.020  1.400
 PJA  CAC  CAW  single    1.499  0.020  1.499
 PJA  CAW  CAK  aromatic  1.380  0.020  1.380
 PJA  CBB  CAN  single    1.454  0.020  1.454
 PJA  CBB  CAX  aromatic  1.411  0.020  1.411
 PJA  CAN  O    double    1.226  0.020  1.226
 PJA  CAK  CAX  aromatic  1.394  0.020  1.394
 PJA  CAX  OAJ  single    1.320  0.020  1.320
 PJA  CAN  H2   single    0.930  0.020  1.080
 PJA  CAL  H5   single    0.930  0.020  1.080
 PJA  CAA  H6   single    0.970  0.020  1.090
 PJA  CAA  H7   single    0.970  0.020  1.090
 PJA  CAA  H8   single    0.970  0.020  1.090
 PJA  CAD  H9   single    0.970  0.020  1.090
 PJA  CAD  H10  single    0.970  0.020  1.090
 PJA  CAD  H11  single    0.970  0.020  1.090
 PJA  CAC  H12  single    0.970  0.020  1.090
 PJA  CAC  H13  single    0.970  0.020  1.090
 PJA  CAC  H14  single    0.970  0.020  1.090
 PJA  CAK  H15  single    0.930  0.020  1.080
 PJA  OAJ  H16  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
 PJA  H2   CAN  CBB  117.69  3.000
 PJA  H2   CAN  O    120.04  3.000
 PJA  CBB  CAN  O    122.27  3.000
 PJA  CAX  CBB  CBF  118.11  3.000
 PJA  CAX  CBB  CAN  120.01  3.000
 PJA  CBF  CBB  CAN  121.87  3.000
 PJA  CBG  CBF  OAS  120.17  3.000
 PJA  CBG  CBF  CBB  121.97  3.000
 PJA  OAS  CBF  CBB  117.84  3.000
 PJA  CBE  OAS  CBF  113.18  3.000
 PJA  CBD  CBE  CBA  120.53  3.000
 PJA  CBA  CBE  OAS  122.06  3.000
 PJA  CBD  CBE  OAS  117.36  3.000
 PJA  CAL  CBA  CAU  118.22  3.000
 PJA  CAU  CBA  CBE  123.96  3.000
 PJA  CAL  CBA  CBE  117.75  3.000
 PJA  OAE  CAU  OAH  127.86  3.000
 PJA  OAE  CAU  CBA  115.83  3.000
 PJA  OAH  CAU  CBA  116.27  3.000
 PJA  H5   CAL  CAZ  120.79  3.000
 PJA  H5   CAL  CBA  117.71  3.000
 PJA  CAZ  CAL  CBA  121.50  3.000
 PJA  CAY  CAZ  OAQ  115.14  3.000
 PJA  CAY  CAZ  CAL  120.97  3.000
 PJA  OAQ  CAZ  CAL  123.89  3.000
 PJA  CAA  OAQ  CAZ  118.77  3.000
 PJA  H8   CAA  H7   108.81  3.000
 PJA  H8   CAA  H6   108.85  3.000
 PJA  H7   CAA  H6   108.83  3.000
 PJA  H8   CAA  OAQ  111.93  3.000
 PJA  H7   CAA  OAQ  111.90  3.000
 PJA  H6   CAA  OAQ  106.42  3.000
 PJA  CBD  CAY  CAD  123.02  3.000
 PJA  CBD  CAY  CAZ  116.59  3.000
 PJA  CAD  CAY  CAZ  120.39  3.000
 PJA  H11  CAD  H10  107.59  3.000
 PJA  H11  CAD  H9   107.07  3.000
 PJA  H10  CAD  H9   107.74  3.000
 PJA  H11  CAD  CAY  111.10  3.000
 PJA  H10  CAD  CAY  112.23  3.000
 PJA  H9   CAD  CAY  110.88  3.000
 PJA  OAR  CBD  CAY  117.75  3.000
 PJA  OAR  CBD  CBE  119.41  3.000
 PJA  CAY  CBD  CBE  122.65  3.000
 PJA  CBC  OAR  CBD  124.57  3.000
 PJA  CBG  CBC  OAG  123.32  3.000
 PJA  CBG  CBC  OAR  119.85  3.000
 PJA  OAG  CBC  OAR  116.79  3.000
 PJA  CAW  CBG  CBC  120.18  3.000
 PJA  CAW  CBG  CBF  119.02  3.000
 PJA  CBC  CBG  CBF  120.14  3.000
 PJA  CAK  CAW  CAC  118.05  3.000
 PJA  CAK  CAW  CBG  119.42  3.000
 PJA  CAC  CAW  CBG  122.52  3.000
 PJA  H14  CAC  H13  107.91  3.000
 PJA  H14  CAC  H12  107.40  3.000
 PJA  H13  CAC  H12  108.04  3.000
 PJA  H14  CAC  CAW  111.12  3.000
 PJA  H13  CAC  CAW  110.00  3.000
 PJA  H12  CAC  CAW  112.20  3.000
 PJA  H15  CAK  CAX  118.69  3.000
 PJA  H15  CAK  CAW  119.93  3.000
 PJA  CAX  CAK  CAW  121.37  3.000
 PJA  OAJ  CAX  CAK  118.45  3.000
 PJA  OAJ  CAX  CBB  121.58  3.000
 PJA  CAK  CAX  CBB  119.96  3.000
 PJA  H16  OAJ  CAX  108.19  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
 PJA  CONST_01  CAW  CBG  CBF  CBB     0.00   0.0  0
 PJA  CONST_02  CAW  CAK  CAX  CBB     0.00   0.0  0
 PJA  CONST_03  CAK  CAW  CBG  CBF     0.00   0.0  0
 PJA  CONST_04  CAK  CAX  CBB  CBF     0.00   0.0  0
 PJA  CONST_05  CAZ  CAY  CBD  CBE     0.00   0.0  0
 PJA  CONST_06  CAZ  CAL  CBA  CBE     0.00   0.0  0
 PJA  CONST_07  CAY  CAZ  CAL  CBA     0.00   0.0  0
 PJA  CONST_08  CAY  CBD  CBE  CBA     0.00   0.0  0
 PJA  CONST_09  CBD  CAY  CAZ  CAL     0.00   0.0  0
 PJA  CONST_10  CBD  CBE  CBA  CAL     0.00   0.0  0
 PJA  CONST_11  CAX  CBB  CBF  CBG     0.00   0.0  0
 PJA  CONST_12  CAX  CAK  CAW  CBG     0.00   0.0  0
 PJA  CONST_13  OAS  CBF  CBB  CAN     0.00   0.0  0
 PJA  CONST_14  CBG  CBF  CBB  CAN   180.00   0.0  0
 PJA  CONST_15  CAK  CAX  CBB  CAN   180.00   0.0  0
 PJA  CONST_16  CAC  CAW  CBG  CBF   180.00   0.0  0
 PJA  CONST_17  OAJ  CAX  CBB  CBF   180.00   0.0  0
 PJA  CONST_18  CAU  CBA  CBE  OAS     0.00   0.0  0
 PJA  CONST_19  CAD  CAY  CBD  CBE   180.00   0.0  0
 PJA  CONST_20  OAQ  CAZ  CAL  CBA   180.00   0.0  0
 PJA  CONST_21  CAZ  CAL  CBA  CAU   180.00   0.0  0
 PJA  CONST_22  CBD  CBE  CBA  CAU   180.00   0.0  0
 PJA  CONST_23  CAD  CAY  CAZ  CAL   180.00   0.0  0
 PJA  CONST_24  CBD  CAY  CAZ  OAQ   180.00   0.0  0
 PJA  CONST_25  OAR  CBD  CAY  CAD     0.00   0.0  0
 PJA  CONST_26  CAC  CAW  CBG  CBC     0.00   0.0  0
 PJA  CONST_27  OAJ  CAX  CAK  CAW   180.00   0.0  0
 PJA  CONST_28  CAX  CAK  CAW  CAC   180.00   0.0  0
 PJA  CONST_29  H15  CAK  CAX  CBB   180.00   0.0  0
 PJA  CONST_30  H5   CAL  CBA  CBE   180.00   0.0  0
 PJA  Var_01    CBD  CBE  OAS  CBF    69.28  30.0  1
 PJA  Var_02    OAR  CBC  CBG  CBF    41.18  30.0  1
 PJA  Var_03    CBG  CBF  OAS  CBE   -63.91  30.0  1
 PJA  Var_04    CBG  CBC  OAR  CBD    14.10  30.0  1
 PJA  Var_05    CBF  CBB  CAN  O    -179.73  30.0  2
 PJA  Var_06    OAH  CAU  CBA  CBE   -41.26  30.0  2
 PJA  Var_07    CAY  CAZ  OAQ  CAA  -179.75  30.0  2
 PJA  Var_08    H9   CAD  CAY  CAZ    52.26  30.0  2
 PJA  Var_09    H12  CAC  CAW  CBG    43.37  30.0  2
 PJA  Var_10    H6   CAA  OAQ  CAZ   179.65  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
 PJA  plan-1  CBA  0.020
 PJA  plan-1  CAU  0.020
 PJA  plan-1  OAH  0.020
 PJA  plan-1  OAE  0.020
 PJA  plan-2  OAS  0.020
 PJA  plan-2  CBE  0.020
 PJA  plan-2  CBA  0.020
 PJA  plan-2  CAU  0.020
 PJA  plan-2  CAL  0.020
 PJA  plan-2  CAZ  0.020
 PJA  plan-2  OAQ  0.020
 PJA  plan-2  CAY  0.020
 PJA  plan-2  CAD  0.020
 PJA  plan-2  CBD  0.020
 PJA  plan-2  OAR  0.020
 PJA  plan-2  H5   0.020
 PJA  plan-3  CAN  0.020
 PJA  plan-3  CBB  0.020
 PJA  plan-3  CBF  0.020
 PJA  plan-3  OAS  0.020
 PJA  plan-3  CBC  0.020
 PJA  plan-3  CBG  0.020
 PJA  plan-3  CAW  0.020
 PJA  plan-3  CAC  0.020
 PJA  plan-3  CAK  0.020
 PJA  plan-3  CAX  0.020
 PJA  plan-3  OAJ  0.020
 PJA  plan-3  H15  0.020
 PJA  plan-4  OAR  0.020
 PJA  plan-4  CBC  0.020
 PJA  plan-4  OAG  0.020
 PJA  plan-4  CBG  0.020
 PJA  plan-5  O    0.020
 PJA  plan-5  CAN  0.020
 PJA  plan-5  CBB  0.020
 PJA  plan-5  H2   0.020

