# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 23:52:21 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  40  26  .  2021-08-19  2023-02-16
;
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  -0.437  -3.0580   3.2666  -0.3579
 PJA  CAN  C  C1    0   0.163  -2.2752   2.4012  -0.7287
 PJA  CBB  C  CR6   0  -0.278  -2.3610   1.0235  -0.2741
 PJA  CBF  C  CR6   0   0.411  -1.4423   0.0474  -0.6769
 PJA  OAS  O  O2    0  -0.510  -0.3714   0.4550  -1.4215
 PJA  CBE  C  CR6   0   0.283   0.8449   0.1927  -0.8342
 PJA  CBA  C  CR6   0  -0.137   1.6630   1.1984  -0.3445
 PJA  CAU  C  C     0   0.516   1.3572   2.6353  -0.5702
 PJA  OAH  O  O     0  -0.423   0.8260   3.0654  -1.5632
 PJA  OAE  O  OH1   0  -0.582   1.7705   3.3947   0.4308
 PJA  CAL  C  CR16  0  -0.420   2.8582   0.8530   0.2880
 PJA  CAZ  C  CR6   0   0.390   3.2298  -0.4760   0.4239
 PJA  OAQ  O  O2    0  -0.459   4.3635  -0.8774   1.0146
 PJA  CAA  C  CH3   0  -0.444   5.2421   0.0974   1.5462
 PJA  CAY  C  CR6   0  -0.099   2.4156  -1.5059  -0.0759
 PJA  CAD  C  CH3   0  -0.708   2.8415  -2.9341   0.0648
 PJA  CBD  C  CR6   0   0.369   1.2376  -1.1331  -0.7010
 PJA  OAR  O  O2    0  -0.467   0.4934  -2.1151  -1.2962
 PJA  CBC  C  C     0   0.575  -0.8150  -2.3273  -1.0593
 PJA  OAG  O  O     0  -0.387  -1.2792  -3.3532  -1.4711
 PJA  CBG  C  CR6   0  -0.274  -1.6097  -1.2945  -0.3646
 PJA  CAW  C  CR6   0   0.121  -2.6905  -1.6759   0.4682
 PJA  CAC  C  CH3   0  -0.731  -2.9161  -3.0954   0.8938
 PJA  CAK  C  CR16  0  -0.404  -3.5594  -0.7120   0.9335
 PJA  CAX  C  CR6   0   0.415  -3.4343   0.6234   0.5514
 PJA  OAJ  O  OH1   0  -0.602  -4.3319   1.4853   0.9875
 PJA  H2   H  H     0   0.256  -1.4923   2.6502  -1.4499
 PJA  H4   H  HOH1  0   0.493   1.6186   4.3299   0.2241
 PJA  H5   H  HCR6  0   0.305   3.4996   1.6411   0.6556
 PJA  H6   H  HCH3  0   0.267   6.0748  -0.4475   1.9824
 PJA  H7   H  HCH3  0   0.235   5.6237   0.7652   0.7699
 PJA  H8   H  HCH3  0   0.235   4.7619   0.6942   2.3253
 PJA  H9   H  HCH3  0   0.258   3.0822  -3.1625   1.1029
 PJA  H10  H  HCH3  0   0.257   2.0727  -3.6286  -0.2609
 PJA  H11  H  HCH3  0   0.261   3.7392  -3.1312  -0.5236
 PJA  H12  H  HCH3  0   0.257  -1.9913  -3.5911   1.1852
 PJA  H13  H  HCH3  0   0.259  -3.5962  -3.1253   1.7424
 PJA  H14  H  HCH3  0   0.270  -3.3599  -3.6793   0.0884
 PJA  H15  H  HCR6  0   0.281  -4.3747  -0.9898   1.5892
 PJA  H16  H  HOH1  0   0.482  -4.1043   2.3782   0.6364

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    1.416  0.020  1.416
 PJA  OAQ  CAZ  single    1.340  0.020  1.340
 PJA  CAD  CAY  single    1.497  0.020  1.497
 PJA  CAZ  CAY  aromatic  1.405  0.020  1.405
 PJA  CAZ  CAL  aromatic  1.387  0.020  1.387
 PJA  CAY  CBD  aromatic  1.385  0.020  1.385
 PJA  CAL  CBA  aromatic  1.396  0.020  1.396
 PJA  CBD  OAR  single    1.368  0.020  1.368
 PJA  CBD  CBE  aromatic  1.389  0.020  1.389
 PJA  OAR  CBC  single    1.347  0.020  1.347
 PJA  CBA  CBE  aromatic  1.386  0.020  1.386
 PJA  CBA  CAU  single    1.486  0.020  1.486
 PJA  CBE  OAS  single    1.376  0.020  1.376
 PJA  OAH  CAU  double    1.206  0.020  1.206
 PJA  OAG  CBC  double    1.199  0.020  1.199
 PJA  CBC  CBG  single    1.477  0.020  1.477
 PJA  CAU  OAE  single    1.323  0.020  1.323
 PJA  OAS  CBF  single    1.367  0.020  1.367
 PJA  CBG  CBF  aromatic  1.388  0.020  1.388
 PJA  CBG  CAW  aromatic  1.417  0.020  1.417
 PJA  CBF  CBB  aromatic  1.400  0.020  1.400
 PJA  CAC  CAW  single    1.499  0.020  1.499
 PJA  CAW  CAK  aromatic  1.379  0.020  1.379
 PJA  CBB  CAN  single    1.453  0.020  1.453
 PJA  CBB  CAX  aromatic  1.412  0.020  1.412
 PJA  CAN  O    double    1.224  0.020  1.224
 PJA  CAK  CAX  aromatic  1.395  0.020  1.395
 PJA  CAX  OAJ  single    1.319  0.020  1.319
 PJA  CAN  H2   single    0.930  0.020  1.080
 PJA  OAE  H4   single    0.850  0.020  0.980
 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  117.68  3.000
 PJA  H2   CAN  O    119.78  3.000
 PJA  CBB  CAN  O    122.52  3.000
 PJA  CAX  CBB  CBF  118.01  3.000
 PJA  CAX  CBB  CAN  119.76  3.000
 PJA  CBF  CBB  CAN  122.16  3.000
 PJA  CBG  CBF  OAS  120.36  3.000
 PJA  CBG  CBF  CBB  122.03  3.000
 PJA  OAS  CBF  CBB  117.59  3.000
 PJA  CBE  OAS  CBF  113.78  3.000
 PJA  CBD  CBE  CBA  119.47  3.000
 PJA  CBA  CBE  OAS  122.30  3.000
 PJA  CBD  CBE  OAS  118.21  3.000
 PJA  CAL  CBA  CAU  118.97  3.000
 PJA  CAU  CBA  CBE  121.77  3.000
 PJA  CAL  CBA  CBE  119.08  3.000
 PJA  OAE  CAU  OAH  123.79  3.000
 PJA  OAE  CAU  CBA  112.08  3.000
 PJA  OAH  CAU  CBA  124.10  3.000
 PJA  H4   OAE  CAU  110.09  3.000
 PJA  H5   CAL  CAZ  120.44  3.000
 PJA  H5   CAL  CBA  118.81  3.000
 PJA  CAZ  CAL  CBA  120.74  3.000
 PJA  CAY  CAZ  OAQ  115.32  3.000
 PJA  CAY  CAZ  CAL  120.83  3.000
 PJA  OAQ  CAZ  CAL  123.85  3.000
 PJA  CAA  OAQ  CAZ  118.97  3.000
 PJA  H8   CAA  H7   109.04  3.000
 PJA  H8   CAA  H6   108.94  3.000
 PJA  H7   CAA  H6   108.91  3.000
 PJA  H8   CAA  OAQ  111.78  3.000
 PJA  H7   CAA  OAQ  111.76  3.000
 PJA  H6   CAA  OAQ  106.32  3.000
 PJA  CBD  CAY  CAD  122.77  3.000
 PJA  CBD  CAY  CAZ  117.15  3.000
 PJA  CAD  CAY  CAZ  120.07  3.000
 PJA  H11  CAD  H10  107.77  3.000
 PJA  H11  CAD  H9   107.10  3.000
 PJA  H10  CAD  H9   107.94  3.000
 PJA  H11  CAD  CAY  110.83  3.000
 PJA  H10  CAD  CAY  112.36  3.000
 PJA  H9   CAD  CAY  110.63  3.000
 PJA  OAR  CBD  CAY  117.76  3.000
 PJA  OAR  CBD  CBE  119.31  3.000
 PJA  CAY  CBD  CBE  122.73  3.000
 PJA  CBC  OAR  CBD  124.41  3.000
 PJA  CBG  CBC  OAG  123.49  3.000
 PJA  CBG  CBC  OAR  119.69  3.000
 PJA  OAG  CBC  OAR  116.78  3.000
 PJA  CAW  CBG  CBC  119.91  3.000
 PJA  CAW  CBG  CBF  118.98  3.000
 PJA  CBC  CBG  CBF  120.37  3.000
 PJA  CAK  CAW  CAC  118.13  3.000
 PJA  CAK  CAW  CBG  119.41  3.000
 PJA  CAC  CAW  CBG  122.46  3.000
 PJA  H14  CAC  H13  107.90  3.000
 PJA  H14  CAC  H12  107.45  3.000
 PJA  H13  CAC  H12  108.04  3.000
 PJA  H14  CAC  CAW  111.04  3.000
 PJA  H13  CAC  CAW  109.97  3.000
 PJA  H12  CAC  CAW  112.29  3.000
 PJA  H15  CAK  CAX  118.64  3.000
 PJA  H15  CAK  CAW  119.98  3.000
 PJA  CAX  CAK  CAW  121.37  3.000
 PJA  OAJ  CAX  CAK  118.31  3.000
 PJA  OAJ  CAX  CBB  121.71  3.000
 PJA  CAK  CAX  CBB  119.98  3.000
 PJA  H16  OAJ  CAX  108.49  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  CONST_31  H4   OAE  CAU  CBA   180.00   0.0  0
 PJA  Var_01    CBD  CBE  OAS  CBF    67.69  30.0  1
 PJA  Var_02    OAR  CBC  CBG  CBF    41.70  30.0  1
 PJA  Var_03    CBG  CBF  OAS  CBE   -61.43  30.0  1
 PJA  Var_04    CBG  CBC  OAR  CBD    14.52  30.0  1
 PJA  Var_05    CBF  CBB  CAN  O    -178.38  30.0  3
 PJA  Var_06    OAH  CAU  CBA  CBE   -33.44  30.0  2
 PJA  Var_07    CAY  CAZ  OAQ  CAA  -180.00  30.0  2
 PJA  Var_08    H9   CAD  CAY  CAZ    52.79  30.0  2
 PJA  Var_09    H12  CAC  CAW  CBG    42.95  30.0  2
 PJA  Var_10    H6   CAA  OAQ  CAZ   179.19  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-1  H4   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

