# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:00:15 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 8-methoxy-6-nitro-naphtho[1,2-e][1,3]benzodioxole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc2c1cc(c3c(cc4OCOc4c23)C(O)=O)[N+]([O-])=O
#
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
 GOQ  GOQ  '8-methoxy-6-nitro-naphtho[1,2-e][1,3]benzodioxole-5-carboxylic acid'  ligand  36  25  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GOQ
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
 GOQ  N    N  N      1   0.332  -0.6164  -2.6995   0.7072
 GOQ  C    C  CH3    0  -0.438   5.4358  -1.6590  -0.1552
 GOQ  C1   C  CR6    0   0.392   3.4891  -0.3077  -0.0369
 GOQ  C10  C  CR66   0  -0.085   2.0737  -0.2614   0.0559
 GOQ  C11  C  CR6    0  -0.090  -2.1973  -0.2467  -0.0178
 GOQ  C12  C  CR16   0  -0.361  -2.9168   0.9432  -0.0048
 GOQ  C13  C  CR56   0   0.343  -2.2034   2.1124   0.0960
 GOQ  C14  C  CR56   0   0.243  -0.8283   2.1328   0.1310
 GOQ  C15  C  CH2    0   0.073  -1.5748   4.2227   0.3078
 GOQ  C16  C  C      0   0.471  -2.9448  -1.4698  -0.4073
 GOQ  C2   C  CR16   0  -0.401   4.2150   0.8653  -0.0681
 GOQ  C3   C  CR16   0  -0.214   3.5373   2.0827  -0.0083
 GOQ  C4   C  CR16   0  -0.387   2.1653   2.1547   0.0721
 GOQ  C5   C  CR66   0   0.191   1.3983   0.9774   0.0953
 GOQ  C6   C  CR66   0  -0.016  -0.0547   0.9710   0.1321
 GOQ  C7   C  CR66   0   0.119  -0.7918  -0.2535   0.1212
 GOQ  C8   C  CR6    0   0.147  -0.0114  -1.4529   0.2665
 GOQ  C9   C  CR16   0  -0.305   1.3373  -1.4674   0.1921
 GOQ  O1   O  O      0  -0.383  -1.4966  -2.6266   1.5354
 GOQ  O2   O  O     -1  -0.364  -0.1744  -3.7369   0.2792
 GOQ  O3   O  O      0  -0.483  -0.4136   3.4152   0.1338
 GOQ  O4   O  O      0  -0.479  -2.6871   3.3724   0.0816
 GOQ  O5   O  O      0  -0.435  -2.4997  -2.3113  -1.1507
 GOQ  O6   O  OH1    0  -0.582  -4.1733  -1.4973   0.0806
 GOQ  H1   H  HCH3   0   0.236   5.8395  -1.1904  -1.0553
 GOQ  H2   H  HCH3   0   0.236   5.9239  -1.2287   0.7224
 GOQ  H3   H  HCH3   0   0.266   5.6434  -2.7248  -0.1880
 GOQ  H4   H  HCR6   0   0.301  -3.9916   0.9608  -0.1163
 GOQ  H5   H  HCH2   0   0.246  -1.5993   4.6142   1.3293
 GOQ  H6   H  HCH2   0   0.256  -1.5686   5.0334  -0.4190
 GOQ  H7   H  HCR6   0   0.292   5.2933   0.8639  -0.1370
 GOQ  H8   H  HCR6   0   0.273   4.1129   2.9985  -0.0309
 GOQ  H9   H  HCR6   0   0.273   1.7071   3.1275   0.1101
 GOQ  H10  H  HCR6   0   0.299   1.8715  -2.3979   0.3187
 GOQ  H11  H  HOH1   0   0.492  -4.6568  -2.2556  -0.2812
 GOQ  O    O  O2     0  -0.461   4.0261  -1.5311  -0.0870

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
 GOQ  O2   N    single    1.206  0.020  1.206
 GOQ  O5   C16  double    1.208  0.020  1.208
 GOQ  O6   C16  single    1.322  0.020  1.322
 GOQ  N    O1   double    1.211  0.020  1.211
 GOQ  N    C8   single    1.454  0.020  1.454
 GOQ  C16  C11  single    1.485  0.020  1.485
 GOQ  C8   C9   aromatic  1.351  0.020  1.351
 GOQ  C8   C7   aromatic  1.438  0.020  1.438
 GOQ  C11  C7   aromatic  1.412  0.020  1.412
 GOQ  C11  C12  aromatic  1.391  0.020  1.391
 GOQ  C    O    single    1.417  0.020  1.417
 GOQ  C9   C10  aromatic  1.420  0.020  1.420
 GOQ  C7   C6   aromatic  1.429  0.020  1.429
 GOQ  C12  C13  aromatic  1.373  0.020  1.373
 GOQ  O    C1   single    1.337  0.020  1.337
 GOQ  C10  C1   aromatic  1.419  0.020  1.419
 GOQ  C10  C5   aromatic  1.412  0.020  1.412
 GOQ  C6   C5   aromatic  1.453  0.020  1.453
 GOQ  C6   C14  aromatic  1.396  0.020  1.396
 GOQ  C13  C14  aromatic  1.376  0.020  1.376
 GOQ  C13  O4   single    1.350  0.020  1.350
 GOQ  C1   C2   aromatic  1.380  0.020  1.380
 GOQ  C5   C4   aromatic  1.405  0.020  1.405
 GOQ  C14  O3   single    1.348  0.020  1.348
 GOQ  O4   C15  single    1.418  0.020  1.418
 GOQ  C2   C3   aromatic  1.395  0.020  1.395
 GOQ  C4   C3   aromatic  1.376  0.020  1.376
 GOQ  O3   C15  single    1.425  0.020  1.425
 GOQ  C    H1   single    0.970  0.020  1.090
 GOQ  C    H2   single    0.970  0.020  1.090
 GOQ  C    H3   single    0.970  0.020  1.090
 GOQ  C12  H4   single    0.930  0.020  1.080
 GOQ  C15  H5   single    0.970  0.020  1.090
 GOQ  C15  H6   single    0.970  0.020  1.090
 GOQ  C2   H7   single    0.930  0.020  1.080
 GOQ  C3   H8   single    0.930  0.020  1.080
 GOQ  C4   H9   single    0.930  0.020  1.080
 GOQ  C9   H10  single    0.930  0.020  1.080
 GOQ  O6   H11  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
 GOQ  O2   N    O1   124.12  3.000
 GOQ  O1   N    C8   117.26  3.000
 GOQ  O2   N    C8   118.51  3.000
 GOQ  H3   C    H2   108.98  3.000
 GOQ  H3   C    H1   108.99  3.000
 GOQ  H2   C    H1   109.14  3.000
 GOQ  H3   C    O    106.27  3.000
 GOQ  H2   C    O    111.73  3.000
 GOQ  H1   C    O    111.63  3.000
 GOQ  C2   C1   C10  119.89  3.000
 GOQ  C2   C1   O    124.45  3.000
 GOQ  C10  C1   O    115.65  3.000
 GOQ  C9   C10  C5   119.65  3.000
 GOQ  C5   C10  C1   120.51  3.000
 GOQ  C9   C10  C1   119.73  3.000
 GOQ  C7   C11  C16  121.51  3.000
 GOQ  C7   C11  C12  121.21  3.000
 GOQ  C16  C11  C12  116.53  3.000
 GOQ  H4   C12  C13  120.68  3.000
 GOQ  H4   C12  C11  121.84  3.000
 GOQ  C13  C12  C11  117.41  3.000
 GOQ  O4   C13  C14  110.16  3.000
 GOQ  O4   C13  C12  127.43  3.000
 GOQ  C14  C13  C12  122.26  3.000
 GOQ  O3   C14  C6   128.43  3.000
 GOQ  O3   C14  C13  108.77  3.000
 GOQ  C6   C14  C13  122.79  3.000
 GOQ  H6   C15  H5   110.91  3.000
 GOQ  H6   C15  O4   110.15  3.000
 GOQ  H5   C15  O4   110.23  3.000
 GOQ  H6   C15  O3   109.62  3.000
 GOQ  H5   C15  O3   109.57  3.000
 GOQ  O4   C15  O3   106.25  3.000
 GOQ  O6   C16  O5   123.72  3.000
 GOQ  O6   C16  C11  112.83  3.000
 GOQ  O5   C16  C11  123.34  3.000
 GOQ  H7   C2   C3   119.27  3.000
 GOQ  H7   C2   C1   121.69  3.000
 GOQ  C3   C2   C1   119.05  3.000
 GOQ  H8   C3   C4   119.16  3.000
 GOQ  H8   C3   C2   118.65  3.000
 GOQ  C4   C3   C2   122.19  3.000
 GOQ  H9   C4   C5   121.63  3.000
 GOQ  H9   C4   C3   118.29  3.000
 GOQ  C5   C4   C3   120.08  3.000
 GOQ  C6   C5   C4   123.35  3.000
 GOQ  C4   C5   C10  118.27  3.000
 GOQ  C6   C5   C10  118.37  3.000
 GOQ  C7   C6   C5   121.28  3.000
 GOQ  C5   C6   C14  123.39  3.000
 GOQ  C7   C6   C14  115.29  3.000
 GOQ  C8   C7   C6   115.71  3.000
 GOQ  C6   C7   C11  120.66  3.000
 GOQ  C8   C7   C11  123.64  3.000
 GOQ  C9   C8   C7   123.03  3.000
 GOQ  C7   C8   N    121.32  3.000
 GOQ  C9   C8   N    115.02  3.000
 GOQ  H10  C9   C8   119.77  3.000
 GOQ  H10  C9   C10  119.11  3.000
 GOQ  C8   C9   C10  120.94  3.000
 GOQ  C15  O3   C14  106.78  3.000
 GOQ  C15  O4   C13  106.08  3.000
 GOQ  H11  O6   C16  110.00  3.000
 GOQ  C1   O    C    118.95  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
 GOQ  CONST_01  C8   C9   C10  C1    180.00   0.0  0
 GOQ  CONST_02  C6   C5   C10  C1    180.00   0.0  0
 GOQ  CONST_03  C4   C5   C10  C1      0.00   0.0  0
 GOQ  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 GOQ  CONST_05  C7   C8   C9   C10     0.00   0.0  0
 GOQ  CONST_06  C3   C2   C1   C10     0.00   0.0  0
 GOQ  CONST_07  C7   C6   C5   C10     0.00   0.0  0
 GOQ  CONST_08  C14  C6   C5   C10   180.00   0.0  0
 GOQ  CONST_09  C3   C4   C5   C10     0.00   0.0  0
 GOQ  CONST_10  C9   C8   C7   C11   180.00   0.0  0
 GOQ  CONST_11  C5   C6   C7   C11   180.00   0.0  0
 GOQ  CONST_12  C14  C6   C7   C11     0.00   0.0  0
 GOQ  CONST_13  C14  C13  C12  C11     0.00   0.0  0
 GOQ  CONST_14  C8   C7   C11  C12   180.00   0.0  0
 GOQ  CONST_15  C6   C7   C11  C12     0.00   0.0  0
 GOQ  CONST_16  C6   C14  C13  C12     0.00   0.0  0
 GOQ  CONST_17  C7   C11  C12  C13     0.00   0.0  0
 GOQ  CONST_18  C7   C6   C14  C13     0.00   0.0  0
 GOQ  CONST_19  C5   C6   C14  C13   180.00   0.0  0
 GOQ  CONST_20  C8   C7   C6   C14   180.00   0.0  0
 GOQ  CONST_21  C4   C5   C6   C14     0.00   0.0  0
 GOQ  CONST_22  C9   C10  C1   C2    180.00   0.0  0
 GOQ  CONST_23  C5   C10  C1   C2      0.00   0.0  0
 GOQ  CONST_24  C5   C4   C3   C2      0.00   0.0  0
 GOQ  CONST_25  C6   C5   C4   C3    180.00   0.0  0
 GOQ  CONST_26  C9   C10  C5   C4    180.00   0.0  0
 GOQ  CONST_27  C7   C6   C5   C4    180.00   0.0  0
 GOQ  CONST_28  C8   C9   C10  C5      0.00   0.0  0
 GOQ  CONST_29  C8   C7   C6   C5      0.00   0.0  0
 GOQ  CONST_30  C9   C8   C7   C6      0.00   0.0  0
 GOQ  CONST_31  C9   C10  C5   C6      0.00   0.0  0
 GOQ  CONST_32  C10  C9   C8   N     180.00   0.0  0
 GOQ  CONST_35  C9   C10  C1   O       0.00   0.0  0
 GOQ  CONST_36  C5   C10  C1   O     180.00   0.0  0
 GOQ  CONST_37  C3   C2   C1   O     180.00   0.0  0
 GOQ  CONST_38  C16  C11  C12  C13   180.00   0.0  0
 GOQ  CONST_41  H10  C9   C10  C1      0.00   0.0  0
 GOQ  CONST_42  H8   C3   C2   C1    180.00   0.0  0
 GOQ  CONST_43  H7   C2   C1   C10   180.00   0.0  0
 GOQ  CONST_44  H9   C4   C5   C10   180.00   0.0  0
 GOQ  CONST_45  H4   C12  C13  C14   180.00   0.0  0
 GOQ  CONST_50  H11  O6   C16  C11   180.00   0.0  0
 GOQ  Var_01    O3   C15  O4   C13    13.45  30.0  1
 GOQ  Var_02    O4   C15  O3   C14   -13.73  30.0  1
 GOQ  Var_03    C6   C14  O3   C15  -172.56  30.0  1
 GOQ  Var_04    C10  C1   O    C    -178.83  30.0  2
 GOQ  Var_05    O5   C16  C11  C12   137.05  30.0  2
 GOQ  Var_06    H1   C    O    C1    -61.22  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
 GOQ  plan-1  N    0.020
 GOQ  plan-1  C1   0.020
 GOQ  plan-1  C10  0.020
 GOQ  plan-1  C11  0.020
 GOQ  plan-1  C12  0.020
 GOQ  plan-1  C13  0.020
 GOQ  plan-1  C14  0.020
 GOQ  plan-1  C16  0.020
 GOQ  plan-1  C2   0.020
 GOQ  plan-1  C3   0.020
 GOQ  plan-1  C4   0.020
 GOQ  plan-1  C5   0.020
 GOQ  plan-1  C6   0.020
 GOQ  plan-1  C7   0.020
 GOQ  plan-1  C8   0.020
 GOQ  plan-1  C9   0.020
 GOQ  plan-1  O3   0.020
 GOQ  plan-1  O4   0.020
 GOQ  plan-1  H4   0.020
 GOQ  plan-1  H7   0.020
 GOQ  plan-1  H8   0.020
 GOQ  plan-1  H9   0.020
 GOQ  plan-1  H10  0.020
 GOQ  plan-1  O    0.020
 GOQ  plan-2  N    0.020
 GOQ  plan-2  C8   0.020
 GOQ  plan-2  O1   0.020
 GOQ  plan-2  O2   0.020
 GOQ  plan-3  C11  0.020
 GOQ  plan-3  C16  0.020
 GOQ  plan-3  O5   0.020
 GOQ  plan-3  O6   0.020
 GOQ  plan-3  H11  0.020

