# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 15:43:13 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 12-[(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]dodecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCCCCCCCNc1ccc(c2nonc12)[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
 C7K  C7K  '12-[(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]dodecanoic acid'  ligand  52  27  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C7K
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
 C7K  C1   C  CR56   0   0.116  -5.6219  -1.0180  -0.0456
 C7K  C2   C  CR56   0   0.182  -6.9909  -0.6281  -0.0651
 C7K  C3   C  CR6    0   0.442  -4.5283  -0.0800  -0.0043
 C7K  N6   N  N      0  -0.130  -7.7083  -1.7211  -0.1001
 C7K  C7   C  CR16   0  -0.408  -4.9079   1.2618   0.0182
 C7K  C10  C  CR16   0  -0.275  -6.2503   1.6440  -0.0018
 C7K  C12  C  CH2    0  -0.263  -2.1125   0.3342   0.0490
 C7K  C15  C  CH2    0  -0.474  -0.8402  -0.4945   0.0202
 C7K  C16  C  CH2    0  -0.419   0.4039   0.3836   0.0508
 C7K  C19  C  CH2    0  -0.412   4.2376  -0.3576   0.0278
 C7K  C20  C  CH2    0  -0.411   5.4875   0.5140   0.0376
 C7K  C21  C  CH2    0  -0.410   6.7825  -0.2885   0.0193
 C7K  C22  C  CH2    0  -0.409   8.0325   0.5832   0.0123
 C7K  C24  C  CH2    0  -0.581  10.5666   0.6598  -0.0314
 C7K  N4   N  N      0  -0.111  -5.5625  -2.3161  -0.0699
 C7K  C5   C  CR6    0   0.197  -7.3088   0.7579  -0.0430
 C7K  N8   N  NH1    0  -0.655  -3.2817  -0.5226   0.0086
 C7K  O9   O  O      0  -0.180  -6.8179  -2.7279  -0.1025
 C7K  N11  N  N      1   0.335  -8.6477   1.2079  -0.0646
 C7K  O13  O  O     -1  -0.417  -8.8712   2.4035  -0.0449
 C7K  O14  O  O      0  -0.410  -9.5224   0.3642  -0.1022
 C7K  C17  C  CH2    0  -0.414   1.6946  -0.4250   0.0262
 C7K  C18  C  CH2    0  -0.413   2.9440   0.4468   0.0496
 C7K  C23  C  CH2    0  -0.402   9.3275  -0.2205  -0.0017
 C7K  C25  C  C      0   0.410  11.9200  -0.0728  -0.0501
 C7K  O26  O  O      0  -0.610  11.9153  -1.3122   0.0878
 C7K  O27  O  OC    -1  -0.635  12.9306   0.6482  -0.1965
 C7K  H1   H  HCR6   0   0.302  -4.1591   2.0388   0.0503
 C7K  H2   H  HCR6   0   0.312  -6.4593   2.7050   0.0165
 C7K  H3   H  HCH2   0   0.253  -2.1403   0.9481   0.9547
 C7K  H4   H  HCH2   0   0.252  -2.1339   1.0173  -0.8055
 C7K  H5   H  HCH2   0   0.239  -0.8298  -1.1762   0.8762
 C7K  H6   H  HCH2   0   0.239  -0.8303  -1.1147  -0.8814
 C7K  H7   H  HCH2   0   0.219   0.3872   1.0684  -0.8037
 C7K  H8   H  HCH2   0   0.219   0.3853   1.0122   0.9476
 C7K  H9   H  HCH2   0   0.207   4.2509  -1.0000  -0.8601
 C7K  H10  H  HCH2   0   0.207   4.2595  -1.0334   0.8902
 C7K  H11  H  HCH2   0   0.205   5.4656   1.1871  -0.8271
 C7K  H12  H  HCH2   0   0.204   6.8092  -0.9547   0.8892
 C7K  H13  H  HCH2   0   0.201   8.0037   1.2468  -0.8599
 C7K  H14  H  HCH2   0   0.202   8.0199   1.2409   0.8895
 C7K  H15  H  HCH2   0   0.213  10.5237   1.3266  -0.9004
 C7K  H16  H  HCH2   0   0.217  10.5583   1.3307   0.8369
 C7K  H17  H  HNH1   0   0.421  -3.1309  -1.5207  -0.0028
 C7K  H18  H  HCH2   0   0.212   1.7117  -1.1082   0.8824
 C7K  H19  H  HCH2   0   0.211   1.7100  -1.0577  -0.8682
 C7K  H20  H  HCH2   0   0.208   2.9265   1.0824   0.9422
 C7K  H21  H  HCH2   0   0.208   2.9258   1.1288  -0.8079
 C7K  H22  H  HCH2   0   0.200   9.3564  -0.8725   0.8762
 C7K  H23  H  HCH2   0   0.199   9.3264  -0.8874  -0.8698
 C7K  H25  H  HCH2   0   0.206   5.4729   1.1596   0.9231
 C7K  H26  H  HCH2   0   0.204   6.7920  -0.9414  -0.8610

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
 C7K  C22  C21  single    1.524  0.020  1.524
 C7K  C22  C23  single    1.524  0.020  1.524
 C7K  C21  C20  single    1.524  0.020  1.524
 C7K  C23  C24  single    1.520  0.020  1.520
 C7K  C20  C19  single    1.524  0.020  1.524
 C7K  C24  C25  single    1.539  0.020  1.539
 C7K  C19  C18  single    1.524  0.020  1.524
 C7K  C25  O26  deloc     1.247  0.020  1.247
 C7K  C25  O27  deloc     1.250  0.020  1.250
 C7K  C18  C17  single    1.524  0.020  1.524
 C7K  C17  C16  single    1.523  0.020  1.523
 C7K  C16  C15  single    1.523  0.020  1.523
 C7K  C15  C12  single    1.519  0.020  1.519
 C7K  C12  N8   single    1.450  0.020  1.450
 C7K  N8   C3   single    1.323  0.020  1.323
 C7K  C3   C1   aromatic  1.441  0.020  1.441
 C7K  C3   C7   aromatic  1.395  0.020  1.395
 C7K  N4   C1   aromatic  1.300  0.020  1.300
 C7K  N4   O9   aromatic  1.322  0.020  1.322
 C7K  C1   C2   aromatic  1.424  0.020  1.424
 C7K  C7   C10  aromatic  1.396  0.020  1.396
 C7K  O9   N6   aromatic  1.344  0.020  1.344
 C7K  C2   N6   aromatic  1.308  0.020  1.308
 C7K  C2   C5   aromatic  1.422  0.020  1.422
 C7K  C10  C5   aromatic  1.381  0.020  1.381
 C7K  C5   N11  single    1.413  0.020  1.413
 C7K  N11  O13  single    1.217  0.020  1.217
 C7K  N11  O14  double    1.216  0.020  1.216
 C7K  C7   H1   single    0.930  0.020  1.080
 C7K  C10  H2   single    0.930  0.020  1.080
 C7K  C12  H3   single    0.970  0.020  1.090
 C7K  C12  H4   single    0.970  0.020  1.090
 C7K  C15  H5   single    0.970  0.020  1.090
 C7K  C15  H6   single    0.970  0.020  1.090
 C7K  C16  H7   single    0.970  0.020  1.090
 C7K  C16  H8   single    0.970  0.020  1.090
 C7K  C19  H9   single    0.970  0.020  1.090
 C7K  C19  H10  single    0.970  0.020  1.090
 C7K  C20  H11  single    0.970  0.020  1.090
 C7K  C21  H12  single    0.970  0.020  1.090
 C7K  C22  H13  single    0.970  0.020  1.090
 C7K  C22  H14  single    0.970  0.020  1.090
 C7K  C24  H15  single    0.970  0.020  1.090
 C7K  C24  H16  single    0.970  0.020  1.090
 C7K  N8   H17  single    0.860  0.020  1.020
 C7K  C17  H18  single    0.970  0.020  1.090
 C7K  C17  H19  single    0.970  0.020  1.090
 C7K  C18  H20  single    0.970  0.020  1.090
 C7K  C18  H21  single    0.970  0.020  1.090
 C7K  C23  H22  single    0.970  0.020  1.090
 C7K  C23  H23  single    0.970  0.020  1.090
 C7K  C20  H25  single    0.970  0.020  1.090
 C7K  C21  H26  single    0.970  0.020  1.090

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
 C7K  N4   C1   C3   128.01  3.000
 C7K  N4   C1   C2   108.50  3.000
 C7K  C3   C1   C2   123.49  3.000
 C7K  C5   C2   N6   133.81  3.000
 C7K  C5   C2   C1   118.79  3.000
 C7K  N6   C2   C1   107.39  3.000
 C7K  N8   C3   C7   125.32  3.000
 C7K  C7   C3   C1   114.84  3.000
 C7K  N8   C3   C1   119.84  3.000
 C7K  O9   N6   C2   105.23  3.000
 C7K  H1   C7   C10  118.06  3.000
 C7K  H1   C7   C3   120.28  3.000
 C7K  C10  C7   C3   121.66  3.000
 C7K  H2   C10  C5   118.81  3.000
 C7K  H2   C10  C7   117.01  3.000
 C7K  C5   C10  C7   124.18  3.000
 C7K  H4   C12  H3   107.19  3.000
 C7K  H4   C12  N8   109.35  3.000
 C7K  H3   C12  N8   109.51  3.000
 C7K  H4   C12  C15  110.01  3.000
 C7K  H3   C12  C15  110.06  3.000
 C7K  N8   C12  C15  110.64  3.000
 C7K  H6   C15  H5   106.94  3.000
 C7K  H6   C15  C16  109.62  3.000
 C7K  H5   C15  C16  109.62  3.000
 C7K  H6   C15  C12  109.42  3.000
 C7K  H5   C15  C12  109.45  3.000
 C7K  C16  C15  C12  111.67  3.000
 C7K  H8   C16  H7   106.25  3.000
 C7K  H8   C16  C17  109.40  3.000
 C7K  H7   C16  C17  109.40  3.000
 C7K  H8   C16  C15  109.48  3.000
 C7K  H7   C16  C15  109.42  3.000
 C7K  C17  C16  C15  112.69  3.000
 C7K  H10  C19  H9   106.02  3.000
 C7K  H10  C19  C18  109.35  3.000
 C7K  H9   C19  C18  109.36  3.000
 C7K  H10  C19  C20  109.35  3.000
 C7K  H9   C19  C20  109.30  3.000
 C7K  C18  C19  C20  113.22  3.000
 C7K  H25  C20  H11  105.98  3.000
 C7K  H25  C20  C21  109.35  3.000
 C7K  H11  C20  C21  109.33  3.000
 C7K  H25  C20  C19  109.34  3.000
 C7K  H11  C20  C19  109.26  3.000
 C7K  C21  C20  C19  113.32  3.000
 C7K  H26  C21  H12  105.97  3.000
 C7K  H26  C21  C22  109.27  3.000
 C7K  H12  C21  C22  109.35  3.000
 C7K  H26  C21  C20  109.32  3.000
 C7K  H12  C21  C20  109.35  3.000
 C7K  C22  C21  C20  113.33  3.000
 C7K  H14  C22  H13  105.85  3.000
 C7K  H14  C22  C23  109.48  3.000
 C7K  H13  C22  C23  109.52  3.000
 C7K  H14  C22  C21  109.27  3.000
 C7K  H13  C22  C21  109.17  3.000
 C7K  C23  C22  C21  113.29  3.000
 C7K  H16  C24  H15  104.78  3.000
 C7K  H16  C24  C25  107.90  3.000
 C7K  H15  C24  C25  108.32  3.000
 C7K  H16  C24  C23  109.42  3.000
 C7K  H15  C24  C23  109.62  3.000
 C7K  C25  C24  C23  116.19  3.000
 C7K  O9   N4   C1   105.57  3.000
 C7K  N11  C5   C10  121.50  3.000
 C7K  N11  C5   C2   121.47  3.000
 C7K  C10  C5   C2   117.03  3.000
 C7K  H17  N8   C12  117.65  3.000
 C7K  H17  N8   C3   118.12  3.000
 C7K  C12  N8   C3   124.22  3.000
 C7K  N4   O9   N6   113.31  3.000
 C7K  O14  N11  O13  123.39  3.000
 C7K  O14  N11  C5   117.47  3.000
 C7K  O13  N11  C5   119.14  3.000
 C7K  H19  C17  H18  106.12  3.000
 C7K  H19  C17  C18  109.36  3.000
 C7K  H18  C17  C18  109.39  3.000
 C7K  H19  C17  C16  109.37  3.000
 C7K  H18  C17  C16  109.37  3.000
 C7K  C18  C17  C16  113.00  3.000
 C7K  H21  C18  H20  106.03  3.000
 C7K  H21  C18  C17  109.29  3.000
 C7K  H20  C18  C17  109.35  3.000
 C7K  H21  C18  C19  109.36  3.000
 C7K  H20  C18  C19  109.36  3.000
 C7K  C17  C18  C19  113.20  3.000
 C7K  H23  C23  H22  105.87  3.000
 C7K  H23  C23  C24  109.76  3.000
 C7K  H22  C23  C24  109.83  3.000
 C7K  H23  C23  C22  109.13  3.000
 C7K  H22  C23  C22  109.22  3.000
 C7K  C24  C23  C22  112.79  3.000
 C7K  O27  C25  O26  126.10  3.000
 C7K  O27  C25  C24  115.96  3.000
 C7K  O26  C25  C24  117.94  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
 C7K  CONST_01  C10  C7   C3   C1      0.00   0.0  0
 C7K  CONST_02  N6   O9   N4   C1      0.00   0.0  0
 C7K  CONST_03  O9   N6   C2   C1      0.00   0.0  0
 C7K  CONST_04  C10  C5   C2   C1      0.00   0.0  0
 C7K  CONST_05  C7   C3   C1   C2      0.00   0.0  0
 C7K  CONST_06  O9   N4   C1   C2      0.00   0.0  0
 C7K  CONST_07  N4   O9   N6   C2      0.00   0.0  0
 C7K  CONST_08  C7   C10  C5   C2      0.00   0.0  0
 C7K  CONST_09  O9   N4   C1   C3    180.00   0.0  0
 C7K  CONST_10  N6   C2   C1   C3    180.00   0.0  0
 C7K  CONST_11  C5   C2   C1   C3      0.00   0.0  0
 C7K  CONST_12  C5   C10  C7   C3      0.00   0.0  0
 C7K  CONST_13  N4   C1   C2   N6      0.00   0.0  0
 C7K  CONST_14  C10  C5   C2   N6    180.00   0.0  0
 C7K  CONST_15  N4   C1   C3   C7    180.00   0.0  0
 C7K  CONST_16  C5   C2   C1   N4    180.00   0.0  0
 C7K  CONST_17  O9   N6   C2   C5    180.00   0.0  0
 C7K  CONST_18  N11  C5   C2   C1    180.00   0.0  0
 C7K  CONST_19  N8   C3   C1   C2    180.00   0.0  0
 C7K  CONST_20  N11  C5   C2   N6      0.00   0.0  0
 C7K  CONST_21  N11  C5   C10  C7    180.00   0.0  0
 C7K  CONST_22  N8   C3   C7   C10   180.00   0.0  0
 C7K  CONST_23  N8   C3   C1   N4      0.00   0.0  0
 C7K  CONST_24  H1   C7   C3   C1    180.00   0.0  0
 C7K  CONST_25  H2   C10  C5   C2    180.00   0.0  0
 C7K  CONST_26  C12  N8   C3   C1    180.00   0.0  0
 C7K  CONST_27  O13  N11  C5   C2    180.00   0.0  0
 C7K  CONST_28  O14  N11  C5   C2      0.00   0.0  0
 C7K  CONST_29  C12  N8   C3   C7      0.00   0.0  0
 C7K  CONST_30  O13  N11  C5   C10     0.00   0.0  0
 C7K  CONST_31  O14  N11  C5   C10   180.00   0.0  0
 C7K  CONST_32  H17  N8   C3   C1      0.00   0.0  0
 C7K  Var_01    C15  C12  N8   C3   -178.65  30.0  1
 C7K  Var_02    C17  C16  C15  C12   179.86  30.0  1
 C7K  Var_03    C18  C17  C16  C15   179.72  30.0  1
 C7K  Var_04    C19  C18  C17  C16   179.89  30.0  1
 C7K  Var_05    N8   C12  C15  C16   179.55  30.0  3
 C7K  Var_06    C22  C21  C20  C19   179.32  30.0  1
 C7K  Var_07    C23  C22  C21  C20   179.83  30.0  1
 C7K  Var_08    C17  C18  C19  C20   179.44  30.0  3
 C7K  Var_09    C24  C23  C22  C21   179.07  30.0  3
 C7K  Var_10    C18  C19  C20  C21   179.86  30.0  3
 C7K  Var_11    C25  C24  C23  C22  -179.88  30.0  3
 C7K  Var_12    O26  C25  C24  C23    -6.66  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
 C7K  plan-1  C1   0.020
 C7K  plan-1  C2   0.020
 C7K  plan-1  C3   0.020
 C7K  plan-1  N6   0.020
 C7K  plan-1  C7   0.020
 C7K  plan-1  C10  0.020
 C7K  plan-1  N4   0.020
 C7K  plan-1  C5   0.020
 C7K  plan-1  N8   0.020
 C7K  plan-1  O9   0.020
 C7K  plan-1  N11  0.020
 C7K  plan-1  H1   0.020
 C7K  plan-1  H2   0.020
 C7K  plan-2  C3   0.020
 C7K  plan-2  C12  0.020
 C7K  plan-2  N8   0.020
 C7K  plan-2  H17  0.020
 C7K  plan-3  C5   0.020
 C7K  plan-3  N11  0.020
 C7K  plan-3  O13  0.020
 C7K  plan-3  O14  0.020
 C7K  plan-4  C24  0.020
 C7K  plan-4  C25  0.020
 C7K  plan-4  O26  0.020
 C7K  plan-4  O27  0.020

