# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:41:42 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: {5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1cc(F)ccc1C(=O)NCc2cccc(c2)[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
 30L  30L  '{5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid'  ligand  38  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_30L
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
 30L  N1   N  NH1    0  -0.619   0.3584   0.5093   0.8815
 30L  C3   C  CH2    0  -0.348   1.2974   1.5707   1.1407
 30L  C4   C  CR6    0   0.111   2.7345   1.1152   1.0685
 30L  C5   C  CR16   0  -0.318   3.1489   0.2200   0.0921
 30L  C6   C  CR6    0   0.280   4.4810  -0.1589   0.0394
 30L  N7   N  N      1   0.329   4.9018  -1.1050  -0.9856
 30L  O8   O  O      0  -0.377   4.0671  -1.5201  -1.7547
 30L  O9   O  O     -1  -0.376   6.0656  -1.4281  -1.0161
 30L  C10  C  CR16   0  -0.281   5.4238   0.3294   0.9322
 30L  C11  C  CR16   0  -0.235   5.0024   1.2224   1.9021
 30L  C12  C  CR16   0  -0.281   3.6709   1.6078   1.9717
 30L  C19  C  C      0   0.513  -0.4563   0.4648  -0.1907
 30L  O20  O  O      0  -0.465  -0.4977   1.3261  -1.0519
 30L  C21  C  CR6    0  -0.185  -1.2938  -0.7736  -0.2617
 30L  C22  C  CR16   0  -0.229  -0.6897  -2.0195  -0.3361
 30L  C24  C  CR16   0  -0.434  -1.4330  -3.1841  -0.4722
 30L  C26  C  CR6    0   0.562  -2.8039  -3.0591  -0.5171
 30L  F27  F  F      0  -0.310  -3.5538  -4.1608  -0.6458
 30L  C28  C  CR16   0  -0.544  -3.4560  -1.8412  -0.4327
 30L  C30  C  CR6    0   0.417  -2.6918  -0.6861  -0.3081
 30L  O31  O  O2     0  -0.445  -3.2119   0.5445  -0.1975
 30L  C32  C  CH2    0  -0.301  -4.6062   0.6905  -0.1704
 30L  C33  C  C      0   0.514  -4.9040   2.1600   0.0070
 30L  O34  O  O      0  -0.417  -4.0777   3.0218   0.1230
 30L  O36  O  OH1    0  -0.591  -6.2135   2.3587   0.0156
 30L  H1   H  HNH1   0   0.414   0.2732  -0.2127   1.5798
 30L  H2   H  HCH2   0   0.282   1.1260   2.3652   0.4141
 30L  H3   H  HCH2   0   0.277   1.0999   1.9970   2.1257
 30L  H4   H  HCR6   0   0.285   2.4390  -0.1798  -0.6184
 30L  H5   H  HCR6   0   0.298   6.4583   0.0238   0.8847
 30L  H6   H  HCR6   0   0.280   5.7157   1.6125   2.6149
 30L  H7   H  HCR6   0   0.274   3.3564   2.2965   2.7464
 30L  H8   H  HCR6   0   0.270   0.3901  -2.0933  -0.3040
 30L  H9   H  HCR6   0   0.285  -0.9560  -4.1519  -0.5419
 30L  H10  H  HCR6   0   0.310  -4.5367  -1.8219  -0.4625
 30L  H11  H  HCH2   0   0.282  -5.0744   0.3410  -1.0982
 30L  H12  H  HCH2   0   0.282  -5.0598   0.1329   0.6578
 30L  H13  H  HOH1   0   0.491  -6.4096   3.3010   0.1294

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
 30L  O9   N7   single    1.208  0.020  1.208
 30L  O8   N7   double    1.208  0.020  1.208
 30L  N7   C6   single    1.457  0.020  1.457
 30L  C10  C6   aromatic  1.387  0.020  1.387
 30L  C10  C11  aromatic  1.384  0.020  1.384
 30L  C6   C5   aromatic  1.386  0.020  1.386
 30L  C11  C12  aromatic  1.388  0.020  1.388
 30L  C5   C4   aromatic  1.388  0.020  1.388
 30L  C12  C4   aromatic  1.391  0.020  1.391
 30L  C4   C3   single    1.509  0.020  1.509
 30L  C3   N1   single    1.441  0.020  1.441
 30L  O20  C19  double    1.219  0.020  1.219
 30L  C19  N1   single    1.347  0.020  1.347
 30L  C19  C21  single    1.497  0.020  1.497
 30L  C22  C21  aromatic  1.387  0.020  1.387
 30L  C22  C24  aromatic  1.388  0.020  1.388
 30L  C21  C30  aromatic  1.401  0.020  1.401
 30L  C24  C26  aromatic  1.377  0.020  1.377
 30L  O34  C33  double    1.200  0.020  1.200
 30L  C30  O31  single    1.341  0.020  1.341
 30L  C30  C28  aromatic  1.391  0.020  1.391
 30L  O31  C32  single    1.402  0.020  1.402
 30L  C26  C28  aromatic  1.384  0.020  1.384
 30L  C26  F27  single    1.339  0.020  1.339
 30L  C33  C32  single    1.510  0.020  1.510
 30L  C33  O36  single    1.324  0.020  1.324
 30L  N1   H1   single    0.860  0.020  1.020
 30L  C3   H2   single    0.970  0.020  1.090
 30L  C3   H3   single    0.970  0.020  1.090
 30L  C5   H4   single    0.930  0.020  1.080
 30L  C10  H5   single    0.930  0.020  1.080
 30L  C11  H6   single    0.930  0.020  1.080
 30L  C12  H7   single    0.930  0.020  1.080
 30L  C22  H8   single    0.930  0.020  1.080
 30L  C24  H9   single    0.930  0.020  1.080
 30L  C28  H10  single    0.930  0.020  1.080
 30L  C32  H11  single    0.970  0.020  1.090
 30L  C32  H12  single    0.970  0.020  1.090
 30L  O36  H13  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
 30L  H1   N1   C19  118.46  3.000
 30L  H1   N1   C3   117.26  3.000
 30L  C19  N1   C3   124.17  3.000
 30L  H3   C3   H2   106.76  3.000
 30L  H3   C3   C4   109.48  3.000
 30L  H2   C3   C4   109.74  3.000
 30L  H3   C3   N1   109.41  3.000
 30L  H2   C3   N1   108.33  3.000
 30L  C4   C3   N1   112.94  3.000
 30L  C12  C4   C5   118.96  3.000
 30L  C12  C4   C3   120.20  3.000
 30L  C5   C4   C3   120.84  3.000
 30L  H4   C5   C6   120.33  3.000
 30L  H4   C5   C4   120.32  3.000
 30L  C6   C5   C4   119.34  3.000
 30L  C10  C6   N7   119.02  3.000
 30L  C10  C6   C5   122.18  3.000
 30L  N7   C6   C5   118.81  3.000
 30L  O9   N7   O8   123.88  3.000
 30L  O8   N7   C6   118.12  3.000
 30L  O9   N7   C6   118.01  3.000
 30L  H5   C10  C11  120.34  3.000
 30L  H5   C10  C6   121.54  3.000
 30L  C11  C10  C6   118.11  3.000
 30L  H6   C11  C12  119.97  3.000
 30L  H6   C11  C10  119.60  3.000
 30L  C12  C11  C10  120.43  3.000
 30L  H7   C12  C11  119.41  3.000
 30L  H7   C12  C4   119.60  3.000
 30L  C11  C12  C4   120.99  3.000
 30L  C21  C19  O20  122.16  3.000
 30L  C21  C19  N1   113.79  3.000
 30L  O20  C19  N1   124.02  3.000
 30L  C30  C21  C22  119.27  3.000
 30L  C30  C21  C19  120.53  3.000
 30L  C22  C21  C19  120.15  3.000
 30L  H8   C22  C24  118.66  3.000
 30L  H8   C22  C21  119.61  3.000
 30L  C24  C22  C21  121.72  3.000
 30L  H9   C24  C26  121.22  3.000
 30L  H9   C24  C22  121.40  3.000
 30L  C26  C24  C22  117.38  3.000
 30L  C28  C26  F27  117.78  3.000
 30L  F27  C26  C24  119.07  3.000
 30L  C28  C26  C24  123.15  3.000
 30L  H10  C28  C30  122.47  3.000
 30L  H10  C28  C26  119.01  3.000
 30L  C30  C28  C26  118.52  3.000
 30L  O31  C30  C28  123.83  3.000
 30L  C28  C30  C21  119.95  3.000
 30L  O31  C30  C21  116.20  3.000
 30L  C32  O31  C30  118.88  3.000
 30L  H12  C32  H11  107.48  3.000
 30L  H12  C32  C33  108.94  3.000
 30L  H11  C32  C33  108.99  3.000
 30L  H12  C32  O31  111.90  3.000
 30L  H11  C32  O31  112.03  3.000
 30L  C33  C32  O31  107.44  3.000
 30L  O36  C33  O34  124.93  3.000
 30L  O36  C33  C32  109.99  3.000
 30L  O34  C33  C32  125.08  3.000
 30L  H13  O36  C33  110.29  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
 30L  CONST_01  C10  C6   C5   C4      0.00   0.0  0
 30L  CONST_02  C10  C11  C12  C4      0.00   0.0  0
 30L  CONST_03  C11  C10  C6   C5      0.00   0.0  0
 30L  CONST_04  C11  C12  C4   C5      0.00   0.0  0
 30L  CONST_05  C12  C11  C10  C6      0.00   0.0  0
 30L  CONST_06  C12  C4   C5   C6      0.00   0.0  0
 30L  CONST_07  C26  C24  C22  C21     0.00   0.0  0
 30L  CONST_08  C26  C28  C30  C21     0.00   0.0  0
 30L  CONST_09  C28  C30  C21  C22     0.00   0.0  0
 30L  CONST_10  C28  C26  C24  C22     0.00   0.0  0
 30L  CONST_11  C30  C21  C22  C24     0.00   0.0  0
 30L  CONST_12  C30  C28  C26  C24     0.00   0.0  0
 30L  CONST_13  C6   C5   C4   C3    180.00   0.0  0
 30L  CONST_14  C11  C12  C4   C3    180.00   0.0  0
 30L  CONST_15  N7   C6   C5   C4    180.00   0.0  0
 30L  CONST_16  C11  C10  C6   N7    180.00   0.0  0
 30L  CONST_17  C24  C22  C21  C19   180.00   0.0  0
 30L  CONST_18  C28  C30  C21  C19   180.00   0.0  0
 30L  CONST_19  O31  C30  C21  C22   180.00   0.0  0
 30L  CONST_20  F27  C26  C24  C22   180.00   0.0  0
 30L  CONST_21  O31  C30  C28  C26   180.00   0.0  0
 30L  CONST_22  C30  C28  C26  F27   180.00   0.0  0
 30L  CONST_23  H6   C11  C12  C4    180.00   0.0  0
 30L  CONST_24  H5   C10  C6   C5    180.00   0.0  0
 30L  CONST_25  H7   C12  C4   C5    180.00   0.0  0
 30L  CONST_26  H4   C5   C6   C10   180.00   0.0  0
 30L  CONST_27  H9   C24  C22  C21   180.00   0.0  0
 30L  CONST_28  H10  C28  C30  C21   180.00   0.0  0
 30L  CONST_29  H8   C22  C24  C26   180.00   0.0  0
 30L  CONST_30  O9   N7   C6   C5    180.00   0.0  0
 30L  CONST_31  O8   N7   C6   C5      0.00   0.0  0
 30L  CONST_32  C10  C6   N7   O8    180.00   0.0  0
 30L  CONST_33  C10  C6   N7   O9      0.00   0.0  0
 30L  CONST_34  C21  C19  N1   C3    180.00   0.0  0
 30L  CONST_35  H1   N1   C19  C21     0.00   0.0  0
 30L  CONST_36  O20  C19  N1   C3      0.00   0.0  0
 30L  CONST_37  H13  O36  C33  C32   180.00   0.0  0
 30L  Var_01    C5   C4   C3   N1     39.87  30.0  2
 30L  Var_02    C22  C21  C19  N1    -60.17  30.0  2
 30L  Var_03    C19  N1   C3   C4   -113.91  30.0  3
 30L  Var_04    C33  C32  O31  C30   178.07  30.0  3
 30L  Var_05    O34  C33  C32  O31    -1.10  30.0  1

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
 30L  plan-1  C3   0.020
 30L  plan-1  C4   0.020
 30L  plan-1  C5   0.020
 30L  plan-1  C6   0.020
 30L  plan-1  N7   0.020
 30L  plan-1  C10  0.020
 30L  plan-1  C11  0.020
 30L  plan-1  C12  0.020
 30L  plan-1  H4   0.020
 30L  plan-1  H5   0.020
 30L  plan-1  H6   0.020
 30L  plan-1  H7   0.020
 30L  plan-2  C19  0.020
 30L  plan-2  C21  0.020
 30L  plan-2  C22  0.020
 30L  plan-2  C24  0.020
 30L  plan-2  C26  0.020
 30L  plan-2  F27  0.020
 30L  plan-2  C28  0.020
 30L  plan-2  C30  0.020
 30L  plan-2  O31  0.020
 30L  plan-2  H8   0.020
 30L  plan-2  H9   0.020
 30L  plan-2  H10  0.020
 30L  plan-3  N1   0.020
 30L  plan-3  C3   0.020
 30L  plan-3  C19  0.020
 30L  plan-3  O20  0.020
 30L  plan-3  C21  0.020
 30L  plan-3  H1   0.020
 30L  plan-4  C6   0.020
 30L  plan-4  N7   0.020
 30L  plan-4  O8   0.020
 30L  plan-4  O9   0.020
 30L  plan-5  C32  0.020
 30L  plan-5  C33  0.020
 30L  plan-5  O34  0.020
 30L  plan-5  O36  0.020
 30L  plan-5  H13  0.020

