# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:39:48 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: {5-chloro-2-[(4-cyano-3-nitrobenzyl)carbamoyl]phenoxy}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1cc(Cl)ccc1C(=O)NCc2ccc(C#N)c(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
 3T4  3T4  '{5-chloro-2-[(4-cyano-3-nitrobenzyl)carbamoyl]phenoxy}acetic acid'  ligand  39  27  .  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_3T4
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
 3T4  C1    C   CR6    0   0.313  -4.0805  -0.3536  -0.2355
 3T4  CL1   CL  CL     0  -0.112   4.3756  -3.5460   1.9422
 3T4  N2    N   N      1   0.336  -4.6471  -1.6207   0.2048
 3T4  O3    O   O     -1  -0.359  -4.0036  -2.6233   0.0206
 3T4  O4    O   O      0  -0.368  -5.7337  -1.5936   0.7295
 3T4  C5    C   CR16   0  -0.315  -2.9191  -0.3786  -0.9794
 3T4  C6    C   CR6    0   0.126  -2.3475   0.8090  -1.4235
 3T4  C7    C   CH2    0  -0.360  -1.0891   0.7726  -2.2518
 3T4  N8    N   NH1    0  -0.629  -0.0582  -0.0338  -1.6471
 3T4  C9    C   C      0   0.529   0.5316   0.3423  -0.4973
 3T4  C10   C   CR6    0  -0.163   1.5207  -0.6374   0.0473
 3T4  C11   C   CR16   0  -0.250   1.1374  -1.9480   0.2872
 3T4  C12   C   CR16   0  -0.237   1.9996  -2.8638   0.8741
 3T4  C13   C   CR6    0  -0.025   3.2699  -2.4359   1.2088
 3T4  C15   C   CR16   0  -0.334   3.6977  -1.1369   0.9718
 3T4  C16   C   CR6    0   0.402   2.8185  -0.2310   0.3875
 3T4  O17   O   O2     0  -0.443   3.1434   1.0353   0.0908
 3T4  C18   C   CH2    0  -0.304   4.4371   1.4861   0.3891
 3T4  C19   C   C      0   0.514   4.5408   2.9178  -0.0780
 3T4  O20   O   O      0  -0.417   3.6685   3.5289  -0.6300
 3T4  O21   O   OH1    0  -0.591   5.7406   3.3989   0.2094
 3T4  O22   O   O      0  -0.457   0.2512   1.3794   0.0770
 3T4  C23   C   CR16   0  -0.274  -2.9592   2.0105  -1.1003
 3T4  C24   C   CR16   0  -0.240  -4.1273   2.0362  -0.3562
 3T4  C25   C   CR6    0   0.002  -4.7087   0.8533   0.0888
 3T4  C26   C   CSP    0   0.083  -5.9007   0.9746   0.8651
 3T4  N27   N   NS     0  -0.237  -6.8469   1.2153   1.4757
 3T4  H5    H   HCR6   0   0.305  -2.4541  -1.3238  -1.2226
 3T4  H7    H   HCH2   0   0.298  -1.3102   0.3399  -3.2275
 3T4  H7A   H   HCH2   0   0.275  -0.7329   1.7898  -2.4258
 3T4  HN8   H   HNH1   0   0.418   0.2710  -0.8496  -2.1368
 3T4  H11   H   HCR6   0   0.271   0.1356  -2.2696   0.0313
 3T4  H12   H   HCR6   0   0.285   1.6819  -3.8789   1.0646
 3T4  H15   H   HCR6   0   0.309   4.7046  -0.8551   1.2453
 3T4  H18   H   HCH2   0   0.283   4.6467   1.4451   1.4643
 3T4  H18A  H   HCH2   0   0.282   5.2062   0.8915  -0.1185
 3T4  H23   H   HCR6   0   0.288  -2.5209   2.9448  -1.4253
 3T4  H24   H   HCR6   0   0.304  -4.5895   2.9811  -0.1078
 3T4  H121  H   HOH1   0   0.491   5.8175   4.3176  -0.0897

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
 3T4  C1   N2    single    1.456  0.020  1.456
 3T4  C1   C5    aromatic  1.379  0.020  1.379
 3T4  C1   C25   aromatic  1.399  0.020  1.399
 3T4  CL1  C13   single    1.730  0.020  1.730
 3T4  N2   O3    single    1.205  0.020  1.205
 3T4  N2   O4    double    1.207  0.020  1.207
 3T4  C5   C6    aromatic  1.391  0.020  1.391
 3T4  C5   H5    single    0.930  0.020  1.080
 3T4  C6   C7    single    1.507  0.020  1.507
 3T4  C6   C23   aromatic  1.386  0.020  1.386
 3T4  C7   N8    single    1.442  0.020  1.442
 3T4  C7   H7    single    0.970  0.020  1.090
 3T4  C7   H7A   single    0.970  0.020  1.090
 3T4  N8   C9    single    1.346  0.020  1.346
 3T4  N8   HN8   single    0.860  0.020  1.020
 3T4  C9   C10   single    1.495  0.020  1.495
 3T4  C9   O22   double    1.218  0.020  1.218
 3T4  C10  C11   aromatic  1.386  0.020  1.386
 3T4  C10  C16   aromatic  1.402  0.020  1.402
 3T4  C11  C12   aromatic  1.388  0.020  1.388
 3T4  C11  H11   single    0.930  0.020  1.080
 3T4  C12  C13   aromatic  1.382  0.020  1.382
 3T4  C12  H12   single    0.930  0.020  1.080
 3T4  C13  C15   aromatic  1.388  0.020  1.388
 3T4  C15  C16   aromatic  1.391  0.020  1.391
 3T4  C15  H15   single    0.930  0.020  1.080
 3T4  C16  O17   single    1.341  0.020  1.341
 3T4  O17  C18   single    1.402  0.020  1.402
 3T4  C18  C19   single    1.510  0.020  1.510
 3T4  C18  H18   single    0.970  0.020  1.090
 3T4  C18  H18A  single    0.970  0.020  1.090
 3T4  C19  O20   double    1.200  0.020  1.200
 3T4  C19  O21   single    1.324  0.020  1.324
 3T4  C23  C24   aromatic  1.385  0.020  1.385
 3T4  C23  H23   single    0.930  0.020  1.080
 3T4  C24  C25   aromatic  1.391  0.020  1.391
 3T4  C24  H24   single    0.930  0.020  1.080
 3T4  C25  C26   single    1.428  0.020  1.428
 3T4  C26  N27   triple    1.152  0.020  1.152
 3T4  O21  H121  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
 3T4  C25   C1   C5   121.25  3.000
 3T4  C25   C1   N2   120.39  3.000
 3T4  C5    C1   N2   118.35  3.000
 3T4  O4    N2   O3   124.45  3.000
 3T4  O4    N2   C1   117.53  3.000
 3T4  O3    N2   C1   118.02  3.000
 3T4  H5    C5   C6   119.87  3.000
 3T4  H5    C5   C1   119.95  3.000
 3T4  C6    C5   C1   120.18  3.000
 3T4  C23   C6   C7   121.16  3.000
 3T4  C23   C6   C5   118.97  3.000
 3T4  C7    C6   C5   119.87  3.000
 3T4  H7A   C7   H7   107.06  3.000
 3T4  H7A   C7   N8   110.77  3.000
 3T4  H7    C7   N8   107.37  3.000
 3T4  H7A   C7   C6   109.72  3.000
 3T4  H7    C7   C6   109.41  3.000
 3T4  N8    C7   C6   112.34  3.000
 3T4  HN8   N8   C9   119.92  3.000
 3T4  HN8   N8   C7   118.87  3.000
 3T4  C9    N8   C7   121.02  3.000
 3T4  O22   C9   C10  122.58  3.000
 3T4  O22   C9   N8   122.67  3.000
 3T4  C10   C9   N8   114.71  3.000
 3T4  C16   C10  C11  119.21  3.000
 3T4  C16   C10  C9   120.73  3.000
 3T4  C11   C10  C9   119.98  3.000
 3T4  H11   C11  C12  118.60  3.000
 3T4  H11   C11  C10  119.71  3.000
 3T4  C12   C11  C10  121.68  3.000
 3T4  H12   C12  C13  121.24  3.000
 3T4  H12   C12  C11  120.78  3.000
 3T4  C13   C12  C11  117.98  3.000
 3T4  C15   C13  C12  122.13  3.000
 3T4  C15   C13  CL1  118.42  3.000
 3T4  C12   C13  CL1  119.45  3.000
 3T4  H15   C15  C16  121.69  3.000
 3T4  H15   C15  C13  119.21  3.000
 3T4  C16   C15  C13  119.10  3.000
 3T4  O17   C16  C15  123.70  3.000
 3T4  O17   C16  C10  116.40  3.000
 3T4  C15   C16  C10  119.88  3.000
 3T4  C18   O17  C16  118.71  3.000
 3T4  H18A  C18  H18  107.43  3.000
 3T4  H18A  C18  C19  108.84  3.000
 3T4  H18   C18  C19  109.02  3.000
 3T4  H18A  C18  O17  111.98  3.000
 3T4  H18   C18  O17  111.90  3.000
 3T4  C19   C18  O17  107.61  3.000
 3T4  O21   C19  O20  125.00  3.000
 3T4  O21   C19  C18  109.85  3.000
 3T4  O20   C19  C18  125.14  3.000
 3T4  H121  O21  C19  110.44  3.000
 3T4  H23   C23  C24  119.14  3.000
 3T4  H23   C23  C6   119.97  3.000
 3T4  C24   C23  C6   120.89  3.000
 3T4  H24   C24  C25  119.42  3.000
 3T4  H24   C24  C23  120.02  3.000
 3T4  C25   C24  C23  120.56  3.000
 3T4  C26   C25  C24  116.78  3.000
 3T4  C26   C25  C1   125.06  3.000
 3T4  C24   C25  C1   118.15  3.000
 3T4  N27   C26  C25  180.00  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
 3T4  CONST_01  C23   C6   C5   C1     0.00   0.0  0
 3T4  CONST_02  C23   C24  C25  C1     0.00   0.0  0
 3T4  CONST_03  C24   C25  C1   C5     0.00   0.0  0
 3T4  CONST_04  C24   C23  C6   C5     0.00   0.0  0
 3T4  CONST_05  C25   C1   C5   C6     0.00   0.0  0
 3T4  CONST_06  C25   C24  C23  C6     0.00   0.0  0
 3T4  CONST_07  C13   C12  C11  C10    0.00   0.0  0
 3T4  CONST_08  C13   C15  C16  C10    0.00   0.0  0
 3T4  CONST_09  C15   C16  C10  C11    0.00   0.0  0
 3T4  CONST_10  C15   C13  C12  C11    0.00   0.0  0
 3T4  CONST_11  C16   C10  C11  C12    0.00   0.0  0
 3T4  CONST_12  C16   C15  C13  C12    0.00   0.0  0
 3T4  CONST_13  C7    C6   C5   C1   180.00   0.0  0
 3T4  CONST_14  C11   C12  C13  CL1  180.00   0.0  0
 3T4  CONST_15  C16   C15  C13  CL1  180.00   0.0  0
 3T4  CONST_16  C6    C5   C1   N2   180.00   0.0  0
 3T4  CONST_17  C24   C25  C1   N2   180.00   0.0  0
 3T4  CONST_18  C26   C25  C1   C5   180.00   0.0  0
 3T4  CONST_19  C24   C23  C6   C7   180.00   0.0  0
 3T4  CONST_20  C12   C11  C10  C9   180.00   0.0  0
 3T4  CONST_21  C15   C16  C10  C9   180.00   0.0  0
 3T4  CONST_22  O17   C16  C10  C11  180.00   0.0  0
 3T4  CONST_23  O17   C16  C15  C13  180.00   0.0  0
 3T4  CONST_24  C26   C25  C24  C23  180.00   0.0  0
 3T4  CONST_25  H24   C24  C25  C1   180.00   0.0  0
 3T4  CONST_26  H23   C23  C6   C5   180.00   0.0  0
 3T4  CONST_27  H12   C12  C11  C10  180.00   0.0  0
 3T4  CONST_28  H15   C15  C16  C10  180.00   0.0  0
 3T4  CONST_29  H11   C11  C12  C13  180.00   0.0  0
 3T4  CONST_30  H5    C5   C6   C23  180.00   0.0  0
 3T4  CONST_31  C5    C1   N2   O3     0.00   0.0  0
 3T4  CONST_32  C25   C1   N2   O3   180.00   0.0  0
 3T4  CONST_33  C5    C1   N2   O4   180.00   0.0  0
 3T4  CONST_34  C25   C1   N2   O4     0.00   0.0  0
 3T4  CONST_35  C10   C9   N8   C7   180.00   0.0  0
 3T4  CONST_36  HN8   N8   C9   C10    0.00   0.0  0
 3T4  CONST_37  O22   C9   N8   C7     0.00   0.0  0
 3T4  CONST_38  H121  O21  C19  C18  180.00   0.0  0
 3T4  Var_01    N8    C7   C6   C5   -50.80  30.0  2
 3T4  Var_02    C11   C10  C9   N8   -55.45  30.0  2
 3T4  Var_03    C9    N8   C7   C6   -67.26  30.0  3
 3T4  Var_04    C19   C18  O17  C16  178.51  30.0  3
 3T4  Var_05    O20   C19  C18  O17   -1.51  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
 3T4  plan-1  C1    0.020
 3T4  plan-1  N2    0.020
 3T4  plan-1  C5    0.020
 3T4  plan-1  C6    0.020
 3T4  plan-1  C7    0.020
 3T4  plan-1  C23   0.020
 3T4  plan-1  C24   0.020
 3T4  plan-1  C25   0.020
 3T4  plan-1  C26   0.020
 3T4  plan-1  N27   0.020
 3T4  plan-1  H5    0.020
 3T4  plan-1  H23   0.020
 3T4  plan-1  H24   0.020
 3T4  plan-2  CL1   0.020
 3T4  plan-2  C9    0.020
 3T4  plan-2  C10   0.020
 3T4  plan-2  C11   0.020
 3T4  plan-2  C12   0.020
 3T4  plan-2  C13   0.020
 3T4  plan-2  C15   0.020
 3T4  plan-2  C16   0.020
 3T4  plan-2  O17   0.020
 3T4  plan-2  H11   0.020
 3T4  plan-2  H12   0.020
 3T4  plan-2  H15   0.020
 3T4  plan-3  C7    0.020
 3T4  plan-3  N8    0.020
 3T4  plan-3  C9    0.020
 3T4  plan-3  C10   0.020
 3T4  plan-3  O22   0.020
 3T4  plan-3  HN8   0.020
 3T4  plan-4  C1    0.020
 3T4  plan-4  N2    0.020
 3T4  plan-4  O3    0.020
 3T4  plan-4  O4    0.020
 3T4  plan-5  C18   0.020
 3T4  plan-5  C19   0.020
 3T4  plan-5  O20   0.020
 3T4  plan-5  O21   0.020
 3T4  plan-5  H121  0.020

