# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 13:41:22 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 4-(acetylamino)-3-[(diaminomethyl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc(cc1NC(N)N)C(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
 ST4  ST4  '4-(acetylamino)-3-[(diaminomethyl)amino]benzoic acid'  ligand  31  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ST4
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
 ST4  C'    C  C     0   0.534   1.1414   0.0426  -3.3326
 ST4  O1'   O  O     0  -0.440   0.1977   0.0797  -4.0865
 ST4  O2'   O  OH1   0  -0.594   2.3986   0.1184  -3.7465
 ST4  C1    C  CR6   0  -0.071   1.0218  -0.0955  -1.8594
 ST4  C2    C  CR16  0  -0.386  -0.2587  -0.1964  -1.3257
 ST4  C3    C  CR6   0   0.364  -0.4635  -0.3296   0.0499
 ST4  N3    N  NH1   0  -0.693  -1.7098  -0.4469   0.6116
 ST4  C3'   C  CH1   0   0.174  -2.9284  -0.0463  -0.0787
 ST4  N1    N  NH2   0  -0.806  -4.0073  -0.4306   0.7984
 ST4  N2    N  NH2   0  -0.788  -3.0731   1.3584  -0.3645
 ST4  C4    C  CR6   0   0.270   0.6777  -0.3806   0.8780
 ST4  N4    N  NH1   0  -0.737   0.4959  -0.5549   2.2637
 ST4  C4'   C  C     0   0.493   0.9562   0.3028   3.2151
 ST4  O4    O  O     0  -0.468   1.5580   1.3245   2.9427
 ST4  CM4   C  CH3   0  -0.789   0.6465  -0.1289   4.6253
 ST4  C5    C  CR16  0  -0.260   1.9485  -0.2783   0.3361
 ST4  C6    C  CR16  0  -0.311   2.1367  -0.1269  -1.0276
 ST4  HO2'  H  HOH1  0   0.487   2.4227   0.1997  -4.7115
 ST4  H2    H  HCR6  0   0.278  -1.1012  -0.1715  -2.0022
 ST4  HN3   H  HNH1  0   0.366  -1.7484  -0.2419   1.6012
 ST4  H3'   H  HCH1  0   0.223  -2.9426  -0.5695  -1.0430
 ST4  HN11  H  HNH2  0   0.355  -4.8852  -0.1555   0.3787
 ST4  HN12  H  HNH2  0   0.353  -4.0301  -1.4373   0.9010
 ST4  HN21  H  HNH2  0   0.344  -2.9132   1.9037   0.4745
 ST4  HN22  H  HNH2  0   0.355  -2.3960   1.6616  -1.0515
 ST4  HN4   H  HNH1  0   0.412   0.0018  -1.3810   2.5707
 ST4  HM41  H  HCH3  0   0.265   1.0114   0.6090   5.3346
 ST4  HM42  H  HCH3  0   0.268  -0.4281  -0.2517   4.7666
 ST4  HM43  H  HCH3  0   0.270   1.1153  -1.0893   4.8439
 ST4  H5    H  HCR6  0   0.269   2.8065  -0.3355   0.9921
 ST4  H6    H  HCR6  0   0.261   3.1398  -0.0479  -1.4203

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
 ST4  C'   O1'   double    1.208  0.020  1.208
 ST4  C'   O2'   single    1.326  0.020  1.326
 ST4  C'   C1    single    1.484  0.020  1.484
 ST4  O2'  HO2'  single    0.850  0.020  0.980
 ST4  C1   C2    aromatic  1.391  0.020  1.391
 ST4  C1   C6    aromatic  1.391  0.020  1.391
 ST4  C2   C3    aromatic  1.397  0.020  1.397
 ST4  C2   H2    single    0.930  0.020  1.080
 ST4  C3   N3    single    1.372  0.020  1.372
 ST4  C3   C4    aromatic  1.411  0.020  1.411
 ST4  N3   C3'   single    1.457  0.020  1.457
 ST4  N3   HN3   single    0.890  0.020  1.040
 ST4  C3'  N1    single    1.443  0.020  1.443
 ST4  C3'  N2    single    1.441  0.020  1.441
 ST4  C3'  H3'   single    0.970  0.020  1.090
 ST4  N1   HN11  single    0.890  0.020  1.040
 ST4  N1   HN12  single    0.890  0.020  1.040
 ST4  N2   HN21  single    0.890  0.020  1.040
 ST4  N2   HN22  single    0.890  0.020  1.040
 ST4  C4   N4    single    1.408  0.020  1.408
 ST4  C4   C5    aromatic  1.385  0.020  1.385
 ST4  N4   C4'   single    1.361  0.020  1.361
 ST4  N4   HN4   single    0.860  0.020  1.020
 ST4  C4'  O4    double    1.217  0.020  1.217
 ST4  C4'  CM4   single    1.507  0.020  1.507
 ST4  CM4  HM41  single    0.970  0.020  1.090
 ST4  CM4  HM42  single    0.970  0.020  1.090
 ST4  CM4  HM43  single    0.970  0.020  1.090
 ST4  C5   C6    aromatic  1.385  0.020  1.385
 ST4  C5   H5    single    0.930  0.020  1.080
 ST4  C6   H6    single    0.930  0.020  1.080

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
 ST4  C1    C'   O2'   113.05  3.000
 ST4  C1    C'   O1'   123.99  3.000
 ST4  O2'   C'   O1'   122.96  3.000
 ST4  HO2'  O2'  C'    109.84  3.000
 ST4  C6    C1   C2    120.44  3.000
 ST4  C6    C1   C'    122.06  3.000
 ST4  C2    C1   C'    117.50  3.000
 ST4  H2    C2   C3    120.28  3.000
 ST4  H2    C2   C1    118.41  3.000
 ST4  C3    C2   C1    121.31  3.000
 ST4  C4    C3   N3    119.43  3.000
 ST4  C4    C3   C2    117.56  3.000
 ST4  N3    C3   C2    122.98  3.000
 ST4  HN3   N3   C3'   112.09  3.000
 ST4  HN3   N3   C3    114.71  3.000
 ST4  C3'   N3   C3    122.85  3.000
 ST4  H3'   C3'  N2    106.81  3.000
 ST4  H3'   C3'  N1    113.44  3.000
 ST4  N2    C3'  N1    107.77  3.000
 ST4  H3'   C3'  N3    107.23  3.000
 ST4  N2    C3'  N3    116.49  3.000
 ST4  N1    C3'  N3    105.32  3.000
 ST4  HN12  N1   HN11  107.03  3.000
 ST4  HN12  N1   C3'   110.08  3.000
 ST4  HN11  N1   C3'   108.93  3.000
 ST4  HN22  N2   HN21  107.19  3.000
 ST4  HN22  N2   C3'   111.09  3.000
 ST4  HN21  N2   C3'   110.15  3.000
 ST4  C5    C4   N4    120.82  3.000
 ST4  C5    C4   C3    120.65  3.000
 ST4  N4    C4   C3    118.52  3.000
 ST4  HN4   N4   C4'   117.92  3.000
 ST4  HN4   N4   C4    117.60  3.000
 ST4  C4'   N4   C4    124.48  3.000
 ST4  CM4   C4'  O4    123.49  3.000
 ST4  CM4   C4'  N4    113.83  3.000
 ST4  O4    C4'  N4    122.68  3.000
 ST4  HM43  CM4  HM42  107.36  3.000
 ST4  HM43  CM4  HM41  108.83  3.000
 ST4  HM42  CM4  HM41  108.83  3.000
 ST4  HM43  CM4  C4'   110.58  3.000
 ST4  HM42  CM4  C4'   110.85  3.000
 ST4  HM41  CM4  C4'   110.32  3.000
 ST4  H5    C5   C6    119.68  3.000
 ST4  H5    C5   C4    119.12  3.000
 ST4  C6    C5   C4    121.19  3.000
 ST4  H6    C6   C5    119.48  3.000
 ST4  H6    C6   C1    121.68  3.000
 ST4  C5    C6   C1    118.83  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
 ST4  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 ST4  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 ST4  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 ST4  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 ST4  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 ST4  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 ST4  CONST_07  C3    C2   C1   C'    180.00   0.0  0
 ST4  CONST_08  C5    C6   C1   C'    180.00   0.0  0
 ST4  CONST_09  N3    C3   C2   C1    180.00   0.0  0
 ST4  CONST_10  N4    C4   C3   C2    180.00   0.0  0
 ST4  CONST_11  C5    C4   C3   N3    180.00   0.0  0
 ST4  CONST_12  C6    C5   C4   N4    180.00   0.0  0
 ST4  CONST_13  H5    C5   C6   C1    180.00   0.0  0
 ST4  CONST_14  H6    C6   C1   C2    180.00   0.0  0
 ST4  CONST_15  H2    C2   C3   C4    180.00   0.0  0
 ST4  CONST_22  O4    C4'  N4   C4      0.00   0.0  0
 ST4  CONST_23  CM4   C4'  N4   C4    180.00   0.0  0
 ST4  CONST_24  HO2'  O2'  C'   C1    180.00   0.0  0
 ST4  Var_01    C2    C1   C'   O1'     0.44  30.0  2
 ST4  Var_02    N1    C3'  N3   C3    175.44  30.0  3
 ST4  Var_03    HN11  N1   C3'  N3    178.66  30.0  3
 ST4  Var_04    HN21  N2   C3'  N3    -50.88  30.0  3
 ST4  Var_05    HM41  CM4  C4'  N4   -178.27  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
 ST4  plan-1  C'    0.020
 ST4  plan-1  C1    0.020
 ST4  plan-1  C2    0.020
 ST4  plan-1  C3    0.020
 ST4  plan-1  N3    0.020
 ST4  plan-1  C4    0.020
 ST4  plan-1  N4    0.020
 ST4  plan-1  C5    0.020
 ST4  plan-1  C6    0.020
 ST4  plan-1  H2    0.020
 ST4  plan-1  H5    0.020
 ST4  plan-1  H6    0.020
 ST4  plan-2  C4    0.020
 ST4  plan-2  N4    0.020
 ST4  plan-2  C4'   0.020
 ST4  plan-2  O4    0.020
 ST4  plan-2  CM4   0.020
 ST4  plan-2  HN4   0.020
 ST4  plan-3  C3    0.020
 ST4  plan-3  N3    0.020
 ST4  plan-3  C3'   0.020
 ST4  plan-3  HN3   0.020
 ST4  plan-4  C'    0.020
 ST4  plan-4  O1'   0.020
 ST4  plan-4  O2'   0.020
 ST4  plan-4  C1    0.020
 ST4  plan-4  HO2'  0.020

