# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 22:09:26 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 4,4'-[propane-1,3-diylbis(oxy)]dibenzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(OCCCOc2ccc(cc2)C(N)=N)cc1
#
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
 TNT  TNT  4,4'-[propane-1,3-diylbis(oxy)]dibenzenecarboximidamide  ligand  43  23  .  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_TNT
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
 TNT  C1    C  CR6   0   0.390  -0.6207   0.0371   3.6084
 TNT  C2    C  CR16  0  -0.336  -1.5187   0.2106   4.6652
 TNT  C3    C  CR16  0  -0.274  -1.0751   0.1569   5.9702
 TNT  C4    C  CR6   0  -0.017   0.2722  -0.0609   6.2673
 TNT  C5    C  CR16  0  -0.267   1.1564  -0.2300   5.2073
 TNT  C6    C  CR16  0  -0.369   0.7247  -0.1902   3.8884
 TNT  C7    C  C     0   0.327   0.7283  -0.1214   7.6812
 TNT  N1    N  N     0  -0.645   0.0338  -0.5737   8.6552
 TNT  N2    N  NH2   0  -0.805   2.0046   0.3131   7.8926
 TNT  C1'   C  CR6   0   0.387  -0.6076   0.0155  -3.5944
 TNT  C2'   C  CR16  0  -0.335  -1.5082   0.1358  -4.6574
 TNT  C3'   C  CR16  0  -0.258  -1.0585   0.0790  -5.9595
 TNT  C4'   C  CR6   0   0.023   0.2977  -0.0860  -6.2503
 TNT  C5'   C  CR16  0  -0.277   1.1826  -0.2109  -5.1852
 TNT  C6'   C  CR16  0  -0.370   0.7452  -0.1659  -3.8673
 TNT  C7'   C  C     0   0.329   0.7462  -0.1412  -7.6654
 TNT  N1'   N  N     0  -0.655  -0.0916  -0.4926  -8.5649
 TNT  N2'   N  NH2   0  -0.823   2.0663   0.1510  -7.8724
 TNT  CA    C  CH2   0  -0.180  -0.2812  -0.0427   1.2531
 TNT  O1    O  O2    0  -0.470  -1.1397   0.1071   2.3717
 TNT  CB    C  CH2   0  -0.495  -1.1282   0.1100   0.0061
 TNT  CA'   C  CH2   0  -0.179  -0.2758  -0.0413  -1.2376
 TNT  O1'   O  O2    0  -0.471  -1.1330   0.0864  -2.3597
 TNT  H2    H  HCR6  0   0.268  -2.5643   0.3937   4.4516
 TNT  H3    H  HCR6  0   0.262  -1.7915   0.3098   6.7679
 TNT  H5    H  HCR6  0   0.265   2.2058  -0.4155   5.3974
 TNT  H6    H  HCR6  0   0.284   1.4503  -0.3391   3.1009
 TNT  HN1   H  H     0   0.330  -0.8421  -0.9607   8.3240
 TNT  HN2   H  HNH2  0   0.382   2.2859   0.3993   8.8564
 TNT  HN3   H  HNH2  0   0.391   2.3638   1.0392   7.2952
 TNT  H2'   H  HCR6  0   0.264  -2.5618   0.2756  -4.4496
 TNT  H3'   H  HCR6  0   0.256  -1.7669   0.1724  -6.7714
 TNT  H5'   H  HCR6  0   0.260   2.2396  -0.3661  -5.3614
 TNT  H6'   H  HCR6  0   0.283   1.4739  -0.2766  -3.0764
 TNT  HN'1  H  H     0   0.322   0.3272  -0.4537  -9.4903
 TNT  HN'2  H  HNH2  0   0.389   2.3636   0.2678  -8.8283
 TNT  HN'3  H  HNH2  0   0.393   2.5136   0.7927  -7.2384
 TNT  HA1   H  HCH2  0   0.231   0.5117   0.7135   1.2761
 TNT  HA2   H  HCH2  0   0.231   0.2002  -1.0269   1.2714
 TNT  HB1   H  HCH2  0   0.251  -1.9162  -0.6471   0.0042
 TNT  HB2   H  HCH2  0   0.251  -1.6067   1.0925   0.0052
 TNT  HA'1  H  HCH2  0   0.230   0.5059   0.7264  -1.2628
 TNT  HA'2  H  HCH2  0   0.230   0.2203  -1.0185  -1.2477

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
 TNT  C1   C2    aromatic  1.398  0.020  1.398
 TNT  C1   C6    aromatic  1.393  0.020  1.393
 TNT  C1   O1    single    1.343  0.020  1.343
 TNT  C2   C3    aromatic  1.379  0.020  1.379
 TNT  C2   H2    single    0.930  0.020  1.080
 TNT  C3   C4    aromatic  1.397  0.020  1.397
 TNT  C3   H3    single    0.930  0.020  1.080
 TNT  C4   C5    aromatic  1.391  0.020  1.391
 TNT  C4   C7    single    1.487  0.020  1.487
 TNT  C5   C6    aromatic  1.388  0.020  1.388
 TNT  C5   H5    single    0.930  0.020  1.080
 TNT  C6   H6    single    0.930  0.020  1.080
 TNT  C7   N1    double    1.279  0.020  1.279
 TNT  C7   N2    single    1.365  0.020  1.365
 TNT  N1   HN1   single    0.890  0.020  1.040
 TNT  N2   HN2   single    0.890  0.020  1.040
 TNT  N2   HN3   single    0.890  0.020  1.040
 TNT  C1'  C2'   aromatic  1.398  0.020  1.398
 TNT  C1'  C6'   aromatic  1.392  0.020  1.392
 TNT  C1'  O1'   single    1.344  0.020  1.344
 TNT  C2'  C3'   aromatic  1.379  0.020  1.379
 TNT  C2'  H2'   single    0.930  0.020  1.080
 TNT  C3'  C4'   aromatic  1.397  0.020  1.397
 TNT  C3'  H3'   single    0.930  0.020  1.080
 TNT  C4'  C5'   aromatic  1.390  0.020  1.390
 TNT  C4'  C7'   single    1.485  0.020  1.485
 TNT  C5'  C6'   aromatic  1.389  0.020  1.389
 TNT  C5'  H5'   single    0.930  0.020  1.080
 TNT  C6'  H6'   single    0.930  0.020  1.080
 TNT  C7'  N1'   double    1.278  0.020  1.278
 TNT  C7'  N2'   single    1.368  0.020  1.368
 TNT  N1'  HN'1  single    0.890  0.020  1.040
 TNT  N2'  HN'2  single    0.890  0.020  1.040
 TNT  N2'  HN'3  single    0.890  0.020  1.040
 TNT  CA   O1    single    1.418  0.020  1.418
 TNT  CA   CB    single    1.515  0.020  1.515
 TNT  CA   HA1   single    0.970  0.020  1.090
 TNT  CA   HA2   single    0.970  0.020  1.090
 TNT  CB   CA'   single    1.515  0.020  1.515
 TNT  CB   HB1   single    0.970  0.020  1.090
 TNT  CB   HB2   single    0.970  0.020  1.090
 TNT  CA'  O1'   single    1.418  0.020  1.418
 TNT  CA'  HA'1  single    0.970  0.020  1.090
 TNT  CA'  HA'2  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
 TNT  O1    C1   C6    124.53  3.000
 TNT  O1    C1   C2    116.20  3.000
 TNT  C6    C1   C2    119.27  3.000
 TNT  H2    C2   C3    120.25  3.000
 TNT  H2    C2   C1    119.49  3.000
 TNT  C3    C2   C1    120.26  3.000
 TNT  H3    C3   C4    120.23  3.000
 TNT  H3    C3   C2    118.59  3.000
 TNT  C4    C3   C2    121.17  3.000
 TNT  C7    C4   C5    121.66  3.000
 TNT  C7    C4   C3    120.29  3.000
 TNT  C5    C4   C3    118.04  3.000
 TNT  H5    C5   C6    118.25  3.000
 TNT  H5    C5   C4    120.22  3.000
 TNT  C6    C5   C4    121.52  3.000
 TNT  H6    C6   C5    118.64  3.000
 TNT  H6    C6   C1    121.63  3.000
 TNT  C5    C6   C1    119.74  3.000
 TNT  N2    C7   N1    120.16  3.000
 TNT  N2    C7   C4    114.91  3.000
 TNT  N1    C7   C4    124.90  3.000
 TNT  HN1   N1   C7    110.82  3.000
 TNT  HN3   N2   HN2   113.98  3.000
 TNT  HN3   N2   C7    118.13  3.000
 TNT  HN2   N2   C7    115.87  3.000
 TNT  O1'   C1'  C6'   124.54  3.000
 TNT  O1'   C1'  C2'   116.24  3.000
 TNT  C6'   C1'  C2'   119.22  3.000
 TNT  H2'   C2'  C3'   120.26  3.000
 TNT  H2'   C2'  C1'   119.46  3.000
 TNT  C3'   C2'  C1'   120.28  3.000
 TNT  H3'   C3'  C4'   119.33  3.000
 TNT  H3'   C3'  C2'   119.46  3.000
 TNT  C4'   C3'  C2'   121.21  3.000
 TNT  C7'   C4'  C5'   122.29  3.000
 TNT  C7'   C4'  C3'   119.73  3.000
 TNT  C5'   C4'  C3'   117.97  3.000
 TNT  H5'   C5'  C6'   117.79  3.000
 TNT  H5'   C5'  C4'   120.64  3.000
 TNT  C6'   C5'  C4'   121.56  3.000
 TNT  H6'   C6'  C5'   118.59  3.000
 TNT  H6'   C6'  C1'   121.67  3.000
 TNT  C5'   C6'  C1'   119.75  3.000
 TNT  N2'   C7'  N1'   125.78  3.000
 TNT  N2'   C7'  C4'   115.32  3.000
 TNT  N1'   C7'  C4'   118.85  3.000
 TNT  HN'1  N1'  C7'   111.10  3.000
 TNT  HN'3  N2'  HN'2  113.10  3.000
 TNT  HN'3  N2'  C7'   118.01  3.000
 TNT  HN'2  N2'  C7'   116.94  3.000
 TNT  HA2   CA   HA1   107.55  3.000
 TNT  HA2   CA   CB    110.48  3.000
 TNT  HA1   CA   CB    110.62  3.000
 TNT  HA2   CA   O1    110.35  3.000
 TNT  HA1   CA   O1    110.40  3.000
 TNT  CB    CA   O1    107.47  3.000
 TNT  CA    O1   C1    119.14  3.000
 TNT  HB2   CB   HB1   107.89  3.000
 TNT  HB2   CB   CA'   109.60  3.000
 TNT  HB1   CB   CA'   109.58  3.000
 TNT  HB2   CB   CA    109.63  3.000
 TNT  HB1   CB   CA    109.55  3.000
 TNT  CA'   CB   CA    110.55  3.000
 TNT  HA'2  CA'  HA'1  107.55  3.000
 TNT  HA'2  CA'  O1'   110.28  3.000
 TNT  HA'1  CA'  O1'   110.48  3.000
 TNT  HA'2  CA'  CB    110.56  3.000
 TNT  HA'1  CA'  CB    110.50  3.000
 TNT  O1'   CA'  CB    107.49  3.000
 TNT  CA'   O1'  C1'   119.08  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
 TNT  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 TNT  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 TNT  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 TNT  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 TNT  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 TNT  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 TNT  CONST_07  C4'   C3'  C2'  C1'     0.00   0.0  0
 TNT  CONST_08  C4'   C5'  C6'  C1'     0.00   0.0  0
 TNT  CONST_09  C5'   C6'  C1'  C2'     0.00   0.0  0
 TNT  CONST_10  C5'   C4'  C3'  C2'     0.00   0.0  0
 TNT  CONST_11  C6'   C1'  C2'  C3'     0.00   0.0  0
 TNT  CONST_12  C6'   C5'  C4'  C3'     0.00   0.0  0
 TNT  CONST_13  C7    C4   C3   C2    180.00   0.0  0
 TNT  CONST_14  O1    C1   C2   C3    180.00   0.0  0
 TNT  CONST_15  O1    C1   C6   C5    180.00   0.0  0
 TNT  CONST_16  C7    C4   C5   C6    180.00   0.0  0
 TNT  CONST_17  C7'   C4'  C3'  C2'   180.00   0.0  0
 TNT  CONST_18  O1'   C1'  C2'  C3'   180.00   0.0  0
 TNT  CONST_19  O1'   C1'  C6'  C5'   180.00   0.0  0
 TNT  CONST_20  C7'   C4'  C5'  C6'   180.00   0.0  0
 TNT  CONST_21  H3    C3   C2   C1    180.00   0.0  0
 TNT  CONST_22  H5    C5   C6   C1    180.00   0.0  0
 TNT  CONST_23  H6    C6   C1   C2    180.00   0.0  0
 TNT  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 TNT  CONST_25  H3'   C3'  C2'  C1'   180.00   0.0  0
 TNT  CONST_26  H5'   C5'  C6'  C1'   180.00   0.0  0
 TNT  CONST_27  H6'   C6'  C1'  C2'   180.00   0.0  0
 TNT  CONST_28  H2'   C2'  C3'  C4'   180.00   0.0  0
 TNT  CONST_29  HN1   N1   C7   C4      0.00   0.0  0
 TNT  CONST_30  HN2   N2   C7   C4    180.00   0.0  0
 TNT  CONST_32  HN'1  N1'  C7'  C4'   180.00   0.0  0
 TNT  CONST_33  HN'2  N2'  C7'  C4'   180.00   0.0  0
 TNT  Var_01    N1    C7   C4   C3     32.80  30.0  2
 TNT  Var_02    N1'   C7'  C4'  C3'   -23.67  30.0  2
 TNT  Var_03    CB    CA   O1   C1   -178.82  30.0  1
 TNT  Var_04    CB    CA'  O1'  C1'   178.69  30.0  1
 TNT  Var_05    O1'   CA'  CB   CA    178.89  30.0  3
 TNT  Var_06    CA'   CB   CA   O1   -179.89  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
 TNT  plan-1  C1    0.020
 TNT  plan-1  C2    0.020
 TNT  plan-1  C3    0.020
 TNT  plan-1  C4    0.020
 TNT  plan-1  C5    0.020
 TNT  plan-1  C6    0.020
 TNT  plan-1  C7    0.020
 TNT  plan-1  O1    0.020
 TNT  plan-1  H2    0.020
 TNT  plan-1  H3    0.020
 TNT  plan-1  H5    0.020
 TNT  plan-1  H6    0.020
 TNT  plan-2  C1'   0.020
 TNT  plan-2  C2'   0.020
 TNT  plan-2  C3'   0.020
 TNT  plan-2  C4'   0.020
 TNT  plan-2  C5'   0.020
 TNT  plan-2  C6'   0.020
 TNT  plan-2  C7'   0.020
 TNT  plan-2  O1'   0.020
 TNT  plan-2  H2'   0.020
 TNT  plan-2  H3'   0.020
 TNT  plan-2  H5'   0.020
 TNT  plan-2  H6'   0.020
 TNT  plan-3  C4    0.020
 TNT  plan-3  C7    0.020
 TNT  plan-3  N1    0.020
 TNT  plan-3  N2    0.020
 TNT  plan-3  HN1   0.020
 TNT  plan-3  HN2   0.020
 TNT  plan-3  HN3   0.020
 TNT  plan-4  C4'   0.020
 TNT  plan-4  C7'   0.020
 TNT  plan-4  N1'   0.020
 TNT  plan-4  N2'   0.020
 TNT  plan-4  HN'1  0.020
 TNT  plan-4  HN'2  0.020
 TNT  plan-4  HN'3  0.020

