# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 03:57:25 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: N-(1H-benzimidazol-2-yl)-N'-(3,5-dichlorobenzyl)propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(Cl)cc(CNCCCNc2[nH]c3ccccc3n2)c1
#
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
 0P4  0P4  N-(1H-benzimidazol-2-yl)-N'-(3,5-dichlorobenzyl)propane-1,3-diamine  ligand  41  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0P4
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
 0P4  CAH  C   CR16  0  -0.244    4.0808  -0.8021  -0.2504
 0P4  CAR  C   CR6   0  -0.024    5.3584  -0.9487  -0.7610
 0P4  CL1  CL  CL    0  -0.118    5.6486  -2.1327  -1.9917
 0P4  CAG  C   CR16  0  -0.193    6.4211  -0.1748  -0.3191
 0P4  CAS  C   CR6   0  -0.026    6.1625   0.7645   0.6644
 0P4  CL2  CL  CL    0  -0.117    7.4607   1.7579   1.2348
 0P4  CAI  C   CR16  0  -0.264    4.8939   0.9372   1.1953
 0P4  CAT  C   CR6   0   0.070    3.8452   0.1468   0.7406
 0P4  CAM  C   CH2   0  -0.306    2.4699   0.2974   1.3367
 0P4  NAO  N   NH1   0  -0.600    1.4363   0.1764   0.3319
 0P4  CAK  C   CH2   0  -0.252    0.0980   0.1913   0.8904
 0P4  CAJ  C   CH2   0  -0.483   -0.9414   0.0139  -0.2047
 0P4  CAL  C   CH2   0  -0.278   -2.3541   0.0158   0.3538
 0P4  NAP  N   NH1   0  -0.686   -3.3113  -0.2024  -0.7121
 0P4  CAU  C   CR5   0   0.671   -4.6443  -0.2075  -0.5005
 0P4  NAQ  N   NR15  0  -0.738   -5.2056   0.3280   0.6200
 0P4  CAW  C   CR56  0   0.334   -6.5706   0.1967   0.4910
 0P4  CAF  C   CR16  0  -0.314   -7.6264   0.5608   1.3076
 0P4  CAD  C   CR16  0  -0.290   -8.9062   0.2649   0.8503
 0P4  CAC  C   CR16  0  -0.273   -9.1049  -0.3699  -0.3783
 0P4  CAE  C   CR16  0  -0.352   -8.0366  -0.7303  -1.1901
 0P4  CAV  C   CR56  0   0.160   -6.7481  -0.4425  -0.7499
 0P4  NAN  N   N     0  -0.536   -5.5318  -0.6833  -1.3431
 0P4  H1   H   HCR6  0   0.275    3.2667  -1.4120  -0.6171
 0P4  H2   H   HCR6  0   0.300    7.4131  -0.2978  -0.7304
 0P4  H3   H   HCR6  0   0.280    4.7208   1.6865   1.9569
 0P4  H4   H   HCH2  0   0.252    2.3215  -0.5010   2.0712
 0P4  H5   H   HCH2  0   0.224    2.4241   1.2396   1.9026
 0P4  H6   H   HNH1  0   0.347    1.5288   0.9397  -0.3287
 0P4  H8   H   HCH2  0   0.226    0.0171  -0.6340   1.6042
 0P4  H9   H   HCH2  0   0.197   -0.1145   1.1118   1.4565
 0P4  H10  H   HCH2  0   0.239   -0.8446   0.8146  -0.9434
 0P4  H11  H   HCH2  0   0.237   -0.7517  -0.9297  -0.7245
 0P4  H12  H   HCH2  0   0.234   -2.4455  -0.7466   1.1374
 0P4  H13  H   HCH2  0   0.236   -2.5514   0.9846   0.8212
 0P4  H14  H   HNH1  0   0.394   -3.0159  -0.8066  -1.4635
 0P4  H15  H   HNR5  0   0.420   -4.7221   0.7481   1.3971
 0P4  H16  H   HCR6  0   0.260   -7.4682   1.0552   2.2574
 0P4  H17  H   HCR6  0   0.247   -9.7616   0.5317   1.4573
 0P4  H18  H   HCR6  0   0.246  -10.1144  -0.5834  -0.7054
 0P4  H19  H   HCR6  0   0.245   -8.2010  -1.2226  -2.1404

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
 0P4  CL2  CAS  single    1.731  0.020  1.731
 0P4  CAS  CAG  aromatic  1.384  0.020  1.384
 0P4  CAS  CAI  aromatic  1.386  0.020  1.386
 0P4  CAG  CAR  aromatic  1.387  0.020  1.387
 0P4  CAI  CAT  aromatic  1.390  0.020  1.390
 0P4  CAR  CL1  single    1.732  0.020  1.732
 0P4  CAR  CAH  aromatic  1.384  0.020  1.384
 0P4  CAT  CAH  aromatic  1.392  0.020  1.392
 0P4  CAT  CAM  single    1.506  0.020  1.506
 0P4  CAM  NAO  single    1.447  0.020  1.447
 0P4  NAO  CAK  single    1.450  0.020  1.450
 0P4  CAK  CAJ  single    1.520  0.020  1.520
 0P4  CAJ  CAL  single    1.519  0.020  1.519
 0P4  CAL  NAP  single    1.449  0.020  1.449
 0P4  NAP  CAU  single    1.350  0.020  1.350
 0P4  CAU  NAQ  aromatic  1.363  0.020  1.363
 0P4  CAU  NAN  aromatic  1.313  0.020  1.313
 0P4  NAQ  CAW  aromatic  1.377  0.020  1.377
 0P4  NAN  CAV  aromatic  1.374  0.020  1.374
 0P4  CAW  CAV  aromatic  1.407  0.020  1.407
 0P4  CAW  CAF  aromatic  1.383  0.020  1.383
 0P4  CAV  CAE  aromatic  1.392  0.020  1.392
 0P4  CAF  CAD  aromatic  1.391  0.020  1.391
 0P4  CAE  CAC  aromatic  1.389  0.020  1.389
 0P4  CAD  CAC  aromatic  1.397  0.020  1.397
 0P4  CAH  H1   single    0.930  0.020  1.080
 0P4  CAG  H2   single    0.930  0.020  1.080
 0P4  CAI  H3   single    0.930  0.020  1.080
 0P4  CAM  H4   single    0.970  0.020  1.090
 0P4  CAM  H5   single    0.970  0.020  1.090
 0P4  NAO  H6   single    0.890  0.020  1.040
 0P4  CAK  H8   single    0.970  0.020  1.090
 0P4  CAK  H9   single    0.970  0.020  1.090
 0P4  CAJ  H10  single    0.970  0.020  1.090
 0P4  CAJ  H11  single    0.970  0.020  1.090
 0P4  CAL  H12  single    0.970  0.020  1.090
 0P4  CAL  H13  single    0.970  0.020  1.090
 0P4  NAP  H14  single    0.890  0.020  1.040
 0P4  NAQ  H15  single    0.860  0.020  1.020
 0P4  CAF  H16  single    0.930  0.020  1.080
 0P4  CAD  H17  single    0.930  0.020  1.080
 0P4  CAC  H18  single    0.930  0.020  1.080
 0P4  CAE  H19  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
 0P4  H1   CAH  CAT  119.89  3.000
 0P4  H1   CAH  CAR  120.68  3.000
 0P4  CAT  CAH  CAR  119.42  3.000
 0P4  CAG  CAR  CL1  118.64  3.000
 0P4  CL1  CAR  CAH  119.30  3.000
 0P4  CAG  CAR  CAH  122.06  3.000
 0P4  H2   CAG  CAS  121.26  3.000
 0P4  H2   CAG  CAR  121.23  3.000
 0P4  CAS  CAG  CAR  117.51  3.000
 0P4  CAI  CAS  CL2  119.25  3.000
 0P4  CAI  CAS  CAG  121.84  3.000
 0P4  CL2  CAS  CAG  118.90  3.000
 0P4  H3   CAI  CAT  120.22  3.000
 0P4  H3   CAI  CAS  120.14  3.000
 0P4  CAT  CAI  CAS  119.64  3.000
 0P4  CAM  CAT  CAI  120.17  3.000
 0P4  CAM  CAT  CAH  120.29  3.000
 0P4  CAI  CAT  CAH  119.53  3.000
 0P4  H5   CAM  H4   105.89  3.000
 0P4  H5   CAM  NAO  113.53  3.000
 0P4  H4   CAM  NAO  107.95  3.000
 0P4  H5   CAM  CAT  109.09  3.000
 0P4  H4   CAM  CAT  108.43  3.000
 0P4  NAO  CAM  CAT  111.66  3.000
 0P4  H6   NAO  CAK  109.11  3.000
 0P4  H6   NAO  CAM  108.94  3.000
 0P4  CAK  NAO  CAM  113.01  3.000
 0P4  H9   CAK  H8   106.31  3.000
 0P4  H9   CAK  CAJ  109.63  3.000
 0P4  H8   CAK  CAJ  109.35  3.000
 0P4  H9   CAK  NAO  112.62  3.000
 0P4  H8   CAK  NAO  108.17  3.000
 0P4  CAJ  CAK  NAO  110.63  3.000
 0P4  H11  CAJ  H10  107.17  3.000
 0P4  H11  CAJ  CAL  109.70  3.000
 0P4  H10  CAJ  CAL  109.25  3.000
 0P4  H11  CAJ  CAK  108.93  3.000
 0P4  H10  CAJ  CAK  109.92  3.000
 0P4  CAL  CAJ  CAK  111.77  3.000
 0P4  H13  CAL  H12  107.18  3.000
 0P4  H13  CAL  NAP  109.18  3.000
 0P4  H12  CAL  NAP  111.45  3.000
 0P4  H13  CAL  CAJ  109.03  3.000
 0P4  H12  CAL  CAJ  109.83  3.000
 0P4  NAP  CAL  CAJ  110.10  3.000
 0P4  H14  NAP  CAU  113.82  3.000
 0P4  H14  NAP  CAL  116.41  3.000
 0P4  CAU  NAP  CAL  122.52  3.000
 0P4  NAN  CAU  NAQ  113.06  3.000
 0P4  NAN  CAU  NAP  124.64  3.000
 0P4  NAQ  CAU  NAP  122.28  3.000
 0P4  H15  NAQ  CAW  126.00  3.000
 0P4  H15  NAQ  CAU  126.92  3.000
 0P4  CAW  NAQ  CAU  107.07  3.000
 0P4  CAV  CAW  CAF  122.94  3.000
 0P4  CAF  CAW  NAQ  132.52  3.000
 0P4  CAV  CAW  NAQ  104.53  3.000
 0P4  H16  CAF  CAD  121.34  3.000
 0P4  H16  CAF  CAW  121.78  3.000
 0P4  CAD  CAF  CAW  116.88  3.000
 0P4  H17  CAD  CAC  119.52  3.000
 0P4  H17  CAD  CAF  119.37  3.000
 0P4  CAC  CAD  CAF  121.11  3.000
 0P4  H18  CAC  CAE  119.30  3.000
 0P4  H18  CAC  CAD  119.21  3.000
 0P4  CAE  CAC  CAD  121.49  3.000
 0P4  H19  CAE  CAV  120.81  3.000
 0P4  H19  CAE  CAC  120.93  3.000
 0P4  CAV  CAE  CAC  118.26  3.000
 0P4  NAN  CAV  CAE  130.28  3.000
 0P4  CAE  CAV  CAW  119.32  3.000
 0P4  NAN  CAV  CAW  110.40  3.000
 0P4  CAV  NAN  CAU  104.93  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
 0P4  CONST_01  CAS  CAG  CAR  CAH     0.00   0.0  0
 0P4  CONST_02  CAS  CAI  CAT  CAH     0.00   0.0  0
 0P4  CONST_03  CAI  CAS  CAG  CAR     0.00   0.0  0
 0P4  CONST_04  CAI  CAT  CAH  CAR     0.00   0.0  0
 0P4  CONST_05  CAT  CAI  CAS  CAG     0.00   0.0  0
 0P4  CONST_06  CAT  CAH  CAR  CAG     0.00   0.0  0
 0P4  CONST_07  CAV  CAW  NAQ  CAU     0.00   0.0  0
 0P4  CONST_08  CAF  CAW  NAQ  CAU   180.00   0.0  0
 0P4  CONST_09  CAW  CAV  NAN  CAU     0.00   0.0  0
 0P4  CONST_10  CAE  CAV  NAN  CAU   180.00   0.0  0
 0P4  CONST_11  CAV  NAN  CAU  NAQ     0.00   0.0  0
 0P4  CONST_12  NAN  CAV  CAW  NAQ     0.00   0.0  0
 0P4  CONST_13  CAE  CAV  CAW  NAQ   180.00   0.0  0
 0P4  CONST_14  CAD  CAF  CAW  NAQ   180.00   0.0  0
 0P4  CONST_15  NAN  CAU  NAQ  CAW     0.00   0.0  0
 0P4  CONST_16  CAC  CAE  CAV  CAW     0.00   0.0  0
 0P4  CONST_17  CAC  CAD  CAF  CAW     0.00   0.0  0
 0P4  CONST_18  NAN  CAV  CAW  CAF   180.00   0.0  0
 0P4  CONST_19  CAE  CAV  CAW  CAF     0.00   0.0  0
 0P4  CONST_20  CAE  CAC  CAD  CAF     0.00   0.0  0
 0P4  CONST_21  CAV  CAW  CAF  CAD     0.00   0.0  0
 0P4  CONST_22  CAV  CAE  CAC  CAD     0.00   0.0  0
 0P4  CONST_23  NAN  CAV  CAE  CAC   180.00   0.0  0
 0P4  CONST_24  CL2  CAS  CAG  CAR   180.00   0.0  0
 0P4  CONST_25  CAM  CAT  CAH  CAR   180.00   0.0  0
 0P4  CONST_26  CAS  CAG  CAR  CL1   180.00   0.0  0
 0P4  CONST_27  CAT  CAH  CAR  CL1   180.00   0.0  0
 0P4  CONST_28  CAM  CAT  CAI  CAS   180.00   0.0  0
 0P4  CONST_29  CAT  CAI  CAS  CL2   180.00   0.0  0
 0P4  CONST_30  CAW  NAQ  CAU  NAP   180.00   0.0  0
 0P4  CONST_31  CAV  NAN  CAU  NAP   180.00   0.0  0
 0P4  CONST_32  H2   CAG  CAR  CAH   180.00   0.0  0
 0P4  CONST_33  H3   CAI  CAT  CAH   180.00   0.0  0
 0P4  CONST_34  H1   CAH  CAR  CAG   180.00   0.0  0
 0P4  CONST_35  H16  CAF  CAW  NAQ     0.00   0.0  0
 0P4  CONST_36  H19  CAE  CAV  CAW   180.00   0.0  0
 0P4  CONST_37  H17  CAD  CAF  CAW   180.00   0.0  0
 0P4  CONST_38  H15  NAQ  CAW  CAF     0.00   0.0  0
 0P4  CONST_39  H18  CAC  CAD  CAF   180.00   0.0  0
 0P4  CONST_42  H14  NAP  CAU  NAQ   180.00   0.0  0
 0P4  Var_01    NAO  CAM  CAT  CAH   -39.78  30.0  2
 0P4  Var_02    CAK  NAO  CAM  CAT   174.56  30.0  3
 0P4  Var_03    CAU  NAP  CAL  CAJ  -177.96  30.0  3
 0P4  Var_04    CAJ  CAK  NAO  CAM  -178.08  30.0  3
 0P4  Var_05    CAL  CAJ  CAK  NAO   179.60  30.0  3
 0P4  Var_06    NAP  CAL  CAJ  CAK  -177.99  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
 0P4  plan-1  CAH  0.020
 0P4  plan-1  CAR  0.020
 0P4  plan-1  CL1  0.020
 0P4  plan-1  CAG  0.020
 0P4  plan-1  CAS  0.020
 0P4  plan-1  CL2  0.020
 0P4  plan-1  CAI  0.020
 0P4  plan-1  CAT  0.020
 0P4  plan-1  CAM  0.020
 0P4  plan-1  H1   0.020
 0P4  plan-1  H2   0.020
 0P4  plan-1  H3   0.020
 0P4  plan-2  NAP  0.020
 0P4  plan-2  CAU  0.020
 0P4  plan-2  NAQ  0.020
 0P4  plan-2  CAW  0.020
 0P4  plan-2  CAF  0.020
 0P4  plan-2  CAD  0.020
 0P4  plan-2  CAC  0.020
 0P4  plan-2  CAE  0.020
 0P4  plan-2  CAV  0.020
 0P4  plan-2  NAN  0.020
 0P4  plan-2  H15  0.020
 0P4  plan-2  H16  0.020
 0P4  plan-2  H17  0.020
 0P4  plan-2  H18  0.020
 0P4  plan-2  H19  0.020
 0P4  plan-3  CAL  0.020
 0P4  plan-3  NAP  0.020
 0P4  plan-3  CAU  0.020
 0P4  plan-3  H14  0.020

