# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:22:52 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N~1~-(4-{2-[(3-chlorophenyl)amino]pyrimidin-4-yl}pyridin-2-yl)ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCNc1cc(ccn1)c2ccnc(Nc3cccc(Cl)c3)n2
#
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
 6LP  6LP  N~1~-(4-{2-[(3-chlorophenyl)amino]pyrimidin-4-yl}pyridin-2-yl)ethane-1,2-diamine  ligand  41  24  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6LP
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
 6LP  C4    C   CR6   0   0.286   1.3399   1.9306  -0.0457
 6LP  C5    C   CR16  0  -0.393   0.9250   3.1973  -0.4557
 6LP  C6    C   CR16  0   0.012  -0.4390   3.3977  -0.5311
 6LP  N1    N   N     0  -0.462  -1.3288   2.4604  -0.2346
 6LP  N3    N   N     0  -0.489   0.4611   0.9860   0.2475
 6LP  CAU   C   CR16  0  -0.320  -3.5754  -1.0809   0.8548
 6LP  CAT   C   CR6   0  -0.024  -4.9424  -1.2686   0.9006
 6LP  CLAV  CL  CL    0  -0.129  -5.5543  -2.8232   1.3690
 6LP  CAS   C   CR16  0  -0.244  -5.8339  -0.2546   0.5854
 6LP  CAR   C   CR16  0  -0.249  -5.3051   0.9727   0.2181
 6LP  CAQ   C   CR16  0  -0.308  -3.9373   1.1985   0.1619
 6LP  CAP   C   CR6   0   0.373  -3.0531   0.1648   0.4825
 6LP  C2    C   CR6   0   0.610  -0.8345   1.2871   0.1435
 6LP  CAF   C   CR6   0   0.168   2.7736   1.5745   0.0619
 6LP  CAE   C   CR16  0  -0.448   3.1573   0.2459   0.0305
 6LP  CAG   C   CR16  0  -0.429   3.7547   2.5607   0.1875
 6LP  CAH   C   CR16  0  -0.057   5.0715   2.1465   0.2679
 6LP  NAI   N   N     0  -0.461   5.4624   0.8818   0.2249
 6LP  CAD   C   CR6   0   0.521   4.5273  -0.0676   0.1085
 6LP  NAC   N   NH1   0  -0.669   4.9713  -1.3431   0.0772
 6LP  CAB   C   CH2   0  -0.261   4.1384  -2.4985  -0.1445
 6LP  CAA   C   CH2   0  -0.315   4.9897  -3.7591  -0.1624
 6LP  NAX   N   NH2   0  -0.799   4.1465  -4.9188  -0.3911
 6LP  H1    H   HCR6  0   0.278   1.6165   3.9821  -0.7211
 6LP  H2    H   HCR6  0   0.280  -0.8369   4.3548  -0.8480
 6LP  H3    H   HCR6  0   0.290  -2.9068  -1.8953   1.1048
 6LP  H4    H   HCR6  0   0.276  -6.9018  -0.4163   0.6250
 6LP  H5    H   HCR6  0   0.268  -5.9775   1.7829  -0.0327
 6LP  H6    H   HCR6  0   0.291  -3.5647   2.1658  -0.1293
 6LP  H7    H   HNH1  0   0.413  -1.1751  -0.5768   0.7409
 6LP  H8    H   HCR6  0   0.273   2.4111  -0.5301  -0.0603
 6LP  H9    H   HCR6  0   0.259   3.5164   3.6132   0.2408
 6LP  H10   H   HCR6  0   0.260   5.8603   2.8836   0.3735
 6LP  H11   H   HNH1  0   0.383   5.9715  -1.4579   0.0361
 6LP  H12   H   HCH2  0   0.230   3.3868  -2.5903   0.6456
 6LP  H13   H   HCH2  0   0.223   3.5955  -2.4166  -1.0953
 6LP  H14   H   HCH2  0   0.206   5.7901  -3.6350  -0.9064
 6LP  H15   H   HCH2  0   0.233   5.4782  -3.8690   0.8089
 6LP  H16   H   HNH2  0   0.344   3.8156  -4.9139  -1.3482
 6LP  H17   H   HNH2  0   0.354   4.7004  -5.7601  -0.2986
 6LP  NAO   N   NH1   0  -0.776  -1.6695   0.2601   0.4683

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
 6LP  CLAV  CAT  single    1.735  0.020  1.735
 6LP  CAT   CAS  aromatic  1.386  0.020  1.386
 6LP  CAT   CAU  aromatic  1.381  0.020  1.381
 6LP  CAS   CAR  aromatic  1.386  0.020  1.386
 6LP  CAU   CAP  aromatic  1.401  0.020  1.401
 6LP  CAR   CAQ  aromatic  1.387  0.020  1.387
 6LP  CAP   CAQ  aromatic  1.398  0.020  1.398
 6LP  CAP   NAO  single    1.387  0.020  1.387
 6LP  C6    N1   aromatic  1.326  0.020  1.326
 6LP  C6    C5   aromatic  1.381  0.020  1.381
 6LP  N1    C2   aromatic  1.328  0.020  1.328
 6LP  CAG   CAH  aromatic  1.383  0.020  1.383
 6LP  CAG   CAF  aromatic  1.397  0.020  1.397
 6LP  C5    C4   aromatic  1.395  0.020  1.395
 6LP  C2    NAO  single    1.363  0.020  1.363
 6LP  C2    N3   aromatic  1.334  0.020  1.334
 6LP  CAH   NAI  aromatic  1.324  0.020  1.324
 6LP  C4    N3   aromatic  1.323  0.020  1.323
 6LP  C4    CAF  single    1.481  0.020  1.481
 6LP  CAF   CAE  aromatic  1.383  0.020  1.383
 6LP  NAI   CAD  aromatic  1.338  0.020  1.338
 6LP  NAX   CAA  single    1.452  0.020  1.452
 6LP  CAE   CAD  aromatic  1.408  0.020  1.408
 6LP  CAD   NAC  single    1.351  0.020  1.351
 6LP  CAB   CAA  single    1.521  0.020  1.521
 6LP  CAB   NAC  single    1.441  0.020  1.441
 6LP  C5    H1   single    0.930  0.020  1.080
 6LP  C6    H2   single    0.930  0.020  1.080
 6LP  CAU   H3   single    0.930  0.020  1.080
 6LP  CAS   H4   single    0.930  0.020  1.080
 6LP  CAR   H5   single    0.930  0.020  1.080
 6LP  CAQ   H6   single    0.930  0.020  1.080
 6LP  NAO   H7   single    0.860  0.020  1.020
 6LP  CAE   H8   single    0.930  0.020  1.080
 6LP  CAG   H9   single    0.930  0.020  1.080
 6LP  CAH   H10  single    0.930  0.020  1.080
 6LP  NAC   H11  single    0.860  0.020  1.020
 6LP  CAB   H12  single    0.970  0.020  1.090
 6LP  CAB   H13  single    0.970  0.020  1.090
 6LP  CAA   H14  single    0.970  0.020  1.090
 6LP  CAA   H15  single    0.970  0.020  1.090
 6LP  NAX   H16  single    0.890  0.020  1.040
 6LP  NAX   H17  single    0.890  0.020  1.040

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
 6LP  CAF   C4   N3    117.08  3.000
 6LP  CAF   C4   C5    121.85  3.000
 6LP  N3    C4   C5    121.06  3.000
 6LP  H1    C5   C6    120.94  3.000
 6LP  H1    C5   C4    122.83  3.000
 6LP  C6    C5   C4    116.22  3.000
 6LP  H2    C6   N1    116.31  3.000
 6LP  H2    C6   C5    120.45  3.000
 6LP  N1    C6   C5    123.24  3.000
 6LP  C2    N1   C6    116.00  3.000
 6LP  C2    N3   C4    117.82  3.000
 6LP  H3    CAU  CAP   119.98  3.000
 6LP  H3    CAU  CAT   120.10  3.000
 6LP  CAP   CAU  CAT   119.92  3.000
 6LP  CAS   CAT  CLAV  119.33  3.000
 6LP  CAS   CAT  CAU   121.99  3.000
 6LP  CLAV  CAT  CAU   118.68  3.000
 6LP  H4    CAS  CAR   121.27  3.000
 6LP  H4    CAS  CAT   121.18  3.000
 6LP  CAR   CAS  CAT   117.55  3.000
 6LP  H5    CAR  CAQ   118.77  3.000
 6LP  H5    CAR  CAS   119.16  3.000
 6LP  CAQ   CAR  CAS   122.07  3.000
 6LP  H6    CAQ  CAP   120.50  3.000
 6LP  H6    CAQ  CAR   119.89  3.000
 6LP  CAP   CAQ  CAR   119.61  3.000
 6LP  NAO   CAP  CAQ   125.31  3.000
 6LP  NAO   CAP  CAU   115.83  3.000
 6LP  CAQ   CAP  CAU   118.86  3.000
 6LP  NAO   C2   N3    113.98  3.000
 6LP  N3    C2   N1    125.66  3.000
 6LP  NAO   C2   N1    120.36  3.000
 6LP  CAG   CAF  CAE   119.04  3.000
 6LP  CAE   CAF  C4    119.85  3.000
 6LP  CAG   CAF  C4    121.11  3.000
 6LP  H8    CAE  CAD   121.13  3.000
 6LP  H8    CAE  CAF   120.01  3.000
 6LP  CAD   CAE  CAF   118.86  3.000
 6LP  H9    CAG  CAH   119.93  3.000
 6LP  H9    CAG  CAF   122.50  3.000
 6LP  CAH   CAG  CAF   117.55  3.000
 6LP  H10   CAH  NAI   115.95  3.000
 6LP  H10   CAH  CAG   119.64  3.000
 6LP  NAI   CAH  CAG   124.42  3.000
 6LP  CAD   NAI  CAH   118.31  3.000
 6LP  NAC   CAD  NAI   116.26  3.000
 6LP  NAC   CAD  CAE   121.93  3.000
 6LP  NAI   CAD  CAE   121.81  3.000
 6LP  H11   NAC  CAB   118.43  3.000
 6LP  H11   NAC  CAD   115.77  3.000
 6LP  CAB   NAC  CAD   124.78  3.000
 6LP  H13   CAB  H12   106.97  3.000
 6LP  H13   CAB  CAA   109.17  3.000
 6LP  H12   CAB  CAA   108.86  3.000
 6LP  H13   CAB  NAC   111.05  3.000
 6LP  H12   CAB  NAC   110.68  3.000
 6LP  CAA   CAB  NAC   110.04  3.000
 6LP  H15   CAA  H14   106.70  3.000
 6LP  H15   CAA  NAX   108.62  3.000
 6LP  H14   CAA  NAX   113.97  3.000
 6LP  H15   CAA  CAB   108.85  3.000
 6LP  H14   CAA  CAB   108.77  3.000
 6LP  NAX   CAA  CAB   109.80  3.000
 6LP  H17   NAX  H16   105.63  3.000
 6LP  H17   NAX  CAA   109.38  3.000
 6LP  H16   NAX  CAA   109.56  3.000
 6LP  H7    NAO  C2    112.89  3.000
 6LP  H7    NAO  CAP   115.40  3.000
 6LP  C2    NAO  CAP   131.72  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
 6LP  CONST_01  N1   C6   C5   C4       0.00   0.0  0
 6LP  CONST_02  N1   C2   N3   C4       0.00   0.0  0
 6LP  CONST_03  CAH  CAG  CAF  C4     180.00   0.0  0
 6LP  CONST_04  CAD  CAE  CAF  C4     180.00   0.0  0
 6LP  CONST_05  C2   N1   C6   C5       0.00   0.0  0
 6LP  CONST_06  C2   N3   C4   C5       0.00   0.0  0
 6LP  CONST_09  N3   C2   N1   C6       0.00   0.0  0
 6LP  CONST_10  N3   C4   C5   C6       0.00   0.0  0
 6LP  CONST_11  CAF  C4   C5   C6     180.00   0.0  0
 6LP  CONST_14  CAR  CAS  CAT  CAU      0.00   0.0  0
 6LP  CONST_15  CAR  CAQ  CAP  CAU      0.00   0.0  0
 6LP  CONST_16  CAQ  CAR  CAS  CAT      0.00   0.0  0
 6LP  CONST_17  CAQ  CAP  CAU  CAT      0.00   0.0  0
 6LP  CONST_18  CAP  CAU  CAT  CAS      0.00   0.0  0
 6LP  CONST_19  CAP  CAQ  CAR  CAS      0.00   0.0  0
 6LP  CONST_20  CAF  C4   N3   C2     180.00   0.0  0
 6LP  CONST_21  NAI  CAH  CAG  CAF      0.00   0.0  0
 6LP  CONST_22  NAI  CAD  CAE  CAF      0.00   0.0  0
 6LP  CONST_23  CAH  CAG  CAF  CAE      0.00   0.0  0
 6LP  CONST_24  CAH  NAI  CAD  CAE      0.00   0.0  0
 6LP  CONST_25  CAD  NAI  CAH  CAG      0.00   0.0  0
 6LP  CONST_26  CAD  CAE  CAF  CAG      0.00   0.0  0
 6LP  CONST_27  NAO  C2   N3   C4     180.00   0.0  0
 6LP  CONST_28  NAO  C2   N1   C6     180.00   0.0  0
 6LP  CONST_29  NAO  CAP  CAU  CAT    180.00   0.0  0
 6LP  CONST_30  CAR  CAS  CAT  CLAV   180.00   0.0  0
 6LP  CONST_31  CAP  CAU  CAT  CLAV   180.00   0.0  0
 6LP  CONST_32  NAO  CAP  CAQ  CAR    180.00   0.0  0
 6LP  CONST_33  NAC  CAD  CAE  CAF    180.00   0.0  0
 6LP  CONST_34  NAC  CAD  NAI  CAH    180.00   0.0  0
 6LP  CONST_35  H2   C6   C5   C4     180.00   0.0  0
 6LP  CONST_36  H9   CAG  CAF  C4       0.00   0.0  0
 6LP  CONST_37  H8   CAE  CAF  C4       0.00   0.0  0
 6LP  CONST_38  H1   C5   C6   N1     180.00   0.0  0
 6LP  CONST_39  H4   CAS  CAT  CAU    180.00   0.0  0
 6LP  CONST_40  H6   CAQ  CAP  CAU    180.00   0.0  0
 6LP  CONST_41  H5   CAR  CAS  CAT    180.00   0.0  0
 6LP  CONST_42  H3   CAU  CAT  CAS    180.00   0.0  0
 6LP  CONST_43  H10  CAH  CAG  CAF    180.00   0.0  0
 6LP  CONST_44  CAB  NAC  CAD  CAE      0.00   0.0  0
 6LP  CONST_45  CAB  NAC  CAD  NAI    180.00   0.0  0
 6LP  CONST_46  H11  NAC  CAD  CAE    180.00   0.0  0
 6LP  Var_01    CAP  NAO  C2   N1       0.49  30.0  2
 6LP  Var_02    C2   NAO  CAP  CAU    178.81  30.0  2
 6LP  Var_03    CAA  CAB  NAC  CAD    177.97  30.0  1
 6LP  Var_04    NAX  CAA  CAB  NAC   -179.78  30.0  3
 6LP  Var_05    H16  NAX  CAA  CAB     70.97  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
 6LP  plan-1  C4    0.020
 6LP  plan-1  C5    0.020
 6LP  plan-1  C6    0.020
 6LP  plan-1  N1    0.020
 6LP  plan-1  N3    0.020
 6LP  plan-1  C2    0.020
 6LP  plan-1  CAF   0.020
 6LP  plan-1  H1    0.020
 6LP  plan-1  H2    0.020
 6LP  plan-1  NAO   0.020
 6LP  plan-2  CAU   0.020
 6LP  plan-2  CAT   0.020
 6LP  plan-2  CLAV  0.020
 6LP  plan-2  CAS   0.020
 6LP  plan-2  CAR   0.020
 6LP  plan-2  CAQ   0.020
 6LP  plan-2  CAP   0.020
 6LP  plan-2  H3    0.020
 6LP  plan-2  H4    0.020
 6LP  plan-2  H5    0.020
 6LP  plan-2  H6    0.020
 6LP  plan-2  NAO   0.020
 6LP  plan-3  C4    0.020
 6LP  plan-3  CAF   0.020
 6LP  plan-3  CAE   0.020
 6LP  plan-3  CAG   0.020
 6LP  plan-3  CAH   0.020
 6LP  plan-3  NAI   0.020
 6LP  plan-3  CAD   0.020
 6LP  plan-3  NAC   0.020
 6LP  plan-3  H8    0.020
 6LP  plan-3  H9    0.020
 6LP  plan-3  H10   0.020
 6LP  plan-4  CAD   0.020
 6LP  plan-4  NAC   0.020
 6LP  plan-4  CAB   0.020
 6LP  plan-4  H11   0.020

