# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 11:23:54 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 6-chloro-N~4~,N~4~-bis[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Cl)cc(n1)N(Cc2cccnc2)Cc3cccnc3
#
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
 7KO  7KO  6-chloro-N~4~,N~4~-bis[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine  ligand  38  23  .  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_7KO
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
 7KO  C5   C   CR16  0  -0.387   1.3002  -0.9905   0.6254
 7KO  C6   C   CR6   0   0.189   1.7792  -2.2759   0.5661
 7KO  N1   N   N     0  -0.476   1.3187  -3.2387  -0.1963
 7KO  C2   C   CR6   0   0.562   0.2881  -2.8843  -0.9786
 7KO  N3   N   N     0  -0.531  -0.2774  -1.6821  -1.0242
 7KO  C4   C   CR6   0   0.592   0.2071  -0.7302  -0.2309
 7KO  CAK  C   CR16  0  -0.175   1.7655   3.2607   1.0971
 7KO  CAL  C   CR16  0  -0.317   2.8701   3.9948   0.7032
 7KO  CAQ  C   CR16  0  -0.072   3.3996   3.7665  -0.5596
 7KO  NAP  N   N     0  -0.399   2.8956   2.8762  -1.4025
 7KO  CAO  C   CR16  0  -0.090   1.8345   2.1760  -1.0141
 7KO  CAJ  C   CR6   0   0.000   1.2216   2.3244   0.2238
 7KO  CAI  C   CH2   0  -0.394   0.0019   1.5354   0.6353
 7KO  NAH  N   NT    0  -0.484  -0.3783   0.4878  -0.2799
 7KO  NAA  N   NH2   0  -0.821  -0.2331  -3.8414  -1.7622
 7KO  CL6  CL  CL    0  -0.109   3.1250  -2.6967   1.5783
 7KO  CAN  C   CH2   0  -0.437  -1.4431   0.7917  -1.2236
 7KO  CAS  C   CR6   0   0.049  -2.8100   0.7006  -0.6003
 7KO  CAT  C   CR16  0  -0.181  -3.3879  -0.5231  -0.2731
 7KO  CAW  C   CR16  0  -0.318  -4.6393  -0.5396   0.3176
 7KO  CAV  C   CR16  0  -0.068  -5.2736   0.6708   0.5659
 7KO  NAU  N   N     0  -0.401  -4.7404   1.8448   0.2560
 7KO  CAR  C   CR16  0  -0.108  -3.5401   1.8476  -0.3132
 7KO  H1   H   HCR6  0   0.286   1.7557  -0.2535   1.2657
 7KO  H3   H   HCR6  0   0.273   3.3170   4.7295   1.3585
 7KO  H4   H   HCR6  0   0.265   4.2646   4.3246  -0.9004
 7KO  H5   H   HCR6  0   0.260   1.4535   1.4567  -1.7315
 7KO  H6   H   HCH2  0   0.282   0.1432   1.1307   1.6403
 7KO  H7   H   HCH2  0   0.298  -0.8419   2.2234   0.7298
 7KO  H8   H   HNH2  0   0.400   0.2502  -4.7165  -1.8626
 7KO  H9   H   HNH2  0   0.400  -0.9008  -3.5903  -2.4698
 7KO  H10  H   HCH2  0   0.280  -1.2780   1.8029  -1.6024
 7KO  H11  H   HCH2  0   0.290  -1.3685   0.1152  -2.0716
 7KO  H12  H   HCR6  0   0.276  -2.8657  -1.4469  -0.4871
 7KO  H13  H   HCR6  0   0.272  -5.1212  -1.4714   0.5803
 7KO  H14  H   HCR6  0   0.265  -6.2530   0.6889   1.0313
 7KO  H15  H   HCR6  0   0.260  -3.1305   2.8221  -0.5646
 7KO  H2   H   HCR6  0   0.271   1.3299   3.4130   2.0778

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
 7KO  CL6  C6   single    1.736  0.020  1.736
 7KO  CAL  CAK  aromatic  1.384  0.020  1.384
 7KO  CAL  CAQ  aromatic  1.388  0.020  1.388
 7KO  CAK  CAJ  aromatic  1.391  0.020  1.391
 7KO  CAQ  NAP  aromatic  1.326  0.020  1.326
 7KO  C6   C5   aromatic  1.373  0.020  1.373
 7KO  C6   N1   aromatic  1.312  0.020  1.312
 7KO  C5   C4   aromatic  1.413  0.020  1.413
 7KO  N1   C2   aromatic  1.341  0.020  1.341
 7KO  CAJ  CAI  single    1.510  0.020  1.510
 7KO  CAJ  CAO  aromatic  1.389  0.020  1.389
 7KO  NAP  CAO  aromatic  1.329  0.020  1.329
 7KO  CAI  NAH  single    1.442  0.020  1.442
 7KO  C4   NAH  single    1.352  0.020  1.352
 7KO  C4   N3   aromatic  1.330  0.020  1.330
 7KO  C2   N3   aromatic  1.329  0.020  1.329
 7KO  C2   NAA  single    1.342  0.020  1.342
 7KO  NAH  CAN  single    1.455  0.020  1.455
 7KO  CAN  CAS  single    1.505  0.020  1.505
 7KO  CAT  CAS  aromatic  1.392  0.020  1.392
 7KO  CAT  CAW  aromatic  1.384  0.020  1.384
 7KO  CAS  CAR  aromatic  1.390  0.020  1.390
 7KO  CAW  CAV  aromatic  1.389  0.020  1.389
 7KO  CAR  NAU  aromatic  1.329  0.020  1.329
 7KO  CAV  NAU  aromatic  1.326  0.020  1.326
 7KO  C5   H1   single    0.930  0.020  1.080
 7KO  CAK  H2   single    0.930  0.020  1.080
 7KO  CAL  H3   single    0.930  0.020  1.080
 7KO  CAQ  H4   single    0.930  0.020  1.080
 7KO  CAO  H5   single    0.930  0.020  1.080
 7KO  CAI  H6   single    0.970  0.020  1.090
 7KO  CAI  H7   single    0.970  0.020  1.090
 7KO  NAA  H8   single    0.890  0.020  1.040
 7KO  NAA  H9   single    0.890  0.020  1.040
 7KO  CAN  H10  single    0.970  0.020  1.090
 7KO  CAN  H11  single    0.970  0.020  1.090
 7KO  CAT  H12  single    0.930  0.020  1.080
 7KO  CAW  H13  single    0.930  0.020  1.080
 7KO  CAV  H14  single    0.930  0.020  1.080
 7KO  CAR  H15  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
 7KO  H1   C5   C4   124.15  3.000
 7KO  H1   C5   C6   121.24  3.000
 7KO  C4   C5   C6   114.59  3.000
 7KO  CL6  C6   N1   115.68  3.000
 7KO  N1   C6   C5   126.15  3.000
 7KO  CL6  C6   C5   118.18  3.000
 7KO  C2   N1   C6   114.51  3.000
 7KO  NAA  C2   N3   117.36  3.000
 7KO  NAA  C2   N1   116.77  3.000
 7KO  N3   C2   N1   125.85  3.000
 7KO  C4   N3   C2   118.14  3.000
 7KO  NAH  C4   N3   117.72  3.000
 7KO  N3   C4   C5   120.76  3.000
 7KO  NAH  C4   C5   121.52  3.000
 7KO  H2   CAK  CAJ  120.36  3.000
 7KO  H2   CAK  CAL  120.26  3.000
 7KO  CAJ  CAK  CAL  119.38  3.000
 7KO  H3   CAL  CAQ  120.36  3.000
 7KO  H3   CAL  CAK  121.20  3.000
 7KO  CAQ  CAL  CAK  118.44  3.000
 7KO  H4   CAQ  NAP  116.69  3.000
 7KO  H4   CAQ  CAL  120.36  3.000
 7KO  NAP  CAQ  CAL  122.95  3.000
 7KO  CAO  NAP  CAQ  118.13  3.000
 7KO  H5   CAO  CAJ  120.34  3.000
 7KO  H5   CAO  NAP  115.86  3.000
 7KO  CAJ  CAO  NAP  123.80  3.000
 7KO  CAI  CAJ  CAO  122.91  3.000
 7KO  CAO  CAJ  CAK  117.31  3.000
 7KO  CAI  CAJ  CAK  119.77  3.000
 7KO  H7   CAI  H6   104.69  3.000
 7KO  H7   CAI  NAH  107.98  3.000
 7KO  H6   CAI  NAH  110.41  3.000
 7KO  H7   CAI  CAJ  108.56  3.000
 7KO  H6   CAI  CAJ  109.86  3.000
 7KO  NAH  CAI  CAJ  114.81  3.000
 7KO  CAN  NAH  CAI  116.93  3.000
 7KO  CAN  NAH  C4   121.90  3.000
 7KO  CAI  NAH  C4   121.14  3.000
 7KO  H9   NAA  H8   117.84  3.000
 7KO  H9   NAA  C2   119.41  3.000
 7KO  H8   NAA  C2   119.51  3.000
 7KO  H11  CAN  H10  107.16  3.000
 7KO  H11  CAN  CAS  110.34  3.000
 7KO  H10  CAN  CAS  109.69  3.000
 7KO  H11  CAN  NAH  109.01  3.000
 7KO  H10  CAN  NAH  107.92  3.000
 7KO  CAS  CAN  NAH  112.55  3.000
 7KO  CAR  CAS  CAT  117.31  3.000
 7KO  CAR  CAS  CAN  120.84  3.000
 7KO  CAT  CAS  CAN  121.84  3.000
 7KO  H12  CAT  CAW  120.69  3.000
 7KO  H12  CAT  CAS  120.22  3.000
 7KO  CAW  CAT  CAS  119.09  3.000
 7KO  H13  CAW  CAV  120.26  3.000
 7KO  H13  CAW  CAT  121.13  3.000
 7KO  CAV  CAW  CAT  118.61  3.000
 7KO  H14  CAV  NAU  116.65  3.000
 7KO  H14  CAV  CAW  120.25  3.000
 7KO  NAU  CAV  CAW  123.10  3.000
 7KO  CAR  NAU  CAV  117.73  3.000
 7KO  H15  CAR  NAU  116.21  3.000
 7KO  H15  CAR  CAS  119.63  3.000
 7KO  NAU  CAR  CAS  124.16  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
 7KO  CONST_01  C2   N1   C6   C5      0.00   0.0  0
 7KO  CONST_02  C2   N3   C4   C5      0.00   0.0  0
 7KO  CONST_03  N3   C4   C5   C6      0.00   0.0  0
 7KO  CONST_04  N3   C2   N1   C6      0.00   0.0  0
 7KO  CONST_05  C4   C5   C6   N1      0.00   0.0  0
 7KO  CONST_06  C4   N3   C2   N1      0.00   0.0  0
 7KO  CONST_07  NAP  CAQ  CAL  CAK     0.00   0.0  0
 7KO  CONST_08  NAP  CAO  CAJ  CAK     0.00   0.0  0
 7KO  CONST_09  CAO  CAJ  CAK  CAL     0.00   0.0  0
 7KO  CONST_10  CAO  NAP  CAQ  CAL     0.00   0.0  0
 7KO  CONST_11  CAJ  CAK  CAL  CAQ     0.00   0.0  0
 7KO  CONST_12  CAJ  CAO  NAP  CAQ     0.00   0.0  0
 7KO  CONST_13  CAV  CAW  CAT  CAS     0.00   0.0  0
 7KO  CONST_14  CAV  NAU  CAR  CAS     0.00   0.0  0
 7KO  CONST_15  NAU  CAR  CAS  CAT     0.00   0.0  0
 7KO  CONST_16  NAU  CAV  CAW  CAT     0.00   0.0  0
 7KO  CONST_17  CAR  CAS  CAT  CAW     0.00   0.0  0
 7KO  CONST_18  CAR  NAU  CAV  CAW     0.00   0.0  0
 7KO  CONST_19  NAH  C4   C5   C6    180.00   0.0  0
 7KO  CONST_20  NAA  C2   N1   C6    180.00   0.0  0
 7KO  CONST_21  CL6  C6   N1   C2    180.00   0.0  0
 7KO  CONST_22  NAH  C4   N3   C2    180.00   0.0  0
 7KO  CONST_23  CL6  C6   C5   C4    180.00   0.0  0
 7KO  CONST_24  NAA  C2   N3   C4    180.00   0.0  0
 7KO  CONST_25  CAI  CAJ  CAK  CAL   180.00   0.0  0
 7KO  CONST_26  CAI  CAJ  CAO  NAP   180.00   0.0  0
 7KO  CONST_27  CAW  CAT  CAS  CAN   180.00   0.0  0
 7KO  CONST_28  NAU  CAR  CAS  CAN   180.00   0.0  0
 7KO  CONST_29  H1   C5   C6   N1    180.00   0.0  0
 7KO  CONST_30  H4   CAQ  CAL  CAK   180.00   0.0  0
 7KO  CONST_31  H5   CAO  CAJ  CAK   180.00   0.0  0
 7KO  CONST_32  H2   CAK  CAL  CAQ   180.00   0.0  0
 7KO  CONST_33  H3   CAL  CAQ  NAP   180.00   0.0  0
 7KO  CONST_34  H13  CAW  CAT  CAS   180.00   0.0  0
 7KO  CONST_35  H15  CAR  CAS  CAT   180.00   0.0  0
 7KO  CONST_36  H14  CAV  CAW  CAT   180.00   0.0  0
 7KO  CONST_37  H12  CAT  CAW  CAV   180.00   0.0  0
 7KO  CONST_38  CAI  NAH  C4   C5      0.00   0.0  0
 7KO  CONST_39  CAN  NAH  C4   C5    180.00   0.0  0
 7KO  CONST_40  CAI  NAH  C4   N3    180.00   0.0  0
 7KO  CONST_41  CAN  NAH  C4   N3      0.00   0.0  0
 7KO  CONST_42  H8   NAA  C2   N1      0.00   0.0  0
 7KO  CONST_43  H9   NAA  C2   N1    180.00   0.0  0
 7KO  Var_01    CAJ  CAI  NAH  C4     83.63  30.0  1
 7KO  Var_02    CAS  CAN  NAH  C4     98.88  30.0  3
 7KO  Var_03    NAH  CAI  CAJ  CAK  -173.03  30.0  2
 7KO  Var_04    CAT  CAS  CAN  NAH   -72.62  30.0  2

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
 7KO  plan-1  C5   0.020
 7KO  plan-1  C6   0.020
 7KO  plan-1  N1   0.020
 7KO  plan-1  C2   0.020
 7KO  plan-1  N3   0.020
 7KO  plan-1  C4   0.020
 7KO  plan-1  NAH  0.020
 7KO  plan-1  NAA  0.020
 7KO  plan-1  CL6  0.020
 7KO  plan-1  H1   0.020
 7KO  plan-2  CAK  0.020
 7KO  plan-2  CAL  0.020
 7KO  plan-2  CAQ  0.020
 7KO  plan-2  NAP  0.020
 7KO  plan-2  CAO  0.020
 7KO  plan-2  CAJ  0.020
 7KO  plan-2  CAI  0.020
 7KO  plan-2  H3   0.020
 7KO  plan-2  H4   0.020
 7KO  plan-2  H5   0.020
 7KO  plan-2  H2   0.020
 7KO  plan-3  CAN  0.020
 7KO  plan-3  CAS  0.020
 7KO  plan-3  CAT  0.020
 7KO  plan-3  CAW  0.020
 7KO  plan-3  CAV  0.020
 7KO  plan-3  NAU  0.020
 7KO  plan-3  CAR  0.020
 7KO  plan-3  H12  0.020
 7KO  plan-3  H13  0.020
 7KO  plan-3  H14  0.020
 7KO  plan-3  H15  0.020
 7KO  plan-4  C4   0.020
 7KO  plan-4  CAI  0.020
 7KO  plan-4  NAH  0.020
 7KO  plan-4  CAN  0.020
 7KO  plan-5  C2   0.020
 7KO  plan-5  NAA  0.020
 7KO  plan-5  H8   0.020
 7KO  plan-5  H9   0.020

