# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:00:08 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 6-(2,6-dibromophenyl)pyrido[2,3-d]pyrimidine-2,7-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc2cc(c(N)nc2n1)c3c(Br)cccc3Br
#
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
 LZJ  LZJ  6-(2,6-dibromophenyl)pyrido[2,3-d]pyrimidine-2,7-diamine  ligand  29  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LZJ
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
 LZJ  BR2   BR  BR    0  -0.012  6.6896  -21.6335  26.8400
 LZJ  C18   C   CR6   0  -0.161  5.9415  -20.3031  25.7339
 LZJ  C17   C   CR16  0  -0.219  6.3859  -18.9973  25.8741
 LZJ  C16   C   CR16  0  -0.257  5.8551  -18.0146  25.0540
 LZJ  C15   C   CR16  0  -0.219  4.8972  -18.3281  24.1032
 LZJ  C14   C   CR6   0  -0.161  4.4699  -19.6417  23.9863
 LZJ  BR1   BR  BR    0  -0.012  3.1798  -20.0568  22.6763
 LZJ  C12   C   CR6   0   0.171  4.9695  -20.6633  24.7977
 LZJ  C9    C   CR6   0  -0.140  4.4965  -22.0565  24.6673
 LZJ  C10   C   CR16  0  -0.181  3.4469  -22.5270  25.3922
 LZJ  C5    C   CR66  0  -0.123  3.0309  -23.8618  25.2290
 LZJ  C6    C   CR16  0  -0.041  1.9672  -24.4634  25.9138
 LZJ  N1    N   N     0  -0.460  1.6132  -25.7063  25.7315
 LZJ  C8    C   CR6   0   0.468  5.1423  -22.9620  23.7550
 LZJ  N13   N   NH2   0  -0.819  6.1751  -22.5296  23.0212
 LZJ  N7    N   N     0  -0.488  4.7625  -24.2172  23.5911
 LZJ  C4    C   CR66  0   0.379  3.7264  -24.6782  24.3042
 LZJ  N3    N   N     0  -0.485  3.3632  -25.9536  24.1132
 LZJ  C2    C   CR6   0   0.549  2.3419  -26.4072  24.8212
 LZJ  N11   N   NH2   0  -0.815  1.9719  -27.6827  24.6485
 LZJ  H17   H   HCR6  0   0.290  7.1361  -18.7423  26.6099
 LZJ  H16   H   HCR6  0   0.285  6.1954  -16.9930  25.1539
 LZJ  H15   H   HCR6  0   0.290  4.4952  -17.5543  23.4637
 LZJ  H10   H   HCR6  0   0.273  2.9308  -21.8799  26.0923
 LZJ  H6    H   HCR6  0   0.274  1.3964  -23.8845  26.6350
 LZJ  H131  H   HNH2  0   0.402  6.6446  -23.1666  22.4009
 LZJ  H132  H   HNH2  0   0.410  6.5534  -21.6036  23.1126
 LZJ  H111  H   HNH2  0   0.401  1.1770  -28.0522  25.1380
 LZJ  H112  H   HNH2  0   0.400  2.4256  -28.2562  23.9602

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
 LZJ  BR2  C18   single    1.885  0.020  1.885
 LZJ  C18  C17   aromatic  1.386  0.020  1.386
 LZJ  C18  C12   aromatic  1.397  0.020  1.397
 LZJ  C17  C16   aromatic  1.386  0.020  1.386
 LZJ  C16  C15   aromatic  1.386  0.020  1.386
 LZJ  C15  C14   aromatic  1.386  0.020  1.386
 LZJ  C14  BR1   single    1.885  0.020  1.885
 LZJ  C14  C12   aromatic  1.397  0.020  1.397
 LZJ  C12  C9    single    1.477  0.020  1.477
 LZJ  C9   C10   aromatic  1.360  0.020  1.360
 LZJ  C9   C8    aromatic  1.438  0.020  1.438
 LZJ  C10  C5    aromatic  1.408  0.020  1.408
 LZJ  C5   C6    aromatic  1.401  0.020  1.401
 LZJ  C5   C4    aromatic  1.416  0.020  1.416
 LZJ  C6   N1    aromatic  1.305  0.020  1.305
 LZJ  N1   C2    aromatic  1.360  0.020  1.360
 LZJ  C8   N13   single    1.339  0.020  1.339
 LZJ  C8   N7    aromatic  1.322  0.020  1.322
 LZJ  N7   C4    aromatic  1.340  0.020  1.340
 LZJ  C4   N3    aromatic  1.340  0.020  1.340
 LZJ  N3   C2    aromatic  1.323  0.020  1.323
 LZJ  C2   N11   single    1.339  0.020  1.339
 LZJ  C17  H17   single    0.930  0.020  1.080
 LZJ  C16  H16   single    0.930  0.020  1.080
 LZJ  C15  H15   single    0.930  0.020  1.080
 LZJ  C10  H10   single    0.930  0.020  1.080
 LZJ  C6   H6    single    0.930  0.020  1.080
 LZJ  N13  H131  single    0.860  0.020  1.020
 LZJ  N13  H132  single    0.860  0.020  1.020
 LZJ  N11  H111  single    0.860  0.020  1.020
 LZJ  N11  H112  single    0.860  0.020  1.020

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
 LZJ  C12   C18  C17   122.26  3.000
 LZJ  C12   C18  BR2   119.17  3.000
 LZJ  C17   C18  BR2   118.57  3.000
 LZJ  H17   C17  C16   120.08  3.000
 LZJ  H17   C17  C18   120.89  3.000
 LZJ  C16   C17  C18   119.03  3.000
 LZJ  H16   C16  C15   119.65  3.000
 LZJ  H16   C16  C17   119.66  3.000
 LZJ  C15   C16  C17   120.69  3.000
 LZJ  H15   C15  C14   120.91  3.000
 LZJ  H15   C15  C16   120.06  3.000
 LZJ  C14   C15  C16   119.03  3.000
 LZJ  C12   C14  BR1   119.17  3.000
 LZJ  C12   C14  C15   122.26  3.000
 LZJ  BR1   C14  C15   118.57  3.000
 LZJ  C9    C12  C14   121.60  3.000
 LZJ  C9    C12  C18   121.69  3.000
 LZJ  C14   C12  C18   116.71  3.000
 LZJ  C8    C9   C10   117.84  3.000
 LZJ  C8    C9   C12   120.39  3.000
 LZJ  C10   C9   C12   121.77  3.000
 LZJ  H10   C10  C5    120.01  3.000
 LZJ  H10   C10  C9    120.36  3.000
 LZJ  C5    C10  C9    119.63  3.000
 LZJ  C4    C5   C6    116.39  3.000
 LZJ  C4    C5   C10   118.51  3.000
 LZJ  C6    C5   C10   125.10  3.000
 LZJ  H6    C6   N1    117.23  3.000
 LZJ  H6    C6   C5    119.63  3.000
 LZJ  N1    C6   C5    123.14  3.000
 LZJ  C2    N1   C6    116.03  3.000
 LZJ  N7    C8   N13   117.42  3.000
 LZJ  N7    C8   C9    123.20  3.000
 LZJ  N13   C8   C9    119.38  3.000
 LZJ  H132  N13  H131  117.67  3.000
 LZJ  H132  N13  C8    122.58  3.000
 LZJ  H131  N13  C8    119.58  3.000
 LZJ  C4    N7   C8    118.89  3.000
 LZJ  N3    C4   N7    117.48  3.000
 LZJ  N3    C4   C5    120.58  3.000
 LZJ  N7    C4   C5    121.94  3.000
 LZJ  C2    N3   C4    117.35  3.000
 LZJ  N11   C2   N3    118.09  3.000
 LZJ  N11   C2   N1    115.40  3.000
 LZJ  N3    C2   N1    126.51  3.000
 LZJ  H112  N11  H111  118.80  3.000
 LZJ  H112  N11  C2    120.49  3.000
 LZJ  H111  N11  C2    120.42  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
 LZJ  CONST_01  C15   C16  C17  C18    0.00  0.0  0
 LZJ  CONST_02  C15   C14  C12  C18    0.00  0.0  0
 LZJ  CONST_05  C14   C12  C18  C17    0.00  0.0  0
 LZJ  CONST_06  C9    C12  C18  C17  180.00  0.0  0
 LZJ  CONST_07  C14   C15  C16  C17    0.00  0.0  0
 LZJ  CONST_08  C12   C18  C17  C16    0.00  0.0  0
 LZJ  CONST_09  C12   C14  C15  C16    0.00  0.0  0
 LZJ  CONST_10  C9    C12  C14  C15  180.00  0.0  0
 LZJ  CONST_13  C5    C10  C9   C12  180.00  0.0  0
 LZJ  CONST_14  N7    C8   C9   C12  180.00  0.0  0
 LZJ  CONST_15  C6    C5   C10  C9   180.00  0.0  0
 LZJ  CONST_16  C4    C5   C10  C9     0.00  0.0  0
 LZJ  CONST_17  C4    N7   C8   C9     0.00  0.0  0
 LZJ  CONST_18  N7    C8   C9   C10    0.00  0.0  0
 LZJ  CONST_19  N1    C6   C5   C10  180.00  0.0  0
 LZJ  CONST_20  N7    C4   C5   C10    0.00  0.0  0
 LZJ  CONST_21  N3    C4   C5   C10  180.00  0.0  0
 LZJ  CONST_22  C8    C9   C10  C5     0.00  0.0  0
 LZJ  CONST_23  C2    N1   C6   C5     0.00  0.0  0
 LZJ  CONST_24  C8    N7   C4   C5     0.00  0.0  0
 LZJ  CONST_25  C2    N3   C4   C5     0.00  0.0  0
 LZJ  CONST_26  N7    C4   C5   C6   180.00  0.0  0
 LZJ  CONST_27  N3    C4   C5   C6     0.00  0.0  0
 LZJ  CONST_28  N3    C2   N1   C6     0.00  0.0  0
 LZJ  CONST_29  C4    C5   C6   N1     0.00  0.0  0
 LZJ  CONST_30  C4    N3   C2   N1     0.00  0.0  0
 LZJ  CONST_31  N3    C4   N7   C8   180.00  0.0  0
 LZJ  CONST_32  C2    N3   C4   N7   180.00  0.0  0
 LZJ  CONST_33  C16   C17  C18  BR2  180.00  0.0  0
 LZJ  CONST_34  C14   C12  C18  BR2  180.00  0.0  0
 LZJ  CONST_35  C9    C12  C18  BR2    0.00  0.0  0
 LZJ  CONST_36  BR1   C14  C12  C18  180.00  0.0  0
 LZJ  CONST_37  BR1   C14  C15  C16  180.00  0.0  0
 LZJ  CONST_38  C9    C12  C14  BR1    0.00  0.0  0
 LZJ  CONST_39  N13   C8   C9   C12    0.00  0.0  0
 LZJ  CONST_40  N13   C8   C9   C10  180.00  0.0  0
 LZJ  CONST_41  N11   C2   N1   C6   180.00  0.0  0
 LZJ  CONST_42  C4    N7   C8   N13  180.00  0.0  0
 LZJ  CONST_43  N11   C2   N3   C4   180.00  0.0  0
 LZJ  CONST_44  H16   C16  C17  C18  180.00  0.0  0
 LZJ  CONST_45  H15   C15  C16  C17  180.00  0.0  0
 LZJ  CONST_46  H17   C17  C16  C15  180.00  0.0  0
 LZJ  CONST_47  H10   C10  C9   C12    0.00  0.0  0
 LZJ  CONST_48  H6    C6   C5   C10    0.00  0.0  0
 LZJ  CONST_49  H131  N13  C8   C9   180.00  0.0  0
 LZJ  CONST_50  H132  N13  C8   C9     0.00  0.0  0
 LZJ  CONST_51  H111  N11  C2   N1     0.00  0.0  0
 LZJ  CONST_52  H112  N11  C2   N1   180.00  0.0  0

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
 LZJ  plan-1  BR2   0.020
 LZJ  plan-1  C18   0.020
 LZJ  plan-1  C17   0.020
 LZJ  plan-1  C16   0.020
 LZJ  plan-1  C15   0.020
 LZJ  plan-1  C14   0.020
 LZJ  plan-1  BR1   0.020
 LZJ  plan-1  C12   0.020
 LZJ  plan-1  C9    0.020
 LZJ  plan-1  H17   0.020
 LZJ  plan-1  H16   0.020
 LZJ  plan-1  H15   0.020
 LZJ  plan-2  C12   0.020
 LZJ  plan-2  C9    0.020
 LZJ  plan-2  C10   0.020
 LZJ  plan-2  C5    0.020
 LZJ  plan-2  C6    0.020
 LZJ  plan-2  N1    0.020
 LZJ  plan-2  C8    0.020
 LZJ  plan-2  N13   0.020
 LZJ  plan-2  N7    0.020
 LZJ  plan-2  C4    0.020
 LZJ  plan-2  N3    0.020
 LZJ  plan-2  C2    0.020
 LZJ  plan-2  N11   0.020
 LZJ  plan-2  H10   0.020
 LZJ  plan-2  H6    0.020
 LZJ  plan-3  C8    0.020
 LZJ  plan-3  N13   0.020
 LZJ  plan-3  H131  0.020
 LZJ  plan-3  H132  0.020
 LZJ  plan-4  C2    0.020
 LZJ  plan-4  N11   0.020
 LZJ  plan-4  H111  0.020
 LZJ  plan-4  H112  0.020

