# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:03:03 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 4-pyridin-3-ylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2cccnc2
#
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
 XDK  XDK  4-pyridin-3-ylpyrimidin-2-amine  ligand  21  13  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XDK
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
 XDK  C7A   C  CR16  0  -0.314  -2.9173   1.4072  -0.2492
 XDK  C3A   C  CR16  0  -0.062  -3.7376   0.3331   0.0647
 XDK  N2A   N  N     0  -0.399  -3.2706  -0.8771   0.3492
 XDK  C1A   C  CR16  0  -0.096  -1.9586  -1.0610   0.3166
 XDK  C5A   C  CR6   0  -0.043  -1.0416  -0.0584   0.0044
 XDK  C4    C  CR6   0   0.289   0.4113  -0.3177  -0.0242
 XDK  N3    N  N     0  -0.488   1.2021   0.7380   0.1117
 XDK  C5    C  CR16  0  -0.399   0.9321  -1.5969  -0.2023
 XDK  C6    C  CR16  0  -0.018   2.3135  -1.6949  -0.2120
 XDK  N1    N  N     0  -0.455   3.1197  -0.6578  -0.0724
 XDK  C2    C  CR6   0   0.551   2.5216   0.5321   0.0782
 XDK  N7    N  NH2   0  -0.826   3.3145   1.6080   0.1960
 XDK  C9    C  CR16  0  -0.164  -1.5486   1.2088  -0.2741
 XDK  H7A   H  HCR6  0   0.276  -3.3457   2.3745  -0.4715
 XDK  H3A   H  HCR6  0   0.271  -4.8144   0.4558   0.0897
 XDK  H9    H  HCR6  0   0.272  -0.8762   2.0214  -0.5140
 XDK  H1A   H  HCR6  0   0.264  -1.6153  -2.0577   0.5714
 XDK  H5    H  HCR6  0   0.268   0.3135  -2.4696  -0.3453
 XDK  H6    H  HCR6  0   0.272   2.7887  -2.6610  -0.3454
 XDK  H71N  H  HNH2  0   0.399   2.9185   2.5117   0.3819
 XDK  H72N  H  HNH2  0   0.400   4.3107   1.4971   0.2545

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
 XDK  C7A  C3A   aromatic  1.387  0.020  1.387
 XDK  C7A  C9    aromatic  1.383  0.020  1.383
 XDK  C3A  N2A   aromatic  1.328  0.020  1.328
 XDK  N2A  C1A   aromatic  1.325  0.020  1.325
 XDK  C1A  C5A   aromatic  1.394  0.020  1.394
 XDK  C5A  C4    single    1.476  0.020  1.476
 XDK  C5A  C9    aromatic  1.393  0.020  1.393
 XDK  C4   N3    aromatic  1.326  0.020  1.326
 XDK  C4   C5    aromatic  1.393  0.020  1.393
 XDK  N3   C2    aromatic  1.336  0.020  1.336
 XDK  C5   C6    aromatic  1.385  0.020  1.385
 XDK  C6   N1    aromatic  1.321  0.020  1.321
 XDK  N1   C2    aromatic  1.340  0.020  1.340
 XDK  C2   N7    single    1.342  0.020  1.342
 XDK  C7A  H7A   single    0.930  0.020  1.080
 XDK  C3A  H3A   single    0.930  0.020  1.080
 XDK  C9   H9    single    0.930  0.020  1.080
 XDK  C1A  H1A   single    0.930  0.020  1.080
 XDK  C5   H5    single    0.930  0.020  1.080
 XDK  C6   H6    single    0.930  0.020  1.080
 XDK  N7   H71N  single    0.860  0.020  1.020
 XDK  N7   H72N  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
 XDK  H7A   C7A  C9    121.12  3.000
 XDK  H7A   C7A  C3A   120.32  3.000
 XDK  C9    C7A  C3A   118.56  3.000
 XDK  H3A   C3A  N2A   116.58  3.000
 XDK  H3A   C3A  C7A   120.32  3.000
 XDK  N2A   C3A  C7A   123.09  3.000
 XDK  C1A   N2A  C3A   117.99  3.000
 XDK  H1A   C1A  C5A   120.35  3.000
 XDK  H1A   C1A  N2A   115.79  3.000
 XDK  C5A   C1A  N2A   123.84  3.000
 XDK  C9    C5A  C4    120.94  3.000
 XDK  C9    C5A  C1A   117.36  3.000
 XDK  C4    C5A  C1A   121.69  3.000
 XDK  C5    C4   N3    121.42  3.000
 XDK  C5    C4   C5A   122.14  3.000
 XDK  N3    C4   C5A   116.43  3.000
 XDK  C2    N3   C4    117.63  3.000
 XDK  H5    C5   C6    120.90  3.000
 XDK  H5    C5   C4    123.05  3.000
 XDK  C6    C5   C4    116.03  3.000
 XDK  H6    C6   N1    116.41  3.000
 XDK  H6    C6   C5    120.05  3.000
 XDK  N1    C6   C5    123.54  3.000
 XDK  C2    N1   C6    115.88  3.000
 XDK  N7    C2   N1    117.26  3.000
 XDK  N7    C2   N3    117.25  3.000
 XDK  N1    C2   N3    125.48  3.000
 XDK  H72N  N7   H71N  118.68  3.000
 XDK  H72N  N7   C2    120.19  3.000
 XDK  H71N  N7   C2    120.33  3.000
 XDK  H9    C9   C5A   120.10  3.000
 XDK  H9    C9   C7A   120.75  3.000
 XDK  C5A   C9   C7A   119.14  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
 XDK  CONST_01  C1A   N2A  C3A  C7A    0.00  0.0  0
 XDK  CONST_02  C1A   C5A  C9   C7A    0.00  0.0  0
 XDK  CONST_03  C4    C5A  C9   C7A  180.00  0.0  0
 XDK  CONST_04  C5A   C9   C7A  C3A    0.00  0.0  0
 XDK  CONST_05  C5A   C1A  N2A  C3A    0.00  0.0  0
 XDK  CONST_06  C9    C7A  C3A  N2A    0.00  0.0  0
 XDK  CONST_07  C4    C5A  C1A  N2A  180.00  0.0  0
 XDK  CONST_08  C9    C5A  C1A  N2A    0.00  0.0  0
 XDK  CONST_11  C2    N3   C4   C5A  180.00  0.0  0
 XDK  CONST_12  C6    C5   C4   C5A  180.00  0.0  0
 XDK  CONST_13  N1    C2   N3   C4     0.00  0.0  0
 XDK  CONST_14  N1    C6   C5   C4     0.00  0.0  0
 XDK  CONST_16  C6    C5   C4   N3     0.00  0.0  0
 XDK  CONST_17  C6    N1   C2   N3     0.00  0.0  0
 XDK  CONST_19  C2    N3   C4   C5     0.00  0.0  0
 XDK  CONST_20  C2    N1   C6   C5     0.00  0.0  0
 XDK  CONST_21  N7    C2   N3   C4   180.00  0.0  0
 XDK  CONST_22  N7    C2   N1   C6   180.00  0.0  0
 XDK  CONST_23  H9    C9   C7A  C3A  180.00  0.0  0
 XDK  CONST_24  H1A   C1A  N2A  C3A  180.00  0.0  0
 XDK  CONST_25  H7A   C7A  C3A  N2A  180.00  0.0  0
 XDK  CONST_26  H3A   C3A  N2A  C1A  180.00  0.0  0
 XDK  CONST_27  H5    C5   C4   C5A    0.00  0.0  0
 XDK  CONST_28  H6    C6   C5   C4   180.00  0.0  0
 XDK  CONST_29  H71N  N7   C2   N3     0.00  0.0  0
 XDK  CONST_30  H72N  N7   C2   N3   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
 XDK  plan-1  C7A   0.020
 XDK  plan-1  C3A   0.020
 XDK  plan-1  N2A   0.020
 XDK  plan-1  C1A   0.020
 XDK  plan-1  C5A   0.020
 XDK  plan-1  C4    0.020
 XDK  plan-1  C9    0.020
 XDK  plan-1  H7A   0.020
 XDK  plan-1  H3A   0.020
 XDK  plan-1  H9    0.020
 XDK  plan-1  H1A   0.020
 XDK  plan-2  C5A   0.020
 XDK  plan-2  C4    0.020
 XDK  plan-2  N3    0.020
 XDK  plan-2  C5    0.020
 XDK  plan-2  C6    0.020
 XDK  plan-2  N1    0.020
 XDK  plan-2  C2    0.020
 XDK  plan-2  N7    0.020
 XDK  plan-2  H5    0.020
 XDK  plan-2  H6    0.020
 XDK  plan-3  C2    0.020
 XDK  plan-3  N7    0.020
 XDK  plan-3  H71N  0.020
 XDK  plan-3  H72N  0.020

