# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 01:30:04 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 5-chloro-6-methyl-N-(2-phenylethyl)-2-pyridin-2-ylpyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(nc(NCCc2ccccc2)c1Cl)c3ccccn3
#
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
 HM2  HM2  5-chloro-6-methyl-N-(2-phenylethyl)-2-pyridin-2-ylpyrimidin-4-amine  ligand  40  23  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HM2
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
 HM2  N1    N   N     0  -0.405   1.6290   2.6633  -0.1802
 HM2  N2    N   N     0  -0.461   0.9795   0.0430   0.0286
 HM2  N3    N   N     0  -0.481   3.2737  -0.5092   0.0109
 HM2  N4    N   NH1   0  -0.678  -0.6515  -1.5682   0.0914
 HM2  C1    C   CR16  0  -0.085   1.9231   3.9533  -0.2375
 HM2  C2    C   CR16  0  -0.312   3.2195   4.4473  -0.1828
 HM2  C3    C   CR16  0  -0.152   4.2581   3.5377  -0.0645
 HM2  C4    C   CR16  0  -0.295   3.9602   2.1859  -0.0069
 HM2  C5    C   CR6   0   0.144   2.6257   1.7907  -0.0668
 HM2  C6    C   CR6   0   0.355   2.2655   0.3472  -0.0057
 HM2  C7    C   CR6   0   0.636   0.6459  -1.2461   0.0729
 HM2  C8    C   CR6   0   0.331   2.9794  -1.8124   0.0590
 HM2  C9    C   CR6   0  -0.247   1.6651  -2.2237   0.0890
 HM2  C10   C   CH2   0  -0.233  -1.7150  -0.5869   0.1321
 HM2  C11   C   CH2   0  -0.560  -3.0598  -1.2739  -0.0826
 HM2  C12   C   CR6   0   0.123  -4.1845  -0.2782  -0.0285
 HM2  C13   C   CR16  0  -0.303  -4.5677   0.4250  -1.1685
 HM2  C14   C   CR16  0  -0.240  -5.5827   1.3707  -1.1123
 HM2  C15   C   CR16  0  -0.271  -6.2307   1.6276   0.0893
 HM2  C16   C   CR16  0  -0.239  -5.8565   0.9331   1.2321
 HM2  C17   C   CR16  0  -0.307  -4.8401  -0.0114   1.1711
 HM2  C18   C   CH3   0  -0.737   4.1153  -2.7825   0.0748
 HM2  CL1   CL  CL    0  -0.110   1.2552  -3.9005   0.1402
 HM2  HN4   H   HNH1  0   0.400  -0.9019  -2.5351   0.2216
 HM2  H1    H   HCR6  0   0.263   1.0850   4.6350  -0.3323
 HM2  H2    H   HCR6  0   0.274   3.4013   5.5120  -0.2321
 HM2  H3    H   HCR6  0   0.275   5.2859   3.8727  -0.0174
 HM2  H4    H   HCR6  0   0.272   4.7424   1.4472   0.0838
 HM2  H101  H   HCH2  0   0.240  -1.7165  -0.0547   1.0890
 HM2  H102  H   HCH2  0   0.247  -1.5520   0.1602  -0.6461
 HM2  H111  H   HCH2  0   0.260  -3.0523  -1.7852  -1.0485
 HM2  H112  H   HCH2  0   0.258  -3.2059  -2.0382   0.6853
 HM2  H13   H   HCR6  0   0.249  -4.0709   0.2267  -2.1114
 HM2  H14   H   HCR6  0   0.254  -5.8697   1.9061  -2.0083
 HM2  H15   H   HCR6  0   0.255  -7.0248   2.3615   0.1329
 HM2  H16   H   HCR6  0   0.254  -6.3590   1.1222   2.1722
 HM2  H17   H   HCR6  0   0.248  -4.5567  -0.5534   2.0663
 HM2  H181  H   HCH3  0   0.261   4.0793  -3.4183   0.9601
 HM2  H182  H   HCH3  0   0.262   4.0791  -3.4411  -0.7942
 HM2  H183  H   HCH3  0   0.261   5.0616  -2.2478   0.0659

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
 HM2  N1   C1    aromatic  1.324  0.020  1.324
 HM2  N1   C5    aromatic  1.330  0.020  1.330
 HM2  N2   C6    aromatic  1.322  0.020  1.322
 HM2  N2   C7    aromatic  1.332  0.020  1.332
 HM2  N3   C6    aromatic  1.323  0.020  1.323
 HM2  N3   C8    aromatic  1.337  0.020  1.337
 HM2  N4   C7    single    1.337  0.020  1.337
 HM2  N4   C10   single    1.448  0.020  1.448
 HM2  N4   HN4   single    0.860  0.020  1.020
 HM2  C1   C2    aromatic  1.388  0.020  1.388
 HM2  C1   H1    single    0.930  0.020  1.080
 HM2  C2   C3    aromatic  1.386  0.020  1.386
 HM2  C2   H2    single    0.930  0.020  1.080
 HM2  C3   C4    aromatic  1.385  0.020  1.385
 HM2  C3   H3    single    0.930  0.020  1.080
 HM2  C4   C5    aromatic  1.393  0.020  1.393
 HM2  C4   H4    single    0.930  0.020  1.080
 HM2  C5   C6    single    1.489  0.020  1.489
 HM2  C7   C9    aromatic  1.412  0.020  1.412
 HM2  C8   C9    aromatic  1.378  0.020  1.378
 HM2  C8   C18   single    1.494  0.020  1.494
 HM2  C9   CL1   single    1.727  0.020  1.727
 HM2  C10  C11   single    1.525  0.020  1.525
 HM2  C10  H101  single    0.970  0.020  1.090
 HM2  C10  H102  single    0.970  0.020  1.090
 HM2  C11  C12   single    1.503  0.020  1.503
 HM2  C11  H111  single    0.970  0.020  1.090
 HM2  C11  H112  single    0.970  0.020  1.090
 HM2  C12  C13   aromatic  1.393  0.020  1.393
 HM2  C12  C17   aromatic  1.393  0.020  1.393
 HM2  C13  C14   aromatic  1.388  0.020  1.388
 HM2  C13  H13   single    0.930  0.020  1.080
 HM2  C14  C15   aromatic  1.389  0.020  1.389
 HM2  C14  H14   single    0.930  0.020  1.080
 HM2  C15  C16   aromatic  1.389  0.020  1.389
 HM2  C15  H15   single    0.930  0.020  1.080
 HM2  C16  C17   aromatic  1.389  0.020  1.389
 HM2  C16  H16   single    0.930  0.020  1.080
 HM2  C17  H17   single    0.930  0.020  1.080
 HM2  C18  H181  single    0.970  0.020  1.090
 HM2  C18  H182  single    0.970  0.020  1.090
 HM2  C18  H183  single    0.970  0.020  1.090

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
 HM2  C5    N1   C1    118.45  3.000
 HM2  C7    N2   C6    117.85  3.000
 HM2  C8    N3   C6    117.63  3.000
 HM2  HN4   N4   C10   117.68  3.000
 HM2  HN4   N4   C7    118.31  3.000
 HM2  C10   N4   C7    123.37  3.000
 HM2  H1    C1   C2    120.09  3.000
 HM2  H1    C1   N1    116.38  3.000
 HM2  C2    C1   N1    123.52  3.000
 HM2  H2    C2   C3    121.62  3.000
 HM2  H2    C2   C1    120.37  3.000
 HM2  C3    C2   C1    118.01  3.000
 HM2  H3    C3   C4    120.30  3.000
 HM2  H3    C3   C2    120.82  3.000
 HM2  C4    C3   C2    118.87  3.000
 HM2  H4    C4   C5    120.23  3.000
 HM2  H4    C4   C3    121.01  3.000
 HM2  C5    C4   C3    118.75  3.000
 HM2  C6    C5   C4    120.33  3.000
 HM2  C6    C5   N1    117.28  3.000
 HM2  C4    C5   N1    122.38  3.000
 HM2  C5    C6   N3    116.34  3.000
 HM2  C5    C6   N2    117.35  3.000
 HM2  N3    C6   N2    126.31  3.000
 HM2  C9    C7   N4    122.24  3.000
 HM2  C9    C7   N2    119.30  3.000
 HM2  N4    C7   N2    118.46  3.000
 HM2  C18   C8   C9    122.10  3.000
 HM2  C18   C8   N3    117.78  3.000
 HM2  C9    C8   N3    120.12  3.000
 HM2  CL1   C9   C8    121.13  3.000
 HM2  CL1   C9   C7    120.08  3.000
 HM2  C8    C9   C7    118.79  3.000
 HM2  H102  C10  H101  106.90  3.000
 HM2  H102  C10  C11   109.86  3.000
 HM2  H101  C10  C11   109.92  3.000
 HM2  H102  C10  N4    109.53  3.000
 HM2  H101  C10  N4    110.80  3.000
 HM2  C11   C10  N4    109.78  3.000
 HM2  H112  C11  H111  107.14  3.000
 HM2  H112  C11  C12   109.75  3.000
 HM2  H111  C11  C12   110.29  3.000
 HM2  H112  C11  C10   109.50  3.000
 HM2  H111  C11  C10   109.21  3.000
 HM2  C12   C11  C10   110.87  3.000
 HM2  C17   C12  C13   118.59  3.000
 HM2  C17   C12  C11   120.67  3.000
 HM2  C13   C12  C11   120.71  3.000
 HM2  H13   C13  C14   119.65  3.000
 HM2  H13   C13  C12   119.56  3.000
 HM2  C14   C13  C12   120.78  3.000
 HM2  H14   C14  C15   120.05  3.000
 HM2  H14   C14  C13   119.82  3.000
 HM2  C15   C14  C13   120.13  3.000
 HM2  H15   C15  C16   120.25  3.000
 HM2  H15   C15  C14   120.17  3.000
 HM2  C16   C15  C14   119.58  3.000
 HM2  H16   C16  C17   119.78  3.000
 HM2  H16   C16  C15   120.14  3.000
 HM2  C17   C16  C15   120.08  3.000
 HM2  H17   C17  C16   119.67  3.000
 HM2  H17   C17  C12   119.49  3.000
 HM2  C16   C17  C12   120.84  3.000
 HM2  H183  C18  H182  108.62  3.000
 HM2  H183  C18  H181  108.79  3.000
 HM2  H182  C18  H181  107.08  3.000
 HM2  H183  C18  C8    110.02  3.000
 HM2  H182  C18  C8    111.00  3.000
 HM2  H181  C18  C8    111.23  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
 HM2  CONST_01  C3    C2   C1   N1     0.00   0.0  0
 HM2  CONST_02  C3    C4   C5   N1     0.00   0.0  0
 HM2  CONST_03  N2    C6   C5   N1     0.00   0.0  0
 HM2  CONST_04  N3    C6   C5   N1   180.00   0.0  0
 HM2  CONST_05  C8    N3   C6   N2     0.00   0.0  0
 HM2  CONST_06  C4    C5   C6   N2   180.00   0.0  0
 HM2  CONST_07  C8    C9   C7   N2     0.00   0.0  0
 HM2  CONST_08  C7    N2   C6   N3     0.00   0.0  0
 HM2  CONST_09  C4    C5   C6   N3     0.00   0.0  0
 HM2  CONST_10  C7    C9   C8   N3     0.00   0.0  0
 HM2  CONST_11  C4    C5   N1   C1     0.00   0.0  0
 HM2  CONST_12  C6    C5   N1   C1   180.00   0.0  0
 HM2  CONST_13  C4    C3   C2   C1     0.00   0.0  0
 HM2  CONST_14  C5    N1   C1   C2     0.00   0.0  0
 HM2  CONST_15  C5    C4   C3   C2     0.00   0.0  0
 HM2  CONST_16  C6    C5   C4   C3   180.00   0.0  0
 HM2  CONST_17  C7    N2   C6   C5   180.00   0.0  0
 HM2  CONST_18  C8    N3   C6   C5   180.00   0.0  0
 HM2  CONST_19  C9    C7   N2   C6     0.00   0.0  0
 HM2  CONST_20  C9    C8   N3   C6     0.00   0.0  0
 HM2  CONST_21  C15   C14  C13  C12    0.00   0.0  0
 HM2  CONST_22  C15   C16  C17  C12    0.00   0.0  0
 HM2  CONST_23  C16   C17  C12  C13    0.00   0.0  0
 HM2  CONST_24  C16   C15  C14  C13    0.00   0.0  0
 HM2  CONST_25  C17   C12  C13  C14    0.00   0.0  0
 HM2  CONST_26  C17   C16  C15  C14    0.00   0.0  0
 HM2  CONST_27  CL1   C9   C7   N2   180.00   0.0  0
 HM2  CONST_28  CL1   C9   C8   N3   180.00   0.0  0
 HM2  CONST_29  C6    N2   C7   N4   180.00   0.0  0
 HM2  CONST_30  C8    C9   C7   N4   180.00   0.0  0
 HM2  CONST_31  C18   C8   N3   C6   180.00   0.0  0
 HM2  CONST_32  C18   C8   C9   C7   180.00   0.0  0
 HM2  CONST_33  C14   C13  C12  C11  180.00   0.0  0
 HM2  CONST_34  C16   C17  C12  C11  180.00   0.0  0
 HM2  CONST_35  H2    C2   C1   N1   180.00   0.0  0
 HM2  CONST_36  H4    C4   C5   N1   180.00   0.0  0
 HM2  CONST_37  H3    C3   C2   C1   180.00   0.0  0
 HM2  CONST_38  H1    C1   C2   C3   180.00   0.0  0
 HM2  CONST_39  H14   C14  C13  C12  180.00   0.0  0
 HM2  CONST_40  H16   C16  C17  C12  180.00   0.0  0
 HM2  CONST_41  H17   C17  C12  C13  180.00   0.0  0
 HM2  CONST_42  H15   C15  C14  C13  180.00   0.0  0
 HM2  CONST_43  H13   C13  C14  C15  180.00   0.0  0
 HM2  CONST_44  C10   N4   C7   N2     0.00   0.0  0
 HM2  CONST_45  C10   N4   C7   C9   180.00   0.0  0
 HM2  CONST_46  HN4   N4   C7   N2   180.00   0.0  0
 HM2  Var_01    C13   C12  C11  C10   86.32  30.0  2
 HM2  Var_02    H181  C18  C8   N3   121.92  30.0  2
 HM2  Var_03    C12   C11  C10  N4   179.32  30.0  3
 HM2  Var_04    C11   C10  N4   C7   170.92  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
 HM2  plan-1  N1   0.020
 HM2  plan-1  C1   0.020
 HM2  plan-1  C2   0.020
 HM2  plan-1  C3   0.020
 HM2  plan-1  C4   0.020
 HM2  plan-1  C5   0.020
 HM2  plan-1  C6   0.020
 HM2  plan-1  H1   0.020
 HM2  plan-1  H2   0.020
 HM2  plan-1  H3   0.020
 HM2  plan-1  H4   0.020
 HM2  plan-2  N2   0.020
 HM2  plan-2  N3   0.020
 HM2  plan-2  N4   0.020
 HM2  plan-2  C5   0.020
 HM2  plan-2  C6   0.020
 HM2  plan-2  C7   0.020
 HM2  plan-2  C8   0.020
 HM2  plan-2  C9   0.020
 HM2  plan-2  C18  0.020
 HM2  plan-2  CL1  0.020
 HM2  plan-3  C11  0.020
 HM2  plan-3  C12  0.020
 HM2  plan-3  C13  0.020
 HM2  plan-3  C14  0.020
 HM2  plan-3  C15  0.020
 HM2  plan-3  C16  0.020
 HM2  plan-3  C17  0.020
 HM2  plan-3  H13  0.020
 HM2  plan-3  H14  0.020
 HM2  plan-3  H15  0.020
 HM2  plan-3  H16  0.020
 HM2  plan-3  H17  0.020
 HM2  plan-4  N4   0.020
 HM2  plan-4  C7   0.020
 HM2  plan-4  C10  0.020
 HM2  plan-4  HN4  0.020

