# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 19:41:29 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: N-[4-(2-methylimidazo[1,2-a]pyridin-3-yl)pyrimidin-2-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1nccc(n1)c2n3ccccc3nc2C
#
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
 HDU  HDU  N-[4-(2-methylimidazo[1,2-a]pyridin-3-yl)pyrimidin-2-yl]acetamide  ligand  33  20  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HDU
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
 HDU  O20   O  O     0  -0.435   0.9357  -0.1059   5.2363
 HDU  C18   C  C     0   0.503  -0.0791   0.3614   4.7706
 HDU  C19   C  CH3   0  -0.793  -1.1558   1.0015   5.6092
 HDU  N17   N  NH1   0  -0.709  -0.3733   0.3878   3.4284
 HDU  C15   C  CR6   0   0.599   0.3559  -0.0700   2.3482
 HDU  N16   N  N     0  -0.482  -0.2561   0.1160   1.1855
 HDU  N14   N  N     0  -0.423   1.5446  -0.6204   2.5338
 HDU  C13   C  CR16  0  -0.012   2.1500  -1.0484   1.4322
 HDU  C12   C  CR16  0  -0.393   1.6058  -0.9313   0.1700
 HDU  C11   C  CR6   0   0.266   0.3572  -0.3090   0.0838
 HDU  C7    C  CR5   0   0.226  -0.3580  -0.1315  -1.1666
 HDU  N6    N  N     0  -0.575   0.2416   0.1016  -2.3921
 HDU  C5    C  CR56  0   0.535  -0.7711   0.1098  -3.3314
 HDU  N8    N  N     0  -0.481  -1.9473  -0.1084  -2.7647
 HDU  C9    C  CR5   0   0.117  -1.7133  -0.2468  -1.4461
 HDU  C10   C  CH3   0  -0.753  -2.8249  -0.5679  -0.5093
 HDU  C4    C  CR16  0  -0.407  -0.4549   0.3491  -4.6808
 HDU  C3    C  CR16  0  -0.148   0.8422   0.5877  -5.0283
 HDU  C2    C  CR16  0  -0.391   1.8463   0.6180  -4.0323
 HDU  C1    C  CR16  0   0.027   1.5322   0.3846  -2.7322
 HDU  H191  H  HCH3  0   0.270  -0.9885   0.7869   6.6609
 HDU  H192  H  HCH3  0   0.278  -1.1392   2.0840   5.4689
 HDU  H193  H  HCH3  0   0.267  -2.1488   0.6513   5.3279
 HDU  H17   H  HNH1  0   0.419  -1.2563   0.8000   3.1646
 HDU  H13   H  HCR6  0   0.280   3.1166  -1.5202   1.5672
 HDU  H12   H  HCR6  0   0.290   2.1169  -1.3451  -0.6860
 HDU  H101  H  HCH3  0   0.253  -2.9746  -1.6481  -0.4482
 HDU  H102  H  HCH3  0   0.258  -2.6306  -0.2021   0.4942
 HDU  H103  H  HCH3  0   0.250  -3.7545  -0.1315  -0.8712
 HDU  H4    H  HCR6  0   0.283  -1.2540   0.3402  -5.4083
 HDU  H3    H  HCR6  0   0.278   1.1064   0.7702  -6.0604
 HDU  H2    H  HCR6  0   0.285   2.8725   0.8355  -4.2884
 HDU  H1    H  HCR6  0   0.318   2.2614   0.4301  -1.9397

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
 HDU  O20  C18   double    1.210  0.020  1.210
 HDU  C18  C19   single    1.507  0.020  1.507
 HDU  C18  N17   single    1.374  0.020  1.374
 HDU  C19  H191  single    0.970  0.020  1.090
 HDU  C19  H192  single    0.970  0.020  1.090
 HDU  C19  H193  single    0.970  0.020  1.090
 HDU  N17  C15   single    1.381  0.020  1.381
 HDU  N17  H17   single    0.860  0.020  1.020
 HDU  C15  N16   aromatic  1.327  0.020  1.327
 HDU  C15  N14   aromatic  1.323  0.020  1.323
 HDU  N16  C11   aromatic  1.331  0.020  1.331
 HDU  N14  C13   aromatic  1.328  0.020  1.328
 HDU  C13  C12   aromatic  1.380  0.020  1.380
 HDU  C13  H13   single    0.930  0.020  1.080
 HDU  C12  C11   aromatic  1.398  0.020  1.398
 HDU  C12  H12   single    0.930  0.020  1.080
 HDU  C11  C7    single    1.451  0.020  1.451
 HDU  C7   N6    aromatic  1.384  0.020  1.384
 HDU  C7   C9    aromatic  1.389  0.020  1.389
 HDU  N6   C5    aromatic  1.381  0.020  1.381
 HDU  N6   C1    aromatic  1.364  0.020  1.364
 HDU  C5   N8    aromatic  1.324  0.020  1.324
 HDU  C5   C4    aromatic  1.406  0.020  1.406
 HDU  N8   C9    aromatic  1.346  0.020  1.346
 HDU  C9   C10   single    1.489  0.020  1.489
 HDU  C10  H101  single    0.970  0.020  1.090
 HDU  C10  H102  single    0.970  0.020  1.090
 HDU  C10  H103  single    0.970  0.020  1.090
 HDU  C4   C3    aromatic  1.364  0.020  1.364
 HDU  C4   H4    single    0.930  0.020  1.080
 HDU  C3   C2    aromatic  1.415  0.020  1.415
 HDU  C3   H3    single    0.930  0.020  1.080
 HDU  C2   C1    aromatic  1.358  0.020  1.358
 HDU  C2   H2    single    0.930  0.020  1.080
 HDU  C1   H1    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
 HDU  N17   C18  C19   112.47  3.000
 HDU  N17   C18  O20   124.24  3.000
 HDU  C19   C18  O20   123.28  3.000
 HDU  H193  C19  H192  107.42  3.000
 HDU  H193  C19  H191  109.07  3.000
 HDU  H192  C19  H191  108.54  3.000
 HDU  H193  C19  C18   111.77  3.000
 HDU  H192  C19  C18   109.80  3.000
 HDU  H191  C19  C18   110.16  3.000
 HDU  H17   N17  C15   113.12  3.000
 HDU  H17   N17  C18   116.76  3.000
 HDU  C15   N17  C18   130.12  3.000
 HDU  N14   C15  N16   126.55  3.000
 HDU  N14   C15  N17   120.16  3.000
 HDU  N16   C15  N17   113.29  3.000
 HDU  C11   N16  C15   117.91  3.000
 HDU  C13   N14  C15   115.30  3.000
 HDU  H13   C13  C12   120.18  3.000
 HDU  H13   C13  N14   116.33  3.000
 HDU  C12   C13  N14   123.49  3.000
 HDU  H12   C12  C11   123.00  3.000
 HDU  H12   C12  C13   120.42  3.000
 HDU  C11   C12  C13   116.53  3.000
 HDU  C7    C11  C12   123.21  3.000
 HDU  C7    C11  N16   116.56  3.000
 HDU  C12   C11  N16   120.19  3.000
 HDU  C9    C7   N6    104.99  3.000
 HDU  C9    C7   C11   130.11  3.000
 HDU  N6    C7   C11   124.75  3.000
 HDU  C1    N6   C5    121.53  3.000
 HDU  C1    N6   C7    131.71  3.000
 HDU  C5    N6   C7    106.59  3.000
 HDU  C4    C5   N8    129.68  3.000
 HDU  C4    C5   N6    119.25  3.000
 HDU  N8    C5   N6    111.06  3.000
 HDU  C9    N8   C5    106.37  3.000
 HDU  C10   C9   N8    120.58  3.000
 HDU  C10   C9   C7    128.31  3.000
 HDU  N8    C9   C7    110.99  3.000
 HDU  H103  C10  H102  108.95  3.000
 HDU  H103  C10  H101  107.34  3.000
 HDU  H102  C10  H101  107.83  3.000
 HDU  H103  C10  C9    109.99  3.000
 HDU  H102  C10  C9    112.05  3.000
 HDU  H101  C10  C9    110.54  3.000
 HDU  H4    C4   C3    122.22  3.000
 HDU  H4    C4   C5    118.57  3.000
 HDU  C3    C4   C5    119.21  3.000
 HDU  H3    C3   C2    119.68  3.000
 HDU  H3    C3   C4    120.35  3.000
 HDU  C2    C3   C4    119.96  3.000
 HDU  H2    C2   C1    118.79  3.000
 HDU  H2    C2   C3    120.79  3.000
 HDU  C1    C2   C3    120.42  3.000
 HDU  H1    C1   C2    122.70  3.000
 HDU  H1    C1   N6    117.74  3.000
 HDU  C2    C1   N6    119.55  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
 HDU  CONST_01  C12   C11  N16  C15    0.00   0.0  0
 HDU  CONST_02  C7    C11  N16  C15  180.00   0.0  0
 HDU  CONST_03  C12   C13  N14  C15    0.00   0.0  0
 HDU  CONST_04  C13   N14  C15  N16    0.00   0.0  0
 HDU  CONST_05  C13   C12  C11  N16    0.00   0.0  0
 HDU  CONST_08  C11   N16  C15  N14    0.00   0.0  0
 HDU  CONST_09  C11   C12  C13  N14    0.00   0.0  0
 HDU  CONST_10  C7    C11  C12  C13  180.00   0.0  0
 HDU  CONST_13  C5    N6   C7   C11  180.00   0.0  0
 HDU  CONST_14  C1    N6   C7   C11    0.00   0.0  0
 HDU  CONST_15  N8    C9   C7   C11  180.00   0.0  0
 HDU  CONST_16  N8    C5   N6   C7     0.00   0.0  0
 HDU  CONST_17  C4    C5   N6   C7   180.00   0.0  0
 HDU  CONST_18  C2    C1   N6   C7   180.00   0.0  0
 HDU  CONST_19  C5    N8   C9   C7     0.00   0.0  0
 HDU  CONST_20  N8    C9   C7   N6     0.00   0.0  0
 HDU  CONST_21  C9    N8   C5   N6     0.00   0.0  0
 HDU  CONST_22  C3    C4   C5   N6     0.00   0.0  0
 HDU  CONST_23  C3    C2   C1   N6     0.00   0.0  0
 HDU  CONST_24  C9    C7   N6   C5     0.00   0.0  0
 HDU  CONST_25  C2    C1   N6   C5     0.00   0.0  0
 HDU  CONST_26  C2    C3   C4   C5     0.00   0.0  0
 HDU  CONST_27  C1    N6   C5   N8   180.00   0.0  0
 HDU  CONST_28  C3    C4   C5   N8   180.00   0.0  0
 HDU  CONST_29  C1    N6   C7   C9   180.00   0.0  0
 HDU  CONST_30  C4    C5   N8   C9   180.00   0.0  0
 HDU  CONST_31  C1    N6   C5   C4     0.00   0.0  0
 HDU  CONST_32  C1    C2   C3   C4     0.00   0.0  0
 HDU  CONST_33  C11   N16  C15  N17  180.00   0.0  0
 HDU  CONST_34  C13   N14  C15  N17  180.00   0.0  0
 HDU  CONST_35  C10   C9   C7   C11    0.00   0.0  0
 HDU  CONST_36  C10   C9   C7   N6   180.00   0.0  0
 HDU  CONST_37  C10   C9   N8   C5   180.00   0.0  0
 HDU  CONST_38  H13   C13  N14  C15  180.00   0.0  0
 HDU  CONST_39  H12   C12  C11  N16  180.00   0.0  0
 HDU  CONST_40  H1    C1   N6   C7     0.00   0.0  0
 HDU  CONST_41  H4    C4   C5   N6   180.00   0.0  0
 HDU  CONST_42  H2    C2   C1   N6   180.00   0.0  0
 HDU  CONST_43  H3    C3   C4   C5   180.00   0.0  0
 HDU  CONST_44  N16   C15  N17  C18  180.00   0.0  0
 HDU  CONST_45  N14   C15  N17  C18    0.00   0.0  0
 HDU  CONST_46  H17   N17  C15  N16    0.00   0.0  0
 HDU  CONST_47  C15   N17  C18  O20    0.00   0.0  0
 HDU  CONST_48  C15   N17  C18  C19  180.00   0.0  0
 HDU  Var_01    H101  C10  C9   C7   -89.00  30.0  2
 HDU  Var_02    H191  C19  C18  O20  -12.21  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
 HDU  plan-1  N17  0.020
 HDU  plan-1  C15  0.020
 HDU  plan-1  N16  0.020
 HDU  plan-1  N14  0.020
 HDU  plan-1  C13  0.020
 HDU  plan-1  C12  0.020
 HDU  plan-1  C11  0.020
 HDU  plan-1  C7   0.020
 HDU  plan-1  H13  0.020
 HDU  plan-1  H12  0.020
 HDU  plan-2  C11  0.020
 HDU  plan-2  C7   0.020
 HDU  plan-2  N6   0.020
 HDU  plan-2  C5   0.020
 HDU  plan-2  N8   0.020
 HDU  plan-2  C9   0.020
 HDU  plan-2  C10  0.020
 HDU  plan-2  C4   0.020
 HDU  plan-2  C3   0.020
 HDU  plan-2  C2   0.020
 HDU  plan-2  C1   0.020
 HDU  plan-2  H4   0.020
 HDU  plan-2  H3   0.020
 HDU  plan-2  H2   0.020
 HDU  plan-2  H1   0.020
 HDU  plan-3  O20  0.020
 HDU  plan-3  C18  0.020
 HDU  plan-3  C19  0.020
 HDU  plan-3  N17  0.020
 HDU  plan-3  C15  0.020
 HDU  plan-3  H17  0.020

