# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 00:22:19 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 2,7-dimethyl-6-[(prop-1-yn-1-ylamino)methyl]quinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#CNCc1cc2C(=O)NC(=Nc2cc1C)C
#
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
 ZD9  ZD9  2,7-dimethyl-6-[(prop-1-yn-1-ylamino)methyl]quinazolin-4(3H)-one  ligand  33  18  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZD9
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
 ZD9  C1    C  CR6   0   0.544  -2.5255  -1.5281  -0.0730
 ZD9  N2    N  NR16  0  -0.688  -3.7714  -0.9948   0.1712
 ZD9  C3    C  CR6   0   0.448  -4.0310   0.3353   0.3376
 ZD9  N4    N  N     0  -0.472  -3.1175   1.2383   0.2798
 ZD9  C5    C  CR66  0   0.263  -1.8266   0.8276   0.0384
 ZD9  C6    C  CR66  0  -0.100  -1.4821  -0.5174  -0.1413
 ZD9  O7    O  O     0  -0.456  -2.3656  -2.7285  -0.2100
 ZD9  C8    C  CR16  0  -0.329  -0.1512  -0.8689  -0.3810
 ZD9  C9    C  CR6   0   0.053   0.8382   0.0873  -0.4467
 ZD9  C10   C  CR6   0   0.102   0.5014   1.4504  -0.2690
 ZD9  C11   C  CR16  0  -0.379  -0.8146   1.7942  -0.0329
 ZD9  C12   C  CH2   0  -0.366   2.2614  -0.3347  -0.6793
 ZD9  N13   N  NH1   0  -0.654   3.0321  -0.2138   0.5570
 ZD9  C14   C  CSP   0   0.023   4.3701  -0.3170   0.4635
 ZD9  C15   C  CSP   0   0.086   5.5718  -0.3502   0.3612
 ZD9  C16   C  CH3   0  -0.782   7.0236  -0.4100   0.2500
 ZD9  C38   C  CH3   0  -0.746   1.5534   2.5150  -0.3442
 ZD9  C39   C  CH3   0  -0.750  -5.4542   0.6933   0.5971
 ZD9  HN2   H  HNR6  0   0.428  -4.5429  -1.6476   0.2285
 ZD9  H8    H  HCR6  0   0.261   0.1029  -1.9128  -0.5205
 ZD9  H11   H  HCR6  0   0.256  -1.0891   2.8332   0.1042
 ZD9  H12   H  HCH2  0   0.253   2.2828  -1.3571  -1.0711
 ZD9  H12A  H  HCH2  0   0.260   2.7362   0.3028  -1.4269
 ZD9  HN13  H  HNH1  0   0.391   2.6360  -0.7432   1.3221
 ZD9  H16   H  HCH3  0   0.261   7.4672  -0.7160   1.1984
 ZD9  H16A  H  HCH3  0   0.256   7.3421  -1.1308  -0.5043
 ZD9  H16B  H  HCH3  0   0.255   7.4518   0.5583  -0.0120
 ZD9  H38   H  HCH3  0   0.251   2.0644   2.4996  -1.3090
 ZD9  H38A  H  HCH3  0   0.256   1.1220   3.5055  -0.2125
 ZD9  H38B  H  HCH3  0   0.260   2.3150   2.3667   0.4211
 ZD9  H39   H  HCH3  0   0.272  -5.8129   0.2064   1.5052
 ZD9  H39A  H  HCH3  0   0.272  -5.5547   1.7685   0.7095
 ZD9  H39B  H  HCH3  0   0.272  -6.0911   0.3614  -0.2243

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
 ZD9  O7   C1    double    1.219  0.020  1.219
 ZD9  C6   C1    single    1.454  0.020  1.454
 ZD9  C1   N2    single    1.377  0.020  1.377
 ZD9  N2   C3    single    1.365  0.020  1.365
 ZD9  N2   HN2   single    0.860  0.020  1.020
 ZD9  C3   N4    double    1.286  0.020  1.286
 ZD9  C3   C39   single    1.490  0.020  1.490
 ZD9  C5   N4    single    1.376  0.020  1.376
 ZD9  C6   C5    aromatic  1.400  0.020  1.400
 ZD9  C5   C11   aromatic  1.401  0.020  1.401
 ZD9  C8   C6    aromatic  1.397  0.020  1.397
 ZD9  C8   C9    aromatic  1.378  0.020  1.378
 ZD9  C8   H8    single    0.930  0.020  1.080
 ZD9  C12  C9    single    1.503  0.020  1.503
 ZD9  C9   C10   aromatic  1.415  0.020  1.415
 ZD9  C10  C38   single    1.499  0.020  1.499
 ZD9  C10  C11   aromatic  1.381  0.020  1.381
 ZD9  C11  H11   single    0.930  0.020  1.080
 ZD9  N13  C12   single    1.462  0.020  1.462
 ZD9  C12  H12   single    0.970  0.020  1.090
 ZD9  C12  H12A  single    0.970  0.020  1.090
 ZD9  C14  N13   single    1.345  0.020  1.345
 ZD9  N13  HN13  single    0.890  0.020  1.040
 ZD9  C15  C14   triple    1.206  0.020  1.206
 ZD9  C16  C15   single    1.457  0.020  1.457
 ZD9  C16  H16   single    0.970  0.020  1.090
 ZD9  C16  H16A  single    0.970  0.020  1.090
 ZD9  C16  H16B  single    0.970  0.020  1.090
 ZD9  C38  H38   single    0.970  0.020  1.090
 ZD9  C38  H38A  single    0.970  0.020  1.090
 ZD9  C38  H38B  single    0.970  0.020  1.090
 ZD9  C39  H39   single    0.970  0.020  1.090
 ZD9  C39  H39A  single    0.970  0.020  1.090
 ZD9  C39  H39B  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
 ZD9  O7    C1   C6    125.81  3.000
 ZD9  C6    C1   N2    112.85  3.000
 ZD9  O7    C1   N2    121.33  3.000
 ZD9  HN2   N2   C3    118.45  3.000
 ZD9  HN2   N2   C1    116.74  3.000
 ZD9  C3    N2   C1    124.81  3.000
 ZD9  C39   C3   N4    121.17  3.000
 ZD9  C39   C3   N2    115.90  3.000
 ZD9  N4    C3   N2    122.93  3.000
 ZD9  C5    N4   C3    117.69  3.000
 ZD9  C11   C5   C6    118.58  3.000
 ZD9  C11   C5   N4    118.72  3.000
 ZD9  C6    C5   N4    122.70  3.000
 ZD9  C8    C6   C5    119.88  3.000
 ZD9  C8    C6   C1    121.11  3.000
 ZD9  C5    C6   C1    119.02  3.000
 ZD9  H8    C8   C9    119.61  3.000
 ZD9  H8    C8   C6    119.21  3.000
 ZD9  C9    C8   C6    121.18  3.000
 ZD9  C12   C9   C10   121.02  3.000
 ZD9  C10   C9   C8    119.44  3.000
 ZD9  C12   C9   C8    119.53  3.000
 ZD9  C38   C10  C11   120.06  3.000
 ZD9  C11   C10  C9    119.22  3.000
 ZD9  C38   C10  C9    120.72  3.000
 ZD9  H11   C11  C10   120.13  3.000
 ZD9  H11   C11  C5    118.18  3.000
 ZD9  C10   C11  C5    121.70  3.000
 ZD9  H12A  C12  H12   106.97  3.000
 ZD9  H12A  C12  N13   107.56  3.000
 ZD9  H12   C12  N13   111.68  3.000
 ZD9  H12A  C12  C9    110.74  3.000
 ZD9  H12   C12  C9    109.64  3.000
 ZD9  N13   C12  C9    110.19  3.000
 ZD9  HN13  N13  C14   113.70  3.000
 ZD9  HN13  N13  C12   112.96  3.000
 ZD9  C14   N13  C12   117.34  3.000
 ZD9  C15   C14  N13   180.00  3.000
 ZD9  C16   C15  C14   180.00  3.000
 ZD9  H16B  C16  H16A  107.81  3.000
 ZD9  H16B  C16  H16   107.35  3.000
 ZD9  H16A  C16  H16   107.28  3.000
 ZD9  H16B  C16  C15   111.90  3.000
 ZD9  H16A  C16  C15   111.76  3.000
 ZD9  H16   C16  C15   110.51  3.000
 ZD9  H38B  C38  H38A  108.41  3.000
 ZD9  H38B  C38  H38   106.95  3.000
 ZD9  H38A  C38  H38   107.78  3.000
 ZD9  H38B  C38  C10   111.02  3.000
 ZD9  H38A  C38  C10   111.23  3.000
 ZD9  H38   C38  C10   111.27  3.000
 ZD9  H39B  C39  H39A  108.97  3.000
 ZD9  H39B  C39  H39   107.39  3.000
 ZD9  H39A  C39  H39   108.99  3.000
 ZD9  H39B  C39  C3    110.69  3.000
 ZD9  H39A  C39  C3    110.14  3.000
 ZD9  H39   C39  C3    110.59  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
 ZD9  CONST_01  C9   C8   C6   C5      0.00   0.0  0
 ZD9  CONST_02  C9   C10  C11  C5      0.00   0.0  0
 ZD9  CONST_03  C10  C11  C5   C6      0.00   0.0  0
 ZD9  CONST_04  C10  C9   C8   C6      0.00   0.0  0
 ZD9  CONST_05  C11  C5   C6   C8      0.00   0.0  0
 ZD9  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 ZD9  CONST_07  N4   C3   N2   C1      0.00   0.0  0
 ZD9  CONST_08  C5   N4   C3   N2      0.00   0.0  0
 ZD9  CONST_09  C6   C1   N2   C3      0.00   0.0  0
 ZD9  CONST_10  C38  C10  C11  C5    180.00   0.0  0
 ZD9  CONST_11  C12  C9   C8   C6    180.00   0.0  0
 ZD9  CONST_12  C38  C10  C9   C8    180.00   0.0  0
 ZD9  CONST_13  C12  C9   C10  C11   180.00   0.0  0
 ZD9  CONST_14  C39  C3   N2   C1    180.00   0.0  0
 ZD9  CONST_15  O7   C1   N2   C3    180.00   0.0  0
 ZD9  CONST_16  C39  C3   N4   C5    180.00   0.0  0
 ZD9  CONST_17  H8   C8   C6   C1      0.00   0.0  0
 ZD9  CONST_18  H11  C11  C5   N4      0.00   0.0  0
 ZD9  CONST_19  HN2  N2   C3   N4    180.00   0.0  0
 ZD9  Var_01    N13  C12  C9   C8   -106.04  30.0  1
 ZD9  Var_02    H39  C39  C3   N2     59.73  30.0  3
 ZD9  Var_03    H38  C38  C10  C9     58.27  30.0  2
 ZD9  Var_04    C14  N13  C12  C9   -168.13  30.0  1
 ZD9  Var_05    H16  C16  C15  C14   -41.48  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
 ZD9  plan-1  C1   0.020
 ZD9  plan-1  N2   0.020
 ZD9  plan-1  C3   0.020
 ZD9  plan-1  N4   0.020
 ZD9  plan-1  C5   0.020
 ZD9  plan-1  C6   0.020
 ZD9  plan-1  O7   0.020
 ZD9  plan-1  C8   0.020
 ZD9  plan-1  C9   0.020
 ZD9  plan-1  C10  0.020
 ZD9  plan-1  C11  0.020
 ZD9  plan-1  C12  0.020
 ZD9  plan-1  C38  0.020
 ZD9  plan-1  C39  0.020
 ZD9  plan-1  HN2  0.020
 ZD9  plan-1  H8   0.020
 ZD9  plan-1  H11  0.020

