# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 04:31:14 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 5-chloro-N~6~-(2,5-dimethoxybenzyl)quinazoline-2,4,6-triamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OC)c(CNc2ccc3nc(N)nc(N)c3c2Cl)c1
#
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
 KA5  KA5  5-chloro-N~6~-(2,5-dimethoxybenzyl)quinazoline-2,4,6-triamine  ligand  43  25  .  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_KA5
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
 KA5  N1    N   N     0  -0.525  -4.8288   1.3431   0.5979
 KA5  C2    C   CR6   0   0.510  -5.7045   0.3903   0.3958
 KA5  N3    N   N     0  -0.508  -5.4270  -0.8709   0.0288
 KA5  C4    C   CR6   0   0.474  -4.1724  -1.2331  -0.1455
 KA5  C5    C   CR66  0   0.054  -3.0870  -0.2879   0.0630
 KA5  C6    C   CR66  0   0.215  -3.5279   1.0065   0.4359
 KA5  C7    C   CR16  0  -0.313  -2.5659   2.0098   0.6595
 KA5  C8    C   CR16  0  -0.339  -1.2302   1.7603   0.5409
 KA5  C9    C   CR6   0   0.446  -0.7460   0.4849   0.1729
 KA5  C10   C   CR6   0  -0.224  -1.6938  -0.5049  -0.0668
 KA5  N11   N   NH2   0  -0.828  -7.0176   0.6644   0.6048
 KA5  N12   N   NH2   0  -0.826  -3.9989  -2.5062  -0.5139
 KA5  CL13  CL  CL    0  -0.133  -1.0356  -2.0474  -0.5513
 KA5  N14   N   NH1   0  -0.678   0.6012   0.2506   0.0234
 KA5  C15   C   CH2   0  -0.338   1.5823   1.2313   0.4425
 KA5  C16   C   CR6   0  -0.004   2.9665   0.7105   0.1765
 KA5  C17   C   CR16  0  -0.376   3.7405   0.2527   1.2263
 KA5  C18   C   CR6   0   0.373   5.0238  -0.2602   1.0223
 KA5  C19   C   CR16  0  -0.377   5.5231  -0.3100  -0.2695
 KA5  C20   C   CR16  0  -0.371   4.7523   0.1496  -1.3370
 KA5  C21   C   CR6   0   0.348   3.4789   0.6577  -1.1304
 KA5  O22   O   O2    0  -0.465   2.6760   1.1251  -2.1091
 KA5  C23   C   CH3   0  -0.435   3.1709   1.1459  -3.4310
 KA5  O24   O   O2    0  -0.478   5.6859  -0.6756   2.1252
 KA5  C25   C   CH3   0  -0.434   6.9827  -1.2077   1.9600
 KA5  H7    H   HCR6  0   0.260  -2.9124   2.9943   0.9448
 KA5  H8    H   HCR6  0   0.287  -0.5321   2.5620   0.7380
 KA5  HN11  H   HNH2  0   0.385  -7.2886   1.6325   0.6372
 KA5  HN1A  H   HNH2  0   0.386  -7.6935   0.0343   0.2082
 KA5  HN12  H   HNH2  0   0.400  -4.8232  -3.0649  -0.6563
 KA5  HN1B  H   HNH2  0   0.407  -3.1098  -2.9195  -0.7157
 KA5  HN14  H   HNH1  0   0.378   0.8918  -0.7003   0.1905
 KA5  H15   H   HCH2  0   0.250   1.4225   2.1613  -0.1078
 KA5  H15A  H   HCH2  0   0.242   1.4917   1.4743   1.5089
 KA5  H17   H   HCR6  0   0.261   3.3435   0.2961   2.2343
 KA5  H19   H   HCR6  0   0.281   6.5088  -0.6991  -0.4848
 KA5  H20   H   HCR6  0   0.281   5.1789   0.0951  -2.3292
 KA5  H23   H   HCH3  0   0.258   2.3869   1.5773  -4.0486
 KA5  H23A  H   HCH3  0   0.225   4.0702   1.7614  -3.5226
 KA5  H23B  H   HCH3  0   0.225   3.3946   0.1418  -3.8023
 KA5  H25   H   HCH3  0   0.225   6.9819  -2.1027   1.3312
 KA5  H25A  H   HCH3  0   0.225   7.6737  -0.4778   1.5289
 KA5  H25B  H   HCH3  0   0.258   7.3376  -1.4787   2.9514

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
 KA5  N1   C2    aromatic  1.310  0.020  1.310
 KA5  N1   C6    aromatic  1.353  0.020  1.353
 KA5  C2   N3    aromatic  1.342  0.020  1.342
 KA5  C2   N11   single    1.358  0.020  1.358
 KA5  N3   C4    aromatic  1.317  0.020  1.317
 KA5  C4   C5    aromatic  1.454  0.020  1.454
 KA5  C4   N12   single    1.337  0.020  1.337
 KA5  C5   C6    aromatic  1.417  0.020  1.417
 KA5  C5   C10   aromatic  1.416  0.020  1.416
 KA5  C6   C7    aromatic  1.408  0.020  1.408
 KA5  C7   C8    aromatic  1.364  0.020  1.364
 KA5  C8   C9    aromatic  1.413  0.020  1.413
 KA5  C9   C10   aromatic  1.391  0.020  1.391
 KA5  C9   N14   single    1.376  0.020  1.376
 KA5  C10  CL13  single    1.746  0.020  1.746
 KA5  N14  C15   single    1.449  0.020  1.449
 KA5  C15  C16   single    1.503  0.020  1.503
 KA5  C16  C17   aromatic  1.382  0.020  1.382
 KA5  C16  C21   aromatic  1.405  0.020  1.405
 KA5  C17  C18   aromatic  1.397  0.020  1.397
 KA5  C18  C19   aromatic  1.386  0.020  1.386
 KA5  C18  O24   single    1.352  0.020  1.352
 KA5  C19  C20   aromatic  1.395  0.020  1.395
 KA5  C20  C21   aromatic  1.386  0.020  1.386
 KA5  C21  O22   single    1.349  0.020  1.349
 KA5  O22  C23   single    1.412  0.020  1.412
 KA5  O24  C25   single    1.411  0.020  1.411
 KA5  C7   H7    single    0.930  0.020  1.080
 KA5  C8   H8    single    0.930  0.020  1.080
 KA5  N11  HN11  single    0.890  0.020  1.040
 KA5  N11  HN1A  single    0.890  0.020  1.040
 KA5  N12  HN12  single    0.860  0.020  1.020
 KA5  N12  HN1B  single    0.860  0.020  1.020
 KA5  N14  HN14  single    0.890  0.020  1.040
 KA5  C15  H15   single    0.970  0.020  1.090
 KA5  C15  H15A  single    0.970  0.020  1.090
 KA5  C17  H17   single    0.930  0.020  1.080
 KA5  C19  H19   single    0.930  0.020  1.080
 KA5  C20  H20   single    0.930  0.020  1.080
 KA5  C23  H23   single    0.970  0.020  1.090
 KA5  C23  H23A  single    0.970  0.020  1.090
 KA5  C23  H23B  single    0.970  0.020  1.090
 KA5  C25  H25   single    0.970  0.020  1.090
 KA5  C25  H25A  single    0.970  0.020  1.090
 KA5  C25  H25B  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
 KA5  C6    N1   C2    116.31  3.000
 KA5  N11   C2   N3    115.57  3.000
 KA5  N11   C2   N1    118.42  3.000
 KA5  N3    C2   N1    125.98  3.000
 KA5  C4    N3   C2    119.42  3.000
 KA5  N12   C4   C5    124.17  3.000
 KA5  N12   C4   N3    114.96  3.000
 KA5  C5    C4   N3    120.87  3.000
 KA5  C10   C5   C6    118.04  3.000
 KA5  C10   C5   C4    128.43  3.000
 KA5  C6    C5   C4    113.52  3.000
 KA5  C7    C6   C5    118.69  3.000
 KA5  C7    C6   N1    117.42  3.000
 KA5  C5    C6   N1    123.89  3.000
 KA5  H7    C7   C8    120.20  3.000
 KA5  H7    C7   C6    118.13  3.000
 KA5  C8    C7   C6    121.66  3.000
 KA5  H8    C8   C9    119.71  3.000
 KA5  H8    C8   C7    118.74  3.000
 KA5  C9    C8   C7    121.56  3.000
 KA5  N14   C9   C10   121.82  3.000
 KA5  N14   C9   C8    121.18  3.000
 KA5  C10   C9   C8    116.98  3.000
 KA5  CL13  C10  C9    114.81  3.000
 KA5  CL13  C10  C5    122.13  3.000
 KA5  C9    C10  C5    123.06  3.000
 KA5  HN1A  N11  HN11  115.77  3.000
 KA5  HN1A  N11  C2    117.57  3.000
 KA5  HN11  N11  C2    117.38  3.000
 KA5  HN1B  N12  HN12  118.03  3.000
 KA5  HN1B  N12  C4    124.34  3.000
 KA5  HN12  N12  C4    117.49  3.000
 KA5  HN14  N14  C15   113.28  3.000
 KA5  HN14  N14  C9    115.15  3.000
 KA5  C15   N14  C9    121.09  3.000
 KA5  H15A  C15  H15   106.79  3.000
 KA5  H15A  C15  C16   108.96  3.000
 KA5  H15   C15  C16   109.92  3.000
 KA5  H15A  C15  N14   112.02  3.000
 KA5  H15   C15  N14   109.36  3.000
 KA5  C16   C15  N14   109.75  3.000
 KA5  C21   C16  C17   119.33  3.000
 KA5  C21   C16  C15   120.91  3.000
 KA5  C17   C16  C15   119.74  3.000
 KA5  H17   C17  C18   119.13  3.000
 KA5  H17   C17  C16   119.20  3.000
 KA5  C18   C17  C16   121.67  3.000
 KA5  O24   C18  C19   124.96  3.000
 KA5  O24   C18  C17   116.34  3.000
 KA5  C19   C18  C17   118.70  3.000
 KA5  H19   C19  C20   118.04  3.000
 KA5  H19   C19  C18   121.80  3.000
 KA5  C20   C19  C18   120.16  3.000
 KA5  H20   C20  C21   121.16  3.000
 KA5  H20   C20  C19   117.88  3.000
 KA5  C21   C20  C19   120.96  3.000
 KA5  O22   C21  C20   124.42  3.000
 KA5  O22   C21  C16   116.41  3.000
 KA5  C20   C21  C16   119.17  3.000
 KA5  C23   O22  C21   118.41  3.000
 KA5  H23B  C23  H23A  108.67  3.000
 KA5  H23B  C23  H23   108.59  3.000
 KA5  H23A  C23  H23   108.79  3.000
 KA5  H23B  C23  O22   112.10  3.000
 KA5  H23A  C23  O22   112.03  3.000
 KA5  H23   C23  O22   106.55  3.000
 KA5  C25   O24  C18   118.05  3.000
 KA5  H25B  C25  H25A  108.63  3.000
 KA5  H25B  C25  H25   108.69  3.000
 KA5  H25A  C25  H25   108.66  3.000
 KA5  H25B  C25  O24   106.68  3.000
 KA5  H25A  C25  O24   112.03  3.000
 KA5  H25   C25  O24   112.03  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
 KA5  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 KA5  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 KA5  CONST_03  C10   C5   C6   N1    180.00   0.0  0
 KA5  CONST_04  C8    C7   C6   N1    180.00   0.0  0
 KA5  CONST_05  C5    C6   N1   C2      0.00   0.0  0
 KA5  CONST_06  C7    C6   N1   C2    180.00   0.0  0
 KA5  CONST_07  C5    C4   N3   C2      0.00   0.0  0
 KA5  CONST_08  C6    N1   C2   N3      0.00   0.0  0
 KA5  CONST_09  C6    C5   C4   N3      0.00   0.0  0
 KA5  CONST_10  C10   C5   C4   N3    180.00   0.0  0
 KA5  CONST_11  C7    C6   C5   C4    180.00   0.0  0
 KA5  CONST_12  C9    C10  C5   C4    180.00   0.0  0
 KA5  CONST_13  C8    C7   C6   C5      0.00   0.0  0
 KA5  CONST_14  C8    C9   C10  C5      0.00   0.0  0
 KA5  CONST_15  C9    C10  C5   C6      0.00   0.0  0
 KA5  CONST_16  C9    C8   C7   C6      0.00   0.0  0
 KA5  CONST_17  C10   C5   C6   C7      0.00   0.0  0
 KA5  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 KA5  CONST_19  C19   C18  C17  C16     0.00   0.0  0
 KA5  CONST_20  C19   C20  C21  C16     0.00   0.0  0
 KA5  CONST_21  C20   C21  C16  C17     0.00   0.0  0
 KA5  CONST_22  C20   C19  C18  C17     0.00   0.0  0
 KA5  CONST_23  C21   C16  C17  C18     0.00   0.0  0
 KA5  CONST_24  C21   C20  C19  C18     0.00   0.0  0
 KA5  CONST_25  N12   C4   N3   C2    180.00   0.0  0
 KA5  CONST_26  N11   C2   N3   C4    180.00   0.0  0
 KA5  CONST_27  CL13  C10  C5   C4      0.00   0.0  0
 KA5  CONST_28  N14   C9   C10  C5    180.00   0.0  0
 KA5  CONST_29  N11   C2   N1   C6    180.00   0.0  0
 KA5  CONST_30  N12   C4   C5   C6    180.00   0.0  0
 KA5  CONST_31  CL13  C10  C5   C6    180.00   0.0  0
 KA5  CONST_32  N14   C9   C8   C7    180.00   0.0  0
 KA5  CONST_33  CL13  C10  C9   C8    180.00   0.0  0
 KA5  CONST_34  N12   C4   C5   C10     0.00   0.0  0
 KA5  CONST_35  C18   C17  C16  C15   180.00   0.0  0
 KA5  CONST_36  C20   C21  C16  C15   180.00   0.0  0
 KA5  CONST_37  O24   C18  C17  C16   180.00   0.0  0
 KA5  CONST_38  O22   C21  C16  C17   180.00   0.0  0
 KA5  CONST_39  O22   C21  C20  C19   180.00   0.0  0
 KA5  CONST_40  O24   C18  C19  C20   180.00   0.0  0
 KA5  CONST_41  H7    C7   C6   N1      0.00   0.0  0
 KA5  CONST_42  H8    C8   C7   C6    180.00   0.0  0
 KA5  CONST_43  H20   C20  C21  C16   180.00   0.0  0
 KA5  CONST_44  H19   C19  C18  C17   180.00   0.0  0
 KA5  CONST_45  H17   C17  C18  C19   180.00   0.0  0
 KA5  CONST_46  C15   N14  C9   C8      0.00   0.0  0
 KA5  CONST_47  C15   N14  C9   C10   180.00   0.0  0
 KA5  CONST_50  HN12  N12  C4   N3      0.00   0.0  0
 KA5  CONST_51  HN1B  N12  C4   N3    180.00   0.0  0
 KA5  Var_01    C16   C15  N14  C9    179.42  30.0  3
 KA5  Var_02    C17   C16  C15  N14  -104.67  30.0  2
 KA5  Var_03    H25   C25  O24  C18   -61.18  30.0  3
 KA5  Var_04    H23   C23  O22  C21  -178.52  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
 KA5  plan-1  C15   0.020
 KA5  plan-1  C16   0.020
 KA5  plan-1  C17   0.020
 KA5  plan-1  C18   0.020
 KA5  plan-1  C19   0.020
 KA5  plan-1  C20   0.020
 KA5  plan-1  C21   0.020
 KA5  plan-1  O22   0.020
 KA5  plan-1  O24   0.020
 KA5  plan-1  H17   0.020
 KA5  plan-1  H19   0.020
 KA5  plan-1  H20   0.020
 KA5  plan-2  N1    0.020
 KA5  plan-2  C2    0.020
 KA5  plan-2  N3    0.020
 KA5  plan-2  C4    0.020
 KA5  plan-2  C5    0.020
 KA5  plan-2  C6    0.020
 KA5  plan-2  C7    0.020
 KA5  plan-2  C8    0.020
 KA5  plan-2  C9    0.020
 KA5  plan-2  C10   0.020
 KA5  plan-2  N11   0.020
 KA5  plan-2  N12   0.020
 KA5  plan-2  CL13  0.020
 KA5  plan-2  N14   0.020
 KA5  plan-2  H7    0.020
 KA5  plan-2  H8    0.020
 KA5  plan-3  C2    0.020
 KA5  plan-3  N11   0.020
 KA5  plan-3  HN11  0.020
 KA5  plan-3  HN1A  0.020
 KA5  plan-4  C4    0.020
 KA5  plan-4  N12   0.020
 KA5  plan-4  HN12  0.020
 KA5  plan-4  HN1B  0.020
 KA5  plan-5  C9    0.020
 KA5  plan-5  N14   0.020
 KA5  plan-5  C15   0.020
 KA5  plan-5  HN14  0.020

