# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 02:52:31 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 6,7-dimethoxy-N-[3-(methylsulfanyl)phenyl]quinazolin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2ncnc(Nc3cccc(SC)c3)c2cc1OC
#
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
 MSQ  MSQ  6,7-dimethoxy-N-[3-(methylsulfanyl)phenyl]quinazolin-4-amine  ligand  40  23  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MSQ
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
 MSQ  N1    N  N     0  -0.485   1.6409  -0.2192  -0.5300
 MSQ  C2    C  CR16  0   0.046   2.7173  -0.2510   0.2655
 MSQ  N3    N  N     0  -0.461   2.7453  -0.2132   1.5660
 MSQ  C4    C  CR66  0   0.241   1.5397  -0.1145   2.1849
 MSQ  C5    C  CR66  0  -0.018   0.3334  -0.0585   1.4672
 MSQ  C6    C  CR6   0   0.540   0.4572  -0.1343   0.0411
 MSQ  C7    C  CR16  0  -0.467   1.5099  -0.0651   3.5949
 MSQ  C8    C  CR6   0   0.338   0.3212   0.0462   4.2670
 MSQ  C9    C  CR6   0   0.356  -0.9069   0.1232   3.5360
 MSQ  C10   C  CR16  0  -0.479  -0.8880   0.0684   2.1683
 MSQ  N12   N  NH1   0  -0.789  -0.6629  -0.1257  -0.7223
 MSQ  C14   C  CR6   0   0.390  -0.8362  -0.1690  -2.1055
 MSQ  C15   C  CR16  0  -0.322   0.1871  -0.0402  -3.0398
 MSQ  C16   C  CR6   0  -0.096  -0.1065  -0.0723  -4.4055
 MSQ  C17   C  CR16  0  -0.288  -1.4138  -0.2339  -4.8474
 MSQ  C18   C  CR16  0  -0.224  -2.4279  -0.3585  -3.9046
 MSQ  C19   C  CR16  0  -0.383  -2.1548  -0.3288  -2.5523
 MSQ  S21   S  S2    0   0.040   1.2781   0.1009  -5.4807
 MSQ  C22   C  CH3   0  -0.795   0.5446   0.1369  -7.1250
 MSQ  O26   O  O2    0  -0.451   0.1859   0.0967   5.5931
 MSQ  C27   C  CH3   0  -0.443   1.3531  -0.0012   6.3904
 MSQ  O31   O  O2    0  -0.458  -2.0028   0.2503   4.2942
 MSQ  C32   C  CH3   0  -0.445  -3.2565   0.3491   3.6455
 MSQ  H21   H  HCR6  0   0.249   3.6716  -0.3210  -0.2468
 MSQ  H71   H  HCR6  0   0.288   2.4544  -0.1170   4.1195
 MSQ  H101  H  HCR6  0   0.283  -1.8246   0.1347   1.6314
 MSQ  H121  H  HNH1  0   0.431  -1.5332  -0.1321  -0.2170
 MSQ  H151  H  HCR6  0   0.291   1.2057   0.0849  -2.7084
 MSQ  H171  H  HCR6  0   0.263  -1.6556  -0.2671  -5.9001
 MSQ  H181  H  HCR6  0   0.263  -3.4503  -0.4845  -4.2364
 MSQ  H191  H  HCR6  0   0.270  -2.9613  -0.4285  -1.8358
 MSQ  H221  H  HCH3  0   0.294   1.3713   0.2866  -7.8166
 MSQ  H222  H  HCH3  0   0.274   0.0520  -0.8018  -7.3713
 MSQ  H223  H  HCH3  0   0.275  -0.1542   0.9642  -7.2342
 MSQ  H271  H  HCH3  0   0.267   1.0227   0.0458   7.4244
 MSQ  H272  H  HCH3  0   0.236   1.8750  -0.9466   6.2249
 MSQ  H273  H  HCH3  0   0.236   2.0438   0.8233   6.1989
 MSQ  H321  H  HCH3  0   0.267  -4.0007   0.4596   4.4294
 MSQ  H322  H  HCH3  0   0.234  -3.3036   1.2200   2.9869
 MSQ  H323  H  HCH3  0   0.234  -3.4836  -0.5486   3.0645

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
 MSQ  N1   C2    aromatic  1.339  0.020  1.339
 MSQ  N1   C6    aromatic  1.317  0.020  1.317
 MSQ  C2   N3    aromatic  1.301  0.020  1.301
 MSQ  C2   H21   single    0.930  0.020  1.080
 MSQ  N3   C4    aromatic  1.359  0.020  1.359
 MSQ  C4   C5    aromatic  1.405  0.020  1.405
 MSQ  C4   C7    aromatic  1.411  0.020  1.411
 MSQ  C5   C6    aromatic  1.433  0.020  1.433
 MSQ  C5   C10   aromatic  1.414  0.020  1.414
 MSQ  C6   N12   single    1.356  0.020  1.356
 MSQ  C7   C8    aromatic  1.370  0.020  1.370
 MSQ  C7   H71   single    0.930  0.020  1.080
 MSQ  C8   C9    aromatic  1.431  0.020  1.431
 MSQ  C8   O26   single    1.334  0.020  1.334
 MSQ  C9   C10   aromatic  1.369  0.020  1.369
 MSQ  C9   O31   single    1.339  0.020  1.339
 MSQ  C10  H101  single    0.930  0.020  1.080
 MSQ  N12  C14   single    1.395  0.020  1.395
 MSQ  N12  H121  single    0.860  0.020  1.020
 MSQ  C14  C15   aromatic  1.392  0.020  1.392
 MSQ  C14  C19   aromatic  1.401  0.020  1.401
 MSQ  C15  C16   aromatic  1.397  0.020  1.397
 MSQ  C15  H151  single    0.930  0.020  1.080
 MSQ  C16  C17   aromatic  1.389  0.020  1.389
 MSQ  C16  S21   single    1.762  0.020  1.762
 MSQ  C17  C18   aromatic  1.390  0.020  1.390
 MSQ  C17  H171  single    0.930  0.020  1.080
 MSQ  C18  C19   aromatic  1.380  0.020  1.380
 MSQ  C18  H181  single    0.930  0.020  1.080
 MSQ  C19  H191  single    0.930  0.020  1.080
 MSQ  S21  C22   single    1.801  0.020  1.801
 MSQ  C22  H221  single    0.970  0.020  1.090
 MSQ  C22  H222  single    0.970  0.020  1.090
 MSQ  C22  H223  single    0.970  0.020  1.090
 MSQ  O26  C27   single    1.417  0.020  1.417
 MSQ  C27  H271  single    0.970  0.020  1.090
 MSQ  C27  H272  single    0.970  0.020  1.090
 MSQ  C27  H273  single    0.970  0.020  1.090
 MSQ  O31  C32   single    1.415  0.020  1.415
 MSQ  C32  H321  single    0.970  0.020  1.090
 MSQ  C32  H322  single    0.970  0.020  1.090
 MSQ  C32  H323  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
 MSQ  C6    N1   C2    117.80  3.000
 MSQ  H21   C2   N3    117.04  3.000
 MSQ  H21   C2   N1    115.34  3.000
 MSQ  N3    C2   N1    127.62  3.000
 MSQ  C4    N3   C2    115.99  3.000
 MSQ  C7    C4   C5    119.40  3.000
 MSQ  C7    C4   N3    118.45  3.000
 MSQ  C5    C4   N3    122.15  3.000
 MSQ  C10   C5   C6    124.93  3.000
 MSQ  C10   C5   C4    119.47  3.000
 MSQ  C6    C5   C4    115.59  3.000
 MSQ  N12   C6   C5    119.25  3.000
 MSQ  N12   C6   N1    119.92  3.000
 MSQ  C5    C6   N1    120.83  3.000
 MSQ  H71   C7   C8    121.57  3.000
 MSQ  H71   C7   C4    117.68  3.000
 MSQ  C8    C7   C4    120.75  3.000
 MSQ  O26   C8   C9    114.75  3.000
 MSQ  O26   C8   C7    125.36  3.000
 MSQ  C9    C8   C7    119.89  3.000
 MSQ  O31   C9   C10   125.52  3.000
 MSQ  O31   C9   C8    114.72  3.000
 MSQ  C10   C9   C8    119.76  3.000
 MSQ  H101  C10  C9    118.79  3.000
 MSQ  H101  C10  C5    120.49  3.000
 MSQ  C9    C10  C5    120.72  3.000
 MSQ  H121  N12  C14   112.97  3.000
 MSQ  H121  N12  C6    115.58  3.000
 MSQ  C14   N12  C6    131.38  3.000
 MSQ  C19   C14  C15   119.23  3.000
 MSQ  C19   C14  N12   115.89  3.000
 MSQ  C15   C14  N12   124.86  3.000
 MSQ  H151  C15  C16   120.10  3.000
 MSQ  H151  C15  C14   119.93  3.000
 MSQ  C16   C15  C14   119.97  3.000
 MSQ  S21   C16  C17   123.84  3.000
 MSQ  S21   C16  C15   115.41  3.000
 MSQ  C17   C16  C15   120.75  3.000
 MSQ  H171  C17  C18   119.65  3.000
 MSQ  H171  C17  C16   121.60  3.000
 MSQ  C18   C17  C16   118.75  3.000
 MSQ  H181  C18  C19   119.34  3.000
 MSQ  H181  C18  C17   119.45  3.000
 MSQ  C19   C18  C17   121.22  3.000
 MSQ  H191  C19  C18   119.92  3.000
 MSQ  H191  C19  C14   120.00  3.000
 MSQ  C18   C19  C14   120.08  3.000
 MSQ  C22   S21  C16   103.83  3.000
 MSQ  H223  C22  H222  110.01  3.000
 MSQ  H223  C22  H221  108.63  3.000
 MSQ  H222  C22  H221  108.58  3.000
 MSQ  H223  C22  S21   111.62  3.000
 MSQ  H222  C22  S21   111.95  3.000
 MSQ  H221  C22  S21   105.88  3.000
 MSQ  C27   O26  C8    118.24  3.000
 MSQ  H273  C27  H272  108.94  3.000
 MSQ  H273  C27  H271  109.05  3.000
 MSQ  H272  C27  H271  109.08  3.000
 MSQ  H273  C27  O26   111.72  3.000
 MSQ  H272  C27  O26   111.59  3.000
 MSQ  H271  C27  O26   106.38  3.000
 MSQ  C32   O31  C9    118.18  3.000
 MSQ  H323  C32  H322  108.98  3.000
 MSQ  H323  C32  H321  108.95  3.000
 MSQ  H322  C32  H321  108.92  3.000
 MSQ  H323  C32  O31   111.74  3.000
 MSQ  H322  C32  O31   111.72  3.000
 MSQ  H321  C32  O31   106.45  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
 MSQ  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 MSQ  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 MSQ  CONST_03  C10   C5   C6   N1    180.00   0.0  0
 MSQ  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 MSQ  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 MSQ  CONST_06  C7    C4   N3   C2    180.00   0.0  0
 MSQ  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 MSQ  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 MSQ  CONST_09  C10   C5   C4   N3    180.00   0.0  0
 MSQ  CONST_10  C8    C7   C4   N3    180.00   0.0  0
 MSQ  CONST_11  C9    C10  C5   C4      0.00   0.0  0
 MSQ  CONST_12  C9    C8   C7   C4      0.00   0.0  0
 MSQ  CONST_13  C8    C7   C4   C5      0.00   0.0  0
 MSQ  CONST_14  C8    C9   C10  C5      0.00   0.0  0
 MSQ  CONST_15  C7    C4   C5   C6    180.00   0.0  0
 MSQ  CONST_16  C9    C10  C5   C6    180.00   0.0  0
 MSQ  CONST_17  C10   C5   C4   C7      0.00   0.0  0
 MSQ  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 MSQ  CONST_19  C17   C16  C15  C14     0.00   0.0  0
 MSQ  CONST_20  C17   C18  C19  C14     0.00   0.0  0
 MSQ  CONST_21  C18   C19  C14  C15     0.00   0.0  0
 MSQ  CONST_22  C18   C17  C16  C15     0.00   0.0  0
 MSQ  CONST_23  C19   C14  C15  C16     0.00   0.0  0
 MSQ  CONST_24  C19   C18  C17  C16     0.00   0.0  0
 MSQ  CONST_25  N12   C6   N1   C2    180.00   0.0  0
 MSQ  CONST_26  N12   C6   C5   C4    180.00   0.0  0
 MSQ  CONST_27  O26   C8   C7   C4    180.00   0.0  0
 MSQ  CONST_28  O31   C9   C10  C5    180.00   0.0  0
 MSQ  CONST_29  O31   C9   C8   C7    180.00   0.0  0
 MSQ  CONST_30  N12   C6   C5   C10     0.00   0.0  0
 MSQ  CONST_31  O26   C8   C9   C10   180.00   0.0  0
 MSQ  CONST_32  C16   C15  C14  N12   180.00   0.0  0
 MSQ  CONST_33  C18   C19  C14  N12   180.00   0.0  0
 MSQ  CONST_34  S21   C16  C15  C14   180.00   0.0  0
 MSQ  CONST_35  S21   C16  C17  C18   180.00   0.0  0
 MSQ  CONST_36  H71   C7   C4   N3      0.00   0.0  0
 MSQ  CONST_37  H21   C2   N3   C4    180.00   0.0  0
 MSQ  CONST_38  H101  C10  C5   C4    180.00   0.0  0
 MSQ  CONST_39  H181  C18  C19  C14   180.00   0.0  0
 MSQ  CONST_40  H191  C19  C14  C15   180.00   0.0  0
 MSQ  CONST_41  H171  C17  C16  C15   180.00   0.0  0
 MSQ  CONST_42  H151  C15  C16  C17   180.00   0.0  0
 MSQ  Var_01    C14   N12  C6   N1     -1.36  30.0  2
 MSQ  Var_02    C15   C14  N12  C6     -9.78  30.0  2
 MSQ  Var_03    H271  C27  O26  C8   -179.15  30.0  3
 MSQ  Var_04    H321  C32  O31  C9   -179.13  30.0  3
 MSQ  Var_05    H221  C22  S21  C16   177.63  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
 MSQ  plan-1  N12   0.020
 MSQ  plan-1  C14   0.020
 MSQ  plan-1  C15   0.020
 MSQ  plan-1  C16   0.020
 MSQ  plan-1  C17   0.020
 MSQ  plan-1  C18   0.020
 MSQ  plan-1  C19   0.020
 MSQ  plan-1  S21   0.020
 MSQ  plan-1  H151  0.020
 MSQ  plan-1  H171  0.020
 MSQ  plan-1  H181  0.020
 MSQ  plan-1  H191  0.020
 MSQ  plan-2  N1    0.020
 MSQ  plan-2  C2    0.020
 MSQ  plan-2  N3    0.020
 MSQ  plan-2  C4    0.020
 MSQ  plan-2  C5    0.020
 MSQ  plan-2  C6    0.020
 MSQ  plan-2  C7    0.020
 MSQ  plan-2  C8    0.020
 MSQ  plan-2  C9    0.020
 MSQ  plan-2  C10   0.020
 MSQ  plan-2  N12   0.020
 MSQ  plan-2  O26   0.020
 MSQ  plan-2  O31   0.020
 MSQ  plan-2  H21   0.020
 MSQ  plan-2  H71   0.020
 MSQ  plan-2  H101  0.020

