# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 16:22:57 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 2-amino-6-(aminomethyl)-8-[(phenylsulfanyl)methyl]quinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cc(CSc2ccccc2)c3N=C(N)NC(=O)c3c1
#
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
 KMB  KMB  2-amino-6-(aminomethyl)-8-[(phenylsulfanyl)methyl]quinazolin-4(3H)-one  ligand  38  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KMB
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
 KMB  C4    C  CH2   0  -0.325   3.6475  -0.1108   2.8784
 KMB  N4    N  NH2   0  -0.797   3.7272  -0.0340   4.3239
 KMB  C6    C  CR6   0   0.079   2.2387   0.0597   2.3679
 KMB  C1    C  CR16  0  -0.323   2.0277   0.3689   1.0165
 KMB  C2    C  CR6   0   0.050   0.7695   0.5247   0.4741
 KMB  C3    C  CR66  0   0.245  -0.3654   0.3642   1.3002
 KMB  N3    N  N     0  -0.510  -1.6050   0.5201   0.7537
 KMB  C8    C  CR6   0   0.664  -2.6301   0.3805   1.5353
 KMB  N2    N  NH2   0  -0.834  -3.8758   0.5653   1.0687
 KMB  N1    N  NR16  0  -0.717  -2.5166   0.0788   2.8649
 KMB  C7    C  CR6   0   0.551  -1.3164  -0.0971   3.5176
 KMB  O1    O  OC    0  -0.459  -1.2892  -0.3599   4.7073
 KMB  C41   C  CR66  0  -0.095  -0.1548   0.0608   2.6547
 KMB  C5    C  CR16  0  -0.353   1.1336  -0.0900   3.1765
 KMB  C9    C  CH2   0  -0.651   0.6020   0.8472  -0.9775
 KMB  S1    S  S2    0   0.056   0.3286  -0.7213  -1.8575
 KMB  C10   C  CR6   0  -0.099   0.1129  -0.2380  -3.5372
 KMB  C11   C  CR16  0  -0.267   0.1376   1.0827  -3.9788
 KMB  C12   C  CR16  0  -0.236  -0.0386   1.3685  -5.3276
 KMB  C13   C  CR16  0  -0.273  -0.2405   0.3509  -6.2475
 KMB  C14   C  CR16  0  -0.241  -0.2682  -0.9670  -5.8060
 KMB  C15   C  CR16  0  -0.271  -0.0924  -1.2634  -4.4646
 KMB  H41   H  HCH2  0   0.216   4.2926   0.6119   2.3596
 KMB  H42   H  HCH2  0   0.244   4.0101  -1.0978   2.5752
 KMB  HN41  H  HNH2  0   0.357   4.6603  -0.2867   4.6204
 KMB  HN42  H  HNH2  0   0.345   3.5877   0.9229   4.6238
 KMB  H1    H  HCR6  0   0.251   2.8902   0.4979   0.3701
 KMB  HN21  H  HNH2  0   0.409  -3.9913   0.6198   0.0711
 KMB  HN22  H  HNH2  0   0.412  -4.6758   0.2538   1.5923
 KMB  HN1   H  HNR6  0   0.425  -3.3540  -0.0215   3.4243
 KMB  H5    H  HCR6  0   0.256   1.2605  -0.3209   4.2258
 KMB  H91   H  HCH2  0   0.292  -0.2514   1.5054  -1.1362
 KMB  H92   H  HCH2  0   0.294   1.4995   1.3270  -1.3690
 KMB  H11   H  HCR6  0   0.268   0.2886   1.8997  -3.2875
 KMB  H12   H  HCR6  0   0.259  -0.0169   2.4004  -5.6540
 KMB  H13   H  HCR6  0   0.256  -0.3756   0.5787  -7.2964
 KMB  H14   H  HCR6  0   0.260  -0.4257  -1.7736  -6.5103
 KMB  H15   H  HCR6  0   0.262  -0.1140  -2.2961  -4.1368

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
 KMB  C4   N4    single    1.450  0.020  1.450
 KMB  C4   C6    single    1.508  0.020  1.508
 KMB  C4   H41   single    0.970  0.020  1.090
 KMB  C4   H42   single    0.970  0.020  1.090
 KMB  N4   HN41  single    0.890  0.020  1.040
 KMB  N4   HN42  single    0.890  0.020  1.040
 KMB  C6   C1    aromatic  1.402  0.020  1.402
 KMB  C6   C5    aromatic  1.378  0.020  1.378
 KMB  C1   C2    aromatic  1.379  0.020  1.379
 KMB  C1   H1    single    0.930  0.020  1.080
 KMB  C2   C3    aromatic  1.413  0.020  1.413
 KMB  C2   C9    single    1.496  0.020  1.496
 KMB  C3   N3    aromatic  1.364  0.020  1.364
 KMB  C3   C41   aromatic  1.404  0.020  1.404
 KMB  N3   C8    aromatic  1.297  0.020  1.297
 KMB  C8   N2    single    1.343  0.020  1.343
 KMB  C8   N1    aromatic  1.368  0.020  1.368
 KMB  N2   HN21  single    0.890  0.020  1.040
 KMB  N2   HN22  single    0.890  0.020  1.040
 KMB  N1   C7    aromatic  1.378  0.020  1.378
 KMB  N1   HN1   single    0.860  0.020  1.020
 KMB  C7   O1    double    1.219  0.020  1.219
 KMB  C7   C41   aromatic  1.456  0.020  1.456
 KMB  C41  C5    aromatic  1.398  0.020  1.398
 KMB  C5   H5    single    0.930  0.020  1.080
 KMB  C9   S1    single    1.819  0.020  1.819
 KMB  C9   H91   single    0.970  0.020  1.090
 KMB  C9   H92   single    0.970  0.020  1.090
 KMB  S1   C10   single    1.761  0.020  1.761
 KMB  C10  C11   aromatic  1.393  0.020  1.393
 KMB  C10  C15   aromatic  1.398  0.020  1.398
 KMB  C11  C12   aromatic  1.390  0.020  1.390
 KMB  C11  H11   single    0.930  0.020  1.080
 KMB  C12  C13   aromatic  1.386  0.020  1.386
 KMB  C12  H12   single    0.930  0.020  1.080
 KMB  C13  C14   aromatic  1.390  0.020  1.390
 KMB  C13  H13   single    0.930  0.020  1.080
 KMB  C14  C15   aromatic  1.385  0.020  1.385
 KMB  C14  H14   single    0.930  0.020  1.080
 KMB  C15  H15   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
 KMB  H42   C4   H41   105.54  3.000
 KMB  H42   C4   C6    108.52  3.000
 KMB  H41   C4   C6    108.31  3.000
 KMB  H42   C4   N4    107.81  3.000
 KMB  H41   C4   N4    113.80  3.000
 KMB  C6    C4   N4    112.51  3.000
 KMB  HN42  N4   HN41  106.05  3.000
 KMB  HN42  N4   C4    109.75  3.000
 KMB  HN41  N4   C4    109.26  3.000
 KMB  C5    C6   C1    117.97  3.000
 KMB  C5    C6   C4    122.58  3.000
 KMB  C1    C6   C4    119.45  3.000
 KMB  H1    C1   C2    118.51  3.000
 KMB  H1    C1   C6    118.72  3.000
 KMB  C2    C1   C6    122.77  3.000
 KMB  C9    C2   C3    120.12  3.000
 KMB  C9    C2   C1    120.53  3.000
 KMB  C3    C2   C1    119.35  3.000
 KMB  C41   C3   N3    123.20  3.000
 KMB  C41   C3   C2    117.92  3.000
 KMB  N3    C3   C2    118.88  3.000
 KMB  C8    N3   C3    117.70  3.000
 KMB  N1    C8   N2    116.42  3.000
 KMB  N1    C8   N3    122.96  3.000
 KMB  N2    C8   N3    120.60  3.000
 KMB  HN22  N2   HN21  116.22  3.000
 KMB  HN22  N2   C8    120.96  3.000
 KMB  HN21  N2   C8    117.29  3.000
 KMB  HN1   N1   C7    116.51  3.000
 KMB  HN1   N1   C8    119.37  3.000
 KMB  C7    N1   C8    124.12  3.000
 KMB  C41   C7   O1    125.75  3.000
 KMB  C41   C7   N1    113.62  3.000
 KMB  O1    C7   N1    120.63  3.000
 KMB  C5    C41  C7    120.16  3.000
 KMB  C5    C41  C3    121.44  3.000
 KMB  C7    C41  C3    118.40  3.000
 KMB  H5    C5   C41   119.55  3.000
 KMB  H5    C5   C6    119.89  3.000
 KMB  C41   C5   C6    120.56  3.000
 KMB  H92   C9   H91   109.07  3.000
 KMB  H92   C9   S1    109.24  3.000
 KMB  H91   C9   S1    109.43  3.000
 KMB  H92   C9   C2    110.55  3.000
 KMB  H91   C9   C2    111.05  3.000
 KMB  S1    C9   C2    107.47  3.000
 KMB  C10   S1   C9    104.07  3.000
 KMB  C15   C10  C11   119.20  3.000
 KMB  C15   C10  S1    116.71  3.000
 KMB  C11   C10  S1    124.09  3.000
 KMB  H11   C11  C12   118.88  3.000
 KMB  H11   C11  C10   121.09  3.000
 KMB  C12   C11  C10   120.02  3.000
 KMB  H12   C12  C13   120.17  3.000
 KMB  H12   C12  C11   119.08  3.000
 KMB  C13   C12  C11   120.76  3.000
 KMB  H13   C13  C14   120.33  3.000
 KMB  H13   C13  C12   120.46  3.000
 KMB  C14   C13  C12   119.21  3.000
 KMB  H14   C14  C15   119.29  3.000
 KMB  H14   C14  C13   120.19  3.000
 KMB  C15   C14  C13   120.52  3.000
 KMB  H15   C15  C14   119.62  3.000
 KMB  H15   C15  C10   120.09  3.000
 KMB  C14   C15  C10   120.28  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
 KMB  CONST_01  C3    C2   C1   C6     0.00   0.0  0
 KMB  CONST_02  C3    C41  C5   C6     0.00   0.0  0
 KMB  CONST_03  C7    C41  C5   C6   180.00   0.0  0
 KMB  CONST_04  C41   C5   C6   C1     0.00   0.0  0
 KMB  CONST_05  N3    C3   C2   C1   180.00   0.0  0
 KMB  CONST_06  C41   C3   C2   C1     0.00   0.0  0
 KMB  CONST_07  C5    C6   C1   C2     0.00   0.0  0
 KMB  CONST_08  C8    N3   C3   C2   180.00   0.0  0
 KMB  CONST_09  C7    C41  C3   C2   180.00   0.0  0
 KMB  CONST_10  C5    C41  C3   C2     0.00   0.0  0
 KMB  CONST_11  N1    C8   N3   C3     0.00   0.0  0
 KMB  CONST_12  N1    C7   C41  C3     0.00   0.0  0
 KMB  CONST_13  C7    C41  C3   N3     0.00   0.0  0
 KMB  CONST_14  C5    C41  C3   N3   180.00   0.0  0
 KMB  CONST_15  C7    N1   C8   N3     0.00   0.0  0
 KMB  CONST_16  C41   C3   N3   C8     0.00   0.0  0
 KMB  CONST_17  C41   C7   N1   C8     0.00   0.0  0
 KMB  CONST_18  C5    C41  C7   N1   180.00   0.0  0
 KMB  CONST_19  C13   C12  C11  C10    0.00   0.0  0
 KMB  CONST_20  C13   C14  C15  C10    0.00   0.0  0
 KMB  CONST_21  C14   C15  C10  C11    0.00   0.0  0
 KMB  CONST_22  C14   C13  C12  C11    0.00   0.0  0
 KMB  CONST_23  C15   C10  C11  C12    0.00   0.0  0
 KMB  CONST_24  C15   C14  C13  C12    0.00   0.0  0
 KMB  CONST_25  C2    C1   C6   C4   180.00   0.0  0
 KMB  CONST_26  C41   C5   C6   C4   180.00   0.0  0
 KMB  CONST_27  C9    C2   C1   C6   180.00   0.0  0
 KMB  CONST_28  N2    C8   N3   C3   180.00   0.0  0
 KMB  CONST_29  O1    C7   C41  C3   180.00   0.0  0
 KMB  CONST_30  C9    C2   C3   N3     0.00   0.0  0
 KMB  CONST_31  O1    C7   N1   C8   180.00   0.0  0
 KMB  CONST_32  C7    N1   C8   N2   180.00   0.0  0
 KMB  CONST_33  C5    C41  C7   O1     0.00   0.0  0
 KMB  CONST_34  C9    C2   C3   C41  180.00   0.0  0
 KMB  CONST_35  C12   C11  C10  S1   180.00   0.0  0
 KMB  CONST_36  C14   C15  C10  S1   180.00   0.0  0
 KMB  CONST_37  H5    C5   C6   C1   180.00   0.0  0
 KMB  CONST_38  H1    C1   C2   C3   180.00   0.0  0
 KMB  CONST_39  HN1   N1   C8   N3   180.00   0.0  0
 KMB  CONST_40  H12   C12  C11  C10  180.00   0.0  0
 KMB  CONST_41  H14   C14  C15  C10  180.00   0.0  0
 KMB  CONST_42  H15   C15  C10  C11  180.00   0.0  0
 KMB  CONST_43  H13   C13  C12  C11  180.00   0.0  0
 KMB  CONST_44  H11   C11  C12  C13  180.00   0.0  0
 KMB  CONST_45  HN21  N2   C8   N3     0.00   0.0  0
 KMB  CONST_46  HN22  N2   C8   N3   180.00   0.0  0
 KMB  Var_01    C1    C6   C4   N4   162.99  30.0  2
 KMB  Var_02    S1    C9   C2   C1    95.41  30.0  2
 KMB  Var_03    C11   C10  S1   C9    -1.16  30.0  2
 KMB  Var_04    HN41  N4   C4   C6   171.83  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
 KMB  plan-1  S1    0.020
 KMB  plan-1  C10   0.020
 KMB  plan-1  C11   0.020
 KMB  plan-1  C12   0.020
 KMB  plan-1  C13   0.020
 KMB  plan-1  C14   0.020
 KMB  plan-1  C15   0.020
 KMB  plan-1  H11   0.020
 KMB  plan-1  H12   0.020
 KMB  plan-1  H13   0.020
 KMB  plan-1  H14   0.020
 KMB  plan-1  H15   0.020
 KMB  plan-2  C4    0.020
 KMB  plan-2  C6    0.020
 KMB  plan-2  C1    0.020
 KMB  plan-2  C2    0.020
 KMB  plan-2  C3    0.020
 KMB  plan-2  N3    0.020
 KMB  plan-2  C8    0.020
 KMB  plan-2  N2    0.020
 KMB  plan-2  N1    0.020
 KMB  plan-2  C7    0.020
 KMB  plan-2  O1    0.020
 KMB  plan-2  C41   0.020
 KMB  plan-2  C5    0.020
 KMB  plan-2  C9    0.020
 KMB  plan-2  H1    0.020
 KMB  plan-2  HN1   0.020
 KMB  plan-2  H5    0.020
 KMB  plan-3  C8    0.020
 KMB  plan-3  N2    0.020
 KMB  plan-3  HN21  0.020
 KMB  plan-3  HN22  0.020

