# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 01:20:55 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 1-{[4-(aminomethyl)phenyl]carbonyl}-5'-fluoro-1'H-spiro[piperidine-4,2'-quinazolin]-4'-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(cc1)C(=O)N2CCC3(CC2)Nc4cccc(F)c4C(=N3)N
#
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
 XXZ  XXZ  1-{[4-(aminomethyl)phenyl]carbonyl}-5'-fluoro-1'H-spiro[piperidine-4,2'-quinazolin]-4'-amine  ligand  49  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XXZ
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
 XXZ  F1    F  F     0  -0.310   5.1541  -1.7868   1.6793
 XXZ  C2    C  CR6   0   0.544   4.6789  -1.4755   0.4631
 XXZ  C3    C  CR16  0  -0.444   5.1113  -2.2385  -0.5994
 XXZ  C4    C  CR16  0  -0.234   4.6288  -1.9250  -1.8665
 XXZ  C1    C  CR16  0  -0.360   3.7197  -0.9041  -2.0542
 XXZ  C6    C  CR6   0   0.406   3.2740  -0.1586  -0.9567
 XXZ  C7    C  CR6   0  -0.315   3.7838  -0.4177   0.3324
 XXZ  CG    C  C     0   0.438   3.3579   0.5239   1.3848
 XXZ  N20   N  N     0  -0.440   2.3618   1.3167   1.2362
 XXZ  N21   N  NH2   0  -0.827   4.0531   0.5606   2.5559
 XXZ  N1    N  NH1   0  -0.707   2.3726   0.8496  -1.0871
 XXZ  C5    C  CT    0   0.214   1.5401   1.1895   0.0609
 XXZ  C10   C  CH2   0  -0.438   0.8641   2.5356  -0.2117
 XXZ  C11   C  CH2   0  -0.349  -0.2209   2.4440  -1.2784
 XXZ  N12   N  NT    0  -0.440  -1.2085   1.4359  -0.9281
 XXZ  C13   C  CH2   0  -0.334  -0.6207   0.1126  -0.7788
 XXZ  C14   C  CH2   0  -0.416   0.4498   0.1260   0.3049
 XXZ  C15   C  C     0   0.517  -2.3879   1.8152  -0.3867
 XXZ  O16   O  O     0  -0.488  -2.6777   2.9878  -0.1834
 XXZ  C18   C  CR16  0  -0.251  -3.7915  -0.1970  -1.0027
 XXZ  NH    N  NH2   0  -0.792  -6.2038  -3.4164   0.3699
 XXZ  C8    C  CR6   0   0.094  -5.3925  -1.1109   0.5599
 XXZ  CD1   C  CR16  0  -0.302  -4.9832  -0.1616   1.4915
 XXZ  CE1   C  CR16  0  -0.258  -4.0064   0.7724   1.1803
 XXZ  CD2   C  CR16  0  -0.275  -4.7847  -1.1125  -0.6941
 XXZ  CZ    C  CR6   0  -0.082  -3.3878   0.7515  -0.0647
 XXZ  H3    H  HCR6  0   0.276   5.8019  -3.0552  -0.4427
 XXZ  H4    H  HCR6  0   0.271   4.9574  -2.5082  -2.7167
 XXZ  H1    H  HCR6  0   0.267   3.3322  -0.6875  -3.0417
 XXZ  H211  H  HNH2  0   0.391   5.0290   0.3215   2.5544
 XXZ  H212  H  HNH2  0   0.380   3.8247   1.3378   3.1558
 XXZ  HN1   H  HNH1  0   0.387   1.9907   0.9885  -2.0096
 XXZ  H101  H  HCH2  0   0.249   1.6196   3.2682  -0.5042
 XXZ  H102  H  HCH2  0   0.246   0.4170   2.8842   0.7216
 XXZ  H111  H  HCH2  0   0.250   0.1996   2.1760  -2.2530
 XXZ  H112  H  HCH2  0   0.276  -0.7082   3.4067  -1.4054
 XXZ  H131  H  HCH2  0   0.281  -1.3821  -0.6216  -0.5324
 XXZ  H132  H  HCH2  0   0.246  -0.2016  -0.1895  -1.7427
 XXZ  H141  H  HCH2  0   0.248   0.9054  -0.8656   0.3766
 XXZ  H142  H  HCH2  0   0.239  -0.0204   0.3299   1.2707
 XXZ  H18   H  HCR6  0   0.265  -3.3371  -0.2172  -1.9859
 XXZ  HNH1  H  HNH2  0   0.344  -5.4286  -3.8212   0.8799
 XXZ  HNH2  H  HNH2  0   0.354  -6.9970  -4.0193   0.5451
 XXZ  HB1   H  HCH2  0   0.243  -7.4164  -1.7413   0.4387
 XXZ  HB2   H  HCH2  0   0.217  -6.6579  -2.0676   1.9799
 XXZ  HD1   H  HCR6  0   0.252  -5.4343  -0.1487   2.4767
 XXZ  HE1   H  HCR6  0   0.257  -3.7147   1.5068   1.9204
 XXZ  HD2   H  HCR6  0   0.251  -5.0885  -1.8415  -1.4340
 XXZ  CB    C  CH2   0  -0.341  -6.4860  -2.0918   0.8955

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
 XXZ  F1   C2    single    1.342  0.020  1.342
 XXZ  C2   C3    aromatic  1.378  0.020  1.378
 XXZ  C2   C7    aromatic  1.392  0.020  1.392
 XXZ  C3   C4    aromatic  1.392  0.020  1.392
 XXZ  C3   H3    single    0.930  0.020  1.080
 XXZ  C4   C1    aromatic  1.380  0.020  1.380
 XXZ  C4   H4    single    0.930  0.020  1.080
 XXZ  C1   C6    aromatic  1.400  0.020  1.400
 XXZ  C1   H1    single    0.930  0.020  1.080
 XXZ  C6   C7    aromatic  1.410  0.020  1.410
 XXZ  C6   N1    single    1.359  0.020  1.359
 XXZ  C7   CG    single    1.475  0.020  1.475
 XXZ  CG   N20   double    1.282  0.020  1.282
 XXZ  CG   N21   single    1.362  0.020  1.362
 XXZ  N20  C5    single    1.440  0.020  1.440
 XXZ  N21  H211  single    0.890  0.020  1.040
 XXZ  N21  H212  single    0.890  0.020  1.040
 XXZ  N1   C5    single    1.458  0.020  1.458
 XXZ  N1   HN1   single    0.890  0.020  1.040
 XXZ  C5   C10   single    1.531  0.020  1.531
 XXZ  C5   C14   single    1.542  0.020  1.542
 XXZ  C10  C11   single    1.524  0.020  1.524
 XXZ  C10  H101  single    0.970  0.020  1.090
 XXZ  C10  H102  single    0.970  0.020  1.090
 XXZ  C11  N12   single    1.454  0.020  1.454
 XXZ  C11  H111  single    0.970  0.020  1.090
 XXZ  C11  H112  single    0.970  0.020  1.090
 XXZ  N12  C13   single    1.456  0.020  1.456
 XXZ  N12  C15   single    1.352  0.020  1.352
 XXZ  C13  C14   single    1.523  0.020  1.523
 XXZ  C13  H131  single    0.970  0.020  1.090
 XXZ  C13  H132  single    0.970  0.020  1.090
 XXZ  C14  H141  single    0.970  0.020  1.090
 XXZ  C14  H142  single    0.970  0.020  1.090
 XXZ  C15  O16   double    1.225  0.020  1.225
 XXZ  C15  CZ    single    1.495  0.020  1.495
 XXZ  C18  CD2   aromatic  1.386  0.020  1.386
 XXZ  C18  CZ    aromatic  1.394  0.020  1.394
 XXZ  C18  H18   single    0.930  0.020  1.080
 XXZ  NH   CB    single    1.453  0.020  1.453
 XXZ  NH   HNH1  single    0.890  0.020  1.040
 XXZ  NH   HNH2  single    0.890  0.020  1.040
 XXZ  CB   C8    single    1.507  0.020  1.507
 XXZ  CB   HB1   single    0.970  0.020  1.090
 XXZ  CB   HB2   single    0.970  0.020  1.090
 XXZ  C8   CD1   aromatic  1.392  0.020  1.392
 XXZ  C8   CD2   aromatic  1.394  0.020  1.394
 XXZ  CD1  CE1   aromatic  1.387  0.020  1.387
 XXZ  CD1  HD1   single    0.930  0.020  1.080
 XXZ  CE1  CZ    aromatic  1.390  0.020  1.390
 XXZ  CE1  HE1   single    0.930  0.020  1.080
 XXZ  CD2  HD2   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
 XXZ  C7    C2   C3    123.39  3.000
 XXZ  C7    C2   F1    119.27  3.000
 XXZ  C3    C2   F1    117.34  3.000
 XXZ  H3    C3   C4    121.58  3.000
 XXZ  H3    C3   C2    120.48  3.000
 XXZ  C4    C3   C2    117.95  3.000
 XXZ  H4    C4   C1    119.47  3.000
 XXZ  H4    C4   C3    119.26  3.000
 XXZ  C1    C4   C3    121.26  3.000
 XXZ  H1    C1   C6    119.65  3.000
 XXZ  H1    C1   C4    120.52  3.000
 XXZ  C6    C1   C4    119.82  3.000
 XXZ  N1    C6   C7    117.64  3.000
 XXZ  N1    C6   C1    122.09  3.000
 XXZ  C7    C6   C1    120.25  3.000
 XXZ  CG    C7   C6    115.51  3.000
 XXZ  CG    C7   C2    127.14  3.000
 XXZ  C6    C7   C2    117.25  3.000
 XXZ  N21   CG   N20   118.65  3.000
 XXZ  N21   CG   C7    118.90  3.000
 XXZ  N20   CG   C7    122.45  3.000
 XXZ  C5    N20  CG    118.92  3.000
 XXZ  H212  N21  H211  113.86  3.000
 XXZ  H212  N21  CG    114.63  3.000
 XXZ  H211  N21  CG    119.20  3.000
 XXZ  HN1   N1   C5    118.17  3.000
 XXZ  HN1   N1   C6    116.19  3.000
 XXZ  C5    N1   C6    118.44  3.000
 XXZ  C14   C5   C10   108.80  3.000
 XXZ  C14   C5   N1    111.55  3.000
 XXZ  C10   C5   N1    108.47  3.000
 XXZ  C14   C5   N20   109.59  3.000
 XXZ  C10   C5   N20   108.64  3.000
 XXZ  N1    C5   N20   109.72  3.000
 XXZ  H102  C10  H101  107.33  3.000
 XXZ  H102  C10  C11   109.02  3.000
 XXZ  H101  C10  C11   110.20  3.000
 XXZ  H102  C10  C5    108.02  3.000
 XXZ  H101  C10  C5    109.40  3.000
 XXZ  C11   C10  C5    112.71  3.000
 XXZ  H112  C11  H111  106.56  3.000
 XXZ  H112  C11  N12   109.74  3.000
 XXZ  H111  C11  N12   107.80  3.000
 XXZ  H112  C11  C10   110.35  3.000
 XXZ  H111  C11  C10   111.37  3.000
 XXZ  N12   C11  C10   110.89  3.000
 XXZ  C15   N12  C13   124.49  3.000
 XXZ  C15   N12  C11   119.64  3.000
 XXZ  C13   N12  C11   112.37  3.000
 XXZ  H132  C13  H131  106.38  3.000
 XXZ  H132  C13  C14   111.11  3.000
 XXZ  H131  C13  C14   109.71  3.000
 XXZ  H132  C13  N12   108.38  3.000
 XXZ  H131  C13  N12   110.77  3.000
 XXZ  C14   C13  N12   110.41  3.000
 XXZ  H142  C14  H141  106.88  3.000
 XXZ  H142  C14  C13   109.13  3.000
 XXZ  H141  C14  C13   109.35  3.000
 XXZ  H142  C14  C5    108.37  3.000
 XXZ  H141  C14  C5    109.94  3.000
 XXZ  C13   C14  C5    112.97  3.000
 XXZ  CZ    C15  O16   119.15  3.000
 XXZ  CZ    C15  N12   118.04  3.000
 XXZ  O16   C15  N12   122.78  3.000
 XXZ  H18   C18  CZ    120.13  3.000
 XXZ  H18   C18  CD2   119.37  3.000
 XXZ  CZ    C18  CD2   120.50  3.000
 XXZ  HNH2  NH   HNH1  105.96  3.000
 XXZ  HNH2  NH   CB    109.17  3.000
 XXZ  HNH1  NH   CB    109.34  3.000
 XXZ  CD2   C8   CD1   118.35  3.000
 XXZ  CD2   C8   CB    121.08  3.000
 XXZ  CD1   C8   CB    120.56  3.000
 XXZ  HD1   CD1  CE1   119.29  3.000
 XXZ  HD1   CD1  C8    119.63  3.000
 XXZ  CE1   CD1  C8    121.09  3.000
 XXZ  HE1   CE1  CZ    120.16  3.000
 XXZ  HE1   CE1  CD1   119.55  3.000
 XXZ  CZ    CE1  CD1   120.28  3.000
 XXZ  HD2   CD2  C8    119.58  3.000
 XXZ  HD2   CD2  C18   119.61  3.000
 XXZ  C8    CD2  C18   120.81  3.000
 XXZ  CE1   CZ   C18   118.95  3.000
 XXZ  CE1   CZ   C15   118.67  3.000
 XXZ  C18   CZ   C15   122.21  3.000
 XXZ  HB2   CB   HB1   105.79  3.000
 XXZ  HB2   CB   C8    108.61  3.000
 XXZ  HB1   CB   C8    108.40  3.000
 XXZ  HB2   CB   NH    114.06  3.000
 XXZ  HB1   CB   NH    107.83  3.000
 XXZ  C8    CB   NH    111.84  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
 XXZ  CONST_01  C1    C4   C3   C2      0.00   0.0  0
 XXZ  CONST_02  C1    C6   C7   C2      0.00   0.0  0
 XXZ  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 XXZ  CONST_04  C6    C1   C4   C3      0.00   0.0  0
 XXZ  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 XXZ  CONST_06  C7    C6   C1   C4      0.00   0.0  0
 XXZ  CONST_07  CD1   C8   CD2  C18     0.00   0.0  0
 XXZ  CONST_08  CD1   CE1  CZ   C18     0.00   0.0  0
 XXZ  CONST_09  CZ    CE1  CD1  C8      0.00   0.0  0
 XXZ  CONST_10  CZ    C18  CD2  C8      0.00   0.0  0
 XXZ  CONST_11  CD2   C8   CD1  CE1     0.00   0.0  0
 XXZ  CONST_12  CD2   C18  CZ   CE1     0.00   0.0  0
 XXZ  CONST_13  C5    N20  CG   C7      0.00   0.0  0
 XXZ  CONST_14  C4    C3   C2   F1    180.00   0.0  0
 XXZ  CONST_15  C6    C7   C2   F1    180.00   0.0  0
 XXZ  CONST_16  CG    C7   C2   F1      0.00   0.0  0
 XXZ  CONST_17  CD2   C18  CZ   C15   180.00   0.0  0
 XXZ  CONST_18  CD1   CE1  CZ   C15   180.00   0.0  0
 XXZ  CONST_19  CB    C8   CD2  C18   180.00   0.0  0
 XXZ  CONST_20  CE1   CD1  C8   CB    180.00   0.0  0
 XXZ  CONST_21  CZ    C15  N12  C11   180.00   0.0  0
 XXZ  CONST_23  C5    N20  CG   N21   180.00   0.0  0
 XXZ  CONST_24  H4    C4   C3   C2    180.00   0.0  0
 XXZ  CONST_25  H1    C1   C4   C3    180.00   0.0  0
 XXZ  CONST_26  H3    C3   C4   C1    180.00   0.0  0
 XXZ  CONST_27  HE1   CE1  CZ   C18   180.00   0.0  0
 XXZ  CONST_28  H18   C18  CD2  C8    180.00   0.0  0
 XXZ  CONST_29  HD2   CD2  C8   CD1   180.00   0.0  0
 XXZ  CONST_30  HD1   CD1  C8   CD2   180.00   0.0  0
 XXZ  CONST_31  O16   C15  N12  C11     0.00   0.0  0
 XXZ  CONST_34  H212  N21  CG   C7    180.00   0.0  0
 XXZ  Var_01    N20   CG   C7   C2   -167.53  30.0  1
 XXZ  Var_02    C5    N1   C6   C1    154.13  30.0  1
 XXZ  Var_03    N20   C5   N1   C6     48.17  30.0  1
 XXZ  Var_04    N1    C5   N20  CG    -36.80  30.0  1
 XXZ  Var_05    C11   C10  C5   N20  -169.50  30.0  3
 XXZ  Var_06    C13   C14  C5   N20   169.10  30.0  3
 XXZ  Var_07    N12   C11  C10  C5     55.33  30.0  1
 XXZ  Var_08    N12   C13  C14  C5    -55.10  30.0  1
 XXZ  Var_09    C13   N12  C11  C10   -59.36  30.0  1
 XXZ  Var_10    C14   C13  N12  C11    59.12  30.0  1
 XXZ  Var_11    C18   CZ   C15  N12   -52.14  30.0  2
 XXZ  Var_12    CD1   C8   CB   NH   -140.63  30.0  2
 XXZ  Var_13    HNH1  NH   CB   C8     69.53  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
 XXZ  plan-1  C15   0.020
 XXZ  plan-1  C18   0.020
 XXZ  plan-1  C8    0.020
 XXZ  plan-1  CD1   0.020
 XXZ  plan-1  CE1   0.020
 XXZ  plan-1  CD2   0.020
 XXZ  plan-1  CZ    0.020
 XXZ  plan-1  H18   0.020
 XXZ  plan-1  HD1   0.020
 XXZ  plan-1  HE1   0.020
 XXZ  plan-1  HD2   0.020
 XXZ  plan-1  CB    0.020
 XXZ  plan-2  F1    0.020
 XXZ  plan-2  C2    0.020
 XXZ  plan-2  C3    0.020
 XXZ  plan-2  C4    0.020
 XXZ  plan-2  C1    0.020
 XXZ  plan-2  C6    0.020
 XXZ  plan-2  C7    0.020
 XXZ  plan-2  CG    0.020
 XXZ  plan-2  N1    0.020
 XXZ  plan-2  H3    0.020
 XXZ  plan-2  H4    0.020
 XXZ  plan-2  H1    0.020
 XXZ  plan-3  C11   0.020
 XXZ  plan-3  N12   0.020
 XXZ  plan-3  C13   0.020
 XXZ  plan-3  C15   0.020
 XXZ  plan-3  O16   0.020
 XXZ  plan-3  CZ    0.020
 XXZ  plan-4  C7    0.020
 XXZ  plan-4  CG    0.020
 XXZ  plan-4  N20   0.020
 XXZ  plan-4  N21   0.020
 XXZ  plan-4  C5    0.020
 XXZ  plan-4  H211  0.020
 XXZ  plan-4  H212  0.020

