# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 07:12:40 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 5-[(4'-amino-5',8'-difluoro-1H,1'H-spiro[piperidine-4,2'-quinazolin]-1-yl)carbonyl]pyridine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2(CCN(CC2)C(=O)c3ccc(nc3)C#N)Nc4c(F)ccc(F)c14
#
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
 B14  B14  5-[(4'-amino-5',8'-difluoro-1H,1'H-spiro[piperidine-4,2'-quinazolin]-1-yl)carbonyl]pyridine-2-carbonitrile  ligand  44  28  .  2022-07-24  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_B14
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
 B14  C1    C  CR6   0   0.472  -4.2859  -1.9468   0.3836
 B14  C2    C  CR16  0  -0.401  -5.6026  -1.7925   0.0348
 B14  C3    C  CR16  0  -0.436  -6.0998  -0.5201  -0.2304
 B14  C4    C  CR6   0   0.542  -5.2481   0.5544  -0.1098
 B14  C4A   C  CR66  0  -0.307  -3.9120   0.4293   0.2619
 B14  C5    C  CR6   0   0.453  -2.9499   1.5221   0.5099
 B14  N6    N  N     0  -0.431  -1.6894   1.3142   0.5992
 B14  C7    C  CR6   0   0.196  -1.1721  -0.0018   0.3327
 B14  N8    N  NR16  0  -0.693  -2.1004  -1.0118   0.8266
 B14  C8A   C  CR66  0   0.234  -3.4099  -0.8650   0.4879
 B14  F9    F  F     0  -0.309  -5.7448   1.7720  -0.3748
 B14  F10   F  F     0  -0.318  -3.7907  -3.1761   0.6233
 B14  C11   C  CH2   0  -0.417  -0.9050  -0.1784  -1.1738
 B14  C12   C  CH2   0  -0.315   0.1815   0.7693  -1.6589
 B14  N13   N  NT    0  -0.445   1.4028   0.5864  -0.8878
 B14  C14   C  CH2   0  -0.321   1.2198   0.7810   0.5436
 B14  C15   C  CH2   0  -0.420   0.1500  -0.1593   1.0836
 B14  C16   C  C     0   0.528   2.4787   0.0169  -1.4549
 B14  O17   O  O     0  -0.477   2.5119  -0.4027  -2.6037
 B14  N18   N  NH2   0  -0.826  -3.4188   2.7908   0.6544
 B14  C19   C  CR6   0  -0.158   3.7376  -0.0652  -0.6458
 B14  C20   C  CR16  0  -0.062   4.3694  -1.3004  -0.5007
 B14  N21   N  N     0  -0.402   5.5325  -1.4524   0.1041
 B14  C22   C  CR6   0   0.202   6.1304  -0.3592   0.5691
 B14  C23   C  CR16  0  -0.263   5.6077   0.9206   0.4658
 B14  C24   C  CR16  0  -0.139   4.3766   1.0628  -0.1543
 B14  C25   C  CSP   0   0.067   7.4009  -0.5633   1.2108
 B14  N26   N  NS    0  -0.232   8.4141  -0.7204   1.7331
 B14  H2    H  HCR6  0   0.295  -6.2442  -2.6593  -0.0508
 B14  H3    H  HCR6  0   0.288  -7.1292  -0.3754  -0.5265
 B14  HN8   H  HNR6  0   0.386  -1.7460  -1.9561   0.8538
 B14  H111  H  HCH2  0   0.238  -0.5970  -1.2105  -1.3661
 B14  H112  H  HCH2  0   0.249  -1.8207  -0.0011  -1.7437
 B14  H121  H  HCH2  0   0.269   0.3912   0.6045  -2.7121
 B14  H122  H  HCH2  0   0.256  -0.1409   1.8070  -1.5446
 B14  H141  H  HCH2  0   0.275   2.1496   0.6041   1.0769
 B14  H142  H  HCH2  0   0.257   0.9316   1.8181   0.7241
 B14  H151  H  HCH2  0   0.254  -0.0081   0.0498   2.1434
 B14  H152  H  HCH2  0   0.237   0.5018  -1.1922   0.9994
 B14  H181  H  HNH2  0   0.383  -2.7410   3.4522   0.9990
 B14  H182  H  HNH2  0   0.393  -4.3491   2.9391   1.0039
 B14  H20   H  HCR6  0   0.290   3.9040  -2.2014  -0.8830
 B14  H23   H  HCR6  0   0.305   6.1439   1.7744   0.8547
 B14  H24   H  HCR6  0   0.299   3.9331   2.0447  -0.2564

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
 B14  C1   C2    aromatic  1.371  0.020  1.371
 B14  C1   C8A   aromatic  1.396  0.020  1.396
 B14  C1   F10   single    1.347  0.020  1.347
 B14  C2   C3    aromatic  1.392  0.020  1.392
 B14  C2   H2    single    0.930  0.020  1.080
 B14  C3   C4    aromatic  1.376  0.020  1.376
 B14  C3   H3    single    0.930  0.020  1.080
 B14  C4   C4A   aromatic  1.393  0.020  1.393
 B14  C4   F9    single    1.341  0.020  1.341
 B14  C4A  C5    single    1.477  0.020  1.477
 B14  C4A  C8A   aromatic  1.407  0.020  1.407
 B14  C5   N6    double    1.281  0.020  1.281
 B14  C5   N18   single    1.360  0.020  1.360
 B14  N6   C7    single    1.439  0.020  1.439
 B14  C7   N8    single    1.458  0.020  1.458
 B14  C7   C11   single    1.540  0.020  1.540
 B14  C7   C15   single    1.529  0.020  1.529
 B14  N8   C8A   single    1.360  0.020  1.360
 B14  N8   HN8   single    0.890  0.020  1.040
 B14  C11  C12   single    1.521  0.020  1.521
 B14  C11  H111  single    0.970  0.020  1.090
 B14  C11  H112  single    0.970  0.020  1.090
 B14  C12  N13   single    1.456  0.020  1.456
 B14  C12  H121  single    0.970  0.020  1.090
 B14  C12  H122  single    0.970  0.020  1.090
 B14  N13  C14   single    1.456  0.020  1.456
 B14  N13  C16   single    1.343  0.020  1.343
 B14  C14  C15   single    1.523  0.020  1.523
 B14  C14  H141  single    0.970  0.020  1.090
 B14  C14  H142  single    0.970  0.020  1.090
 B14  C15  H151  single    0.970  0.020  1.090
 B14  C15  H152  single    0.970  0.020  1.090
 B14  C16  O17   double    1.223  0.020  1.223
 B14  C16  C19   single    1.499  0.020  1.499
 B14  N18  H181  single    0.890  0.020  1.040
 B14  N18  H182  single    0.890  0.020  1.040
 B14  C19  C20   aromatic  1.395  0.020  1.395
 B14  C19  C24   aromatic  1.387  0.020  1.387
 B14  C20  N21   aromatic  1.320  0.020  1.320
 B14  C20  H20   single    0.930  0.020  1.080
 B14  N21  C22   aromatic  1.330  0.020  1.330
 B14  C22  C23   aromatic  1.386  0.020  1.386
 B14  C22  C25   single    1.438  0.020  1.438
 B14  C23  C24   aromatic  1.386  0.020  1.386
 B14  C23  H23   single    0.930  0.020  1.080
 B14  C24  H24   single    0.930  0.020  1.080
 B14  C25  N26   triple    1.151  0.020  1.151

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
 B14  F10   C1   C8A   117.60  3.000
 B14  F10   C1   C2    120.08  3.000
 B14  C8A   C1   C2    122.31  3.000
 B14  H2    C2   C3    120.37  3.000
 B14  H2    C2   C1    119.97  3.000
 B14  C3    C2   C1    119.64  3.000
 B14  H3    C3   C4    120.59  3.000
 B14  H3    C3   C2    120.99  3.000
 B14  C4    C3   C2    118.42  3.000
 B14  F9    C4   C4A   119.31  3.000
 B14  F9    C4   C3    117.52  3.000
 B14  C4A   C4   C3    123.16  3.000
 B14  C8A   C4A  C5    114.92  3.000
 B14  C8A   C4A  C4    117.91  3.000
 B14  C5    C4A  C4    127.11  3.000
 B14  N18   C5   N6    118.90  3.000
 B14  N18   C5   C4A   118.90  3.000
 B14  N6    C5   C4A   122.19  3.000
 B14  C7    N6   C5    119.30  3.000
 B14  C15   C7   C11   108.58  3.000
 B14  C15   C7   N8    108.24  3.000
 B14  C11   C7   N8    111.24  3.000
 B14  C15   C7   N6    108.31  3.000
 B14  C11   C7   N6    110.39  3.000
 B14  N8    C7   N6    109.99  3.000
 B14  HN8   N8   C8A   116.48  3.000
 B14  HN8   N8   C7    115.71  3.000
 B14  C8A   N8   C7    116.98  3.000
 B14  N8    C8A  C4A   118.87  3.000
 B14  N8    C8A  C1    122.62  3.000
 B14  C4A   C8A  C1    118.50  3.000
 B14  H112  C11  H111  107.29  3.000
 B14  H112  C11  C12   109.33  3.000
 B14  H111  C11  C12   109.30  3.000
 B14  H112  C11  C7    110.25  3.000
 B14  H111  C11  C7    109.20  3.000
 B14  C12   C11  C7    111.37  3.000
 B14  H122  C12  H121  107.60  3.000
 B14  H122  C12  N13   108.14  3.000
 B14  H121  C12  N13   109.41  3.000
 B14  H122  C12  C11   110.34  3.000
 B14  H121  C12  C11   110.65  3.000
 B14  N13   C12  C11   110.61  3.000
 B14  C16   N13  C14   124.93  3.000
 B14  C16   N13  C12   120.11  3.000
 B14  C14   N13  C12   113.48  3.000
 B14  H142  C14  H141  107.43  3.000
 B14  H142  C14  C15   110.03  3.000
 B14  H141  C14  C15   109.05  3.000
 B14  H142  C14  N13   108.83  3.000
 B14  H141  C14  N13   110.68  3.000
 B14  C15   C14  N13   110.75  3.000
 B14  H152  C15  H151  107.58  3.000
 B14  H152  C15  C14   109.25  3.000
 B14  H151  C15  C14   109.13  3.000
 B14  H152  C15  C7    109.72  3.000
 B14  H151  C15  C7    109.38  3.000
 B14  C14   C15  C7    111.70  3.000
 B14  C19   C16  O17   117.73  3.000
 B14  C19   C16  N13   117.91  3.000
 B14  O17   C16  N13   124.31  3.000
 B14  H182  N18  H181  114.01  3.000
 B14  H182  N18  C5    119.59  3.000
 B14  H181  N18  C5    114.62  3.000
 B14  C24   C19  C20   118.35  3.000
 B14  C24   C19  C16   122.27  3.000
 B14  C20   C19  C16   119.02  3.000
 B14  H20   C20  N21   116.39  3.000
 B14  H20   C20  C19   120.32  3.000
 B14  N21   C20  C19   123.28  3.000
 B14  C22   N21  C20   117.51  3.000
 B14  C25   C22  C23   119.83  3.000
 B14  C25   C22  N21   115.89  3.000
 B14  C23   C22  N21   124.28  3.000
 B14  H23   C23  C24   121.38  3.000
 B14  H23   C23  C22   121.03  3.000
 B14  C24   C23  C22   117.59  3.000
 B14  H24   C24  C23   119.96  3.000
 B14  H24   C24  C19   121.05  3.000
 B14  C23   C24  C19   118.98  3.000
 B14  N26   C25  C22   180.00  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
 B14  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 B14  CONST_02  C4    C4A  C8A  C1      0.00   0.0  0
 B14  CONST_03  C4A   C8A  C1   C2      0.00   0.0  0
 B14  CONST_04  C4A   C4   C3   C2      0.00   0.0  0
 B14  CONST_05  C8A   C1   C2   C3      0.00   0.0  0
 B14  CONST_06  C8A   C4A  C4   C3      0.00   0.0  0
 B14  CONST_07  C22   N21  C20  C19     0.00   0.0  0
 B14  CONST_08  C22   C23  C24  C19     0.00   0.0  0
 B14  CONST_09  C23   C24  C19  C20     0.00   0.0  0
 B14  CONST_10  C23   C22  N21  C20     0.00   0.0  0
 B14  CONST_11  C24   C19  C20  N21     0.00   0.0  0
 B14  CONST_12  C24   C23  C22  N21     0.00   0.0  0
 B14  CONST_13  C7    N6   C5   C4A     0.00   0.0  0
 B14  CONST_14  F9    C4   C3   C2    180.00   0.0  0
 B14  CONST_15  F10   C1   C2   C3    180.00   0.0  0
 B14  CONST_16  F10   C1   C8A  C4A   180.00   0.0  0
 B14  CONST_17  F9    C4   C4A  C5      0.00   0.0  0
 B14  CONST_18  F10   C1   C8A  N8      0.00   0.0  0
 B14  CONST_19  F9    C4   C4A  C8A   180.00   0.0  0
 B14  CONST_20  N21   C20  C19  C16   180.00   0.0  0
 B14  CONST_21  C23   C24  C19  C16   180.00   0.0  0
 B14  CONST_22  C25   C22  N21  C20   180.00   0.0  0
 B14  CONST_23  C25   C22  C23  C24   180.00   0.0  0
 B14  CONST_24  C19   C16  N13  C12   180.00   0.0  0
 B14  CONST_26  N18   C5   N6   C7    180.00   0.0  0
 B14  CONST_27  H3    C3   C2   C1    180.00   0.0  0
 B14  CONST_28  H2    C2   C3   C4    180.00   0.0  0
 B14  CONST_29  H23   C23  C24  C19   180.00   0.0  0
 B14  CONST_30  H24   C24  C19  C20   180.00   0.0  0
 B14  CONST_31  H20   C20  N21  C22   180.00   0.0  0
 B14  CONST_32  O17   C16  N13  C12     0.00   0.0  0
 B14  CONST_34  H181  N18  C5   C4A   180.00   0.0  0
 B14  Var_01    C7    N8   C8A  C1    152.63  30.0  1
 B14  Var_02    N6    C5   C4A  C4   -166.49  30.0  1
 B14  Var_03    N8    C7   N6   C5    -36.60  30.0  1
 B14  Var_04    C8A   N8   C7   N6     48.60  30.0  1
 B14  Var_05    C12   C11  C7   N6     64.13  30.0  3
 B14  Var_06    C14   C15  C7   N6    -65.73  30.0  3
 B14  Var_07    N13   C12  C11  C7     56.07  30.0  1
 B14  Var_08    N13   C14  C15  C7    -55.57  30.0  1
 B14  Var_09    C14   N13  C12  C11   -57.58  30.0  1
 B14  Var_10    C15   C14  N13  C12    57.17  30.0  1
 B14  Var_11    C20   C19  C16  N13   127.21  30.0  2

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
 B14  plan-1  C16   0.020
 B14  plan-1  C19   0.020
 B14  plan-1  C20   0.020
 B14  plan-1  N21   0.020
 B14  plan-1  C22   0.020
 B14  plan-1  C23   0.020
 B14  plan-1  C24   0.020
 B14  plan-1  C25   0.020
 B14  plan-1  N26   0.020
 B14  plan-1  H20   0.020
 B14  plan-1  H23   0.020
 B14  plan-1  H24   0.020
 B14  plan-2  C1    0.020
 B14  plan-2  C2    0.020
 B14  plan-2  C3    0.020
 B14  plan-2  C4    0.020
 B14  plan-2  C4A   0.020
 B14  plan-2  C5    0.020
 B14  plan-2  N8    0.020
 B14  plan-2  C8A   0.020
 B14  plan-2  F9    0.020
 B14  plan-2  F10   0.020
 B14  plan-2  H2    0.020
 B14  plan-2  H3    0.020
 B14  plan-3  C12   0.020
 B14  plan-3  N13   0.020
 B14  plan-3  C14   0.020
 B14  plan-3  C16   0.020
 B14  plan-3  O17   0.020
 B14  plan-3  C19   0.020
 B14  plan-4  C4A   0.020
 B14  plan-4  C5    0.020
 B14  plan-4  N6    0.020
 B14  plan-4  C7    0.020
 B14  plan-4  N18   0.020
 B14  plan-4  H181  0.020
 B14  plan-4  H182  0.020

