# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:26:43 2021
#   Inital geometry file: a 136 line input string
#   Ligand name: (3~{R},4~{R})-~{N}-cyclohexyl-4-[(3-methyl-2-oxidanylidene-1~{H}-1,7-naphthyridin-8-yl)amino]piperidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=Cc2ccnc(N[C@@H]3CCNC[C@H]3C(=O)NC4CCCCC4)c2NC1=O
#
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
 QAZ  QAZ  (3~{R},4~{R})-~{N}-cyclohexyl-4-[(3-methyl-2-oxidanylidene-1~{H}-1,7-naphthyridin-8-yl)amino]piperidine-3-carboxamide  ligand  57  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QAZ
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
 QAZ  C17  C  CH1   0  -0.104  14.6548   5.8712   5.6881
 QAZ  C22  C  CH2   0  -0.299  16.2680   6.8557   4.0553
 QAZ  C01  C  CH3   0  -0.711  11.2420   5.7920  12.8677
 QAZ  C05  C  CR6   0  -0.111  12.0134   5.5687  11.6106
 QAZ  C06  C  CR16  0  -0.193  12.8884   4.5543  11.4485
 QAZ  C08  C  CR66  0   0.125  13.6207   4.3600  10.2315
 QAZ  C09  C  CR16  0  -0.427  14.5139   3.2911  10.0329
 QAZ  C11  C  CR16  0  -0.068  15.1324   3.1930   8.8172
 QAZ  N13  N  N     0  -0.483  14.9633   4.0799   7.8276
 QAZ  C14  C  CR6   0   0.526  14.1550   5.1080   7.9908
 QAZ  N15  N  NH1   0  -0.698  13.9974   5.9966   6.9714
 QAZ  C19  C  CH2   0  -0.427  15.6219   7.0221   5.4231
 QAZ  N25  N  NH1   0  -0.597  15.2423   6.7948   3.0305
 QAZ  C27  C  CH2   0  -0.276  14.3640   5.6569   3.2124
 QAZ  C30  C  CH1   0  -0.360  13.6301   5.7887   4.5524
 QAZ  C32  C  C     0   0.556  12.5870   4.6893   4.6900
 QAZ  O33  O  O     0  -0.511  11.4571   4.8545   4.2425
 QAZ  N34  N  NH1   0  -0.638  12.9740   3.5462   5.2728
 QAZ  C36  C  CH1   0  -0.050  12.0984   2.4090   5.4850
 QAZ  C38  C  CH2   0  -0.446  12.4574   1.7160   6.7963
 QAZ  C41  C  CH2   0  -0.435  11.5567   0.5111   7.0462
 QAZ  C44  C  CH2   0  -0.431  11.5958  -0.4721   5.8809
 QAZ  C47  C  CH2   0  -0.440  11.2465   0.2220   4.5684
 QAZ  C50  C  CH2   0  -0.423  12.1513   1.4245   4.3171
 QAZ  C53  C  CR66  0   0.220  13.4179   5.2651   9.2003
 QAZ  N54  N  NR16  0  -0.753  12.5054   6.2768   9.3753
 QAZ  C56  C  CR6   0   0.516  11.7718   6.5010  10.5087
 QAZ  O57  O  O     0  -0.479  10.9662   7.4218  10.5656
 QAZ  H1   H  HCH1  0   0.256  15.2521   4.9577   5.7151
 QAZ  H2   H  HCH2  0   0.195  16.8993   5.9525   4.0733
 QAZ  H3   H  HCH2  0   0.241  16.9268   7.7012   3.8503
 QAZ  H4   H  HCH3  0   0.248  11.4926   5.0432  13.6167
 QAZ  H5   H  HCH3  0   0.251  11.4495   6.7776  13.2872
 QAZ  H6   H  HCH3  0   0.251  10.1671   5.7457  12.6855
 QAZ  H8   H  HCR6  0   0.261  14.6900   2.5656  10.8152
 QAZ  H9   H  HCR6  0   0.257  15.8089   2.3736   8.6058
 QAZ  H10  H  HNH1  0   0.389  13.6605   6.9199   7.1891
 QAZ  H11  H  HCH2  0   0.246  16.3903   7.0424   6.1984
 QAZ  H12  H  HCH2  0   0.226  15.0870   7.9765   5.4625
 QAZ  H13  H  HNH1  0   0.358  15.6742   6.7423   2.1174
 QAZ  H15  H  HCH2  0   0.247  13.6398   5.6342   2.3961
 QAZ  H16  H  HCH2  0   0.198  14.9012   4.6934   3.1969
 QAZ  H17  H  HCH1  0   0.253  13.0674   6.7276   4.5284
 QAZ  H18  H  HNH1  0   0.397  13.9134   3.4649   5.6308
 QAZ  H19  H  HCH1  0   0.231  11.0775   2.7940   5.5659
 QAZ  H20  H  HCH2  0   0.216  13.5026   1.3876   6.7566
 QAZ  H21  H  HCH2  0   0.238  12.3842   2.4264   7.6238
 QAZ  H22  H  HCH2  0   0.214  10.5281   0.8560   7.1963
 QAZ  H23  H  HCH2  0   0.232  11.8541   0.0174   7.9740
 QAZ  H24  H  HCH2  0   0.229  10.9094  -1.3018   6.0650
 QAZ  H25  H  HCH2  0   0.210  12.5986  -0.9070   5.8059
 QAZ  H26  H  HCH2  0   0.213  10.2034   0.5552   4.6016
 QAZ  H27  H  HCH2  0   0.232  11.3200  -0.4792   3.7342
 QAZ  H28  H  HCH2  0   0.211  13.1850   1.0871   4.1830
 QAZ  H29  H  HCH2  0   0.234  11.8610   1.9328   3.3946
 QAZ  H30  H  HNR6  0   0.408  12.2836   6.8911   8.6041
 QAZ  H7   H  HCR6  0   0.271  13.0553   3.8517  12.2571

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
 QAZ  N25  C27  single    1.449  0.020  1.449
 QAZ  N25  C22  single    1.451  0.020  1.451
 QAZ  C27  C30  single    1.533  0.020  1.533
 QAZ  C22  C19  single    1.522  0.020  1.522
 QAZ  O33  C32  double    1.227  0.020  1.227
 QAZ  C50  C47  single    1.526  0.020  1.526
 QAZ  C50  C36  single    1.528  0.020  1.528
 QAZ  C30  C32  single    1.522  0.020  1.522
 QAZ  C30  C17  single    1.532  0.020  1.532
 QAZ  C47  C44  single    1.525  0.020  1.525
 QAZ  C32  N34  single    1.340  0.020  1.340
 QAZ  N34  C36  single    1.451  0.020  1.451
 QAZ  C19  C17  single    1.527  0.020  1.527
 QAZ  C36  C38  single    1.526  0.020  1.526
 QAZ  C17  N15  single    1.447  0.020  1.447
 QAZ  C44  C41  single    1.525  0.020  1.525
 QAZ  C38  C41  single    1.525  0.020  1.525
 QAZ  N15  C14  single    1.362  0.020  1.362
 QAZ  N13  C14  aromatic  1.318  0.020  1.318
 QAZ  N13  C11  aromatic  1.340  0.020  1.340
 QAZ  C14  C53  aromatic  1.425  0.020  1.425
 QAZ  C11  C09  aromatic  1.368  0.020  1.368
 QAZ  C53  N54  single    1.374  0.020  1.374
 QAZ  C53  C08  aromatic  1.387  0.020  1.387
 QAZ  N54  C56  single    1.369  0.020  1.369
 QAZ  C09  C08  aromatic  1.407  0.020  1.407
 QAZ  C08  C06  single    1.434  0.020  1.434
 QAZ  C56  O57  double    1.225  0.020  1.225
 QAZ  C56  C05  single    1.463  0.020  1.463
 QAZ  C06  C05  double    1.349  0.020  1.349
 QAZ  C05  C01  single    1.492  0.020  1.492
 QAZ  C17  H1   single    0.970  0.020  1.090
 QAZ  C22  H2   single    0.970  0.020  1.090
 QAZ  C22  H3   single    0.970  0.020  1.090
 QAZ  C01  H4   single    0.970  0.020  1.090
 QAZ  C01  H5   single    0.970  0.020  1.090
 QAZ  C01  H6   single    0.970  0.020  1.090
 QAZ  C06  H7   single    0.930  0.020  1.080
 QAZ  C09  H8   single    0.930  0.020  1.080
 QAZ  C11  H9   single    0.930  0.020  1.080
 QAZ  N15  H10  single    0.890  0.020  1.040
 QAZ  C19  H11  single    0.970  0.020  1.090
 QAZ  C19  H12  single    0.970  0.020  1.090
 QAZ  N25  H13  single    0.890  0.020  1.040
 QAZ  C27  H15  single    0.970  0.020  1.090
 QAZ  C27  H16  single    0.970  0.020  1.090
 QAZ  C30  H17  single    0.970  0.020  1.090
 QAZ  N34  H18  single    0.860  0.020  1.020
 QAZ  C36  H19  single    0.970  0.020  1.090
 QAZ  C38  H20  single    0.970  0.020  1.090
 QAZ  C38  H21  single    0.970  0.020  1.090
 QAZ  C41  H22  single    0.970  0.020  1.090
 QAZ  C41  H23  single    0.970  0.020  1.090
 QAZ  C44  H24  single    0.970  0.020  1.090
 QAZ  C44  H25  single    0.970  0.020  1.090
 QAZ  C47  H26  single    0.970  0.020  1.090
 QAZ  C47  H27  single    0.970  0.020  1.090
 QAZ  C50  H28  single    0.970  0.020  1.090
 QAZ  C50  H29  single    0.970  0.020  1.090
 QAZ  N54  H30  single    0.860  0.020  1.020

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
 QAZ  H1   C17  C30  109.83  3.000
 QAZ  H1   C17  C19  106.77  3.000
 QAZ  C30  C17  C19  109.61  3.000
 QAZ  H1   C17  N15  107.41  3.000
 QAZ  C19  C17  N15  112.11  3.000
 QAZ  C30  C17  N15  110.99  3.000
 QAZ  H3   C22  H2   106.99  3.000
 QAZ  H3   C22  N25  109.06  3.000
 QAZ  H2   C22  N25  112.46  3.000
 QAZ  H3   C22  C19  109.90  3.000
 QAZ  H2   C22  C19  108.55  3.000
 QAZ  N25  C22  C19  109.83  3.000
 QAZ  H6   C01  H5   106.85  3.000
 QAZ  H6   C01  H4   108.22  3.000
 QAZ  H5   C01  H4   108.24  3.000
 QAZ  H6   C01  C05  111.24  3.000
 QAZ  H5   C01  C05  111.16  3.000
 QAZ  H4   C01  C05  110.97  3.000
 QAZ  C56  C05  C06  119.70  3.000
 QAZ  C06  C05  C01  123.30  3.000
 QAZ  C56  C05  C01  116.98  3.000
 QAZ  H7   C06  C08  117.82  3.000
 QAZ  H7   C06  C05  119.83  3.000
 QAZ  C08  C06  C05  122.35  3.000
 QAZ  C53  C08  C09  118.92  3.000
 QAZ  C09  C08  C06  123.17  3.000
 QAZ  C53  C08  C06  117.90  3.000
 QAZ  H8   C09  C11  121.43  3.000
 QAZ  H8   C09  C08  120.72  3.000
 QAZ  C11  C09  C08  117.84  3.000
 QAZ  H9   C11  N13  115.81  3.000
 QAZ  H9   C11  C09  120.67  3.000
 QAZ  N13  C11  C09  123.52  3.000
 QAZ  C14  N13  C11  120.16  3.000
 QAZ  C53  C14  N15  120.24  3.000
 QAZ  C53  C14  N13  120.56  3.000
 QAZ  N15  C14  N13  119.17  3.000
 QAZ  H10  N15  C14  118.39  3.000
 QAZ  H10  N15  C17  115.05  3.000
 QAZ  C14  N15  C17  123.69  3.000
 QAZ  H12  C19  H11  107.58  3.000
 QAZ  H12  C19  C22  109.59  3.000
 QAZ  H11  C19  C22  109.97  3.000
 QAZ  H12  C19  C17  109.97  3.000
 QAZ  H11  C19  C17  109.67  3.000
 QAZ  C22  C19  C17  110.03  3.000
 QAZ  H13  N25  C27  109.36  3.000
 QAZ  H13  N25  C22  109.74  3.000
 QAZ  C27  N25  C22  111.88  3.000
 QAZ  H16  C27  H15  107.12  3.000
 QAZ  H16  C27  C30  108.68  3.000
 QAZ  H15  C27  C30  109.74  3.000
 QAZ  H16  C27  N25  112.89  3.000
 QAZ  H15  C27  N25  108.95  3.000
 QAZ  C30  C27  N25  109.41  3.000
 QAZ  H17  C30  C32  105.62  3.000
 QAZ  H17  C30  C27  107.49  3.000
 QAZ  C32  C30  C27  110.18  3.000
 QAZ  H17  C30  C17  108.29  3.000
 QAZ  C32  C30  C17  115.49  3.000
 QAZ  C27  C30  C17  109.41  3.000
 QAZ  N34  C32  O33  122.65  3.000
 QAZ  N34  C32  C30  117.23  3.000
 QAZ  O33  C32  C30  120.08  3.000
 QAZ  H18  N34  C36  116.56  3.000
 QAZ  H18  N34  C32  119.47  3.000
 QAZ  C36  N34  C32  123.91  3.000
 QAZ  H19  C36  C50  108.39  3.000
 QAZ  H19  C36  C38  108.41  3.000
 QAZ  C50  C36  C38  110.85  3.000
 QAZ  H19  C36  N34  107.35  3.000
 QAZ  C38  C36  N34  109.86  3.000
 QAZ  C50  C36  N34  111.85  3.000
 QAZ  H21  C38  H20  106.62  3.000
 QAZ  H21  C38  C41  110.48  3.000
 QAZ  H20  C38  C41  109.41  3.000
 QAZ  H21  C38  C36  109.85  3.000
 QAZ  H20  C38  C36  109.22  3.000
 QAZ  C41  C38  C36  111.14  3.000
 QAZ  H23  C41  H22  106.37  3.000
 QAZ  H23  C41  C44  110.52  3.000
 QAZ  H22  C41  C44  109.37  3.000
 QAZ  H23  C41  C38  109.61  3.000
 QAZ  H22  C41  C38  109.17  3.000
 QAZ  C44  C41  C38  111.65  3.000
 QAZ  H25  C44  H24  106.56  3.000
 QAZ  H25  C44  C47  109.35  3.000
 QAZ  H24  C44  C47  110.29  3.000
 QAZ  H25  C44  C41  109.37  3.000
 QAZ  H24  C44  C41  110.17  3.000
 QAZ  C47  C44  C41  111.00  3.000
 QAZ  H27  C47  H26  106.41  3.000
 QAZ  H27  C47  C50  109.89  3.000
 QAZ  H26  C47  C50  109.26  3.000
 QAZ  H27  C47  C44  110.47  3.000
 QAZ  H26  C47  C44  109.29  3.000
 QAZ  C50  C47  C44  111.38  3.000
 QAZ  H29  C50  H28  106.89  3.000
 QAZ  H29  C50  C47  110.38  3.000
 QAZ  H28  C50  C47  109.69  3.000
 QAZ  H29  C50  C36  109.65  3.000
 QAZ  H28  C50  C36  108.94  3.000
 QAZ  C47  C50  C36  111.18  3.000
 QAZ  N54  C53  C14  122.20  3.000
 QAZ  N54  C53  C08  118.89  3.000
 QAZ  C14  C53  C08  118.91  3.000
 QAZ  H30  N54  C56  114.50  3.000
 QAZ  H30  N54  C53  119.76  3.000
 QAZ  C56  N54  C53  125.61  3.000
 QAZ  O57  C56  N54  120.94  3.000
 QAZ  O57  C56  C05  123.55  3.000
 QAZ  N54  C56  C05  115.51  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
 QAZ  CONST_01  N13  C14  C53  C08    0.00   0.0  0
 QAZ  CONST_02  N13  C11  C09  C08    0.00   0.0  0
 QAZ  CONST_03  C14  N13  C11  C09    0.00   0.0  0
 QAZ  CONST_04  C14  C53  C08  C09    0.00   0.0  0
 QAZ  CONST_05  C53  C14  N13  C11    0.00   0.0  0
 QAZ  CONST_06  C53  C08  C09  C11    0.00   0.0  0
 QAZ  CONST_07  C53  N54  C56  C05    0.00   0.0  0
 QAZ  CONST_08  N15  C14  C53  C08  180.00   0.0  0
 QAZ  CONST_09  N15  C14  N13  C11  180.00   0.0  0
 QAZ  CONST_10  N54  C53  C14  N15    0.00   0.0  0
 QAZ  CONST_11  N13  C14  N15  C17    0.00   0.0  0
 QAZ  CONST_12  C53  C14  N15  C17  180.00   0.0  0
 QAZ  CONST_13  O57  C56  N54  C53  180.00   0.0  0
 QAZ  CONST_14  H8   C09  C08  C06    0.00   0.0  0
 QAZ  CONST_15  H9   C11  C09  C08  180.00   0.0  0
 QAZ  CONST_16  H30  N54  C56  C05  180.00   0.0  0
 QAZ  CONST_17  C36  N34  C32  C30  180.00   0.0  0
 QAZ  CONST_19  C36  N34  C32  O33    0.00   0.0  0
 QAZ  CONST_20  H18  N34  C32  C30    0.00   0.0  0
 QAZ  Var_01    N25  C22  C19  C17   57.65  30.0  1
 QAZ  Var_02    C30  C27  N25  C22   62.34  30.0  1
 QAZ  Var_03    C27  N25  C22  C19  -61.93  30.0  1
 QAZ  Var_04    C44  C47  C50  C36  -55.79  30.0  1
 QAZ  Var_05    C44  C41  C38  C36   55.51  30.0  1
 QAZ  Var_06    C47  C44  C41  C38  -55.02  30.0  1
 QAZ  Var_07    C50  C47  C44  C41   55.08  30.0  1
 QAZ  Var_08    H4   C01  C05  C06    0.68  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 QAZ  chir_01  C17  C30  C19  N15  negativ
 QAZ  chir_02  C30  C17  C32  C27  positiv
 QAZ  chir_03  C36  N34  C50  C38  negativ

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
 QAZ  plan-1  C30  0.020
 QAZ  plan-1  C32  0.020
 QAZ  plan-1  O33  0.020
 QAZ  plan-1  N34  0.020
 QAZ  plan-1  C36  0.020
 QAZ  plan-1  H18  0.020
 QAZ  plan-2  C01  0.020
 QAZ  plan-2  C05  0.020
 QAZ  plan-2  C06  0.020
 QAZ  plan-2  C08  0.020
 QAZ  plan-2  C09  0.020
 QAZ  plan-2  C11  0.020
 QAZ  plan-2  N13  0.020
 QAZ  plan-2  C14  0.020
 QAZ  plan-2  N15  0.020
 QAZ  plan-2  C53  0.020
 QAZ  plan-2  N54  0.020
 QAZ  plan-2  C56  0.020
 QAZ  plan-2  O57  0.020
 QAZ  plan-2  H8   0.020
 QAZ  plan-2  H9   0.020
 QAZ  plan-2  H30  0.020
 QAZ  plan-2  H7   0.020
 QAZ  plan-3  C17  0.020
 QAZ  plan-3  C14  0.020
 QAZ  plan-3  N15  0.020
 QAZ  plan-3  H10  0.020

