# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul 10 02:24:08 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 2-{[4-(4-hydroxypiperidin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)c2ccccc2N(C)c3nc(Nc4ccc(cc4)N5CCC(O)CC5)ncc13
#
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
 ZTX  ZTX  2-{[4-(4-hydroxypiperidin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one  ligand  58  32  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZTX
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
 ZTX  N1    N  N     0  -0.461  -0.6860  -0.8361  -0.1569
 ZTX  C2    C  CR6   0   0.588  -0.8209   0.4817  -0.2405
 ZTX  N3    N  N     0  -0.484  -1.9781   1.1277  -0.4184
 ZTX  C4    C  CR6   0   0.482  -3.0641   0.4101  -0.5980
 ZTX  C5    C  CR6   0   0.144  -3.0161  -0.9900  -0.6517
 ZTX  C6    C  CR16  0  -0.037  -1.7826  -1.5484  -0.3771
 ZTX  CAB   C  C     0   0.550  -5.3460  -1.7114  -0.6381
 ZTX  CAC   C  CR6   0  -0.101  -5.7013  -0.6309   0.3246
 ZTX  CAD   C  CR6   0   0.298  -5.2662   0.6957   0.2113
 ZTX  NAE   N  NT    0  -0.570  -4.2780   1.0690  -0.7267
 ZTX  CAF   C  CH3   0  -0.561  -4.2214   2.4627  -1.1375
 ZTX  CAH   C  CR16  0  -0.249  -6.7645   1.3143   2.0064
 ZTX  CAI   C  CR16  0  -0.255  -7.1716  -0.0052   2.1449
 ZTX  CAK   C  CR16  0  -0.287  -6.6502  -0.9602   1.2931
 ZTX  CAL   C  CR16  0  -0.299  -5.8224   1.6607   1.0535
 ZTX  NAN   N  NH1   0  -0.761   0.2674   1.2845  -0.1319
 ZTX  CAO   C  CR6   0   0.329   1.6172   0.9339  -0.0172
 ZTX  CAP   C  CR16  0  -0.324   2.5613   1.7912  -0.5883
 ZTX  CAQ   C  CR16  0  -0.308   3.9138   1.5405  -0.4767
 ZTX  CAR   C  CR6   0   0.335   4.3911   0.4064   0.1920
 ZTX  NAS   N  NT    0  -0.505   5.7725   0.1893   0.2857
 ZTX  CAT   C  CH2   0  -0.311   6.4793   0.0809  -0.9865
 ZTX  CAU   C  CH2   0  -0.461   7.9798   0.2378  -0.7994
 ZTX  CAV   C  CH1   0   0.067   8.5008  -0.7799   0.1989
 ZTX  OAW   O  OH1   0  -0.674   9.8844  -0.5620   0.3787
 ZTX  CAX   C  CH2   0  -0.472   7.7167  -0.6527   1.4975
 ZTX  CAY   C  CH2   0  -0.317   6.2223  -0.7975   1.2481
 ZTX  CAZ   C  CR16  0  -0.346   3.4411  -0.4427   0.7618
 ZTX  CBA   C  CR16  0  -0.283   2.0789  -0.1807   0.6743
 ZTX  NBG   N  NT    0  -0.556  -4.0851  -1.7715  -1.1255
 ZTX  CBH   C  CH3   0  -0.547  -3.7881  -2.7942  -2.1218
 ZTX  H6    H  HCR6  0   0.286  -1.6644  -2.6274  -0.3644
 ZTX  HAF   H  HCH3  0   0.240  -3.8262   3.1342  -0.3730
 ZTX  HAFA  H  HCH3  0   0.267  -3.5882   2.5443  -2.0174
 ZTX  HAFB  H  HCH3  0   0.260  -5.2243   2.7854  -1.4082
 ZTX  HAH   H  HCR6  0   0.268  -7.1702   2.0816   2.6526
 ZTX  HAI   H  HCR6  0   0.262  -7.8990  -0.2818   2.8959
 ZTX  HAK   H  HCR6  0   0.264  -6.9885  -1.9849   1.3680
 ZTX  HAL   H  HCR6  0   0.279  -5.5104   2.6929   0.9807
 ZTX  HNAN  H  HNH1  0   0.405   0.0764   2.2586  -0.3092
 ZTX  HAP   H  HCR6  0   0.264   2.2313   2.6779  -1.1168
 ZTX  HAQ   H  HCR6  0   0.260   4.6115   2.2456  -0.9112
 ZTX  HAT   H  HCH2  0   0.211   6.2658  -0.8908  -1.4595
 ZTX  HATA  H  HCH2  0   0.256   6.1194   0.8472  -1.6711
 ZTX  HAU   H  HCH2  0   0.241   8.4733   0.1158  -1.7665
 ZTX  HAUA  H  HCH2  0   0.226   8.1975   1.2479  -0.4392
 ZTX  HAV   H  HCH1  0   0.188   8.3221  -1.7868  -0.2118
 ZTX  HOAW  H  HOH1  0   0.447  10.2089  -1.2078   1.0141
 ZTX  HAX   H  HCH2  0   0.239   8.0310  -1.4164   2.2148
 ZTX  HAXA  H  HCH2  0   0.225   7.9184   0.3247   1.9461
 ZTX  HAY   H  HCH2  0   0.252   5.6869  -0.6498   2.1870
 ZTX  HAYA  H  HCH2  0   0.207   6.0056  -1.8248   0.9126
 ZTX  HAZ   H  HCR6  0   0.264   3.7476  -1.3361   1.2893
 ZTX  HBA   H  HCR6  0   0.265   1.3855  -0.8642   1.1396
 ZTX  HBH   H  HCH3  0   0.251  -3.6647  -3.7795  -1.6713
 ZTX  HBHA  H  HCH3  0   0.264  -4.5878  -2.8485  -2.8566
 ZTX  HBHB  H  HCH3  0   0.258  -2.8686  -2.5266  -2.6348
 ZTX  OAA   O  O     0  -0.472  -6.1927  -2.5241  -0.9776

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
 ZTX  C2   N1    aromatic  1.327  0.020  1.327
 ZTX  N1   C6    aromatic  1.326  0.020  1.326
 ZTX  NAN  C2    single    1.357  0.020  1.357
 ZTX  N3   C2    aromatic  1.337  0.020  1.337
 ZTX  N3   C4    aromatic  1.314  0.020  1.314
 ZTX  NAE  C4    single    1.387  0.020  1.387
 ZTX  C4   C5    aromatic  1.402  0.020  1.402
 ZTX  C5   C6    aromatic  1.382  0.020  1.382
 ZTX  C5   NBG   single    1.406  0.020  1.406
 ZTX  C6   H6    single    0.930  0.020  1.080
 ZTX  CAB  OAA   double    1.222  0.020  1.222
 ZTX  CAC  CAB   single    1.490  0.020  1.490
 ZTX  CAB  NBG   single    1.353  0.020  1.353
 ZTX  CAD  CAC   aromatic  1.401  0.020  1.401
 ZTX  CAK  CAC   aromatic  1.395  0.020  1.395
 ZTX  CAL  CAD   aromatic  1.396  0.020  1.396
 ZTX  CAD  NAE   single    1.413  0.020  1.413
 ZTX  CAF  NAE   single    1.454  0.020  1.454
 ZTX  CAF  HAF   single    0.970  0.020  1.090
 ZTX  CAF  HAFA  single    0.970  0.020  1.090
 ZTX  CAF  HAFB  single    0.970  0.020  1.090
 ZTX  CAH  CAL   aromatic  1.384  0.020  1.384
 ZTX  CAH  CAI   aromatic  1.388  0.020  1.388
 ZTX  CAH  HAH   single    0.930  0.020  1.080
 ZTX  CAI  CAK   aromatic  1.382  0.020  1.382
 ZTX  CAI  HAI   single    0.930  0.020  1.080
 ZTX  CAK  HAK   single    0.930  0.020  1.080
 ZTX  CAL  HAL   single    0.930  0.020  1.080
 ZTX  CAO  NAN   single    1.399  0.020  1.399
 ZTX  NAN  HNAN  single    0.860  0.020  1.020
 ZTX  CAP  CAO   aromatic  1.397  0.020  1.397
 ZTX  CBA  CAO   aromatic  1.391  0.020  1.391
 ZTX  CAQ  CAP   aromatic  1.380  0.020  1.380
 ZTX  CAP  HAP   single    0.930  0.020  1.080
 ZTX  CAR  CAQ   aromatic  1.400  0.020  1.400
 ZTX  CAQ  HAQ   single    0.930  0.020  1.080
 ZTX  NAS  CAR   single    1.401  0.020  1.401
 ZTX  CAR  CAZ   aromatic  1.396  0.020  1.396
 ZTX  CAT  NAS   single    1.459  0.020  1.459
 ZTX  NAS  CAY   single    1.450  0.020  1.450
 ZTX  CAU  CAT   single    1.520  0.020  1.520
 ZTX  CAT  HAT   single    0.970  0.020  1.090
 ZTX  CAT  HATA  single    0.970  0.020  1.090
 ZTX  CAU  CAV   single    1.518  0.020  1.518
 ZTX  CAU  HAU   single    0.970  0.020  1.090
 ZTX  CAU  HAUA  single    0.970  0.020  1.090
 ZTX  OAW  CAV   single    1.412  0.020  1.412
 ZTX  CAV  CAX   single    1.522  0.020  1.522
 ZTX  CAV  HAV   single    0.970  0.020  1.090
 ZTX  OAW  HOAW  single    0.850  0.020  0.980
 ZTX  CAX  CAY   single    1.522  0.020  1.522
 ZTX  CAX  HAX   single    0.970  0.020  1.090
 ZTX  CAX  HAXA  single    0.970  0.020  1.090
 ZTX  CAY  HAY   single    0.970  0.020  1.090
 ZTX  CAY  HAYA  single    0.970  0.020  1.090
 ZTX  CAZ  CBA   aromatic  1.390  0.020  1.390
 ZTX  CAZ  HAZ   single    0.930  0.020  1.080
 ZTX  CBA  HBA   single    0.930  0.020  1.080
 ZTX  NBG  CBH   single    1.458  0.020  1.458
 ZTX  CBH  HBH   single    0.970  0.020  1.090
 ZTX  CBH  HBHA  single    0.970  0.020  1.090
 ZTX  CBH  HBHB  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
 ZTX  C6    N1   C2    116.03  3.000
 ZTX  NAN   C2   N3    114.77  3.000
 ZTX  N3    C2   N1    125.17  3.000
 ZTX  NAN   C2   N1    120.06  3.000
 ZTX  C4    N3   C2    118.01  3.000
 ZTX  NAE   C4   C5    120.05  3.000
 ZTX  C5    C4   N3    121.48  3.000
 ZTX  NAE   C4   N3    118.46  3.000
 ZTX  NBG   C5   C6    121.40  3.000
 ZTX  NBG   C5   C4    122.80  3.000
 ZTX  C6    C5   C4    115.26  3.000
 ZTX  H6    C6   C5    120.09  3.000
 ZTX  H6    C6   N1    116.23  3.000
 ZTX  C5    C6   N1    123.65  3.000
 ZTX  NBG   CAB  CAC   119.15  3.000
 ZTX  NBG   CAB  OAA   121.07  3.000
 ZTX  CAC   CAB  OAA   119.78  3.000
 ZTX  CAK   CAC  CAD   119.40  3.000
 ZTX  CAK   CAC  CAB   116.07  3.000
 ZTX  CAD   CAC  CAB   124.09  3.000
 ZTX  CAL   CAD  NAE   119.77  3.000
 ZTX  NAE   CAD  CAC   121.41  3.000
 ZTX  CAL   CAD  CAC   118.82  3.000
 ZTX  CAF   NAE  CAD   117.91  3.000
 ZTX  CAF   NAE  C4    116.57  3.000
 ZTX  CAD   NAE  C4    115.15  3.000
 ZTX  HAFB  CAF  HAFA  108.26  3.000
 ZTX  HAFB  CAF  HAF   109.00  3.000
 ZTX  HAFA  CAF  HAF   108.05  3.000
 ZTX  HAFB  CAF  NAE   108.59  3.000
 ZTX  HAFA  CAF  NAE   108.87  3.000
 ZTX  HAF   CAF  NAE   113.94  3.000
 ZTX  HAH   CAH  CAL   119.27  3.000
 ZTX  HAH   CAH  CAI   120.30  3.000
 ZTX  CAL   CAH  CAI   120.42  3.000
 ZTX  HAI   CAI  CAK   120.34  3.000
 ZTX  HAI   CAI  CAH   120.65  3.000
 ZTX  CAK   CAI  CAH   119.01  3.000
 ZTX  HAK   CAK  CAI   119.60  3.000
 ZTX  HAK   CAK  CAC   118.97  3.000
 ZTX  CAI   CAK  CAC   121.43  3.000
 ZTX  HAL   CAL  CAH   118.80  3.000
 ZTX  HAL   CAL  CAD   120.30  3.000
 ZTX  CAH   CAL  CAD   120.89  3.000
 ZTX  HNAN  NAN  CAO   116.05  3.000
 ZTX  HNAN  NAN  C2    113.93  3.000
 ZTX  CAO   NAN  C2    129.21  3.000
 ZTX  CBA   CAO  CAP   118.08  3.000
 ZTX  CBA   CAO  NAN   124.19  3.000
 ZTX  CAP   CAO  NAN   117.68  3.000
 ZTX  HAP   CAP  CAQ   119.11  3.000
 ZTX  HAP   CAP  CAO   119.71  3.000
 ZTX  CAQ   CAP  CAO   121.18  3.000
 ZTX  HAQ   CAQ  CAR   119.95  3.000
 ZTX  HAQ   CAQ  CAP   118.73  3.000
 ZTX  CAR   CAQ  CAP   121.32  3.000
 ZTX  CAZ   CAR  NAS   123.32  3.000
 ZTX  CAZ   CAR  CAQ   117.10  3.000
 ZTX  NAS   CAR  CAQ   119.56  3.000
 ZTX  CAY   NAS  CAT   112.20  3.000
 ZTX  CAY   NAS  CAR   117.10  3.000
 ZTX  CAT   NAS  CAR   115.51  3.000
 ZTX  HATA  CAT  HAT   106.66  3.000
 ZTX  HATA  CAT  CAU   109.33  3.000
 ZTX  HAT   CAT  CAU   109.58  3.000
 ZTX  HATA  CAT  NAS   109.62  3.000
 ZTX  HAT   CAT  NAS   110.24  3.000
 ZTX  CAU   CAT  NAS   111.29  3.000
 ZTX  HAUA  CAU  HAU   107.73  3.000
 ZTX  HAUA  CAU  CAV   109.52  3.000
 ZTX  HAU   CAU  CAV   110.63  3.000
 ZTX  HAUA  CAU  CAT   109.40  3.000
 ZTX  HAU   CAU  CAT   108.99  3.000
 ZTX  CAV   CAU  CAT   110.52  3.000
 ZTX  HAV   CAV  CAX   108.11  3.000
 ZTX  HAV   CAV  OAW   110.33  3.000
 ZTX  CAX   CAV  OAW   112.53  3.000
 ZTX  HAV   CAV  CAU   108.17  3.000
 ZTX  CAX   CAV  CAU   109.16  3.000
 ZTX  OAW   CAV  CAU   108.46  3.000
 ZTX  HOAW  OAW  CAV   108.11  3.000
 ZTX  HAXA  CAX  HAX   107.57  3.000
 ZTX  HAXA  CAX  CAY   109.46  3.000
 ZTX  HAX   CAX  CAY   108.85  3.000
 ZTX  HAXA  CAX  CAV   109.23  3.000
 ZTX  HAX   CAX  CAV   110.67  3.000
 ZTX  CAY   CAX  CAV   110.98  3.000
 ZTX  HAYA  CAY  HAY   106.96  3.000
 ZTX  HAYA  CAY  CAX   109.37  3.000
 ZTX  HAY   CAY  CAX   109.15  3.000
 ZTX  HAYA  CAY  NAS   111.79  3.000
 ZTX  HAY   CAY  NAS   109.08  3.000
 ZTX  CAX   CAY  NAS   110.40  3.000
 ZTX  HAZ   CAZ  CBA   117.65  3.000
 ZTX  HAZ   CAZ  CAR   120.57  3.000
 ZTX  CBA   CAZ  CAR   121.78  3.000
 ZTX  HBA   CBA  CAZ   118.90  3.000
 ZTX  HBA   CBA  CAO   120.58  3.000
 ZTX  CAZ   CBA  CAO   120.52  3.000
 ZTX  CBH   NBG  CAB   117.84  3.000
 ZTX  CBH   NBG  C5    117.71  3.000
 ZTX  CAB   NBG  C5    124.21  3.000
 ZTX  HBHB  CBH  HBHA  108.40  3.000
 ZTX  HBHB  CBH  HBH   108.78  3.000
 ZTX  HBHA  CBH  HBH   108.50  3.000
 ZTX  HBHB  CBH  NBG   108.80  3.000
 ZTX  HBHA  CBH  NBG   110.30  3.000
 ZTX  HBH   CBH  NBG   111.99  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
 ZTX  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 ZTX  CONST_02  C5   C6   N1   C2      0.00   0.0  0
 ZTX  CONST_03  C6   N1   C2   N3      0.00   0.0  0
 ZTX  CONST_04  CAH  CAI  CAK  CAC     0.00   0.0  0
 ZTX  CONST_05  CAI  CAH  CAL  CAD     0.00   0.0  0
 ZTX  CONST_06  CAL  CAH  CAI  CAK     0.00   0.0  0
 ZTX  CONST_07  CAR  CAQ  CAP  CAO     0.00   0.0  0
 ZTX  CONST_08  CAR  CAZ  CBA  CAO     0.00   0.0  0
 ZTX  CONST_09  CAZ  CBA  CAO  CAP     0.00   0.0  0
 ZTX  CONST_10  CAZ  CAR  CAQ  CAP     0.00   0.0  0
 ZTX  CONST_11  CBA  CAO  CAP  CAQ     0.00   0.0  0
 ZTX  CONST_12  CBA  CAZ  CAR  CAQ     0.00   0.0  0
 ZTX  CONST_13  NAS  CAR  CAQ  CAP   180.00   0.0  0
 ZTX  CONST_14  CBA  CAZ  CAR  NAS   180.00   0.0  0
 ZTX  CONST_15  NAN  C2   N3   C4    180.00   0.0  0
 ZTX  CONST_16  NAN  C2   N1   C6    180.00   0.0  0
 ZTX  CONST_17  CAQ  CAP  CAO  NAN   180.00   0.0  0
 ZTX  CONST_18  CAZ  CBA  CAO  NAN   180.00   0.0  0
 ZTX  CONST_19  H6   C6   N1   C2    180.00   0.0  0
 ZTX  CONST_20  HAI  CAI  CAK  CAC   180.00   0.0  0
 ZTX  CONST_21  HAH  CAH  CAL  CAD   180.00   0.0  0
 ZTX  CONST_22  HAK  CAK  CAI  CAH   180.00   0.0  0
 ZTX  CONST_23  HAL  CAL  CAH  CAI   180.00   0.0  0
 ZTX  CONST_24  HAQ  CAQ  CAP  CAO   180.00   0.0  0
 ZTX  CONST_25  HAZ  CAZ  CBA  CAO   180.00   0.0  0
 ZTX  CONST_26  HBA  CBA  CAO  CAP   180.00   0.0  0
 ZTX  CONST_27  HAP  CAP  CAQ  CAR   180.00   0.0  0
 ZTX  Var_01    CAT  NAS  CAR  CAQ   -59.07  30.0  2
 ZTX  Var_02    CAU  CAT  NAS  CAR   164.10  30.0  1
 ZTX  Var_03    CAX  CAY  NAS  CAR  -164.81  30.0  1
 ZTX  Var_04    CAV  CAU  CAT  NAS    56.27  30.0  1
 ZTX  Var_05    CAV  CAX  CAY  NAS   -57.18  30.0  1
 ZTX  Var_06    CAO  NAN  C2   N1      4.53  30.0  1
 ZTX  Var_07    CAP  CAO  NAN  C2    147.49  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
 ZTX  chir_01  CAV  CAU  OAW  CAX  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
 ZTX  plan-1  NAN  0.020
 ZTX  plan-1  CAO  0.020
 ZTX  plan-1  CAP  0.020
 ZTX  plan-1  CAQ  0.020
 ZTX  plan-1  CAR  0.020
 ZTX  plan-1  NAS  0.020
 ZTX  plan-1  CAZ  0.020
 ZTX  plan-1  CBA  0.020
 ZTX  plan-1  HAP  0.020
 ZTX  plan-1  HAQ  0.020
 ZTX  plan-1  HAZ  0.020
 ZTX  plan-1  HBA  0.020
 ZTX  plan-2  N1   0.020
 ZTX  plan-2  C2   0.020
 ZTX  plan-2  N3   0.020
 ZTX  plan-2  C4   0.020
 ZTX  plan-2  C5   0.020
 ZTX  plan-2  C6   0.020
 ZTX  plan-2  NAE  0.020
 ZTX  plan-2  NAN  0.020
 ZTX  plan-2  NBG  0.020
 ZTX  plan-2  H6   0.020
 ZTX  plan-3  CAB  0.020
 ZTX  plan-3  CAC  0.020
 ZTX  plan-3  CAD  0.020
 ZTX  plan-3  NAE  0.020
 ZTX  plan-3  CAH  0.020
 ZTX  plan-3  CAI  0.020
 ZTX  plan-3  CAK  0.020
 ZTX  plan-3  CAL  0.020
 ZTX  plan-3  HAH  0.020
 ZTX  plan-3  HAI  0.020
 ZTX  plan-3  HAK  0.020
 ZTX  plan-3  HAL  0.020
 ZTX  plan-4  C5   0.020
 ZTX  plan-4  CAB  0.020
 ZTX  plan-4  CAC  0.020
 ZTX  plan-4  NBG  0.020
 ZTX  plan-4  CBH  0.020
 ZTX  plan-4  OAA  0.020

