# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 07:49:55 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-{4-[(4-methylpiperazin-1-yl)carbonyl]phenyl}-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C(=O)c2ccc(cc2)C3=CC(=O)c4ccccc4O3
#
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
 1VF  1VF  2-{4-[(4-methylpiperazin-1-yl)carbonyl]phenyl}-4H-chromen-4-one  ligand  46  26  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1VF
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
 1VF  CAD  C  CH2   0  -0.314   5.5996  -0.3070   0.8756
 1VF  CAC  C  CH2   0  -0.280   6.4290  -0.2318  -0.3933
 1VF  NAB  N  NT    0  -0.416   6.2181   1.0339  -1.0650
 1VF  CAA  C  CH3   0  -0.517   7.0570   1.1657  -2.2345
 1VF  CAG  C  CH2   0  -0.269   4.8183   1.2095  -1.3866
 1VF  CAF  C  CH2   0  -0.320   3.9565   1.1611  -0.1348
 1VF  NAE  N  NT    0  -0.456   4.1930  -0.0742   0.5938
 1VF  CAH  C  C     0   0.523   3.2707  -1.0179   0.8607
 1VF  OAI  O  O     0  -0.486   3.5505  -2.1460   1.2465
 1VF  CAJ  C  CR6   0  -0.078   1.8259  -0.6461   0.7225
 1VF  CAO  C  CR16  0  -0.254   0.9705  -1.5006   0.0364
 1VF  CAN  C  CR16  0  -0.267  -0.3853  -1.2308  -0.0367
 1VF  CAK  C  CR16  0  -0.234   1.2959   0.4677   1.3682
 1VF  CAL  C  CR16  0  -0.300  -0.0606   0.7294   1.3151
 1VF  CAM  C  CR6   0   0.027  -0.9198  -0.1145   0.6103
 1VF  CAP  C  CR6   0   0.417  -2.3595   0.1698   0.5570
 1VF  OAZ  O  O     0  -0.466  -2.9743  -0.4810  -0.4369
 1VF  CAY  C  CR66  0   0.371  -4.3070  -0.3545  -0.6288
 1VF  CAX  C  CR16  0  -0.327  -4.8615  -1.0865  -1.6745
 1VF  CAW  C  CR16  0  -0.249  -6.2168  -0.9809  -1.9094
 1VF  CAV  C  CR16  0  -0.244  -7.0183  -0.1551  -1.1155
 1VF  CAU  C  CR16  0  -0.293  -6.4546   0.5628  -0.0837
 1VF  CAT  C  CR66  0  -0.130  -5.0833   0.4728   0.1772
 1VF  CAR  C  CR6   0   0.467  -4.4496   1.2145   1.2746
 1VF  OAS  O  O     0  -0.441  -5.0785   1.9565   2.0177
 1VF  CAQ  C  CR16  0  -0.526  -3.0287   0.9829   1.4039
 1VF  H1   H  HCH2  0   0.267   5.7234  -1.2770   1.3480
 1VF  H2   H  HCH2  0   0.247   5.9399   0.4584   1.5800
 1VF  H3   H  HCH2  0   0.245   7.4841  -0.3251  -0.1257
 1VF  H4   H  HCH2  0   0.199   6.1834  -1.0890  -1.0445
 1VF  H6   H  HCH3  0   0.195   6.8618   0.3970  -2.9978
 1VF  H7   H  HCH3  0   0.235   6.9025   2.1417  -2.6965
 1VF  H8   H  HCH3  0   0.235   8.1076   1.0923  -1.9489
 1VF  H9   H  HCH2  0   0.247   4.6769   2.1835  -1.8606
 1VF  H10  H  HCH2  0   0.197   4.4577   0.4467  -2.0992
 1VF  H11  H  HCH2  0   0.247   4.1907   2.0125   0.5110
 1VF  H12  H  HCH2  0   0.274   2.9136   1.2435  -0.4275
 1VF  H13  H  HCR6  0   0.271   1.3618  -2.3814  -0.4551
 1VF  H14  H  HCR6  0   0.270  -1.0202  -1.9099  -0.5882
 1VF  H15  H  HCR6  0   0.278   1.9400   1.1401   1.9202
 1VF  H16  H  HCR6  0   0.270  -0.4384   1.6120   1.8126
 1VF  H17  H  HCR6  0   0.286  -4.2331  -1.7224  -2.2840
 1VF  H18  H  HCR6  0   0.277  -6.6604  -1.5439  -2.7196
 1VF  H19  H  HCR6  0   0.269  -8.0787  -0.0813  -1.3139
 1VF  H20  H  HCR6  0   0.271  -7.0659   1.2050   0.5361
 1VF  H21  H  HCR6  0   0.282  -2.5023   1.4672   2.2138

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
 1VF  CAV  CAU  aromatic  1.378  0.020  1.378
 1VF  CAV  CAW  aromatic  1.398  0.020  1.398
 1VF  CAU  CAT  aromatic  1.399  0.020  1.399
 1VF  CAW  CAX  aromatic  1.380  0.020  1.380
 1VF  OAS  CAR  double    1.224  0.020  1.224
 1VF  CAT  CAR  single    1.468  0.020  1.468
 1VF  CAT  CAY  aromatic  1.392  0.020  1.392
 1VF  CAR  CAQ  single    1.445  0.020  1.445
 1VF  CAX  CAY  aromatic  1.392  0.020  1.392
 1VF  CAY  OAZ  single    1.352  0.020  1.352
 1VF  CAQ  CAP  double    1.351  0.020  1.351
 1VF  OAZ  CAP  single    1.338  0.020  1.338
 1VF  CAP  CAM  single    1.468  0.020  1.468
 1VF  CAM  CAN  aromatic  1.396  0.020  1.396
 1VF  CAM  CAL  aromatic  1.395  0.020  1.395
 1VF  CAN  CAO  aromatic  1.384  0.020  1.384
 1VF  CAL  CAK  aromatic  1.383  0.020  1.383
 1VF  CAO  CAJ  aromatic  1.390  0.020  1.390
 1VF  CAK  CAJ  aromatic  1.392  0.020  1.392
 1VF  CAJ  CAH  single    1.498  0.020  1.498
 1VF  CAH  OAI  double    1.225  0.020  1.225
 1VF  CAH  NAE  single    1.346  0.020  1.346
 1VF  CAD  NAE  single    1.453  0.020  1.453
 1VF  CAD  CAC  single    1.518  0.020  1.518
 1VF  NAE  CAF  single    1.454  0.020  1.454
 1VF  CAC  NAB  single    1.448  0.020  1.448
 1VF  CAF  CAG  single    1.521  0.020  1.521
 1VF  NAB  CAG  single    1.447  0.020  1.447
 1VF  NAB  CAA  single    1.445  0.020  1.445
 1VF  CAD  H1   single    0.970  0.020  1.090
 1VF  CAD  H2   single    0.970  0.020  1.090
 1VF  CAC  H3   single    0.970  0.020  1.090
 1VF  CAC  H4   single    0.970  0.020  1.090
 1VF  CAA  H6   single    0.970  0.020  1.090
 1VF  CAA  H7   single    0.970  0.020  1.090
 1VF  CAA  H8   single    0.970  0.020  1.090
 1VF  CAG  H9   single    0.970  0.020  1.090
 1VF  CAG  H10  single    0.970  0.020  1.090
 1VF  CAF  H11  single    0.970  0.020  1.090
 1VF  CAF  H12  single    0.970  0.020  1.090
 1VF  CAO  H13  single    0.930  0.020  1.080
 1VF  CAN  H14  single    0.930  0.020  1.080
 1VF  CAK  H15  single    0.930  0.020  1.080
 1VF  CAL  H16  single    0.930  0.020  1.080
 1VF  CAX  H17  single    0.930  0.020  1.080
 1VF  CAW  H18  single    0.930  0.020  1.080
 1VF  CAV  H19  single    0.930  0.020  1.080
 1VF  CAU  H20  single    0.930  0.020  1.080
 1VF  CAQ  H21  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
 1VF  H2   CAD  H1   108.01  3.000
 1VF  H2   CAD  NAE  108.29  3.000
 1VF  H1   CAD  NAE  109.74  3.000
 1VF  H2   CAD  CAC  109.48  3.000
 1VF  H1   CAD  CAC  110.21  3.000
 1VF  NAE  CAD  CAC  111.03  3.000
 1VF  H4   CAC  H3   107.04  3.000
 1VF  H4   CAC  NAB  111.87  3.000
 1VF  H3   CAC  NAB  109.20  3.000
 1VF  H4   CAC  CAD  109.46  3.000
 1VF  H3   CAC  CAD  108.59  3.000
 1VF  NAB  CAC  CAD  110.57  3.000
 1VF  CAG  NAB  CAA  111.76  3.000
 1VF  CAA  NAB  CAC  111.74  3.000
 1VF  CAG  NAB  CAC  110.49  3.000
 1VF  H8   CAA  H7   107.91  3.000
 1VF  H8   CAA  H6   107.78  3.000
 1VF  H7   CAA  H6   107.82  3.000
 1VF  H8   CAA  NAB  109.94  3.000
 1VF  H7   CAA  NAB  110.00  3.000
 1VF  H6   CAA  NAB  113.23  3.000
 1VF  H10  CAG  H9   107.07  3.000
 1VF  H10  CAG  CAF  108.92  3.000
 1VF  H9   CAG  CAF  108.20  3.000
 1VF  H10  CAG  NAB  112.05  3.000
 1VF  H9   CAG  NAB  109.26  3.000
 1VF  CAF  CAG  NAB  111.19  3.000
 1VF  H12  CAF  H11  107.79  3.000
 1VF  H12  CAF  NAE  110.83  3.000
 1VF  H11  CAF  NAE  109.31  3.000
 1VF  H12  CAF  CAG  108.65  3.000
 1VF  H11  CAF  CAG  109.87  3.000
 1VF  NAE  CAF  CAG  110.34  3.000
 1VF  CAH  NAE  CAF  125.71  3.000
 1VF  CAF  NAE  CAD  113.00  3.000
 1VF  CAH  NAE  CAD  120.82  3.000
 1VF  CAJ  CAH  OAI  118.56  3.000
 1VF  OAI  CAH  NAE  123.48  3.000
 1VF  CAJ  CAH  NAE  117.93  3.000
 1VF  CAK  CAJ  CAO  119.10  3.000
 1VF  CAK  CAJ  CAH  121.52  3.000
 1VF  CAO  CAJ  CAH  119.10  3.000
 1VF  H13  CAO  CAN  119.27  3.000
 1VF  H13  CAO  CAJ  120.14  3.000
 1VF  CAN  CAO  CAJ  120.59  3.000
 1VF  H14  CAN  CAM  120.92  3.000
 1VF  H14  CAN  CAO  118.67  3.000
 1VF  CAM  CAN  CAO  120.41  3.000
 1VF  H15  CAK  CAL  119.07  3.000
 1VF  H15  CAK  CAJ  120.46  3.000
 1VF  CAL  CAK  CAJ  120.47  3.000
 1VF  H16  CAL  CAM  120.73  3.000
 1VF  H16  CAL  CAK  118.66  3.000
 1VF  CAM  CAL  CAK  120.60  3.000
 1VF  CAP  CAM  CAL  120.32  3.000
 1VF  CAL  CAM  CAN  118.80  3.000
 1VF  CAP  CAM  CAN  120.88  3.000
 1VF  CAQ  CAP  OAZ  122.06  3.000
 1VF  OAZ  CAP  CAM  112.54  3.000
 1VF  CAQ  CAP  CAM  125.40  3.000
 1VF  CAY  OAZ  CAP  120.86  3.000
 1VF  CAT  CAY  CAX  121.71  3.000
 1VF  CAX  CAY  OAZ  116.75  3.000
 1VF  CAT  CAY  OAZ  121.54  3.000
 1VF  H17  CAX  CAW  121.31  3.000
 1VF  H17  CAX  CAY  120.07  3.000
 1VF  CAW  CAX  CAY  118.63  3.000
 1VF  H18  CAW  CAV  119.84  3.000
 1VF  H18  CAW  CAX  119.38  3.000
 1VF  CAV  CAW  CAX  120.78  3.000
 1VF  H19  CAV  CAU  120.20  3.000
 1VF  H19  CAV  CAW  119.89  3.000
 1VF  CAU  CAV  CAW  119.91  3.000
 1VF  H20  CAU  CAT  119.03  3.000
 1VF  H20  CAU  CAV  120.49  3.000
 1VF  CAT  CAU  CAV  120.48  3.000
 1VF  CAR  CAT  CAU  122.01  3.000
 1VF  CAR  CAT  CAY  119.50  3.000
 1VF  CAU  CAT  CAY  118.50  3.000
 1VF  CAQ  CAR  OAS  123.23  3.000
 1VF  CAQ  CAR  CAT  114.22  3.000
 1VF  OAS  CAR  CAT  122.56  3.000
 1VF  H21  CAQ  CAR  118.30  3.000
 1VF  H21  CAQ  CAP  119.88  3.000
 1VF  CAR  CAQ  CAP  121.81  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
 1VF  CONST_01  CAM  CAN  CAO  CAJ    0.00   0.0  0
 1VF  CONST_02  CAM  CAL  CAK  CAJ    0.00   0.0  0
 1VF  CONST_03  CAL  CAM  CAN  CAO    0.00   0.0  0
 1VF  CONST_04  CAL  CAK  CAJ  CAO    0.00   0.0  0
 1VF  CONST_05  CAK  CAL  CAM  CAN    0.00   0.0  0
 1VF  CONST_06  CAK  CAJ  CAO  CAN    0.00   0.0  0
 1VF  CONST_07  CAV  CAU  CAT  CAY    0.00   0.0  0
 1VF  CONST_08  CAV  CAW  CAX  CAY    0.00   0.0  0
 1VF  CONST_09  CAU  CAV  CAW  CAX    0.00   0.0  0
 1VF  CONST_10  CAU  CAT  CAY  CAX    0.00   0.0  0
 1VF  CONST_11  CAT  CAU  CAV  CAW    0.00   0.0  0
 1VF  CONST_12  CAT  CAY  CAX  CAW    0.00   0.0  0
 1VF  CONST_13  CAP  CAM  CAN  CAO  180.00   0.0  0
 1VF  CONST_14  CAP  CAM  CAL  CAK  180.00   0.0  0
 1VF  CONST_15  CAN  CAO  CAJ  CAH  180.00   0.0  0
 1VF  CONST_16  CAL  CAK  CAJ  CAH  180.00   0.0  0
 1VF  CONST_17  CAJ  CAH  NAE  CAD  180.00   0.0  0
 1VF  CONST_19  H14  CAN  CAO  CAJ  180.00   0.0  0
 1VF  CONST_20  H16  CAL  CAK  CAJ  180.00   0.0  0
 1VF  CONST_21  H15  CAK  CAJ  CAO  180.00   0.0  0
 1VF  CONST_22  H13  CAO  CAJ  CAK  180.00   0.0  0
 1VF  CONST_23  H17  CAX  CAY  OAZ    0.00   0.0  0
 1VF  CONST_24  H20  CAU  CAT  CAY  180.00   0.0  0
 1VF  CONST_25  H18  CAW  CAX  CAY  180.00   0.0  0
 1VF  CONST_26  H19  CAV  CAW  CAX  180.00   0.0  0
 1VF  CONST_27  OAI  CAH  NAE  CAD    0.00   0.0  0
 1VF  CONST_28  OAI  CAH  NAE  CAF  180.00   0.0  0
 1VF  Var_01    CAG  CAF  NAE  CAD   52.99  30.0  1
 1VF  Var_02    CAG  NAB  CAC  CAD  -58.37  30.0  1
 1VF  Var_03    CAF  NAE  CAD  CAC  -53.38  30.0  1
 1VF  Var_04    CAF  CAG  NAB  CAC   58.71  30.0  1
 1VF  Var_05    NAE  CAD  CAC  NAB   55.34  30.0  1
 1VF  Var_06    NAE  CAF  CAG  NAB  -55.32  30.0  1
 1VF  Var_07    CAQ  CAP  CAM  CAN  161.52  30.0  2
 1VF  Var_08    CAR  CAQ  CAP  CAM  179.60  30.0  1
 1VF  Var_09    CAT  CAR  CAQ  CAP    1.28  30.0  1
 1VF  Var_10    CAT  CAY  OAZ  CAP    1.31  30.0  1
 1VF  Var_11    CAQ  CAR  CAT  CAY   -0.41  30.0  1
 1VF  Var_12    CAO  CAJ  CAH  NAE  133.03  30.0  2
 1VF  Var_13    H6   CAA  NAB  CAC   61.37  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
 1VF  plan-1  CAH  0.020
 1VF  plan-1  CAJ  0.020
 1VF  plan-1  CAO  0.020
 1VF  plan-1  CAN  0.020
 1VF  plan-1  CAK  0.020
 1VF  plan-1  CAL  0.020
 1VF  plan-1  CAM  0.020
 1VF  plan-1  CAP  0.020
 1VF  plan-1  H13  0.020
 1VF  plan-1  H14  0.020
 1VF  plan-1  H15  0.020
 1VF  plan-1  H16  0.020
 1VF  plan-2  OAZ  0.020
 1VF  plan-2  CAY  0.020
 1VF  plan-2  CAX  0.020
 1VF  plan-2  CAW  0.020
 1VF  plan-2  CAV  0.020
 1VF  plan-2  CAU  0.020
 1VF  plan-2  CAT  0.020
 1VF  plan-2  CAR  0.020
 1VF  plan-2  H17  0.020
 1VF  plan-2  H18  0.020
 1VF  plan-2  H19  0.020
 1VF  plan-2  H20  0.020
 1VF  plan-3  CAD  0.020
 1VF  plan-3  CAF  0.020
 1VF  plan-3  NAE  0.020
 1VF  plan-3  CAH  0.020
 1VF  plan-3  OAI  0.020
 1VF  plan-3  CAJ  0.020
 1VF  plan-4  CAT  0.020
 1VF  plan-4  CAR  0.020
 1VF  plan-4  OAS  0.020
 1VF  plan-4  CAQ  0.020

