# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 23:51:17 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-[6-azanyl-1-[(3-fluorophenyl)methyl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-N-methyl-benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C1=C(N)N(Cc2cccc(F)c2)C(=O)NC1=O)[S](=O)(=O)c3ccccc3
#
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
 LD6  LD6  N-[6-azanyl-1-[(3-fluorophenyl)methyl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-N-methyl-benzenesulfonamide  ligand  45  28  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LD6
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
 LD6  CAY   C  CR16  0  -0.440  -4.0812   0.0357  -0.5404
 LD6  CAZ   C  CR6   0   0.549  -5.2209   0.6753  -0.9846
 LD6  FBB   F  F     0  -0.313  -5.5731   0.5363  -2.2718
 LD6  CBA   C  CR16  0  -0.418  -6.0126   1.4498  -0.1578
 LD6  CAX   C  CR16  0  -0.225  -5.6337   1.5828   1.1693
 LD6  CAW   C  CR16  0  -0.308  -4.4895   0.9549   1.6437
 LD6  CAV   C  CR6   0   0.075  -3.7096   0.1786   0.7926
 LD6  CAU   C  CH2   0  -0.409  -2.4953  -0.5279   1.3426
 LD6  NAQ   N  NR6   0  -0.600  -1.3740  -0.5796   0.4123
 LD6  CAR   C  CR6   0   0.691  -0.6083   0.5400   0.1848
 LD6  NAS   N  NH2   0  -0.817  -0.9815   1.6795   0.7628
 LD6  CAP   C  CR6   0   0.723  -1.0911  -1.7968  -0.1946
 LD6  OAO   O  O     0  -0.473  -1.7834  -2.7782  -0.0212
 LD6  NAG   N  NR16  0  -0.743   0.0050  -1.8093  -0.9964
 LD6  CAH   C  CR6   0   0.584   0.8669  -0.7507  -1.2709
 LD6  OAA   O  O     0  -0.464   1.7928  -0.9112  -2.0483
 LD6  CAI   C  CR6   0  -0.099   0.5315   0.4609  -0.5993
 LD6  NAJ   N  N     0  -0.632   1.2757   1.6376  -0.8303
 LD6  CAB   C  CH3   0  -0.523   1.3771   2.1539  -2.1958
 LD6  SAK   S  S     0   1.375   2.5660   1.8844   0.1977
 LD6  OAT   O  OS    0  -0.654   3.1968   3.1270  -0.2196
 LD6  OAC   O  OS    0  -0.649   2.0558   1.7613   1.5531
 LD6  CAL   C  CR6   0  -0.172   3.6983   0.5551  -0.0743
 LD6  CAM   C  CR16  0  -0.232   4.6307   0.6624  -1.0976
 LD6  CAN   C  CR16  0  -0.245   5.4803  -0.4040  -1.3438
 LD6  CAF   C  CR16  0  -0.237   5.3937  -1.5573  -0.5744
 LD6  CAE   C  CR16  0  -0.240   4.4628  -1.6462   0.4518
 LD6  CAD   C  CR16  0  -0.233   3.6080  -0.5860   0.7107
 LD6  HAY   H  HCR6  0   0.277  -3.5010  -0.5605  -1.2331
 LD6  HBA   H  HCR6  0   0.284  -6.8979   1.9382  -0.5424
 LD6  HAX   H  HCR6  0   0.274  -6.2314   2.1887   1.8367
 LD6  HAW   H  HCR6  0   0.269  -4.2023   1.0723   2.6814
 LD6  HAU1  H  HCH2  0   0.299  -2.1646  -0.0569   2.2692
 LD6  HAU2  H  HCH2  0   0.321  -2.7534  -1.5530   1.5975
 LD6  HAS1  H  HNH2  0   0.428  -1.9036   1.8286   1.1345
 LD6  HAS2  H  HNH2  0   0.419  -0.4511   2.5074   0.5463
 LD6  HAG   H  HNR6  0   0.425   0.1994  -2.6876  -1.4606
 LD6  HAB1  H  HCH3  0   0.261   1.5754   3.2217  -2.1831
 LD6  HAB2  H  HCH3  0   0.243   2.1393   1.6484  -2.7895
 LD6  HAB3  H  HCH3  0   0.262   0.4111   1.9964  -2.6692
 LD6  HAM   H  HCR6  0   0.278   4.7034   1.5625  -1.6933
 LD6  HAD   H  HCR6  0   0.282   2.8880  -0.6541   1.5144
 LD6  HAN   H  HCR6  0   0.270   6.2132  -0.3328  -2.1361
 LD6  HAF   H  HCR6  0   0.269   6.0597  -2.3871  -0.7717
 LD6  HAE   H  HCR6  0   0.269   4.4033  -2.5411   1.0565

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
 LD6  CAY  CAZ   aromatic  1.380  0.020  1.380
 LD6  CAY  CAV   aromatic  1.391  0.020  1.391
 LD6  CAZ  FBB   single    1.342  0.020  1.342
 LD6  CAZ  CBA   aromatic  1.382  0.020  1.382
 LD6  CBA  CAX   aromatic  1.387  0.020  1.387
 LD6  CAX  CAW   aromatic  1.389  0.020  1.389
 LD6  CAW  CAV   aromatic  1.391  0.020  1.391
 LD6  CAV  CAU   single    1.509  0.020  1.509
 LD6  CAU  NAQ   single    1.458  0.020  1.458
 LD6  NAQ  CAR   single    1.375  0.020  1.375
 LD6  NAQ  CAP   single    1.389  0.020  1.389
 LD6  CAR  NAS   single    1.331  0.020  1.331
 LD6  CAR  CAI   double    1.386  0.020  1.386
 LD6  CAP  OAO   double    1.213  0.020  1.213
 LD6  CAP  NAG   single    1.358  0.020  1.358
 LD6  NAG  CAH   single    1.392  0.020  1.392
 LD6  CAH  OAA   double    1.220  0.020  1.220
 LD6  CAH  CAI   single    1.425  0.020  1.425
 LD6  CAI  NAJ   single    1.411  0.020  1.411
 LD6  NAJ  CAB   single    1.463  0.020  1.463
 LD6  NAJ  SAK   single    1.668  0.020  1.668
 LD6  SAK  OAT   double    1.455  0.020  1.455
 LD6  SAK  OAC   double    1.453  0.020  1.453
 LD6  SAK  CAL   single    1.767  0.020  1.767
 LD6  CAL  CAM   aromatic  1.389  0.020  1.389
 LD6  CAL  CAD   aromatic  1.388  0.020  1.388
 LD6  CAM  CAN   aromatic  1.386  0.020  1.386
 LD6  CAN  CAF   aromatic  1.389  0.020  1.389
 LD6  CAF  CAE   aromatic  1.388  0.020  1.388
 LD6  CAE  CAD   aromatic  1.386  0.020  1.386
 LD6  CAY  HAY   single    0.930  0.020  1.080
 LD6  CBA  HBA   single    0.930  0.020  1.080
 LD6  CAX  HAX   single    0.930  0.020  1.080
 LD6  CAW  HAW   single    0.930  0.020  1.080
 LD6  CAU  HAU1  single    0.970  0.020  1.090
 LD6  CAU  HAU2  single    0.970  0.020  1.090
 LD6  NAS  HAS1  single    0.890  0.020  1.040
 LD6  NAS  HAS2  single    0.890  0.020  1.040
 LD6  NAG  HAG   single    0.860  0.020  1.020
 LD6  CAB  HAB1  single    0.970  0.020  1.090
 LD6  CAB  HAB2  single    0.970  0.020  1.090
 LD6  CAB  HAB3  single    0.970  0.020  1.090
 LD6  CAM  HAM   single    0.930  0.020  1.080
 LD6  CAD  HAD   single    0.930  0.020  1.080
 LD6  CAN  HAN   single    0.930  0.020  1.080
 LD6  CAF  HAF   single    0.930  0.020  1.080
 LD6  CAE  HAE   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
 LD6  HAY   CAY  CAV   121.77  3.000
 LD6  HAY   CAY  CAZ   119.46  3.000
 LD6  CAV   CAY  CAZ   118.77  3.000
 LD6  CBA   CAZ  FBB   118.79  3.000
 LD6  CBA   CAZ  CAY   122.69  3.000
 LD6  FBB   CAZ  CAY   118.52  3.000
 LD6  HBA   CBA  CAX   121.38  3.000
 LD6  HBA   CBA  CAZ   120.60  3.000
 LD6  CAX   CBA  CAZ   118.02  3.000
 LD6  HAX   CAX  CAW   119.86  3.000
 LD6  HAX   CAX  CBA   119.56  3.000
 LD6  CAW   CAX  CBA   120.58  3.000
 LD6  HAW   CAW  CAV   119.86  3.000
 LD6  HAW   CAW  CAX   119.79  3.000
 LD6  CAV   CAW  CAX   120.35  3.000
 LD6  CAU   CAV  CAW   119.31  3.000
 LD6  CAU   CAV  CAY   121.08  3.000
 LD6  CAW   CAV  CAY   119.59  3.000
 LD6  HAU2  CAU  HAU1  106.25  3.000
 LD6  HAU2  CAU  NAQ   107.38  3.000
 LD6  HAU1  CAU  NAQ   108.92  3.000
 LD6  HAU2  CAU  CAV   109.63  3.000
 LD6  HAU1  CAU  CAV   110.58  3.000
 LD6  NAQ   CAU  CAV   113.77  3.000
 LD6  CAP   NAQ  CAR   121.85  3.000
 LD6  CAP   NAQ  CAU   117.81  3.000
 LD6  CAR   NAQ  CAU   120.32  3.000
 LD6  CAI   CAR  NAS   121.68  3.000
 LD6  CAI   CAR  NAQ   120.33  3.000
 LD6  NAS   CAR  NAQ   117.97  3.000
 LD6  HAS2  NAS  HAS1  116.15  3.000
 LD6  HAS2  NAS  CAR   117.58  3.000
 LD6  HAS1  NAS  CAR   123.01  3.000
 LD6  NAG   CAP  OAO   122.50  3.000
 LD6  NAG   CAP  NAQ   115.49  3.000
 LD6  OAO   CAP  NAQ   122.01  3.000
 LD6  HAG   NAG  CAH   116.77  3.000
 LD6  HAG   NAG  CAP   115.70  3.000
 LD6  CAH   NAG  CAP   127.51  3.000
 LD6  CAI   CAH  OAA   126.22  3.000
 LD6  CAI   CAH  NAG   114.06  3.000
 LD6  OAA   CAH  NAG   119.70  3.000
 LD6  NAJ   CAI  CAH   120.50  3.000
 LD6  NAJ   CAI  CAR   118.60  3.000
 LD6  CAH   CAI  CAR   120.58  3.000
 LD6  SAK   NAJ  CAB   117.99  3.000
 LD6  SAK   NAJ  CAI   115.49  3.000
 LD6  CAB   NAJ  CAI   118.91  3.000
 LD6  HAB3  CAB  HAB2  108.47  3.000
 LD6  HAB3  CAB  HAB1  108.04  3.000
 LD6  HAB2  CAB  HAB1  109.54  3.000
 LD6  HAB3  CAB  NAJ   107.08  3.000
 LD6  HAB2  CAB  NAJ   113.14  3.000
 LD6  HAB1  CAB  NAJ   110.40  3.000
 LD6  CAL   SAK  OAC   107.74  3.000
 LD6  CAL   SAK  OAT   108.69  3.000
 LD6  OAC   SAK  OAT   119.48  3.000
 LD6  CAL   SAK  NAJ   106.82  3.000
 LD6  OAC   SAK  NAJ   106.90  3.000
 LD6  OAT   SAK  NAJ   106.56  3.000
 LD6  CAD   CAL  CAM   121.60  3.000
 LD6  CAD   CAL  SAK   119.32  3.000
 LD6  CAM   CAL  SAK   119.05  3.000
 LD6  HAM   CAM  CAN   120.09  3.000
 LD6  HAM   CAM  CAL   121.01  3.000
 LD6  CAN   CAM  CAL   118.90  3.000
 LD6  HAN   CAN  CAF   120.18  3.000
 LD6  HAN   CAN  CAM   119.67  3.000
 LD6  CAF   CAN  CAM   120.15  3.000
 LD6  HAF   CAF  CAE   119.89  3.000
 LD6  HAF   CAF  CAN   119.82  3.000
 LD6  CAE   CAF  CAN   120.29  3.000
 LD6  HAE   CAE  CAD   119.63  3.000
 LD6  HAE   CAE  CAF   120.21  3.000
 LD6  CAD   CAE  CAF   120.17  3.000
 LD6  HAD   CAD  CAE   120.09  3.000
 LD6  HAD   CAD  CAL   121.03  3.000
 LD6  CAE   CAD  CAL   118.89  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
 LD6  CONST_01  CAX   CBA  CAZ  CAY     0.00   0.0  0
 LD6  CONST_02  CAX   CAW  CAV  CAY     0.00   0.0  0
 LD6  CONST_03  CAW   CAV  CAY  CAZ     0.00   0.0  0
 LD6  CONST_04  CAW   CAX  CBA  CAZ     0.00   0.0  0
 LD6  CONST_05  CAV   CAY  CAZ  CBA     0.00   0.0  0
 LD6  CONST_06  CAV   CAW  CAX  CBA     0.00   0.0  0
 LD6  CONST_07  CAF   CAN  CAM  CAL     0.00   0.0  0
 LD6  CONST_08  CAF   CAE  CAD  CAL     0.00   0.0  0
 LD6  CONST_09  CAE   CAD  CAL  CAM     0.00   0.0  0
 LD6  CONST_10  CAE   CAF  CAN  CAM     0.00   0.0  0
 LD6  CONST_11  CAD   CAL  CAM  CAN     0.00   0.0  0
 LD6  CONST_12  CAD   CAE  CAF  CAN     0.00   0.0  0
 LD6  CONST_13  CAH   NAG  CAP  NAQ     0.00   0.0  0
 LD6  CONST_14  NAG   CAP  NAQ  CAR     0.00   0.0  0
 LD6  CONST_15  CAI   CAR  NAQ  CAP     0.00   0.0  0
 LD6  CONST_16  CAI   CAH  NAG  CAP     0.00   0.0  0
 LD6  CONST_17  CAU   CAV  CAY  CAZ   180.00   0.0  0
 LD6  CONST_18  CAV   CAY  CAZ  FBB   180.00   0.0  0
 LD6  CONST_19  CAX   CBA  CAZ  FBB   180.00   0.0  0
 LD6  CONST_20  CAU   CAV  CAW  CAX   180.00   0.0  0
 LD6  CONST_21  CAN   CAM  CAL  SAK   180.00   0.0  0
 LD6  CONST_22  CAE   CAD  CAL  SAK   180.00   0.0  0
 LD6  CONST_23  CAI   CAR  NAQ  CAU   180.00   0.0  0
 LD6  CONST_24  NAG   CAP  NAQ  CAU   180.00   0.0  0
 LD6  CONST_25  OAO   CAP  NAQ  CAR   180.00   0.0  0
 LD6  CONST_26  CAP   NAQ  CAR  NAS   180.00   0.0  0
 LD6  CONST_27  OAA   CAH  NAG  CAP   180.00   0.0  0
 LD6  CONST_28  CAH   NAG  CAP  OAO   180.00   0.0  0
 LD6  CONST_29  HBA   CBA  CAZ  CAY   180.00   0.0  0
 LD6  CONST_30  HAW   CAW  CAV  CAY   180.00   0.0  0
 LD6  CONST_31  HAX   CAX  CBA  CAZ   180.00   0.0  0
 LD6  CONST_32  HAY   CAY  CAZ  CBA   180.00   0.0  0
 LD6  CONST_33  HAN   CAN  CAM  CAL   180.00   0.0  0
 LD6  CONST_34  HAE   CAE  CAD  CAL   180.00   0.0  0
 LD6  CONST_35  HAD   CAD  CAL  CAM   180.00   0.0  0
 LD6  CONST_36  HAF   CAF  CAN  CAM   180.00   0.0  0
 LD6  CONST_37  HAM   CAM  CAN  CAF   180.00   0.0  0
 LD6  CONST_38  HAG   NAG  CAP  NAQ   180.00   0.0  0
 LD6  CONST_39  NAS   CAR  NAQ  CAU     0.00   0.0  0
 LD6  CONST_40  OAO   CAP  NAQ  CAU     0.00   0.0  0
 LD6  CONST_42  HAS2  NAS  CAR  NAQ   180.00   0.0  0
 LD6  Var_01    NAQ   CAU  CAV  CAY    38.00  30.0  2
 LD6  Var_02    CAR   NAQ  CAU  CAV    75.57  30.0  3
 LD6  Var_03    CAB   NAJ  CAI  CAR  -115.71  30.0  2
 LD6  Var_04    CAL   SAK  NAJ  CAI    63.27  30.0  3
 LD6  Var_05    CAM   CAL  SAK  NAJ    85.62  30.0  2
 LD6  Var_06    HAB1  CAB  NAJ  CAI   155.32  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
 LD6  plan-1  CAY   0.020
 LD6  plan-1  CAZ   0.020
 LD6  plan-1  FBB   0.020
 LD6  plan-1  CBA   0.020
 LD6  plan-1  CAX   0.020
 LD6  plan-1  CAW   0.020
 LD6  plan-1  CAV   0.020
 LD6  plan-1  CAU   0.020
 LD6  plan-1  HAY   0.020
 LD6  plan-1  HBA   0.020
 LD6  plan-1  HAX   0.020
 LD6  plan-1  HAW   0.020
 LD6  plan-2  CAU   0.020
 LD6  plan-2  NAQ   0.020
 LD6  plan-2  CAR   0.020
 LD6  plan-2  NAS   0.020
 LD6  plan-2  CAP   0.020
 LD6  plan-2  OAO   0.020
 LD6  plan-2  NAG   0.020
 LD6  plan-2  CAH   0.020
 LD6  plan-2  OAA   0.020
 LD6  plan-2  CAI   0.020
 LD6  plan-2  NAJ   0.020
 LD6  plan-2  HAS1  0.020
 LD6  plan-2  HAS2  0.020
 LD6  plan-2  HAG   0.020
 LD6  plan-3  SAK   0.020
 LD6  plan-3  CAL   0.020
 LD6  plan-3  CAM   0.020
 LD6  plan-3  CAN   0.020
 LD6  plan-3  CAF   0.020
 LD6  plan-3  CAE   0.020
 LD6  plan-3  CAD   0.020
 LD6  plan-3  HAM   0.020
 LD6  plan-3  HAD   0.020
 LD6  plan-3  HAN   0.020
 LD6  plan-3  HAF   0.020
 LD6  plan-3  HAE   0.020

