# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:25:54 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 2-(carbamoylamino)-5-(4-fluorophenyl)thiophene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)Nc1sc(cc1C(N)=O)c2ccc(F)cc2
#
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
 NM7  NM7  2-(carbamoylamino)-5-(4-fluorophenyl)thiophene-3-carboxamide  ligand  29  19  .  2022-07-22  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_NM7
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
 NM7  NAA   N  NH2   0  -0.844   4.7748  -2.0746   0.2599
 NM7  NAB   N  NH2   0  -0.818   2.0064   3.6098  -0.3521
 NM7  OAC   O  O     0  -0.508   2.5901  -2.6949   0.2907
 NM7  OAD   O  O     0  -0.517   3.6808   2.1276  -0.1332
 NM7  CAF   C  CR16  0  -0.394  -4.0127  -1.3299  -0.4010
 NM7  CAG   C  CR16  0  -0.391  -4.2976   0.8884   0.5088
 NM7  CAH   C  CR16  0  -0.304  -2.6397  -1.1382  -0.4141
 NM7  CAI   C  CR16  0  -0.307  -2.9235   1.0594   0.5022
 NM7  CAJ   C  CR15  0  -0.255   0.0537   1.4382  -0.0930
 NM7  NAK   N  NH1   0  -0.740   3.1196  -0.5032   0.0990
 NM7  SAL   S  S2    0   0.252   0.4681  -1.0810   0.1517
 NM7  CAM   C  C     0   0.692   3.4543  -1.8320   0.2158
 NM7  CAO   C  CR6   0   0.514  -4.8209  -0.3089   0.0579
 NM7  CAP   C  CR6   0   0.133  -2.0699   0.0558   0.0351
 NM7  CAQ   C  CR5   0  -0.218  -0.6249   0.2677   0.0165
 NM7  CAR   C  CR5   0  -0.061   1.4717   1.2871  -0.0754
 NM7  CAS   C  CR5   0   0.112   1.8391  -0.0406   0.0513
 NM7  HNAA  H  HNH2  0   0.412   5.4607  -1.3640   0.0706
 NM7  HNAB  H  HNH2  0   0.412   5.0904  -3.0293   0.2493
 NM7  HNAC  H  HNH2  0   0.408   2.6560   4.3727  -0.4508
 NM7  HNAD  H  HNH2  0   0.415   1.0302   3.8303  -0.4337
 NM7  HAF   H  HCR6  0   0.284  -4.4426  -2.2572  -0.7555
 NM7  HAG   H  HCR6  0   0.283  -4.9493   1.6717   0.8729
 NM7  HAH   H  HCR6  0   0.264  -2.0138  -1.9344  -0.7984
 NM7  HAI   H  HCR6  0   0.266  -2.5130   1.9850   0.8836
 NM7  HAJ   H  HCR5  0   0.265  -0.4559   2.3858  -0.2030
 NM7  HNAK  H  HNH1  0   0.433   3.8195   0.2336   0.0458
 NM7  CAN   C  C     0   0.526   2.4695   2.3636  -0.1885
 NM7  FAE   F  F     0  -0.314  -6.1516  -0.4835   0.0700

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
 NM7  NAA  CAM   single    1.343  0.020  1.343
 NM7  NAA  HNAA  single    0.860  0.020  1.020
 NM7  NAA  HNAB  single    0.860  0.020  1.020
 NM7  NAB  CAN   single    1.340  0.020  1.340
 NM7  NAB  HNAC  single    0.860  0.020  1.020
 NM7  NAB  HNAD  single    0.860  0.020  1.020
 NM7  CAM  OAC   double    1.224  0.020  1.224
 NM7  OAD  CAN   double    1.235  0.020  1.235
 NM7  CAO  FAE   single    1.342  0.020  1.342
 NM7  CAH  CAF   aromatic  1.386  0.020  1.386
 NM7  CAF  CAO   aromatic  1.381  0.020  1.381
 NM7  CAF  HAF   single    0.930  0.020  1.080
 NM7  CAI  CAG   aromatic  1.385  0.020  1.385
 NM7  CAO  CAG   aromatic  1.382  0.020  1.382
 NM7  CAG  HAG   single    0.930  0.020  1.080
 NM7  CAH  CAP   aromatic  1.397  0.020  1.397
 NM7  CAH  HAH   single    0.930  0.020  1.080
 NM7  CAP  CAI   aromatic  1.398  0.020  1.398
 NM7  CAI  HAI   single    0.930  0.020  1.080
 NM7  CAR  CAJ   aromatic  1.426  0.020  1.426
 NM7  CAJ  CAQ   aromatic  1.357  0.020  1.357
 NM7  CAJ  HAJ   single    0.930  0.020  1.080
 NM7  NAK  CAM   single    1.375  0.020  1.375
 NM7  NAK  CAS   single    1.362  0.020  1.362
 NM7  NAK  HNAK  single    0.860  0.020  1.020
 NM7  CAS  SAL   aromatic  1.724  0.020  1.724
 NM7  SAL  CAQ   aromatic  1.741  0.020  1.741
 NM7  CAN  CAR   single    1.472  0.020  1.472
 NM7  CAQ  CAP   single    1.461  0.020  1.461
 NM7  CAR  CAS   aromatic  1.383  0.020  1.383

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
 NM7  HNAB  NAA  HNAA  117.05  3.000
 NM7  HNAB  NAA  CAM   118.67  3.000
 NM7  HNAA  NAA  CAM   122.46  3.000
 NM7  HNAD  NAB  HNAC  116.93  3.000
 NM7  HNAD  NAB  CAN   123.39  3.000
 NM7  HNAC  NAB  CAN   119.59  3.000
 NM7  HAF   CAF  CAO   120.67  3.000
 NM7  HAF   CAF  CAH   120.60  3.000
 NM7  CAO   CAF  CAH   118.73  3.000
 NM7  HAG   CAG  CAO   120.58  3.000
 NM7  HAG   CAG  CAI   120.65  3.000
 NM7  CAO   CAG  CAI   118.76  3.000
 NM7  HAH   CAH  CAP   120.43  3.000
 NM7  HAH   CAH  CAF   118.29  3.000
 NM7  CAP   CAH  CAF   121.27  3.000
 NM7  HAI   CAI  CAP   120.02  3.000
 NM7  HAI   CAI  CAG   118.71  3.000
 NM7  CAP   CAI  CAG   121.26  3.000
 NM7  HAJ   CAJ  CAR   124.23  3.000
 NM7  HAJ   CAJ  CAQ   121.88  3.000
 NM7  CAR   CAJ  CAQ   113.88  3.000
 NM7  HNAK  NAK  CAS   113.49  3.000
 NM7  HNAK  NAK  CAM   122.46  3.000
 NM7  CAS   NAK  CAM   124.04  3.000
 NM7  CAS   SAL  CAQ    91.56  3.000
 NM7  NAK   CAM  OAC   120.98  3.000
 NM7  NAK   CAM  NAA   114.61  3.000
 NM7  OAC   CAM  NAA   124.40  3.000
 NM7  CAG   CAO  CAF   121.83  3.000
 NM7  CAG   CAO  FAE   119.02  3.000
 NM7  CAF   CAO  FAE   119.15  3.000
 NM7  CAQ   CAP  CAI   120.28  3.000
 NM7  CAQ   CAP  CAH   121.56  3.000
 NM7  CAI   CAP  CAH   118.16  3.000
 NM7  CAP   CAQ  SAL   120.51  3.000
 NM7  CAP   CAQ  CAJ   128.37  3.000
 NM7  SAL   CAQ  CAJ   111.12  3.000
 NM7  CAS   CAR  CAN   121.92  3.000
 NM7  CAS   CAR  CAJ   111.52  3.000
 NM7  CAN   CAR  CAJ   126.55  3.000
 NM7  CAR   CAS  SAL   111.92  3.000
 NM7  CAR   CAS  NAK   125.37  3.000
 NM7  SAL   CAS  NAK   122.72  3.000
 NM7  CAR   CAN  OAD   121.43  3.000
 NM7  CAR   CAN  NAB   117.09  3.000
 NM7  OAD   CAN  NAB   121.48  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
 NM7  CONST_01  CAI   CAP  CAH  CAF    0.00  0.0  0
 NM7  CONST_02  CAQ   CAP  CAH  CAF  180.00  0.0  0
 NM7  CONST_03  CAI   CAG  CAO  CAF    0.00  0.0  0
 NM7  CONST_04  CAH   CAP  CAI  CAG    0.00  0.0  0
 NM7  CONST_05  CAQ   CAP  CAI  CAG  180.00  0.0  0
 NM7  CONST_06  CAH   CAF  CAO  CAG    0.00  0.0  0
 NM7  CONST_11  SAL   CAS  CAR  CAJ    0.00  0.0  0
 NM7  CONST_12  CAS   SAL  CAQ  CAJ    0.00  0.0  0
 NM7  CONST_13  CAR   CAJ  CAQ  SAL    0.00  0.0  0
 NM7  CONST_14  CAP   CAH  CAF  CAO    0.00  0.0  0
 NM7  CONST_15  CAP   CAI  CAG  CAO    0.00  0.0  0
 NM7  CONST_16  CAR   CAJ  CAQ  CAP  180.00  0.0  0
 NM7  CONST_17  CAS   SAL  CAQ  CAP  180.00  0.0  0
 NM7  CONST_18  CAS   CAR  CAJ  CAQ    0.00  0.0  0
 NM7  CONST_19  CAR   CAS  SAL  CAQ    0.00  0.0  0
 NM7  CONST_20  CAH   CAF  CAO  FAE  180.00  0.0  0
 NM7  CONST_21  CAI   CAG  CAO  FAE  180.00  0.0  0
 NM7  CONST_22  NAK   CAS  CAR  CAJ  180.00  0.0  0
 NM7  CONST_23  CAQ   SAL  CAS  NAK  180.00  0.0  0
 NM7  CONST_24  CAN   CAR  CAS  SAL  180.00  0.0  0
 NM7  CONST_25  CAQ   CAJ  CAR  CAN  180.00  0.0  0
 NM7  CONST_26  HAG   CAG  CAO  CAF  180.00  0.0  0
 NM7  CONST_27  HAF   CAF  CAO  CAG  180.00  0.0  0
 NM7  CONST_28  HAI   CAI  CAP  CAH  180.00  0.0  0
 NM7  CONST_29  HAH   CAH  CAP  CAI  180.00  0.0  0
 NM7  CONST_30  HAJ   CAJ  CAQ  SAL  180.00  0.0  0
 NM7  CONST_31  CAS   CAR  CAN  NAB  180.00  0.0  0
 NM7  CONST_32  CAM   NAK  CAS  SAL    0.00  0.0  0
 NM7  CONST_33  CAR   CAS  NAK  CAM  180.00  0.0  0
 NM7  CONST_34  HNAK  NAK  CAS  SAL  180.00  0.0  0
 NM7  CONST_35  CAS   NAK  CAM  OAC    0.00  0.0  0
 NM7  CONST_36  CAS   NAK  CAM  NAA  180.00  0.0  0
 NM7  CONST_37  HNAC  NAB  CAN  CAR  180.00  0.0  0
 NM7  CONST_38  HNAD  NAB  CAN  CAR    0.00  0.0  0
 NM7  CONST_39  HNAA  NAA  CAM  OAC  180.00  0.0  0
 NM7  CONST_40  HNAB  NAA  CAM  OAC    0.00  0.0  0

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
 NM7  plan-1  CAF   0.020
 NM7  plan-1  CAG   0.020
 NM7  plan-1  CAH   0.020
 NM7  plan-1  CAI   0.020
 NM7  plan-1  CAO   0.020
 NM7  plan-1  CAP   0.020
 NM7  plan-1  CAQ   0.020
 NM7  plan-1  HAF   0.020
 NM7  plan-1  HAG   0.020
 NM7  plan-1  HAH   0.020
 NM7  plan-1  HAI   0.020
 NM7  plan-1  FAE   0.020
 NM7  plan-2  NAA   0.020
 NM7  plan-2  OAC   0.020
 NM7  plan-2  NAK   0.020
 NM7  plan-2  CAM   0.020
 NM7  plan-2  CAS   0.020
 NM7  plan-2  HNAA  0.020
 NM7  plan-2  HNAB  0.020
 NM7  plan-2  HNAK  0.020
 NM7  plan-3  NAB   0.020
 NM7  plan-3  OAD   0.020
 NM7  plan-3  CAJ   0.020
 NM7  plan-3  NAK   0.020
 NM7  plan-3  SAL   0.020
 NM7  plan-3  CAP   0.020
 NM7  plan-3  CAQ   0.020
 NM7  plan-3  CAR   0.020
 NM7  plan-3  CAS   0.020
 NM7  plan-3  HNAC  0.020
 NM7  plan-3  HNAD  0.020
 NM7  plan-3  HAJ   0.020
 NM7  plan-3  CAN   0.020

