# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 12:20:01 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: N-[2-(2-methyl-1H-indol-3-yl)ethyl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c2ccccc2c1CCNC(=O)c3sccc3
#
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
 N23  N23  N-[2-(2-methyl-1H-indol-3-yl)ethyl]thiophene-2-carboxamide  ligand  36  20  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N23
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
 N23  CAO   C  CH3   0  -0.739   2.4291   3.2945   0.1123
 N23  CAB   C  CR5   0   0.283   2.8856   1.8803   0.1560
 N23  NAA   N  NR15  0  -0.729   4.1789   1.5516  -0.1602
 N23  CAE   C  CR56  0   0.338   4.3501   0.2005  -0.0775
 N23  CAR   C  CR16  0  -0.312   5.4767  -0.5880  -0.2988
 N23  CAT   C  CR16  0  -0.288   5.3418  -1.9550  -0.1347
 N23  CAS   C  CR16  0  -0.269   4.1160  -2.5256   0.2433
 N23  CAQ   C  CR16  0  -0.379   3.0016  -1.7378   0.4640
 N23  CAD   C  CR56  0   0.058   3.1088  -0.3521   0.3051
 N23  CAC   C  CR5   0  -0.034   2.1899   0.7367   0.4533
 N23  CAN   C  CH2   0  -0.589   0.7432   0.6175   0.7983
 N23  CAP   C  CH2   0  -0.235  -0.0928   0.2538  -0.4260
 N23  NAM   N  NH1   0  -0.670  -1.4825   0.0747  -0.0589
 N23  CAG   C  C     0   0.554  -2.4727   0.0628  -0.9666
 N23  OAK   O  O     0  -0.486  -2.2817   0.2270  -2.1644
 N23  CAF   C  CR5   0  -0.317  -3.8430  -0.1552  -0.4525
 N23  CAI   C  CR15  0  -0.188  -4.9253  -0.4691  -1.2263
 N23  CAL   C  CR15  0  -0.175  -6.1144  -0.6256  -0.4737
 N23  CAJ   C  CR15  0  -0.451  -5.9177  -0.4189   0.8594
 N23  SAH   S  S2    0   0.234  -4.2915  -0.0325   1.2082
 N23  HAO   H  HCH3  0   0.257   2.2046   3.6104  -0.9087
 N23  HAOA  H  HCH3  0   0.253   1.5258   3.4306   0.7040
 N23  HAOB  H  HCH3  0   0.254   3.1900   3.9708   0.5038
 N23  HNAA  H  HNR5  0   0.404   4.8972   2.2172  -0.3940
 N23  HAR   H  HCR6  0   0.256   6.4228  -0.1504  -0.5917
 N23  HAT   H  HCR6  0   0.247   6.1969  -2.5971  -0.3024
 N23  HAS   H  HCR6  0   0.244   4.0462  -3.5994   0.3610
 N23  HAQ   H  HCR6  0   0.238   2.0605  -2.1885   0.7570
 N23  HAN   H  HCH2  0   0.248   0.6093  -0.1475   1.5707
 N23  HANA  H  HCH2  0   0.254   0.3676   1.5522   1.2223
 N23  HAP   H  HCH2  0   0.245  -0.0186   1.0500  -1.1672
 N23  HAPA  H  HCH2  0   0.239   0.3032  -0.6555  -0.8901
 N23  HNAM  H  HNH1  0   0.402  -1.6644  -0.2404   0.8815
 N23  HAI   H  HCR5  0   0.273  -4.8673  -0.5898  -2.2983
 N23  HAL   H  HCR5  0   0.275  -7.0733  -0.8782  -0.9016
 N23  HAJ   H  HCR5  0   0.307  -6.6451  -0.4653   1.6551

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
 N23  CAO  CAB   single    1.487  0.020  1.487
 N23  CAB  NAA   aromatic  1.371  0.020  1.371
 N23  CAB  CAC   aromatic  1.371  0.020  1.371
 N23  NAA  CAE   aromatic  1.364  0.020  1.364
 N23  CAE  CAR   aromatic  1.393  0.020  1.393
 N23  CAE  CAD   aromatic  1.412  0.020  1.412
 N23  CAR  CAT   aromatic  1.383  0.020  1.383
 N23  CAT  CAS   aromatic  1.404  0.020  1.404
 N23  CAS  CAQ   aromatic  1.383  0.020  1.383
 N23  CAQ  CAD   aromatic  1.399  0.020  1.399
 N23  CAD  CAC   aromatic  1.432  0.020  1.432
 N23  CAC  CAN   single    1.492  0.020  1.492
 N23  CAN  CAP   single    1.526  0.020  1.526
 N23  CAP  NAM   single    1.449  0.020  1.449
 N23  NAM  CAG   single    1.343  0.020  1.343
 N23  CAG  OAK   double    1.224  0.020  1.224
 N23  CAG  CAF   single    1.480  0.020  1.480
 N23  CAF  CAI   aromatic  1.367  0.020  1.367
 N23  CAF  SAH   aromatic  1.725  0.020  1.725
 N23  CAI  CAL   aromatic  1.416  0.020  1.416
 N23  CAL  CAJ   aromatic  1.363  0.020  1.363
 N23  CAJ  SAH   aromatic  1.708  0.020  1.708
 N23  CAO  HAO   single    0.970  0.020  1.090
 N23  CAO  HAOA  single    0.970  0.020  1.090
 N23  CAO  HAOB  single    0.970  0.020  1.090
 N23  NAA  HNAA  single    0.860  0.020  1.020
 N23  CAR  HAR   single    0.930  0.020  1.080
 N23  CAT  HAT   single    0.930  0.020  1.080
 N23  CAS  HAS   single    0.930  0.020  1.080
 N23  CAQ  HAQ   single    0.930  0.020  1.080
 N23  CAN  HAN   single    0.970  0.020  1.090
 N23  CAN  HANA  single    0.970  0.020  1.090
 N23  CAP  HAP   single    0.970  0.020  1.090
 N23  CAP  HAPA  single    0.970  0.020  1.090
 N23  NAM  HNAM  single    0.860  0.020  1.020
 N23  CAI  HAI   single    0.930  0.020  1.080
 N23  CAL  HAL   single    0.930  0.020  1.080
 N23  CAJ  HAJ   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
 N23  HAOB  CAO  HAOA  107.84  3.000
 N23  HAOB  CAO  HAO   107.44  3.000
 N23  HAOA  CAO  HAO   107.55  3.000
 N23  HAOB  CAO  CAB   111.41  3.000
 N23  HAOA  CAO  CAB   110.97  3.000
 N23  HAO   CAO  CAB   111.45  3.000
 N23  CAC   CAB  NAA   109.18  3.000
 N23  CAC   CAB  CAO   130.08  3.000
 N23  NAA   CAB  CAO   120.72  3.000
 N23  HNAA  NAA  CAE   125.39  3.000
 N23  HNAA  NAA  CAB   124.61  3.000
 N23  CAE   NAA  CAB   109.98  3.000
 N23  CAD   CAE  CAR   122.19  3.000
 N23  CAD   CAE  NAA   107.08  3.000
 N23  CAR   CAE  NAA   130.73  3.000
 N23  HAR   CAR  CAT   121.11  3.000
 N23  HAR   CAR  CAE   121.39  3.000
 N23  CAT   CAR  CAE   117.49  3.000
 N23  HAT   CAT  CAS   119.37  3.000
 N23  HAT   CAT  CAR   119.39  3.000
 N23  CAS   CAT  CAR   121.25  3.000
 N23  HAS   CAS  CAQ   119.73  3.000
 N23  HAS   CAS  CAT   119.26  3.000
 N23  CAQ   CAS  CAT   121.01  3.000
 N23  HAQ   CAQ  CAD   120.61  3.000
 N23  HAQ   CAQ  CAS   120.40  3.000
 N23  CAD   CAQ  CAS   118.98  3.000
 N23  CAC   CAD  CAQ   133.79  3.000
 N23  CAC   CAD  CAE   107.13  3.000
 N23  CAQ   CAD  CAE   119.08  3.000
 N23  CAN   CAC  CAD   125.82  3.000
 N23  CAN   CAC  CAB   127.50  3.000
 N23  CAD   CAC  CAB   106.62  3.000
 N23  HANA  CAN  HAN   106.37  3.000
 N23  HANA  CAN  CAP   109.07  3.000
 N23  HAN   CAN  CAP   109.40  3.000
 N23  HANA  CAN  CAC   110.77  3.000
 N23  HAN   CAN  CAC   109.71  3.000
 N23  CAP   CAN  CAC   111.38  3.000
 N23  HAPA  CAP  HAP   107.08  3.000
 N23  HAPA  CAP  NAM   110.59  3.000
 N23  HAP   CAP  NAM   109.13  3.000
 N23  HAPA  CAP  CAN   109.86  3.000
 N23  HAP   CAP  CAN   109.51  3.000
 N23  NAM   CAP  CAN   110.59  3.000
 N23  HNAM  NAM  CAG   119.63  3.000
 N23  HNAM  NAM  CAP   116.62  3.000
 N23  CAG   NAM  CAP   122.49  3.000
 N23  CAF   CAG  OAK   120.28  3.000
 N23  CAF   CAG  NAM   116.69  3.000
 N23  OAK   CAG  NAM   123.02  3.000
 N23  SAH   CAF  CAI   110.82  3.000
 N23  SAH   CAF  CAG   124.39  3.000
 N23  CAI   CAF  CAG   124.78  3.000
 N23  HAI   CAI  CAL   124.07  3.000
 N23  HAI   CAI  CAF   123.01  3.000
 N23  CAL   CAI  CAF   112.92  3.000
 N23  HAL   CAL  CAJ   123.43  3.000
 N23  HAL   CAL  CAI   124.12  3.000
 N23  CAJ   CAL  CAI   112.45  3.000
 N23  HAJ   CAJ  SAH   120.07  3.000
 N23  HAJ   CAJ  CAL   128.12  3.000
 N23  SAH   CAJ  CAL   111.80  3.000
 N23  CAJ   SAH  CAF    92.00  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
 N23  CONST_01  CAR   CAE  NAA  CAB   180.00   0.0  0
 N23  CONST_02  CAD   CAE  NAA  CAB     0.00   0.0  0
 N23  CONST_03  CAE   CAD  CAC  CAB     0.00   0.0  0
 N23  CONST_04  CAQ   CAD  CAC  CAB   180.00   0.0  0
 N23  CONST_05  CAD   CAC  CAB  NAA     0.00   0.0  0
 N23  CONST_06  CAT   CAR  CAE  NAA   180.00   0.0  0
 N23  CONST_07  CAQ   CAD  CAE  NAA   180.00   0.0  0
 N23  CONST_08  CAC   CAD  CAE  NAA     0.00   0.0  0
 N23  CONST_09  CAC   CAB  NAA  CAE     0.00   0.0  0
 N23  CONST_10  CAS   CAT  CAR  CAE     0.00   0.0  0
 N23  CONST_11  CAS   CAQ  CAD  CAE     0.00   0.0  0
 N23  CONST_12  CAQ   CAD  CAE  CAR     0.00   0.0  0
 N23  CONST_13  CAC   CAD  CAE  CAR   180.00   0.0  0
 N23  CONST_14  CAQ   CAS  CAT  CAR     0.00   0.0  0
 N23  CONST_15  CAD   CAE  CAR  CAT     0.00   0.0  0
 N23  CONST_16  CAD   CAQ  CAS  CAT     0.00   0.0  0
 N23  CONST_17  CAC   CAD  CAQ  CAS   180.00   0.0  0
 N23  CONST_18  CAJ   CAL  CAI  CAF     0.00   0.0  0
 N23  CONST_19  CAL   CAJ  SAH  CAF     0.00   0.0  0
 N23  CONST_20  CAJ   SAH  CAF  CAI     0.00   0.0  0
 N23  CONST_21  SAH   CAJ  CAL  CAI     0.00   0.0  0
 N23  CONST_22  SAH   CAF  CAI  CAL     0.00   0.0  0
 N23  CONST_23  CAE   NAA  CAB  CAO   180.00   0.0  0
 N23  CONST_24  CAD   CAC  CAB  CAO   180.00   0.0  0
 N23  CONST_25  CAN   CAC  CAB  NAA   180.00   0.0  0
 N23  CONST_26  CAN   CAC  CAD  CAE   180.00   0.0  0
 N23  CONST_27  CAN   CAC  CAD  CAQ     0.00   0.0  0
 N23  CONST_28  CAL   CAI  CAF  CAG   180.00   0.0  0
 N23  CONST_29  CAJ   SAH  CAF  CAG   180.00   0.0  0
 N23  CONST_30  HAR   CAR  CAE  NAA     0.00   0.0  0
 N23  CONST_31  HAT   CAT  CAR  CAE   180.00   0.0  0
 N23  CONST_32  HAQ   CAQ  CAD  CAE   180.00   0.0  0
 N23  CONST_33  HNAA  NAA  CAE  CAR     0.00   0.0  0
 N23  CONST_34  HAS   CAS  CAT  CAR   180.00   0.0  0
 N23  CONST_35  HAL   CAL  CAI  CAF   180.00   0.0  0
 N23  CONST_36  HAJ   CAJ  SAH  CAF   180.00   0.0  0
 N23  CONST_37  HAI   CAI  CAL  CAJ   180.00   0.0  0
 N23  CONST_38  CAF   CAG  NAM  CAP   180.00   0.0  0
 N23  CONST_39  HNAM  NAM  CAG  CAF     0.00   0.0  0
 N23  CONST_40  OAK   CAG  NAM  CAP     0.00   0.0  0
 N23  Var_01    CAP   CAN  CAC  CAB    96.27  30.0  2
 N23  Var_02    CAI   CAF  CAG  NAM  -165.96  30.0  2
 N23  Var_03    HAO   CAO  CAB  NAA    79.98  30.0  2
 N23  Var_04    NAM   CAP  CAN  CAC   177.05  30.0  3
 N23  Var_05    CAG   NAM  CAP  CAN   163.95  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
 N23  plan-1  CAG   0.020
 N23  plan-1  CAF   0.020
 N23  plan-1  CAI   0.020
 N23  plan-1  CAL   0.020
 N23  plan-1  CAJ   0.020
 N23  plan-1  SAH   0.020
 N23  plan-1  HAI   0.020
 N23  plan-1  HAL   0.020
 N23  plan-1  HAJ   0.020
 N23  plan-2  CAO   0.020
 N23  plan-2  CAB   0.020
 N23  plan-2  NAA   0.020
 N23  plan-2  CAE   0.020
 N23  plan-2  CAR   0.020
 N23  plan-2  CAT   0.020
 N23  plan-2  CAS   0.020
 N23  plan-2  CAQ   0.020
 N23  plan-2  CAD   0.020
 N23  plan-2  CAC   0.020
 N23  plan-2  CAN   0.020
 N23  plan-2  HNAA  0.020
 N23  plan-2  HAR   0.020
 N23  plan-2  HAT   0.020
 N23  plan-2  HAS   0.020
 N23  plan-2  HAQ   0.020
 N23  plan-3  CAP   0.020
 N23  plan-3  NAM   0.020
 N23  plan-3  CAG   0.020
 N23  plan-3  OAK   0.020
 N23  plan-3  CAF   0.020
 N23  plan-3  HNAM  0.020

