# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 05:26:37 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: ~{N}-[(1~{S})-1-(1,5-dimethylpyrazol-4-yl)ethyl]-1-ethyl-3-methyl-2-oxidanylidene-quinoxaline-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)C(=Nc2cc(ccc12)C(=O)N[C@@H](C)c3cnn(C)c3C)C
#
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
 9L5  9L5  ~{N}-[(1~{S})-1-(1,5-dimethylpyrazol-4-yl)ethyl]-1-ethyl-3-methyl-2-oxidanylidene-quinoxaline-6-carboxamide  ligand  49  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9L5
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
 9L5  CAA  C  CH3   0  -0.663   3.7600   3.0189  -1.7375
 9L5  CAB  C  CH3   0  -0.726   6.1210  -1.8708  -0.0644
 9L5  CAC  C  CH3   0  -0.750  -4.3267   0.0539  -1.7165
 9L5  CAD  C  CH3   0  -0.660  -3.6233  -2.2939   2.2934
 9L5  CAE  C  CH3   0  -0.522  -6.4916   2.0208  -0.8693
 9L5  CAH  C  CR16  0  -0.290   0.2158   0.5393   0.1077
 9L5  CAI  C  CR16  0  -0.321   1.4123   1.2119  -0.0200
 9L5  CAJ  C  CR15  0  -0.086  -5.3203   0.1415   1.8146
 9L5  CAK  C  CR16  0  -0.353   1.3608  -1.5548   0.1954
 9L5  CAL  C  CH2   0  -0.351   3.9444   2.5736  -0.2971
 9L5  CAP  C  C     0   0.553  -1.1068  -1.6223   0.3326
 9L5  CAQ  C  CR6   0  -0.041   0.1701  -0.8541   0.2242
 9L5  CAR  C  CR6   0   0.096   4.8637  -1.0722  -0.0550
 9L5  CAS  C  CR5   0   0.415  -4.8390   0.2226  -0.3314
 9L5  CAT  C  CR5   0  -0.178  -4.5073  -0.4482   0.8329
 9L5  CAU  C  CR6   0   0.525   5.0088   0.3943  -0.2093
 9L5  CAV  C  CR66  0   0.204   2.5833  -0.8958   0.0808
 9L5  CAW  C  CR66  0   0.418   2.6193   0.5048  -0.0297
 9L5  CAX  C  CH1   0  -0.176  -3.4848  -1.5320   0.9801
 9L5  NAM  N  N     0  -0.294  -6.0850   1.0884   1.3057
 9L5  NAN  N  N     0  -0.383   3.7300  -1.6524   0.0748
 9L5  NAO  N  NH1   0  -0.645  -2.1544  -0.9526   0.8376
 9L5  NAY  N  NR5   0  -0.316  -5.7757   1.1293   0.0101
 9L5  NAZ  N  NR6   0  -0.571   3.8481   1.1206  -0.1487
 9L5  OAF  O  O     0  -0.494  -1.1712  -2.7900  -0.0309
 9L5  H1   H  HCH3  0   0.241   4.5206   2.5800  -2.3825
 9L5  H2   H  HCH3  0   0.236   2.7804   2.7459  -2.1307
 9L5  H3   H  HCH3  0   0.247   3.8532   4.1027  -1.7985
 9L5  H4   H  HCH3  0   0.257   5.8941  -2.9258   0.0676
 9L5  H5   H  HCH3  0   0.260   6.6619  -1.7415  -1.0031
 9L5  H6   H  HCH3  0   0.259   6.7938  -1.5517   0.7331
 9L5  H7   H  HCH3  0   0.261  -3.8243   0.9539  -2.0757
 9L5  H8   H  HCH3  0   0.264  -3.6058  -0.7602  -1.7549
 9L5  H9   H  HCH3  0   0.261  -5.1272  -0.1778  -2.4207
 9L5  H10  H  HCH3  0   0.236  -4.6082  -2.7558   2.3661
 9L5  H11  H  HCH3  0   0.245  -2.8751  -3.0829   2.3557
 9L5  H12  H  HCH3  0   0.227  -3.4929  -1.6337   3.1519
 9L5  H13  H  HCH3  0   0.257  -7.4289   1.5755  -1.2021
 9L5  H14  H  HCH3  0   0.266  -6.7050   2.9466  -0.3424
 9L5  H15  H  HCH3  0   0.260  -5.8845   2.2501  -1.7411
 9L5  H16  H  HCR6  0   0.264  -0.6931   1.1268   0.0869
 9L5  H17  H  HCR6  0   0.290   1.3855   2.2862  -0.1215
 9L5  H18  H  HCR5  0   0.254  -5.3746  -0.0900   2.8682
 9L5  H19  H  HCR6  0   0.270   1.3719  -2.6345   0.2683
 9L5  H20  H  HCH2  0   0.283   4.9211   2.8757   0.0698
 9L5  H21  H  HCH2  0   0.271   3.2125   3.0381   0.3603
 9L5  H22  H  HCH1  0   0.256  -3.6032  -2.2441   0.1598
 9L5  H23  H  HNH1  0   0.404  -2.0097  -0.0468   1.2542
 9L5  OAG  O  O     0  -0.459   6.0995   0.9142  -0.3736

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
 9L5  OAG  CAU  double    1.219  0.020  1.219
 9L5  CAA  CAL  single    1.519  0.020  1.519
 9L5  CAB  CAR  single    1.490  0.020  1.490
 9L5  CAU  CAR  single    1.482  0.020  1.482
 9L5  CAU  NAZ  single    1.371  0.020  1.371
 9L5  CAL  NAZ  single    1.464  0.020  1.464
 9L5  CAR  NAN  double    1.280  0.020  1.280
 9L5  NAZ  CAW  single    1.380  0.020  1.380
 9L5  NAN  CAV  single    1.374  0.020  1.374
 9L5  CAW  CAV  aromatic  1.405  0.020  1.405
 9L5  CAW  CAI  aromatic  1.399  0.020  1.399
 9L5  CAV  CAK  aromatic  1.394  0.020  1.394
 9L5  CAI  CAH  aromatic  1.379  0.020  1.379
 9L5  CAK  CAQ  aromatic  1.382  0.020  1.382
 9L5  CAH  CAQ  aromatic  1.399  0.020  1.399
 9L5  CAQ  CAP  single    1.494  0.020  1.494
 9L5  CAP  OAF  double    1.225  0.020  1.225
 9L5  CAP  NAO  single    1.342  0.020  1.342
 9L5  NAO  CAX  single    1.458  0.020  1.458
 9L5  CAD  CAX  single    1.525  0.020  1.525
 9L5  CAX  CAT  single    1.497  0.020  1.497
 9L5  CAT  CAS  aromatic  1.384  0.020  1.384
 9L5  CAT  CAJ  aromatic  1.404  0.020  1.404
 9L5  CAC  CAS  single    1.486  0.020  1.486
 9L5  CAS  NAY  aromatic  1.348  0.020  1.348
 9L5  CAJ  NAM  aromatic  1.319  0.020  1.319
 9L5  NAY  NAM  aromatic  1.333  0.020  1.333
 9L5  NAY  CAE  single    1.442  0.020  1.442
 9L5  CAA  H1   single    0.970  0.020  1.090
 9L5  CAA  H2   single    0.970  0.020  1.090
 9L5  CAA  H3   single    0.970  0.020  1.090
 9L5  CAB  H4   single    0.970  0.020  1.090
 9L5  CAB  H5   single    0.970  0.020  1.090
 9L5  CAB  H6   single    0.970  0.020  1.090
 9L5  CAC  H7   single    0.970  0.020  1.090
 9L5  CAC  H8   single    0.970  0.020  1.090
 9L5  CAC  H9   single    0.970  0.020  1.090
 9L5  CAD  H10  single    0.970  0.020  1.090
 9L5  CAD  H11  single    0.970  0.020  1.090
 9L5  CAD  H12  single    0.970  0.020  1.090
 9L5  CAE  H13  single    0.970  0.020  1.090
 9L5  CAE  H14  single    0.970  0.020  1.090
 9L5  CAE  H15  single    0.970  0.020  1.090
 9L5  CAH  H16  single    0.930  0.020  1.080
 9L5  CAI  H17  single    0.930  0.020  1.080
 9L5  CAJ  H18  single    0.930  0.020  1.080
 9L5  CAK  H19  single    0.930  0.020  1.080
 9L5  CAL  H20  single    0.970  0.020  1.090
 9L5  CAL  H21  single    0.970  0.020  1.090
 9L5  CAX  H22  single    0.970  0.020  1.090
 9L5  NAO  H23  single    0.860  0.020  1.020

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
 9L5  H3   CAA  H2   107.81  3.000
 9L5  H3   CAA  H1   107.93  3.000
 9L5  H2   CAA  H1   108.24  3.000
 9L5  H3   CAA  CAL  109.53  3.000
 9L5  H2   CAA  CAL  112.19  3.000
 9L5  H1   CAA  CAL  111.01  3.000
 9L5  H6   CAB  H5   106.77  3.000
 9L5  H6   CAB  H4   108.89  3.000
 9L5  H5   CAB  H4   108.84  3.000
 9L5  H6   CAB  CAR  111.04  3.000
 9L5  H5   CAB  CAR  111.12  3.000
 9L5  H4   CAB  CAR  110.08  3.000
 9L5  H9   CAC  H8   107.73  3.000
 9L5  H9   CAC  H7   107.48  3.000
 9L5  H8   CAC  H7   107.48  3.000
 9L5  H9   CAC  CAS  111.88  3.000
 9L5  H8   CAC  CAS  110.25  3.000
 9L5  H7   CAC  CAS  111.82  3.000
 9L5  H12  CAD  H11  108.14  3.000
 9L5  H12  CAD  H10  108.18  3.000
 9L5  H11  CAD  H10  108.05  3.000
 9L5  H12  CAD  CAX  111.39  3.000
 9L5  H11  CAD  CAX  110.42  3.000
 9L5  H10  CAD  CAX  110.56  3.000
 9L5  H15  CAE  H14  108.60  3.000
 9L5  H15  CAE  H13  108.77  3.000
 9L5  H14  CAE  H13  109.11  3.000
 9L5  H15  CAE  NAY  110.01  3.000
 9L5  H14  CAE  NAY  109.18  3.000
 9L5  H13  CAE  NAY  111.13  3.000
 9L5  H16  CAH  CAQ  120.98  3.000
 9L5  H16  CAH  CAI  117.53  3.000
 9L5  CAQ  CAH  CAI  121.47  3.000
 9L5  H17  CAI  CAW  121.59  3.000
 9L5  H17  CAI  CAH  118.21  3.000
 9L5  CAW  CAI  CAH  120.19  3.000
 9L5  H18  CAJ  NAM  120.06  3.000
 9L5  H18  CAJ  CAT  128.39  3.000
 9L5  NAM  CAJ  CAT  111.55  3.000
 9L5  H19  CAK  CAV  117.93  3.000
 9L5  H19  CAK  CAQ  120.89  3.000
 9L5  CAV  CAK  CAQ  121.18  3.000
 9L5  H21  CAL  H20  106.38  3.000
 9L5  H21  CAL  NAZ  108.56  3.000
 9L5  H20  CAL  NAZ  107.52  3.000
 9L5  H21  CAL  CAA  111.48  3.000
 9L5  H20  CAL  CAA  110.36  3.000
 9L5  NAZ  CAL  CAA  112.29  3.000
 9L5  OAF  CAP  NAO  123.13  3.000
 9L5  NAO  CAP  CAQ  115.97  3.000
 9L5  OAF  CAP  CAQ  120.91  3.000
 9L5  CAP  CAQ  CAK  118.50  3.000
 9L5  CAP  CAQ  CAH  123.10  3.000
 9L5  CAK  CAQ  CAH  118.37  3.000
 9L5  NAN  CAR  CAU  123.08  3.000
 9L5  NAN  CAR  CAB  120.34  3.000
 9L5  CAU  CAR  CAB  116.57  3.000
 9L5  NAY  CAS  CAT  106.23  3.000
 9L5  NAY  CAS  CAC  123.51  3.000
 9L5  CAT  CAS  CAC  130.26  3.000
 9L5  CAX  CAT  CAS  126.67  3.000
 9L5  CAS  CAT  CAJ  104.23  3.000
 9L5  CAX  CAT  CAJ  129.09  3.000
 9L5  OAG  CAU  NAZ  122.52  3.000
 9L5  NAZ  CAU  CAR  115.91  3.000
 9L5  OAG  CAU  CAR  121.58  3.000
 9L5  NAN  CAV  CAW  121.81  3.000
 9L5  CAW  CAV  CAK  120.02  3.000
 9L5  NAN  CAV  CAK  118.17  3.000
 9L5  NAZ  CAW  CAV  118.32  3.000
 9L5  CAV  CAW  CAI  118.75  3.000
 9L5  NAZ  CAW  CAI  122.92  3.000
 9L5  H22  CAX  NAO  106.52  3.000
 9L5  H22  CAX  CAT  108.90  3.000
 9L5  NAO  CAX  CAT  109.02  3.000
 9L5  H22  CAX  CAD  108.13  3.000
 9L5  CAT  CAX  CAD  112.61  3.000
 9L5  NAO  CAX  CAD  111.44  3.000
 9L5  NAY  NAM  CAJ  105.21  3.000
 9L5  CAV  NAN  CAR  119.34  3.000
 9L5  H23  NAO  CAX  116.62  3.000
 9L5  H23  NAO  CAP  119.48  3.000
 9L5  CAX  NAO  CAP  123.42  3.000
 9L5  NAM  NAY  CAS  112.77  3.000
 9L5  NAM  NAY  CAE  119.77  3.000
 9L5  CAS  NAY  CAE  127.32  3.000
 9L5  CAW  NAZ  CAU  121.44  3.000
 9L5  CAW  NAZ  CAL  120.69  3.000
 9L5  CAU  NAZ  CAL  117.76  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
 9L5  CONST_01  CAV  CAW  CAI  CAH     0.00   0.0  0
 9L5  CONST_02  CAV  CAK  CAQ  CAH     0.00   0.0  0
 9L5  CONST_03  CAK  CAV  CAW  CAI     0.00   0.0  0
 9L5  CONST_04  CAK  CAQ  CAH  CAI     0.00   0.0  0
 9L5  CONST_05  NAY  CAS  CAT  CAJ     0.00   0.0  0
 9L5  CONST_06  CAS  NAY  NAM  CAJ     0.00   0.0  0
 9L5  CONST_07  CAW  CAV  CAK  CAQ     0.00   0.0  0
 9L5  CONST_08  CAW  CAI  CAH  CAQ     0.00   0.0  0
 9L5  CONST_09  NAM  CAJ  CAT  CAS     0.00   0.0  0
 9L5  CONST_10  NAM  NAY  CAS  CAT     0.00   0.0  0
 9L5  CONST_11  NAY  NAM  CAJ  CAT     0.00   0.0  0
 9L5  CONST_12  CAW  NAZ  CAU  CAR     0.00   0.0  0
 9L5  CONST_13  CAJ  CAT  CAS  CAC   180.00   0.0  0
 9L5  CONST_14  NAM  NAY  CAS  CAC   180.00   0.0  0
 9L5  CONST_15  CAT  CAS  NAY  CAE   180.00   0.0  0
 9L5  CONST_16  CAJ  NAM  NAY  CAE   180.00   0.0  0
 9L5  CONST_17  CAP  CAQ  CAH  CAI   180.00   0.0  0
 9L5  CONST_18  CAV  CAK  CAQ  CAP   180.00   0.0  0
 9L5  CONST_19  NAY  CAS  CAT  CAX   180.00   0.0  0
 9L5  CONST_20  NAM  CAJ  CAT  CAX   180.00   0.0  0
 9L5  CONST_21  CAR  CAU  NAZ  CAL   180.00   0.0  0
 9L5  CONST_22  OAG  CAU  NAZ  CAW   180.00   0.0  0
 9L5  CONST_23  H19  CAK  CAQ  CAH   180.00   0.0  0
 9L5  CONST_24  H16  CAH  CAQ  CAK   180.00   0.0  0
 9L5  CONST_25  H17  CAI  CAH  CAQ   180.00   0.0  0
 9L5  CONST_26  H18  CAJ  CAT  CAS   180.00   0.0  0
 9L5  CONST_27  OAG  CAU  NAZ  CAL     0.00   0.0  0
 9L5  CONST_28  CAX  NAO  CAP  CAQ   180.00   0.0  0
 9L5  CONST_29  H23  NAO  CAP  CAQ     0.00   0.0  0
 9L5  CONST_30  OAF  CAP  NAO  CAX     0.00   0.0  0
 9L5  Var_01    CAU  NAZ  CAL  CAA    92.77  30.0  3
 9L5  Var_02    OAF  CAP  CAQ  CAH   154.02  30.0  2
 9L5  Var_03    H13  CAE  NAY  CAS    92.09  30.0  2
 9L5  Var_04    H7   CAC  CAS  CAT  -117.39  30.0  2
 9L5  Var_05    H4   CAB  CAR  CAU   179.31  30.0  3
 9L5  Var_06    H1   CAA  CAL  NAZ   -60.16  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
 9L5  chir_01  CAX  NAO  CAD  CAT  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
 9L5  plan-1  CAC  0.020
 9L5  plan-1  CAE  0.020
 9L5  plan-1  CAJ  0.020
 9L5  plan-1  CAS  0.020
 9L5  plan-1  CAT  0.020
 9L5  plan-1  CAX  0.020
 9L5  plan-1  NAM  0.020
 9L5  plan-1  NAY  0.020
 9L5  plan-1  H18  0.020
 9L5  plan-2  CAB  0.020
 9L5  plan-2  CAH  0.020
 9L5  plan-2  CAI  0.020
 9L5  plan-2  CAK  0.020
 9L5  plan-2  CAL  0.020
 9L5  plan-2  CAP  0.020
 9L5  plan-2  CAQ  0.020
 9L5  plan-2  CAR  0.020
 9L5  plan-2  CAU  0.020
 9L5  plan-2  CAV  0.020
 9L5  plan-2  CAW  0.020
 9L5  plan-2  NAN  0.020
 9L5  plan-2  NAZ  0.020
 9L5  plan-2  H16  0.020
 9L5  plan-2  H17  0.020
 9L5  plan-2  H19  0.020
 9L5  plan-2  OAG  0.020
 9L5  plan-3  CAP  0.020
 9L5  plan-3  CAQ  0.020
 9L5  plan-3  CAX  0.020
 9L5  plan-3  NAO  0.020
 9L5  plan-3  OAF  0.020
 9L5  plan-3  H23  0.020

