# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 22:07:52 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: N-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butyl]-6-(trifluoromethyl)-3,4-dihydropyrrolo[1,2-a]pyrazine-2(1H)-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCNC(=O)N1CCn2c(C1)ccc2C(F)(F)F)Cc3cc(F)c(F)cc3F
#
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
 D3C  D3C  N-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butyl]-6-(trifluoromethyl)-3,4-dihydropyrrolo[1,2-a]pyrazine-2(1H)-carboxamide  ligand  50  30  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D3C
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
 D3C  FBB  F  F     0  -0.320  -7.6632  -1.0724  -1.0976
 D3C  CBA  C  CT    0   1.063  -7.7982  -0.3121   0.0038
 D3C  FBC  F  F     0  -0.321  -8.2525   0.8794  -0.4312
 D3C  FBD  F  F     0  -0.300  -8.7711  -0.8522   0.7410
 D3C  CAX  C  CR5   0   0.025  -6.5507  -0.2048   0.7831
 D3C  CAY  C  CR15  0  -0.347  -6.3502  -0.4823   2.1136
 D3C  CAZ  C  CR15  0  -0.394  -4.9957  -0.2153   2.3898
 D3C  CAV  C  CR5   0   0.333  -4.4177   0.2154   1.2172
 D3C  CAU  C  CH2   0  -0.344  -3.0016   0.6268   0.9596
 D3C  NAW  N  NR5   0  -0.533  -5.3664   0.2298   0.2481
 D3C  CAT  C  CH2   0  -0.292  -5.0823   0.5862  -1.1333
 D3C  CAS  C  CH2   0  -0.332  -3.8507   1.4637  -1.1665
 D3C  NAQ  N  NT    0  -0.521  -2.7648   0.8306  -0.4527
 D3C  CAP  C  C     0   0.749  -1.5214   0.7559  -1.0272
 D3C  OAR  O  O     0  -0.543  -1.3578   0.9107  -2.2332
 D3C  NAO  N  NH1   0  -0.700  -0.4881   0.4649  -0.1971
 D3C  CAN  C  CH2   0  -0.220   0.8701   0.4244  -0.7040
 D3C  CAL  C  CH2   0  -0.473   1.8270   0.0287   0.4081
 D3C  CAK  C  CH1   0  -0.094   3.2842   0.0468  -0.0421
 D3C  NAM  N  NH2   0  -0.786   3.4804  -0.9026  -1.1226
 D3C  CAJ  C  CH2   0  -0.511   4.2064  -0.1763   1.1755
 D3C  CAD  C  CR6   0  -0.065   5.6584  -0.0956   0.8114
 D3C  CAC  C  CR16  0  -0.458   6.4078  -1.2414   0.5530
 D3C  CAB  C  CR6   0   0.405   7.7299  -1.1551   0.1705
 D3C  FAI  F  F     0  -0.306   8.4385  -2.2639  -0.0693
 D3C  CAA  C  CR6   0   0.399   8.3373   0.0792   0.0297
 D3C  FAH  F  F     0  -0.301   9.6163   0.1436  -0.3462
 D3C  CAF  C  CR16  0  -0.551   7.6292   1.2368   0.2758
 D3C  CAE  C  CR6   0   0.532   6.3066   1.1216   0.6588
 D3C  FAG  F  F     0  -0.306   5.6215   2.2517   0.8909
 D3C  H1   H  HCR5  0   0.263  -7.0932  -0.8344   2.8115
 D3C  H2   H  HCR5  0   0.254  -4.4934  -0.3268   3.3379
 D3C  H3   H  HCH2  0   0.268  -2.7730   1.5297   1.5410
 D3C  H4   H  HCH2  0   0.280  -2.3558  -0.1689   1.3338
 D3C  H5   H  HCH2  0   0.269  -4.9255  -0.3167  -1.7254
 D3C  H6   H  HCH2  0   0.269  -5.9211   1.1348  -1.5569
 D3C  H7   H  HCH2  0   0.285  -3.5617   1.6314  -2.1993
 D3C  H8   H  HCH2  0   0.254  -4.0790   2.4390  -0.7215
 D3C  H9   H  HNH1  0   0.408  -0.5823   0.6503   0.7879
 D3C  H10  H  HCH2  0   0.237   0.9329  -0.2939  -1.5200
 D3C  H11  H  HCH2  0   0.217   1.1682   1.3982  -1.1092
 D3C  H12  H  HCH2  0   0.235   1.7148   0.7208   1.2488
 D3C  H13  H  HCH2  0   0.233   1.5708  -0.9679   0.7841
 D3C  H14  H  HCH1  0   0.236   3.4983   1.0425  -0.4449
 D3C  H15  H  HNH2  0   0.351   4.4231  -0.8412  -1.4861
 D3C  H16  H  HNH2  0   0.338   3.3694  -1.8491  -0.7755
 D3C  H18  H  HCH2  0   0.254   3.9676   0.5540   1.9519
 D3C  H19  H  HCH2  0   0.253   3.9970  -1.1629   1.5978
 D3C  H20  H  HCR6  0   0.296   5.9540  -2.2184   0.6635
 D3C  H21  H  HCR6  0   0.313   8.0987   2.2058   0.1661

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
 D3C  FBD  CBA  single    1.335  0.020  1.335
 D3C  CBA  FBB  single    1.345  0.020  1.345
 D3C  CBA  FBC  single    1.347  0.020  1.347
 D3C  CBA  CAX  single    1.475  0.020  1.475
 D3C  CAY  CAX  aromatic  1.374  0.020  1.374
 D3C  CAY  CAZ  aromatic  1.408  0.020  1.408
 D3C  CAX  NAW  aromatic  1.370  0.020  1.370
 D3C  CAZ  CAV  aromatic  1.376  0.020  1.376
 D3C  NAW  CAV  aromatic  1.356  0.020  1.356
 D3C  NAW  CAT  single    1.455  0.020  1.455
 D3C  CAV  CAU  single    1.497  0.020  1.497
 D3C  CAT  CAS  single    1.513  0.020  1.513
 D3C  CAU  NAQ  single    1.446  0.020  1.446
 D3C  CAS  NAQ  single    1.446  0.020  1.446
 D3C  NAQ  CAP  single    1.372  0.020  1.372
 D3C  OAR  CAP  double    1.227  0.020  1.227
 D3C  CAP  NAO  single    1.357  0.020  1.357
 D3C  NAO  CAN  single    1.450  0.020  1.450
 D3C  CAN  CAL  single    1.520  0.020  1.520
 D3C  CAL  CAK  single    1.525  0.020  1.525
 D3C  CAK  NAM  single    1.452  0.020  1.452
 D3C  CAK  CAJ  single    1.544  0.020  1.544
 D3C  CAJ  CAD  single    1.499  0.020  1.499
 D3C  CAC  CAD  aromatic  1.393  0.020  1.393
 D3C  CAC  CAB  aromatic  1.379  0.020  1.379
 D3C  FAI  CAB  single    1.338  0.020  1.338
 D3C  CAD  CAE  aromatic  1.387  0.020  1.387
 D3C  CAB  CAA  aromatic  1.383  0.020  1.383
 D3C  CAE  FAG  single    1.342  0.020  1.342
 D3C  CAE  CAF  aromatic  1.382  0.020  1.382
 D3C  CAA  CAF  aromatic  1.379  0.020  1.379
 D3C  CAA  FAH  single    1.335  0.020  1.335
 D3C  CAY  H1   single    0.930  0.020  1.080
 D3C  CAZ  H2   single    0.930  0.020  1.080
 D3C  CAU  H3   single    0.970  0.020  1.090
 D3C  CAU  H4   single    0.970  0.020  1.090
 D3C  CAT  H5   single    0.970  0.020  1.090
 D3C  CAT  H6   single    0.970  0.020  1.090
 D3C  CAS  H7   single    0.970  0.020  1.090
 D3C  CAS  H8   single    0.970  0.020  1.090
 D3C  NAO  H9   single    0.890  0.020  1.040
 D3C  CAN  H10  single    0.970  0.020  1.090
 D3C  CAN  H11  single    0.970  0.020  1.090
 D3C  CAL  H12  single    0.970  0.020  1.090
 D3C  CAL  H13  single    0.970  0.020  1.090
 D3C  CAK  H14  single    0.970  0.020  1.090
 D3C  NAM  H15  single    0.890  0.020  1.040
 D3C  NAM  H16  single    0.890  0.020  1.040
 D3C  CAJ  H18  single    0.970  0.020  1.090
 D3C  CAJ  H19  single    0.970  0.020  1.090
 D3C  CAC  H20  single    0.930  0.020  1.080
 D3C  CAF  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
 D3C  CAX  CBA  FBD  110.74  3.000
 D3C  CAX  CBA  FBC  113.04  3.000
 D3C  FBD  CBA  FBC  106.88  3.000
 D3C  CAX  CBA  FBB  112.88  3.000
 D3C  FBC  CBA  FBB  105.62  3.000
 D3C  FBD  CBA  FBB  107.26  3.000
 D3C  NAW  CAX  CAY  108.42  3.000
 D3C  NAW  CAX  CBA  123.22  3.000
 D3C  CAY  CAX  CBA  128.35  3.000
 D3C  H1   CAY  CAZ  126.71  3.000
 D3C  H1   CAY  CAX  126.31  3.000
 D3C  CAZ  CAY  CAX  106.98  3.000
 D3C  H2   CAZ  CAV  125.84  3.000
 D3C  H2   CAZ  CAY  126.93  3.000
 D3C  CAV  CAZ  CAY  107.23  3.000
 D3C  NAW  CAV  CAU  122.40  3.000
 D3C  CAU  CAV  CAZ  129.04  3.000
 D3C  NAW  CAV  CAZ  108.56  3.000
 D3C  H4   CAU  H3   107.15  3.000
 D3C  H4   CAU  NAQ  109.92  3.000
 D3C  H3   CAU  NAQ  111.54  3.000
 D3C  H4   CAU  CAV  107.48  3.000
 D3C  H3   CAU  CAV  109.38  3.000
 D3C  NAQ  CAU  CAV  111.20  3.000
 D3C  CAT  NAW  CAV  122.99  3.000
 D3C  CAT  NAW  CAX  128.12  3.000
 D3C  CAV  NAW  CAX  108.80  3.000
 D3C  H6   CAT  H5   108.47  3.000
 D3C  H6   CAT  CAS  109.07  3.000
 D3C  H5   CAT  CAS  110.56  3.000
 D3C  H6   CAT  NAW  110.04  3.000
 D3C  H5   CAT  NAW  109.91  3.000
 D3C  CAS  CAT  NAW  108.79  3.000
 D3C  H8   CAS  H7   107.71  3.000
 D3C  H8   CAS  NAQ  110.23  3.000
 D3C  H7   CAS  NAQ  109.73  3.000
 D3C  H8   CAS  CAT  109.73  3.000
 D3C  H7   CAS  CAT  109.10  3.000
 D3C  NAQ  CAS  CAT  110.29  3.000
 D3C  CAP  NAQ  CAS  119.86  3.000
 D3C  CAP  NAQ  CAU  123.34  3.000
 D3C  CAS  NAQ  CAU  114.89  3.000
 D3C  NAO  CAP  OAR  121.79  3.000
 D3C  NAO  CAP  NAQ  116.46  3.000
 D3C  OAR  CAP  NAQ  121.72  3.000
 D3C  H9   NAO  CAN  115.76  3.000
 D3C  H9   NAO  CAP  119.20  3.000
 D3C  CAN  NAO  CAP  120.35  3.000
 D3C  H11  CAN  H10  107.06  3.000
 D3C  H11  CAN  CAL  109.30  3.000
 D3C  H10  CAN  CAL  109.90  3.000
 D3C  H11  CAN  NAO  111.05  3.000
 D3C  H10  CAN  NAO  109.53  3.000
 D3C  CAL  CAN  NAO  109.95  3.000
 D3C  H13  CAL  H12  106.71  3.000
 D3C  H13  CAL  CAK  109.60  3.000
 D3C  H12  CAL  CAK  108.49  3.000
 D3C  H13  CAL  CAN  109.92  3.000
 D3C  H12  CAL  CAN  109.44  3.000
 D3C  CAK  CAL  CAN  112.49  3.000
 D3C  H14  CAK  CAJ  107.74  3.000
 D3C  H14  CAK  NAM  107.13  3.000
 D3C  CAJ  CAK  NAM  114.32  3.000
 D3C  H14  CAK  CAL  107.82  3.000
 D3C  CAJ  CAK  CAL  109.65  3.000
 D3C  NAM  CAK  CAL  109.94  3.000
 D3C  H16  NAM  H15  106.34  3.000
 D3C  H16  NAM  CAK  109.93  3.000
 D3C  H15  NAM  CAK  110.70  3.000
 D3C  H19  CAJ  H18  106.67  3.000
 D3C  H19  CAJ  CAD  109.14  3.000
 D3C  H18  CAJ  CAD  110.39  3.000
 D3C  H19  CAJ  CAK  108.70  3.000
 D3C  H18  CAJ  CAK  109.47  3.000
 D3C  CAD  CAJ  CAK  112.29  3.000
 D3C  CAE  CAD  CAC  116.73  3.000
 D3C  CAE  CAD  CAJ  121.76  3.000
 D3C  CAC  CAD  CAJ  121.45  3.000
 D3C  H20  CAC  CAB  119.11  3.000
 D3C  H20  CAC  CAD  119.84  3.000
 D3C  CAB  CAC  CAD  121.04  3.000
 D3C  CAA  CAB  FAI  119.27  3.000
 D3C  CAA  CAB  CAC  120.34  3.000
 D3C  FAI  CAB  CAC  120.38  3.000
 D3C  CAF  CAA  FAH  120.11  3.000
 D3C  FAH  CAA  CAB  119.52  3.000
 D3C  CAF  CAA  CAB  120.37  3.000
 D3C  H21  CAF  CAE  121.20  3.000
 D3C  H21  CAF  CAA  120.71  3.000
 D3C  CAE  CAF  CAA  118.09  3.000
 D3C  FAG  CAE  CAF  117.80  3.000
 D3C  CAF  CAE  CAD  123.42  3.000
 D3C  FAG  CAE  CAD  118.78  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
 D3C  CONST_01  CAV  CAZ  CAY  CAX     0.00   0.0  0
 D3C  CONST_02  CAZ  CAV  NAW  CAX     0.00   0.0  0
 D3C  CONST_03  CAV  NAW  CAX  CAY     0.00   0.0  0
 D3C  CONST_04  NAW  CAV  CAZ  CAY     0.00   0.0  0
 D3C  CONST_05  NAW  CAX  CAY  CAZ     0.00   0.0  0
 D3C  CONST_06  CAA  CAB  CAC  CAD     0.00   0.0  0
 D3C  CONST_07  CAA  CAF  CAE  CAD     0.00   0.0  0
 D3C  CONST_08  CAF  CAE  CAD  CAC     0.00   0.0  0
 D3C  CONST_09  CAF  CAA  CAB  CAC     0.00   0.0  0
 D3C  CONST_10  CAE  CAD  CAC  CAB     0.00   0.0  0
 D3C  CONST_11  CAE  CAF  CAA  CAB     0.00   0.0  0
 D3C  CONST_12  CAZ  CAY  CAX  CBA   180.00   0.0  0
 D3C  CONST_13  CAV  NAW  CAX  CBA   180.00   0.0  0
 D3C  CONST_14  CAT  NAW  CAX  CBA     0.00   0.0  0
 D3C  CONST_15  CAB  CAC  CAD  CAJ   180.00   0.0  0
 D3C  CONST_16  CAF  CAE  CAD  CAJ   180.00   0.0  0
 D3C  CONST_17  FAI  CAB  CAC  CAD   180.00   0.0  0
 D3C  CONST_18  FAG  CAE  CAD  CAC   180.00   0.0  0
 D3C  CONST_19  FAH  CAA  CAB  CAC   180.00   0.0  0
 D3C  CONST_20  CAF  CAA  CAB  FAI   180.00   0.0  0
 D3C  CONST_21  FAG  CAE  CAF  CAA   180.00   0.0  0
 D3C  CONST_22  CAE  CAF  CAA  FAH   180.00   0.0  0
 D3C  CONST_23  H2   CAZ  CAY  CAX   180.00   0.0  0
 D3C  CONST_24  H1   CAY  CAZ  CAV   180.00   0.0  0
 D3C  CONST_25  H21  CAF  CAE  CAD   180.00   0.0  0
 D3C  CONST_26  H20  CAC  CAB  CAA   180.00   0.0  0
 D3C  CONST_27  OAR  CAP  NAQ  CAU   180.00   0.0  0
 D3C  CONST_29  NAO  CAP  NAQ  CAU     0.00   0.0  0
 D3C  CONST_31  CAN  NAO  CAP  NAQ   180.00   0.0  0
 D3C  CONST_33  CAN  NAO  CAP  OAR     0.00   0.0  0
 D3C  Var_01    CAS  CAT  NAW  CAX   159.47  30.0  1
 D3C  Var_02    NAQ  CAU  CAV  CAZ   171.87  30.0  1
 D3C  Var_03    CAS  NAQ  CAU  CAV    38.98  30.0  1
 D3C  Var_04    CAT  CAS  NAQ  CAU   -63.29  30.0  1
 D3C  Var_05    NAQ  CAS  CAT  NAW    52.45  30.0  1
 D3C  Var_06    CAY  CAX  CBA  FBB  -125.82  30.0  2
 D3C  Var_07    CAC  CAD  CAJ  CAK   -96.99  30.0  2
 D3C  Var_08    CAL  CAN  NAO  CAP  -177.95  30.0  3
 D3C  Var_09    CAK  CAL  CAN  NAO  -176.67  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
 D3C  chir_01  CAK  CAL  NAM  CAJ  positiv

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
 D3C  plan-1  CAJ  0.020
 D3C  plan-1  CAD  0.020
 D3C  plan-1  CAC  0.020
 D3C  plan-1  CAB  0.020
 D3C  plan-1  FAI  0.020
 D3C  plan-1  CAA  0.020
 D3C  plan-1  FAH  0.020
 D3C  plan-1  CAF  0.020
 D3C  plan-1  CAE  0.020
 D3C  plan-1  FAG  0.020
 D3C  plan-1  H20  0.020
 D3C  plan-1  H21  0.020
 D3C  plan-2  CBA  0.020
 D3C  plan-2  CAX  0.020
 D3C  plan-2  CAY  0.020
 D3C  plan-2  CAZ  0.020
 D3C  plan-2  CAV  0.020
 D3C  plan-2  CAU  0.020
 D3C  plan-2  NAW  0.020
 D3C  plan-2  CAT  0.020
 D3C  plan-2  H1   0.020
 D3C  plan-2  H2   0.020
 D3C  plan-3  CAU  0.020
 D3C  plan-3  CAS  0.020
 D3C  plan-3  NAQ  0.020
 D3C  plan-3  CAP  0.020
 D3C  plan-3  OAR  0.020
 D3C  plan-3  NAO  0.020
 D3C  plan-3  CAN  0.020
 D3C  plan-3  H9   0.020

