# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 22:04:52 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (2R)-2-(1H-indol-3-ylmethyl)-1,4-dihydropyrido[2,3-b]pyrazin-3(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1Nc2ncccc2N[C@@H]1Cc3c[nH]c4ccccc34
#
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
 I5R  I5R  (2R)-2-(1H-indol-3-ylmethyl)-1,4-dihydropyrido[2,3-b]pyrazin-3(2H)-one  ligand  35  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I5R
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
 I5R  O    O  O     0  -0.455  -1.3966  -3.4114  -0.2241
 I5R  C    C  C     0   0.538  -1.6070  -2.2283  -0.0435
 I5R  NAL  N  NH1   0  -0.693  -2.8380  -1.6745  -0.1852
 I5R  CAR  C  CR6   0   0.445  -3.1183  -0.3254   0.0021
 I5R  NAK  N  N     0  -0.425  -4.2759   0.1270  -0.4210
 I5R  CAE  C  CR16  0  -0.100  -4.5648   1.4115  -0.2097
 I5R  CAD  C  CR16  0  -0.329  -3.6938   2.2754   0.4269
 I5R  CAF  C  CR16  0  -0.242  -2.4659   1.7906   0.8658
 I5R  CAQ  C  CR6   0   0.224  -2.1574   0.4552   0.6646
 I5R  N    N  NH1   0  -0.659  -1.0191  -0.1791   1.1094
 I5R  CA   C  CH1   0  -0.261  -0.4985  -1.2431   0.2780
 I5R  CB   C  CH2   0  -0.558   0.1372  -0.7481  -1.0420
 I5R  CG   C  CR5   0   0.013   1.2272   0.2339  -0.7875
 I5R  CD2  C  CR56  0   0.033   2.5432  -0.0475  -0.2934
 I5R  CE3  C  CR16  0  -0.375   3.2233  -1.2257   0.0368
 I5R  CZ3  C  CR16  0  -0.267   4.5241  -1.1411   0.4932
 I5R  CH2  C  CR16  0  -0.284   5.1650   0.1023   0.6270
 I5R  CZ2  C  CR16  0  -0.304   4.5202   1.2814   0.3060
 I5R  CE2  C  CR56  0   0.354   3.2068   1.1917  -0.1527
 I5R  NE1  N  NR15  0  -0.686   2.3338   2.1665  -0.5380
 I5R  CD1  C  CR15  0  -0.079   1.1529   1.5932  -0.9138
 I5R  H1   H  HNH1  0   0.409  -3.5953  -2.2652  -0.5044
 I5R  H2   H  HCR6  0   0.260  -5.5297   1.7531  -0.5631
 I5R  H3   H  HCR6  0   0.268  -3.9610   3.3123   0.5758
 I5R  H4   H  HCR6  0   0.277  -1.7620   2.4404   1.3714
 I5R  H5   H  HNH1  0   0.390  -0.3051   0.4321   1.4779
 I5R  H6   H  HCH1  0   0.296   0.2522  -1.7819   0.8577
 I5R  H7   H  HCH2  0   0.264   0.5165  -1.6145  -1.5908
 I5R  H8   H  HCH2  0   0.263  -0.6335  -0.2923  -1.6699
 I5R  H9   H  HCR6  0   0.240   2.7414  -2.1904  -0.0690
 I5R  H10  H  HCR6  0   0.246   5.0617  -2.0442   0.7517
 I5R  H11  H  HCR6  0   0.250   6.1846   0.1372   0.9889
 I5R  H12  H  HCR6  0   0.259   5.0173   2.2377   0.4097
 I5R  H13  H  HNR5  0   0.410   2.5285   3.1533  -0.5626
 I5R  H14  H  HCR5  0   0.281   0.3295   2.2024  -1.2540

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
 I5R  O    C    double    1.215  0.020  1.215
 I5R  C    CA   single    1.517  0.020  1.517
 I5R  C    NAL  single    1.357  0.020  1.357
 I5R  CA   N    single    1.447  0.020  1.447
 I5R  CA   CB   single    1.547  0.020  1.547
 I5R  N    CAQ  single    1.377  0.020  1.377
 I5R  CD1  NE1  aromatic  1.365  0.020  1.365
 I5R  CD1  CG   aromatic  1.367  0.020  1.367
 I5R  NAL  CAR  single    1.391  0.020  1.391
 I5R  NE1  CE2  aromatic  1.364  0.020  1.364
 I5R  CB   CG   single    1.489  0.020  1.489
 I5R  CAQ  CAR  aromatic  1.404  0.020  1.404
 I5R  CAQ  CAF  aromatic  1.385  0.020  1.385
 I5R  CG   CD2  aromatic  1.434  0.020  1.434
 I5R  CAR  NAK  aromatic  1.313  0.020  1.313
 I5R  CAF  CAD  aromatic  1.391  0.020  1.391
 I5R  CE2  CD2  aromatic  1.413  0.020  1.413
 I5R  CE2  CZ2  aromatic  1.394  0.020  1.394
 I5R  NAK  CAE  aromatic  1.333  0.020  1.333
 I5R  CD2  CE3  aromatic  1.400  0.020  1.400
 I5R  CAD  CAE  aromatic  1.382  0.020  1.382
 I5R  CZ2  CH2  aromatic  1.382  0.020  1.382
 I5R  CE3  CZ3  aromatic  1.381  0.020  1.381
 I5R  CH2  CZ3  aromatic  1.405  0.020  1.405
 I5R  NAL  H1   single    0.860  0.020  1.020
 I5R  CAE  H2   single    0.930  0.020  1.080
 I5R  CAD  H3   single    0.930  0.020  1.080
 I5R  CAF  H4   single    0.930  0.020  1.080
 I5R  N    H5   single    0.890  0.020  1.040
 I5R  CA   H6   single    0.970  0.020  1.090
 I5R  CB   H7   single    0.970  0.020  1.090
 I5R  CB   H8   single    0.970  0.020  1.090
 I5R  CE3  H9   single    0.930  0.020  1.080
 I5R  CZ3  H10  single    0.930  0.020  1.080
 I5R  CH2  H11  single    0.930  0.020  1.080
 I5R  CZ2  H12  single    0.930  0.020  1.080
 I5R  NE1  H13  single    0.860  0.020  1.020
 I5R  CD1  H14  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
 I5R  CA   C    NAL  114.82  3.000
 I5R  NAL  C    O    122.60  3.000
 I5R  CA   C    O    122.48  3.000
 I5R  H1   NAL  CAR  117.25  3.000
 I5R  H1   NAL  C    118.26  3.000
 I5R  CAR  NAL  C    124.37  3.000
 I5R  CAQ  CAR  NAK  124.32  3.000
 I5R  NAK  CAR  NAL  117.94  3.000
 I5R  CAQ  CAR  NAL  117.71  3.000
 I5R  CAE  NAK  CAR  118.16  3.000
 I5R  H2   CAE  CAD  120.97  3.000
 I5R  H2   CAE  NAK  116.44  3.000
 I5R  CAD  CAE  NAK  122.59  3.000
 I5R  H3   CAD  CAF  120.59  3.000
 I5R  H3   CAD  CAE  120.48  3.000
 I5R  CAF  CAD  CAE  118.93  3.000
 I5R  H4   CAF  CAQ  120.09  3.000
 I5R  H4   CAF  CAD  120.78  3.000
 I5R  CAQ  CAF  CAD  119.12  3.000
 I5R  N    CAQ  CAF  125.54  3.000
 I5R  CAF  CAQ  CAR  116.88  3.000
 I5R  N    CAQ  CAR  117.52  3.000
 I5R  H5   N    CA   113.60  3.000
 I5R  H5   N    CAQ  115.07  3.000
 I5R  CA   N    CAQ  116.78  3.000
 I5R  H6   CA   CB   109.20  3.000
 I5R  H6   CA   N    107.79  3.000
 I5R  CB   CA   N    113.76  3.000
 I5R  H6   CA   C    107.14  3.000
 I5R  CB   CA   C    109.10  3.000
 I5R  N    CA   C    109.65  3.000
 I5R  H8   CB   H7   106.65  3.000
 I5R  H8   CB   CG   109.82  3.000
 I5R  H7   CB   CG   110.76  3.000
 I5R  H8   CB   CA   109.50  3.000
 I5R  H7   CB   CA   108.50  3.000
 I5R  CG   CB   CA   111.47  3.000
 I5R  CD1  CG   CD2  106.08  3.000
 I5R  CD2  CG   CB   126.97  3.000
 I5R  CD1  CG   CB   126.88  3.000
 I5R  CE2  CD2  CE3  119.11  3.000
 I5R  CE3  CD2  CG   133.83  3.000
 I5R  CE2  CD2  CG   107.06  3.000
 I5R  H9   CE3  CZ3  120.37  3.000
 I5R  H9   CE3  CD2  120.68  3.000
 I5R  CZ3  CE3  CD2  118.95  3.000
 I5R  H10  CZ3  CH2  119.28  3.000
 I5R  H10  CZ3  CE3  119.71  3.000
 I5R  CH2  CZ3  CE3  121.01  3.000
 I5R  H11  CH2  CZ2  119.32  3.000
 I5R  H11  CH2  CZ3  119.34  3.000
 I5R  CZ2  CH2  CZ3  121.34  3.000
 I5R  H12  CZ2  CE2  121.39  3.000
 I5R  H12  CZ2  CH2  121.15  3.000
 I5R  CE2  CZ2  CH2  117.46  3.000
 I5R  NE1  CE2  CZ2  130.53  3.000
 I5R  CZ2  CE2  CD2  122.12  3.000
 I5R  NE1  CE2  CD2  107.34  3.000
 I5R  H13  NE1  CD1  124.92  3.000
 I5R  H13  NE1  CE2  125.73  3.000
 I5R  CD1  NE1  CE2  109.34  3.000
 I5R  H14  CD1  NE1  120.64  3.000
 I5R  H14  CD1  CG   129.18  3.000
 I5R  NE1  CD1  CG   110.18  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
 I5R  CONST_01  CAD  CAF  CAQ  CAR     0.00   0.0  0
 I5R  CONST_02  CAD  CAE  NAK  CAR     0.00   0.0  0
 I5R  CONST_03  CAF  CAQ  CAR  NAK     0.00   0.0  0
 I5R  CONST_04  CAF  CAD  CAE  NAK     0.00   0.0  0
 I5R  CONST_05  CAQ  CAR  NAK  CAE     0.00   0.0  0
 I5R  CONST_06  CAQ  CAF  CAD  CAE     0.00   0.0  0
 I5R  CONST_07  CE2  NE1  CD1  CG      0.00   0.0  0
 I5R  CONST_08  NE1  CE2  CD2  CG      0.00   0.0  0
 I5R  CONST_09  CZ2  CE2  CD2  CG    180.00   0.0  0
 I5R  CONST_10  CZ3  CE3  CD2  CG    180.00   0.0  0
 I5R  CONST_11  NE1  CD1  CG   CD2     0.00   0.0  0
 I5R  CONST_12  CD1  NE1  CE2  CD2     0.00   0.0  0
 I5R  CONST_13  CH2  CZ2  CE2  CD2     0.00   0.0  0
 I5R  CONST_14  CH2  CZ3  CE3  CD2     0.00   0.0  0
 I5R  CONST_15  CD1  CG   CD2  CE3   180.00   0.0  0
 I5R  CONST_16  NE1  CE2  CD2  CE3   180.00   0.0  0
 I5R  CONST_17  CZ2  CE2  CD2  CE3     0.00   0.0  0
 I5R  CONST_18  CZ2  CH2  CZ3  CE3     0.00   0.0  0
 I5R  CONST_19  CE2  CD2  CE3  CZ3     0.00   0.0  0
 I5R  CONST_20  CE2  CZ2  CH2  CZ3     0.00   0.0  0
 I5R  CONST_21  NE1  CE2  CZ2  CH2   180.00   0.0  0
 I5R  CONST_22  CD1  NE1  CE2  CZ2   180.00   0.0  0
 I5R  CONST_23  CD1  CG   CD2  CE2     0.00   0.0  0
 I5R  CONST_24  CA   C    NAL  CAR     0.00   0.0  0
 I5R  CONST_25  NE1  CD1  CG   CB    180.00   0.0  0
 I5R  CONST_26  CE2  CD2  CG   CB    180.00   0.0  0
 I5R  CONST_27  CE3  CD2  CG   CB      0.00   0.0  0
 I5R  CONST_28  CAR  NAL  C    O     180.00   0.0  0
 I5R  CONST_29  H4   CAF  CAQ  CAR   180.00   0.0  0
 I5R  CONST_30  H2   CAE  NAK  CAR   180.00   0.0  0
 I5R  CONST_31  H3   CAD  CAE  NAK   180.00   0.0  0
 I5R  CONST_32  H13  NE1  CD1  CG    180.00   0.0  0
 I5R  CONST_33  H9   CE3  CD2  CG      0.00   0.0  0
 I5R  CONST_34  H14  CD1  CG   CD2   180.00   0.0  0
 I5R  CONST_35  H12  CZ2  CE2  CD2   180.00   0.0  0
 I5R  CONST_36  H10  CZ3  CE3  CD2   180.00   0.0  0
 I5R  CONST_37  H11  CH2  CZ3  CE3   180.00   0.0  0
 I5R  CONST_38  H1   NAL  C    CA    180.00   0.0  0
 I5R  Var_01    CAQ  CAR  NAL  C     -15.05  30.0  1
 I5R  Var_02    CA   N    CAQ  CAR    35.85  30.0  1
 I5R  Var_03    CD1  CG   CB   CA   -102.03  30.0  2

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
 I5R  chir_01  CA  C  N  CB  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
 I5R  plan-1  CB   0.020
 I5R  plan-1  CG   0.020
 I5R  plan-1  CD2  0.020
 I5R  plan-1  CE3  0.020
 I5R  plan-1  CZ3  0.020
 I5R  plan-1  CH2  0.020
 I5R  plan-1  CZ2  0.020
 I5R  plan-1  CE2  0.020
 I5R  plan-1  NE1  0.020
 I5R  plan-1  CD1  0.020
 I5R  plan-1  H9   0.020
 I5R  plan-1  H10  0.020
 I5R  plan-1  H11  0.020
 I5R  plan-1  H12  0.020
 I5R  plan-1  H13  0.020
 I5R  plan-1  H14  0.020
 I5R  plan-2  NAL  0.020
 I5R  plan-2  CAR  0.020
 I5R  plan-2  NAK  0.020
 I5R  plan-2  CAE  0.020
 I5R  plan-2  CAD  0.020
 I5R  plan-2  CAF  0.020
 I5R  plan-2  CAQ  0.020
 I5R  plan-2  N    0.020
 I5R  plan-2  H2   0.020
 I5R  plan-2  H3   0.020
 I5R  plan-2  H4   0.020
 I5R  plan-3  O    0.020
 I5R  plan-3  C    0.020
 I5R  plan-3  NAL  0.020
 I5R  plan-3  CAR  0.020
 I5R  plan-3  CA   0.020
 I5R  plan-3  H1   0.020

