# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 17:16:19 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: N-(3-chloropyridin-4-yl)-2-(3-methyl-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=Nc2n(CC(=O)Nc3ccncc3Cl)ccc2C1=O
#
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
 YND  YND  "N-(3-chloropyridin-4-yl)-2-(3-methyl-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)acetamide"
  ligand  34  22  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YND
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
 YND  C1    C   CH3   0  -0.516  -19.1167  -4.0681  17.7642
 YND  N     N   NR5   0  -0.494  -18.8148  -2.9055  12.4704
 YND  CA    C   CH2   0  -0.470  -19.2262  -1.7572  11.7232
 YND  C     C   C     0   0.551  -20.6557  -1.9052  11.2147
 YND  O     O   O     0  -0.418  -21.3939  -2.7794  11.6020
 YND  CAD   C   CR16  0  -0.061  -24.4361  -1.3122   9.0333
 YND  CAE   C   CR16  0  -0.379  -23.3009  -1.5899   9.7733
 YND  CAF   C   CR15  0  -0.414  -18.0752  -4.9682  12.9266
 YND  CAG   C   CR15  0  -0.011  -18.2884  -4.0588  11.9334
 YND  CAH   C   CR16  0   0.154  -19.4722  -2.5573  15.8903
 YND  CAI   C   CR16  0  -0.039  -23.4915   0.4814   8.0350
 YND  CAP   C   CR6   0  -0.211  -22.3089   0.2929   8.7275
 YND  CAQ   C   CR6   0   0.554  -22.1798  -0.7697   9.6313
 YND  CAR   C   CR6   0   0.534  -18.5303  -4.7626  15.4964
 YND  CAS   C   CR56  0  -0.149  -18.5029  -4.3476  14.1317
 YND  CAT   C   CR56  0   0.508  -18.9618  -3.0798  13.8050
 YND  NAK   N   N     0  -0.404  -24.5476  -0.3037   8.1782
 YND  NAL   N   N     0  -0.454  -19.4566  -2.1628  14.6610
 YND  NAM   N   NH1   0  -0.749  -20.9845  -0.9452  10.3018
 YND  NAN   N   NR6   0  -0.512  -19.0460  -3.7657  16.3416
 YND  OAB   O   O     0  -0.474  -18.1648  -5.8350  15.9502
 YND  H1    H   HCH3  0   0.260  -19.5167  -3.2065  18.2902
 YND  H2    H   HCH3  0   0.261  -19.7673  -4.9211  17.9436
 YND  H3    H   HCH3  0   0.261  -18.1271  -4.2892  18.1578
 YND  HA2   H   HCH2  0   0.318  -18.5383  -1.6048  10.8892
 YND  HA1   H   HCH2  0   0.324  -19.1644  -0.8667  12.3527
 YND  HAD   H   HCR6  0   0.274  -25.3038  -1.9519   9.1456
 YND  HAE   H   HCR6  0   0.304  -23.3002  -2.4337  10.4416
 YND  HAF   H   HCR5  0   0.256  -17.6588  -5.9550  12.8071
 YND  HAG   H   HCR5  0   0.292  -18.0966  -4.1267  10.8744
 YND  HAH   H   HCR6  0   0.291  -19.8516  -1.8859  16.6508
 YND  HAI   H   HCR6  0   0.287  -23.5732   1.3074   7.3373
 YND  HNA   H   HNH1  0   0.422  -20.2566  -0.2800  10.0774
 YND  CLAC  CL  CL    0  -0.097  -20.9991   1.3871   8.4504

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
 YND  CLAC  CAP  single    1.729  0.020  1.729
 YND  CAI   NAK  aromatic  1.324  0.020  1.324
 YND  CAI   CAP  aromatic  1.383  0.020  1.383
 YND  NAK   CAD  aromatic  1.327  0.020  1.327
 YND  CAP   CAQ  aromatic  1.401  0.020  1.401
 YND  CAD   CAE  aromatic  1.383  0.020  1.383
 YND  CAQ   CAE  aromatic  1.396  0.020  1.396
 YND  CAQ   NAM  single    1.382  0.020  1.382
 YND  NAM   C    single    1.365  0.020  1.365
 YND  C     O    double    1.208  0.020  1.208
 YND  C     CA   single    1.524  0.020  1.524
 YND  CA    N    single    1.430  0.020  1.430
 YND  CAG   N    aromatic  1.377  0.020  1.377
 YND  CAG   CAF  aromatic  1.363  0.020  1.363
 YND  N     CAT  aromatic  1.354  0.020  1.354
 YND  CAF   CAS  aromatic  1.421  0.020  1.421
 YND  CAT   CAS  aromatic  1.387  0.020  1.387
 YND  CAT   NAL  single    1.348  0.020  1.348
 YND  CAS   CAR  single    1.427  0.020  1.427
 YND  NAL   CAH  double    1.291  0.020  1.291
 YND  CAR   OAB  double    1.221  0.020  1.221
 YND  CAR   NAN  single    1.405  0.020  1.405
 YND  CAH   NAN  single    1.358  0.020  1.358
 YND  NAN   C1   single    1.456  0.020  1.456
 YND  C1    H1   single    0.970  0.020  1.090
 YND  C1    H2   single    0.970  0.020  1.090
 YND  C1    H3   single    0.970  0.020  1.090
 YND  CA    HA2  single    0.970  0.020  1.090
 YND  CA    HA1  single    0.970  0.020  1.090
 YND  CAD   HAD  single    0.930  0.020  1.080
 YND  CAE   HAE  single    0.930  0.020  1.080
 YND  CAF   HAF  single    0.930  0.020  1.080
 YND  CAG   HAG  single    0.930  0.020  1.080
 YND  CAH   HAH  single    0.930  0.020  1.080
 YND  CAI   HAI  single    0.930  0.020  1.080
 YND  NAM   HNA  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
 YND  H3    C1   H2   108.97  3.000
 YND  H3    C1   H1   108.73  3.000
 YND  H2    C1   H1   108.79  3.000
 YND  H3    C1   NAN  110.58  3.000
 YND  H2    C1   NAN  110.68  3.000
 YND  H1    C1   NAN  109.05  3.000
 YND  CAT   N    CAG  108.55  3.000
 YND  CAT   N    CA   125.94  3.000
 YND  CAG   N    CA   125.36  3.000
 YND  HA1   CA   HA2  106.91  3.000
 YND  HA1   CA   C    108.93  3.000
 YND  HA2   CA   C    110.46  3.000
 YND  HA1   CA   N    109.70  3.000
 YND  HA2   CA   N    109.26  3.000
 YND  C     CA   N    111.47  3.000
 YND  NAM   C    O    125.18  3.000
 YND  O     C    CA   122.44  3.000
 YND  NAM   C    CA   112.38  3.000
 YND  HAD   CAD  NAK  116.62  3.000
 YND  HAD   CAD  CAE  118.89  3.000
 YND  NAK   CAD  CAE  124.49  3.000
 YND  HAE   CAE  CAQ  121.54  3.000
 YND  HAE   CAE  CAD  119.34  3.000
 YND  CAQ   CAE  CAD  119.12  3.000
 YND  HAF   CAF  CAS  127.59  3.000
 YND  HAF   CAF  CAG  126.19  3.000
 YND  CAS   CAF  CAG  106.22  3.000
 YND  HAG   CAG  CAF  130.21  3.000
 YND  HAG   CAG  N    120.25  3.000
 YND  CAF   CAG  N    109.54  3.000
 YND  HAH   CAH  NAN  115.34  3.000
 YND  HAH   CAH  NAL  118.90  3.000
 YND  NAN   CAH  NAL  125.76  3.000
 YND  HAI   CAI  NAK  117.47  3.000
 YND  HAI   CAI  CAP  119.36  3.000
 YND  NAK   CAI  CAP  123.17  3.000
 YND  CLAC  CAP  CAQ  120.90  3.000
 YND  CAQ   CAP  CAI  120.34  3.000
 YND  CLAC  CAP  CAI  118.76  3.000
 YND  NAM   CAQ  CAP  119.28  3.000
 YND  NAM   CAQ  CAE  124.80  3.000
 YND  CAP   CAQ  CAE  115.92  3.000
 YND  OAB   CAR  NAN  120.64  3.000
 YND  NAN   CAR  CAS  112.09  3.000
 YND  OAB   CAR  CAS  127.27  3.000
 YND  CAT   CAS  CAR  118.99  3.000
 YND  CAR   CAS  CAF  133.61  3.000
 YND  CAT   CAS  CAF  107.39  3.000
 YND  NAL   CAT  CAS  126.40  3.000
 YND  NAL   CAT  N    125.31  3.000
 YND  CAS   CAT  N    108.29  3.000
 YND  CAI   NAK  CAD  116.97  3.000
 YND  CAT   NAL  CAH  113.64  3.000
 YND  HNA   NAM  CAQ  115.56  3.000
 YND  HNA   NAM  C    115.95  3.000
 YND  CAQ   NAM  C    128.48  3.000
 YND  CAR   NAN  CAH  123.12  3.000
 YND  CAH   NAN  C1   119.61  3.000
 YND  CAR   NAN  C1   117.27  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
 YND  CONST_01  CAS   CAF  CAG  N       0.00   0.0  0
 YND  CONST_02  CAF   CAS  CAT  N       0.00   0.0  0
 YND  CONST_03  CAP   CAI  NAK  CAD     0.00   0.0  0
 YND  CONST_04  CAP   CAQ  CAE  CAD     0.00   0.0  0
 YND  CONST_05  CAI   NAK  CAD  CAE     0.00   0.0  0
 YND  CONST_06  CAI   CAP  CAQ  CAE     0.00   0.0  0
 YND  CONST_07  CAT   N    CAG  CAF     0.00   0.0  0
 YND  CONST_08  CAS   CAT  N    CAG     0.00   0.0  0
 YND  CONST_09  CAT   CAS  CAF  CAG     0.00   0.0  0
 YND  CONST_10  NAK   CAI  CAP  CAQ     0.00   0.0  0
 YND  CONST_11  NAK   CAD  CAE  CAQ     0.00   0.0  0
 YND  CONST_12  CAS   CAR  NAN  CAH     0.00   0.0  0
 YND  CONST_13  NAL   CAH  NAN  CAR     0.00   0.0  0
 YND  CONST_14  NAN   CAH  NAL  CAT     0.00   0.0  0
 YND  CONST_15  CAF   CAG  N    CA    180.00   0.0  0
 YND  CONST_16  CAS   CAT  N    CA    180.00   0.0  0
 YND  CONST_17  NAL   CAT  N    CA      0.00   0.0  0
 YND  CONST_18  NAM   CAQ  CAE  CAD   180.00   0.0  0
 YND  CONST_19  CLAC  CAP  CAQ  CAE   180.00   0.0  0
 YND  CONST_20  NAM   CAQ  CAP  CAI   180.00   0.0  0
 YND  CONST_21  CLAC  CAP  CAI  NAK   180.00   0.0  0
 YND  CONST_22  CAS   CAR  NAN  C1    180.00   0.0  0
 YND  CONST_23  NAL   CAH  NAN  C1    180.00   0.0  0
 YND  CONST_24  OAB   CAR  NAN  CAH   180.00   0.0  0
 YND  CONST_25  HAF   CAF  CAG  N     180.00   0.0  0
 YND  CONST_26  HAI   CAI  NAK  CAD   180.00   0.0  0
 YND  CONST_27  HAD   CAD  NAK  CAI   180.00   0.0  0
 YND  CONST_28  HAE   CAE  CAQ  CAP   180.00   0.0  0
 YND  CONST_29  HAI   CAI  CAP  CAQ   180.00   0.0  0
 YND  CONST_30  HAD   CAD  CAE  CAQ   180.00   0.0  0
 YND  CONST_31  HAF   CAF  CAS  CAR     0.00   0.0  0
 YND  CONST_32  HAG   CAG  CAF  CAS   180.00   0.0  0
 YND  CONST_33  HAG   CAG  N    CAT   180.00   0.0  0
 YND  CONST_34  HAF   CAF  CAS  CAT   180.00   0.0  0
 YND  CONST_35  HAE   CAE  CAD  NAK   180.00   0.0  0
 YND  CONST_36  HAH   CAH  NAN  CAR   180.00   0.0  0
 YND  CONST_37  HAH   CAH  NAL  CAT   180.00   0.0  0
 YND  CONST_38  CAP   CAQ  NAM  C     180.00   0.0  0
 YND  CONST_39  CAE   CAQ  NAM  C       0.00   0.0  0
 YND  CONST_40  OAB   CAR  NAN  C1      0.00   0.0  0
 YND  CONST_41  HNA   NAM  CAQ  CAE   180.00   0.0  0
 YND  CONST_42  HNA   NAM  CAQ  CAP     0.00   0.0  0
 YND  CONST_43  HAH   CAH  NAN  C1      0.00   0.0  0
 YND  CONST_44  CAQ   NAM  C    CA    180.00   0.0  0
 YND  CONST_45  CAQ   NAM  C    O       0.00   0.0  0
 YND  CONST_46  HNA   NAM  C    CA      0.00   0.0  0
 YND  CONST_47  HNA   NAM  C    O     180.00   0.0  0
 YND  Var_01    CAG   N    CA   C      85.11  30.0  2
 YND  Var_02    CAT   N    CA   C     -89.98  30.0  2
 YND  Var_03    HA2   CA   N    CAG   -37.26  30.0  1
 YND  Var_04    HA1   CA   N    CAG  -154.15  30.0  1
 YND  Var_05    H1    C1   NAN  CAH    -0.96  30.0  3
 YND  Var_06    H2    C1   NAN  CAH   118.67  30.0  3
 YND  Var_07    H3    C1   NAN  CAH  -120.47  30.0  3
 YND  Var_08    H1    C1   NAN  CAR   179.07  30.0  3
 YND  Var_09    H2    C1   NAN  CAR   -61.29  30.0  3
 YND  Var_10    H3    C1   NAN  CAR    59.56  30.0  3
 YND  Var_11    HA2   CA   N    CAT   147.66  30.0  1
 YND  Var_12    HA1   CA   N    CAT    30.76  30.0  1
 YND  Var_13    NAM   C    CA   N    -168.72  30.0  2
 YND  Var_14    O     C    CA   N      11.75  30.0  2
 YND  Var_15    HA2   CA   C    O     133.42  30.0  3
 YND  Var_16    HA1   CA   C    O    -109.44  30.0  3
 YND  Var_17    HA2   CA   C    NAM   -47.05  30.0  3
 YND  Var_18    HA1   CA   C    NAM    70.09  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
 YND  plan-1  CAD   0.020
 YND  plan-1  CAE   0.020
 YND  plan-1  CAI   0.020
 YND  plan-1  CAP   0.020
 YND  plan-1  CAQ   0.020
 YND  plan-1  NAK   0.020
 YND  plan-1  NAM   0.020
 YND  plan-1  HAD   0.020
 YND  plan-1  HAE   0.020
 YND  plan-1  HAI   0.020
 YND  plan-1  CLAC  0.020
 YND  plan-2  CA    0.020
 YND  plan-2  C     0.020
 YND  plan-2  O     0.020
 YND  plan-2  CAQ   0.020
 YND  plan-2  NAM   0.020
 YND  plan-2  HNA   0.020
 YND  plan-3  C1    0.020
 YND  plan-3  N     0.020
 YND  plan-3  CA    0.020
 YND  plan-3  CAF   0.020
 YND  plan-3  CAG   0.020
 YND  plan-3  CAH   0.020
 YND  plan-3  CAR   0.020
 YND  plan-3  CAS   0.020
 YND  plan-3  CAT   0.020
 YND  plan-3  NAL   0.020
 YND  plan-3  NAN   0.020
 YND  plan-3  OAB   0.020
 YND  plan-3  HAF   0.020
 YND  plan-3  HAG   0.020
 YND  plan-3  HAH   0.020

