# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 23:28:05 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-(pyridin-4-yl)-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NCCc2[nH]c(cc12)c3ccncc3
#
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
 0SY  0SY  2-(pyridin-4-yl)-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one  ligand  27  16  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0SY
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
 0SY  CAF  C  CR15  0  -0.416   0.3542   1.0129  -0.0358
 0SY  CAO  C  CR5   0  -0.132   1.6439   0.4403   0.0022
 0SY  CAL  C  C     0   0.475   2.9645   1.0648   0.0273
 0SY  OAA  O  O     0  -0.493   3.1360   2.2747   0.1267
 0SY  NAJ  N  NH1   0  -0.650   3.9880   0.1772  -0.0227
 0SY  CAG  C  CH2   0  -0.284   3.8339  -1.2075  -0.4434
 0SY  CAH  C  CH2   0  -0.527   2.6312  -1.8690   0.2213
 0SY  CAP  C  CR5   0   0.363   1.4915  -0.9274   0.0983
 0SY  NAK  N  NR15  0  -0.721   0.1766  -1.1947   0.1162
 0SY  CAN  C  CR5   0   0.370  -0.5495  -0.0253   0.0299
 0SY  CAM  C  CR6   0   0.165  -2.0001  -0.0024   0.0090
 0SY  CAD  C  CR16  0  -0.385  -2.7758  -1.1638   0.0283
 0SY  CAB  C  CR16  0  -0.061  -4.1567  -1.0595   0.0042
 0SY  NAI  N  N     0  -0.415  -4.8141   0.0928  -0.0375
 0SY  CAC  C  CR16  0  -0.058  -4.0775   1.2006  -0.0551
 0SY  CAE  C  CR16  0  -0.408  -2.6959   1.2096  -0.0333
 0SY  H1   H  HCR5  0   0.260   0.1209   2.0628  -0.1132
 0SY  H2   H  HNH1  0   0.397   4.9165   0.5686  -0.0774
 0SY  H3   H  HCH2  0   0.242   3.7211  -1.2677  -1.5309
 0SY  H4   H  HCH2  0   0.275   2.4274  -2.8268  -0.2588
 0SY  H5   H  HNR5  0   0.421  -0.2091  -2.1234   0.1851
 0SY  H6   H  HCR6  0   0.255  -2.3380  -2.1526   0.0595
 0SY  H7   H  HCR6  0   0.265  -4.7587  -1.9614   0.0180
 0SY  H8   H  HCR6  0   0.265  -4.6173   2.1406  -0.0880
 0SY  H9   H  HCR6  0   0.261  -2.1743   2.1569  -0.0478
 0SY  H10  H  HCH2  0   0.265   4.7452  -1.7406  -0.1801
 0SY  H11  H  HCH2  0   0.270   2.8387  -2.0725   1.2765

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
 0SY  CAB  NAI  aromatic  1.327  0.020  1.327
 0SY  CAB  CAD  aromatic  1.385  0.020  1.385
 0SY  NAI  CAC  aromatic  1.330  0.020  1.330
 0SY  CAD  CAM  aromatic  1.397  0.020  1.397
 0SY  CAC  CAE  aromatic  1.382  0.020  1.382
 0SY  CAM  CAE  aromatic  1.398  0.020  1.398
 0SY  CAM  CAN  single    1.451  0.020  1.451
 0SY  CAF  CAN  aromatic  1.378  0.020  1.378
 0SY  CAF  CAO  aromatic  1.412  0.020  1.412
 0SY  CAN  NAK  aromatic  1.379  0.020  1.379
 0SY  OAA  CAL  double    1.226  0.020  1.226
 0SY  CAO  CAL  single    1.461  0.020  1.461
 0SY  CAO  CAP  aromatic  1.379  0.020  1.379
 0SY  CAL  NAJ  single    1.356  0.020  1.356
 0SY  NAK  CAP  aromatic  1.342  0.020  1.342
 0SY  CAP  CAH  single    1.483  0.020  1.483
 0SY  NAJ  CAG  single    1.455  0.020  1.455
 0SY  CAH  CAG  single    1.525  0.020  1.525
 0SY  CAF  H1   single    0.930  0.020  1.080
 0SY  NAJ  H2   single    0.890  0.020  1.040
 0SY  CAG  H3   single    0.970  0.020  1.090
 0SY  CAH  H4   single    0.970  0.020  1.090
 0SY  NAK  H5   single    0.860  0.020  1.020
 0SY  CAD  H6   single    0.930  0.020  1.080
 0SY  CAB  H7   single    0.930  0.020  1.080
 0SY  CAC  H8   single    0.930  0.020  1.080
 0SY  CAE  H9   single    0.930  0.020  1.080
 0SY  CAG  H10  single    0.970  0.020  1.090
 0SY  CAH  H11  single    0.970  0.020  1.090

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
 0SY  H1   CAF  CAN  126.52  3.000
 0SY  H1   CAF  CAO  126.48  3.000
 0SY  CAN  CAF  CAO  106.99  3.000
 0SY  CAP  CAO  CAL  121.49  3.000
 0SY  CAP  CAO  CAF  107.65  3.000
 0SY  CAL  CAO  CAF  130.76  3.000
 0SY  NAJ  CAL  OAA  122.92  3.000
 0SY  NAJ  CAL  CAO  113.70  3.000
 0SY  OAA  CAL  CAO  123.34  3.000
 0SY  H2   NAJ  CAG  116.80  3.000
 0SY  H2   NAJ  CAL  116.27  3.000
 0SY  CAG  NAJ  CAL  123.62  3.000
 0SY  H10  CAG  H3   107.44  3.000
 0SY  H10  CAG  CAH  110.03  3.000
 0SY  H3   CAG  CAH  109.13  3.000
 0SY  H10  CAG  NAJ  107.91  3.000
 0SY  H3   CAG  NAJ  110.50  3.000
 0SY  CAH  CAG  NAJ  111.73  3.000
 0SY  H11  CAH  H4   107.25  3.000
 0SY  H11  CAH  CAP  110.10  3.000
 0SY  H4   CAH  CAP  112.17  3.000
 0SY  H11  CAH  CAG  110.57  3.000
 0SY  H4   CAH  CAG  109.66  3.000
 0SY  CAP  CAH  CAG  107.13  3.000
 0SY  NAK  CAP  CAH  128.70  3.000
 0SY  CAH  CAP  CAO  123.38  3.000
 0SY  NAK  CAP  CAO  107.86  3.000
 0SY  H5   NAK  CAN  125.73  3.000
 0SY  H5   NAK  CAP  124.02  3.000
 0SY  CAN  NAK  CAP  110.25  3.000
 0SY  CAM  CAN  NAK  122.72  3.000
 0SY  NAK  CAN  CAF  107.25  3.000
 0SY  CAM  CAN  CAF  130.02  3.000
 0SY  CAE  CAM  CAD  116.41  3.000
 0SY  CAE  CAM  CAN  120.77  3.000
 0SY  CAD  CAM  CAN  122.82  3.000
 0SY  H6   CAD  CAB  118.22  3.000
 0SY  H6   CAD  CAM  122.39  3.000
 0SY  CAB  CAD  CAM  119.40  3.000
 0SY  H7   CAB  NAI  116.58  3.000
 0SY  H7   CAB  CAD  119.38  3.000
 0SY  NAI  CAB  CAD  124.04  3.000
 0SY  CAC  NAI  CAB  116.68  3.000
 0SY  H8   CAC  CAE  119.51  3.000
 0SY  H8   CAC  NAI  116.52  3.000
 0SY  CAE  CAC  NAI  123.97  3.000
 0SY  H9   CAE  CAC  119.19  3.000
 0SY  H9   CAE  CAM  121.31  3.000
 0SY  CAC  CAE  CAM  119.50  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
 0SY  CONST_01  CAD  CAM  CAN  CAF   180.00   0.0  0
 0SY  CONST_02  CAE  CAM  CAN  CAF     0.00   0.0  0
 0SY  CONST_03  CAP  NAK  CAN  CAF     0.00   0.0  0
 0SY  CONST_04  NAK  CAP  CAO  CAF     0.00   0.0  0
 0SY  CONST_05  CAM  CAN  CAF  CAO   180.00   0.0  0
 0SY  CONST_06  NAK  CAN  CAF  CAO     0.00   0.0  0
 0SY  CONST_07  CAN  NAK  CAP  CAO     0.00   0.0  0
 0SY  CONST_08  CAN  CAF  CAO  CAP     0.00   0.0  0
 0SY  CONST_09  CAM  CAN  NAK  CAP   180.00   0.0  0
 0SY  CONST_10  CAD  CAM  CAN  NAK     0.00   0.0  0
 0SY  CONST_11  CAE  CAM  CAN  NAK   180.00   0.0  0
 0SY  CONST_12  CAB  CAD  CAM  CAN   180.00   0.0  0
 0SY  CONST_13  CAC  CAE  CAM  CAN   180.00   0.0  0
 0SY  CONST_14  NAI  CAB  CAD  CAM     0.00   0.0  0
 0SY  CONST_15  NAI  CAC  CAE  CAM     0.00   0.0  0
 0SY  CONST_16  CAC  NAI  CAB  CAD     0.00   0.0  0
 0SY  CONST_17  CAC  CAE  CAM  CAD     0.00   0.0  0
 0SY  CONST_18  CAE  CAC  NAI  CAB     0.00   0.0  0
 0SY  CONST_19  CAE  CAM  CAD  CAB     0.00   0.0  0
 0SY  CONST_21  CAG  NAJ  CAL  OAA   180.00   0.0  0
 0SY  CONST_22  H5   NAK  CAN  CAF   180.00   0.0  0
 0SY  CONST_23  H1   CAF  CAO  CAL     0.00   0.0  0
 0SY  CONST_24  H6   CAD  CAM  CAN     0.00   0.0  0
 0SY  CONST_25  H9   CAE  CAM  CAN     0.00   0.0  0
 0SY  CONST_26  H7   CAB  CAD  CAM   180.00   0.0  0
 0SY  CONST_27  H8   CAC  CAE  CAM   180.00   0.0  0
 0SY  CONST_28  H2   NAJ  CAL  CAO   180.00   0.0  0
 0SY  Var_01    NAJ  CAL  CAO  CAF  -176.07  30.0  1
 0SY  Var_02    CAG  CAH  CAP  CAO   -27.24  30.0  1
 0SY  Var_03    CAH  CAG  NAJ  CAL   -46.50  30.0  1
 0SY  Var_04    CAP  CAH  CAG  NAJ    46.81  30.0  1

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
 0SY  plan-1  CAN  0.020
 0SY  plan-1  CAM  0.020
 0SY  plan-1  CAD  0.020
 0SY  plan-1  CAB  0.020
 0SY  plan-1  NAI  0.020
 0SY  plan-1  CAC  0.020
 0SY  plan-1  CAE  0.020
 0SY  plan-1  H6   0.020
 0SY  plan-1  H7   0.020
 0SY  plan-1  H8   0.020
 0SY  plan-1  H9   0.020
 0SY  plan-2  CAF  0.020
 0SY  plan-2  CAO  0.020
 0SY  plan-2  CAL  0.020
 0SY  plan-2  CAH  0.020
 0SY  plan-2  CAP  0.020
 0SY  plan-2  NAK  0.020
 0SY  plan-2  CAN  0.020
 0SY  plan-2  CAM  0.020
 0SY  plan-2  H1   0.020
 0SY  plan-2  H5   0.020
 0SY  plan-3  CAO  0.020
 0SY  plan-3  CAL  0.020
 0SY  plan-3  OAA  0.020
 0SY  plan-3  NAJ  0.020
 0SY  plan-3  CAG  0.020
 0SY  plan-3  H2   0.020

