# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 06:09:17 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (2~{R})-2-azanyl-~{N}-(4-ethanoyl-5-pyridin-3-yl-1,3-thiazol-2-yl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N)C(=O)Nc1sc(c2cccnc2)c(n1)C(C)=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
 G5Z  G5Z  (2~{R})-2-azanyl-~{N}-(4-ethanoyl-5-pyridin-3-yl-1,3-thiazol-2-yl)propanamide  ligand  34  20  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G5Z
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
 G5Z  N    N  NH2   0  -0.779  -5.9960   0.2570  -0.6113
 G5Z  CA   C  CH1   0  -0.249  -4.9153  -0.6262  -0.2287
 G5Z  C    C  C     0   0.547  -3.6277   0.1808  -0.1408
 G5Z  O    O  O     0  -0.415  -3.6004   1.3650   0.0906
 G5Z  CB   C  CH3   0  -0.666  -5.1274  -1.3659   1.0993
 G5Z  CAA  C  CH3   0  -0.767   0.2933   3.6109   0.3086
 G5Z  CAN  C  C     0   0.330   1.2135   2.4256   0.2583
 G5Z  CAP  C  CR6   0  -0.033   2.6600  -0.4235   0.0003
 G5Z  CAQ  C  CR5   0   0.300  -1.1958  -0.1688  -0.1844
 G5Z  CAR  C  CR5   0   0.259   0.5755   1.1049   0.0352
 G5Z  CAS  C  CR5   0  -0.266   1.2341  -0.0924  -0.0317
 G5Z  NAK  N  N     0  -0.401  -0.7880   1.0434  -0.0593
 G5Z  NAL  N  NH1   0  -0.722  -2.4970  -0.5899  -0.2991
 G5Z  OAD  O  O     0  -0.387   2.4130   2.5240   0.4031
 G5Z  SAM  S  S2    0   0.261   0.0757  -1.3585  -0.2051
 G5Z  H1   H  HNH2  0   0.356  -6.8482  -0.2856  -0.6757
 G5Z  H2   H  HNH2  0   0.345  -6.1566   0.9400   0.1196
 G5Z  H4   H  HCH1  0   0.269  -4.7997  -1.3734  -1.0205
 G5Z  H5   H  HCH3  0   0.249  -6.0548  -1.9370   1.0517
 G5Z  H6   H  HCH3  0   0.232  -4.3209  -2.0663   1.3216
 G5Z  H7   H  HCH3  0   0.235  -5.2051  -0.6612   1.9288
 G5Z  H8   H  HCH3  0   0.267  -0.2708   3.6934  -0.6213
 G5Z  H9   H  HCH3  0   0.269  -0.4400   3.4945   1.1070
 G5Z  H10  H  HCH3  0   0.259   0.8617   4.5244   0.4673
 G5Z  H14  H  HNH1  0   0.432  -2.6404  -1.5659  -0.5118
 G5Z  C1   C  CR16  0  -0.179   3.1878  -1.2704   0.9682
 G5Z  C2   C  CR16  0  -0.318   4.5419  -1.5648   0.9348
 G5Z  C3   C  CR16  0  -0.061   5.3153  -1.0072  -0.0698
 G5Z  N1   N  N     0  -0.401   4.8188  -0.2097  -1.0118
 G5Z  C5   C  CR16  0  -0.058   3.5272   0.0693  -0.9751
 G5Z  H3   H  HCR6  0   0.277   2.5550  -1.6839   1.7435
 G5Z  H11  H  HCR6  0   0.278   4.9903  -2.2119   1.6754
 G5Z  H12  H  HCR6  0   0.271   6.3778  -1.2155  -0.1217
 G5Z  H13  H  HCR6  0   0.265   3.1433   0.7082  -1.7629

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
 G5Z  CAP  CAS  single    1.464  0.020  1.464
 G5Z  CAA  CAN  single    1.501  0.020  1.501
 G5Z  CAS  SAM  aromatic  1.725  0.020  1.725
 G5Z  CAS  CAR  aromatic  1.368  0.020  1.368
 G5Z  CAN  CAR  single    1.484  0.020  1.484
 G5Z  CAN  OAD  double    1.212  0.020  1.212
 G5Z  SAM  CAQ  aromatic  1.741  0.020  1.741
 G5Z  CAR  NAK  aromatic  1.368  0.020  1.368
 G5Z  O    C    double    1.207  0.020  1.207
 G5Z  NAK  CAQ  aromatic  1.285  0.020  1.285
 G5Z  CAQ  NAL  single    1.372  0.020  1.372
 G5Z  C    NAL  single    1.378  0.020  1.378
 G5Z  C    CA   single    1.522  0.020  1.522
 G5Z  CB   CA   single    1.535  0.020  1.535
 G5Z  CA   N    single    1.447  0.020  1.447
 G5Z  N    H1   single    0.890  0.020  1.040
 G5Z  N    H2   single    0.890  0.020  1.040
 G5Z  CA   H4   single    0.970  0.020  1.090
 G5Z  CB   H5   single    0.970  0.020  1.090
 G5Z  CB   H6   single    0.970  0.020  1.090
 G5Z  CB   H7   single    0.970  0.020  1.090
 G5Z  CAA  H8   single    0.970  0.020  1.090
 G5Z  CAA  H9   single    0.970  0.020  1.090
 G5Z  CAA  H10  single    0.970  0.020  1.090
 G5Z  NAL  H14  single    0.860  0.020  1.020
 G5Z  CAP  C1   aromatic  1.390  0.020  1.390
 G5Z  C1   C2   aromatic  1.386  0.020  1.386
 G5Z  C2   C3   aromatic  1.385  0.020  1.385
 G5Z  C3   N1   aromatic  1.330  0.020  1.330
 G5Z  N1   C5   aromatic  1.322  0.020  1.322
 G5Z  C5   CAP  aromatic  1.395  0.020  1.395
 G5Z  C1   H3   single    0.930  0.020  1.080
 G5Z  C2   H11  single    0.930  0.020  1.080
 G5Z  C3   H12  single    0.930  0.020  1.080
 G5Z  C5   H13  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
 G5Z  H2   N    H1   105.89  3.000
 G5Z  H2   N    CA   109.82  3.000
 G5Z  H1   N    CA   108.56  3.000
 G5Z  H4   CA   CB   108.14  3.000
 G5Z  H4   CA   C    108.32  3.000
 G5Z  CB   CA   C    108.81  3.000
 G5Z  H4   CA   N    107.71  3.000
 G5Z  CB   CA   N    114.82  3.000
 G5Z  C    CA   N    108.87  3.000
 G5Z  NAL  C    O    123.53  3.000
 G5Z  NAL  C    CA   113.02  3.000
 G5Z  O    C    CA   123.40  3.000
 G5Z  H7   CB   H6   108.20  3.000
 G5Z  H7   CB   H5   108.11  3.000
 G5Z  H6   CB   H5   107.54  3.000
 G5Z  H7   CB   CA   110.87  3.000
 G5Z  H6   CB   CA   112.56  3.000
 G5Z  H5   CB   CA   109.40  3.000
 G5Z  H10  CAA  H9   109.53  3.000
 G5Z  H10  CAA  H8   109.34  3.000
 G5Z  H9   CAA  H8   106.53  3.000
 G5Z  H10  CAA  CAN  110.34  3.000
 G5Z  H9   CAA  CAN  110.64  3.000
 G5Z  H8   CAA  CAN  110.37  3.000
 G5Z  OAD  CAN  CAR  121.05  3.000
 G5Z  OAD  CAN  CAA  122.58  3.000
 G5Z  CAR  CAN  CAA  116.37  3.000
 G5Z  C5   CAP  C1   117.77  3.000
 G5Z  C5   CAP  CAS  120.68  3.000
 G5Z  C1   CAP  CAS  121.51  3.000
 G5Z  SAM  CAQ  NAL  118.80  3.000
 G5Z  NAL  CAQ  NAK  126.76  3.000
 G5Z  SAM  CAQ  NAK  114.45  3.000
 G5Z  NAK  CAR  CAS  115.92  3.000
 G5Z  NAK  CAR  CAN  118.61  3.000
 G5Z  CAS  CAR  CAN  125.41  3.000
 G5Z  SAM  CAS  CAR  108.90  3.000
 G5Z  CAR  CAS  CAP  131.73  3.000
 G5Z  SAM  CAS  CAP  119.36  3.000
 G5Z  CAR  NAK  CAQ  111.43  3.000
 G5Z  H14  NAL  CAQ  116.68  3.000
 G5Z  H14  NAL  C    116.66  3.000
 G5Z  CAQ  NAL  C    126.65  3.000
 G5Z  CAS  SAM  CAQ   89.30  3.000
 G5Z  H3   C1   C2   120.46  3.000
 G5Z  H3   C1   CAP  120.62  3.000
 G5Z  C2   C1   CAP  118.91  3.000
 G5Z  H11  C2   C3   120.42  3.000
 G5Z  H11  C2   C1   121.06  3.000
 G5Z  C3   C2   C1   118.52  3.000
 G5Z  H12  C3   N1   116.55  3.000
 G5Z  H12  C3   C2   120.32  3.000
 G5Z  N1   C3   C2   123.13  3.000
 G5Z  C5   N1   C3   118.13  3.000
 G5Z  H13  C5   N1   116.75  3.000
 G5Z  H13  C5   CAP  119.73  3.000
 G5Z  N1   C5   CAP  123.52  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
 G5Z  CONST_01  CAQ  SAM  CAS  CAP   180.00   0.0  0
 G5Z  CONST_02  NAK  CAR  CAS  CAP   180.00   0.0  0
 G5Z  CONST_03  C3   C2   C1   CAP     0.00   0.0  0
 G5Z  CONST_04  C3   N1   C5   CAP     0.00   0.0  0
 G5Z  CONST_05  CAR  CAS  SAM  CAQ     0.00   0.0  0
 G5Z  CONST_06  CAS  CAR  NAK  CAQ     0.00   0.0  0
 G5Z  CONST_09  SAM  CAQ  NAK  CAR     0.00   0.0  0
 G5Z  CONST_10  C2   C1   CAP  CAS   180.00   0.0  0
 G5Z  CONST_11  N1   C5   CAP  CAS   180.00   0.0  0
 G5Z  CONST_12  NAK  CAQ  SAM  CAS     0.00   0.0  0
 G5Z  CONST_13  SAM  CAS  CAR  NAK     0.00   0.0  0
 G5Z  CONST_16  N1   C5   CAP  C1      0.00   0.0  0
 G5Z  CONST_17  N1   C3   C2   C1      0.00   0.0  0
 G5Z  CONST_18  C5   CAP  C1   C2      0.00   0.0  0
 G5Z  CONST_19  C5   N1   C3   C2      0.00   0.0  0
 G5Z  CONST_20  CAP  CAS  CAR  CAN     0.00   0.0  0
 G5Z  CONST_21  SAM  CAS  CAR  CAN   180.00   0.0  0
 G5Z  CONST_22  CAQ  NAK  CAR  CAN   180.00   0.0  0
 G5Z  CONST_23  NAL  CAQ  NAK  CAR   180.00   0.0  0
 G5Z  CONST_24  NAL  CAQ  SAM  CAS   180.00   0.0  0
 G5Z  CONST_25  H11  C2   C1   CAP   180.00   0.0  0
 G5Z  CONST_26  H3   C1   CAP  CAS     0.00   0.0  0
 G5Z  CONST_27  H13  C5   CAP  CAS     0.00   0.0  0
 G5Z  CONST_28  H12  C3   C2   C1    180.00   0.0  0
 G5Z  CONST_29  SAM  CAQ  NAL  C     180.00   0.0  0
 G5Z  CONST_30  NAK  CAQ  NAL  C       0.00   0.0  0
 G5Z  CONST_31  H14  NAL  CAQ  NAK   180.00   0.0  0
 G5Z  CONST_32  CAQ  NAL  C    CA    180.00   0.0  0
 G5Z  CONST_33  CAQ  NAL  C    O       0.00   0.0  0
 G5Z  Var_01    CAS  CAR  CAN  CAA  -179.43  30.0  2
 G5Z  Var_02    H8   CAA  CAN  CAR   -58.58  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
 G5Z  chir_01  CA  C  CB  N  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
 G5Z  plan-1  CAN  0.020
 G5Z  plan-1  CAP  0.020
 G5Z  plan-1  CAQ  0.020
 G5Z  plan-1  CAR  0.020
 G5Z  plan-1  CAS  0.020
 G5Z  plan-1  NAK  0.020
 G5Z  plan-1  NAL  0.020
 G5Z  plan-1  SAM  0.020
 G5Z  plan-2  CAP  0.020
 G5Z  plan-2  CAS  0.020
 G5Z  plan-2  C1   0.020
 G5Z  plan-2  C2   0.020
 G5Z  plan-2  C3   0.020
 G5Z  plan-2  N1   0.020
 G5Z  plan-2  C5   0.020
 G5Z  plan-2  H3   0.020
 G5Z  plan-2  H11  0.020
 G5Z  plan-2  H12  0.020
 G5Z  plan-2  H13  0.020
 G5Z  plan-3  CA   0.020
 G5Z  plan-3  C    0.020
 G5Z  plan-3  O    0.020
 G5Z  plan-3  CAQ  0.020
 G5Z  plan-3  NAL  0.020
 G5Z  plan-3  H14  0.020
 G5Z  plan-4  CAA  0.020
 G5Z  plan-4  CAN  0.020
 G5Z  plan-4  CAR  0.020
 G5Z  plan-4  OAD  0.020

