# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 00:11:20 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (3Z)-6-hydroxy-3-[hydroxy(sulfanyl)methylidene]-5-[2-(methylsulfanyl)ethyl]pyrazin-2(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCCC1=N\C(=C(O)/S)C(=O)N=C1O
#
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
 HM7  HM7  (3Z)-6-hydroxy-3-[hydroxy(sulfanyl)methylidene]-5-[2-(methylsulfanyl)ethyl]pyrazin-2(3H)-one  ligand  25  15  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HM7
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
 HM7  CBS   C  CH2   0  -0.543   2.4144   0.2524  -0.0092
 HM7  CBR   C  CH2   0  -0.488   1.7816  -1.1291  -0.0346
 HM7  CAA   C  CR6   0   0.151   0.2847  -1.0722  -0.0184
 HM7  NAB   N  N     0  -0.395  -0.3376   0.0473  -0.0143
 HM7  CAI   C  CR6   0   0.454  -0.5144  -2.2906  -0.0111
 HM7  OAJ   O  OH1   0  -0.576   0.1698  -3.4169  -0.0200
 HM7  NAH   N  N     0  -0.487  -1.8002  -2.3085   0.0020
 HM7  CAF   C  CR6   0   0.438  -2.5084  -1.1207   0.0076
 HM7  OAG   O  O     0  -0.457  -3.7299  -1.1417   0.0224
 HM7  CA    C  CR6   0   0.026  -1.6991   0.0926  -0.0038
 HM7  C     C  C     0   0.130  -2.2144   1.3782  -0.0096
 HM7  SAE   S  S2    0  -0.049  -1.0636   2.6891  -0.0222
 HM7  CBU   C  CH3   0  -0.762   4.6943   1.8157   0.0080
 HM7  SBT   S  S2    0  -0.043   4.2198   0.0744  -0.0304
 HM7  OXT   O  OH1   0  -0.510  -3.5005   1.5839  -0.0073
 HM7  HBS1  H  HCH2  0   0.265   2.0996   0.8369  -0.8745
 HM7  HBS2  H  HCH2  0   0.265   2.1138   0.7958   0.8875
 HM7  HBR1  H  HCH2  0   0.270   2.1110  -1.6733  -0.9255
 HM7  HBR2  H  HCH2  0   0.270   2.1310  -1.7149   0.8212
 HM7  HAJ   H  HOH1  0   0.486  -0.4397  -4.1704  -0.0130
 HM7  HAE   H  HSH1  0   0.249  -1.9643   3.6817  -0.0312
 HM7  HBU1  H  HCH3  0   0.261   4.3079   2.3490  -0.8598
 HM7  HBU2  H  HCH3  0   0.261   4.3421   2.3012   0.9174
 HM7  HBU3  H  HCH3  0   0.274   5.7816   1.8624  -0.0123
 HM7  HXT   H  HOH1  0   0.508  -3.7465   2.5184  -0.0193

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
 HM7  CBS  CBR   single  1.520  0.020  1.520
 HM7  CBR  CAA   single  1.498  0.020  1.498
 HM7  CAA  NAB   double  1.281  0.020  1.281
 HM7  CAA  CAI   single  1.457  0.020  1.457
 HM7  NAB  CA    single  1.362  0.020  1.362
 HM7  CAI  OAJ   single  1.318  0.020  1.318
 HM7  CAI  NAH   double  1.286  0.020  1.286
 HM7  NAH  CAF   single  1.383  0.020  1.383
 HM7  CAF  OAG   double  1.222  0.020  1.222
 HM7  CAF  CA    single  1.458  0.020  1.458
 HM7  CA   C     double  1.385  0.020  1.385
 HM7  C    SAE   single  1.744  0.020  1.744
 HM7  C    OXT   single  1.302  0.020  1.302
 HM7  CBS  SBT   single  1.814  0.020  1.814
 HM7  CBU  SBT   single  1.805  0.020  1.805
 HM7  CBS  HBS1  single  0.970  0.020  1.090
 HM7  CBS  HBS2  single  0.970  0.020  1.090
 HM7  CBR  HBR1  single  0.970  0.020  1.090
 HM7  CBR  HBR2  single  0.970  0.020  1.090
 HM7  OAJ  HAJ   single  0.850  0.020  0.980
 HM7  SAE  HAE   single  1.200  0.020  1.300
 HM7  CBU  HBU1  single  0.970  0.020  1.090
 HM7  CBU  HBU2  single  0.970  0.020  1.090
 HM7  CBU  HBU3  single  0.970  0.020  1.090
 HM7  OXT  HXT   single  0.850  0.020  0.980

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
 HM7  HBS2  CBS  HBS1  107.80  3.000
 HM7  HBS2  CBS  SBT   109.44  3.000
 HM7  HBS1  CBS  SBT   109.30  3.000
 HM7  HBS2  CBS  CBR   110.60  3.000
 HM7  HBS1  CBS  CBR   110.71  3.000
 HM7  SBT   CBS  CBR   108.96  3.000
 HM7  HBR2  CBR  HBR1  105.92  3.000
 HM7  HBR2  CBR  CAA   109.32  3.000
 HM7  HBR1  CBR  CAA   109.17  3.000
 HM7  HBR2  CBR  CBS   109.91  3.000
 HM7  HBR1  CBR  CBS   109.89  3.000
 HM7  CAA   CBR  CBS   112.42  3.000
 HM7  CAI   CAA  NAB   117.67  3.000
 HM7  CAI   CAA  CBR   121.08  3.000
 HM7  NAB   CAA  CBR   121.24  3.000
 HM7  CA    NAB  CAA   120.97  3.000
 HM7  NAH   CAI  OAJ   120.48  3.000
 HM7  NAH   CAI  CAA   124.06  3.000
 HM7  OAJ   CAI  CAA   115.46  3.000
 HM7  HAJ   OAJ  CAI   109.75  3.000
 HM7  CAF   NAH  CAI   120.01  3.000
 HM7  CA    CAF  OAG   124.69  3.000
 HM7  CA    CAF  NAH   115.49  3.000
 HM7  OAG   CAF  NAH   119.82  3.000
 HM7  C     CA   CAF   124.45  3.000
 HM7  C     CA   NAB   113.74  3.000
 HM7  CAF   CA   NAB   121.80  3.000
 HM7  OXT   C    SAE   122.19  3.000
 HM7  OXT   C    CA    120.93  3.000
 HM7  SAE   C    CA    116.88  3.000
 HM7  HAE   SAE  C      96.50  3.000
 HM7  HBU3  CBU  HBU2  108.63  3.000
 HM7  HBU3  CBU  HBU1  108.58  3.000
 HM7  HBU2  CBU  HBU1  109.40  3.000
 HM7  HBU3  CBU  SBT   107.67  3.000
 HM7  HBU2  CBU  SBT   111.26  3.000
 HM7  HBU1  CBU  SBT   111.22  3.000
 HM7  CBU   SBT  CBS    99.59  3.000
 HM7  HXT   OXT  C     113.84  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
 HM7  Var_01  NAB   CAA  CBR  CBS    1.46  30.0  3
 HM7  Var_02  SAE   C    CA   NAB   -0.24  30.0  2
 HM7  Var_03  SBT   CBS  CBR  CAA  179.97  30.0  1
 HM7  Var_04  HBU1  CBU  SBT  CBS  -60.54  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
 HM7  plan-1  CBR  0.020
 HM7  plan-1  CAA  0.020
 HM7  plan-1  NAB  0.020
 HM7  plan-1  CAI  0.020
 HM7  plan-1  OAJ  0.020
 HM7  plan-1  NAH  0.020
 HM7  plan-1  CAF  0.020
 HM7  plan-1  OAG  0.020
 HM7  plan-1  CA   0.020
 HM7  plan-1  C    0.020

