# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:08:31 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 6-(3-carbamimidamidopropyl)-3,5-dihydroxypyrazine-2-carbothioic S-acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NCCCc1nc(C(S)=O)c(O)nc1O
#
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
 HM9  HM9  '6-(3-carbamimidamidopropyl)-3,5-dihydroxypyrazine-2-carbothioic S-acid'  L-peptide  31  18  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_HM9
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
 HM9  C     C  C     0   0.161  -3.5617  -1.2711  -0.2303
 HM9  SAE   S  S2    0  -0.183  -2.7885  -2.8124   0.2465
 HM9  CAC   C  CR6   0   0.048  -2.6608  -0.1239  -0.0500
 HM9  NAB   N  N     0  -0.367  -1.4459  -0.3931   0.4184
 HM9  CAF   C  CR6   0   0.497  -3.0064   1.2032  -0.3361
 HM9  OAG   O  OH1   0  -0.574  -4.1958   1.5144  -0.8114
 HM9  NAH   N  N     0  -0.444  -2.1411   2.1814  -0.1317
 HM9  CAI   C  CR6   0   0.449  -0.9521   1.8874   0.3367
 HM9  OAJ   O  OH1   0  -0.569  -0.1497   2.9248   0.5149
 HM9  CAA   C  CR6   0   0.107  -0.5674   0.5522   0.6250
 HM9  CBW   C  CH2   0  -0.567   0.8033   0.1906   1.1109
 HM9  CBX   C  CH2   0  -0.456   1.8406   0.1926  -0.0146
 HM9  CBY   C  CH2   0  -0.255   3.2087  -0.2385   0.4879
 HM9  NBZ   N  NH1   0  -0.631   4.1566  -0.2479  -0.6098
 HM9  CCA   C  C     0   0.517   5.4887  -0.5488  -0.4406
 HM9  NCC   N  N     0  -0.713   6.1214  -1.1242  -1.3968
 HM9  NCB   N  NH2   0  -0.826   6.0133  -0.2106   0.7833
 HM9  OXT   O  O     0  -0.365  -4.6899  -1.2089  -0.6453
 HM9  HAE   H  HSH1  0   0.238  -3.8618  -3.5566  -0.0504
 HM9  HAG   H  HOH1  0   0.485  -4.2443   2.4731  -0.9386
 HM9  HAJ   H  HOH1  0   0.498   0.6940   2.6703   0.9092
 HM9  HBW1  H  HCH2  0   0.259   1.1208   0.8558   1.9218
 HM9  HBW2  H  HCH2  0   0.284   0.7448  -0.8056   1.5515
 HM9  HBX1  H  HCH2  0   0.252   1.5064  -0.4847  -0.8057
 HM9  HBX2  H  HCH2  0   0.237   1.9252   1.1842  -0.4686
 HM9  HBY1  H  HCH2  0   0.230   3.5317   0.4653   1.2576
 HM9  HBY2  H  HCH2  0   0.225   3.1293  -1.2207   0.9714
 HM9  HBZ   H  HNH1  0   0.372   3.7972  -0.6804  -1.4482
 HM9  HCC   H  H     0   0.314   7.1080  -1.2043  -1.1798
 HM9  HCB1  H  HNH2  0   0.388   5.6183   0.5887   1.2531
 HM9  HCB2  H  HNH2  0   0.390   7.0192  -0.2167   0.8361

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
 HM9  C    SAE   single    1.789  0.020  1.789
 HM9  C    CAC   single    1.470  0.020  1.470
 HM9  C    OXT   double    1.204  0.020  1.204
 HM9  CAC  NAB   aromatic  1.330  0.020  1.330
 HM9  CAC  CAF   aromatic  1.401  0.020  1.401
 HM9  NAB  CAA   aromatic  1.307  0.020  1.307
 HM9  CAF  OAG   single    1.318  0.020  1.318
 HM9  CAF  NAH   aromatic  1.322  0.020  1.322
 HM9  NAH  CAI   aromatic  1.311  0.020  1.311
 HM9  CAI  OAJ   single    1.323  0.020  1.323
 HM9  CAI  CAA   aromatic  1.419  0.020  1.419
 HM9  CAA  CBW   single    1.499  0.020  1.499
 HM9  CBW  CBX   single    1.531  0.020  1.531
 HM9  CBX  CBY   single    1.520  0.020  1.520
 HM9  CBY  NBZ   single    1.450  0.020  1.450
 HM9  NBZ  CCA   single    1.376  0.020  1.376
 HM9  CCA  NCC   double    1.283  0.020  1.283
 HM9  CCA  NCB   single    1.374  0.020  1.374
 HM9  SAE  HAE   single    1.200  0.020  1.300
 HM9  OAG  HAG   single    0.850  0.020  0.980
 HM9  OAJ  HAJ   single    0.850  0.020  0.980
 HM9  CBW  HBW1  single    0.970  0.020  1.090
 HM9  CBW  HBW2  single    0.970  0.020  1.090
 HM9  CBX  HBX1  single    0.970  0.020  1.090
 HM9  CBX  HBX2  single    0.970  0.020  1.090
 HM9  CBY  HBY1  single    0.970  0.020  1.090
 HM9  CBY  HBY2  single    0.970  0.020  1.090
 HM9  NBZ  HBZ   single    0.890  0.020  1.040
 HM9  NCC  HCC   single    0.890  0.020  1.040
 HM9  NCB  HCB1  single    0.890  0.020  1.040
 HM9  NCB  HCB2  single    0.890  0.020  1.040

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
 HM9  OXT   C    CAC   125.20  3.000
 HM9  OXT   C    SAE   122.78  3.000
 HM9  CAC   C    SAE   112.01  3.000
 HM9  HAE   SAE  C      94.20  3.000
 HM9  CAF   CAC  NAB   119.28  3.000
 HM9  CAF   CAC  C     124.27  3.000
 HM9  NAB   CAC  C     116.44  3.000
 HM9  CAA   NAB  CAC   121.57  3.000
 HM9  NAH   CAF  OAG   118.15  3.000
 HM9  NAH   CAF  CAC   120.53  3.000
 HM9  OAG   CAF  CAC   121.32  3.000
 HM9  HAG   OAG  CAF   109.05  3.000
 HM9  CAI   NAH  CAF   118.88  3.000
 HM9  CAA   CAI  OAJ   123.08  3.000
 HM9  CAA   CAI  NAH   121.96  3.000
 HM9  OAJ   CAI  NAH   114.97  3.000
 HM9  HAJ   OAJ  CAI   112.22  3.000
 HM9  CBW   CAA  CAI   122.74  3.000
 HM9  CBW   CAA  NAB   119.44  3.000
 HM9  CAI   CAA  NAB   117.79  3.000
 HM9  HBW2  CBW  HBW1  105.73  3.000
 HM9  HBW2  CBW  CBX   109.54  3.000
 HM9  HBW1  CBW  CBX   110.30  3.000
 HM9  HBW2  CBW  CAA   107.60  3.000
 HM9  HBW1  CBW  CAA   111.01  3.000
 HM9  CBX   CBW  CAA   112.40  3.000
 HM9  HBX2  CBX  HBX1  106.55  3.000
 HM9  HBX2  CBX  CBY   108.95  3.000
 HM9  HBX1  CBX  CBY   109.79  3.000
 HM9  HBX2  CBX  CBW   111.03  3.000
 HM9  HBX1  CBX  CBW   108.90  3.000
 HM9  CBY   CBX  CBW   111.50  3.000
 HM9  HBY2  CBY  HBY1  106.72  3.000
 HM9  HBY2  CBY  NBZ   112.01  3.000
 HM9  HBY1  CBY  NBZ   110.14  3.000
 HM9  HBY2  CBY  CBX   109.53  3.000
 HM9  HBY1  CBY  CBX   108.46  3.000
 HM9  NBZ   CBY  CBX   109.87  3.000
 HM9  HBZ   NBZ  CCA   110.67  3.000
 HM9  HBZ   NBZ  CBY   113.49  3.000
 HM9  CCA   NBZ  CBY   122.76  3.000
 HM9  NCB   CCA  NCC   125.87  3.000
 HM9  NCB   CCA  NBZ   115.17  3.000
 HM9  NCC   CCA  NBZ   118.94  3.000
 HM9  HCC   NCC  CCA   110.86  3.000
 HM9  HCB2  NCB  HCB1  111.82  3.000
 HM9  HCB2  NCB  CCA   115.25  3.000
 HM9  HCB1  NCB  CCA   117.44  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
 HM9  CONST_01  CAI   CAA  NAB  CAC     0.00   0.0  0
 HM9  CONST_02  CAI   NAH  CAF  CAC     0.00   0.0  0
 HM9  CONST_03  NAH   CAF  CAC  NAB     0.00   0.0  0
 HM9  CONST_04  NAH   CAI  CAA  NAB     0.00   0.0  0
 HM9  CONST_05  CAA   NAB  CAC  CAF     0.00   0.0  0
 HM9  CONST_06  CAA   CAI  NAH  CAF     0.00   0.0  0
 HM9  CONST_07  CAA   NAB  CAC  C     180.00   0.0  0
 HM9  CONST_08  NAH   CAF  CAC  C     180.00   0.0  0
 HM9  CONST_09  CBW   CAA  NAB  CAC   180.00   0.0  0
 HM9  CONST_10  OAG   CAF  CAC  NAB   180.00   0.0  0
 HM9  CONST_11  OAJ   CAI  CAA  NAB   180.00   0.0  0
 HM9  CONST_12  OAJ   CAI  NAH  CAF   180.00   0.0  0
 HM9  CONST_13  CAI   NAH  CAF  OAG   180.00   0.0  0
 HM9  CONST_14  CBW   CAA  CAI  NAH   180.00   0.0  0
 HM9  CONST_17  HCC   NCC  CCA  NBZ   180.00   0.0  0
 HM9  CONST_19  HCB2  NCB  CCA  NBZ   180.00   0.0  0
 HM9  CONST_20  HBZ   NBZ  CCA  NCC     0.00   0.0  0
 HM9  Var_01    NAB   CAC  C    SAE     0.29  30.0  2
 HM9  Var_02    CBX   CBW  CAA  NAB   100.95  30.0  2
 HM9  Var_03    CBY   CBX  CBW  CAA  -177.38  30.0  3
 HM9  Var_04    NBZ   CBY  CBX  CBW   178.95  30.0  3
 HM9  Var_05    CCA   NBZ  CBY  CBX   177.41  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
 HM9  plan-1  C     0.020
 HM9  plan-1  CAC   0.020
 HM9  plan-1  NAB   0.020
 HM9  plan-1  CAF   0.020
 HM9  plan-1  OAG   0.020
 HM9  plan-1  NAH   0.020
 HM9  plan-1  CAI   0.020
 HM9  plan-1  OAJ   0.020
 HM9  plan-1  CAA   0.020
 HM9  plan-1  CBW   0.020
 HM9  plan-2  CBY   0.020
 HM9  plan-2  NBZ   0.020
 HM9  plan-2  CCA   0.020
 HM9  plan-2  NCC   0.020
 HM9  plan-2  NCB   0.020
 HM9  plan-2  HBZ   0.020
 HM9  plan-2  HCC   0.020
 HM9  plan-2  HCB1  0.020
 HM9  plan-2  HCB2  0.020
 HM9  plan-3  C     0.020
 HM9  plan-3  SAE   0.020
 HM9  plan-3  CAC   0.020
 HM9  plan-3  OXT   0.020

