# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 00:36:30 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (2R,3R,4S)-3-(acetylamino)-4-carbamimidamido-2-[methyl(propyl)carbamoyl]-3,4-dihydro-2H-pyran-6-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN(C)C(=O)[C@@H]1OC(=C[C@H](NC(N)=N)[C@H]1NC(C)=O)C(O)=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
 G20  G20  '(2R,3R,4S)-3-(acetylamino)-4-carbamimidamido-2-[methyl(propyl)carbamoyl]-3,4-dihydro-2H-pyran-6-carboxylic acid (non-preferred name)'  L-saccharide  46  24  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G20
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
 G20  C1    C  C      0   0.373   3.3643  -0.0051  -2.1205
 G20  O1A   O  O      0  -0.589   3.5078  -0.0787  -3.3543
 G20  O1B   O  OC    -1  -0.594   4.2453   0.1432  -1.2585
 G20  C2    C  C      0   0.165   1.9324  -0.1135  -1.6056
 G20  C3    C  C1     0  -0.361   0.8752  -0.2969  -2.3968
 G20  C4    C  CH1    0  -0.071  -0.5397  -0.3313  -1.8980
 G20  C5    C  CH1    0  -0.122  -0.5915   0.1402  -0.4473
 G20  N5    N  NH1    0  -0.634  -1.8363  -0.2472   0.1604
 G20  C10   C  C      0   0.527  -2.5455   0.5302   1.0040
 G20  O10   O  O      0  -0.491  -2.1934   1.6543   1.3269
 G20  C11   C  CH3    0  -0.785  -3.8055  -0.0986   1.5430
 G20  C6    C  CH1    0  -0.050   0.6187  -0.4446   0.3041
 G20  O6    O  O2     0  -0.472   1.8321  -0.0044  -0.2575
 G20  C7    C  C      0   0.530   0.6185   0.0544   1.7480
 G20  O7    O  O      0  -0.492   1.1339   1.1357   1.9899
 G20  N8    N  NT     0  -0.449   0.0029  -0.6775   2.6941
 G20  C81   C  CH3    0  -0.543  -0.5216  -2.0201   2.5540
 G20  C9    C  CH2    0  -0.295  -0.1340  -0.1069   4.0266
 G20  C91   C  CH2    0  -0.428   1.0585  -0.3848   4.9336
 G20  C92   C  CH3    0  -0.668   0.8204   0.1425   6.3414
 G20  NE    N  NH1    0  -0.642  -1.4330   0.4754  -2.6977
 G20  CZ    C  C      0   0.559  -1.9698  -0.0230  -3.8596
 G20  NH1   N  N      0  -0.712  -1.8653  -1.2663  -4.1511
 G20  NH2   N  NH2    0  -0.843  -2.5741   0.9436  -4.6324
 G20  H3    H  H      0   0.250   1.0359  -0.4053  -3.4598
 G20  H4    H  HCH1   0   0.266  -0.9169  -1.3568  -1.9539
 G20  H5    H  HCH1   0   0.280  -0.5146   1.2304  -0.4084
 G20  HN5   H  HNH1   0   0.402  -2.1986  -1.1595  -0.0681
 G20  H111  H  HCH3   0   0.270  -4.6328   0.6040   1.4549
 G20  H112  H  HCH3   0   0.251  -4.0780  -1.0256   1.0423
 G20  H113  H  HCH3   0   0.266  -3.6730  -0.3117   2.6051
 G20  H6    H  HCH1   0   0.262   0.5784  -1.5361   0.2245
 G20  H811  H  HCH3   0   0.260  -0.2374  -2.4845   1.6168
 G20  H812  H  HCH3   0   0.255  -0.1358  -2.6501   3.3567
 G20  H813  H  HCH3   0   0.244  -1.6111  -2.0250   2.6178
 G20  H91   H  HCH2   0   0.240  -1.0391  -0.5303   4.4695
 G20  H92   H  HCH2   0   0.249  -0.3015   0.9665   3.9410
 G20  H911  H  HCH2   0   0.229   1.9521   0.0760   4.5074
 G20  H912  H  HCH2   0   0.222   1.2476  -1.4611   4.9706
 G20  H921  H  HCH3   0   0.234   1.6803  -0.0441   6.9843
 G20  H922  H  HCH3   0   0.222   0.6384   1.2187   6.3370
 G20  H923  H  HCH3   0   0.221  -0.0460  -0.3360   6.8018
 G20  HNE   H  HNH1   0   0.378  -1.2077   1.4596  -2.7113
 G20  HN1   H  H      0   0.318  -2.3886  -1.4824  -4.9913
 G20  HN21  H  HNH2   0   0.386  -3.1840   0.5983  -5.3556
 G20  HN22  H  HNH2   0   0.384  -2.9754   1.7278  -4.1415

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
 G20  C1   O1A   deloc   1.244  0.020  1.244
 G20  C1   O1B   deloc   1.241  0.020  1.241
 G20  C1   C2    single  1.526  0.020  1.526
 G20  C2   C3    double  1.333  0.020  1.333
 G20  C2   O6    single  1.356  0.020  1.356
 G20  C3   C4    single  1.501  0.020  1.501
 G20  C3   H3    single  0.930  0.020  1.080
 G20  C4   C5    single  1.526  0.020  1.526
 G20  C4   NE    single  1.445  0.020  1.445
 G20  C4   H4    single  0.970  0.020  1.090
 G20  C5   N5    single  1.438  0.020  1.438
 G20  C5   C6    single  1.540  0.020  1.540
 G20  C5   H5    single  0.970  0.020  1.090
 G20  N5   C10   single  1.349  0.020  1.349
 G20  N5   HN5   single  0.860  0.020  1.020
 G20  C10  O10   double  1.221  0.020  1.221
 G20  C10  C11   single  1.508  0.020  1.508
 G20  C11  H111  single  0.970  0.020  1.090
 G20  C11  H112  single  0.970  0.020  1.090
 G20  C11  H113  single  0.970  0.020  1.090
 G20  C6   O6    single  1.408  0.020  1.408
 G20  C6   C7    single  1.528  0.020  1.528
 G20  C6   H6    single  0.970  0.020  1.090
 G20  C7   O7    double  1.222  0.020  1.222
 G20  C7   N8    single  1.345  0.020  1.345
 G20  N8   C81   single  1.448  0.020  1.448
 G20  N8   C9    single  1.456  0.020  1.456
 G20  C81  H811  single  0.970  0.020  1.090
 G20  C81  H812  single  0.970  0.020  1.090
 G20  C81  H813  single  0.970  0.020  1.090
 G20  C9   C91   single  1.524  0.020  1.524
 G20  C9   H91   single  0.970  0.020  1.090
 G20  C9   H92   single  0.970  0.020  1.090
 G20  C91  C92   single  1.522  0.020  1.522
 G20  C91  H911  single  0.970  0.020  1.090
 G20  C91  H912  single  0.970  0.020  1.090
 G20  C92  H921  single  0.970  0.020  1.090
 G20  C92  H922  single  0.970  0.020  1.090
 G20  C92  H923  single  0.970  0.020  1.090
 G20  NE   CZ    single  1.374  0.020  1.374
 G20  NE   HNE   single  0.890  0.020  1.040
 G20  CZ   NH1   double  1.281  0.020  1.281
 G20  CZ   NH2   single  1.377  0.020  1.377
 G20  NH1  HN1   single  0.890  0.020  1.040
 G20  NH2  HN21  single  0.890  0.020  1.040
 G20  NH2  HN22  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
 G20  C2    C1   O1B   116.12  3.000
 G20  C2    C1   O1A   116.03  3.000
 G20  O1B   C1   O1A   127.86  3.000
 G20  O6    C2   C3    122.85  3.000
 G20  O6    C2   C1    113.53  3.000
 G20  C3    C2   C1    123.63  3.000
 G20  H3    C3   C4    117.71  3.000
 G20  H3    C3   C2    118.67  3.000
 G20  C4    C3   C2    123.61  3.000
 G20  H4    C4   NE    106.37  3.000
 G20  H4    C4   C5    109.05  3.000
 G20  NE    C4   C5    109.42  3.000
 G20  H4    C4   C3    109.24  3.000
 G20  NE    C4   C3    112.72  3.000
 G20  C5    C4   C3    109.93  3.000
 G20  H5    C5   C6    107.81  3.000
 G20  H5    C5   N5    108.32  3.000
 G20  C6    C5   N5    111.82  3.000
 G20  H5    C5   C4    109.84  3.000
 G20  C6    C5   C4    108.65  3.000
 G20  N5    C5   C4    110.35  3.000
 G20  HN5   N5   C10   118.33  3.000
 G20  HN5   N5   C5    117.33  3.000
 G20  C10   N5   C5    124.34  3.000
 G20  C11   C10  O10   122.02  3.000
 G20  C11   C10  N5    115.00  3.000
 G20  O10   C10  N5    122.97  3.000
 G20  H113  C11  H112  108.17  3.000
 G20  H113  C11  H111  107.27  3.000
 G20  H112  C11  H111  108.79  3.000
 G20  H113  C11  C10   109.14  3.000
 G20  H112  C11  C10   113.58  3.000
 G20  H111  C11  C10   109.69  3.000
 G20  H6    C6   C7    113.22  3.000
 G20  H6    C6   O6    108.33  3.000
 G20  C7    C6   O6    105.96  3.000
 G20  H6    C6   C5    108.31  3.000
 G20  C7    C6   C5    109.69  3.000
 G20  O6    C6   C5    111.35  3.000
 G20  C6    O6   C2    115.79  3.000
 G20  N8    C7   O7    122.36  3.000
 G20  N8    C7   C6    119.15  3.000
 G20  O7    C7   C6    118.43  3.000
 G20  C9    N8   C81   114.70  3.000
 G20  C9    N8   C7    118.26  3.000
 G20  C81   N8   C7    127.02  3.000
 G20  H813  C81  H812  107.90  3.000
 G20  H813  C81  H811  108.08  3.000
 G20  H812  C81  H811  107.22  3.000
 G20  H813  C81  N8    111.11  3.000
 G20  H812  C81  N8    109.64  3.000
 G20  H811  C81  N8    112.70  3.000
 G20  H92   C9   H91   106.62  3.000
 G20  H92   C9   C91   110.29  3.000
 G20  H91   C9   C91   109.65  3.000
 G20  H92   C9   N8    109.18  3.000
 G20  H91   C9   N8    107.27  3.000
 G20  C91   C9   N8    113.56  3.000
 G20  H912  C91  H911  106.68  3.000
 G20  H912  C91  C92   109.68  3.000
 G20  H911  C91  C92   110.05  3.000
 G20  H912  C91  C9    109.58  3.000
 G20  H911  C91  C9    109.34  3.000
 G20  C92   C91  C9    111.40  3.000
 G20  H923  C92  H922  107.55  3.000
 G20  H923  C92  H921  107.60  3.000
 G20  H922  C92  H921  107.62  3.000
 G20  H923  C92  C91   111.25  3.000
 G20  H922  C92  C91   111.35  3.000
 G20  H921  C92  C91   111.28  3.000
 G20  HNE   NE   CZ    115.43  3.000
 G20  HNE   NE   C4    114.43  3.000
 G20  CZ    NE   C4    120.48  3.000
 G20  NH2   CZ   NH1   126.10  3.000
 G20  NH2   CZ   NE    113.05  3.000
 G20  NH1   CZ   NE    120.84  3.000
 G20  HN1   NH1  CZ    110.70  3.000
 G20  HN22  NH2  HN21  112.03  3.000
 G20  HN22  NH2  CZ    116.56  3.000
 G20  HN21  NH2  CZ    115.34  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
 G20  CONST_01  O10   C10  N5   C5      0.00   0.0  0
 G20  CONST_02  C11   C10  N5   C5    180.00   0.0  0
 G20  CONST_03  C81   N8   C7   C6      0.00   0.0  0
 G20  CONST_04  C9    N8   C7   C6    180.00   0.0  0
 G20  CONST_05  NH1   CZ   NE   C4      0.00   0.0  0
 G20  CONST_06  NH2   CZ   NE   C4    180.00   0.0  0
 G20  CONST_07  C81   N8   C7   O7    180.00   0.0  0
 G20  CONST_08  C9    N8   C7   O7      0.00   0.0  0
 G20  CONST_09  HN5   N5   C10  O10   180.00   0.0  0
 G20  CONST_10  HN1   NH1  CZ   NE    180.00   0.0  0
 G20  Var_01    O6    C2   C3   C4      3.30  30.0  1
 G20  Var_02    C3    C2   C1   O1A     1.01  30.0  2
 G20  Var_03    C91   C9   N8   C7    -87.91  30.0  3
 G20  Var_04    C92   C91  C9   N8   -175.77  30.0  3
 G20  Var_05    H111  C11  C10  N5   -132.68  30.0  3
 G20  Var_06    H811  C81  N8   C7      9.09  30.0  3
 G20  Var_07    H921  C92  C91  C9   -179.15  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
 G20  chir_01  C4  C3  C5  NE  negativ
 G20  chir_02  C5  N5  C6  C4  negativ
 G20  chir_03  C6  O6  C7  C5  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
 G20  plan-1  C5    0.020
 G20  plan-1  N5    0.020
 G20  plan-1  C10   0.020
 G20  plan-1  O10   0.020
 G20  plan-1  C11   0.020
 G20  plan-1  HN5   0.020
 G20  plan-2  C6    0.020
 G20  plan-2  C7    0.020
 G20  plan-2  O7    0.020
 G20  plan-2  N8    0.020
 G20  plan-2  C81   0.020
 G20  plan-2  C9    0.020
 G20  plan-3  C4    0.020
 G20  plan-3  NE    0.020
 G20  plan-3  CZ    0.020
 G20  plan-3  NH1   0.020
 G20  plan-3  NH2   0.020
 G20  plan-3  HNE   0.020
 G20  plan-3  HN1   0.020
 G20  plan-3  HN21  0.020
 G20  plan-3  HN22  0.020
 G20  plan-4  C1    0.020
 G20  plan-4  O1A   0.020
 G20  plan-4  O1B   0.020
 G20  plan-4  C2    0.020

