# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 03:29:00 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (3Z)-4-{[(4-amino-2-methylpyrimidin-5-yl)methyl](formyl)amino}-3-sulfanylpent-3-en-1-yl trihydrogen diphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CN(C=O)C(/C)=C(\S)CCO[P](O)(=O)O[P](O)(O)=O)c(N)n1
#
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
 G8G  G8G  '(3Z)-4-{[(4-amino-2-methylpyrimidin-5-yl)methyl](formyl)amino}-3-sulfanylpent-3-en-1-yl trihydrogen diphosphate'  ligand  47  27  .  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_G8G
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
 G8G  S01  S  S2    0  -0.162  -1.3014   2.4406  -1.8204
 G8G  C02  C  C     0  -0.167  -1.2589   1.1607  -0.6039
 G8G  C03  C  CH2   0  -0.545  -0.0703   0.2560  -0.7791
 G8G  C04  C  CH2   0  -0.146   1.1469   0.8448  -0.0880
 G8G  O05  O  O2    0  -0.575   2.2789   0.0150  -0.4045
 G8G  P06  P  P     0   1.473   3.5481  -0.0274   0.5452
 G8G  O07  O  O2    0  -0.682   4.3274  -1.2013  -0.2498
 G8G  P08  P  P     0   1.462   5.9174  -1.5180  -0.1889
 G8G  O09  O  O     0  -0.687   6.5523  -1.2466   1.1079
 G8G  O10  O  OH1   0  -0.718   5.8175  -3.0147  -0.7029
 G8G  O11  O  OH1   0  -0.724   6.5633  -0.6314  -1.3366
 G8G  O12  O  O     0  -0.675   3.3259  -0.2671   1.9766
 G8G  O13  O  OH1   0  -0.735   4.3931   1.2996   0.3132
 G8G  C14  C  C     0   0.302  -2.1592   1.0076   0.3720
 G8G  C15  C  CH3   0  -0.717  -2.0744  -0.0512   1.4331
 G8G  N16  N  NT    0  -0.483  -3.3217   1.8306   0.4033
 G8G  C17  C  C1    0   0.248  -3.4769   2.7474   1.3813
 G8G  O18  O  O     0  -0.466  -2.6440   3.0089   2.2252
 G8G  C19  C  CH2   0  -0.420  -4.3836   1.5566  -0.5627
 G8G  C20  C  CR6   0  -0.046  -4.8142   0.1256  -0.5302
 G8G  C21  C  CR6   0   0.468  -5.5410  -0.4445   0.5366
 G8G  N22  N  NH2   0  -0.824  -5.9274   0.2726   1.6058
 G8G  N23  N  N     0  -0.466  -5.8404  -1.7455   0.5390
 G8G  C24  C  CR6   0   0.355  -5.4395  -2.4851  -0.4848
 G8G  C25  C  CH3   0  -0.729  -5.8121  -3.9342  -0.4720
 G8G  N26  N  N     0  -0.445  -4.7560  -2.0457  -1.5358
 G8G  C27  C  CR16  0  -0.064  -4.4577  -0.7479  -1.5306
 G8G  H1   H  HSH1  0   0.244  -2.0542   3.3332  -1.1677
 G8G  H2   H  HCH2  0   0.280  -0.2828  -0.7363  -0.3809
 G8G  H3   H  HCH2  0   0.281   0.1430   0.1272  -1.8439
 G8G  H4   H  HCH2  0   0.255   1.3398   1.8598  -0.4395
 G8G  H5   H  HCH2  0   0.248   0.9894   0.8792   0.9924
 G8G  H6   H  HOH1  0   0.513   6.6629  -3.4846  -0.7363
 G8G  H7   H  HOH1  0   0.504   6.2578  -0.7982  -2.2393
 G8G  H8   H  HOH1  0   0.502   4.5034   1.5979  -0.6005
 G8G  H9   H  HCH3  0   0.253  -2.6121  -0.9520   1.1272
 G8G  H10  H  HCH3  0   0.249  -1.0490  -0.3373   1.6577
 G8G  H11  H  HCH3  0   0.260  -2.5242   0.2941   2.3621
 G8G  H12  H  H     0   0.203  -4.4515   3.2586   1.3313
 G8G  H13  H  HCH2  0   0.281  -5.2111   2.2399  -0.3531
 G8G  H14  H  HCH2  0   0.278  -4.0377   1.7997  -1.5701
 G8G  H15  H  HNH2  0   0.401  -5.9574   1.2761   1.5742
 G8G  H16  H  HNH2  0   0.400  -6.5546  -0.1613   2.2628
 G8G  H17  H  HCH3  0   0.258  -6.6636  -4.1058  -1.1340
 G8G  H18  H  HCH3  0   0.250  -4.9912  -4.5489  -0.8382
 G8G  H19  H  HCH3  0   0.247  -6.0911  -4.2628   0.5261
 G8G  H20  H  HCR6  0   0.262  -3.8907  -0.3764  -2.3804

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
 G8G  C25  C24  single    1.496  0.020  1.496
 G8G  N26  C24  aromatic  1.328  0.020  1.328
 G8G  N26  C27  aromatic  1.332  0.020  1.332
 G8G  C24  N23  aromatic  1.325  0.020  1.325
 G8G  C27  C20  aromatic  1.375  0.020  1.375
 G8G  N23  C21  aromatic  1.335  0.020  1.335
 G8G  C20  C21  aromatic  1.411  0.020  1.411
 G8G  C20  C19  single    1.495  0.020  1.495
 G8G  C21  N22  single    1.344  0.020  1.344
 G8G  C15  C14  single    1.501  0.020  1.501
 G8G  C19  N16  single    1.462  0.020  1.462
 G8G  C14  N16  single    1.425  0.020  1.425
 G8G  C14  C02  double    1.337  0.020  1.337
 G8G  N16  C17  single    1.349  0.020  1.349
 G8G  O12  P06  double    1.468  0.020  1.468
 G8G  O05  P06  single    1.586  0.020  1.586
 G8G  O05  C04  single    1.439  0.020  1.439
 G8G  C03  C02  single    1.504  0.020  1.504
 G8G  C03  C04  single    1.519  0.020  1.519
 G8G  O13  P06  single    1.590  0.020  1.590
 G8G  C02  S01  single    1.766  0.020  1.766
 G8G  P06  O07  single    1.618  0.020  1.618
 G8G  C17  O18  double    1.214  0.020  1.214
 G8G  O07  P08  single    1.622  0.020  1.622
 G8G  O09  P08  double    1.469  0.020  1.469
 G8G  P08  O10  single    1.586  0.020  1.586
 G8G  P08  O11  single    1.588  0.020  1.588
 G8G  S01  H1   single    1.200  0.020  1.300
 G8G  C03  H2   single    0.970  0.020  1.090
 G8G  C03  H3   single    0.970  0.020  1.090
 G8G  C04  H4   single    0.970  0.020  1.090
 G8G  C04  H5   single    0.970  0.020  1.090
 G8G  O10  H6   single    0.850  0.020  0.980
 G8G  O11  H7   single    0.850  0.020  0.980
 G8G  O13  H8   single    0.850  0.020  0.980
 G8G  C15  H9   single    0.970  0.020  1.090
 G8G  C15  H10  single    0.970  0.020  1.090
 G8G  C15  H11  single    0.970  0.020  1.090
 G8G  C17  H12  single    0.930  0.020  1.080
 G8G  C19  H13  single    0.970  0.020  1.090
 G8G  C19  H14  single    0.970  0.020  1.090
 G8G  N22  H15  single    0.890  0.020  1.040
 G8G  N22  H16  single    0.890  0.020  1.040
 G8G  C25  H17  single    0.970  0.020  1.090
 G8G  C25  H18  single    0.970  0.020  1.090
 G8G  C25  H19  single    0.970  0.020  1.090
 G8G  C27  H20  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
 G8G  H1   S01  C02   99.26  3.000
 G8G  C14  C02  C03  123.26  3.000
 G8G  C03  C02  S01  112.00  3.000
 G8G  C14  C02  S01  124.73  3.000
 G8G  H3   C03  H2   106.65  3.000
 G8G  H3   C03  C04  109.42  3.000
 G8G  H2   C03  C04  110.06  3.000
 G8G  H3   C03  C02  109.78  3.000
 G8G  H2   C03  C02  110.55  3.000
 G8G  C04  C03  C02  110.31  3.000
 G8G  H5   C04  H4   108.34  3.000
 G8G  H5   C04  O05  110.44  3.000
 G8G  H4   C04  O05  109.06  3.000
 G8G  H5   C04  C03  110.29  3.000
 G8G  H4   C04  C03  110.84  3.000
 G8G  O05  C04  C03  107.87  3.000
 G8G  P06  O05  C04  120.89  3.000
 G8G  O13  P06  O12  111.03  3.000
 G8G  O13  P06  O07  106.13  3.000
 G8G  O12  P06  O07  115.69  3.000
 G8G  O07  P06  O05   96.35  3.000
 G8G  O13  P06  O05  108.40  3.000
 G8G  O12  P06  O05  117.84  3.000
 G8G  P08  O07  P06  126.53  3.000
 G8G  O11  P08  O10  108.57  3.000
 G8G  O11  P08  O09  111.05  3.000
 G8G  O10  P08  O09  119.19  3.000
 G8G  O11  P08  O07  105.22  3.000
 G8G  O10  P08  O07   96.33  3.000
 G8G  O09  P08  O07  114.87  3.000
 G8G  H6   O10  P08  114.48  3.000
 G8G  H7   O11  P08  116.73  3.000
 G8G  H8   O13  P06  117.11  3.000
 G8G  N16  C14  C15  115.97  3.000
 G8G  N16  C14  C02  119.97  3.000
 G8G  C15  C14  C02  123.97  3.000
 G8G  H11  C15  H10  107.26  3.000
 G8G  H11  C15  H9   107.28  3.000
 G8G  H10  C15  H9   107.75  3.000
 G8G  H11  C15  C14  110.86  3.000
 G8G  H10  C15  C14  112.62  3.000
 G8G  H9   C15  C14  110.84  3.000
 G8G  C19  N16  C17  121.52  3.000
 G8G  C17  N16  C14  120.15  3.000
 G8G  C19  N16  C14  118.04  3.000
 G8G  H12  C17  O18  122.57  3.000
 G8G  H12  C17  N16  112.59  3.000
 G8G  O18  C17  N16  124.83  3.000
 G8G  H14  C19  H13  106.11  3.000
 G8G  H14  C19  C20  108.92  3.000
 G8G  H13  C19  C20  112.09  3.000
 G8G  H14  C19  N16  109.73  3.000
 G8G  H13  C19  N16  107.82  3.000
 G8G  C20  C19  N16  111.99  3.000
 G8G  C27  C20  C21  115.27  3.000
 G8G  C21  C20  C19  123.47  3.000
 G8G  C27  C20  C19  121.18  3.000
 G8G  N23  C21  N22  117.00  3.000
 G8G  N22  C21  C20  122.26  3.000
 G8G  N23  C21  C20  120.70  3.000
 G8G  H16  N22  H15  115.62  3.000
 G8G  H16  N22  C21  117.92  3.000
 G8G  H15  N22  C21  121.11  3.000
 G8G  C24  N23  C21  118.34  3.000
 G8G  N26  C24  C25  117.08  3.000
 G8G  N26  C24  N23  125.61  3.000
 G8G  C25  C24  N23  117.29  3.000
 G8G  H19  C25  H18  109.36  3.000
 G8G  H19  C25  H17  107.99  3.000
 G8G  H18  C25  H17  107.17  3.000
 G8G  H19  C25  C24  111.37  3.000
 G8G  H18  C25  C24  110.86  3.000
 G8G  H17  C25  C24  109.95  3.000
 G8G  C27  N26  C24  115.75  3.000
 G8G  H20  C27  N26  116.54  3.000
 G8G  H20  C27  C20  119.13  3.000
 G8G  N26  C27  C20  124.32  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
 G8G  CONST_01  C24  N26  C27  C20     0.00   0.0  0
 G8G  CONST_02  C24  N23  C21  C20     0.00   0.0  0
 G8G  CONST_03  N26  C24  N23  C21     0.00   0.0  0
 G8G  CONST_04  N26  C27  C20  C21     0.00   0.0  0
 G8G  CONST_05  C27  N26  C24  N23     0.00   0.0  0
 G8G  CONST_06  C27  C20  C21  N23     0.00   0.0  0
 G8G  CONST_07  N26  C27  C20  C19   180.00   0.0  0
 G8G  CONST_08  N23  C21  C20  C19   180.00   0.0  0
 G8G  CONST_09  C25  C24  N23  C21   180.00   0.0  0
 G8G  CONST_10  C24  N23  C21  N22   180.00   0.0  0
 G8G  CONST_11  C27  C20  C21  N22   180.00   0.0  0
 G8G  CONST_12  C27  N26  C24  C25   180.00   0.0  0
 G8G  CONST_13  H20  C27  C20  C21   180.00   0.0  0
 G8G  CONST_15  H16  N22  C21  C20   180.00   0.0  0
 G8G  CONST_16  O18  C17  N16  C14     0.00   0.0  0
 G8G  CONST_17  C19  N16  C17  O18   180.00   0.0  0
 G8G  Var_01    C27  C20  C19  N16  -105.93  30.0  2
 G8G  Var_02    H17  C25  C24  N23   101.30  30.0  2
 G8G  Var_03    C20  C19  N16  C14    52.91  30.0  2
 G8G  Var_04    C15  C14  C02  S01  -177.24   0.0  2
 G8G  Var_05    C04  C03  C02  S01    84.83  30.0  1
 G8G  Var_06    C19  N16  C14  C02    74.33  30.0  2
 G8G  Var_07    O05  C04  C03  C02  -174.08  30.0  3
 G8G  Var_08    O12  P06  O05  C04    50.84  30.0  3
 G8G  Var_09    O09  P08  O07  P06    33.20  30.0  3
 G8G  Var_10    H9   C15  C14  C02   -91.68  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
 G8G  chir_01  P06  O05  O13  O07  both

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
 G8G  plan-1  C19  0.020
 G8G  plan-1  C20  0.020
 G8G  plan-1  C21  0.020
 G8G  plan-1  N22  0.020
 G8G  plan-1  N23  0.020
 G8G  plan-1  C24  0.020
 G8G  plan-1  C25  0.020
 G8G  plan-1  N26  0.020
 G8G  plan-1  C27  0.020
 G8G  plan-1  H20  0.020
 G8G  plan-2  C14  0.020
 G8G  plan-2  N16  0.020
 G8G  plan-2  C17  0.020
 G8G  plan-2  O18  0.020
 G8G  plan-2  C19  0.020
 G8G  plan-2  H12  0.020
 G8G  plan-3  C21  0.020
 G8G  plan-3  N22  0.020
 G8G  plan-3  H15  0.020
 G8G  plan-3  H16  0.020
 G8G  plan-4  S01  0.020
 G8G  plan-4  C02  0.020
 G8G  plan-4  C03  0.020
 G8G  plan-4  C14  0.020
 G8G  plan-4  C15  0.020
 G8G  plan-4  N16  0.020

