# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 22:54:21 2021
#   Inital geometry file: a 132 line input string
#   Ligand name: 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=C(NC=O)C(=O)N1)C[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
#
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
 GKS  GKS  1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol  ligand  51  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GKS
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
 GKS  PG   P  P     0   1.373  -10.9310  1.2656  67.6867
 GKS  O1G  O  O     0  -0.672  -11.5867  0.1024  68.2990
 GKS  O2G  O  OH1   0  -0.731  -10.2811  2.3562  68.6332
 GKS  O3G  O  OH1   0  -0.635   -9.7976  0.9955  66.6162
 GKS  O3B  O  O2    0  -0.721  -11.9427  2.2187  66.8285
 GKS  PB   P  P     0   1.430  -13.1914  3.0975  67.3041
 GKS  O1B  O  O     0  -0.636  -14.2557  3.1357  66.2861
 GKS  O2B  O  OH1   0  -0.591  -13.5680  2.6105  68.7554
 GKS  O3A  O  O2    0  -0.661  -12.4521  4.4886  67.5866
 GKS  PA   P  P     0   1.449  -12.9794  5.9867  67.9530
 GKS  O1A  O  OH1   0  -0.666  -14.4032  5.6238  68.5507
 GKS  O2A  O  O     0  -0.739  -11.9996  6.6910  68.7862
 GKS  O5'  O  O2    0  -0.550  -13.1930  6.7007  66.5615
 GKS  C5'  C  CH2   0  -0.295  -14.3044  6.5236  65.6659
 GKS  C4'  C  CR15  0   0.108  -13.8005  6.4057  64.2480
 GKS  O4'  O  O     0  -0.504  -13.1082  7.5783  63.8704
 GKS  C3'  C  CR15  0  -0.069  -12.8475  5.2251  63.9765
 GKS  O3'  O  OH1   0  -0.725  -13.4963  4.0353  63.6274
 GKS  C2'  C  CH2   0  -0.481  -12.0027  5.7809  62.8440
 GKS  C1'  C  CR15  0   0.001  -11.8816  7.2517  63.2221
 GKS  C9   C  CH2   0  -0.502  -10.7212  7.5550  64.1761
 GKS  C4   C  CR6   0   0.230   -9.3966  7.2441  63.5574
 GKS  N3   N  N     0  -0.593   -9.1116  7.9484  62.4427
 GKS  C2   C  CR6   0   0.703   -7.9774  7.6983  61.8346
 GKS  N2   N  NH2   0  -0.817   -7.6604  8.3560  60.7182
 GKS  N1   N  NR16  0  -0.727   -7.1024  6.7701  62.2909
 GKS  C6   C  CR6   0   0.505   -7.3130  6.0055  63.4309
 GKS  O6   O  O     0  -0.421   -6.4784  5.1890  63.7887
 GKS  C5   C  CR6   0   0.034   -8.5599  6.2954  64.0841
 GKS  N7   N  NH1   0  -0.718   -8.8641  5.5804  65.2582
 GKS  C8   C  C1    0   0.240   -9.2819  4.3009  65.2405
 GKS  O8   O  O     0  -0.325   -9.5615  3.6695  64.2412
 GKS  H1   H  HOH1  0   0.515   -9.8745  2.0045  69.4384
 GKS  H2   H  HOH1  0   0.525   -9.9248  0.2019  66.0776
 GKS  H3   H  HOH1  0   0.554  -14.3172  1.9981  68.8098
 GKS  H4   H  HOH1  0   0.523  -14.8707  6.3498  68.9905
 GKS  H5   H  HCH2  0   0.223  -14.9553  7.3921  65.7756
 GKS  H6   H  HCH2  0   0.268  -14.8902  5.6356  65.9094
 GKS  H7   H  HCR5  0   0.246  -14.6950  6.2867  63.6178
 GKS  H8   H  HCR5  0   0.270  -12.1949  5.0653  64.8453
 GKS  H9   H  HOH1  0   0.433  -13.8003  3.6134  64.4437
 GKS  H10  H  HCH2  0   0.271  -12.5400  5.6765  61.8977
 GKS  H11  H  HCH2  0   0.274  -11.0401  5.2772  62.7493
 GKS  H12  H  HCR5  0   0.223  -11.7841  7.8854  62.3377
 GKS  H13  H  HCH2  0   0.233  -10.8488  7.0064  65.1081
 GKS  H14  H  HCH2  0   0.302  -10.7453  8.6207  64.4210
 GKS  H15  H  HNH2  0   0.407   -8.2555  9.1106  60.4216
 GKS  H16  H  HNH2  0   0.437   -6.7442  8.2976  60.3069
 GKS  H18  H  HNH1  0   0.387   -8.6024  5.9729  66.1509
 GKS  H19  H  H     0   0.199   -9.3745  3.8867  66.2554
 GKS  H20  H  HNR6  0   0.416   -6.2349  6.6123  61.7926

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
 GKS  N2   C2   single  1.334  0.020  1.334
 GKS  C2   N1   single  1.355  0.020  1.355
 GKS  C2   N3   double  1.311  0.020  1.311
 GKS  N1   C6   single  1.389  0.020  1.389
 GKS  N3   C4   single  1.349  0.020  1.349
 GKS  C6   O6   double  1.221  0.020  1.221
 GKS  C6   C5   single  1.437  0.020  1.437
 GKS  C2'  C1'  single  1.523  0.020  1.523
 GKS  C2'  C3'  single  1.518  0.020  1.518
 GKS  C4   C5   double  1.370  0.020  1.370
 GKS  C4   C9   single  1.495  0.020  1.495
 GKS  C1'  C9   single  1.533  0.020  1.533
 GKS  C1'  O4'  single  1.425  0.020  1.425
 GKS  C5   N7   single  1.408  0.020  1.408
 GKS  O3'  C3'  single  1.399  0.020  1.399
 GKS  O8   C8   double  1.215  0.020  1.215
 GKS  C3'  C4'  single  1.541  0.020  1.541
 GKS  O4'  C4'  single  1.413  0.020  1.413
 GKS  N7   C8   single  1.346  0.020  1.346
 GKS  C4'  C5'  single  1.509  0.020  1.509
 GKS  O1B  PB   double  1.473  0.020  1.473
 GKS  C5'  O5'  single  1.438  0.020  1.438
 GKS  O5'  PA   single  1.578  0.020  1.578
 GKS  PB   O3A  single  1.600  0.020  1.600
 GKS  PB   O2B  single  1.576  0.020  1.576
 GKS  PB   O3B  single  1.599  0.020  1.599
 GKS  O3A  PA   single  1.630  0.020  1.630
 GKS  O3B  PG   single  1.634  0.020  1.634
 GKS  PA   O2A  double  1.466  0.020  1.466
 GKS  PA   O1A  single  1.586  0.020  1.586
 GKS  PG   O1G  double  1.469  0.020  1.469
 GKS  PG   O3G  single  1.582  0.020  1.582
 GKS  PG   O2G  single  1.584  0.020  1.584
 GKS  O2G  H1   single  0.850  0.020  0.980
 GKS  O3G  H2   single  0.850  0.020  0.980
 GKS  O2B  H3   single  0.850  0.020  0.980
 GKS  O1A  H4   single  0.850  0.020  0.980
 GKS  C5'  H5   single  0.970  0.020  1.090
 GKS  C5'  H6   single  0.970  0.020  1.090
 GKS  C4'  H7   single  0.970  0.020  1.090
 GKS  C3'  H8   single  0.970  0.020  1.090
 GKS  O3'  H9   single  0.850  0.020  0.980
 GKS  C2'  H10  single  0.970  0.020  1.090
 GKS  C2'  H11  single  0.970  0.020  1.090
 GKS  C1'  H12  single  0.970  0.020  1.090
 GKS  C9   H13  single  0.970  0.020  1.090
 GKS  C9   H14  single  0.970  0.020  1.090
 GKS  N2   H15  single  0.860  0.020  1.020
 GKS  N2   H16  single  0.860  0.020  1.020
 GKS  N7   H18  single  0.860  0.020  1.020
 GKS  C8   H19  single  0.930  0.020  1.080
 GKS  N1   H20  single  0.860  0.020  1.020

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
 GKS  O3B  PG   O3G  100.82  3.000
 GKS  O3G  PG   O2G  103.18  3.000
 GKS  O3B  PG   O2G   99.58  3.000
 GKS  O2G  PG   O1G  118.65  3.000
 GKS  O3G  PG   O1G  117.81  3.000
 GKS  O3B  PG   O1G  113.86  3.000
 GKS  H1   O2G  PG   114.79  3.000
 GKS  H2   O3G  PG   115.00  3.000
 GKS  PB   O3B  PG   130.39  3.000
 GKS  O3A  PB   O2B  102.49  3.000
 GKS  O2B  PB   O1B  118.13  3.000
 GKS  O3A  PB   O1B  115.66  3.000
 GKS  O2B  PB   O3B  106.89  3.000
 GKS  O3A  PB   O3B   99.76  3.000
 GKS  O1B  PB   O3B  111.89  3.000
 GKS  H3   O2B  PB   115.57  3.000
 GKS  PA   O3A  PB   133.56  3.000
 GKS  O5'  PA   O2A  111.96  3.000
 GKS  O2A  PA   O1A  119.70  3.000
 GKS  O5'  PA   O1A  108.32  3.000
 GKS  O1A  PA   O3A   99.49  3.000
 GKS  O2A  PA   O3A  110.67  3.000
 GKS  O5'  PA   O3A  105.15  3.000
 GKS  H4   O1A  PA   115.64  3.000
 GKS  C5'  O5'  PA   126.71  3.000
 GKS  H6   C5'  H5   107.76  3.000
 GKS  H6   C5'  C4'  108.98  3.000
 GKS  H5   C5'  C4'  110.84  3.000
 GKS  H6   C5'  O5'  112.09  3.000
 GKS  H5   C5'  O5'  107.49  3.000
 GKS  C4'  C5'  O5'  109.67  3.000
 GKS  H7   C4'  C3'  108.59  3.000
 GKS  H7   C4'  O4'  109.57  3.000
 GKS  C3'  C4'  O4'  106.60  3.000
 GKS  H7   C4'  C5'  105.96  3.000
 GKS  O4'  C4'  C5'  110.47  3.000
 GKS  C3'  C4'  C5'  115.57  3.000
 GKS  C1'  O4'  C4'  110.67  3.000
 GKS  H8   C3'  C2'  108.22  3.000
 GKS  H8   C3'  O3'  110.43  3.000
 GKS  C2'  C3'  O3'  112.52  3.000
 GKS  H8   C3'  C4'  109.85  3.000
 GKS  O3'  C3'  C4'  114.11  3.000
 GKS  C2'  C3'  C4'  101.24  3.000
 GKS  H9   O3'  C3'  107.80  3.000
 GKS  H11  C2'  H10  108.33  3.000
 GKS  H11  C2'  C1'  113.41  3.000
 GKS  H10  C2'  C1'  110.25  3.000
 GKS  H11  C2'  C3'  112.76  3.000
 GKS  H10  C2'  C3'  109.71  3.000
 GKS  C1'  C2'  C3'  102.27  3.000
 GKS  H12  C1'  C9   108.76  3.000
 GKS  H12  C1'  C2'  111.48  3.000
 GKS  C9   C1'  C2'  113.94  3.000
 GKS  H12  C1'  O4'  108.19  3.000
 GKS  C9   C1'  O4'  108.85  3.000
 GKS  C2'  C1'  O4'  105.40  3.000
 GKS  H14  C9   H13  107.26  3.000
 GKS  H14  C9   C4   108.36  3.000
 GKS  H13  C9   C4   110.69  3.000
 GKS  H14  C9   C1'  108.39  3.000
 GKS  H13  C9   C1'  110.14  3.000
 GKS  C4   C9   C1'  111.85  3.000
 GKS  C5   C4   N3   123.37  3.000
 GKS  C5   C4   C9   121.74  3.000
 GKS  N3   C4   C9   114.88  3.000
 GKS  C2   N3   C4   117.80  3.000
 GKS  N1   C2   N2   117.79  3.000
 GKS  N1   C2   N3   122.22  3.000
 GKS  N2   C2   N3   119.98  3.000
 GKS  H16  N2   H15  117.50  3.000
 GKS  H16  N2   C2   122.00  3.000
 GKS  H15  N2   C2   118.44  3.000
 GKS  H20  N1   C6   116.62  3.000
 GKS  H20  N1   C2   119.62  3.000
 GKS  C6   N1   C2   123.76  3.000
 GKS  C5   C6   O6   126.49  3.000
 GKS  C5   C6   N1   113.18  3.000
 GKS  O6   C6   N1   120.33  3.000
 GKS  N7   C5   C6   117.64  3.000
 GKS  N7   C5   C4   122.70  3.000
 GKS  C6   C5   C4   119.66  3.000
 GKS  H18  N7   C8   117.49  3.000
 GKS  H18  N7   C5   118.95  3.000
 GKS  C8   N7   C5   122.60  3.000
 GKS  H19  C8   O8   122.95  3.000
 GKS  H19  C8   N7   111.83  3.000
 GKS  O8   C8   N7   125.20  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
 GKS  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 GKS  CONST_02  C6   N1   C2   N3      0.00   0.0  0
 GKS  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 GKS  CONST_04  N2   C2   N3   C4    180.00   0.0  0
 GKS  CONST_05  O6   C6   N1   C2    180.00   0.0  0
 GKS  CONST_06  C6   N1   C2   N2    180.00   0.0  0
 GKS  CONST_07  H20  N1   C2   N3    180.00   0.0  0
 GKS  CONST_08  H15  N2   C2   N3      0.00   0.0  0
 GKS  CONST_09  H16  N2   C2   N3    180.00   0.0  0
 GKS  CONST_10  O8   C8   N7   C5      0.00   0.0  0
 GKS  CONST_11  H18  N7   C8   O8    180.00   0.0  0
 GKS  Var_01    N3   C4   C9   C1'    61.04  30.0  1
 GKS  Var_02    C8   N7   C5   C4    104.08  30.0  2
 GKS  Var_03    C4'  C5'  O5'  PA   -136.37  30.0  1
 GKS  Var_04    O1B  PB   O3B  PG   -145.72  30.0  1
 GKS  Var_05    O5'  PA   O3A  PB    -89.58  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
 GKS  chir_03  C4'  C3'  O4'  C5'  positiv
 GKS  chir_04  C3'  O3'  C4'  C2'  positiv
 GKS  chir_05  C1'  O4'  C2'  C9   positiv
 GKS  chir_06  PB   O3A  O2B  O3B  both
 GKS  chir_07  PA   O2A  O3A  O5'  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
 GKS  plan-1  C9   0.020
 GKS  plan-1  C4   0.020
 GKS  plan-1  N3   0.020
 GKS  plan-1  C2   0.020
 GKS  plan-1  N2   0.020
 GKS  plan-1  N1   0.020
 GKS  plan-1  C6   0.020
 GKS  plan-1  O6   0.020
 GKS  plan-1  C5   0.020
 GKS  plan-1  N7   0.020
 GKS  plan-1  H15  0.020
 GKS  plan-1  H16  0.020
 GKS  plan-1  H20  0.020
 GKS  plan-2  C5   0.020
 GKS  plan-2  N7   0.020
 GKS  plan-2  C8   0.020
 GKS  plan-2  O8   0.020
 GKS  plan-2  H18  0.020
 GKS  plan-2  H19  0.020

