# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 08:17:25 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=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
 2KH  2KH  5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine  ligand  45  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2KH
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
 2KH  PA   P  P     0   1.458  63.6575  20.3962  94.5490
 2KH  O1A  O  O     0  -0.681  64.8928  20.5400  95.3410
 2KH  O2A  O  OH1   0  -0.768  62.2665  20.2865  95.2761
 2KH  N3A  N  NH1   0  -0.984  63.7754  19.0244  93.5561
 2KH  O5'  O  O2    0  -0.584  63.4864  21.6743  93.6135
 2KH  PB   P  P     0   1.490  62.7172  17.9343  92.8943
 2KH  O1B  O  OH1   0  -0.735  61.3286  18.6817  93.0303
 2KH  O2B  O  O     0  -0.661  63.1360  17.3964  91.5876
 2KH  O3B  O  O2    0  -0.675  62.6088  16.6863  93.9437
 2KH  PG   P  P     0   1.502  61.9397  16.6387  95.4066
 2KH  O1G  O  OH1   0  -0.711  60.4691  16.1993  95.0445
 2KH  O2G  O  O     0  -0.715  62.1037  17.8938  96.1853
 2KH  O3G  O  OH1   0  -0.701  62.5725  15.3473  96.0539
 2KH  C5'  C  CH2   0  -0.223  62.4139  21.9645  92.7195
 2KH  C4'  C  CH1   0   0.015  62.9260  22.1932  91.3187
 2KH  O4'  O  O2    0  -0.498  63.8653  23.2639  91.2914
 2KH  C1'  C  CH1   0   0.176  64.8355  23.0505  90.3125
 2KH  C2'  C  CH1   0  -0.054  64.4509  21.7567  89.5704
 2KH  O2'  O  OH1   0  -0.658  63.5848  22.0308  88.5068
 2KH  C3'  C  CH1   0   0.004  63.6566  21.0297  90.6569
 2KH  O3'  O  OH1   0  -0.667  62.7480  20.0763  90.2051
 2KH  N1   N  NR6   0  -0.567  66.1676  22.9480  90.9448
 2KH  C6   C  CR16  0   0.077  66.3417  22.7284  92.2780
 2KH  C2   C  CR6   0   0.740  67.2490  23.0898  90.1015
 2KH  O2   O  O     0  -0.482  67.1221  23.2828  88.9086
 2KH  N3   N  NR16  0  -0.731  68.4718  22.9944  90.7065
 2KH  C4   C  CR6   0   0.566  68.7415  22.7599  92.0476
 2KH  O4   O  O     0  -0.466  69.8906  22.6919  92.4437
 2KH  C5   C  CR16  0  -0.512  67.5537  22.6230  92.8506
 2KH  H1   H  HOH1  0   0.500  62.1142  19.4029  95.7224
 2KH  H2   H  HNH1  0   0.451  64.7417  18.7655  93.3766
 2KH  H3   H  HOH1  0   0.517  60.5957  18.2986  92.5256
 2KH  H4   H  HOH1  0   0.517  59.8098  16.3556  95.7364
 2KH  H5   H  HOH1  0   0.516  63.4254  15.4808  96.4923
 2KH  H6   H  HCH2  0   0.274  61.9125  22.8605  93.0883
 2KH  H7   H  HCH2  0   0.259  61.6720  21.1659  92.6831
 2KH  H8   H  HCH1  0   0.257  62.0466  22.4555  90.7156
 2KH  H9   H  HCH1  0   0.286  64.8744  23.9067  89.6354
 2KH  H10  H  HCH1  0   0.265  65.3329  21.1929  89.2481
 2KH  H11  H  HOH1  0   0.461  64.0768  22.4970  87.8232
 2KH  H12  H  HCH1  0   0.234  64.3790  20.5978  91.3606
 2KH  H13  H  HOH1  0   0.458  63.1280  19.1953  90.2939
 2KH  H14  H  HCR6  0   0.334  65.4444  22.6508  92.8697
 2KH  H15  H  HNR6  0   0.427  69.2681  23.1019  90.0898
 2KH  H16  H  HCR6  0   0.289  67.6417  22.4506  93.9121

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
 2KH  O2'  C2'  single  1.399  0.020  1.399
 2KH  O3'  C3'  single  1.392  0.020  1.392
 2KH  C2'  C3'  single  1.530  0.020  1.530
 2KH  C2'  C1'  single  1.540  0.020  1.540
 2KH  O2   C2   double  1.215  0.020  1.215
 2KH  C3'  C4'  single  1.525  0.020  1.525
 2KH  C1'  N1   single  1.478  0.020  1.478
 2KH  C1'  O4'  single  1.395  0.020  1.395
 2KH  C2   N1   single  1.379  0.020  1.379
 2KH  C2   N3   single  1.368  0.020  1.368
 2KH  C4'  O4'  single  1.425  0.020  1.425
 2KH  C4'  C5'  single  1.509  0.020  1.509
 2KH  N1   C6   single  1.362  0.020  1.362
 2KH  N3   C4   single  1.388  0.020  1.388
 2KH  C5'  O5'  single  1.426  0.020  1.426
 2KH  C6   C5   double  1.345  0.020  1.345
 2KH  C4   C5   single  1.440  0.020  1.440
 2KH  C4   O4   double  1.217  0.020  1.217
 2KH  O2B  PB   double  1.474  0.020  1.474
 2KH  O5'  PA   single  1.593  0.020  1.593
 2KH  N3A  PB   single  1.657  0.020  1.657
 2KH  N3A  PA   single  1.698  0.020  1.698
 2KH  PB   O1B  single  1.583  0.020  1.583
 2KH  PB   O3B  single  1.634  0.020  1.634
 2KH  PA   O1A  double  1.474  0.020  1.474
 2KH  PA   O2A  single  1.573  0.020  1.573
 2KH  O3B  PG   single  1.609  0.020  1.609
 2KH  PG   O2G  double  1.486  0.020  1.486
 2KH  PG   O1G  single  1.577  0.020  1.577
 2KH  PG   O3G  single  1.577  0.020  1.577
 2KH  O2A  H1   single  0.850  0.020  0.980
 2KH  N3A  H2   single  0.860  0.020  1.020
 2KH  O1B  H3   single  0.850  0.020  0.980
 2KH  O1G  H4   single  0.850  0.020  0.980
 2KH  O3G  H5   single  0.850  0.020  0.980
 2KH  C5'  H6   single  0.970  0.020  1.090
 2KH  C5'  H7   single  0.970  0.020  1.090
 2KH  C4'  H8   single  0.970  0.020  1.090
 2KH  C1'  H9   single  0.970  0.020  1.090
 2KH  C2'  H10  single  0.970  0.020  1.090
 2KH  O2'  H11  single  0.850  0.020  0.980
 2KH  C3'  H12  single  0.970  0.020  1.090
 2KH  O3'  H13  single  0.850  0.020  0.980
 2KH  C6   H14  single  0.930  0.020  1.080
 2KH  N3   H15  single  0.860  0.020  1.020
 2KH  C5   H16  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
 2KH  O5'  PA   N3A  108.20  3.000
 2KH  N3A  PA   O2A  105.99  3.000
 2KH  O5'  PA   O2A  103.43  3.000
 2KH  O2A  PA   O1A  119.95  3.000
 2KH  N3A  PA   O1A  109.56  3.000
 2KH  O5'  PA   O1A  109.10  3.000
 2KH  H1   O2A  PA   113.69  3.000
 2KH  H2   N3A  PB   111.66  3.000
 2KH  H2   N3A  PA   112.04  3.000
 2KH  PB   N3A  PA   136.12  3.000
 2KH  C5'  O5'  PA   127.74  3.000
 2KH  O3B  PB   O2B  108.03  3.000
 2KH  O3B  PB   O1B  104.31  3.000
 2KH  O2B  PB   O1B  119.85  3.000
 2KH  O3B  PB   N3A  106.75  3.000
 2KH  O1B  PB   N3A  102.44  3.000
 2KH  O2B  PB   N3A  114.37  3.000
 2KH  H3   O1B  PB   115.61  3.000
 2KH  PG   O3B  PB   129.34  3.000
 2KH  O3G  PG   O2G  115.61  3.000
 2KH  O3G  PG   O1G  103.90  3.000
 2KH  O2G  PG   O1G  117.29  3.000
 2KH  O3G  PG   O3B  103.33  3.000
 2KH  O1G  PG   O3B  100.79  3.000
 2KH  O2G  PG   O3B  113.92  3.000
 2KH  H4   O1G  PG   115.21  3.000
 2KH  H5   O3G  PG   115.24  3.000
 2KH  H7   C5'  H6   107.46  3.000
 2KH  H7   C5'  C4'  108.11  3.000
 2KH  H6   C5'  C4'  110.20  3.000
 2KH  H7   C5'  O5'  112.56  3.000
 2KH  H6   C5'  O5'  107.51  3.000
 2KH  C4'  C5'  O5'  110.95  3.000
 2KH  H8   C4'  C3'  109.12  3.000
 2KH  H8   C4'  O4'  109.75  3.000
 2KH  C3'  C4'  O4'  104.44  3.000
 2KH  H8   C4'  C5'  105.91  3.000
 2KH  O4'  C4'  C5'  110.82  3.000
 2KH  C3'  C4'  C5'  116.74  3.000
 2KH  C1'  O4'  C4'  110.92  3.000
 2KH  H9   C1'  N1   106.71  3.000
 2KH  H9   C1'  C2'  111.64  3.000
 2KH  N1   C1'  C2'  111.89  3.000
 2KH  H9   C1'  O4'  109.87  3.000
 2KH  N1   C1'  O4'  109.71  3.000
 2KH  C2'  C1'  O4'  107.04  3.000
 2KH  H10  C2'  C3'  112.49  3.000
 2KH  H10  C2'  O2'  112.07  3.000
 2KH  C3'  C2'  O2'  108.16  3.000
 2KH  H10  C2'  C1'  111.90  3.000
 2KH  C3'  C2'  C1'  100.76  3.000
 2KH  O2'  C2'  C1'  110.87  3.000
 2KH  H11  O2'  C2'  108.57  3.000
 2KH  H12  C3'  O3'  111.61  3.000
 2KH  H12  C3'  C2'  107.51  3.000
 2KH  O3'  C3'  C2'  115.71  3.000
 2KH  H12  C3'  C4'  109.72  3.000
 2KH  C2'  C3'  C4'  101.21  3.000
 2KH  O3'  C3'  C4'  110.52  3.000
 2KH  H13  O3'  C3'  109.81  3.000
 2KH  C2   N1   C6   121.00  3.000
 2KH  C6   N1   C1'  123.02  3.000
 2KH  C2   N1   C1'  115.98  3.000
 2KH  H14  C6   C5   120.74  3.000
 2KH  H14  C6   N1   116.27  3.000
 2KH  C5   C6   N1   122.99  3.000
 2KH  N3   C2   O2   122.60  3.000
 2KH  N3   C2   N1   115.06  3.000
 2KH  O2   C2   N1   122.34  3.000
 2KH  H15  N3   C4   116.97  3.000
 2KH  H15  N3   C2   115.23  3.000
 2KH  C4   N3   C2   127.80  3.000
 2KH  C5   C4   O4   126.28  3.000
 2KH  O4   C4   N3   120.48  3.000
 2KH  C5   C4   N3   113.24  3.000
 2KH  H16  C5   C4   119.77  3.000
 2KH  H16  C5   C6   120.32  3.000
 2KH  C4   C5   C6   119.90  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
 2KH  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 2KH  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 2KH  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 2KH  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 2KH  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 2KH  CONST_06  O2   C2   N1   C6    180.00   0.0  0
 2KH  CONST_07  O4   C4   N3   C2    180.00   0.0  0
 2KH  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 2KH  CONST_09  H15  N3   C2   N1    180.00   0.0  0
 2KH  Var_01    C4'  C5'  O5'  PA   -123.86  30.0  1
 2KH  Var_02    O2B  PB   N3A  PA    148.06  30.0  3
 2KH  Var_03    PB   N3A  PA   O1A   151.21  30.0  1
 2KH  Var_04    O2G  PG   O3B  PB    -35.88  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
 2KH  chir_03  C4'  C3'  O4'  C5'  positiv
 2KH  chir_04  C1'  O4'  N1   C2'  negativ
 2KH  chir_05  C2'  O2'  C1'  C3'  negativ
 2KH  chir_06  C3'  O3'  C4'  C2'  positiv
 2KH  chir_07  PA   N3A  O1A  O2A  both
 2KH  chir_08  PB   O1B  O3B  N3A  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
 2KH  plan-1  C1'  0.020
 2KH  plan-1  N1   0.020
 2KH  plan-1  C6   0.020
 2KH  plan-1  C2   0.020
 2KH  plan-1  O2   0.020
 2KH  plan-1  N3   0.020
 2KH  plan-1  C4   0.020
 2KH  plan-1  O4   0.020
 2KH  plan-1  C5   0.020
 2KH  plan-1  H14  0.020
 2KH  plan-1  H15  0.020
 2KH  plan-1  H16  0.020

