# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:06:17 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: (2R,4S,6R)-4-amino-5,5-dihydroxy-4,6-dimethyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](C[C@](C)(N)C1(O)O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=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
 AKM  AKM  '(2R,4S,6R)-4-amino-5,5-dihydroxy-4,6-dimethyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  63  36  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AKM
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
 AKM  O2P  O  OP    -1  -0.790  -0.5427   1.1796   1.9139
 AKM  P    P  P      0   1.345  -0.1905   2.1042   0.7925
 AKM  O1P  O  O      0  -0.801   0.0472   3.5594   1.0471
 AKM  OPP  O  O2     0  -0.734   1.0339   1.4664  -0.0994
 AKM  P2   P  P      0   1.327   2.6177   1.7585   0.2029
 AKM  O3P  O  O      0  -0.788   2.8658   1.8944   1.6698
 AKM  O1   O  O2     0  -0.631   3.0956   0.2578  -0.3153
 AKM  C1   C  CH1    0   0.328   4.4366  -0.0820  -0.1782
 AKM  C2   C  CH2    0  -0.475   4.9481  -0.6710  -1.4786
 AKM  C3   C  CT     0   0.007   6.3752  -1.2186  -1.3597
 AKM  C3M  C  CH3    0  -0.659   7.3848  -0.0666  -1.2759
 AKM  N3   N  NH2    0  -0.781   6.6425  -2.0217  -2.5528
 AKM  C4   C  CT     0   0.513   6.4161  -2.1515  -0.1193
 AKM  O4A  O  OH1    0  -0.664   5.6608  -3.2809  -0.4580
 AKM  O4B  O  OH1    0  -0.667   7.7535  -2.4912   0.1082
 AKM  C5   C  CH1    0  -0.078   5.7818  -1.5184   1.1503
 AKM  C6   C  CH3    0  -0.682   6.6177  -0.5130   1.9346
 AKM  O5   O  O2     0  -0.484   4.4884  -1.0341   0.8561
 AKM  O4P  O  OP    -1  -0.785   3.1367   2.7798  -0.7583
 AKM  O5'  O  O2     0  -0.622  -1.2931   1.9317  -0.4204
 AKM  C5'  C  CH2    0  -0.155  -2.5978   2.4041  -0.1603
 AKM  C4'  C  CH1    0   0.013  -3.5376   1.9018  -1.2275
 AKM  C3'  C  CH1    0   0.023  -4.9470   2.4819  -1.0995
 AKM  O3'  O  OH1    0  -0.669  -5.0219   3.6655  -1.8542
 AKM  C2'  C  CH2    0  -0.561  -5.8252   1.3397  -1.6110
 AKM  C1'  C  CH1    0   0.218  -4.9643   0.0825  -1.4608
 AKM  O4'  O  O2     0  -0.489  -3.6700   0.4945  -1.1307
 AKM  N11  N  NT     0  -0.567  -5.4244  -0.8990  -0.4790
 AKM  C21  C  C      0   0.742  -5.5975  -0.5290   0.8348
 AKM  O21  O  O      0  -0.471  -5.4307   0.6011   1.2419
 AKM  N31  N  NH1    0  -0.732  -5.9839  -1.5495   1.6632
 AKM  C41  C  C      0   0.552  -6.2188  -2.8753   1.3417
 AKM  O41  O  O      0  -0.460  -6.5694  -3.6610   2.2037
 AKM  C51  C  C      0  -0.196  -6.0064  -3.1941  -0.0564
 AKM  C5A  C  CH3    0  -0.717  -6.2306  -4.5905  -0.5525
 AKM  C61  C  C1     0   0.078  -5.6198  -2.1967  -0.8712
 AKM  H2   H  HCH1   0   0.180   5.0411   0.7976   0.0942
 AKM  H3   H  HCH2   0   0.245   4.2781  -1.4744  -1.7934
 AKM  H4   H  HCH2   0   0.239   4.9171   0.1027  -2.2520
 AKM  H5   H  HCH3   0   0.222   7.2373   0.6173  -0.4432
 AKM  H6   H  HCH3   0   0.236   8.4062  -0.4408  -1.2163
 AKM  H7   H  HCH3   0   0.230   7.3037   0.5282  -2.1880
 AKM  H8   H  HNH2   0   0.340   6.5905  -1.4076  -3.3589
 AKM  H9   H  HNH2   0   0.338   7.6041  -2.3434  -2.5316
 AKM  H11  H  HOH1   0   0.446   5.3678  -3.7267   0.3446
 AKM  H12  H  HOH1   0   0.449   7.8221  -3.0357   0.9015
 AKM  H13  H  HCH1   0   0.244   5.6139  -2.3525   1.8459
 AKM  H14  H  HCH3   0   0.245   6.0999  -0.2762   2.8641
 AKM  H15  H  HCH3   0   0.235   7.5862  -0.9355   2.1969
 AKM  H16  H  HCH3   0   0.234   6.7974   0.4255   1.4165
 AKM  H18  H  HCH2   0   0.213  -2.9618   2.0688   0.8180
 AKM  H19  H  HCH2   0   0.214  -2.6285   3.5002  -0.1668
 AKM  H20  H  HCH1   0   0.227  -3.1447   2.1684  -2.2204
 AKM  H21  H  HCH1   0   0.233  -5.1721   2.6807  -0.0481
 AKM  H22  H  HOH1   0   0.457  -5.8338   4.1217  -1.6153
 AKM  H23  H  HCH2   0   0.275  -6.7854   1.2635  -1.1033
 AKM  H24  H  HCH2   0   0.267  -6.0269   1.4962  -2.6723
 AKM  H25  H  HCH1   0   0.253  -4.9517  -0.4710  -2.4031
 AKM  H26  H  HNH1   0   0.424  -6.1163  -1.2886   2.6328
 AKM  H27  H  HCH3   0   0.252  -6.3107  -5.2892   0.2770
 AKM  H28  H  HCH3   0   0.251  -7.1513  -4.6662  -1.1321
 AKM  H29  H  HCH3   0   0.250  -5.4115  -4.9242  -1.1886
 AKM  H30  H  H      0   0.316  -5.4417  -2.3821  -1.9227

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
 AKM  O4A  C4   single  1.400  0.020  1.400
 AKM  C6   C5   single  1.525  0.020  1.525
 AKM  O3P  P2   deloc   1.494  0.020  1.494
 AKM  C5   O5   single  1.412  0.020  1.412
 AKM  C5   C4   single  1.554  0.020  1.554
 AKM  O5   C1   single  1.407  0.020  1.407
 AKM  C4   O4B  single  1.399  0.020  1.399
 AKM  C4   C3   single  1.553  0.020  1.553
 AKM  O1   P2   single  1.658  0.020  1.658
 AKM  O1   C1   single  1.390  0.020  1.390
 AKM  N3   C3   single  1.463  0.020  1.463
 AKM  P2   O4P  deloc   1.495  0.020  1.495
 AKM  P2   OPP  single  1.639  0.020  1.639
 AKM  C2   C1   single  1.517  0.020  1.517
 AKM  C2   C3   single  1.533  0.020  1.533
 AKM  C3   C3M  single  1.534  0.020  1.534
 AKM  O3'  C3'  single  1.406  0.020  1.406
 AKM  OPP  P    single  1.644  0.020  1.644
 AKM  C3'  C4'  single  1.529  0.020  1.529
 AKM  C3'  C2'  single  1.529  0.020  1.529
 AKM  P    O1P  deloc   1.496  0.020  1.496
 AKM  P    O2P  deloc   1.495  0.020  1.495
 AKM  P    O5'  single  1.648  0.020  1.648
 AKM  C4'  C5'  single  1.508  0.020  1.508
 AKM  C4'  O4'  single  1.417  0.020  1.417
 AKM  C5'  O5'  single  1.412  0.020  1.412
 AKM  C2'  C1'  single  1.531  0.020  1.531
 AKM  O4'  C1'  single  1.398  0.020  1.398
 AKM  C1'  N11  single  1.462  0.020  1.462
 AKM  O21  C21  double  1.213  0.020  1.213
 AKM  N11  C21  single  1.376  0.020  1.376
 AKM  N11  C61  single  1.370  0.020  1.370
 AKM  C21  N31  single  1.370  0.020  1.370
 AKM  C61  C51  double  1.345  0.020  1.345
 AKM  N31  C41  single  1.384  0.020  1.384
 AKM  C51  C41  single  1.450  0.020  1.450
 AKM  C51  C5A  single  1.499  0.020  1.499
 AKM  C41  O41  double  1.218  0.020  1.218
 AKM  C1   H2   single  0.970  0.020  1.090
 AKM  C2   H3   single  0.970  0.020  1.090
 AKM  C2   H4   single  0.970  0.020  1.090
 AKM  C3M  H5   single  0.970  0.020  1.090
 AKM  C3M  H6   single  0.970  0.020  1.090
 AKM  C3M  H7   single  0.970  0.020  1.090
 AKM  N3   H8   single  0.890  0.020  1.040
 AKM  N3   H9   single  0.890  0.020  1.040
 AKM  O4A  H11  single  0.850  0.020  0.980
 AKM  O4B  H12  single  0.850  0.020  0.980
 AKM  C5   H13  single  0.970  0.020  1.090
 AKM  C6   H14  single  0.970  0.020  1.090
 AKM  C6   H15  single  0.970  0.020  1.090
 AKM  C6   H16  single  0.970  0.020  1.090
 AKM  C5'  H18  single  0.970  0.020  1.090
 AKM  C5'  H19  single  0.970  0.020  1.090
 AKM  C4'  H20  single  0.970  0.020  1.090
 AKM  C3'  H21  single  0.970  0.020  1.090
 AKM  O3'  H22  single  0.850  0.020  0.980
 AKM  C2'  H23  single  0.970  0.020  1.090
 AKM  C2'  H24  single  0.970  0.020  1.090
 AKM  C1'  H25  single  0.970  0.020  1.090
 AKM  N31  H26  single  0.860  0.020  1.020
 AKM  C5A  H27  single  0.970  0.020  1.090
 AKM  C5A  H28  single  0.970  0.020  1.090
 AKM  C5A  H29  single  0.970  0.020  1.090
 AKM  C61  H30  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
 AKM  O5'  P    OPP   93.35  3.000
 AKM  O5'  P    O1P  109.47  3.000
 AKM  OPP  P    O1P  110.57  3.000
 AKM  O5'  P    O2P  109.24  3.000
 AKM  O1P  P    O2P  120.74  3.000
 AKM  OPP  P    O2P  110.03  3.000
 AKM  P2   OPP  P    123.42  3.000
 AKM  O4P  P2   O1   108.49  3.000
 AKM  O4P  P2   O3P  120.75  3.000
 AKM  O1   P2   O3P  109.96  3.000
 AKM  O4P  P2   OPP  109.79  3.000
 AKM  O1   P2   OPP   93.42  3.000
 AKM  O3P  P2   OPP  110.97  3.000
 AKM  C1   O1   P2   117.94  3.000
 AKM  H2   C1   O5   109.78  3.000
 AKM  H2   C1   C2   109.70  3.000
 AKM  O5   C1   C2   110.80  3.000
 AKM  H2   C1   O1   111.01  3.000
 AKM  C2   C1   O1   109.62  3.000
 AKM  O5   C1   O1   105.87  3.000
 AKM  H4   C2   H3   107.39  3.000
 AKM  H4   C2   C3   109.49  3.000
 AKM  H3   C2   C3   109.31  3.000
 AKM  H4   C2   C1   108.77  3.000
 AKM  H3   C2   C1   109.02  3.000
 AKM  C3   C2   C1   112.72  3.000
 AKM  C4   C3   N3   108.48  3.000
 AKM  N3   C3   C3M  109.67  3.000
 AKM  C4   C3   C3M  112.97  3.000
 AKM  C3M  C3   C2   110.40  3.000
 AKM  N3   C3   C2   107.63  3.000
 AKM  C4   C3   C2   107.52  3.000
 AKM  H7   C3M  H6   107.61  3.000
 AKM  H7   C3M  H5   106.68  3.000
 AKM  H6   C3M  H5   107.54  3.000
 AKM  H7   C3M  C3   108.33  3.000
 AKM  H6   C3M  C3   111.22  3.000
 AKM  H5   C3M  C3   115.13  3.000
 AKM  H9   N3   H8   104.91  3.000
 AKM  H9   N3   C3   109.29  3.000
 AKM  H8   N3   C3   107.84  3.000
 AKM  C5   C4   O4B  110.88  3.000
 AKM  O4B  C4   O4A  111.06  3.000
 AKM  C5   C4   O4A  107.83  3.000
 AKM  O4B  C4   C3   107.52  3.000
 AKM  C5   C4   C3   113.40  3.000
 AKM  O4A  C4   C3   106.09  3.000
 AKM  H11  O4A  C4   109.61  3.000
 AKM  H12  O4B  C4   109.80  3.000
 AKM  H13  C5   O5   104.61  3.000
 AKM  H13  C5   C6   104.99  3.000
 AKM  O5   C5   C6   112.53  3.000
 AKM  H13  C5   C4   105.68  3.000
 AKM  O5   C5   C4   110.08  3.000
 AKM  C6   C5   C4   117.72  3.000
 AKM  H16  C6   H15  107.63  3.000
 AKM  H16  C6   H14  107.30  3.000
 AKM  H15  C6   H14  107.54  3.000
 AKM  H16  C6   C5   114.51  3.000
 AKM  H15  C6   C5   110.84  3.000
 AKM  H14  C6   C5   108.75  3.000
 AKM  C5   O5   C1   114.77  3.000
 AKM  C5'  O5'  P    116.59  3.000
 AKM  H19  C5'  H18  107.56  3.000
 AKM  H19  C5'  C4'  108.14  3.000
 AKM  H18  C5'  C4'  108.82  3.000
 AKM  H19  C5'  O5'  111.05  3.000
 AKM  H18  C5'  O5'  111.65  3.000
 AKM  C4'  C5'  O5'  109.52  3.000
 AKM  H20  C4'  O4'  109.61  3.000
 AKM  H20  C4'  C3'  108.22  3.000
 AKM  O4'  C4'  C3'  106.55  3.000
 AKM  H20  C4'  C5'  109.59  3.000
 AKM  O4'  C4'  C5'  109.92  3.000
 AKM  C3'  C4'  C5'  112.87  3.000
 AKM  H21  C3'  C2'  109.83  3.000
 AKM  H21  C3'  O3'  110.62  3.000
 AKM  C2'  C3'  O3'  114.76  3.000
 AKM  H21  C3'  C4'  109.83  3.000
 AKM  C2'  C3'  C4'  102.59  3.000
 AKM  O3'  C3'  C4'  108.88  3.000
 AKM  H22  O3'  C3'  108.13  3.000
 AKM  H24  C2'  H23  107.49  3.000
 AKM  H24  C2'  C1'  108.48  3.000
 AKM  H23  C2'  C1'  113.12  3.000
 AKM  H24  C2'  C3'  108.92  3.000
 AKM  H23  C2'  C3'  113.76  3.000
 AKM  C1'  C2'  C3'  104.93  3.000
 AKM  H25  C1'  N11  104.04  3.000
 AKM  H25  C1'  O4'  110.01  3.000
 AKM  N11  C1'  O4'  109.30  3.000
 AKM  H25  C1'  C2'  109.74  3.000
 AKM  N11  C1'  C2'  116.11  3.000
 AKM  O4'  C1'  C2'  107.56  3.000
 AKM  C1'  O4'  C4'  111.29  3.000
 AKM  C61  N11  C21  120.68  3.000
 AKM  C61  N11  C1'  119.24  3.000
 AKM  C21  N11  C1'  120.01  3.000
 AKM  N31  C21  O21  122.01  3.000
 AKM  N31  C21  N11  114.37  3.000
 AKM  O21  C21  N11  123.63  3.000
 AKM  H26  N31  C41  116.54  3.000
 AKM  H26  N31  C21  115.08  3.000
 AKM  C41  N31  C21  128.38  3.000
 AKM  C51  C41  O41  125.65  3.000
 AKM  O41  C41  N31  120.16  3.000
 AKM  C51  C41  N31  114.19  3.000
 AKM  C61  C51  C5A  122.24  3.000
 AKM  C5A  C51  C41  120.14  3.000
 AKM  C61  C51  C41  117.61  3.000
 AKM  H29  C5A  H28  107.64  3.000
 AKM  H29  C5A  H27  107.69  3.000
 AKM  H28  C5A  H27  107.38  3.000
 AKM  H29  C5A  C51  111.48  3.000
 AKM  H28  C5A  C51  111.52  3.000
 AKM  H27  C5A  C51  110.93  3.000
 AKM  H30  C61  C51  120.59  3.000
 AKM  H30  C61  N11  114.64  3.000
 AKM  C51  C61  N11  124.77  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
 AKM  CONST_01  N31  C21  N11  C1'   180.00   0.0  0
 AKM  CONST_02  C41  N31  C21  N11     0.00   0.0  0
 AKM  CONST_03  C51  C41  N31  C21     0.00   0.0  0
 AKM  CONST_04  C61  N11  C21  N31     0.00   0.0  0
 AKM  CONST_05  O21  C21  N11  C1'     0.00   0.0  0
 AKM  CONST_06  O41  C41  N31  C21   180.00   0.0  0
 AKM  CONST_07  C61  N11  C21  O21   180.00   0.0  0
 AKM  CONST_08  C41  N31  C21  O21   180.00   0.0  0
 AKM  CONST_09  H26  N31  C21  N11   180.00   0.0  0
 AKM  Var_01    H27  C5A  C51  C41   -13.77  30.0  3
 AKM  Var_02    C4'  C5'  O5'  P    -167.52  30.0  2
 AKM  Var_03    O4P  P2   O1   C1     72.42  30.0  3
 AKM  Var_04    O3P  P2   OPP  P      34.60  30.0  1
 AKM  Var_05    O5'  P    OPP  P2    157.32  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
 AKM  chir_03  C1   O5   O1   C2   positiv
 AKM  chir_04  C3   C3M  C2   C4   positiv
 AKM  chir_05  C5   O5   C6   C4   positiv
 AKM  chir_06  C4'  C3'  C5'  O4'  negativ
 AKM  chir_07  C3'  O3'  C4'  C2'  positiv
 AKM  chir_08  C1'  O4'  N11  C2'  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
 AKM  plan-1  C1'  0.020
 AKM  plan-1  N11  0.020
 AKM  plan-1  C21  0.020
 AKM  plan-1  O21  0.020
 AKM  plan-1  N31  0.020
 AKM  plan-1  C41  0.020
 AKM  plan-1  O41  0.020
 AKM  plan-1  C51  0.020
 AKM  plan-1  C5A  0.020
 AKM  plan-1  C61  0.020
 AKM  plan-1  H26  0.020
 AKM  plan-1  H30  0.020

