# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 11:17:51 2021
#   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  65  36  .  2022-03-11  2022-11-17
;
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  OH1   0  -0.716  20.6314  21.1776  -16.3394
 AKM  P    P  P     0   1.493  20.9616  22.4606  -17.2050
 AKM  O1P  O  O     0  -0.679  22.3540  22.9307  -17.2679
 AKM  OPP  O  O2    0  -0.686  20.4434  22.1208  -18.7070
 AKM  P2   P  P     0   1.489  18.9653  22.0681  -19.3653
 AKM  O3P  O  O     0  -0.663  19.0059  21.3203  -20.6307
 AKM  O1   O  O2    0  -0.617  18.1272  21.4757  -18.1534
 AKM  C1   C  CH1   0   0.304  16.7142  21.7109  -18.0135
 AKM  C2   C  CH2   0  -0.563  16.1928  20.6991  -17.0054
 AKM  C3   C  CT    0   0.044  14.6980  20.4580  -17.2216
 AKM  C3M  C  CH3   0  -0.702  13.9130  21.7524  -17.0046
 AKM  N3   N  NH2   0  -0.832  14.2535  19.4219  -16.2919
 AKM  C4   C  CT    0   0.520  14.5172  19.8572  -18.6804
 AKM  O4A  O  OH1   0  -0.687  14.5478  18.4836  -18.6062
 AKM  O4B  O  OH1   0  -0.670  13.2629  20.2014  -19.2178
 AKM  C5   C  CH1   0  -0.036  15.6877  20.3024  -19.5907
 AKM  C6   C  CH3   0  -0.679  15.3878  20.2865  -21.0720
 AKM  O5   O  O2    0  -0.493  16.0841  21.6271  -19.2376
 AKM  O4P  O  OH1   0  -0.733  18.4900  23.5832  -19.4381
 AKM  O5'  O  O2    0  -0.591  19.8789  23.4433  -16.5929
 AKM  C5'  C  CH2   0  -0.184  19.9984  24.8642  -16.7524
 AKM  C4'  C  CR15  0   0.004  18.6623  25.4833  -16.4420
 AKM  C3'  C  CR15  0   0.022  18.6591  27.0004  -16.6133
 AKM  O3'  O  OH1   0  -0.658  18.4555  27.3202  -17.9594
 AKM  C2'  C  CH2   0  -0.575  17.5339  27.4113  -15.6624
 AKM  C1'  C  CR15  0   0.173  17.4954  26.2939  -14.6122
 AKM  O4'  O  O     0  -0.487  18.3381  25.2649  -15.0838
 AKM  N11  N  NR6   0  -0.562  17.9661  26.6891  -13.2943
 AKM  C21  C  CR6   0   0.735  17.1979  26.4092  -12.1856
 AKM  O21  O  O     0  -0.482  16.1096  25.8736  -12.2346
 AKM  N31  N  NR16  0  -0.736  17.7627  26.7959  -10.9987
 AKM  C41  C  CR6   0   0.562  18.9910  27.3970  -10.7919
 AKM  O41  O  O     0  -0.450  19.3587  27.6850   -9.6685
 AKM  C51  C  CR6   0  -0.183  19.7544  27.6344  -12.0028
 AKM  C5A  C  CH3   0  -0.708  21.1001  28.2711  -11.8955
 AKM  C61  C  CR16  0   0.074  19.2053  27.2642  -13.1703
 AKM  H1   H  HOH1  0   0.509  21.2374  20.4353  -16.4720
 AKM  H2   H  HCH1  0   0.264  16.5837  22.7362  -17.6613
 AKM  H3   H  HCH2  0   0.276  16.7391  19.7559  -17.0989
 AKM  H4   H  HCH2  0   0.281  16.3732  21.0685  -15.9934
 AKM  H5   H  HCH3  0   0.249  14.1522  22.1604  -16.0213
 AKM  H6   H  HCH3  0   0.239  14.1345  22.5257  -17.7408
 AKM  H7   H  HCH3  0   0.247  12.8383  21.5691  -17.0306
 AKM  H8   H  HNH2  0   0.378  14.8244  19.3869  -15.4577
 AKM  H9   H  HNH2  0   0.373  13.2988  19.5773  -15.9940
 AKM  H11  H  HOH1  0   0.449  14.3728  18.3010  -17.6501
 AKM  H12  H  HOH1  0   0.454  13.2049  21.1554  -19.3423
 AKM  H13  H  HCH1  0   0.238  16.5183  19.6118  -19.4070
 AKM  H14  H  HCH3  0   0.239  15.0527  19.2966  -21.3789
 AKM  H15  H  HCH3  0   0.227  14.6181  21.0061  -21.3500
 AKM  H16  H  HCH3  0   0.243  16.2932  20.5225  -21.6305
 AKM  H17  H  HOH1  0   0.507  18.5444  23.9807  -20.3182
 AKM  H18  H  HCH2  0   0.256  20.2781  25.1270  -17.7747
 AKM  H19  H  HCH2  0   0.256  20.7672  25.2430  -16.0750
 AKM  H20  H  HCR5  0   0.247  17.8944  25.0517  -17.0993
 AKM  H21  H  HCR5  0   0.227  19.6170  27.4097  -16.2601
 AKM  H22  H  HOH1  0   0.462  18.6038  28.2637  -18.0753
 AKM  H23  H  HCH2  0   0.286  17.6667  28.4016  -15.2274
 AKM  H24  H  HCH2  0   0.284  16.5912  27.4174  -16.2122
 AKM  H25  H  HCR5  0   0.279  16.4808  25.9245  -14.4758
 AKM  H26  H  HNR6  0   0.427  17.2048  26.6087  -10.1743
 AKM  H27  H  HCH3  0   0.249  21.7771  27.6713  -11.2861
 AKM  H28  H  HCH3  0   0.248  21.5523  28.3928  -12.8786
 AKM  H29  H  HCH3  0   0.249  21.0352  29.2563  -11.4318
 AKM  H30  H  HCR6  0   0.309  19.7402  27.4198  -14.0971

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  1.376  0.020  1.376
 AKM  C6   C5   single  1.511  0.020  1.511
 AKM  O3P  P2   double  1.470  0.020  1.470
 AKM  C5   O5   single  1.427  0.020  1.427
 AKM  C5   C4   single  1.548  0.020  1.548
 AKM  O5   C1   single  1.379  0.020  1.379
 AKM  C4   O4B  single  1.407  0.020  1.407
 AKM  C4   C3   single  1.588  0.020  1.588
 AKM  O1   P2   single  1.588  0.020  1.588
 AKM  O1   C1   single  1.439  0.020  1.439
 AKM  N3   C3   single  1.461  0.020  1.461
 AKM  P2   O4P  single  1.590  0.020  1.590
 AKM  P2   OPP  single  1.619  0.020  1.619
 AKM  C2   C1   single  1.520  0.020  1.520
 AKM  C2   C3   single  1.529  0.020  1.529
 AKM  C3   C3M  single  1.529  0.020  1.529
 AKM  O3'  C3'  single  1.398  0.020  1.398
 AKM  OPP  P    single  1.625  0.020  1.625
 AKM  C3'  C4'  single  1.527  0.020  1.527
 AKM  C3'  C2'  single  1.529  0.020  1.529
 AKM  P    O1P  double  1.471  0.020  1.471
 AKM  P    O2P  single  1.583  0.020  1.583
 AKM  P    O5'  single  1.585  0.020  1.585
 AKM  C4'  C5'  single  1.505  0.020  1.505
 AKM  C4'  O4'  single  1.413  0.020  1.413
 AKM  C5'  O5'  single  1.435  0.020  1.435
 AKM  C2'  C1'  single  1.534  0.020  1.534
 AKM  O4'  C1'  single  1.411  0.020  1.411
 AKM  C1'  N11  single  1.454  0.020  1.454
 AKM  O21  C21  double  1.214  0.020  1.214
 AKM  N11  C21  single  1.378  0.020  1.378
 AKM  N11  C61  single  1.372  0.020  1.372
 AKM  C21  N31  single  1.370  0.020  1.370
 AKM  C61  C51  double  1.342  0.020  1.342
 AKM  N31  C41  single  1.383  0.020  1.383
 AKM  C51  C41  single  1.451  0.020  1.451
 AKM  C51  C5A  single  1.493  0.020  1.493
 AKM  C41  O41  double  1.217  0.020  1.217
 AKM  O2P  H1   single  0.850  0.020  0.980
 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  O4P  H17  single  0.850  0.020  0.980
 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  H1   O2P  P    114.61  3.000
 AKM  O5'  P    OPP  105.59  3.000
 AKM  O5'  P    O1P  117.71  3.000
 AKM  OPP  P    O1P  109.22  3.000
 AKM  O5'  P    O2P   98.56  3.000
 AKM  O1P  P    O2P  118.68  3.000
 AKM  OPP  P    O2P  105.64  3.000
 AKM  P2   OPP  P    132.37  3.000
 AKM  O4P  P2   O1   103.46  3.000
 AKM  O4P  P2   O3P  116.97  3.000
 AKM  O1   P2   O3P  118.79  3.000
 AKM  O4P  P2   OPP  105.10  3.000
 AKM  O1   P2   OPP  100.59  3.000
 AKM  O3P  P2   OPP  109.95  3.000
 AKM  C1   O1   P2   122.09  3.000
 AKM  H2   C1   O5   106.78  3.000
 AKM  H2   C1   C2   111.71  3.000
 AKM  O5   C1   C2   113.04  3.000
 AKM  H2   C1   O1   107.59  3.000
 AKM  C2   C1   O1   107.00  3.000
 AKM  O5   C1   O1   110.63  3.000
 AKM  H4   C2   H3   106.75  3.000
 AKM  H4   C2   C3   110.22  3.000
 AKM  H3   C2   C3   109.88  3.000
 AKM  H4   C2   C1   109.43  3.000
 AKM  H3   C2   C1   110.23  3.000
 AKM  C3   C2   C1   110.27  3.000
 AKM  C4   C3   N3   106.35  3.000
 AKM  N3   C3   C3M  110.72  3.000
 AKM  C4   C3   C3M  113.08  3.000
 AKM  C3M  C3   C2   110.38  3.000
 AKM  N3   C3   C2   108.61  3.000
 AKM  C4   C3   C2   107.50  3.000
 AKM  H7   C3M  H6   107.66  3.000
 AKM  H7   C3M  H5   107.48  3.000
 AKM  H6   C3M  H5   107.39  3.000
 AKM  H7   C3M  C3   111.11  3.000
 AKM  H6   C3M  C3   113.59  3.000
 AKM  H5   C3M  C3   109.38  3.000
 AKM  H9   N3   H8   107.16  3.000
 AKM  H9   N3   C3   111.42  3.000
 AKM  H8   N3   C3   112.18  3.000
 AKM  C5   C4   O4B  112.27  3.000
 AKM  O4B  C4   O4A  106.53  3.000
 AKM  C5   C4   O4A  107.58  3.000
 AKM  O4B  C4   C3   111.09  3.000
 AKM  C5   C4   C3   110.20  3.000
 AKM  O4A  C4   C3   109.00  3.000
 AKM  H11  O4A  C4   103.45  3.000
 AKM  H12  O4B  C4   110.19  3.000
 AKM  H13  C5   O5   109.45  3.000
 AKM  H13  C5   C6   107.95  3.000
 AKM  O5   C5   C6   107.90  3.000
 AKM  H13  C5   C4   107.05  3.000
 AKM  O5   C5   C4   109.35  3.000
 AKM  C6   C5   C4   115.04  3.000
 AKM  H16  C6   H15  108.24  3.000
 AKM  H16  C6   H14  107.94  3.000
 AKM  H15  C6   H14  108.12  3.000
 AKM  H16  C6   C5   109.58  3.000
 AKM  H15  C6   C5   112.53  3.000
 AKM  H14  C6   C5   110.29  3.000
 AKM  C5   O5   C1   113.76  3.000
 AKM  H17  O4P  P2   114.62  3.000
 AKM  C5'  O5'  P    120.94  3.000
 AKM  H19  C5'  H18  108.47  3.000
 AKM  H19  C5'  C4'  110.75  3.000
 AKM  H18  C5'  C4'  108.75  3.000
 AKM  H19  C5'  O5'  109.45  3.000
 AKM  H18  C5'  O5'  111.33  3.000
 AKM  C4'  C5'  O5'  108.09  3.000
 AKM  H20  C4'  O4'  110.72  3.000
 AKM  H20  C4'  C3'  108.76  3.000
 AKM  O4'  C4'  C3'  105.12  3.000
 AKM  H20  C4'  C5'  109.60  3.000
 AKM  O4'  C4'  C5'  109.77  3.000
 AKM  C3'  C4'  C5'  112.80  3.000
 AKM  H21  C3'  C2'  109.94  3.000
 AKM  H21  C3'  O3'  110.54  3.000
 AKM  C2'  C3'  O3'  115.46  3.000
 AKM  H21  C3'  C4'  109.39  3.000
 AKM  C2'  C3'  C4'  101.46  3.000
 AKM  O3'  C3'  C4'  109.61  3.000
 AKM  H22  O3'  C3'  108.53  3.000
 AKM  H24  C2'  H23  107.53  3.000
 AKM  H24  C2'  C1'  109.11  3.000
 AKM  H23  C2'  C1'  113.06  3.000
 AKM  H24  C2'  C3'  108.89  3.000
 AKM  H23  C2'  C3'  113.75  3.000
 AKM  C1'  C2'  C3'  104.38  3.000
 AKM  H25  C1'  N11  106.29  3.000
 AKM  H25  C1'  O4'  110.55  3.000
 AKM  N11  C1'  O4'  107.92  3.000
 AKM  H25  C1'  C2'  110.88  3.000
 AKM  N11  C1'  C2'  114.48  3.000
 AKM  O4'  C1'  C2'  106.70  3.000
 AKM  C1'  O4'  C4'  110.21  3.000
 AKM  C61  N11  C21  121.08  3.000
 AKM  C61  N11  C1'  119.23  3.000
 AKM  C21  N11  C1'  119.58  3.000
 AKM  N31  C21  O21  121.94  3.000
 AKM  N31  C21  N11  114.20  3.000
 AKM  O21  C21  N11  123.86  3.000
 AKM  H26  N31  C41  116.60  3.000
 AKM  H26  N31  C21  115.21  3.000
 AKM  C41  N31  C21  128.19  3.000
 AKM  C51  C41  O41  124.95  3.000
 AKM  O41  C41  N31  120.62  3.000
 AKM  C51  C41  N31  114.43  3.000
 AKM  C61  C51  C5A  123.30  3.000
 AKM  C5A  C51  C41  118.96  3.000
 AKM  C61  C51  C41  117.74  3.000
 AKM  H29  C5A  H28  107.92  3.000
 AKM  H29  C5A  H27  107.23  3.000
 AKM  H28  C5A  H27  107.95  3.000
 AKM  H29  C5A  C51  111.24  3.000
 AKM  H28  C5A  C51  110.92  3.000
 AKM  H27  C5A  C51  111.42  3.000
 AKM  H30  C61  C51  120.23  3.000
 AKM  H30  C61  N11  115.45  3.000
 AKM  C51  C61  N11  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
 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    60.07  30.0  3
 AKM  Var_02    C4'  C5'  O5'  P     163.43  30.0  1
 AKM  Var_03    O4P  P2   O1   C1     46.37  30.0  3
 AKM  Var_04    O3P  P2   OPP  P    -162.72  30.0  1
 AKM  Var_05    O5'  P    OPP  P2    -28.14  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
 AKM  chir_09  P    O1P  O2P  O5'  both
 AKM  chir_10  P2   O4P  O1   O3P  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
 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

