# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  1 04:24:45 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(S)-hydroxy{[(2R,3S)-2,3,4-trihydroxy-3-methylbutyl]oxy}phosphoryl]oxy}phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](O)(CO)[C@H](O)CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N
#
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
 CDM  CDM  5'-O-[(R)-hydroxy{[(S)-hydroxy{[(2R,3S)-2,3,4-trihydroxy-3-methylbutyl]oxy}phosphoryl]oxy}phosphoryl]cytidine  ligand  56  33  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CDM
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
 CDM  N1    N  NR6    0  -0.566  -0.9871  -0.7475  -4.1015
 CDM  C2    C  CR6    0   0.605  -1.5372   0.5145  -3.8004
 CDM  N3    N  N      0  -0.541  -2.8798   0.6455  -3.8309
 CDM  C4    C  CR6    0   0.514  -3.6632  -0.3668  -4.1437
 CDM  C5    C  CR16   0  -0.475  -3.1411  -1.6574  -4.4646
 CDM  C6    C  CR16   0   0.096  -1.8022  -1.7858  -4.4177
 CDM  O2    O  O      0  -0.503  -0.7968   1.4471  -3.5271
 CDM  N4    N  NH2    0  -0.808  -4.9799  -0.1668  -4.1581
 CDM  C1'   C  CH1    0   0.243   0.4440  -0.9861  -4.0577
 CDM  C2'   C  CH1    0  -0.062   1.3042  -0.1404  -4.9953
 CDM  O2'   O  OH1    0  -0.660   1.2838  -0.7039  -6.2779
 CDM  C3'   C  CH1    0  -0.036   2.6625  -0.2331  -4.2905
 CDM  C4'   C  CH1    0  -0.020   2.2516  -0.2160  -2.8218
 CDM  O4'   O  O2     0  -0.489   0.9432  -0.7883  -2.7689
 CDM  O3'   O  OH1    0  -0.672   3.2915  -1.4581  -4.5727
 CDM  C5'   C  CH2    0  -0.153   2.2726   1.1804  -2.2343
 CDM  O5'   O  O2     0  -0.617   1.7955   1.1361  -0.9044
 CDM  PA    P  P      0   1.336   2.6319   1.9899   0.2211
 CDM  O1A   O  O      0  -0.796   3.9135   1.2887   0.5438
 CDM  O2A   O  OP    -1  -0.787   2.6284   3.4398  -0.1465
 CDM  O3A   O  O2     0  -0.729   1.5258   1.7255   1.4120
 CDM  PB    P  P      0   1.367   1.9265   1.4255   2.9664
 CDM  O1B   O  OP    -1  -0.780   2.9195   2.4213   3.4671
 CDM  O2B   O  O      0  -0.798   2.1959  -0.0501   3.1551
 CDM  O3B   O  O2     0  -0.616   0.4299   1.7574   3.5420
 CDM  C1M   C  CH2    0  -0.211   0.0685   1.3141   4.8474
 CDM  C2M   C  CH1    0   0.031  -0.5866  -0.0671   4.8143
 CDM  O2M   O  OH1    0  -0.718   0.3443  -1.1078   4.6871
 CDM  C3M   C  CT     0   0.154  -1.4502  -0.3334   6.0682
 CDM  C4M   C  CH2    0  -0.147  -2.0789  -1.7244   5.9359
 CDM  C5M   C  CH3    0  -0.680  -0.6368  -0.2201   7.3507
 CDM  O3M   O  OH1    0  -0.675  -2.4697   0.6485   6.1513
 CDM  O4M   O  OH1    0  -0.671  -2.9538  -1.9480   7.0169
 CDM  H5    H  HCR6   0   0.289  -3.7748  -2.4932  -4.7193
 CDM  H6    H  HCR6   0   0.320  -1.3178  -2.7285  -4.6330
 CDM  H41   H  HNH2   0   0.403  -5.3577   0.7305  -3.9058
 CDM  H42   H  HNH2   0   0.414  -5.6234  -0.9090  -4.3685
 CDM  H1'   H  HCH1   0   0.240   0.5628  -2.0359  -4.3532
 CDM  H2'   H  HCH1   0   0.267   0.9700   0.8983  -5.0041
 CDM  HO'2  H  HOH1   0   0.468   1.5185  -0.0252  -6.9180
 CDM  H3'   H  HCH1   0   0.243   3.3111   0.6164  -4.5425
 CDM  H4'   H  HCH1   0   0.248   2.9252  -0.8470  -2.2320
 CDM  H3T   H  HOH1   0   0.447   3.1869  -1.6304  -5.5164
 CDM  H5'1  H  HCH2   0   0.229   1.6581   1.8641  -2.8238
 CDM  H5'2  H  HCH2   0   0.212   3.3081   1.5351  -2.2951
 CDM  H1M1  H  HCH2   0   0.235  -0.6378   2.0475   5.2364
 CDM  H1M2  H  HCH2   0   0.217   0.9335   1.3100   5.5210
 CDM  H2M1  H  HCH1   0   0.187  -1.2809  -0.0569   3.9526
 CDM  H2M2  H  HOH1   0   0.453   1.0687  -0.8080   4.0854
 CDM  H4M1  H  HCH2   0   0.190  -2.6164  -1.7725   4.9749
 CDM  H4M2  H  HCH2   0   0.207  -1.2890  -2.4802   5.8969
 CDM  H5M1  H  HCH3   0   0.229   0.2044  -0.9120   7.3347
 CDM  H5M2  H  HCH3   0   0.233  -0.2398   0.7872   7.4856
 CDM  H5M3  H  HCH3   0   0.239  -1.2463  -0.4523   8.2235
 CDM  H3M   H  HOH1   0   0.442  -3.0413   0.5693   5.3793
 CDM  H4M   H  HOH1   0   0.454  -3.2663  -2.8546   6.9576

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
 CDM  N1   C2    single  1.409  0.020  1.409
 CDM  N1   C6    single  1.357  0.020  1.357
 CDM  N1   C1'   single  1.452  0.020  1.452
 CDM  C2   N3    single  1.349  0.020  1.349
 CDM  C2   O2    double  1.222  0.020  1.222
 CDM  N3   C4    double  1.318  0.020  1.318
 CDM  C4   C5    single  1.429  0.020  1.429
 CDM  C4   N4    single  1.332  0.020  1.332
 CDM  C5   C6    double  1.346  0.020  1.346
 CDM  C5   H5    single  0.930  0.020  1.080
 CDM  C6   H6    single  0.930  0.020  1.080
 CDM  N4   H41   single  0.860  0.020  1.020
 CDM  N4   H42   single  0.860  0.020  1.020
 CDM  C1'  C2'   single  1.528  0.020  1.528
 CDM  C1'  O4'   single  1.396  0.020  1.396
 CDM  C1'  H1'   single  0.970  0.020  1.090
 CDM  C2'  O2'   single  1.401  0.020  1.401
 CDM  C2'  C3'   single  1.533  0.020  1.533
 CDM  C2'  H2'   single  0.970  0.020  1.090
 CDM  O2'  HO'2  single  0.850  0.020  0.980
 CDM  C3'  C4'   single  1.525  0.020  1.525
 CDM  C3'  O3'   single  1.406  0.020  1.406
 CDM  C3'  H3'   single  0.970  0.020  1.090
 CDM  C4'  O4'   single  1.429  0.020  1.429
 CDM  C4'  C5'   single  1.515  0.020  1.515
 CDM  C4'  H4'   single  0.970  0.020  1.090
 CDM  O3'  H3T   single  0.850  0.020  0.980
 CDM  C5'  O5'   single  1.414  0.020  1.414
 CDM  C5'  H5'1  single  0.970  0.020  1.090
 CDM  C5'  H5'2  single  0.970  0.020  1.090
 CDM  O5'  PA    single  1.642  0.020  1.642
 CDM  PA   O1A   deloc   1.496  0.020  1.496
 CDM  PA   O2A   deloc   1.496  0.020  1.496
 CDM  PA   O3A   single  1.647  0.020  1.647
 CDM  O3A  PB    single  1.633  0.020  1.633
 CDM  PB   O1B   deloc   1.493  0.020  1.493
 CDM  PB   O2B   deloc   1.512  0.020  1.512
 CDM  PB   O3B   single  1.638  0.020  1.638
 CDM  O3B  C1M   single  1.425  0.020  1.425
 CDM  C1M  C2M   single  1.529  0.020  1.529
 CDM  C1M  H1M1  single  0.970  0.020  1.090
 CDM  C1M  H1M2  single  0.970  0.020  1.090
 CDM  C2M  O2M   single  1.402  0.020  1.402
 CDM  C2M  C3M   single  1.546  0.020  1.546
 CDM  C2M  H2M1  single  0.970  0.020  1.090
 CDM  O2M  H2M2  single  0.850  0.020  0.980
 CDM  C3M  C4M   single  1.532  0.020  1.532
 CDM  C3M  C5M   single  1.523  0.020  1.523
 CDM  C3M  O3M   single  1.418  0.020  1.418
 CDM  C4M  O4M   single  1.409  0.020  1.409
 CDM  C4M  H4M1  single  0.970  0.020  1.090
 CDM  C4M  H4M2  single  0.970  0.020  1.090
 CDM  C5M  H5M1  single  0.970  0.020  1.090
 CDM  C5M  H5M2  single  0.970  0.020  1.090
 CDM  C5M  H5M3  single  0.970  0.020  1.090
 CDM  O3M  H3M   single  0.850  0.020  0.980
 CDM  O4M  H4M   single  0.850  0.020  0.980

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
 CDM  C1'   N1   C6    118.25  3.000
 CDM  C1'   N1   C2    121.71  3.000
 CDM  C6    N1   C2    120.03  3.000
 CDM  O2    C2   N3    122.27  3.000
 CDM  O2    C2   N1    119.66  3.000
 CDM  N3    C2   N1    118.07  3.000
 CDM  C4    N3   C2    121.49  3.000
 CDM  N4    C4   C5    119.64  3.000
 CDM  N4    C4   N3    118.36  3.000
 CDM  C5    C4   N3    122.00  3.000
 CDM  H5    C5   C6    121.22  3.000
 CDM  H5    C5   C4    122.54  3.000
 CDM  C6    C5   C4    116.23  3.000
 CDM  H6    C6   C5    121.45  3.000
 CDM  H6    C6   N1    116.37  3.000
 CDM  C5    C6   N1    122.17  3.000
 CDM  H42   N4   H41   118.10  3.000
 CDM  H42   N4   C4    121.64  3.000
 CDM  H41   N4   C4    120.17  3.000
 CDM  H1'   C1'  O4'   110.21  3.000
 CDM  H1'   C1'  C2'   107.66  3.000
 CDM  O4'   C1'  C2'   106.66  3.000
 CDM  H1'   C1'  N1    104.83  3.000
 CDM  O4'   C1'  N1    110.92  3.000
 CDM  C2'   C1'  N1    116.46  3.000
 CDM  H2'   C2'  C3'   109.43  3.000
 CDM  H2'   C2'  O2'   111.78  3.000
 CDM  C3'   C2'  O2'   114.17  3.000
 CDM  H2'   C2'  C1'   111.06  3.000
 CDM  C3'   C2'  C1'   100.56  3.000
 CDM  O2'   C2'  C1'   109.33  3.000
 CDM  HO'2  O2'  C2'   108.77  3.000
 CDM  H3'   C3'  O3'   111.33  3.000
 CDM  H3'   C3'  C4'   111.81  3.000
 CDM  O3'   C3'  C4'   108.88  3.000
 CDM  H3'   C3'  C2'   111.78  3.000
 CDM  O3'   C3'  C2'   110.90  3.000
 CDM  C4'   C3'  C2'   101.73  3.000
 CDM  H4'   C4'  C5'   108.27  3.000
 CDM  H4'   C4'  O4'   108.21  3.000
 CDM  C5'   C4'  O4'   111.56  3.000
 CDM  H4'   C4'  C3'   110.27  3.000
 CDM  C5'   C4'  C3'   112.33  3.000
 CDM  O4'   C4'  C3'   106.13  3.000
 CDM  C4'   O4'  C1'   110.48  3.000
 CDM  H3T   O3'  C3'   107.67  3.000
 CDM  H5'2  C5'  H5'1  107.40  3.000
 CDM  H5'2  C5'  O5'   112.41  3.000
 CDM  H5'1  C5'  O5'   109.73  3.000
 CDM  H5'2  C5'  C4'   106.85  3.000
 CDM  H5'1  C5'  C4'   111.09  3.000
 CDM  O5'   C5'  C4'   109.34  3.000
 CDM  PA    O5'  C5'   117.18  3.000
 CDM  O3A   PA   O2A   109.38  3.000
 CDM  O3A   PA   O1A   110.13  3.000
 CDM  O2A   PA   O1A   120.62  3.000
 CDM  O3A   PA   O5'    94.02  3.000
 CDM  O2A   PA   O5'   109.54  3.000
 CDM  O1A   PA   O5'   109.91  3.000
 CDM  PB    O3A  PA    123.58  3.000
 CDM  O3B   PB   O2B   108.47  3.000
 CDM  O3B   PB   O1B   110.78  3.000
 CDM  O2B   PB   O1B   119.39  3.000
 CDM  O3B   PB   O3A    94.19  3.000
 CDM  O2B   PB   O3A   109.99  3.000
 CDM  O1B   PB   O3A   111.10  3.000
 CDM  C1M   O3B  PB    119.38  3.000
 CDM  H1M2  C1M  H1M1  107.13  3.000
 CDM  H1M2  C1M  C2M   110.36  3.000
 CDM  H1M1  C1M  C2M   109.75  3.000
 CDM  H1M2  C1M  O3B   111.34  3.000
 CDM  H1M1  C1M  O3B   106.37  3.000
 CDM  C2M   C1M  O3B   111.70  3.000
 CDM  H2M1  C2M  C3M   106.42  3.000
 CDM  H2M1  C2M  O2M   110.66  3.000
 CDM  C3M   C2M  O2M   108.46  3.000
 CDM  H2M1  C2M  C1M   106.10  3.000
 CDM  C3M   C2M  C1M   112.18  3.000
 CDM  O2M   C2M  C1M   112.83  3.000
 CDM  H2M2  O2M  C2M   108.46  3.000
 CDM  O3M   C3M  C5M   106.45  3.000
 CDM  O3M   C3M  C4M   109.80  3.000
 CDM  C5M   C3M  C4M   111.07  3.000
 CDM  O3M   C3M  C2M   109.27  3.000
 CDM  C5M   C3M  C2M   111.83  3.000
 CDM  C4M   C3M  C2M   108.40  3.000
 CDM  H4M2  C4M  H4M1  106.91  3.000
 CDM  H4M2  C4M  O4M   111.48  3.000
 CDM  H4M1  C4M  O4M   111.06  3.000
 CDM  H4M2  C4M  C3M   109.51  3.000
 CDM  H4M1  C4M  C3M   108.36  3.000
 CDM  O4M   C4M  C3M   109.43  3.000
 CDM  H5M3  C5M  H5M2  107.53  3.000
 CDM  H5M3  C5M  H5M1  107.96  3.000
 CDM  H5M2  C5M  H5M1  107.90  3.000
 CDM  H5M3  C5M  C3M   111.10  3.000
 CDM  H5M2  C5M  C3M   111.54  3.000
 CDM  H5M1  C5M  C3M   110.66  3.000
 CDM  H3M   O3M  C3M   108.82  3.000
 CDM  H4M   O4M  C4M   107.73  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
 CDM  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 CDM  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 CDM  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 CDM  CONST_04  C1'   N1   C2   N3    180.00   0.0  0
 CDM  CONST_05  N4    C4   N3   C2    180.00   0.0  0
 CDM  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 CDM  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 CDM  CONST_08  C1'   N1   C2   O2      0.00   0.0  0
 CDM  CONST_09  H41   N4   C4   N3      0.00   0.0  0
 CDM  CONST_10  H42   N4   C4   N3    180.00   0.0  0
 CDM  Var_01    O1A   PA   O5'  C5'   -74.25  30.0  3
 CDM  Var_02    O1B   PB   O3A  PA     48.95  30.0  3
 CDM  Var_03    C2M   C1M  O3B  PB    -91.38  30.0  3
 CDM  Var_04    H5'1  C5'  O5'  PA   -102.21  30.0  1

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
 CDM  chir_01  C1'  N1   C2'  O4'  negativ
 CDM  chir_02  C2'  O2'  C3'  C1'  positiv
 CDM  chir_03  C3'  O3'  C2'  C4'  negativ
 CDM  chir_04  C4'  O4'  C3'  C5'  negativ
 CDM  chir_07  C2M  C1M  O2M  C3M  negativ
 CDM  chir_08  C3M  C5M  C4M  C2M  positiv

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
 CDM  plan-1  N1   0.020
 CDM  plan-1  C2   0.020
 CDM  plan-1  N3   0.020
 CDM  plan-1  C4   0.020
 CDM  plan-1  C5   0.020
 CDM  plan-1  C6   0.020
 CDM  plan-1  O2   0.020
 CDM  plan-1  N4   0.020
 CDM  plan-1  C1'  0.020
 CDM  plan-1  H5   0.020
 CDM  plan-1  H6   0.020
 CDM  plan-1  H41  0.020
 CDM  plan-1  H42  0.020

