# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 09:46:46 2021
#   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  58  33  .  2021-08-07  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.558  49.2416  -15.6656  31.4614
 CDM  C2    C  CR6   0   0.597  48.0623  -16.0984  32.0965
 CDM  N3    N  N     0  -0.543  48.1295  -17.2011  32.8698
 CDM  C4    C  CR6   0   0.519  49.2587  -17.8631  33.0234
 CDM  C5    C  CR16  0  -0.483  50.4708  -17.4571  32.3828
 CDM  C6    C  CR16  0   0.100  50.4005  -16.3535  31.6163
 CDM  O2    O  O     0  -0.516  47.0233  -15.4733  31.9356
 CDM  N4    N  NH2   0  -0.808  49.2571  -18.9454  33.7987
 CDM  C1'   C  CR15  0   0.186  49.2215  -14.4901  30.6142
 CDM  C2'   C  CR15  0   0.004  50.0558  -13.3212  31.1366
 CDM  O2'   O  OH1   0  -0.653  49.3400  -12.6384  32.1151
 CDM  C3'   C  CR15  0  -0.053  50.3371  -12.5569  29.8413
 CDM  C4'   C  CR15  0  -0.018  50.4942  -13.7072  28.8307
 CDM  O4'   O  O     0  -0.496  49.7777  -14.8161  29.3656
 CDM  O3'   O  OH1   0  -0.665  49.2134  -11.7648  29.5606
 CDM  C5'   C  CH2   0  -0.206  51.9212  -14.0960  28.5234
 CDM  O5'   O  O2    0  -0.588  52.6041  -14.3965  29.7453
 CDM  PA    P  P     0   1.520  54.1872  -14.4176  29.8427
 CDM  O1A   O  O     0  -0.666  54.9103  -13.2090  29.4253
 CDM  O2A   O  OH1   0  -0.723  54.3248  -14.9269  31.3346
 CDM  O3A   O  O2    0  -0.712  54.6251  -15.6696  28.9074
 CDM  PB    P  P     0   1.488  54.6604  -17.2655  29.1746
 CDM  O1B   O  OH1   0  -0.742  53.1815  -17.4887  29.7228
 CDM  O2B   O  O     0  -0.667  55.7703  -17.7467  30.0069
 CDM  O3B   O  O2    0  -0.571  54.7266  -17.8305  27.7005
 CDM  C1M   C  CH2   0  -0.190  53.7700  -17.4816  26.6859
 CDM  C2M   C  CH1   0   0.011  53.7389  -18.6024  25.6695
 CDM  O2M   O  OH1   0  -0.668  53.1709  -19.7237  26.2985
 CDM  C3M   C  CT    0   0.157  52.9572  -18.1887  24.4010
 CDM  C4M   C  CH2   0  -0.171  52.7157  -19.4055  23.5062
 CDM  C5M   C  CH3   0  -0.719  51.5953  -17.5794  24.7286
 CDM  O3M   O  OH1   0  -0.674  53.7992  -17.2499  23.7567
 CDM  O4M   O  OH1   0  -0.673  53.9105  -20.1302  23.3349
 CDM  H5    H  HCR6  0   0.285  51.3960  -18.0006  32.5021
 CDM  H6    H  HCR6  0   0.315  51.2639  -15.9810  31.0855
 CDM  H41   H  HNH2  0   0.415  50.0936  -19.4772  33.9621
 CDM  H42   H  HNH2  0   0.404  48.4170  -19.2249  34.2760
 CDM  H1'   H  HCR5  0   0.270  48.1763  -14.1895  30.5209
 CDM  H2'   H  HCR5  0   0.242  51.0111  -13.6971  31.5252
 CDM  HO'2  H  HOH1  0   0.462  49.9239  -12.0005  32.5368
 CDM  H3'   H  HCR5  0   0.254  51.2494  -11.9502  29.9035
 CDM  H4'   H  HCR5  0   0.272  50.0518  -13.4204  27.8695
 CDM  H3T   H  HOH1  0   0.457  49.3638  -11.3093  28.7265
 CDM  H5'1  H  HCH2  0   0.256  51.9404  -14.9709  27.8692
 CDM  H5'2  H  HCH2  0   0.264  52.4055  -13.2678  28.0006
 CDM  HO2A  H  HOH1  0   0.514  55.1490  -14.6702  31.7720
 CDM  HO1B  H  HOH1  0   0.507  53.0420  -18.3435  30.1537
 CDM  H1M1  H  HCH2  0   0.237  52.7801  -17.3489  27.1301
 CDM  H1M2  H  HCH2  0   0.261  54.0753  -16.5449  26.2192
 CDM  H2M1  H  HCH1  0   0.241  54.7730  -18.8047  25.3619
 CDM  H2M2  H  HOH1  0   0.457  53.4463  -20.5090  25.8150
 CDM  H4M1  H  HCH2  0   0.207  51.9278  -20.0254  23.9504
 CDM  H4M2  H  HCH2  0   0.216  52.3212  -19.0432  22.5461
 CDM  H5M1  H  HCH3  0   0.247  51.0096  -17.4353  23.8176
 CDM  H5M2  H  HCH3  0   0.242  51.0192  -18.2273  25.3895
 CDM  H5M3  H  HCH3  0   0.245  51.6918  -16.6028  25.2053
 CDM  H3M   H  HOH1  0   0.451  53.3149  -16.8540  23.0243
 CDM  H4M   H  HOH1  0   0.460  53.7078  -20.9316  22.8441

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  1.408  0.020  1.408
 CDM  N1   C6    single  1.357  0.020  1.357
 CDM  N1   C1'   single  1.449  0.020  1.449
 CDM  C2   N3    single  1.349  0.020  1.349
 CDM  C2   O2    double  1.223  0.020  1.223
 CDM  N3   C4    double  1.318  0.020  1.318
 CDM  C4   C5    single  1.430  0.020  1.430
 CDM  C4   N4    single  1.331  0.020  1.331
 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  1.405  0.020  1.405
 CDM  C1'  H1'   single  0.970  0.020  1.090
 CDM  C2'  O2'   single  1.391  0.020  1.391
 CDM  C2'  C3'   single  1.530  0.020  1.530
 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  1.539  0.020  1.539
 CDM  C3'  O3'   single  1.403  0.020  1.403
 CDM  C3'  H3'   single  0.970  0.020  1.090
 CDM  C4'  O4'   single  1.425  0.020  1.425
 CDM  C4'  C5'   single  1.511  0.020  1.511
 CDM  C4'  H4'   single  0.970  0.020  1.090
 CDM  O3'  H3T   single  0.850  0.020  0.980
 CDM  C5'  O5'   single  1.432  0.020  1.432
 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  1.586  0.020  1.586
 CDM  PA   O1A   double  1.469  0.020  1.469
 CDM  PA   O2A   single  1.582  0.020  1.582
 CDM  PA   O3A   single  1.623  0.020  1.623
 CDM  O2A  HO2A  single  0.850  0.020  0.980
 CDM  O3A  PB    single  1.619  0.020  1.619
 CDM  PB   O1B   single  1.593  0.020  1.593
 CDM  PB   O2B   double  1.468  0.020  1.468
 CDM  PB   O3B   single  1.580  0.020  1.580
 CDM  O1B  HO1B  single  0.850  0.020  0.980
 CDM  O3B  C1M   single  1.437  0.020  1.437
 CDM  C1M  C2M   single  1.513  0.020  1.513
 CDM  C1M  H1M1  single  0.970  0.020  1.090
 CDM  C1M  H1M2  single  0.970  0.020  1.090
 CDM  C2M  O2M   single  1.406  0.020  1.406
 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  1.530  0.020  1.530
 CDM  C3M  C5M   single  1.528  0.020  1.528
 CDM  C3M  O3M   single  1.416  0.020  1.416
 CDM  C4M  O4M   single  1.408  0.020  1.408
 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    119.34  3.000
 CDM  C1'   N1   C2    120.10  3.000
 CDM  C6    N1   C2    120.55  3.000
 CDM  O2    C2   N3    122.38  3.000
 CDM  O2    C2   N1    119.69  3.000
 CDM  N3    C2   N1    117.93  3.000
 CDM  C4    N3   C2    121.35  3.000
 CDM  N4    C4   C5    119.52  3.000
 CDM  N4    C4   N3    118.37  3.000
 CDM  C5    C4   N3    122.11  3.000
 CDM  H5    C5   C6    121.37  3.000
 CDM  H5    C5   C4    122.28  3.000
 CDM  C6    C5   C4    116.35  3.000
 CDM  H6    C6   C5    121.41  3.000
 CDM  H6    C6   N1    116.88  3.000
 CDM  C5    C6   N1    121.71  3.000
 CDM  H42   N4   H41   118.11  3.000
 CDM  H42   N4   C4    120.22  3.000
 CDM  H41   N4   C4    121.60  3.000
 CDM  H1'   C1'  O4'   111.53  3.000
 CDM  H1'   C1'  C2'   109.96  3.000
 CDM  O4'   C1'  C2'   105.38  3.000
 CDM  H1'   C1'  N1    106.65  3.000
 CDM  O4'   C1'  N1    109.01  3.000
 CDM  C2'   C1'  N1    114.39  3.000
 CDM  H2'   C2'  C3'   108.11  3.000
 CDM  H2'   C2'  O2'   111.52  3.000
 CDM  C3'   C2'  O2'   116.41  3.000
 CDM  H2'   C2'  C1'   109.52  3.000
 CDM  C3'   C2'  C1'   101.13  3.000
 CDM  O2'   C2'  C1'   109.57  3.000
 CDM  HO'2  O2'  C2'   108.74  3.000
 CDM  H3'   C3'  O3'   111.41  3.000
 CDM  H3'   C3'  C4'   111.44  3.000
 CDM  O3'   C3'  C4'   111.86  3.000
 CDM  H3'   C3'  C2'   112.40  3.000
 CDM  O3'   C3'  C2'   107.70  3.000
 CDM  C4'   C3'  C2'   101.61  3.000
 CDM  H4'   C4'  C5'   105.67  3.000
 CDM  H4'   C4'  O4'   109.26  3.000
 CDM  C5'   C4'  O4'   110.56  3.000
 CDM  H4'   C4'  C3'   109.82  3.000
 CDM  C5'   C4'  C3'   114.98  3.000
 CDM  O4'   C4'  C3'   106.50  3.000
 CDM  C4'   O4'  C1'   110.61  3.000
 CDM  H3T   O3'  C3'   108.39  3.000
 CDM  H5'2  C5'  H5'1  108.22  3.000
 CDM  H5'2  C5'  O5'   110.85  3.000
 CDM  H5'1  C5'  O5'   109.54  3.000
 CDM  H5'2  C5'  C4'   108.73  3.000
 CDM  H5'1  C5'  C4'   110.15  3.000
 CDM  O5'   C5'  C4'   109.33  3.000
 CDM  PA    O5'  C5'   122.09  3.000
 CDM  O3A   PA   O2A   105.76  3.000
 CDM  O3A   PA   O1A   109.76  3.000
 CDM  O2A   PA   O1A   119.33  3.000
 CDM  O3A   PA   O5'   104.13  3.000
 CDM  O2A   PA   O5'    98.57  3.000
 CDM  O1A   PA   O5'   117.57  3.000
 CDM  HO2A  O2A  PA    114.51  3.000
 CDM  PB    O3A  PA    132.17  3.000
 CDM  O3B   PB   O2B   112.33  3.000
 CDM  O3B   PB   O1B   108.05  3.000
 CDM  O2B   PB   O1B   117.44  3.000
 CDM  O3B   PB   O3A   101.51  3.000
 CDM  O2B   PB   O3A   115.67  3.000
 CDM  O1B   PB   O3A   100.06  3.000
 CDM  HO1B  O1B  PB    114.26  3.000
 CDM  C1M   O3B  PB    122.95  3.000
 CDM  H1M2  C1M  H1M1  108.86  3.000
 CDM  H1M2  C1M  C2M   110.77  3.000
 CDM  H1M1  C1M  C2M   110.13  3.000
 CDM  H1M2  C1M  O3B   108.93  3.000
 CDM  H1M1  C1M  O3B   110.20  3.000
 CDM  C2M   C1M  O3B   107.94  3.000
 CDM  H2M1  C2M  C3M   107.20  3.000
 CDM  H2M1  C2M  O2M   111.04  3.000
 CDM  C3M   C2M  O2M   112.10  3.000
 CDM  H2M1  C2M  C1M   107.78  3.000
 CDM  C3M   C2M  C1M   111.29  3.000
 CDM  O2M   C2M  C1M   107.37  3.000
 CDM  H2M2  O2M  C2M   108.09  3.000
 CDM  O3M   C3M  C5M   111.30  3.000
 CDM  O3M   C3M  C4M   110.80  3.000
 CDM  C5M   C3M  C4M   107.58  3.000
 CDM  O3M   C3M  C2M   104.48  3.000
 CDM  C5M   C3M  C2M   112.43  3.000
 CDM  C4M   C3M  C2M   110.29  3.000
 CDM  H4M2  C4M  H4M1  106.39  3.000
 CDM  H4M2  C4M  O4M   111.59  3.000
 CDM  H4M1  C4M  O4M   111.59  3.000
 CDM  H4M2  C4M  C3M   107.78  3.000
 CDM  H4M1  C4M  C3M   109.04  3.000
 CDM  O4M   C4M  C3M   110.29  3.000
 CDM  H5M3  C5M  H5M2  108.29  3.000
 CDM  H5M3  C5M  H5M1  107.08  3.000
 CDM  H5M2  C5M  H5M1  107.49  3.000
 CDM  H5M3  C5M  C3M   111.83  3.000
 CDM  H5M2  C5M  C3M   111.36  3.000
 CDM  H5M1  C5M  C3M   110.60  3.000
 CDM  H3M   O3M  C3M   108.63  3.000
 CDM  H4M   O4M  C4M   108.20  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
 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    180.00   0.0  0
 CDM  CONST_10  H42   N4   C4   N3      0.00   0.0  0
 CDM  Var_01    O1A   PA   O5'  C5'    55.41  30.0  3
 CDM  Var_02    O1B   PB   O3A  PA     51.12  30.0  3
 CDM  Var_03    C2M   C1M  O3B  PB   -154.91  30.0  3
 CDM  Var_04    H5'1  C5'  O5'  PA     77.76  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
 CDM  chir_09  PA   O1A  O2A  O3A  both
 CDM  chir_10  PB   O1B  O2B  O3B  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
 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

