# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 26 21:29:16 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: 5'-O-[(R)-{[(S)-{[(2R,3S)-2,4-dihydroxy-3-methyl-3-(phosphonooxy)butyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@](CO)(O[P](O)(O)=O)[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
 SUD  SUD  5'-O-[(R)-{[(S)-{[(2R,3S)-2,4-dihydroxy-3-methyl-3-(phosphonooxy)butyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine  ligand  59  37  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SUD
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
 SUD  C1    C  CH2    0  -0.167   3.7399   0.4212   0.4539
 SUD  N1    N  NR6    0  -0.566  -5.8202  -0.5236  -0.7565
 SUD  C3    C  CR6    0   0.604  -5.3867  -1.3230   0.3206
 SUD  N3    N  N      0  -0.541  -5.4875  -2.6629   0.1983
 SUD  C4    C  CR6    0   0.515  -5.9752  -3.2197  -0.8917
 SUD  C5    C  CR16   0  -0.476  -6.4201  -2.4424  -2.0048
 SUD  C6    C  CR16   0   0.096  -6.3116  -1.1068  -1.8793
 SUD  O8    O  O      0  -0.502  -4.9401  -0.7924   1.3262
 SUD  N4    N  NH2    0  -0.808  -6.0518  -4.5482  -0.9443
 SUD  C1'   C  CH1    0   0.243  -5.7257   0.9249  -0.7202
 SUD  C2'   C  CH1    0  -0.061  -6.4681   1.6265   0.4156
 SUD  O2'   O  OH1    0  -0.661  -7.8212   1.7555   0.0731
 SUD  C3'   C  CH1    0  -0.037  -5.7057   2.9548   0.4756
 SUD  C4'   C  CH1    0  -0.024  -4.2798   2.5139   0.1596
 SUD  O4'   O  O2     0  -0.489  -4.3939   1.3350  -0.6412
 SUD  O3'   O  OH1    0  -0.672  -6.1449   3.8314  -0.5319
 SUD  C5'   C  CH2    0  -0.145  -3.4618   2.2570   1.4078
 SUD  O5'   O  O2     0  -0.620  -2.1772   1.8143   1.0269
 SUD  PA    P  P      0   1.338  -0.9621   2.0604   2.1120
 SUD  O1A   O  O      0  -0.793  -0.6535   3.5236   2.1768
 SUD  O2A   O  OP    -1  -0.801  -1.2385   1.2904   3.3646
 SUD  O3A   O  O2     0  -0.737   0.1536   1.2880   1.1889
 SUD  PB    P  P      0   1.337   1.5184   0.6137   1.8092
 SUD  O1B   O  O      0  -0.804   2.0728   1.4720   2.9034
 SUD  O2B   O  O2     0  -0.620   2.3835   0.8337   0.4305
 SUD  O3B   O  OP    -1  -0.794   1.3019  -0.8507   2.0324
 SUD  C27   C  CH1    0  -0.007   4.3121   0.5410  -0.9501
 SUD  C28   C  CT     0   0.208   5.7012  -0.1370  -1.0664
 SUD  C29   C  CH2    0  -0.143   6.2947   0.1001  -2.4562
 SUD  O30   O  OH1    0  -0.683   5.3935  -0.3311  -3.4538
 SUD  O31   O  O2     0  -0.674   5.4431  -1.5042  -0.8823
 SUD  C32   C  CH3    0  -0.735   6.6819   0.4546  -0.0483
 SUD  O33   O  OH1    0  -0.667   4.3138   1.8818  -1.3932
 SUD  P34   P  P      0   1.237   6.5676  -2.6629  -0.3343
 SUD  O35   O  O      0  -0.893   7.8602  -2.4142  -1.1101
 SUD  O36   O  OP    -1  -0.897   6.6909  -2.4445   1.1700
 SUD  O37   O  OP    -1  -0.900   5.8306  -3.9406  -0.7212
 SUD  H11   H  HCH2   0   0.215   3.8362  -0.6138   0.7941
 SUD  H12   H  HCH2   0   0.196   4.3099   1.0464   1.1529
 SUD  H5    H  HCR6   0   0.289  -6.8173  -2.8899  -2.9028
 SUD  H6    H  HCR6   0   0.319  -6.6151  -0.4392  -2.6739
 SUD  HN41  H  HNH2   0   0.414  -6.3981  -5.0241  -1.7586
 SUD  HN42  H  HNH2   0   0.403  -5.7271  -5.1055  -0.1724
 SUD  H1'   H  HCH1   0   0.238  -6.1716   1.2589  -1.6654
 SUD  H2'   H  HCH1   0   0.269  -6.3396   1.0909   1.3573
 SUD  H1    H  HOH1   0   0.468  -8.3329   1.8753   0.8787
 SUD  H3'   H  HCH1   0   0.242  -5.7765   3.4188   1.4686
 SUD  H4'   H  HCH1   0   0.247  -3.7728   3.2833  -0.4329
 SUD  H2    H  HOH1   0   0.446  -7.1086   3.7899  -0.5543
 SUD  H5'1  H  HCH2   0   0.225  -3.9508   1.5197   2.0498
 SUD  H5'2  H  HCH2   0   0.207  -3.4165   3.2029   1.9615
 SUD  H27   H  HCH1   0   0.227   3.6382   0.0126  -1.6310
 SUD  H291  H  HCH2   0   0.171   6.5388   1.1636  -2.5748
 SUD  H292  H  HCH2   0   0.204   7.2315  -0.4650  -2.4957
 SUD  H30   H  HOH1   0   0.448   5.8092  -0.1828  -4.3070
 SUD  H321  H  HCH3   0   0.200   6.7121   1.5451  -0.1072
 SUD  H322  H  HCH3   0   0.242   6.4270   0.1698   0.9694
 SUD  H323  H  HCH3   0   0.238   7.6907   0.0922  -0.2408
 SUD  H33   H  HOH1   0   0.434   4.8416   2.4100  -0.7858

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
 SUD  C1   O2B   single  1.418  0.020  1.418
 SUD  C1   C27   single  1.521  0.020  1.521
 SUD  C1   H11   single  0.970  0.020  1.090
 SUD  C1   H12   single  0.970  0.020  1.090
 SUD  N1   C3    single  1.410  0.020  1.410
 SUD  N1   C6    single  1.357  0.020  1.357
 SUD  N1   C1'   single  1.452  0.020  1.452
 SUD  C3   N3    single  1.349  0.020  1.349
 SUD  C3   O8    double  1.222  0.020  1.222
 SUD  N3   C4    double  1.318  0.020  1.318
 SUD  C4   C5    single  1.429  0.020  1.429
 SUD  C4   N4    single  1.332  0.020  1.332
 SUD  C5   C6    double  1.346  0.020  1.346
 SUD  C5   H5    single  0.930  0.020  1.080
 SUD  C6   H6    single  0.930  0.020  1.080
 SUD  N4   HN41  single  0.860  0.020  1.020
 SUD  N4   HN42  single  0.860  0.020  1.020
 SUD  C1'  C2'   single  1.528  0.020  1.528
 SUD  C1'  O4'   single  1.396  0.020  1.396
 SUD  C1'  H1'   single  0.970  0.020  1.090
 SUD  C2'  O2'   single  1.402  0.020  1.402
 SUD  C2'  C3'   single  1.533  0.020  1.533
 SUD  C2'  H2'   single  0.970  0.020  1.090
 SUD  O2'  H1    single  0.850  0.020  0.980
 SUD  C3'  C4'   single  1.526  0.020  1.526
 SUD  C3'  O3'   single  1.406  0.020  1.406
 SUD  C3'  H3'   single  0.970  0.020  1.090
 SUD  C4'  O4'   single  1.430  0.020  1.430
 SUD  C4'  C5'   single  1.514  0.020  1.514
 SUD  C4'  H4'   single  0.970  0.020  1.090
 SUD  O3'  H2    single  0.850  0.020  0.980
 SUD  C5'  O5'   single  1.411  0.020  1.411
 SUD  C5'  H5'1  single  0.970  0.020  1.090
 SUD  C5'  H5'2  single  0.970  0.020  1.090
 SUD  O5'  PA    single  1.648  0.020  1.648
 SUD  PA   O1A   deloc   1.497  0.020  1.497
 SUD  PA   O2A   deloc   1.496  0.020  1.496
 SUD  PA   O3A   single  1.641  0.020  1.641
 SUD  O3A  PB    single  1.644  0.020  1.644
 SUD  PB   O1B   deloc   1.497  0.020  1.497
 SUD  PB   O2B   single  1.642  0.020  1.642
 SUD  PB   O3B   deloc   1.497  0.020  1.497
 SUD  C27  C28   single  1.550  0.020  1.550
 SUD  C27  O33   single  1.412  0.020  1.412
 SUD  C27  H27   single  0.970  0.020  1.090
 SUD  C28  C29   single  1.530  0.020  1.530
 SUD  C28  O31   single  1.403  0.020  1.403
 SUD  C28  C32   single  1.533  0.020  1.533
 SUD  C29  O30   single  1.412  0.020  1.412
 SUD  C29  H291  single  0.970  0.020  1.090
 SUD  C29  H292  single  0.970  0.020  1.090
 SUD  O30  H30   single  0.850  0.020  0.980
 SUD  O31  P34   single  1.705  0.020  1.705
 SUD  C32  H321  single  0.970  0.020  1.090
 SUD  C32  H322  single  0.970  0.020  1.090
 SUD  C32  H323  single  0.970  0.020  1.090
 SUD  O33  H33   single  0.850  0.020  0.980
 SUD  P34  O35   deloc   1.528  0.020  1.528
 SUD  P34  O36   deloc   1.525  0.020  1.525
 SUD  P34  O37   deloc   1.525  0.020  1.525

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
 SUD  H12   C1   H11   107.17  3.000
 SUD  H12   C1   C27   110.35  3.000
 SUD  H11   C1   C27   109.19  3.000
 SUD  H12   C1   O2B   109.97  3.000
 SUD  H11   C1   O2B   111.38  3.000
 SUD  C27   C1   O2B   108.77  3.000
 SUD  C1'   N1   C6    118.22  3.000
 SUD  C1'   N1   C3    121.78  3.000
 SUD  C6    N1   C3    119.98  3.000
 SUD  O8    C3   N3    122.23  3.000
 SUD  O8    C3   N1    119.68  3.000
 SUD  N3    C3   N1    118.09  3.000
 SUD  C4    N3   C3    121.49  3.000
 SUD  N4    C4   C5    119.61  3.000
 SUD  N4    C4   N3    118.39  3.000
 SUD  C5    C4   N3    122.00  3.000
 SUD  H5    C5   C6    121.25  3.000
 SUD  H5    C5   C4    122.50  3.000
 SUD  C6    C5   C4    116.24  3.000
 SUD  H6    C6   C5    121.44  3.000
 SUD  H6    C6   N1    116.37  3.000
 SUD  C5    C6   N1    122.19  3.000
 SUD  HN42  N4   HN41  118.09  3.000
 SUD  HN42  N4   C4    120.25  3.000
 SUD  HN41  N4   C4    121.62  3.000
 SUD  H1'   C1'  O4'   110.31  3.000
 SUD  H1'   C1'  C2'   107.65  3.000
 SUD  O4'   C1'  C2'   106.66  3.000
 SUD  H1'   C1'  N1    104.82  3.000
 SUD  O4'   C1'  N1    110.90  3.000
 SUD  C2'   C1'  N1    116.43  3.000
 SUD  H2'   C2'  C3'   109.45  3.000
 SUD  H2'   C2'  O2'   111.71  3.000
 SUD  C3'   C2'  O2'   114.20  3.000
 SUD  H2'   C2'  C1'   111.04  3.000
 SUD  C3'   C2'  C1'   100.69  3.000
 SUD  O2'   C2'  C1'   109.26  3.000
 SUD  H1    O2'  C2'   108.68  3.000
 SUD  H3'   C3'  O3'   111.37  3.000
 SUD  H3'   C3'  C4'   111.69  3.000
 SUD  O3'   C3'  C4'   108.89  3.000
 SUD  H3'   C3'  C2'   111.69  3.000
 SUD  O3'   C3'  C2'   110.91  3.000
 SUD  C4'   C3'  C2'   101.91  3.000
 SUD  H4'   C4'  C5'   108.36  3.000
 SUD  H4'   C4'  O4'   108.25  3.000
 SUD  C5'   C4'  O4'   111.40  3.000
 SUD  H4'   C4'  C3'   109.98  3.000
 SUD  C5'   C4'  C3'   112.53  3.000
 SUD  O4'   C4'  C3'   106.24  3.000
 SUD  C4'   O4'  C1'   110.50  3.000
 SUD  H2    O3'  C3'   107.57  3.000
 SUD  H5'2  C5'  H5'1  107.68  3.000
 SUD  H5'2  C5'  O5'   111.67  3.000
 SUD  H5'1  C5'  O5'   110.74  3.000
 SUD  H5'2  C5'  C4'   106.98  3.000
 SUD  H5'1  C5'  C4'   110.90  3.000
 SUD  O5'   C5'  C4'   108.81  3.000
 SUD  PA    O5'  C5'   116.54  3.000
 SUD  O3A   PA   O2A   110.75  3.000
 SUD  O3A   PA   O1A   110.14  3.000
 SUD  O2A   PA   O1A   120.33  3.000
 SUD  O3A   PA   O5'    93.48  3.000
 SUD  O2A   PA   O5'   109.77  3.000
 SUD  O1A   PA   O5'   109.06  3.000
 SUD  PB    O3A  PA    123.04  3.000
 SUD  O3B   PB   O2B   109.42  3.000
 SUD  O3B   PB   O1B   120.36  3.000
 SUD  O2B   PB   O1B   109.98  3.000
 SUD  O3B   PB   O3A   109.72  3.000
 SUD  O2B   PB   O3A    93.76  3.000
 SUD  O1B   PB   O3A   110.37  3.000
 SUD  PB    O2B  C1    116.81  3.000
 SUD  H27   C27  O33   105.31  3.000
 SUD  H27   C27  C28   107.10  3.000
 SUD  O33   C27  C28   113.00  3.000
 SUD  H27   C27  C1    107.75  3.000
 SUD  O33   C27  C1    111.40  3.000
 SUD  C28   C27  C1    111.84  3.000
 SUD  C32   C28  O31   113.99  3.000
 SUD  C32   C28  C29   107.18  3.000
 SUD  O31   C28  C29   109.97  3.000
 SUD  C32   C28  C27   110.78  3.000
 SUD  O31   C28  C27   104.57  3.000
 SUD  C29   C28  C27   110.37  3.000
 SUD  H292  C29  H291  107.82  3.000
 SUD  H292  C29  O30   111.29  3.000
 SUD  H291  C29  O30   111.20  3.000
 SUD  H292  C29  C28   106.54  3.000
 SUD  H291  C29  C28   109.55  3.000
 SUD  O30   C29  C28   110.30  3.000
 SUD  H30   O30  C29   107.71  3.000
 SUD  P34   O31  C28   125.66  3.000
 SUD  H323  C32  H322  107.19  3.000
 SUD  H323  C32  H321  107.28  3.000
 SUD  H322  C32  H321  108.57  3.000
 SUD  H323  C32  C28   110.29  3.000
 SUD  H322  C32  C28   111.76  3.000
 SUD  H321  C32  C28   111.54  3.000
 SUD  H33   O33  C27   108.89  3.000
 SUD  O37   P34  O36   114.17  3.000
 SUD  O37   P34  O35   114.61  3.000
 SUD  O36   P34  O35   114.15  3.000
 SUD  O37   P34  O31    99.74  3.000
 SUD  O36   P34  O31   105.85  3.000
 SUD  O35   P34  O31   106.50  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
 SUD  CONST_01  C4    N3   C3   N1     0.00   0.0  0
 SUD  CONST_02  C5    C4   N3   C3     0.00   0.0  0
 SUD  CONST_03  C6    N1   C3   N3     0.00   0.0  0
 SUD  CONST_04  C1'   N1   C3   N3   180.00   0.0  0
 SUD  CONST_05  N4    C4   N3   C3   180.00   0.0  0
 SUD  CONST_06  O8    C3   N3   C4   180.00   0.0  0
 SUD  CONST_07  O8    C3   N1   C6   180.00   0.0  0
 SUD  CONST_08  C1'   N1   C3   O8     0.00   0.0  0
 SUD  CONST_09  HN41  N4   C4   N3   180.00   0.0  0
 SUD  CONST_10  HN42  N4   C4   N3     0.00   0.0  0
 SUD  Var_01    O3A   PB   O2B  C1   178.34  30.0  1
 SUD  Var_02    O1A   PA   O5'  C5'  -70.91  30.0  3
 SUD  Var_03    C27   C1   O2B  PB   172.88  30.0  1
 SUD  Var_04    O35   P34  O31  C28  -45.47  30.0  3
 SUD  Var_05    H5'1  C5'  O5'  PA   -82.15  30.0  2

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
 SUD  chir_01  C1'  N1   C2'  O4'  negativ
 SUD  chir_02  C2'  O2'  C3'  C1'  positiv
 SUD  chir_03  C3'  O3'  C2'  C4'  negativ
 SUD  chir_04  C4'  O4'  C3'  C5'  negativ
 SUD  chir_07  C27  C1   C28  O33  positiv
 SUD  chir_08  C28  C32  C29  C27  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
 SUD  plan-1  N1    0.020
 SUD  plan-1  C3    0.020
 SUD  plan-1  N3    0.020
 SUD  plan-1  C4    0.020
 SUD  plan-1  C5    0.020
 SUD  plan-1  C6    0.020
 SUD  plan-1  O8    0.020
 SUD  plan-1  N4    0.020
 SUD  plan-1  C1'   0.020
 SUD  plan-1  H5    0.020
 SUD  plan-1  H6    0.020
 SUD  plan-1  HN41  0.020
 SUD  plan-1  HN42  0.020

