# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:22:47 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 5'-O-[(S)-{[(R)-(2-aminoethyl)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[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
 0RC  0RC  5'-O-[(S)-{[(R)-(2-aminoethyl)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine  ligand  47  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0RC
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
 0RC  O3B   O  O     0  -0.683  -3.6210  -1.8364  -1.3134
 0RC  PB    P  P     0   1.386  -4.1216  -0.8121  -0.3766
 0RC  O2B   O  OH1   0  -0.743  -5.1995   0.1288  -1.0950
 0RC  C1B   C  CH2   0  -0.751  -4.8056  -1.3910   1.1772
 0RC  C14   C  CH2   0  -0.279  -5.9423  -2.3919   0.9719
 0RC  N15   N  NH2   0  -0.795  -6.3999  -2.8707   2.2641
 0RC  O3A   O  O2    0  -0.693  -2.9650   0.2205   0.1625
 0RC  PA    P  P     0   1.475  -2.1571   1.3122  -0.7078
 0RC  O1A   O  O     0  -0.692  -2.1075   1.0791  -2.1586
 0RC  O2A   O  OH1   0  -0.724  -2.8462   2.7060  -0.3803
 0RC  O5'   O  O2    0  -0.580  -0.7856   1.2547   0.0928
 0RC  C5'   C  CH2   0  -0.187   0.3812   1.8797  -0.4670
 0RC  C4'   C  CR15  0   0.019   1.4540   1.9299   0.5885
 0RC  C3'   C  CR15  0  -0.037   2.7207   2.6133   0.0684
 0RC  O3'   O  OH1   0  -0.662   2.6739   3.9851   0.3684
 0RC  C2'   C  CR15  0  -0.042   3.8417   1.8752   0.8240
 0RC  O2'   O  OH1   0  -0.676   4.1536   2.5484   2.0169
 0RC  O4'   O  O     0  -0.489   1.8261   0.6194   0.9599
 0RC  C1'   C  CR15  0   0.202   3.2029   0.5293   1.2070
 0RC  N1    N  NR6   0  -0.556   3.7375  -0.6547   0.5568
 0RC  C6    C  CR16  0   0.102   4.1813  -1.6811   1.3247
 0RC  C5    C  CR16  0  -0.476   4.6439  -2.8241   0.7845
 0RC  C4    C  CR6   0   0.517   4.6239  -2.9033  -0.6423
 0RC  N4    N  NH2   0  -0.807   5.0588  -4.0076  -1.2449
 0RC  N3    N  N     0  -0.540   4.1825  -1.9127  -1.3930
 0RC  C2    C  CR6   0   0.606   3.7314  -0.7691  -0.8427
 0RC  O2    O  O     0  -0.510   3.3235   0.1691  -1.5139
 0RC  HO2B  H  HOH1  0   0.498  -5.6724   0.7557  -0.5309
 0RC  H1B1  H  HCH2  0   0.300  -3.9974  -1.8584   1.7443
 0RC  H1B2  H  HCH2  0   0.291  -5.1506  -0.5305   1.7575
 0RC  H141  H  HCH2  0   0.213  -6.7325  -1.9297   0.3664
 0RC  H142  H  HCH2  0   0.239  -5.5712  -3.2454   0.4022
 0RC  H151  H  HNH2  0   0.344  -6.8821  -2.1253   2.7512
 0RC  H152  H  HNH2  0   0.355  -7.0891  -3.5984   2.1249
 0RC  HO2A  H  HOH1  0   0.503  -2.8908   2.9592   0.5522
 0RC  H5'1  H  HCH2  0   0.255   0.7241   1.3071  -1.3307
 0RC  H5'2  H  HCH2  0   0.251   0.1590   2.9019  -0.7857
 0RC  H4'   H  HCR5  0   0.246   1.0832   2.4820   1.4636
 0RC  H3'   H  HCR5  0   0.266   2.8344   2.4481  -1.0032
 0RC  HO3'  H  HOH1  0   0.471   3.1795   4.4668  -0.2938
 0RC  H2'   H  HCR5  0   0.249   4.7352   1.7431   0.2049
 0RC  HO2'  H  HOH1  0   0.448   3.9308   3.4797   1.8805
 0RC  H1'   H  HCR5  0   0.256   3.3833   0.3710   2.2743
 0RC  H6    H  HCR6  0   0.321   4.1461  -1.5314   2.3950
 0RC  H5    H  HCR6  0   0.290   4.9990  -3.6342   1.4032
 0RC  HN41  H  HNH2  0   0.415   5.4067  -4.7907  -0.7209
 0RC  HN42  H  HNH2  0   0.404   5.0413  -4.0786  -2.2481

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
 0RC  O2   C2    double  1.224  0.020  1.224
 0RC  N3   C2    single  1.347  0.020  1.347
 0RC  N3   C4    double  1.319  0.020  1.319
 0RC  C2   N1    single  1.404  0.020  1.404
 0RC  N15  C14   single  1.452  0.020  1.452
 0RC  O4'  C1'   single  1.402  0.020  1.402
 0RC  O4'  C4'   single  1.412  0.020  1.412
 0RC  N4   C4    single  1.331  0.020  1.331
 0RC  C4   C5    single  1.429  0.020  1.429
 0RC  N1   C1'   single  1.453  0.020  1.453
 0RC  N1   C6    single  1.357  0.020  1.357
 0RC  C1'  C2'   single  1.538  0.020  1.538
 0RC  C4'  C5'   single  1.506  0.020  1.506
 0RC  C4'  C3'   single  1.530  0.020  1.530
 0RC  C14  C1B   single  1.528  0.020  1.528
 0RC  C5   C6    double  1.346  0.020  1.346
 0RC  C5'  O5'   single  1.437  0.020  1.437
 0RC  O3'  C3'   single  1.405  0.020  1.405
 0RC  C1B  PB    single  1.794  0.020  1.794
 0RC  C3'  C2'   single  1.540  0.020  1.540
 0RC  C2'  O2'   single  1.405  0.020  1.405
 0RC  O5'  PA    single  1.589  0.020  1.589
 0RC  O3A  PB    single  1.642  0.020  1.642
 0RC  O3A  PA    single  1.613  0.020  1.613
 0RC  PB   O3B   double  1.476  0.020  1.476
 0RC  PB   O2B   single  1.601  0.020  1.601
 0RC  PA   O1A   double  1.470  0.020  1.470
 0RC  PA   O2A   single  1.589  0.020  1.589
 0RC  O2B  HO2B  single  0.850  0.020  0.980
 0RC  C1B  H1B1  single  0.970  0.020  1.090
 0RC  C1B  H1B2  single  0.970  0.020  1.090
 0RC  C14  H141  single  0.970  0.020  1.090
 0RC  C14  H142  single  0.970  0.020  1.090
 0RC  N15  H151  single  0.890  0.020  1.040
 0RC  N15  H152  single  0.890  0.020  1.040
 0RC  O2A  HO2A  single  0.850  0.020  0.980
 0RC  C5'  H5'1  single  0.970  0.020  1.090
 0RC  C5'  H5'2  single  0.970  0.020  1.090
 0RC  C4'  H4'   single  0.970  0.020  1.090
 0RC  C3'  H3'   single  0.970  0.020  1.090
 0RC  O3'  HO3'  single  0.850  0.020  0.980
 0RC  C2'  H2'   single  0.970  0.020  1.090
 0RC  O2'  HO2'  single  0.850  0.020  0.980
 0RC  C1'  H1'   single  0.970  0.020  1.090
 0RC  C6   H6    single  0.930  0.020  1.080
 0RC  C5   H5    single  0.930  0.020  1.080
 0RC  N4   HN41  single  0.860  0.020  1.020
 0RC  N4   HN42  single  0.860  0.020  1.020

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
 0RC  O3A   PB   C1B   100.79  3.000
 0RC  O3A   PB   O2B   104.60  3.000
 0RC  C1B   PB   O2B   108.76  3.000
 0RC  O2B   PB   O3B   110.58  3.000
 0RC  O3A   PB   O3B   113.96  3.000
 0RC  C1B   PB   O3B   117.08  3.000
 0RC  HO2B  O2B  PB    116.65  3.000
 0RC  H1B2  C1B  H1B1  107.14  3.000
 0RC  H1B2  C1B  C14   110.60  3.000
 0RC  H1B1  C1B  C14   109.87  3.000
 0RC  H1B2  C1B  PB    109.03  3.000
 0RC  H1B1  C1B  PB    107.79  3.000
 0RC  C14   C1B  PB    112.24  3.000
 0RC  H142  C14  H141  106.63  3.000
 0RC  H142  C14  N15   108.29  3.000
 0RC  H141  C14  N15   113.76  3.000
 0RC  H142  C14  C1B   109.24  3.000
 0RC  H141  C14  C1B   109.50  3.000
 0RC  N15   C14  C1B   109.32  3.000
 0RC  H152  N15  H151  105.74  3.000
 0RC  H152  N15  C14   109.24  3.000
 0RC  H151  N15  C14   109.60  3.000
 0RC  PA    O3A  PB    126.97  3.000
 0RC  O5'   PA   O2A   107.59  3.000
 0RC  O2A   PA   O1A   110.92  3.000
 0RC  O5'   PA   O1A   117.54  3.000
 0RC  O2A   PA   O3A   105.38  3.000
 0RC  O1A   PA   O3A   116.23  3.000
 0RC  O5'   PA   O3A    97.81  3.000
 0RC  HO2A  O2A  PA    116.64  3.000
 0RC  C5'   O5'  PA    119.25  3.000
 0RC  H5'2  C5'  H5'1  108.88  3.000
 0RC  H5'2  C5'  C4'   108.54  3.000
 0RC  H5'1  C5'  C4'   110.38  3.000
 0RC  H5'2  C5'  O5'   110.80  3.000
 0RC  H5'1  C5'  O5'   109.58  3.000
 0RC  C4'   C5'  O5'   108.66  3.000
 0RC  H4'   C4'  O4'   110.22  3.000
 0RC  H4'   C4'  C3'   109.00  3.000
 0RC  O4'   C4'  C3'   106.60  3.000
 0RC  H4'   C4'  C5'   109.54  3.000
 0RC  C3'   C4'  C5'   111.49  3.000
 0RC  O4'   C4'  C5'   109.95  3.000
 0RC  H3'   C3'  C2'   109.49  3.000
 0RC  H3'   C3'  O3'   111.18  3.000
 0RC  C2'   C3'  O3'   112.79  3.000
 0RC  H3'   C3'  C4'   110.65  3.000
 0RC  C2'   C3'  C4'   102.81  3.000
 0RC  O3'   C3'  C4'   109.63  3.000
 0RC  HO3'  O3'  C3'   108.92  3.000
 0RC  H2'   C2'  C1'   111.97  3.000
 0RC  H2'   C2'  O2'   110.90  3.000
 0RC  C1'   C2'  O2'   107.46  3.000
 0RC  H2'   C2'  C3'   111.98  3.000
 0RC  O2'   C2'  C3'   110.40  3.000
 0RC  C1'   C2'  C3'   103.84  3.000
 0RC  HO2'  O2'  C2'   106.88  3.000
 0RC  C1'   O4'  C4'   111.40  3.000
 0RC  H1'   C1'  N1    104.95  3.000
 0RC  H1'   C1'  O4'   110.07  3.000
 0RC  N1    C1'  O4'   109.57  3.000
 0RC  H1'   C1'  C2'   107.52  3.000
 0RC  N1    C1'  C2'   116.67  3.000
 0RC  O4'   C1'  C2'   107.92  3.000
 0RC  C2    N1   C6    120.26  3.000
 0RC  C6    N1   C1'   118.93  3.000
 0RC  C2    N1   C1'   120.72  3.000
 0RC  H6    C6   C5    121.73  3.000
 0RC  H6    C6   N1    116.42  3.000
 0RC  C5    C6   N1    121.85  3.000
 0RC  H5    C5   C4    122.36  3.000
 0RC  H5    C5   C6    121.35  3.000
 0RC  C4    C5   C6    116.29  3.000
 0RC  N3    C4   N4    118.34  3.000
 0RC  N4    C4   C5    119.57  3.000
 0RC  N3    C4   C5    122.09  3.000
 0RC  HN42  N4   HN41  118.12  3.000
 0RC  HN42  N4   C4    120.30  3.000
 0RC  HN41  N4   C4    121.58  3.000
 0RC  C2    N3   C4    121.15  3.000
 0RC  O2    C2   N3    122.59  3.000
 0RC  N3    C2   N1    118.35  3.000
 0RC  O2    C2   N1    119.06  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
 0RC  CONST_01  N3    C2   N1   C1'   180.00   0.0  0
 0RC  CONST_02  C4    N3   C2   N1      0.00   0.0  0
 0RC  CONST_03  N3    C2   N1   C6      0.00   0.0  0
 0RC  CONST_04  C2    N3   C4   C5      0.00   0.0  0
 0RC  CONST_05  O2    C2   N1   C1'     0.00   0.0  0
 0RC  CONST_06  O2    C2   N1   C6    180.00   0.0  0
 0RC  CONST_07  O2    C2   N3   C4    180.00   0.0  0
 0RC  CONST_08  C2    N3   C4   N4    180.00   0.0  0
 0RC  CONST_09  HN41  N4   C4   C5      0.00   0.0  0
 0RC  CONST_10  HN42  N4   C4   C5    180.00   0.0  0
 0RC  Var_01    C4'   C5'  O5'  PA    168.67  30.0  1
 0RC  Var_02    C14   C1B  PB   O3B   -56.07  30.0  1
 0RC  Var_03    N15   C14  C1B  PB    177.01  30.0  1
 0RC  Var_04    O5'   PA   O3A  PB   -147.70  30.0  3
 0RC  Var_05    H151  N15  C14  C1B    70.04  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
 0RC  chir_03  C4'  O4'  C5'  C3'  positiv
 0RC  chir_04  C3'  O3'  C4'  C2'  positiv
 0RC  chir_05  C2'  O2'  C3'  C1'  positiv
 0RC  chir_06  C1'  O4'  N1   C2'  negativ
 0RC  chir_07  PB   O3A  O3B  O2B  both
 0RC  chir_08  PA   O1A  O3A  O5'  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
 0RC  plan-1  C1'   0.020
 0RC  plan-1  N1    0.020
 0RC  plan-1  C6    0.020
 0RC  plan-1  C5    0.020
 0RC  plan-1  C4    0.020
 0RC  plan-1  N4    0.020
 0RC  plan-1  N3    0.020
 0RC  plan-1  C2    0.020
 0RC  plan-1  O2    0.020
 0RC  plan-1  H6    0.020
 0RC  plan-1  H5    0.020
 0RC  plan-1  HN41  0.020
 0RC  plan-1  HN42  0.020

