# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue May 19 21:43:09 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: 5'-O-[(S)-{[(R)-(2-{[(2-aminophenyl)carbonyl]oxy}ethoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OCCOC(=O)c3ccccc3N)[C@@H](O)[C@H]2O
#
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
 1AA  1AA  5'-O-[(S)-{[(R)-(2-{[(2-aminophenyl)carbonyl]oxy}ethoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine  ligand  59  37  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1AA
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
 1AA  O1    O  O      0  -0.508  -5.9047  -0.2441  -0.6415
 1AA  C1    C  CR6    0   0.603  -6.0141   0.9417  -0.3628
 1AA  N4    N  N      0  -0.541  -6.7474   1.7969  -1.1025
 1AA  C9'   C  CR6    0   0.515  -6.8595   3.0673  -0.7665
 1AA  N3    N  NH2    0  -0.808  -7.5985   3.8617  -1.5384
 1AA  C8'   C  CR16   0  -0.477  -6.2143   3.6070   0.3887
 1AA  C7'   C  CR16   0   0.101  -5.4718   2.7479   1.1124
 1AA  N2    N  NR6    0  -0.556  -5.3579   1.4398   0.7750
 1AA  C2    C  CR15   0   0.207  -4.4962   0.5794   1.5678
 1AA  O2'   O  O      0  -0.491  -3.3983   0.1839   0.7944
 1AA  C3    C  CR15   0  -0.044  -5.1462  -0.6854   2.1570
 1AA  O4'   O  OH1    0  -0.677  -4.8651  -0.7142   3.5336
 1AA  C4    C  CR15   0  -0.036  -4.4189  -1.8339   1.4331
 1AA  O3'   O  OH1    0  -0.664  -4.1502  -2.9252   2.2790
 1AA  C5    C  CR15   0   0.022  -3.1072  -1.1870   0.9910
 1AA  C6    C  CH2    0  -0.162  -2.5697  -1.7914  -0.2825
 1AA  O2    O  O2     0  -0.620  -1.3514  -1.1711  -0.6352
 1AA  P1    P  P      0   1.337  -0.2309  -2.1070  -1.3990
 1AA  O1'   O  O      0  -0.801  -0.7866  -2.6059  -2.6959
 1AA  O9    O  OP    -1  -0.789   0.3619  -3.0630  -0.4123
 1AA  O3    O  O2     0  -0.736   0.7981  -0.8545  -1.6530
 1AA  P2    P  P      0   1.349   1.8125  -0.7735  -2.9424
 1AA  O8    O  O      0  -0.796   1.1432  -0.0875  -4.0909
 1AA  O7    O  OP    -1  -0.801   2.5079  -2.0829  -3.1409
 1AA  O4    O  O2     0  -0.612   2.8264   0.2906  -2.1977
 1AA  C7    C  CH2    0  -0.178   3.9218   0.7636  -2.9489
 1AA  C8    C  CH2    0  -0.203   4.7692   1.6597  -2.0869
 1AA  O5    O  O2     0  -0.459   5.2902   0.8698  -1.0170
 1AA  C9    C  C      0   0.632   6.0756   1.4566  -0.1255
 1AA  O6    O  O      0  -0.480   6.3955   2.6261  -0.2164
 1AA  C1'   C  CR6    0  -0.184   6.4934   0.5498   0.9544
 1AA  C2'   C  CR16   0  -0.273   5.9794  -0.7557   1.0144
 1AA  C3'   C  CR16   0  -0.281   6.3283  -1.6310   2.0177
 1AA  C4'   C  CR16   0  -0.240   7.2204  -1.2004   3.0026
 1AA  C5'   C  CR16   0  -0.334   7.7417   0.0710   2.9732
 1AA  C6'   C  CR6    0   0.347   7.4010   0.9846   1.9534
 1AA  N1    N  NH2    0  -0.864   7.9819   2.2077   1.9606
 1AA  HN31  H  HNH2   0   0.403  -8.0503   3.4933  -2.3579
 1AA  HN32  H  HNH2   0   0.414  -7.7192   4.8367  -1.3289
 1AA  H8'   H  HCR6   0   0.289  -6.3025   4.6454   0.6690
 1AA  H7'   H  HCR6   0   0.320  -4.9373   3.0648   1.9975
 1AA  H2    H  HCR5   0   0.251  -4.1660   1.2018   2.4059
 1AA  H3    H  HCR5   0   0.245  -6.2269  -0.7080   1.9818
 1AA  H4'   H  HOH1   0   0.447  -4.6343  -1.6281   3.7511
 1AA  H4    H  HCR5   0   0.259  -5.0014  -2.1435   0.5639
 1AA  H6    H  HOH1   0   0.469  -4.8696  -3.5597   2.2043
 1AA  H5    H  HCR5   0   0.230  -2.3614  -1.3035   1.7916
 1AA  H61   H  HCH2   0   0.213  -2.4503  -2.8669  -0.1044
 1AA  H62   H  HCH2   0   0.217  -3.3085  -1.6703  -1.0822
 1AA  H71   H  HCH2   0   0.217   4.5296  -0.0634  -3.3342
 1AA  H72   H  HCH2   0   0.221   3.5935   1.3533  -3.8124
 1AA  H81   H  HCH2   0   0.241   5.5808   2.0738  -2.6894
 1AA  H82   H  HCH2   0   0.241   4.1799   2.4906  -1.6918
 1AA  H2'   H  HCR6   0   0.261   5.2834  -1.0827   0.2544
 1AA  H3'   H  HCR6   0   0.252   5.9163  -2.6301   2.0430
 1AA  H1    H  HCR6   0   0.261   7.5094  -1.8707   3.8023
 1AA  H5'   H  HCR6   0   0.262   8.4306   0.3897   3.7466
 1AA  HN11  H  HNH2   0   0.390   8.4541   2.5033   2.7972
 1AA  HN12  H  HNH2   0   0.401   7.6160   2.9300   1.3656

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
 1AA  O1   C1    double    1.223  0.020  1.223
 1AA  C1   N4    single    1.348  0.020  1.348
 1AA  C1   N2    single    1.405  0.020  1.405
 1AA  N4   C9'   double    1.319  0.020  1.319
 1AA  C9'  N3    single    1.332  0.020  1.332
 1AA  C9'  C8'   single    1.429  0.020  1.429
 1AA  N3   HN31  single    0.860  0.020  1.020
 1AA  N3   HN32  single    0.860  0.020  1.020
 1AA  C8'  C7'   double    1.347  0.020  1.347
 1AA  C8'  H8'   single    0.930  0.020  1.080
 1AA  C7'  N2    single    1.356  0.020  1.356
 1AA  C7'  H7'   single    0.930  0.020  1.080
 1AA  N2   C2    single    1.453  0.020  1.453
 1AA  C2   O2'   single    1.400  0.020  1.400
 1AA  C2   C3    single    1.539  0.020  1.539
 1AA  C2   H2    single    0.970  0.020  1.090
 1AA  O2'  C5    single    1.415  0.020  1.415
 1AA  C3   O4'   single    1.405  0.020  1.405
 1AA  C3   C4    single    1.540  0.020  1.540
 1AA  C3   H3    single    0.970  0.020  1.090
 1AA  O4'  H4'   single    0.850  0.020  0.980
 1AA  C4   O3'   single    1.407  0.020  1.407
 1AA  C4   C5    single    1.528  0.020  1.528
 1AA  C4   H4    single    0.970  0.020  1.090
 1AA  O3'  H6    single    0.850  0.020  0.980
 1AA  C5   C6    single    1.509  0.020  1.509
 1AA  C5   H5    single    0.970  0.020  1.090
 1AA  C6   O2    single    1.412  0.020  1.412
 1AA  C6   H61   single    0.970  0.020  1.090
 1AA  C6   H62   single    0.970  0.020  1.090
 1AA  O2   P1    single    1.648  0.020  1.648
 1AA  P1   O1'   deloc     1.497  0.020  1.497
 1AA  P1   O9    deloc     1.496  0.020  1.496
 1AA  P1   O3    single    1.641  0.020  1.641
 1AA  O3   P2    single    1.643  0.020  1.643
 1AA  P2   O8    deloc     1.496  0.020  1.496
 1AA  P2   O7    deloc     1.496  0.020  1.496
 1AA  P2   O4    single    1.648  0.020  1.648
 1AA  O4   C7    single    1.410  0.020  1.410
 1AA  C7   C8    single    1.505  0.020  1.505
 1AA  C7   H71   single    0.970  0.020  1.090
 1AA  C7   H72   single    0.970  0.020  1.090
 1AA  C8   O5    single    1.428  0.020  1.428
 1AA  C8   H81   single    0.970  0.020  1.090
 1AA  C8   H82   single    0.970  0.020  1.090
 1AA  O5   C9    single    1.325  0.020  1.325
 1AA  C9   O6    double    1.216  0.020  1.216
 1AA  C9   C1'   single    1.471  0.020  1.471
 1AA  C1'  C2'   aromatic  1.404  0.020  1.404
 1AA  C1'  C6'   aromatic  1.418  0.020  1.418
 1AA  C2'  C3'   aromatic  1.376  0.020  1.376
 1AA  C2'  H2'   single    0.930  0.020  1.080
 1AA  C3'  C4'   aromatic  1.397  0.020  1.397
 1AA  C3'  H3'   single    0.930  0.020  1.080
 1AA  C4'  C5'   aromatic  1.374  0.020  1.374
 1AA  C4'  H1    single    0.930  0.020  1.080
 1AA  C5'  C6'   aromatic  1.411  0.020  1.411
 1AA  C5'  H5'   single    0.930  0.020  1.080
 1AA  C6'  N1    single    1.354  0.020  1.354
 1AA  N1   HN11  single    0.890  0.020  1.040
 1AA  N1   HN12  single    0.890  0.020  1.040

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
 1AA  N2    C1   N4    118.28  3.000
 1AA  N2    C1   O1    119.12  3.000
 1AA  N4    C1   O1    122.61  3.000
 1AA  C9'   N4   C1    121.17  3.000
 1AA  C8'   C9'  N3    119.60  3.000
 1AA  C8'   C9'  N4    122.10  3.000
 1AA  N3    C9'  N4    118.30  3.000
 1AA  HN32  N3   HN31  118.13  3.000
 1AA  HN32  N3   C9'   121.65  3.000
 1AA  HN31  N3   C9'   120.21  3.000
 1AA  H8'   C8'  C7'   121.29  3.000
 1AA  H8'   C8'  C9'   122.45  3.000
 1AA  C7'   C8'  C9'   116.26  3.000
 1AA  H7'   C7'  N2    116.42  3.000
 1AA  H7'   C7'  C8'   121.70  3.000
 1AA  N2    C7'  C8'   121.88  3.000
 1AA  C2    N2   C7'   119.04  3.000
 1AA  C2    N2   C1    120.60  3.000
 1AA  C7'   N2   C1    120.30  3.000
 1AA  H2    C2   C3    107.55  3.000
 1AA  H2    C2   O2'   110.30  3.000
 1AA  C3    C2   O2'   108.09  3.000
 1AA  H2    C2   N2    105.06  3.000
 1AA  C3    C2   N2    116.42  3.000
 1AA  O2'   C2   N2    109.32  3.000
 1AA  C5    O2'  C2    110.99  3.000
 1AA  H3    C3   C4    112.05  3.000
 1AA  H3    C3   O4'   110.72  3.000
 1AA  C4    C3   O4'   110.53  3.000
 1AA  H3    C3   C2    111.87  3.000
 1AA  C4    C3   C2    103.50  3.000
 1AA  O4'   C3   C2    107.89  3.000
 1AA  H4'   O4'  C3    106.70  3.000
 1AA  H4    C4   C5    110.36  3.000
 1AA  H4    C4   O3'   111.15  3.000
 1AA  C5    C4   O3'   109.79  3.000
 1AA  H4    C4   C3    109.51  3.000
 1AA  C5    C4   C3    103.04  3.000
 1AA  O3'   C4   C3    112.71  3.000
 1AA  H6    O3'  C4    108.79  3.000
 1AA  H5    C5   C6    109.28  3.000
 1AA  H5    C5   C4    109.05  3.000
 1AA  C6    C5   C4    112.37  3.000
 1AA  H5    C5   O2'   110.06  3.000
 1AA  C6    C5   O2'   110.13  3.000
 1AA  C4    C5   O2'   105.89  3.000
 1AA  H62   C6   H61   107.48  3.000
 1AA  H62   C6   O2    110.56  3.000
 1AA  H61   C6   O2    112.18  3.000
 1AA  H62   C6   C5    109.37  3.000
 1AA  H61   C6   C5    107.13  3.000
 1AA  O2    C6   C5    110.02  3.000
 1AA  P1    O2   C6    116.94  3.000
 1AA  O3    P1   O9    109.96  3.000
 1AA  O3    P1   O1'   110.68  3.000
 1AA  O9    P1   O1'   120.37  3.000
 1AA  O3    P1   O2     93.71  3.000
 1AA  O9    P1   O2    109.07  3.000
 1AA  O1'   P1   O2    109.79  3.000
 1AA  P2    O3   P1    123.12  3.000
 1AA  O4    P2   O7    109.83  3.000
 1AA  O4    P2   O8    109.04  3.000
 1AA  O7    P2   O8    120.50  3.000
 1AA  O4    P2   O3     93.27  3.000
 1AA  O7    P2   O3    110.37  3.000
 1AA  O8    P2   O3    110.42  3.000
 1AA  C7    O4   P2    117.00  3.000
 1AA  H72   C7   H71   107.16  3.000
 1AA  H72   C7   C8    107.44  3.000
 1AA  H71   C7   C8    109.78  3.000
 1AA  H72   C7   O4    111.56  3.000
 1AA  H71   C7   O4    111.40  3.000
 1AA  C8    C7   O4    109.40  3.000
 1AA  H82   C8   H81   108.17  3.000
 1AA  H82   C8   O5    110.26  3.000
 1AA  H81   C8   O5    110.60  3.000
 1AA  H82   C8   C7    110.87  3.000
 1AA  H81   C8   C7    109.16  3.000
 1AA  O5    C8   C7    107.77  3.000
 1AA  C9    O5   C8    118.38  3.000
 1AA  C1'   C9   O6    124.97  3.000
 1AA  C1'   C9   O5    112.92  3.000
 1AA  O6    C9   O5    122.11  3.000
 1AA  C6'   C1'  C2'   119.29  3.000
 1AA  C6'   C1'  C9    120.67  3.000
 1AA  C2'   C1'  C9    120.04  3.000
 1AA  H2'   C2'  C3'   118.89  3.000
 1AA  H2'   C2'  C1'   119.13  3.000
 1AA  C3'   C2'  C1'   121.98  3.000
 1AA  H3'   C3'  C4'   120.78  3.000
 1AA  H3'   C3'  C2'   120.55  3.000
 1AA  C4'   C3'  C2'   118.67  3.000
 1AA  H1    C4'  C5'   119.16  3.000
 1AA  H1    C4'  C3'   120.03  3.000
 1AA  C5'   C4'  C3'   120.82  3.000
 1AA  H5'   C5'  C6'   118.61  3.000
 1AA  H5'   C5'  C4'   119.86  3.000
 1AA  C6'   C5'  C4'   121.52  3.000
 1AA  N1    C6'  C5'   118.52  3.000
 1AA  N1    C6'  C1'   123.73  3.000
 1AA  C5'   C6'  C1'   117.72  3.000
 1AA  HN12  N1   HN11  116.91  3.000
 1AA  HN12  N1   C6'   119.34  3.000
 1AA  HN11  N1   C6'   118.14  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
 1AA  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 1AA  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 1AA  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 1AA  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 1AA  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 1AA  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 1AA  CONST_07  C8'   C9'  N4   C1      0.00   0.0  0
 1AA  CONST_08  C7'   N2   C1   N4      0.00   0.0  0
 1AA  CONST_09  C2    N2   C1   N4    180.00   0.0  0
 1AA  CONST_10  N2    C1   N4   C9'     0.00   0.0  0
 1AA  CONST_11  C3'   C2'  C1'  C9    180.00   0.0  0
 1AA  CONST_12  C5'   C6'  C1'  C9    180.00   0.0  0
 1AA  CONST_13  N1    C6'  C1'  C2'   180.00   0.0  0
 1AA  CONST_14  N1    C6'  C5'  C4'   180.00   0.0  0
 1AA  CONST_15  C9'   N4   C1   O1    180.00   0.0  0
 1AA  CONST_16  C7'   N2   C1   O1    180.00   0.0  0
 1AA  CONST_17  C2    N2   C1   O1      0.00   0.0  0
 1AA  CONST_18  N3    C9'  N4   C1    180.00   0.0  0
 1AA  CONST_19  H3'   C3'  C2'  C1'   180.00   0.0  0
 1AA  CONST_20  H5'   C5'  C6'  C1'   180.00   0.0  0
 1AA  CONST_21  H1    C4'  C3'  C2'   180.00   0.0  0
 1AA  CONST_22  H2'   C2'  C3'  C4'   180.00   0.0  0
 1AA  CONST_23  HN11  N1   C6'  C1'   180.00   0.0  0
 1AA  CONST_24  HN12  N1   C6'  C1'     0.00   0.0  0
 1AA  CONST_25  HN31  N3   C9'  N4      0.00   0.0  0
 1AA  CONST_26  HN32  N3   C9'  N4    180.00   0.0  0
 1AA  Var_01    C2'   C1'  C9   O5     -4.66  30.0  2
 1AA  Var_02    C1'   C9   O5   C8    177.39  30.0  3
 1AA  Var_03    O1'   P1   O2   C6     61.23  30.0  3
 1AA  Var_04    O8    P2   O3   P1     89.83  30.0  3
 1AA  Var_05    C8    C7   O4   P2   -177.00  30.0  3
 1AA  Var_06    O5    C8   C7   O4     63.37  30.0  3
 1AA  Var_07    H61   C6   O2   P1     28.31  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
 1AA  chir_01  C2  N2   O2'  C3  positiv
 1AA  chir_02  C3  O4'  C2   C4  negativ
 1AA  chir_03  C4  O3'  C5   C3  positiv
 1AA  chir_04  C5  O2'  C4   C6  negativ

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
 1AA  plan-1  O1    0.020
 1AA  plan-1  C1    0.020
 1AA  plan-1  N4    0.020
 1AA  plan-1  C9'   0.020
 1AA  plan-1  N3    0.020
 1AA  plan-1  C8'   0.020
 1AA  plan-1  C7'   0.020
 1AA  plan-1  N2    0.020
 1AA  plan-1  C2    0.020
 1AA  plan-1  HN31  0.020
 1AA  plan-1  HN32  0.020
 1AA  plan-1  H8'   0.020
 1AA  plan-1  H7'   0.020
 1AA  plan-2  C9    0.020
 1AA  plan-2  C1'   0.020
 1AA  plan-2  C2'   0.020
 1AA  plan-2  C3'   0.020
 1AA  plan-2  C4'   0.020
 1AA  plan-2  C5'   0.020
 1AA  plan-2  C6'   0.020
 1AA  plan-2  N1    0.020
 1AA  plan-2  H2'   0.020
 1AA  plan-2  H3'   0.020
 1AA  plan-2  H1    0.020
 1AA  plan-2  H5'   0.020
 1AA  plan-3  C6'   0.020
 1AA  plan-3  N1    0.020
 1AA  plan-3  HN11  0.020
 1AA  plan-3  HN12  0.020
 1AA  plan-4  O5    0.020
 1AA  plan-4  C9    0.020
 1AA  plan-4  O6    0.020
 1AA  plan-4  C1'   0.020

