# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:16:53 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 CA0  CA0  5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine  ligand  41  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CA0
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
 CA0  N1    N  N     0  -0.474  -3.6366   2.7448   1.4235
 CA0  C2    C  CR16  0   0.044  -3.5869   1.5612   2.0278
 CA0  N3    N  N     0  -0.457  -2.9222   0.4787   1.6608
 CA0  C4    C  CR56  0   0.486  -2.2426   0.6776   0.5349
 CA0  C5    C  CR56  0  -0.001  -2.1962   1.8475  -0.2042
 CA0  C6    C  CR6   0   0.458  -2.9443   2.9297   0.2933
 CA0  N6    N  NH2   0  -0.816  -2.9761   4.1208  -0.3053
 CA0  N7    N  N     0  -0.446  -1.3763   1.7035  -1.2937
 CA0  C8    C  CR15  0   0.103  -0.9439   0.4822  -1.2150
 CA0  N9    N  NR5   0  -0.540  -1.4411  -0.2037  -0.1371
 CA0  PA    P  P     0   1.488   2.8575   0.1419  -0.7575
 CA0  CB    C  C     0   0.724   1.6399   2.1128   0.4737
 CA0  C1'   C  CH1   0   0.210  -1.0784  -1.5223   0.3076
 CA0  O1A   O  OH1   0  -0.717   4.3551   0.6245  -0.5916
 CA0  O1B   O  O     0  -0.481   2.0872   2.9227  -0.3006
 CA0  C2'   C  CH1   0  -0.057  -1.1812  -2.6075  -0.7640
 CA0  O2'   O  OH1   0  -0.652  -2.4907  -3.0841  -0.8268
 CA0  O2A   O  O     0  -0.688   2.3139   0.4056  -2.0986
 CA0  N2B   N  NH2   0  -0.808   0.7407   2.3226   1.4332
 CA0  C3'   C  CH1   0  -0.030  -0.1475  -3.6221  -0.2596
 CA0  O3'   O  OH1   0  -0.665  -0.6605  -4.3752   0.8060
 CA0  O3A   O  O2    0  -0.593   2.0327   0.8034   0.4779
 CA0  C4'   C  CH1   0  -0.027   0.9351  -2.6948   0.2810
 CA0  O4'   O  O2    0  -0.482   0.2611  -1.5208   0.7241
 CA0  C5'   C  CH2   0  -0.196   1.9639  -2.3528  -0.7809
 CA0  O5'   O  O2    0  -0.575   2.8872  -1.3762  -0.2866
 CA0  H2    H  HCR6  0   0.253  -4.1679   1.4794   2.9402
 CA0  HN6   H  HNH2  0   0.411  -2.5074   4.2738  -1.1807
 CA0  HN6A  H  HNH2  0   0.404  -3.5649   4.8527   0.0532
 CA0  H8    H  HCR5  0   0.291  -0.2566   0.0305  -1.9137
 CA0  H1'   H  HCH1  0   0.266  -1.7495  -1.7559   1.1406
 CA0  HO1A  H  HOH1  0   0.506   4.7550   0.5357   0.2846
 CA0  H2'   H  HCH1  0   0.252  -0.8506  -2.2185  -1.7352
 CA0  HO2'  H  HOH1  0   0.471  -2.6151  -3.5463  -1.6620
 CA0  HN2B  H  HNH2  0   0.417   0.4193   1.5845   2.0359
 CA0  HN2A  H  HNH2  0   0.418   0.3646   3.2452   1.5666
 CA0  H3'   H  HCH1  0   0.258   0.2262  -4.2614  -1.0705
 CA0  HO3'  H  HOH1  0   0.451  -1.5389  -4.6856   0.5563
 CA0  H4'   H  HCH1  0   0.275   1.4452  -3.1474   1.1364
 CA0  H5'   H  HCH2  0   0.274   2.5442  -3.2444  -1.0199
 CA0  H5'A  H  HCH2  0   0.242   1.4984  -2.0057  -1.7070

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
 CA0  C2   N1    aromatic  1.330  0.020  1.330
 CA0  C6   N1    aromatic  1.338  0.020  1.338
 CA0  N3   C2    aromatic  1.322  0.020  1.322
 CA0  C2   H2    single    0.930  0.020  1.080
 CA0  C4   N3    aromatic  1.330  0.020  1.330
 CA0  N9   C4    aromatic  1.368  0.020  1.368
 CA0  C4   C5    aromatic  1.385  0.020  1.385
 CA0  N7   C5    aromatic  1.371  0.020  1.371
 CA0  C5   C6    aromatic  1.407  0.020  1.407
 CA0  C6   N6    single    1.333  0.020  1.333
 CA0  N6   HN6   single    0.860  0.020  1.020
 CA0  N6   HN6A  single    0.860  0.020  1.020
 CA0  C8   N7    aromatic  1.298  0.020  1.298
 CA0  N9   C8    aromatic  1.371  0.020  1.371
 CA0  C8   H8    single    0.930  0.020  1.080
 CA0  C1'  N9    single    1.438  0.020  1.438
 CA0  O2A  PA    double    1.471  0.020  1.471
 CA0  O1A  PA    single    1.582  0.020  1.582
 CA0  PA   O3A   single    1.626  0.020  1.626
 CA0  PA   O5'   single    1.590  0.020  1.590
 CA0  N2B  CB    single    1.332  0.020  1.332
 CA0  O1B  CB    double    1.206  0.020  1.206
 CA0  CB   O3A   single    1.367  0.020  1.367
 CA0  O4'  C1'   single    1.403  0.020  1.403
 CA0  C2'  C1'   single    1.529  0.020  1.529
 CA0  C1'  H1'   single    0.970  0.020  1.090
 CA0  O1A  HO1A  single    0.850  0.020  0.980
 CA0  O2'  C2'   single    1.395  0.020  1.395
 CA0  C3'  C2'   single    1.534  0.020  1.534
 CA0  C2'  H2'   single    0.970  0.020  1.090
 CA0  O2'  HO2'  single    0.850  0.020  0.980
 CA0  N2B  HN2B  single    0.860  0.020  1.020
 CA0  N2B  HN2A  single    0.860  0.020  1.020
 CA0  O3'  C3'   single    1.402  0.020  1.402
 CA0  C4'  C3'   single    1.525  0.020  1.525
 CA0  C3'  H3'   single    0.970  0.020  1.090
 CA0  O3'  HO3'  single    0.850  0.020  0.980
 CA0  C4'  C5'   single    1.518  0.020  1.518
 CA0  C4'  O4'   single    1.424  0.020  1.424
 CA0  C4'  H4'   single    0.970  0.020  1.090
 CA0  O5'  C5'   single    1.432  0.020  1.432
 CA0  C5'  H5'   single    0.970  0.020  1.090
 CA0  C5'  H5'A  single    0.970  0.020  1.090

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
 CA0  C6    N1   C2    119.17  3.000
 CA0  H2    C2   N3    116.17  3.000
 CA0  H2    C2   N1    115.42  3.000
 CA0  N3    C2   N1    128.41  3.000
 CA0  C4    N3   C2    111.68  3.000
 CA0  N9    C4   C5    105.22  3.000
 CA0  C5    C4   N3    126.53  3.000
 CA0  N9    C4   N3    128.24  3.000
 CA0  N7    C5   C6    132.83  3.000
 CA0  C6    C5   C4    116.33  3.000
 CA0  N7    C5   C4    110.82  3.000
 CA0  N6    C6   C5    122.77  3.000
 CA0  N6    C6   N1    119.36  3.000
 CA0  C5    C6   N1    117.87  3.000
 CA0  HN6A  N6   HN6   118.23  3.000
 CA0  HN6A  N6   C6    120.28  3.000
 CA0  HN6   N6   C6    121.07  3.000
 CA0  C8    N7   C5    104.47  3.000
 CA0  H8    C8   N9    122.04  3.000
 CA0  H8    C8   N7    124.53  3.000
 CA0  N9    C8   N7    113.43  3.000
 CA0  C1'   N9   C8    127.62  3.000
 CA0  C1'   N9   C4    125.92  3.000
 CA0  C8    N9   C4    106.05  3.000
 CA0  O5'   PA   O3A    99.96  3.000
 CA0  O5'   PA   O2A   116.63  3.000
 CA0  O3A   PA   O2A   115.61  3.000
 CA0  O5'   PA   O1A   104.04  3.000
 CA0  O3A   PA   O1A   106.04  3.000
 CA0  O2A   PA   O1A   113.00  3.000
 CA0  O3A   CB   N2B   110.04  3.000
 CA0  O3A   CB   O1B   122.58  3.000
 CA0  N2B   CB   O1B   127.37  3.000
 CA0  H1'   C1'  O4'   111.08  3.000
 CA0  H1'   C1'  C2'   109.92  3.000
 CA0  O4'   C1'  C2'   105.85  3.000
 CA0  H1'   C1'  N9    106.04  3.000
 CA0  C2'   C1'  N9    114.66  3.000
 CA0  O4'   C1'  N9    109.37  3.000
 CA0  HO1A  O1A  PA    117.28  3.000
 CA0  H2'   C2'  C3'   108.82  3.000
 CA0  H2'   C2'  O2'   111.35  3.000
 CA0  C3'   C2'  O2'   114.93  3.000
 CA0  H2'   C2'  C1'   110.40  3.000
 CA0  C3'   C2'  C1'   101.17  3.000
 CA0  O2'   C2'  C1'   109.71  3.000
 CA0  HO2'  O2'  C2'   108.93  3.000
 CA0  HN2A  N2B  HN2B  118.33  3.000
 CA0  HN2A  N2B  CB    119.53  3.000
 CA0  HN2B  N2B  CB    122.14  3.000
 CA0  H3'   C3'  C4'   111.98  3.000
 CA0  H3'   C3'  O3'   111.90  3.000
 CA0  C4'   C3'  O3'   108.49  3.000
 CA0  H3'   C3'  C2'   111.81  3.000
 CA0  C4'   C3'  C2'   101.12  3.000
 CA0  O3'   C3'  C2'   111.02  3.000
 CA0  HO3'  O3'  C3'   108.02  3.000
 CA0  CB    O3A  PA    122.21  3.000
 CA0  H4'   C4'  C5'   108.92  3.000
 CA0  H4'   C4'  O4'   108.57  3.000
 CA0  C5'   C4'  O4'   110.65  3.000
 CA0  H4'   C4'  C3'   110.90  3.000
 CA0  O4'   C4'  C3'   105.99  3.000
 CA0  C5'   C4'  C3'   111.74  3.000
 CA0  C4'   O4'  C1'   111.02  3.000
 CA0  H5'A  C5'  H5'   107.49  3.000
 CA0  H5'A  C5'  O5'   110.51  3.000
 CA0  H5'   C5'  O5'   106.87  3.000
 CA0  H5'A  C5'  C4'   112.07  3.000
 CA0  H5'   C5'  C4'   109.26  3.000
 CA0  O5'   C5'  C4'   110.44  3.000
 CA0  C5'   O5'  PA    122.48  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
 CA0  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 CA0  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 CA0  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 CA0  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 CA0  CONST_05  N9    C4   N3   C2    180.00   0.0  0
 CA0  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 CA0  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 CA0  CONST_08  C8    N9   C4   N3    180.00   0.0  0
 CA0  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 CA0  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 CA0  CONST_11  N7    C8   N9   C4      0.00   0.0  0
 CA0  CONST_12  C8    N7   C5   C4      0.00   0.0  0
 CA0  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 CA0  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 CA0  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 CA0  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 CA0  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 CA0  CONST_18  C1'   N9   C4   N3      0.00   0.0  0
 CA0  CONST_19  C1'   N9   C4   C5    180.00   0.0  0
 CA0  CONST_20  C1'   N9   C8   N7    180.00   0.0  0
 CA0  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 CA0  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 CA0  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 CA0  CONST_24  H2    C2   N3   C4    180.00   0.0  0
 CA0  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 CA0  CONST_26  HN6   N6   C6   N1    180.00   0.0  0
 CA0  CONST_27  HN6A  N6   C6   N1      0.00   0.0  0
 CA0  Var_01    C4'   C5'  O5'  PA   -106.33  30.0  3
 CA0  Var_02    N2B   CB   O3A  PA    166.04  30.0  1
 CA0  Var_03    O2A   PA   O3A  CB    -47.93  30.0  1
 CA0  Var_04    HN2B  N2B  CB   O1B   179.81  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
 CA0  chir_02  C1'  N9   O4'  C2'  positiv
 CA0  chir_03  C2'  O2'  C1'  C3'  negativ
 CA0  chir_04  C3'  O3'  C4'  C2'  positiv
 CA0  chir_05  C4'  O4'  C3'  C5'  negativ
 CA0  chir_06  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
 CA0  plan-1  N1    0.020
 CA0  plan-1  C2    0.020
 CA0  plan-1  N3    0.020
 CA0  plan-1  C4    0.020
 CA0  plan-1  C5    0.020
 CA0  plan-1  C6    0.020
 CA0  plan-1  N6    0.020
 CA0  plan-1  N7    0.020
 CA0  plan-1  C8    0.020
 CA0  plan-1  N9    0.020
 CA0  plan-1  C1'   0.020
 CA0  plan-1  H2    0.020
 CA0  plan-1  H8    0.020
 CA0  plan-2  C6    0.020
 CA0  plan-2  N6    0.020
 CA0  plan-2  HN6   0.020
 CA0  plan-2  HN6A  0.020
 CA0  plan-3  CB    0.020
 CA0  plan-3  O1B   0.020
 CA0  plan-3  N2B   0.020
 CA0  plan-3  O3A   0.020

