# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:03:31 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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
 ABM  ABM  5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine  ligand  38  23  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ABM
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
 ABM  P     P  P      0   1.268  -1.6104   0.3176   3.5239
 ABM  CM    C  CH3    0  -0.950  -2.5664  -1.2109   3.7504
 ABM  O2P   O  O      0  -0.805  -1.4920   1.0671   4.8246
 ABM  O3P   O  OP    -1  -0.794  -2.0907   1.0660   2.3019
 ABM  O5'   O  O2     0  -0.627  -0.1491  -0.3918   3.1768
 ABM  C5'   C  CH2    0  -0.142   0.8966   0.4120   2.6928
 ABM  C4'   C  CR15   0  -0.045   1.7817  -0.4291   1.7913
 ABM  O4'   O  O      0  -0.489   1.0187  -1.0216   0.7344
 ABM  C3'   C  CR15   0  -0.030   2.8584   0.3982   1.1055
 ABM  O3'   O  OH1    0  -0.669   3.9473  -0.4346   0.8019
 ABM  C2'   C  CR15   0  -0.050   2.1269   0.8304  -0.1682
 ABM  O2'   O  OH1    0  -0.652   2.9557   1.1577  -1.2429
 ABM  C1'   C  CR15   0   0.226   1.3217  -0.4291  -0.4919
 ABM  N9    N  NR5    0  -0.542   0.0956  -0.1675  -1.2106
 ABM  C8    C  CR15   0   0.066  -1.0810   0.3211  -0.7041
 ABM  N7    N  N      0  -0.460  -1.9977   0.4815  -1.6154
 ABM  C5    C  CR5    0  -0.012  -1.3996   0.0841  -2.7824
 ABM  C6    C  C      0   0.451  -1.8498   0.0161  -4.1132
 ABM  N6    N  NH2    0  -0.818  -3.0841   0.3725  -4.4755
 ABM  N1    N  N      0  -0.475  -0.9987  -0.4345  -5.0417
 ABM  C2    C  C1     0   0.040   0.2263  -0.8012  -4.6720
 ABM  N3    N  N      0  -0.455   0.7618  -0.7804  -3.4645
 ABM  C4    C  CR5    0   0.486  -0.0956  -0.3263  -2.5524
 ABM  HM1   H  HCH3   0   0.247  -3.5943  -0.9561   4.0112
 ABM  HM2   H  HCH3   0   0.244  -2.5900  -1.8074   2.8388
 ABM  HM3   H  HCH3   0   0.244  -2.1614  -1.8253   4.5546
 ABM  H5'1  H  HCH2   0   0.201   0.5193   1.2846   2.1459
 ABM  H5'2  H  HCH2   0   0.222   1.5135   0.7952   3.5150
 ABM  H4'   H  HCR5   0   0.259   2.2252  -1.2386   2.3789
 ABM  H3'   H  HCR5   0   0.250   3.1641   1.2602   1.7140
 ABM  HO3'  H  HOH1   0   0.449   4.4545  -0.0154   0.0968
 ABM  H2'   H  HCR5   0   0.248   1.4372   1.6494   0.0720
 ABM  HO2'  H  HOH1   0   0.469   3.2272   2.0769  -1.1558
 ABM  H1'   H  HCR5   0   0.257   1.9112  -1.0972  -1.1303
 ABM  H8    H  HCR5   0   0.329  -1.2268   0.5230   0.3515
 ABM  HN61  H  HNH2   0   0.402  -3.3488   0.3680  -5.4453
 ABM  HN62  H  HNH2   0   0.410  -3.7265   0.7621  -3.8085
 ABM  H2    H  H      0   0.249   0.8651  -1.1612  -5.4717

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
 ABM  P    CM    single    1.817  0.020  1.817
 ABM  P    O2P   deloc     1.506  0.020  1.506
 ABM  P    O3P   deloc     1.511  0.020  1.511
 ABM  P    O5'   single    1.661  0.020  1.661
 ABM  CM   HM1   single    0.970  0.020  1.090
 ABM  CM   HM2   single    0.970  0.020  1.090
 ABM  CM   HM3   single    0.970  0.020  1.090
 ABM  O5'  C5'   single    1.405  0.020  1.405
 ABM  C5'  C4'   single    1.518  0.020  1.518
 ABM  C5'  H5'1  single    0.970  0.020  1.090
 ABM  C5'  H5'2  single    0.970  0.020  1.090
 ABM  C4'  O4'   single    1.432  0.020  1.432
 ABM  C4'  C3'   single    1.521  0.020  1.521
 ABM  C4'  H4'   single    0.970  0.020  1.090
 ABM  O4'  C1'   single    1.395  0.020  1.395
 ABM  C3'  O3'   single    1.404  0.020  1.404
 ABM  C3'  C2'   single    1.531  0.020  1.531
 ABM  C3'  H3'   single    0.970  0.020  1.090
 ABM  O3'  HO3'  single    0.850  0.020  0.980
 ABM  C2'  O2'   single    1.396  0.020  1.396
 ABM  C2'  C1'   single    1.530  0.020  1.530
 ABM  C2'  H2'   single    0.970  0.020  1.090
 ABM  O2'  HO2'  single    0.850  0.020  0.980
 ABM  C1'  N9    single    1.445  0.020  1.445
 ABM  C1'  H1'   single    0.970  0.020  1.090
 ABM  N9   C8    aromatic  1.371  0.020  1.371
 ABM  N9   C4    aromatic  1.365  0.020  1.365
 ABM  C8   N7    aromatic  1.302  0.020  1.302
 ABM  C8   H8    single    0.930  0.020  1.080
 ABM  N7   C5    aromatic  1.370  0.020  1.370
 ABM  C5   C6    aromatic  1.406  0.020  1.406
 ABM  C5   C4    aromatic  1.386  0.020  1.386
 ABM  C6   N6    single    1.335  0.020  1.335
 ABM  C6   N1    aromatic  1.338  0.020  1.338
 ABM  N6   HN61  single    0.860  0.020  1.020
 ABM  N6   HN62  single    0.860  0.020  1.020
 ABM  N1   C2    aromatic  1.331  0.020  1.331
 ABM  C2   N3    aromatic  1.321  0.020  1.321
 ABM  C2   H2    single    0.930  0.020  1.080
 ABM  N3   C4    aromatic  1.332  0.020  1.332

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
 ABM  O5'   P    O3P   108.80  3.000
 ABM  O5'   P    O2P   108.90  3.000
 ABM  O3P   P    O2P   118.48  3.000
 ABM  O5'   P    CM     97.45  3.000
 ABM  O3P   P    CM    110.50  3.000
 ABM  O2P   P    CM    110.63  3.000
 ABM  HM3   CM   HM2   108.47  3.000
 ABM  HM3   CM   HM1   107.78  3.000
 ABM  HM2   CM   HM1   107.90  3.000
 ABM  HM3   CM   P     111.75  3.000
 ABM  HM2   CM   P     111.57  3.000
 ABM  HM1   CM   P     109.22  3.000
 ABM  C5'   O5'  P     118.85  3.000
 ABM  H5'2  C5'  H5'1  106.81  3.000
 ABM  H5'2  C5'  C4'   108.11  3.000
 ABM  H5'1  C5'  C4'   110.20  3.000
 ABM  H5'2  C5'  O5'   111.11  3.000
 ABM  H5'1  C5'  O5'   111.77  3.000
 ABM  C4'   C5'  O5'   108.76  3.000
 ABM  H4'   C4'  C3'   110.95  3.000
 ABM  H4'   C4'  O4'   107.83  3.000
 ABM  C3'   C4'  O4'   105.63  3.000
 ABM  H4'   C4'  C5'   109.11  3.000
 ABM  C3'   C4'  C5'   112.28  3.000
 ABM  O4'   C4'  C5'   110.91  3.000
 ABM  C1'   O4'  C4'   110.94  3.000
 ABM  H3'   C3'  C2'   111.86  3.000
 ABM  H3'   C3'  O3'   111.68  3.000
 ABM  C2'   C3'  O3'   110.98  3.000
 ABM  H3'   C3'  C4'   111.96  3.000
 ABM  C2'   C3'  C4'   100.98  3.000
 ABM  O3'   C3'  C4'   108.90  3.000
 ABM  HO3'  O3'  C3'   107.95  3.000
 ABM  H2'   C2'  C1'   109.27  3.000
 ABM  H2'   C2'  O2'   111.51  3.000
 ABM  C1'   C2'  O2'   110.04  3.000
 ABM  H2'   C2'  C3'   109.20  3.000
 ABM  C1'   C2'  C3'   101.25  3.000
 ABM  O2'   C2'  C3'   115.02  3.000
 ABM  HO2'  O2'  C2'   108.76  3.000
 ABM  H1'   C1'  N9    106.08  3.000
 ABM  H1'   C1'  C2'   110.00  3.000
 ABM  N9    C1'  C2'   113.75  3.000
 ABM  H1'   C1'  O4'   111.71  3.000
 ABM  N9    C1'  O4'   109.25  3.000
 ABM  C2'   C1'  O4'   106.14  3.000
 ABM  C4    N9   C8    106.53  3.000
 ABM  C4    N9   C1'   125.93  3.000
 ABM  C8    N9   C1'   127.51  3.000
 ABM  H8    C8   N7    124.29  3.000
 ABM  H8    C8   N9    122.77  3.000
 ABM  N7    C8   N9    112.92  3.000
 ABM  C5    N7   C8    104.65  3.000
 ABM  C4    C5   C6    116.35  3.000
 ABM  C4    C5   N7    110.80  3.000
 ABM  C6    C5   N7    132.86  3.000
 ABM  N1    C6   N6    119.33  3.000
 ABM  N1    C6   C5    118.00  3.000
 ABM  N6    C6   C5    122.67  3.000
 ABM  HN62  N6   HN61  118.28  3.000
 ABM  HN62  N6   C6    120.97  3.000
 ABM  HN61  N6   C6    120.27  3.000
 ABM  C2    N1   C6    119.05  3.000
 ABM  H2    C2   N3    116.12  3.000
 ABM  H2    C2   N1    115.38  3.000
 ABM  N3    C2   N1    128.50  3.000
 ABM  C4    N3   C2    111.74  3.000
 ABM  N3    C4   C5    126.36  3.000
 ABM  N3    C4   N9    128.53  3.000
 ABM  C5    C4   N9    105.10  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
 ABM  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 ABM  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 ABM  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 ABM  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 ABM  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 ABM  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 ABM  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 ABM  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 ABM  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 ABM  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 ABM  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 ABM  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 ABM  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 ABM  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 ABM  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 ABM  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 ABM  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 ABM  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 ABM  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 ABM  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 ABM  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 ABM  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 ABM  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 ABM  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 ABM  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 ABM  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 ABM  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 ABM  Var_01    C4'   C5'  O5'  P    -150.05  30.0  3
 ABM  Var_02    HM1   CM   P    O2P    65.63  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
 ABM  chir_02  C4'  C5'  O4'  C3'  negativ
 ABM  chir_03  C3'  O3'  C4'  C2'  positiv
 ABM  chir_04  C2'  O2'  C3'  C1'  positiv
 ABM  chir_05  C1'  O4'  N9   C2'  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
 ABM  plan-1  C1'   0.020
 ABM  plan-1  N9    0.020
 ABM  plan-1  C8    0.020
 ABM  plan-1  N7    0.020
 ABM  plan-1  C5    0.020
 ABM  plan-1  C6    0.020
 ABM  plan-1  N6    0.020
 ABM  plan-1  N1    0.020
 ABM  plan-1  C2    0.020
 ABM  plan-1  N3    0.020
 ABM  plan-1  C4    0.020
 ABM  plan-1  H8    0.020
 ABM  plan-1  H2    0.020
 ABM  plan-2  C6    0.020
 ABM  plan-2  N6    0.020
 ABM  plan-2  HN61  0.020
 ABM  plan-2  HN62  0.020

