# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 20:45:43 2021
#   Inital geometry file: a 94 line input string
#   Ligand name: 5'-O-[(R)-hydroxy(methoxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[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
 XM7  XM7  5'-O-[(R)-hydroxy(methoxy)phosphoryl]adenosine  ligand  40  24  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XM7
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
 XM7  C2    C  CR16  0   0.040   4.5082   1.7071  -20.3424
 XM7  N1    N  N     0  -0.473   4.2413   2.8275  -19.6759
 XM7  C6    C  CR6   0   0.457   4.6186   2.9328  -18.3970
 XM7  C4'   C  CH1   0   0.016   8.3777  -2.4872  -17.2639
 XM7  C3'   C  CH1   0  -0.040   8.8950  -1.5351  -18.3403
 XM7  C2'   C  CH1   0  -0.046   7.6922  -1.4662  -19.2880
 XM7  C1'   C  CH1   0   0.184   6.5335  -1.5096  -18.2942
 XM7  C8    C  CR15  0   0.104   6.2807   0.4061  -16.6254
 XM7  C5    C  CR56  0  -0.002   5.2867   1.8389  -17.8152
 XM7  C4    C  CR56  0   0.487   5.4954   0.7423  -18.6361
 XM7  C22   C  CH3   0  -0.418   5.4636  -2.5913  -14.2501
 XM7  N9    N  NR5   0  -0.541   6.1459  -0.1710  -17.8590
 XM7  N7    N  N     0  -0.449   5.7849   1.6076  -16.5611
 XM7  N3    N  N     0  -0.458   5.1259   0.6214  -19.9102
 XM7  N6    N  NH2   0  -0.816   4.3592   4.0576  -17.7294
 XM7  O3'   O  OH1   0  -0.654  10.0524  -2.0529  -18.9291
 XM7  O4'   O  O2    0  -0.492   6.9774  -2.2392  -17.1905
 XM7  O2'   O  OH1   0  -0.663   7.6083  -2.6205  -20.0759
 XM7  OP3   O  O2    0  -0.587   6.6441  -1.9347  -13.7756
 XM7  OP2   O  OH1   0  -0.733   7.6813  -4.1403  -12.9486
 XM7  OP1   O  O     0  -0.698   8.9539  -1.8388  -12.7979
 XM7  P     P  P     0   1.474   8.0223  -2.7037  -13.5450
 XM7  H4'   H  HCR6  0   0.252   4.1727   1.6877  -21.3738
 XM7  H1    H  HCH1  0   0.261   8.5471  -3.5245  -17.5772
 XM7  H3'   H  HCH1  0   0.251   9.0731  -0.5403  -17.9103
 XM7  H2'   H  HCH1  0   0.266   7.6847  -0.5538  -19.8954
 XM7  H1'   H  HCH1  0   0.288   5.6483  -1.9799  -18.7307
 XM7  H5''  H  HCR5  0   0.285   6.7374  -0.1093  -15.7962
 XM7  H5'   H  HCH2  0   0.269  10.1020  -2.4078  -16.0173
 XM7  H2    H  HCH2  0   0.236   8.8655  -1.2273  -15.5933
 XM7  H9    H  HCH3  0   0.247   4.8085  -1.8176  -14.6426
 XM7  H10   H  HCH3  0   0.238   5.6760  -3.3025  -15.0462
 XM7  H11   H  HCH3  0   0.245   4.9606  -3.1018  -13.4301
 XM7  H61   H  HNH2  0   0.404   3.8274   4.7924  -18.1631
 XM7  H62   H  HNH2  0   0.411   4.5773   4.1427  -16.7522
 XM7  HO3'  H  HOH1  0   0.471  10.5301  -1.3363  -19.3593
 XM7  HO2'  H  HOH1  0   0.454   8.4993  -2.8414  -20.3736
 XM7  HOP2  H  HOH1  0   0.506   7.4876  -4.1380  -12.0011
 XM7  C5'   C  CH2   0  -0.188   9.0251  -2.2580  -15.9228
 XM7  O5'   O  O2    0  -0.589   8.5163  -3.2048  -14.9788

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
 XM7  C2   N3    aromatic  1.322  0.020  1.322
 XM7  C2   N1    aromatic  1.331  0.020  1.331
 XM7  O2'  C2'   single    1.400  0.020  1.400
 XM7  N3   C4    aromatic  1.332  0.020  1.332
 XM7  N1   C6    aromatic  1.338  0.020  1.338
 XM7  C2'  C1'   single    1.527  0.020  1.527
 XM7  C2'  C3'   single    1.533  0.020  1.533
 XM7  C4   N9    aromatic  1.364  0.020  1.364
 XM7  C4   C5    aromatic  1.386  0.020  1.386
 XM7  O3'  C3'   single    1.398  0.020  1.398
 XM7  C6   C5    aromatic  1.408  0.020  1.408
 XM7  C6   N6    single    1.334  0.020  1.334
 XM7  C1'  N9    single    1.460  0.020  1.460
 XM7  C1'  O4'   single    1.396  0.020  1.396
 XM7  N9   C8    aromatic  1.369  0.020  1.369
 XM7  C3'  C4'   single    1.527  0.020  1.527
 XM7  C5   N7    aromatic  1.369  0.020  1.369
 XM7  C4'  O4'   single    1.424  0.020  1.424
 XM7  C4'  C5'   single    1.507  0.020  1.507
 XM7  C8   N7    aromatic  1.301  0.020  1.301
 XM7  C5'  O5'   single    1.431  0.020  1.431
 XM7  O5'  P     single    1.597  0.020  1.597
 XM7  P    OP1   double    1.474  0.020  1.474
 XM7  P    OP2   single    1.592  0.020  1.592
 XM7  P    OP3   single    1.595  0.020  1.595
 XM7  OP3  C22   single    1.432  0.020  1.432
 XM7  C2   H4'   single    0.930  0.020  1.080
 XM7  C4'  H1    single    0.970  0.020  1.090
 XM7  C3'  H3'   single    0.970  0.020  1.090
 XM7  C2'  H2'   single    0.970  0.020  1.090
 XM7  C1'  H1'   single    0.970  0.020  1.090
 XM7  C8   H5''  single    0.930  0.020  1.080
 XM7  C5'  H5'   single    0.970  0.020  1.090
 XM7  C5'  H2    single    0.970  0.020  1.090
 XM7  C22  H9    single    0.970  0.020  1.090
 XM7  C22  H10   single    0.970  0.020  1.090
 XM7  C22  H11   single    0.970  0.020  1.090
 XM7  N6   H61   single    0.860  0.020  1.020
 XM7  N6   H62   single    0.860  0.020  1.020
 XM7  O3'  HO3'  single    0.850  0.020  0.980
 XM7  O2'  HO2'  single    0.850  0.020  0.980
 XM7  OP2  HOP2  single    0.850  0.020  0.980

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
 XM7  H4'   C2   N3   116.15  3.000
 XM7  H4'   C2   N1   115.42  3.000
 XM7  N3    C2   N1   128.43  3.000
 XM7  C6    N1   C2   119.25  3.000
 XM7  N6    C6   C5   122.75  3.000
 XM7  N6    C6   N1   119.35  3.000
 XM7  C5    C6   N1   117.90  3.000
 XM7  H1    C4'  O4'  109.35  3.000
 XM7  H1    C4'  C5'  109.38  3.000
 XM7  O4'   C4'  C5'  110.50  3.000
 XM7  H1    C4'  C3'  109.63  3.000
 XM7  C5'   C4'  C3'  112.77  3.000
 XM7  O4'   C4'  C3'  105.12  3.000
 XM7  H3'   C3'  O3'  111.48  3.000
 XM7  H3'   C3'  C2'  109.19  3.000
 XM7  O3'   C3'  C2'  113.95  3.000
 XM7  H3'   C3'  C4'  110.09  3.000
 XM7  O3'   C3'  C4'  110.26  3.000
 XM7  C2'   C3'  C4'  101.42  3.000
 XM7  H2'   C2'  O2'  111.97  3.000
 XM7  H2'   C2'  C1'  112.28  3.000
 XM7  O2'   C2'  C1'  107.30  3.000
 XM7  H2'   C2'  C3'  112.67  3.000
 XM7  C1'   C2'  C3'  101.05  3.000
 XM7  O2'   C2'  C3'  110.97  3.000
 XM7  H1'   C1'  O4'  110.39  3.000
 XM7  H1'   C1'  N9   107.36  3.000
 XM7  O4'   C1'  N9   109.15  3.000
 XM7  H1'   C1'  C2'  111.52  3.000
 XM7  O4'   C1'  C2'  106.75  3.000
 XM7  N9    C1'  C2'  111.68  3.000
 XM7  H5''  C8   N7   124.39  3.000
 XM7  H5''  C8   N9   122.25  3.000
 XM7  N7    C8   N9   113.35  3.000
 XM7  N7    C5   C4   110.74  3.000
 XM7  N7    C5   C6   133.04  3.000
 XM7  C4    C5   C6   116.21  3.000
 XM7  N3    C4   N9   128.05  3.000
 XM7  N9    C4   C5   105.32  3.000
 XM7  N3    C4   C5   126.64  3.000
 XM7  H11   C22  H10  109.54  3.000
 XM7  H11   C22  H9   109.10  3.000
 XM7  H10   C22  H9   108.58  3.000
 XM7  H11   C22  OP3  110.26  3.000
 XM7  H10   C22  OP3  112.40  3.000
 XM7  H9    C22  OP3  106.86  3.000
 XM7  C4    N9   C8   106.15  3.000
 XM7  C8    N9   C1'  128.99  3.000
 XM7  C4    N9   C1'  124.79  3.000
 XM7  C5    N7   C8   104.44  3.000
 XM7  C4    N3   C2   111.58  3.000
 XM7  H62   N6   H61  118.19  3.000
 XM7  H62   N6   C6   121.07  3.000
 XM7  H61   N6   C6   120.23  3.000
 XM7  HO3'  O3'  C3'  108.86  3.000
 XM7  C1'   O4'  C4'  111.29  3.000
 XM7  HO2'  O2'  C2'  107.88  3.000
 XM7  P     OP3  C22  122.63  3.000
 XM7  HOP2  OP2  P    114.06  3.000
 XM7  OP1   P    OP2  118.34  3.000
 XM7  OP2   P    OP3  107.70  3.000
 XM7  OP1   P    OP3  109.66  3.000
 XM7  OP3   P    O5'  106.78  3.000
 XM7  OP2   P    O5'   96.86  3.000
 XM7  OP1   P    O5'  116.32  3.000
 XM7  H2    C5'  H5'  107.42  3.000
 XM7  H2    C5'  O5'  111.90  3.000
 XM7  H5'   C5'  O5'  108.50  3.000
 XM7  H2    C5'  C4'  110.41  3.000
 XM7  H5'   C5'  C4'  109.03  3.000
 XM7  O5'   C5'  C4'  109.51  3.000
 XM7  P     O5'  C5'  119.66  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
 XM7  CONST_01  N9    C4   N3   C2    180.00   0.0  0
 XM7  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 XM7  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 XM7  CONST_04  C4    N3   C2   N1      0.00   0.0  0
 XM7  CONST_05  C4    C5   C6   N1      0.00   0.0  0
 XM7  CONST_06  N7    C5   C6   N1    180.00   0.0  0
 XM7  CONST_07  N3    C2   N1   C6      0.00   0.0  0
 XM7  CONST_08  N3    C4   C5   C6      0.00   0.0  0
 XM7  CONST_09  N9    C4   C5   C6    180.00   0.0  0
 XM7  CONST_10  C8    N7   C5   C6    180.00   0.0  0
 XM7  CONST_11  N3    C4   N9   C8    180.00   0.0  0
 XM7  CONST_12  C5    C4   N9   C8      0.00   0.0  0
 XM7  CONST_13  C4    C5   N7   C8      0.00   0.0  0
 XM7  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 XM7  CONST_15  N7    C8   N9   C4      0.00   0.0  0
 XM7  CONST_16  N7    C5   C4   N9      0.00   0.0  0
 XM7  CONST_17  N3    C4   C5   N7    180.00   0.0  0
 XM7  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 XM7  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 XM7  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 XM7  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 XM7  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 XM7  CONST_23  N6    C6   C5   N7      0.00   0.0  0
 XM7  CONST_24  H4'   C2   N1   C6    180.00   0.0  0
 XM7  CONST_25  H5''  C8   N9   C1'     0.00   0.0  0
 XM7  CONST_26  H61   N6   C6   N1      0.00   0.0  0
 XM7  CONST_27  H62   N6   C6   N1    180.00   0.0  0
 XM7  Var_01    OP1   P    O5'  C5'   -50.25  30.0  3
 XM7  Var_02    O5'   P    OP3  C22    64.90  30.0  1
 XM7  Var_03    H5'   C5'  O5'  P     109.05  30.0  2
 XM7  Var_04    H9    C22  OP3  P    -160.48  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
 XM7  chir_01  C4'  C3'  O4'  C5'  positiv
 XM7  chir_02  C3'  O3'  C2'  C4'  negativ
 XM7  chir_03  C2'  O2'  C1'  C3'  negativ
 XM7  chir_04  C1'  O4'  N9   C2'  negativ
 XM7  chir_05  P    OP1  OP2  OP3  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
 XM7  plan-1  C2    0.020
 XM7  plan-1  N1    0.020
 XM7  plan-1  C6    0.020
 XM7  plan-1  C1'   0.020
 XM7  plan-1  C8    0.020
 XM7  plan-1  C5    0.020
 XM7  plan-1  C4    0.020
 XM7  plan-1  N9    0.020
 XM7  plan-1  N7    0.020
 XM7  plan-1  N3    0.020
 XM7  plan-1  N6    0.020
 XM7  plan-1  H4'   0.020
 XM7  plan-1  H5''  0.020
 XM7  plan-2  C6    0.020
 XM7  plan-2  N6    0.020
 XM7  plan-2  H61   0.020
 XM7  plan-2  H62   0.020

