# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 09:46:05 2021
#   Inital geometry file: a 137 line input string
#   Ligand name: 5'-O-[(R)-({5-[(3R)-1,2-dithiolan-3-yl]pentanoyl}oxy)(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)OC(=O)CCCC[C@@H]4CCSS4)[C@@H](O)[C@H]3O
#
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
 LAQ  LAQ  5'-O-[(R)-({5-[(3R)-1,2-dithiolan-3-yl]pentanoyl}oxy)(hydroxy)phosphoryl]adenosine  ligand  60  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LAQ
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
 LAQ  O2P   O  OH1   0  -0.727  38.9429  23.5990   7.0560
 LAQ  P     P  P     0   1.480  39.0510  24.8452   6.0748
 LAQ  O1P   O  O     0  -0.671  37.8167  25.3638   5.4717
 LAQ  O3P   O  O2    0  -0.597  39.7977  25.8084   7.1634
 LAQ  C10   C  C     0   0.616  40.1073  27.1090   6.8953
 LAQ  C11   C  CH2   0  -0.591  40.6530  27.7899   8.1125
 LAQ  C12   C  CH2   0  -0.431  41.1154  29.2154   7.8602
 LAQ  C13   C  CH2   0  -0.432  41.5086  29.9171   9.1558
 LAQ  C14   C  CH2   0  -0.420  42.0409  31.3219   8.8957
 LAQ  C15   C  CH1   0  -0.382  42.0835  32.2207  10.1202
 LAQ  S15   S  S2    0  -0.051  43.1360  31.5075  11.4372
 LAQ  S17   S  S2    0  -0.075  43.0388  33.2574  12.5616
 LAQ  C17   C  CH2   0  -0.547  42.8734  34.3966  11.1230
 LAQ  C16   C  CH2   0  -0.404  42.6915  33.5889   9.8387
 LAQ  O10   O  O     0  -0.400  39.9198  27.5965   5.8214
 LAQ  O5'   O  O2    0  -0.580  40.1383  24.4990   4.9729
 LAQ  C5'   C  CH2   0  -0.193  41.4083  23.9013   5.2650
 LAQ  C4'   C  CH1   0  -0.003  42.4843  24.6803   4.5576
 LAQ  C3'   C  CH1   0  -0.011  43.8899  24.1093   4.7899
 LAQ  O3'   O  OH1   0  -0.653  44.2187  23.0200   3.9920
 LAQ  C2'   C  CH1   0  -0.074  44.7541  25.3567   4.5827
 LAQ  O2'   O  OH1   0  -0.666  44.9194  25.5009   3.1974
 LAQ  C1'   C  CH1   0   0.162  43.8527  26.4697   5.1445
 LAQ  O4'   O  O2    0  -0.487  42.5332  25.9966   5.0844
 LAQ  N9    N  NR5   0  -0.531  44.1551  26.8312   6.5124
 LAQ  C8    C  CR15  0   0.104  43.9572  26.0909   7.6474
 LAQ  N7    N  N     0  -0.444  44.2926  26.7153   8.7369
 LAQ  C5    C  CR56  0  -0.001  44.7376  27.9382   8.3060
 LAQ  C6    C  CR6   0   0.458  45.2174  29.0750   8.9812
 LAQ  N6    N  NH2   0  -0.813  45.3647  29.1198  10.3073
 LAQ  N1    N  N     0  -0.467  45.5527  30.1425   8.2485
 LAQ  C2    C  CR16  0   0.043  45.4219  30.0895   6.9256
 LAQ  N3    N  N     0  -0.456  44.9878  29.0852   6.1833
 LAQ  C4    C  CR56  0   0.494  44.6573  28.0325   6.9262
 LAQ  HO2P  H  HOH1  0   0.509  38.4235  22.8624   6.7032
 LAQ  H111  H  HCH2  0   0.294  39.8605  27.7719   8.8692
 LAQ  H112  H  HCH2  0   0.281  41.4614  27.1814   8.5287
 LAQ  H121  H  HCH2  0   0.233  41.9612  29.2185   7.1667
 LAQ  H122  H  HCH2  0   0.242  40.3182  29.7864   7.3780
 LAQ  H131  H  HCH2  0   0.232  40.6362  29.9649   9.8156
 LAQ  H132  H  HCH2  0   0.223  42.2611  29.3212   9.6838
 LAQ  H141  H  HCH2  0   0.243  43.0353  31.2659   8.4444
 LAQ  H142  H  HCH2  0   0.248  41.3974  31.8215   8.1645
 LAQ  H15   H  HCH1  0   0.284  41.0769  32.3310  10.5344
 LAQ  H171  H  HCH2  0   0.285  43.7504  35.0383  11.0658
 LAQ  H172  H  HCH2  0   0.283  42.0033  35.0166  11.3319
 LAQ  H161  H  HCH2  0   0.251  43.6577  33.4485   9.3511
 LAQ  H162  H  HCH2  0   0.269  42.0513  34.1445   9.1493
 LAQ  H5'1  H  HCH2  0   0.270  41.3953  22.8740   4.8980
 LAQ  H5'2  H  HCH2  0   0.241  41.6060  23.8716   6.3400
 LAQ  H4'   H  HCH1  0   0.258  42.2661  24.7110   3.4816
 LAQ  H3'   H  HCH1  0   0.262  43.9848  23.7769   5.8297
 LAQ  HO3'  H  HOH1  0   0.451  44.3961  23.3420   3.0996
 LAQ  H2'   H  HCH1  0   0.282  45.7119  25.3078   5.1096
 LAQ  HO2'  H  HOH1  0   0.473  45.6574  26.0927   3.0222
 LAQ  H1'   H  HCH1  0   0.281  43.9662  27.3874   4.5610
 LAQ  H8    H  HCR5  0   0.295  43.5531  25.0900   7.6182
 LAQ  HN61  H  HNH2  0   0.409  45.0039  28.3794  10.8843
 LAQ  HN62  H  HNH2  0   0.399  45.5413  30.0060  10.7506
 LAQ  H2    H  HCR6  0   0.255  45.7091  30.9893   6.3925

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
 LAQ  O2P  P     single    1.590  0.020  1.590
 LAQ  O2P  HO2P  single    0.850  0.020  0.980
 LAQ  P    O1P   double    1.468  0.020  1.468
 LAQ  P    O5'   single    1.586  0.020  1.586
 LAQ  P    O3P   single    1.634  0.020  1.634
 LAQ  O3P  C10   single    1.364  0.020  1.364
 LAQ  C10  O10   double    1.194  0.020  1.194
 LAQ  C10  C11   single    1.498  0.020  1.498
 LAQ  C11  C12   single    1.520  0.020  1.520
 LAQ  C11  H111  single    0.970  0.020  1.090
 LAQ  C11  H112  single    0.970  0.020  1.090
 LAQ  C12  C13   single    1.525  0.020  1.525
 LAQ  C12  H121  single    0.970  0.020  1.090
 LAQ  C12  H122  single    0.970  0.020  1.090
 LAQ  C13  C14   single    1.525  0.020  1.525
 LAQ  C13  H131  single    0.970  0.020  1.090
 LAQ  C13  H132  single    0.970  0.020  1.090
 LAQ  C14  C15   single    1.520  0.020  1.520
 LAQ  C14  H141  single    0.970  0.020  1.090
 LAQ  C14  H142  single    0.970  0.020  1.090
 LAQ  C15  C16   single    1.523  0.020  1.523
 LAQ  C15  S15   single    1.831  0.020  1.831
 LAQ  C15  H15   single    0.970  0.020  1.090
 LAQ  S15  S17   single    2.082  0.020  2.082
 LAQ  S17  C17   single    1.842  0.020  1.842
 LAQ  C17  C16   single    1.528  0.020  1.528
 LAQ  C17  H171  single    0.970  0.020  1.090
 LAQ  C17  H172  single    0.970  0.020  1.090
 LAQ  C16  H161  single    0.970  0.020  1.090
 LAQ  C16  H162  single    0.970  0.020  1.090
 LAQ  O5'  C5'   single    1.434  0.020  1.434
 LAQ  C5'  C4'   single    1.505  0.020  1.505
 LAQ  C5'  H5'1  single    0.970  0.020  1.090
 LAQ  C5'  H5'2  single    0.970  0.020  1.090
 LAQ  C4'  O4'   single    1.419  0.020  1.419
 LAQ  C4'  C3'   single    1.535  0.020  1.535
 LAQ  C4'  H4'   single    0.970  0.020  1.090
 LAQ  C3'  C2'   single    1.532  0.020  1.532
 LAQ  C3'  O3'   single    1.390  0.020  1.390
 LAQ  C3'  H3'   single    0.970  0.020  1.090
 LAQ  O3'  HO3'  single    0.850  0.020  0.980
 LAQ  C2'  O2'   single    1.403  0.020  1.403
 LAQ  C2'  C1'   single    1.538  0.020  1.538
 LAQ  C2'  H2'   single    0.970  0.020  1.090
 LAQ  O2'  HO2'  single    0.850  0.020  0.980
 LAQ  C1'  O4'   single    1.403  0.020  1.403
 LAQ  C1'  N9    single    1.447  0.020  1.447
 LAQ  C1'  H1'   single    0.970  0.020  1.090
 LAQ  N9   C4    aromatic  1.366  0.020  1.366
 LAQ  N9   C8    aromatic  1.369  0.020  1.369
 LAQ  C8   N7    aromatic  1.300  0.020  1.300
 LAQ  C8   H8    single    0.930  0.020  1.080
 LAQ  N7   C5    aromatic  1.371  0.020  1.371
 LAQ  C5   C4    aromatic  1.385  0.020  1.385
 LAQ  C5   C6    aromatic  1.407  0.020  1.407
 LAQ  C6   N1    aromatic  1.337  0.020  1.337
 LAQ  C6   N6    single    1.335  0.020  1.335
 LAQ  N6   HN61  single    0.890  0.020  1.040
 LAQ  N6   HN62  single    0.890  0.020  1.040
 LAQ  N1   C2    aromatic  1.330  0.020  1.330
 LAQ  C2   N3    aromatic  1.322  0.020  1.322
 LAQ  C2   H2    single    0.930  0.020  1.080
 LAQ  N3   C4    aromatic  1.330  0.020  1.330

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
 LAQ  HO2P  O2P  P     114.09  3.000
 LAQ  O5'   P    O3P   106.15  3.000
 LAQ  O3P   P    O1P   116.71  3.000
 LAQ  O5'   P    O1P   111.59  3.000
 LAQ  O3P   P    O2P    94.70  3.000
 LAQ  O5'   P    O2P   107.72  3.000
 LAQ  O1P   P    O2P   118.24  3.000
 LAQ  C10   O3P  P     122.34  3.000
 LAQ  O10   C10  C11   127.05  3.000
 LAQ  C11   C10  O3P   110.89  3.000
 LAQ  O10   C10  O3P   122.04  3.000
 LAQ  H112  C11  H111  105.22  3.000
 LAQ  H112  C11  C12   111.10  3.000
 LAQ  H111  C11  C12   110.49  3.000
 LAQ  H112  C11  C10   109.00  3.000
 LAQ  H111  C11  C10   106.88  3.000
 LAQ  C12   C11  C10   113.73  3.000
 LAQ  H122  C12  H121  106.43  3.000
 LAQ  H122  C12  C13   108.82  3.000
 LAQ  H121  C12  C13   109.75  3.000
 LAQ  H122  C12  C11   109.97  3.000
 LAQ  H121  C12  C11   110.07  3.000
 LAQ  C13   C12  C11   111.66  3.000
 LAQ  H132  C13  H131  106.30  3.000
 LAQ  H132  C13  C14   110.10  3.000
 LAQ  H131  C13  C14   109.93  3.000
 LAQ  H132  C13  C12   109.65  3.000
 LAQ  H131  C13  C12   109.06  3.000
 LAQ  C14   C13  C12   111.66  3.000
 LAQ  H142  C14  H141  106.40  3.000
 LAQ  H142  C14  C15   106.55  3.000
 LAQ  H141  C14  C15   109.72  3.000
 LAQ  H142  C14  C13   109.22  3.000
 LAQ  H141  C14  C13   109.92  3.000
 LAQ  C15   C14  C13   114.67  3.000
 LAQ  H15   C15  C16   110.28  3.000
 LAQ  H15   C15  S15   107.21  3.000
 LAQ  C16   C15  S15   104.68  3.000
 LAQ  H15   C15  C14   109.81  3.000
 LAQ  S15   C15  C14   111.44  3.000
 LAQ  C16   C15  C14   113.18  3.000
 LAQ  S17   S15  C15    91.97  3.000
 LAQ  C17   S17  S15    95.86  3.000
 LAQ  H172  C17  H171  108.56  3.000
 LAQ  H172  C17  C16   111.54  3.000
 LAQ  H171  C17  C16   111.32  3.000
 LAQ  H172  C17  S17   105.91  3.000
 LAQ  H171  C17  S17   109.46  3.000
 LAQ  C16   C17  S17   109.89  3.000
 LAQ  H162  C16  H161  107.59  3.000
 LAQ  H162  C16  C17   109.35  3.000
 LAQ  H161  C16  C17   109.77  3.000
 LAQ  H162  C16  C15   109.84  3.000
 LAQ  H161  C16  C15   108.68  3.000
 LAQ  C17   C16  C15   111.53  3.000
 LAQ  C5'   O5'  P     123.82  3.000
 LAQ  H5'2  C5'  H5'1  107.90  3.000
 LAQ  H5'2  C5'  C4'   110.30  3.000
 LAQ  H5'1  C5'  C4'   109.74  3.000
 LAQ  H5'2  C5'  O5'   111.83  3.000
 LAQ  H5'1  C5'  O5'   108.27  3.000
 LAQ  C4'   C5'  O5'   108.77  3.000
 LAQ  H4'   C4'  O4'   110.16  3.000
 LAQ  H4'   C4'  C3'   109.92  3.000
 LAQ  O4'   C4'  C3'   104.92  3.000
 LAQ  H4'   C4'  C5'   109.45  3.000
 LAQ  C3'   C4'  C5'   113.02  3.000
 LAQ  O4'   C4'  C5'   109.29  3.000
 LAQ  H3'   C3'  C2'   109.06  3.000
 LAQ  H3'   C3'  O3'   106.65  3.000
 LAQ  C2'   C3'  O3'   115.29  3.000
 LAQ  H3'   C3'  C4'   109.62  3.000
 LAQ  O3'   C3'  C4'   114.92  3.000
 LAQ  C2'   C3'  C4'   101.15  3.000
 LAQ  HO3'  O3'  C3'   108.23  3.000
 LAQ  H2'   C2'  C1'   111.67  3.000
 LAQ  H2'   C2'  O2'   112.15  3.000
 LAQ  C1'   C2'  O2'   110.81  3.000
 LAQ  H2'   C2'  C3'   113.11  3.000
 LAQ  C1'   C2'  C3'   102.08  3.000
 LAQ  O2'   C2'  C3'   106.49  3.000
 LAQ  HO2'  O2'  C2'   109.48  3.000
 LAQ  H1'   C1'  N9    105.86  3.000
 LAQ  H1'   C1'  O4'   110.96  3.000
 LAQ  N9    C1'  O4'   108.74  3.000
 LAQ  H1'   C1'  C2'   110.58  3.000
 LAQ  N9    C1'  C2'   113.80  3.000
 LAQ  O4'   C1'  C2'   106.94  3.000
 LAQ  C1'   O4'  C4'   111.17  3.000
 LAQ  C4    N9   C8    106.11  3.000
 LAQ  C8    N9   C1'   128.19  3.000
 LAQ  C4    N9   C1'   125.65  3.000
 LAQ  H8    C8   N7    124.37  3.000
 LAQ  H8    C8   N9    122.20  3.000
 LAQ  N7    C8   N9    113.43  3.000
 LAQ  C5    N7   C8    104.41  3.000
 LAQ  C4    C5   C6    116.29  3.000
 LAQ  C6    C5   N7    132.91  3.000
 LAQ  C4    C5   N7    110.79  3.000
 LAQ  N1    C6   N6    119.32  3.000
 LAQ  N6    C6   C5    122.79  3.000
 LAQ  N1    C6   C5    117.88  3.000
 LAQ  HN62  N6   HN61  117.29  3.000
 LAQ  HN62  N6   C6    119.10  3.000
 LAQ  HN61  N6   C6    120.37  3.000
 LAQ  C2    N1   C6    119.23  3.000
 LAQ  H2    C2   N3    116.17  3.000
 LAQ  H2    C2   N1    115.45  3.000
 LAQ  N3    C2   N1    128.38  3.000
 LAQ  C4    N3   C2    111.66  3.000
 LAQ  N3    C4   C5    126.56  3.000
 LAQ  N3    C4   N9    128.17  3.000
 LAQ  C5    C4   N9    105.26  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
 LAQ  CONST_01  N7    C5   C4   N9      0.00   0.0  0
 LAQ  CONST_02  C6    C5   C4   N9    180.00   0.0  0
 LAQ  CONST_03  C2    N3   C4   N9    180.00   0.0  0
 LAQ  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 LAQ  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 LAQ  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 LAQ  CONST_07  C4    C5   N7   C8      0.00   0.0  0
 LAQ  CONST_08  C6    C5   N7   C8    180.00   0.0  0
 LAQ  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 LAQ  CONST_10  N3    C4   C5   N7    180.00   0.0  0
 LAQ  CONST_11  N1    C6   C5   N7    180.00   0.0  0
 LAQ  CONST_12  C2    N3   C4   C5      0.00   0.0  0
 LAQ  CONST_13  C2    N1   C6   C5      0.00   0.0  0
 LAQ  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 LAQ  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 LAQ  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 LAQ  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 LAQ  CONST_18  C5    C4   N9   C1'   180.00   0.0  0
 LAQ  CONST_19  N3    C4   N9   C1'     0.00   0.0  0
 LAQ  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 LAQ  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 LAQ  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 LAQ  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 LAQ  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 LAQ  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 LAQ  CONST_26  HN61  N6   C6   C5      0.00   0.0  0
 LAQ  CONST_27  HN62  N6   C6   C5    180.00   0.0  0
 LAQ  Var_01    S17   C17  C16  C15    25.66  30.0  1
 LAQ  Var_02    C16   C17  S17  S15     7.59  30.0  1
 LAQ  Var_03    C4'   C5'  O5'  P    -131.83  30.0  3
 LAQ  Var_04    C15   C14  C13  C12   163.54  30.0  3
 LAQ  Var_05    O10   C10  O3P  P      -4.42  30.0  3
 LAQ  Var_06    C12   C11  C10  O3P   175.75  30.0  3
 LAQ  Var_07    O5'   P    O3P  C10    73.32  30.0  1
 LAQ  Var_08    C13   C12  C11  C10   173.36  30.0  3
 LAQ  Var_09    C14   C13  C12  C11   177.04  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
 LAQ  chir_02  C15  C14  C16  S15  positiv
 LAQ  chir_03  C4'  C5'  O4'  C3'  negativ
 LAQ  chir_04  C3'  O3'  C4'  C2'  positiv
 LAQ  chir_05  C2'  O2'  C3'  C1'  positiv
 LAQ  chir_06  C1'  O4'  N9   C2'  negativ
 LAQ  chir_07  P    O1P  O5'  O3P  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
 LAQ  plan-1  C6    0.020
 LAQ  plan-1  N6    0.020
 LAQ  plan-1  HN61  0.020
 LAQ  plan-1  HN62  0.020
 LAQ  plan-2  C1'   0.020
 LAQ  plan-2  N9    0.020
 LAQ  plan-2  C8    0.020
 LAQ  plan-2  N7    0.020
 LAQ  plan-2  C5    0.020
 LAQ  plan-2  C6    0.020
 LAQ  plan-2  N6    0.020
 LAQ  plan-2  N1    0.020
 LAQ  plan-2  C2    0.020
 LAQ  plan-2  N3    0.020
 LAQ  plan-2  C4    0.020
 LAQ  plan-2  H8    0.020
 LAQ  plan-2  H2    0.020
 LAQ  plan-3  O3P   0.020
 LAQ  plan-3  C10   0.020
 LAQ  plan-3  C11   0.020
 LAQ  plan-3  O10   0.020

