# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 15:43:22 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 5'-O-{(S)-hydroxy[(4-methyl-2-oxopentanoyl)oxy]phosphoryl}adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC(=O)C(=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
 QA7  QA7  5'-O-{(S)-hydroxy[(4-methyl-2-oxopentanoyl)oxy]phosphoryl}adenosine  ligand  53  31  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QA7
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
 QA7  C01   C  CH3   0  -0.683   4.2174   2.4815   2.0141
 QA7  C02   C  CH1   0  -0.271   3.1978   2.9711   0.9911
 QA7  C03   C  CH3   0  -0.657   3.5592   4.3741   0.5127
 QA7  C04   C  CH2   0  -0.512   3.1129   2.0359  -0.2103
 QA7  C05   C  C     0   0.277   2.5348   0.6874   0.0726
 QA7  C06   C  C     0   0.548   2.6215  -0.3242  -1.0885
 QA7  C10   C  CH2   0  -0.164  -0.2691  -3.9791  -0.8511
 QA7  C11   C  CH1   0  -0.007  -0.8056  -3.4793   0.4728
 QA7  C12   C  CH1   0  -0.086  -2.3326  -3.4945   0.4908
 QA7  C13   C  CH1   0   0.060  -2.6514  -2.0733   0.0048
 QA7  C14   C  CH1   0   0.247  -1.5343  -1.2740   0.6747
 QA7  C16   C  CR15  0   0.092  -0.7113   0.0947  -1.2689
 QA7  C18   C  CR56  0  -0.018  -0.5772   2.0164  -0.3964
 QA7  C19   C  CR6   0   0.434  -0.3873   3.3653  -0.0416
 QA7  C21   C  CR16  0   0.053  -1.1712   2.8223   2.0494
 QA7  C23   C  CR56  0   0.512  -1.0884   1.1867   0.5872
 QA7  N15   N  NR5   0  -0.539  -1.1858  -0.0479   0.0069
 QA7  N17   N  N     0  -0.503  -0.3395   1.3099  -1.5492
 QA7  N20   N  N     0  -0.491  -0.7026   3.7344   1.2062
 QA7  N22   N  N     0  -0.457  -1.4053   1.5389   1.8277
 QA7  N24   N  NH2   0  -0.816   0.1055   4.2719  -0.8880
 QA7  O07   O  O2    0  -0.515   2.0932  -1.5043  -0.7481
 QA7  O09   O  O2    0  -0.560   1.1579  -3.7966  -0.9128
 QA7  O25   O  O2    0  -0.565  -0.4199  -2.1239   0.6832
 QA7  O26   O  OH1   0  -0.598  -3.8953  -1.5819   0.4029
 QA7  O27   O  OH1   0  -0.641  -2.7601  -3.6810   1.8152
 QA7  O28   O  O     0  -0.717   1.0842  -2.2589  -3.0262
 QA7  O29   O  OH1   0  -0.645   3.2626  -3.2861  -2.1798
 QA7  O30   O  O     0  -0.338   3.1293  -0.0883  -2.1436
 QA7  O31   O  O     0  -0.371   1.9711   0.3624   1.0822
 QA7  P08   P  P     0   1.476   1.8327  -2.7064  -1.8448
 QA7  H013  H  HCH3  0   0.256   5.2112   2.4151   1.5655
 QA7  H011  H  HCH3  0   0.234   4.2811   3.1752   2.8542
 QA7  H012  H  HCH3  0   0.252   3.9673   1.5002   2.4193
 QA7  H021  H  HCH1  0   0.256   2.2144   3.0176   1.4705
 QA7  H033  H  HCH3  0   0.195   4.5365   4.3810   0.0241
 QA7  H031  H  HCH3  0   0.235   2.8270   4.7554  -0.2010
 QA7  H032  H  HCH3  0   0.254   3.6019   5.0723   1.3515
 QA7  H042  H  HCH2  0   0.263   2.4939   2.4810  -1.0002
 QA7  H041  H  HCH2  0   0.262   4.0990   1.9124  -0.6686
 QA7  H102  H  HCH2  0   0.194  -0.4610  -5.0488  -0.9388
 QA7  H101  H  HCH2  0   0.252  -0.7538  -3.4870  -1.6977
 QA7  H111  H  HCH1  0   0.277  -0.4003  -4.0929   1.2834
 QA7  H121  H  HCH1  0   0.258  -2.7466  -4.2564  -0.1824
 QA7  H131  H  HCH1  0   0.175  -2.5364  -2.0341  -1.0848
 QA7  H141  H  HCH1  0   0.287  -1.8304  -0.9897   1.6901
 QA7  H161  H  HCR5  0   0.316  -0.6551  -0.7351  -1.9562
 QA7  H211  H  HCR6  0   0.289  -1.4104   3.1843   3.0417
 QA7  H242  H  HNH2  0   0.412   0.2804   4.0395  -1.8534
 QA7  H241  H  HNH2  0   0.380   0.1778   5.2372  -0.6086
 QA7  H261  H  HOH1  0   0.467  -4.5636  -1.8704  -0.2312
 QA7  H271  H  HOH1  0   0.416  -3.6896  -3.4215   1.8754
 QA7  H1    H  HOH1  0   0.522   3.7686  -3.6827  -1.4531

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
 QA7  O27  C12   single    1.404  0.020  1.404
 QA7  O26  C13   single    1.395  0.020  1.395
 QA7  C13  C12   single    1.535  0.020  1.535
 QA7  C13  C14   single    1.528  0.020  1.528
 QA7  C12  C11   single    1.527  0.020  1.527
 QA7  C11  C10   single    1.513  0.020  1.513
 QA7  C11  O25   single    1.425  0.020  1.425
 QA7  C14  O25   single    1.402  0.020  1.402
 QA7  C14  N15   single    1.439  0.020  1.439
 QA7  N22  C21   aromatic  1.323  0.020  1.323
 QA7  N22  C23   aromatic  1.328  0.020  1.328
 QA7  C21  N20   aromatic  1.328  0.020  1.328
 QA7  C10  O09   single    1.440  0.020  1.440
 QA7  C23  N15   aromatic  1.368  0.020  1.368
 QA7  C23  C18   aromatic  1.385  0.020  1.385
 QA7  N15  C16   aromatic  1.369  0.020  1.369
 QA7  O09  P08   single    1.585  0.020  1.585
 QA7  O28  P08   double    1.468  0.020  1.468
 QA7  N20  C19   aromatic  1.339  0.020  1.339
 QA7  C18  C19   aromatic  1.408  0.020  1.408
 QA7  C18  N17   aromatic  1.373  0.020  1.373
 QA7  C16  N17   aromatic  1.301  0.020  1.301
 QA7  C19  N24   single    1.335  0.020  1.335
 QA7  P08  O29   single    1.579  0.020  1.579
 QA7  P08  O07   single    1.648  0.020  1.648
 QA7  O07  C06   single    1.337  0.020  1.337
 QA7  C06  O30   double    1.195  0.020  1.195
 QA7  C06  C05   single    1.542  0.020  1.542
 QA7  O31  C05   double    1.201  0.020  1.201
 QA7  C05  C04   single    1.494  0.020  1.494
 QA7  C04  C02   single    1.525  0.020  1.525
 QA7  C02  C03   single    1.526  0.020  1.526
 QA7  C02  C01   single    1.525  0.020  1.525
 QA7  C01  H013  single    0.970  0.020  1.090
 QA7  C01  H011  single    0.970  0.020  1.090
 QA7  C01  H012  single    0.970  0.020  1.090
 QA7  C02  H021  single    0.970  0.020  1.090
 QA7  C03  H033  single    0.970  0.020  1.090
 QA7  C03  H031  single    0.970  0.020  1.090
 QA7  C03  H032  single    0.970  0.020  1.090
 QA7  C04  H042  single    0.970  0.020  1.090
 QA7  C04  H041  single    0.970  0.020  1.090
 QA7  C10  H102  single    0.970  0.020  1.090
 QA7  C10  H101  single    0.970  0.020  1.090
 QA7  C11  H111  single    0.970  0.020  1.090
 QA7  C12  H121  single    0.970  0.020  1.090
 QA7  C13  H131  single    0.970  0.020  1.090
 QA7  C14  H141  single    0.970  0.020  1.090
 QA7  C16  H161  single    0.930  0.020  1.080
 QA7  C21  H211  single    0.930  0.020  1.080
 QA7  N24  H242  single    0.860  0.020  1.020
 QA7  N24  H241  single    0.860  0.020  1.020
 QA7  O26  H261  single    0.850  0.020  0.980
 QA7  O27  H271  single    0.850  0.020  0.980
 QA7  O29  H1    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
 QA7  H012  C01  H011  107.41  3.000
 QA7  H012  C01  H013  107.85  3.000
 QA7  H011  C01  H013  107.56  3.000
 QA7  H012  C01  C02   112.63  3.000
 QA7  H011  C01  C02   110.57  3.000
 QA7  H013  C01  C02   110.62  3.000
 QA7  H021  C02  C04   108.72  3.000
 QA7  H021  C02  C03   108.11  3.000
 QA7  C04   C02  C03   109.28  3.000
 QA7  H021  C02  C01   108.68  3.000
 QA7  C03   C02  C01   110.32  3.000
 QA7  C04   C02  C01   111.65  3.000
 QA7  H032  C03  H031  107.77  3.000
 QA7  H032  C03  H033  107.72  3.000
 QA7  H031  C03  H033  107.78  3.000
 QA7  H032  C03  C02   110.88  3.000
 QA7  H031  C03  C02   111.56  3.000
 QA7  H033  C03  C02   110.96  3.000
 QA7  H041  C04  H042  104.62  3.000
 QA7  H041  C04  C05   109.03  3.000
 QA7  H042  C04  C05   106.50  3.000
 QA7  H041  C04  C02   110.42  3.000
 QA7  H042  C04  C02   110.47  3.000
 QA7  C05   C04  C02   115.21  3.000
 QA7  O31   C05  C06   118.79  3.000
 QA7  O31   C05  C04   125.80  3.000
 QA7  C06   C05  C04   115.32  3.000
 QA7  O30   C06  O07   124.55  3.000
 QA7  O30   C06  C05   124.01  3.000
 QA7  O07   C06  C05   111.41  3.000
 QA7  H101  C10  H102  107.54  3.000
 QA7  H101  C10  O09   110.45  3.000
 QA7  H102  C10  O09   107.18  3.000
 QA7  H101  C10  C11   111.83  3.000
 QA7  H102  C10  C11   109.39  3.000
 QA7  O09   C10  C11   110.30  3.000
 QA7  H111  C11  O25   108.89  3.000
 QA7  H111  C11  C12   110.85  3.000
 QA7  O25   C11  C12   106.17  3.000
 QA7  H111  C11  C10   109.35  3.000
 QA7  O25   C11  C10   110.33  3.000
 QA7  C12   C11  C10   111.19  3.000
 QA7  H121  C12  O27   111.81  3.000
 QA7  H121  C12  C13   111.72  3.000
 QA7  O27   C12  C13   111.00  3.000
 QA7  H121  C12  C11   112.13  3.000
 QA7  C13   C12  C11   101.22  3.000
 QA7  O27   C12  C11   108.47  3.000
 QA7  H131  C13  O26   111.38  3.000
 QA7  H131  C13  C14   109.89  3.000
 QA7  O26   C13  C14   110.02  3.000
 QA7  H131  C13  C12   109.02  3.000
 QA7  C14   C13  C12   101.16  3.000
 QA7  O26   C13  C12   114.88  3.000
 QA7  H141  C14  O25   111.51  3.000
 QA7  H141  C14  N15   105.94  3.000
 QA7  O25   C14  N15   109.09  3.000
 QA7  H141  C14  C13   110.15  3.000
 QA7  N15   C14  C13   114.79  3.000
 QA7  O25   C14  C13   105.47  3.000
 QA7  H161  C16  N17   124.48  3.000
 QA7  H161  C16  N15   122.12  3.000
 QA7  N17   C16  N15   113.40  3.000
 QA7  N17   C18  C23   110.61  3.000
 QA7  N17   C18  C19   132.96  3.000
 QA7  C23   C18  C19   116.42  3.000
 QA7  N24   C19  N20   119.39  3.000
 QA7  N24   C19  C18   122.74  3.000
 QA7  N20   C19  C18   117.86  3.000
 QA7  H211  C21  N22   116.02  3.000
 QA7  H211  C21  N20   115.48  3.000
 QA7  N22   C21  N20   128.49  3.000
 QA7  N22   C23  N15   128.23  3.000
 QA7  N15   C23  C18   105.42  3.000
 QA7  N22   C23  C18   126.35  3.000
 QA7  C23   N15  C16   106.07  3.000
 QA7  C16   N15  C14   127.25  3.000
 QA7  C23   N15  C14   126.12  3.000
 QA7  C18   N17  C16   104.49  3.000
 QA7  C21   N20  C19   119.05  3.000
 QA7  C23   N22  C21   111.81  3.000
 QA7  H241  N24  H242  118.28  3.000
 QA7  H241  N24  C19   120.10  3.000
 QA7  H242  N24  C19   120.98  3.000
 QA7  P08   O07  C06   122.48  3.000
 QA7  P08   O09  C10   122.30  3.000
 QA7  C14   O25  C11   111.15  3.000
 QA7  H261  O26  C13   108.94  3.000
 QA7  H271  O27  C12   108.41  3.000
 QA7  H1    O29  P08   117.61  3.000
 QA7  O29   P08  O28   113.76  3.000
 QA7  O29   P08  O09   104.94  3.000
 QA7  O28   P08  O09   117.75  3.000
 QA7  O29   P08  O07   105.42  3.000
 QA7  O28   P08  O07   113.18  3.000
 QA7  O09   P08  O07   100.24  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
 QA7  CONST_01  N22   C23  N15  C16   180.00   0.0  0
 QA7  CONST_02  C18   C23  N15  C16     0.00   0.0  0
 QA7  CONST_03  C23   C18  N17  C16     0.00   0.0  0
 QA7  CONST_04  C19   C18  N17  C16   180.00   0.0  0
 QA7  CONST_05  C21   N22  C23  C18     0.00   0.0  0
 QA7  CONST_06  C21   N20  C19  C18     0.00   0.0  0
 QA7  CONST_07  N15   C16  N17  C18     0.00   0.0  0
 QA7  CONST_08  N22   C21  N20  C19     0.00   0.0  0
 QA7  CONST_09  N22   C23  C18  C19     0.00   0.0  0
 QA7  CONST_10  N15   C23  C18  C19   180.00   0.0  0
 QA7  CONST_11  N15   C23  N22  C21   180.00   0.0  0
 QA7  CONST_12  N20   C21  N22  C23     0.00   0.0  0
 QA7  CONST_13  N17   C16  N15  C23     0.00   0.0  0
 QA7  CONST_14  N20   C19  C18  C23     0.00   0.0  0
 QA7  CONST_15  N17   C18  C23  N15     0.00   0.0  0
 QA7  CONST_16  N22   C23  C18  N17   180.00   0.0  0
 QA7  CONST_17  N20   C19  C18  N17   180.00   0.0  0
 QA7  CONST_18  N22   C23  N15  C14     0.00   0.0  0
 QA7  CONST_19  C18   C23  N15  C14   180.00   0.0  0
 QA7  CONST_20  N17   C16  N15  C14   180.00   0.0  0
 QA7  CONST_21  N24   C19  N20  C21   180.00   0.0  0
 QA7  CONST_22  N24   C19  C18  C23   180.00   0.0  0
 QA7  CONST_23  N24   C19  C18  N17     0.00   0.0  0
 QA7  CONST_24  H161  C16  N15  C14     0.00   0.0  0
 QA7  CONST_25  H211  C21  N20  C19   180.00   0.0  0
 QA7  CONST_26  H242  N24  C19  C18     0.00   0.0  0
 QA7  CONST_27  H241  N24  C19  C18   180.00   0.0  0
 QA7  Var_01    C05   C04  C02  C01    67.99  30.0  2
 QA7  Var_02    C06   C05  C04  C02  -172.09  30.0  1
 QA7  Var_03    O07   C06  C05  C04   179.48  30.0  1
 QA7  Var_04    O09   P08  O07  C06  -177.71  30.0  2
 QA7  Var_05    H033  C03  C02  C01    61.33  30.0  3
 QA7  Var_06    H013  C01  C02  C03   -62.11  30.0  3
 QA7  Var_07    H102  C10  O09  P08   132.40  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
 QA7  chir_01  C11  C12  C10  O25  negativ
 QA7  chir_02  C12  O27  C13  C11  negativ
 QA7  chir_03  C13  O26  C14  C12  negativ
 QA7  chir_04  C14  O25  N15  C13  negativ
 QA7  chir_05  P08  O28  O29  O07  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
 QA7  plan-1  C14   0.020
 QA7  plan-1  C16   0.020
 QA7  plan-1  C18   0.020
 QA7  plan-1  C19   0.020
 QA7  plan-1  C21   0.020
 QA7  plan-1  C23   0.020
 QA7  plan-1  N15   0.020
 QA7  plan-1  N17   0.020
 QA7  plan-1  N20   0.020
 QA7  plan-1  N22   0.020
 QA7  plan-1  N24   0.020
 QA7  plan-1  H161  0.020
 QA7  plan-1  H211  0.020
 QA7  plan-2  C19   0.020
 QA7  plan-2  N24   0.020
 QA7  plan-2  H242  0.020
 QA7  plan-2  H241  0.020
 QA7  plan-3  C04   0.020
 QA7  plan-3  C05   0.020
 QA7  plan-3  C06   0.020
 QA7  plan-3  O31   0.020
 QA7  plan-4  C05   0.020
 QA7  plan-4  C06   0.020
 QA7  plan-4  O07   0.020
 QA7  plan-4  O30   0.020

