# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:28:49 2021
#   Inital geometry file: a 112 line input string
#   Ligand name: 5'-O-[(S)-butoxy(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCO[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
 WT7  WT7  5'-O-[(S)-butoxy(hydroxy)phosphoryl]adenosine  ligand  49  27  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WT7
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
 WT7  C11  C  CH1   0  -0.014  -13.2565   7.5423  -26.3949
 WT7  C10  C  CH2   0  -0.180  -12.3468   6.8967  -25.3851
 WT7  C01  C  CH3   0  -0.684  -14.6610   4.0161  -22.4474
 WT7  C02  C  CH2   0  -0.425  -13.6413   2.8857  -22.4460
 WT7  C03  C  CH2   0  -0.462  -13.3205   2.3262  -23.8303
 WT7  C04  C  CH2   0  -0.194  -12.8545   3.3454  -24.8453
 WT7  C13  C  CH1   0   0.176  -15.4192   7.1922  -27.1639
 WT7  C15  C  CR15  0   0.132  -16.3152   5.8951  -25.1759
 WT7  C17  C  CR56  0  -0.003  -18.3553   5.7275  -25.6838
 WT7  C18  C  CR6   0   0.458  -19.7366   5.4865  -25.8055
 WT7  C21  C  CR16  0   0.044  -19.6553   6.6052  -27.8161
 WT7  C23  C  CR56  0   0.489  -17.7618   6.4264  -26.7231
 WT7  C24  C  CH1   0  -0.052  -15.2850   8.6775  -26.8132
 WT7  C26  C  CH1   0  -0.012  -14.1306   8.6544  -25.8092
 WT7  N14  N  NR5   0  -0.534  -16.4441   6.5253  -26.3816
 WT7  N16  N  N     0  -0.447  -17.4308   5.4028  -24.7259
 WT7  N19  N  NH2   0  -0.815  -20.4407   4.8376  -24.8771
 WT7  N20  N  N     0  -0.473  -20.3570   5.9458  -26.8981
 WT7  N22  N  N     0  -0.457  -18.3650   6.8931  -27.8140
 WT7  O05  O  O2    0  -0.591  -11.7218   4.0535  -24.3075
 WT7  O07  O  O     0  -0.694   -9.9665   3.9846  -26.2516
 WT7  O08  O  OH1   0  -0.736   -9.8702   5.5536  -24.1487
 WT7  O09  O  O2    0  -0.591  -11.5648   5.9103  -26.0556
 WT7  O12  O  O2    0  -0.492  -14.1864   6.5860  -26.8901
 WT7  O25  O  OH1   0  -0.661  -14.9303   9.3494  -27.9903
 WT7  O27  O  OH1   0  -0.660  -13.5016   9.8984  -25.7382
 WT7  P06  P  P     0   1.486  -10.7086   4.8044  -25.2772
 WT7  H1   H  HCH1  0   0.257  -12.6568   7.9480  -27.2189
 WT7  H2   H  HCH2  0   0.260  -11.6972   7.6601  -24.9481
 WT7  H3   H  HCH2  0   0.225  -12.9326   6.4539  -24.5718
 WT7  H4   H  HCH3  0   0.241  -14.9456   4.2879  -21.4310
 WT7  H5   H  HCH3  0   0.211  -14.2629   4.9203  -22.9114
 WT7  H6   H  HCH3  0   0.225  -15.5726   3.7397  -22.9812
 WT7  H7   H  HCH2  0   0.232  -14.0176   2.0624  -21.8341
 WT7  H8   H  HCH2  0   0.225  -12.7239   3.2225  -21.9581
 WT7  H9   H  HCH2  0   0.237  -14.2139   1.8568  -24.2527
 WT7  H10  H  HCH2  0   0.243  -12.5707   1.5362  -23.7419
 WT7  H11  H  HCH2  0   0.221  -13.6459   4.0653  -25.0715
 WT7  H12  H  HCH2  0   0.257  -12.5868   2.8472  -25.7802
 WT7  H13  H  HCH1  0   0.284  -15.6969   7.0673  -28.2143
 WT7  H14  H  HCR5  0   0.258  -15.3654   5.8178  -24.6726
 WT7  H15  H  HCR6  0   0.253  -20.2206   6.9501  -28.6753
 WT7  H16  H  HCH1  0   0.268  -16.2090   9.0739  -26.3772
 WT7  H17  H  HCH1  0   0.244  -14.5190   8.3417  -24.8299
 WT7  H18  H  HNH2  0   0.404  -21.4085   4.6189  -25.0401
 WT7  H19  H  HNH2  0   0.411  -19.9866   4.4162  -24.0861
 WT7  H20  H  HOH1  0   0.505   -9.0285   5.9157  -24.4579
 WT7  H21  H  HOH1  0   0.460  -14.6561  10.2441  -27.7601
 WT7  H22  H  HOH1  0   0.470  -13.1032  10.0081  -24.8704

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
 WT7  O25  C24  single    1.401  0.020  1.401
 WT7  N22  C21  aromatic  1.322  0.020  1.322
 WT7  N22  C23  aromatic  1.331  0.020  1.331
 WT7  C21  N20  aromatic  1.330  0.020  1.330
 WT7  C13  C24  single    1.532  0.020  1.532
 WT7  C13  O12  single    1.401  0.020  1.401
 WT7  C13  N14  single    1.452  0.020  1.452
 WT7  C24  C26  single    1.530  0.020  1.530
 WT7  O12  C11  single    1.423  0.020  1.423
 WT7  C23  N14  aromatic  1.365  0.020  1.365
 WT7  C23  C17  aromatic  1.386  0.020  1.386
 WT7  N20  C18  aromatic  1.338  0.020  1.338
 WT7  N14  C15  aromatic  1.367  0.020  1.367
 WT7  C11  C26  single    1.531  0.020  1.531
 WT7  C11  C10  single    1.505  0.020  1.505
 WT7  O27  C26  single    1.396  0.020  1.396
 WT7  O07  P06  double    1.474  0.020  1.474
 WT7  C17  C18  aromatic  1.407  0.020  1.407
 WT7  C17  N16  aromatic  1.370  0.020  1.370
 WT7  C18  N19  single    1.334  0.020  1.334
 WT7  O09  C10  single    1.426  0.020  1.426
 WT7  O09  P06  single    1.601  0.020  1.601
 WT7  C15  N16  aromatic  1.300  0.020  1.300
 WT7  C04  O05  single    1.440  0.020  1.440
 WT7  C04  C03  single    1.512  0.020  1.512
 WT7  P06  O05  single    1.591  0.020  1.591
 WT7  P06  O08  single    1.593  0.020  1.593
 WT7  C03  C02  single    1.527  0.020  1.527
 WT7  C01  C02  single    1.522  0.020  1.522
 WT7  C11  H1   single    0.970  0.020  1.090
 WT7  C10  H2   single    0.970  0.020  1.090
 WT7  C10  H3   single    0.970  0.020  1.090
 WT7  C01  H4   single    0.970  0.020  1.090
 WT7  C01  H5   single    0.970  0.020  1.090
 WT7  C01  H6   single    0.970  0.020  1.090
 WT7  C02  H7   single    0.970  0.020  1.090
 WT7  C02  H8   single    0.970  0.020  1.090
 WT7  C03  H9   single    0.970  0.020  1.090
 WT7  C03  H10  single    0.970  0.020  1.090
 WT7  C04  H11  single    0.970  0.020  1.090
 WT7  C04  H12  single    0.970  0.020  1.090
 WT7  C13  H13  single    0.970  0.020  1.090
 WT7  C15  H14  single    0.930  0.020  1.080
 WT7  C21  H15  single    0.930  0.020  1.080
 WT7  C24  H16  single    0.970  0.020  1.090
 WT7  C26  H17  single    0.970  0.020  1.090
 WT7  N19  H18  single    0.860  0.020  1.020
 WT7  N19  H19  single    0.860  0.020  1.020
 WT7  O08  H20  single    0.850  0.020  0.980
 WT7  O25  H21  single    0.850  0.020  0.980
 WT7  O27  H22  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
 WT7  H1   C11  O12  110.15  3.000
 WT7  H1   C11  C26  109.32  3.000
 WT7  O12  C11  C26  104.37  3.000
 WT7  H1   C11  C10  109.41  3.000
 WT7  C26  C11  C10  113.58  3.000
 WT7  O12  C11  C10  109.90  3.000
 WT7  H3   C10  H2   107.65  3.000
 WT7  H3   C10  O09  111.26  3.000
 WT7  H2   C10  O09  110.18  3.000
 WT7  H3   C10  C11  110.38  3.000
 WT7  H2   C10  C11  109.13  3.000
 WT7  O09  C10  C11  108.22  3.000
 WT7  H6   C01  H5   107.84  3.000
 WT7  H6   C01  H4   107.52  3.000
 WT7  H5   C01  H4   106.56  3.000
 WT7  H6   C01  C02  111.82  3.000
 WT7  H5   C01  C02  111.79  3.000
 WT7  H4   C01  C02  111.05  3.000
 WT7  H8   C02  H7   105.75  3.000
 WT7  H8   C02  C03  109.96  3.000
 WT7  H7   C02  C03  107.69  3.000
 WT7  H8   C02  C01  109.51  3.000
 WT7  H7   C02  C01  109.23  3.000
 WT7  C03  C02  C01  114.32  3.000
 WT7  H10  C03  H9   106.34  3.000
 WT7  H10  C03  C04  109.28  3.000
 WT7  H9   C03  C04  106.36  3.000
 WT7  H10  C03  C02  109.62  3.000
 WT7  H9   C03  C02  109.61  3.000
 WT7  C04  C03  C02  115.23  3.000
 WT7  H12  C04  H11  107.49  3.000
 WT7  H12  C04  O05  110.56  3.000
 WT7  H11  C04  O05  108.83  3.000
 WT7  H12  C04  C03  110.03  3.000
 WT7  H11  C04  C03  111.07  3.000
 WT7  O05  C04  C03  108.85  3.000
 WT7  H13  C13  O12  111.21  3.000
 WT7  H13  C13  N14  106.61  3.000
 WT7  O12  C13  N14  108.50  3.000
 WT7  H13  C13  C24  110.66  3.000
 WT7  N14  C13  C24  112.58  3.000
 WT7  O12  C13  C24  107.32  3.000
 WT7  H14  C15  N16  124.59  3.000
 WT7  H14  C15  N14  121.89  3.000
 WT7  N16  C15  N14  113.52  3.000
 WT7  N16  C17  C23  110.78  3.000
 WT7  N16  C17  C18  133.00  3.000
 WT7  C23  C17  C18  116.22  3.000
 WT7  N20  C18  N19  119.39  3.000
 WT7  N19  C18  C17  122.77  3.000
 WT7  N20  C18  C17  117.84  3.000
 WT7  H15  C21  N22  116.14  3.000
 WT7  H15  C21  N20  115.43  3.000
 WT7  N22  C21  N20  128.43  3.000
 WT7  N22  C23  N14  128.11  3.000
 WT7  N14  C23  C17  105.21  3.000
 WT7  N22  C23  C17  126.68  3.000
 WT7  H16  C24  O25  111.98  3.000
 WT7  H16  C24  C26  112.36  3.000
 WT7  O25  C24  C26  111.57  3.000
 WT7  H16  C24  C13  111.58  3.000
 WT7  C26  C24  C13  101.63  3.000
 WT7  O25  C24  C13  107.15  3.000
 WT7  H17  C26  O27  111.56  3.000
 WT7  H17  C26  C24  108.81  3.000
 WT7  O27  C26  C24  111.09  3.000
 WT7  H17  C26  C11  109.64  3.000
 WT7  O27  C26  C11  114.18  3.000
 WT7  C24  C26  C11  100.99  3.000
 WT7  C23  N14  C15  106.17  3.000
 WT7  C15  N14  C13  128.37  3.000
 WT7  C23  N14  C13  125.46  3.000
 WT7  C17  N16  C15  104.32  3.000
 WT7  H19  N19  H18  118.12  3.000
 WT7  H19  N19  C18  120.90  3.000
 WT7  H18  N19  C18  120.08  3.000
 WT7  C21  N20  C18  119.28  3.000
 WT7  C23  N22  C21  111.55  3.000
 WT7  P06  O05  C04  120.36  3.000
 WT7  H20  O08  P06  114.06  3.000
 WT7  P06  O09  C10  122.85  3.000
 WT7  C13  O12  C11  110.63  3.000
 WT7  H21  O25  C24  108.46  3.000
 WT7  H22  O27  C26  109.54  3.000
 WT7  O09  P06  O08  107.52  3.000
 WT7  O08  P06  O07  117.70  3.000
 WT7  O09  P06  O07  109.40  3.000
 WT7  O08  P06  O05   97.20  3.000
 WT7  O09  P06  O05  106.38  3.000
 WT7  O07  P06  O05  117.46  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
 WT7  CONST_01  N22  C23  N14  C15   180.00   0.0  0
 WT7  CONST_02  C17  C23  N14  C15     0.00   0.0  0
 WT7  CONST_03  C23  C17  N16  C15     0.00   0.0  0
 WT7  CONST_04  C18  C17  N16  C15   180.00   0.0  0
 WT7  CONST_05  C21  N22  C23  C17     0.00   0.0  0
 WT7  CONST_06  C21  N20  C18  C17     0.00   0.0  0
 WT7  CONST_07  N14  C15  N16  C17     0.00   0.0  0
 WT7  CONST_08  N22  C21  N20  C18     0.00   0.0  0
 WT7  CONST_09  N22  C23  C17  C18     0.00   0.0  0
 WT7  CONST_10  N14  C23  C17  C18   180.00   0.0  0
 WT7  CONST_11  N14  C23  N22  C21   180.00   0.0  0
 WT7  CONST_12  N20  C21  N22  C23     0.00   0.0  0
 WT7  CONST_13  N16  C15  N14  C23     0.00   0.0  0
 WT7  CONST_14  N20  C18  C17  C23     0.00   0.0  0
 WT7  CONST_15  N16  C17  C23  N14     0.00   0.0  0
 WT7  CONST_16  N22  C23  C17  N16   180.00   0.0  0
 WT7  CONST_17  N20  C18  C17  N16   180.00   0.0  0
 WT7  CONST_18  N22  C23  N14  C13     0.00   0.0  0
 WT7  CONST_19  C17  C23  N14  C13   180.00   0.0  0
 WT7  CONST_20  N16  C15  N14  C13   180.00   0.0  0
 WT7  CONST_21  N19  C18  N20  C21   180.00   0.0  0
 WT7  CONST_22  N19  C18  C17  C23   180.00   0.0  0
 WT7  CONST_23  N19  C18  C17  N16     0.00   0.0  0
 WT7  CONST_24  H14  C15  N14  C13     0.00   0.0  0
 WT7  CONST_25  H15  C21  N20  C18   180.00   0.0  0
 WT7  CONST_26  H18  N19  C18  C17   180.00   0.0  0
 WT7  CONST_27  H19  N19  C18  C17     0.00   0.0  0
 WT7  Var_01    O07  P06  O09  C10  -177.19  30.0  3
 WT7  Var_02    C04  C03  C02  C01    55.21  30.0  1
 WT7  Var_03    O05  C04  C03  C02    54.98  30.0  2
 WT7  Var_04    H4   C01  C02  C03   172.72  30.0  3
 WT7  Var_05    H2   C10  O09  P06    74.04  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
 WT7  chir_01  C11  O12  C26  C10  negativ
 WT7  chir_02  C13  O12  N14  C24  negativ
 WT7  chir_03  C24  O25  C13  C26  negativ
 WT7  chir_04  C26  O27  C11  C24  positiv
 WT7  chir_05  P06  O09  O05  O08  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
 WT7  plan-1  C13  0.020
 WT7  plan-1  C15  0.020
 WT7  plan-1  C17  0.020
 WT7  plan-1  C18  0.020
 WT7  plan-1  C21  0.020
 WT7  plan-1  C23  0.020
 WT7  plan-1  N14  0.020
 WT7  plan-1  N16  0.020
 WT7  plan-1  N19  0.020
 WT7  plan-1  N20  0.020
 WT7  plan-1  N22  0.020
 WT7  plan-1  H14  0.020
 WT7  plan-1  H15  0.020
 WT7  plan-2  C18  0.020
 WT7  plan-2  N19  0.020
 WT7  plan-2  H18  0.020
 WT7  plan-2  H19  0.020

