# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 23:47:45 2022
#   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  48  27  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.008  -13.3564   7.4572  -26.4795
 WT7  C10  C  CH2    0  -0.164  -12.5733   6.8080  -25.3670
 WT7  C01  C  CH3    0  -0.682  -14.7782   3.7300  -22.6467
 WT7  C02  C  CH2    0  -0.419  -13.5982   2.8105  -22.3612
 WT7  C03  C  CH2    0  -0.455  -12.9438   2.2287  -23.6115
 WT7  C04  C  CH2    0  -0.177  -12.4664   3.2551  -24.6202
 WT7  C13  C  CH1    0   0.186  -15.4680   7.0862  -27.3891
 WT7  C15  C  CR15   0   0.104  -16.3194   5.5366  -25.5544
 WT7  C17  C  CR56   0  -0.001  -18.4066   5.7917  -25.7440
 WT7  C18  C  CR6    0   0.455  -19.8131   5.7907  -25.6874
 WT7  C21  C  CR16   0   0.038  -19.7890   7.3135  -27.4133
 WT7  C23  C  CR56   0   0.484  -17.8337   6.6157  -26.7003
 WT7  C24  C  CH1    0  -0.050  -15.3538   8.5788  -27.0839
 WT7  C26  C  CH1    0  -0.017  -14.2865   8.5728  -25.9926
 WT7  N14  N  NR5    0  -0.538  -16.4871   6.4460  -26.5612
 WT7  N16  N  N      0  -0.453  -17.4411   5.1244  -25.0379
 WT7  N19  N  NH2    0  -0.816  -20.5017   5.0457  -24.8215
 WT7  N20  N  N      0  -0.471  -20.4757   6.5731  -26.5470
 WT7  N22  N  N      0  -0.458  -18.4788   7.3998  -27.5631
 WT7  O05  O  O2     0  -0.622  -11.5914   4.1735  -23.9876
 WT7  O07  O  O      0  -0.784   -9.7482   4.2738  -25.7851
 WT7  O08  O  OP    -1  -0.788  -10.0255   6.1127  -23.9337
 WT7  O09  O  O2     0  -0.628  -11.6766   5.8596  -25.8998
 WT7  O12  O  O2     0  -0.494  -14.2276   6.5143  -27.1108
 WT7  O25  O  OH1    0  -0.659  -14.8978   9.1989  -28.2553
 WT7  O27  O  OH1    0  -0.659  -13.6880   9.8313  -25.8935
 WT7  P06  P  P      0   1.370  -10.5985   5.1172  -24.8912
 WT7  H1   H  HCH1   0   0.238  -12.6636   7.8645  -27.2257
 WT7  H2   H  HCH2   0   0.219  -12.0371   7.6002  -24.8309
 WT7  H3   H  HCH2   0   0.214  -13.2677   6.3495  -24.6503
 WT7  H4   H  HCH3   0   0.230  -15.2852   4.0152  -21.7244
 WT7  H5   H  HCH3   0   0.226  -14.4609   4.6525  -23.1357
 WT7  H6   H  HCH3   0   0.215  -15.5153   3.2490  -23.2933
 WT7  H7   H  HCH2   0   0.220  -13.9321   1.9794  -21.7347
 WT7  H8   H  HCH2   0   0.216  -12.8534   3.3485  -21.7704
 WT7  H9   H  HCH2   0   0.218  -13.6579   1.5780  -24.1262
 WT7  H10  H  HCH2   0   0.224  -12.1044   1.5915  -23.3188
 WT7  H11  H  HCH2   0   0.210  -13.3229   3.7879  -25.0493
 WT7  H12  H  HCH2   0   0.213  -11.9679   2.7404  -25.4488
 WT7  H13  H  HCH1   0   0.281  -15.7463   6.9159  -28.4335
 WT7  H14  H  HCR5   0   0.298  -15.3426   5.2037  -25.2437
 WT7  H15  H  HCR6   0   0.249  -20.3881   7.9236  -28.0811
 WT7  H16  H  HCH1   0   0.262  -16.3025   9.0052  -26.7384
 WT7  H17  H  HCH1   0   0.239  -14.7549   8.2719  -25.0446
 WT7  H18  H  HNH2   0   0.402  -21.5063   5.0821  -24.8082
 WT7  H19  H  HNH2   0   0.410  -20.0358   4.4558  -24.1546
 WT7  H21  H  HOH1   0   0.456  -14.5735  10.0776  -28.0288
 WT7  H22  H  HOH1   0   0.465  -13.1945   9.8882  -25.0698

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    1.402  0.020  1.402
 WT7  N22  C21  aromatic  1.322  0.020  1.322
 WT7  N22  C23  aromatic  1.332  0.020  1.332
 WT7  C21  N20  aromatic  1.330  0.020  1.330
 WT7  C13  C24  single    1.528  0.020  1.528
 WT7  C13  O12  single    1.394  0.020  1.394
 WT7  C13  N14  single    1.461  0.020  1.461
 WT7  C24  C26  single    1.527  0.020  1.527
 WT7  O12  C11  single    1.431  0.020  1.431
 WT7  C23  N14  aromatic  1.364  0.020  1.364
 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    1.532  0.020  1.532
 WT7  C11  C10  single    1.507  0.020  1.507
 WT7  O27  C26  single    1.397  0.020  1.397
 WT7  O07  P06  deloc     1.494  0.020  1.494
 WT7  C17  C18  aromatic  1.408  0.020  1.408
 WT7  C17  N16  aromatic  1.370  0.020  1.370
 WT7  C18  N19  single    1.334  0.020  1.334
 WT7  O09  C10  single    1.410  0.020  1.410
 WT7  O09  P06  single    1.653  0.020  1.653
 WT7  C15  N16  aromatic  1.302  0.020  1.302
 WT7  C04  O05  single    1.417  0.020  1.417
 WT7  C04  C03  single    1.516  0.020  1.516
 WT7  P06  O05  single    1.641  0.020  1.641
 WT7  P06  O08  deloc     1.495  0.020  1.495
 WT7  C03  C02  single    1.526  0.020  1.526
 WT7  C01  C02  single    1.523  0.020  1.523
 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  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  109.22  3.000
 WT7  H1   C11  C26  109.23  3.000
 WT7  O12  C11  C26  104.51  3.000
 WT7  H1   C11  C10  109.51  3.000
 WT7  C26  C11  C10  113.23  3.000
 WT7  O12  C11  C10  110.99  3.000
 WT7  H3   C10  H2   106.97  3.000
 WT7  H3   C10  O09  111.59  3.000
 WT7  H2   C10  O09  111.08  3.000
 WT7  H3   C10  C11  109.45  3.000
 WT7  H2   C10  C11  107.68  3.000
 WT7  O09  C10  C11  109.95  3.000
 WT7  H6   C01  H5   107.66  3.000
 WT7  H6   C01  H4   107.59  3.000
 WT7  H5   C01  H4   107.04  3.000
 WT7  H6   C01  C02  111.59  3.000
 WT7  H5   C01  C02  111.66  3.000
 WT7  H4   C01  C02  111.08  3.000
 WT7  H8   C02  H7   105.83  3.000
 WT7  H8   C02  C03  109.78  3.000
 WT7  H7   C02  C03  108.10  3.000
 WT7  H8   C02  C01  109.41  3.000
 WT7  H7   C02  C01  109.26  3.000
 WT7  C03  C02  C01  114.13  3.000
 WT7  H10  C03  H9   106.27  3.000
 WT7  H10  C03  C04  109.32  3.000
 WT7  H9   C03  C04  107.15  3.000
 WT7  H10  C03  C02  109.38  3.000
 WT7  H9   C03  C02  109.40  3.000
 WT7  C04  C03  C02  114.95  3.000
 WT7  H12  C04  H11  106.72  3.000
 WT7  H12  C04  O05  111.17  3.000
 WT7  H11  C04  O05  110.00  3.000
 WT7  H12  C04  C03  109.18  3.000
 WT7  H11  C04  C03  110.09  3.000
 WT7  O05  C04  C03  109.64  3.000
 WT7  H13  C13  O12  110.68  3.000
 WT7  H13  C13  N14  107.17  3.000
 WT7  O12  C13  N14  109.14  3.000
 WT7  H13  C13  C24  111.21  3.000
 WT7  N14  C13  C24  111.54  3.000
 WT7  O12  C13  C24  107.13  3.000
 WT7  H14  C15  N16  124.67  3.000
 WT7  H14  C15  N14  121.93  3.000
 WT7  N16  C15  N14  113.40  3.000
 WT7  N16  C17  C23  110.72  3.000
 WT7  N16  C17  C18  133.10  3.000
 WT7  C23  C17  C18  116.17  3.000
 WT7  N20  C18  N19  119.21  3.000
 WT7  N19  C18  C17  122.84  3.000
 WT7  N20  C18  C17  117.95  3.000
 WT7  H15  C21  N22  116.16  3.000
 WT7  H15  C21  N20  115.39  3.000
 WT7  N22  C21  N20  128.46  3.000
 WT7  N22  C23  N14  128.10  3.000
 WT7  N14  C23  C17  105.29  3.000
 WT7  N22  C23  C17  126.61  3.000
 WT7  H16  C24  O25  111.90  3.000
 WT7  H16  C24  C26  112.42  3.000
 WT7  O25  C24  C26  111.82  3.000
 WT7  H16  C24  C13  112.23  3.000
 WT7  C26  C24  C13  101.03  3.000
 WT7  O25  C24  C13  106.83  3.000
 WT7  H17  C26  O27  111.59  3.000
 WT7  H17  C26  C24  108.64  3.000
 WT7  O27  C26  C24  110.29  3.000
 WT7  H17  C26  C11  109.48  3.000
 WT7  O27  C26  C11  114.74  3.000
 WT7  C24  C26  C11  101.54  3.000
 WT7  C23  N14  C15  106.19  3.000
 WT7  C15  N14  C13  128.57  3.000
 WT7  C23  N14  C13  125.19  3.000
 WT7  C17  N16  C15  104.40  3.000
 WT7  H19  N19  H18  118.41  3.000
 WT7  H19  N19  C18  121.29  3.000
 WT7  H18  N19  C18  120.28  3.000
 WT7  C21  N20  C18  119.21  3.000
 WT7  C23  N22  C21  111.60  3.000
 WT7  P06  O05  C04  120.03  3.000
 WT7  P06  O09  C10  119.11  3.000
 WT7  C13  O12  C11  111.07  3.000
 WT7  H21  O25  C24  108.45  3.000
 WT7  H22  O27  C26  109.50  3.000
 WT7  O09  P06  O08  109.98  3.000
 WT7  O08  P06  O07  122.73  3.000
 WT7  O09  P06  O07  105.05  3.000
 WT7  O08  P06  O05  105.20  3.000
 WT7  O09  P06  O05  101.52  3.000
 WT7  O07  P06  O05  110.43  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  -175.68  30.0  3
 WT7  Var_02    C04  C03  C02  C01    56.06  30.0  1
 WT7  Var_03    O05  C04  C03  C02    55.01  30.0  1
 WT7  Var_04    H4   C01  C02  C03   172.78  30.0  3
 WT7  Var_05    H2   C10  O09  P06    54.97  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

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

