# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 05:44:34 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: [6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)hexyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(CCCCCC[P](O)(O)=O)cnc2C(=O)N1
#
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
 6MS  6MS  '[6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)hexyl]phosphonic acid'  ligand  39  21  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6MS
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
 6MS  C12  C  CH2   0  -0.301   1.3236   1.1735  -1.1408
 6MS  P18  P  P     0   1.373  -6.2377  -0.4066   0.0904
 6MS  O01  O  O     0  -0.477   6.7885   0.2656   1.0953
 6MS  C02  C  CR6   0   0.499   5.7083  -0.0398   0.6168
 6MS  N03  N  NR16  0  -0.728   5.3885  -1.3833   0.3828
 6MS  C04  C  CR6   0   0.686   4.2201  -1.8547  -0.1465
 6MS  N05  N  NH2   0  -0.835   4.1226  -3.1799  -0.3158
 6MS  N06  N  N     0  -0.513   3.2331  -1.0729  -0.5066
 6MS  C07  C  CR56  0   0.496   3.4920   0.2281  -0.3065
 6MS  C08  C  CR56  0  -0.089   4.6326   0.8066   0.2233
 6MS  N09  N  N     0  -0.448   4.5082   2.1709   0.2650
 6MS  C10  C  CR15  0   0.089   3.3281   2.4017  -0.2265
 6MS  N11  N  NR5   0  -0.494   2.6644   1.2633  -0.5973
 6MS  C13  C  CH2   0  -0.434   0.2950   0.7550  -0.1003
 6MS  C14  C  CH2   0  -0.425  -1.1057   0.6841  -0.6942
 6MS  C15  C  CH2   0  -0.407  -2.1494   0.2413   0.3225
 6MS  C16  C  CH2   0  -0.432  -3.5543   0.1796  -0.2635
 6MS  C17  C  CH2   0  -0.758  -4.5767  -0.2878   0.7714
 6MS  O19  O  OH1   0  -0.753  -6.7118   1.0930  -0.2629
 6MS  O20  O  O     0  -0.722  -6.3954  -1.2530  -1.1179
 6MS  O21  O  OH1   0  -0.747  -7.0818  -0.8663   1.3812
 6MS  H1   H  HCH2  0   0.266   1.0743   2.1511  -1.5546
 6MS  H2   H  HCH2  0   0.261   1.3394   0.4664  -1.9717
 6MS  H3   H  HNH2  0   0.415   4.7875  -3.8148   0.0911
 6MS  H4   H  HNH2  0   0.412   3.2309  -3.5603  -0.5822
 6MS  H6   H  HCR5  0   0.285   2.8780   3.3751  -0.3556
 6MS  H7   H  HCH2  0   0.234   0.5726  -0.2199   0.3103
 6MS  H8   H  HCH2  0   0.231   0.3117   1.4663   0.7305
 6MS  H9   H  HCH2  0   0.221  -1.3823   1.6642  -1.0969
 6MS  H10  H  HCH2  0   0.221  -1.1079  -0.0082  -1.5428
 6MS  H11  H  HCH2  0   0.220  -1.8770  -0.7431   0.7166
 6MS  H12  H  HCH2  0   0.219  -2.1433   0.9270   1.1762
 6MS  H13  H  HCH2  0   0.233  -3.8335   1.1657  -0.6442
 6MS  H14  H  HCH2  0   0.234  -3.5626  -0.4993  -1.1204
 6MS  H15  H  HCH2  0   0.281  -4.5915   0.3880   1.6312
 6MS  H16  H  HCH2  0   0.283  -4.3032  -1.2758   1.1511
 6MS  H17  H  HOH1  0   0.488  -6.6722   1.7216   0.4694
 6MS  H18  H  HOH1  0   0.492  -7.9884  -1.1375   1.1815
 6MS  H5   H  HNR6  0   0.424   6.1074  -2.0527   0.6275

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
 6MS  O20  P18  double    1.484  0.020  1.484
 6MS  O21  P18  single    1.609  0.020  1.609
 6MS  P18  C17  single    1.799  0.020  1.799
 6MS  P18  O19  single    1.612  0.020  1.612
 6MS  C16  C17  single    1.528  0.020  1.528
 6MS  C16  C15  single    1.523  0.020  1.523
 6MS  C14  C15  single    1.523  0.020  1.523
 6MS  C14  C13  single    1.523  0.020  1.523
 6MS  C12  C13  single    1.522  0.020  1.522
 6MS  C12  N11  single    1.450  0.020  1.450
 6MS  N11  C10  aromatic  1.369  0.020  1.369
 6MS  N11  C07  aromatic  1.357  0.020  1.357
 6MS  C10  N09  aromatic  1.299  0.020  1.299
 6MS  C07  N06  single    1.342  0.020  1.342
 6MS  C07  C08  aromatic  1.384  0.020  1.384
 6MS  N06  C04  double    1.310  0.020  1.310
 6MS  N09  C08  aromatic  1.371  0.020  1.371
 6MS  C08  C02  single    1.424  0.020  1.424
 6MS  C04  N05  single    1.339  0.020  1.339
 6MS  C04  N03  single    1.367  0.020  1.367
 6MS  C02  N03  single    1.401  0.020  1.401
 6MS  C02  O01  double    1.220  0.020  1.220
 6MS  C12  H1   single    0.970  0.020  1.090
 6MS  C12  H2   single    0.970  0.020  1.090
 6MS  N05  H3   single    0.890  0.020  1.040
 6MS  N05  H4   single    0.890  0.020  1.040
 6MS  C10  H6   single    0.930  0.020  1.080
 6MS  C13  H7   single    0.970  0.020  1.090
 6MS  C13  H8   single    0.970  0.020  1.090
 6MS  C14  H9   single    0.970  0.020  1.090
 6MS  C14  H10  single    0.970  0.020  1.090
 6MS  C15  H11  single    0.970  0.020  1.090
 6MS  C15  H12  single    0.970  0.020  1.090
 6MS  C16  H13  single    0.970  0.020  1.090
 6MS  C16  H14  single    0.970  0.020  1.090
 6MS  C17  H15  single    0.970  0.020  1.090
 6MS  C17  H16  single    0.970  0.020  1.090
 6MS  O19  H17  single    0.850  0.020  0.980
 6MS  O21  H18  single    0.850  0.020  0.980
 6MS  N03  H5   single    0.860  0.020  1.020

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
 6MS  H2   C12  H1   107.17  3.000
 6MS  H2   C12  C13  110.62  3.000
 6MS  H1   C12  C13  110.58  3.000
 6MS  H2   C12  N11  108.19  3.000
 6MS  H1   C12  N11  107.35  3.000
 6MS  C13  C12  N11  112.70  3.000
 6MS  O21  P18  O20  115.76  3.000
 6MS  O21  P18  O19  106.69  3.000
 6MS  O20  P18  O19  108.72  3.000
 6MS  O19  P18  C17  107.04  3.000
 6MS  O21  P18  C17  101.51  3.000
 6MS  O20  P18  C17  116.37  3.000
 6MS  C08  C02  N03  110.57  3.000
 6MS  N03  C02  O01  120.51  3.000
 6MS  C08  C02  O01  128.92  3.000
 6MS  H5   N03  C04  118.21  3.000
 6MS  H5   N03  C02  115.58  3.000
 6MS  C04  N03  C02  126.21  3.000
 6MS  N06  C04  N05  120.07  3.000
 6MS  N05  C04  N03  116.90  3.000
 6MS  N06  C04  N03  123.02  3.000
 6MS  H4   N05  H3   117.06  3.000
 6MS  H4   N05  C04  118.19  3.000
 6MS  H3   N05  C04  121.70  3.000
 6MS  C07  N06  C04  113.11  3.000
 6MS  N11  C07  C08  105.41  3.000
 6MS  C08  C07  N06  128.42  3.000
 6MS  N11  C07  N06  126.17  3.000
 6MS  N09  C08  C07  110.66  3.000
 6MS  N09  C08  C02  130.67  3.000
 6MS  C07  C08  C02  118.67  3.000
 6MS  C10  N09  C08  104.35  3.000
 6MS  H6   C10  N11  121.00  3.000
 6MS  H6   C10  N09  125.72  3.000
 6MS  N11  C10  N09  113.28  3.000
 6MS  C10  N11  C07  106.30  3.000
 6MS  C07  N11  C12  126.67  3.000
 6MS  C10  N11  C12  126.98  3.000
 6MS  H8   C13  H7   106.90  3.000
 6MS  H8   C13  C14  109.91  3.000
 6MS  H7   C13  C14  109.78  3.000
 6MS  H8   C13  C12  109.27  3.000
 6MS  H7   C13  C12  109.28  3.000
 6MS  C14  C13  C12  111.58  3.000
 6MS  H10  C14  H9   106.28  3.000
 6MS  H10  C14  C15  109.40  3.000
 6MS  H9   C14  C15  109.43  3.000
 6MS  H10  C14  C13  109.47  3.000
 6MS  H9   C14  C13  109.51  3.000
 6MS  C15  C14  C13  112.55  3.000
 6MS  H12  C15  H11  106.32  3.000
 6MS  H12  C15  C16  109.30  3.000
 6MS  H11  C15  C16  109.36  3.000
 6MS  H12  C15  C14  109.55  3.000
 6MS  H11  C15  C14  109.35  3.000
 6MS  C16  C15  C14  112.76  3.000
 6MS  H14  C16  H13  106.57  3.000
 6MS  H14  C16  C17  109.62  3.000
 6MS  H13  C16  C17  109.92  3.000
 6MS  H14  C16  C15  109.49  3.000
 6MS  H13  C16  C15  109.45  3.000
 6MS  C17  C16  C15  111.65  3.000
 6MS  H16  C17  H15  106.78  3.000
 6MS  H16  C17  C16  110.14  3.000
 6MS  H15  C17  C16  110.65  3.000
 6MS  H16  C17  P18  107.62  3.000
 6MS  H15  C17  P18  109.02  3.000
 6MS  C16  C17  P18  112.43  3.000
 6MS  H17  O19  P18  115.29  3.000
 6MS  H18  O21  P18  113.96  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
 6MS  CONST_01  N09  C10  N11  C07     0.00   0.0  0
 6MS  CONST_02  C10  N09  C08  C07     0.00   0.0  0
 6MS  CONST_03  C10  N11  C07  C08     0.00   0.0  0
 6MS  CONST_04  N11  C10  N09  C08     0.00   0.0  0
 6MS  CONST_05  N11  C07  C08  N09     0.00   0.0  0
 6MS  CONST_06  N06  C04  N03  C02     0.00   0.0  0
 6MS  CONST_07  C07  N06  C04  N03     0.00   0.0  0
 6MS  CONST_08  C08  C02  N03  C04     0.00   0.0  0
 6MS  CONST_09  N09  C10  N11  C12   180.00   0.0  0
 6MS  CONST_10  N06  C07  N11  C12     0.00   0.0  0
 6MS  CONST_11  C08  C07  N11  C12   180.00   0.0  0
 6MS  CONST_12  C04  N03  C02  O01   180.00   0.0  0
 6MS  CONST_13  N05  C04  N03  C02   180.00   0.0  0
 6MS  CONST_14  C07  N06  C04  N05   180.00   0.0  0
 6MS  CONST_15  H6   C10  N11  C07   180.00   0.0  0
 6MS  CONST_16  H5   N03  C04  N06   180.00   0.0  0
 6MS  CONST_17  H3   N05  C04  N03     0.00   0.0  0
 6MS  CONST_18  H4   N05  C04  N03   180.00   0.0  0
 6MS  Var_01    C13  C12  N11  C07    76.35  30.0  2
 6MS  Var_02    C14  C13  C12  N11   179.35  30.0  3
 6MS  Var_03    C15  C14  C13  C12   178.91  30.0  2
 6MS  Var_04    C15  C16  C17  P18  -178.61  30.0  1
 6MS  Var_05    C16  C15  C14  C13   179.54  30.0  3
 6MS  Var_06    C17  C16  C15  C14   179.12  30.0  1
 6MS  Var_07    O20  P18  C17  C16    54.96  30.0  2

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
 6MS  plan-1  C12  0.020
 6MS  plan-1  O01  0.020
 6MS  plan-1  C02  0.020
 6MS  plan-1  N03  0.020
 6MS  plan-1  C04  0.020
 6MS  plan-1  N05  0.020
 6MS  plan-1  N06  0.020
 6MS  plan-1  C07  0.020
 6MS  plan-1  C08  0.020
 6MS  plan-1  N09  0.020
 6MS  plan-1  C10  0.020
 6MS  plan-1  N11  0.020
 6MS  plan-1  H3   0.020
 6MS  plan-1  H4   0.020
 6MS  plan-1  H6   0.020
 6MS  plan-1  H5   0.020

