# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 20:47:21 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: (2~{S})-2-[[[(2~{R})-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-oxidanyl-phosphoryl]amino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Cn1cnc2c(N)ncnc12)OC[P](O)(=O)N[C@@H](CCC(O)=O)C(O)=O
#
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
 RE5  RE5  '(2~{S})-2-[[[(2~{R})-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-oxidanyl-phosphoryl]amino]pentanedioic acid'  ligand  49  28  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RE5
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
 RE5  C04  C  CH1   0  -0.212  17.3073  27.8845  171.2057
 RE5  C05  C  C     0   0.577  18.2957  28.8982  170.6395
 RE5  C08  C  CH2   0  -0.452  16.2988  28.4780  172.1930
 RE5  C09  C  CH2   0  -0.546  15.2262  27.4388  172.5256
 RE5  C10  C  C     0   0.550  14.2873  27.8970  173.6040
 RE5  C13  C  CH2   0  -0.429  18.6595  24.0909  172.0459
 RE5  C15  C  CH1   0   0.042  16.8445  22.5264  171.9905
 RE5  C16  C  CH3   0  -0.678  16.3190  22.6331  170.5706
 RE5  C17  C  CH2   0  -0.353  15.7862  22.0859  172.9951
 RE5  C19  C  CR56  0   0.483  13.5508  23.1409  172.4966
 RE5  C21  C  CR16  0   0.033  11.8820  22.7029  171.1391
 RE5  C23  C  CR6   0   0.441  11.6928  24.6157  172.4031
 RE5  C25  C  CR56  0   0.013  12.9347  24.2890  172.9748
 RE5  C27  C  CR15  0   0.116  14.7607  24.1342  174.0144
 RE5  N03  N  NH1   0  -0.766  17.9989  26.7744  171.8096
 RE5  N18  N  NR5   0  -0.486  14.7305  23.0583  173.1752
 RE5  N20  N  N     0  -0.452  13.0614  22.3067  171.5807
 RE5  N22  N  N     0  -0.474  11.1890  23.7871  171.4830
 RE5  N26  N  N     0  -0.456  13.7062  24.8918  173.9328
 RE5  O01  O  O     0  -0.712  17.9175  25.3702  169.6219
 RE5  O06  O  O     0  -0.447  19.4629  28.6571  170.4455
 RE5  O07  O  OH1   0  -0.581  17.7303  30.0508  170.3337
 RE5  O11  O  O     0  -0.459  13.1258  28.1870  173.4393
 RE5  O12  O  OH1   0  -0.591  14.8895  27.9877  174.7840
 RE5  O14  O  O2    0  -0.480  17.3667  23.7520  172.4689
 RE5  O28  O  OH1   0  -0.761  20.2330  25.7467  170.7841
 RE5  P02  P  P     0   1.307  18.6360  25.5246  170.9164
 RE5  H1   H  HCH1  0   0.303  16.7530  27.5079  170.3383
 RE5  H2   H  HCH2  0   0.257  16.8262  28.7969  173.0956
 RE5  H3   H  HCH2  0   0.267  15.8304  29.3638  171.7648
 RE5  H4   H  HCH2  0   0.260  14.6412  27.2148  171.6332
 RE5  H5   H  HCH2  0   0.286  15.7072  26.5130  172.8424
 RE5  H6   H  HCH2  0   0.261  19.1774  23.2626  171.5477
 RE5  H7   H  HCH2  0   0.274  19.2650  24.3573  172.9187
 RE5  H8   H  HCH1  0   0.231  17.6234  21.7516  172.0214
 RE5  H9   H  HCH3  0   0.229  15.8543  21.6935  170.2727
 RE5  H10  H  HCH3  0   0.230  15.5803  23.4281  170.4727
 RE5  H11  H  HCH3  0   0.244  17.1250  22.8445  169.8694
 RE5  H12  H  HCH2  0   0.277  15.3399  21.1472  172.6690
 RE5  H13  H  HCH2  0   0.283  16.2488  21.9070  173.9659
 RE5  H14  H  HCR6  0   0.249  11.4130  22.0700  170.3929
 RE5  H15  H  HCR5  0   0.289  15.5957  24.2998  174.6782
 RE5  H16  H  HNH1  0   0.399  18.4508  26.9919  172.6890
 RE5  H17  H  HNH2  0   0.397  10.1944  25.9644  172.2127
 RE5  H18  H  HNH2  0   0.407  11.4558  26.4378  173.2734
 RE5  H19  H  HOH1  0   0.489  18.3790  30.6496  169.9327
 RE5  H20  H  HOH1  0   0.479  14.2592  28.2940  175.4527
 RE5  H21  H  HOH1  0   0.484  20.4460  26.6585  170.5324
 RE5  N24  N  NH2   0  -0.823  10.9967  25.7028  172.7609

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
 RE5  C16  C15  single    1.518  0.020  1.518
 RE5  C21  N22  aromatic  1.332  0.020  1.332
 RE5  C21  N20  aromatic  1.320  0.020  1.320
 RE5  O01  P02  double    1.489  0.020  1.489
 RE5  O06  C05  double    1.208  0.020  1.208
 RE5  N22  C23  aromatic  1.337  0.020  1.337
 RE5  N20  C19  aromatic  1.332  0.020  1.332
 RE5  O07  C05  single    1.320  0.020  1.320
 RE5  C05  C04  single    1.525  0.020  1.525
 RE5  C15  O14  single    1.416  0.020  1.416
 RE5  C15  C17  single    1.524  0.020  1.524
 RE5  O28  P02  single    1.618  0.020  1.618
 RE5  P02  N03  single    1.663  0.020  1.663
 RE5  P02  C13  single    1.825  0.020  1.825
 RE5  C23  N24  single    1.340  0.020  1.340
 RE5  C23  C25  aromatic  1.406  0.020  1.406
 RE5  C19  C25  aromatic  1.388  0.020  1.388
 RE5  C19  N18  aromatic  1.363  0.020  1.363
 RE5  O14  C13  single    1.402  0.020  1.402
 RE5  C25  N26  aromatic  1.370  0.020  1.370
 RE5  C17  N18  single    1.447  0.020  1.447
 RE5  N03  C04  single    1.441  0.020  1.441
 RE5  N18  C27  aromatic  1.365  0.020  1.365
 RE5  C04  C08  single    1.531  0.020  1.531
 RE5  N26  C27  aromatic  1.301  0.020  1.301
 RE5  C08  C09  single    1.530  0.020  1.530
 RE5  C09  C10  single    1.502  0.020  1.502
 RE5  O11  C10  double    1.208  0.020  1.208
 RE5  C10  O12  single    1.328  0.020  1.328
 RE5  C04  H1   single    0.970  0.020  1.090
 RE5  C08  H2   single    0.970  0.020  1.090
 RE5  C08  H3   single    0.970  0.020  1.090
 RE5  C09  H4   single    0.970  0.020  1.090
 RE5  C09  H5   single    0.970  0.020  1.090
 RE5  C13  H6   single    0.970  0.020  1.090
 RE5  C13  H7   single    0.970  0.020  1.090
 RE5  C15  H8   single    0.970  0.020  1.090
 RE5  C16  H9   single    0.970  0.020  1.090
 RE5  C16  H10  single    0.970  0.020  1.090
 RE5  C16  H11  single    0.970  0.020  1.090
 RE5  C17  H12  single    0.970  0.020  1.090
 RE5  C17  H13  single    0.970  0.020  1.090
 RE5  C21  H14  single    0.930  0.020  1.080
 RE5  C27  H15  single    0.930  0.020  1.080
 RE5  N03  H16  single    0.890  0.020  1.040
 RE5  N24  H17  single    0.890  0.020  1.040
 RE5  N24  H18  single    0.890  0.020  1.040
 RE5  O07  H19  single    0.850  0.020  0.980
 RE5  O12  H20  single    0.850  0.020  0.980
 RE5  O28  H21  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
 RE5  H1   C04  N03  108.04  3.000
 RE5  H1   C04  C08  108.08  3.000
 RE5  N03  C04  C08  110.15  3.000
 RE5  H1   C04  C05  105.21  3.000
 RE5  C08  C04  C05  114.12  3.000
 RE5  N03  C04  C05  110.90  3.000
 RE5  O07  C05  O06  123.45  3.000
 RE5  O07  C05  C04  112.89  3.000
 RE5  O06  C05  C04  123.61  3.000
 RE5  H3   C08  H2   107.15  3.000
 RE5  H3   C08  C09  109.65  3.000
 RE5  H2   C08  C09  110.91  3.000
 RE5  H3   C08  C04  110.17  3.000
 RE5  H2   C08  C04  109.14  3.000
 RE5  C09  C08  C04  109.80  3.000
 RE5  H5   C09  H4   107.46  3.000
 RE5  H5   C09  C10  109.04  3.000
 RE5  H4   C09  C10  108.36  3.000
 RE5  H5   C09  C08  109.31  3.000
 RE5  H4   C09  C08  109.74  3.000
 RE5  C10  C09  C08  112.78  3.000
 RE5  O12  C10  O11  122.73  3.000
 RE5  O12  C10  C09  112.05  3.000
 RE5  O11  C10  C09  125.19  3.000
 RE5  H7   C13  H6   106.54  3.000
 RE5  H7   C13  P02  108.01  3.000
 RE5  H6   C13  P02  108.56  3.000
 RE5  H7   C13  O14  109.16  3.000
 RE5  H6   C13  O14  112.96  3.000
 RE5  P02  C13  O14  111.39  3.000
 RE5  H8   C15  O14  109.85  3.000
 RE5  H8   C15  C17  105.65  3.000
 RE5  O14  C15  C17  106.47  3.000
 RE5  H8   C15  C16  108.74  3.000
 RE5  C17  C15  C16  113.36  3.000
 RE5  O14  C15  C16  112.52  3.000
 RE5  H11  C16  H10  107.60  3.000
 RE5  H11  C16  H9   107.88  3.000
 RE5  H10  C16  H9   108.39  3.000
 RE5  H11  C16  C15  111.08  3.000
 RE5  H10  C16  C15  111.72  3.000
 RE5  H9   C16  C15  110.05  3.000
 RE5  H13  C17  H12  107.40  3.000
 RE5  H13  C17  N18  108.00  3.000
 RE5  H12  C17  N18  108.51  3.000
 RE5  H13  C17  C15  109.86  3.000
 RE5  H12  C17  C15  109.64  3.000
 RE5  N18  C17  C15  113.24  3.000
 RE5  N20  C19  N18  128.48  3.000
 RE5  N18  C19  C25  105.23  3.000
 RE5  N20  C19  C25  126.29  3.000
 RE5  H14  C21  N22  115.31  3.000
 RE5  H14  C21  N20  116.18  3.000
 RE5  N22  C21  N20  128.51  3.000
 RE5  N24  C23  N22  119.41  3.000
 RE5  N24  C23  C25  122.62  3.000
 RE5  N22  C23  C25  117.96  3.000
 RE5  N26  C25  C23  132.83  3.000
 RE5  N26  C25  C19  110.79  3.000
 RE5  C23  C25  C19  116.38  3.000
 RE5  H15  C27  N26  125.18  3.000
 RE5  H15  C27  N18  121.08  3.000
 RE5  N26  C27  N18  113.74  3.000
 RE5  H16  N03  P02  117.20  3.000
 RE5  H16  N03  C04  114.39  3.000
 RE5  P02  N03  C04  122.53  3.000
 RE5  C27  N18  C19  106.11  3.000
 RE5  C27  N18  C17  126.18  3.000
 RE5  C19  N18  C17  127.60  3.000
 RE5  C21  N20  C19  111.74  3.000
 RE5  C23  N22  C21  119.10  3.000
 RE5  C27  N26  C25  104.13  3.000
 RE5  H19  O07  C05  110.40  3.000
 RE5  H20  O12  C10  109.87  3.000
 RE5  C15  O14  C13  116.58  3.000
 RE5  H21  O28  P02  111.54  3.000
 RE5  O28  P02  O01  114.81  3.000
 RE5  O28  P02  N03  108.60  3.000
 RE5  O01  P02  N03  111.11  3.000
 RE5  N03  P02  C13  105.24  3.000
 RE5  O28  P02  C13   98.38  3.000
 RE5  O01  P02  C13  117.57  3.000
 RE5  H18  N24  H17  116.82  3.000
 RE5  H18  N24  C23  119.43  3.000
 RE5  H17  N24  C23  118.67  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
 RE5  CONST_01  N22  C21  N20  C19    0.00   0.0  0
 RE5  CONST_02  N22  C23  C25  C19    0.00   0.0  0
 RE5  CONST_03  C27  N26  C25  C19    0.00   0.0  0
 RE5  CONST_04  N26  C27  N18  C19    0.00   0.0  0
 RE5  CONST_05  C25  C23  N22  C21    0.00   0.0  0
 RE5  CONST_06  C25  C19  N20  C21    0.00   0.0  0
 RE5  CONST_07  N18  C19  N20  C21  180.00   0.0  0
 RE5  CONST_08  N20  C21  N22  C23    0.00   0.0  0
 RE5  CONST_09  N20  C19  C25  C23    0.00   0.0  0
 RE5  CONST_10  N18  C19  C25  C23  180.00   0.0  0
 RE5  CONST_11  C27  N26  C25  C23  180.00   0.0  0
 RE5  CONST_12  C27  N18  C19  C25    0.00   0.0  0
 RE5  CONST_13  N18  C27  N26  C25    0.00   0.0  0
 RE5  CONST_14  N20  C19  N18  C27  180.00   0.0  0
 RE5  CONST_15  N26  C25  C19  N18    0.00   0.0  0
 RE5  CONST_16  N26  C25  C19  N20  180.00   0.0  0
 RE5  CONST_17  N26  C25  C23  N22  180.00   0.0  0
 RE5  CONST_18  N20  C19  N18  C17    0.00   0.0  0
 RE5  CONST_19  C25  C19  N18  C17  180.00   0.0  0
 RE5  CONST_20  N26  C27  N18  C17  180.00   0.0  0
 RE5  CONST_21  N24  C23  C25  C19  180.00   0.0  0
 RE5  CONST_22  N24  C23  N22  C21  180.00   0.0  0
 RE5  CONST_23  N26  C25  C23  N24    0.00   0.0  0
 RE5  CONST_24  H14  C21  N20  C19  180.00   0.0  0
 RE5  CONST_25  H15  C27  N18  C19  180.00   0.0  0
 RE5  CONST_26  H17  N24  C23  C25  180.00   0.0  0
 RE5  CONST_28  H19  O07  C05  C04  180.00   0.0  0
 RE5  CONST_29  H20  O12  C10  C09  180.00   0.0  0
 RE5  Var_01    C19  N18  C17  C15   91.13  30.0  2
 RE5  Var_02    O01  P02  N03  C04  -25.47  30.0  2
 RE5  Var_03    C10  C09  C08  C04  173.67  30.0  3
 RE5  Var_04    O11  C10  C09  C08  110.02  30.0  3
 RE5  Var_05    P02  C13  O14  C15  111.34  30.0  3
 RE5  Var_06    O14  C13  P02  N03   61.44  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
 RE5  chir_01  C04  C05  N03  C08  negativ
 RE5  chir_02  C15  O14  C16  C17  positiv
 RE5  chir_03  P02  O28  N03  C13  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
 RE5  plan-1  C17  0.020
 RE5  plan-1  C19  0.020
 RE5  plan-1  C21  0.020
 RE5  plan-1  C23  0.020
 RE5  plan-1  C25  0.020
 RE5  plan-1  C27  0.020
 RE5  plan-1  N18  0.020
 RE5  plan-1  N20  0.020
 RE5  plan-1  N22  0.020
 RE5  plan-1  N26  0.020
 RE5  plan-1  H14  0.020
 RE5  plan-1  H15  0.020
 RE5  plan-1  N24  0.020
 RE5  plan-2  C23  0.020
 RE5  plan-2  H17  0.020
 RE5  plan-2  H18  0.020
 RE5  plan-2  N24  0.020
 RE5  plan-3  C04  0.020
 RE5  plan-3  C05  0.020
 RE5  plan-3  O06  0.020
 RE5  plan-3  O07  0.020
 RE5  plan-3  H19  0.020
 RE5  plan-4  C09  0.020
 RE5  plan-4  C10  0.020
 RE5  plan-4  O11  0.020
 RE5  plan-4  O12  0.020
 RE5  plan-4  H20  0.020

