# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 21:01:12 2022
#   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  46  28  .  2022-03-23  2022-03-23
;
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  -0.115  16.7426  26.9532  171.8074
 RE5  C05  C  C      0   0.405  16.5326  27.6967  170.4675
 RE5  C08  C  CH2    0  -0.455  16.0659  27.7379  172.9352
 RE5  C09  C  CH2    0  -0.569  14.5792  27.9980  172.7156
 RE5  C10  C  C      0   0.438  13.8737  28.5570  173.9588
 RE5  C13  C  CH2    0  -0.442  19.0312  24.1097  172.0784
 RE5  C15  C  CH1    0   0.058  17.1547  22.6883  171.5382
 RE5  C16  C  CH3    0  -0.692  16.6812  23.1904  170.1840
 RE5  C17  C  CH2    0  -0.350  16.0369  22.0476  172.3588
 RE5  C19  C  CR56   0   0.474  13.8716  23.3189  172.1459
 RE5  C21  C  CR16   0   0.030  12.1768  23.2789  170.7510
 RE5  C23  C  CR6    0   0.420  12.1325  24.9261  172.3660
 RE5  C25  C  CR56   0  -0.002  13.3368  24.3837  172.8593
 RE5  C27  C  CR15   0   0.113  15.1377  23.8686  173.8327
 RE5  N03  N  NH1    0  -0.802  18.1479  26.7972  172.1485
 RE5  N18  N  NR5    0  -0.486  15.0369  23.0052  172.7803
 RE5  N20  N  N      0  -0.460  13.3299  22.7253  171.0824
 RE5  N22  N  N      0  -0.476  11.5664  24.3181  171.3118
 RE5  N26  N  N      0  -0.452  14.1435  24.7031  173.9222
 RE5  O01  O  O      0  -0.799  18.7757  25.7355  169.8539
 RE5  O06  O  O      0  -0.618  17.1773  28.7494  170.2898
 RE5  O07  O  OC    -1  -0.627  15.6774  27.2116  169.6949
 RE5  O11  O  O      0  -0.605  12.7644  28.0510  174.2792
 RE5  O12  O  OC    -1  -0.590  14.4331  29.4886  174.5615
 RE5  O14  O  O2     0  -0.488  17.6994  23.7050  172.3394
 RE5  O28  O  OP    -1  -0.811  20.6285  26.1996  171.6432
 RE5  P02  P  P      0   1.210  19.2160  25.7880  171.2972
 RE5  H1   H  HCH1   0   0.181  16.2299  25.9849  171.7348
 RE5  H2   H  HCH2   0   0.203  16.1946  27.1698  173.8642
 RE5  H3   H  HCH2   0   0.202  16.5949  28.6835  173.0764
 RE5  H4   H  HCH2   0   0.222  14.4521  28.7242  171.9051
 RE5  H5   H  HCH2   0   0.209  14.0923  27.0815  172.3810
 RE5  H6   H  HCH2   0   0.203  19.5590  23.3674  171.4636
 RE5  H7   H  HCH2   0   0.213  19.5534  24.1346  173.0414
 RE5  H8   H  HCH1   0   0.212  17.8985  21.8939  171.3725
 RE5  H9   H  HCH3   0   0.218  16.2116  22.3821  169.6225
 RE5  H10  H  HCH3   0   0.222  15.9603  24.0033  170.2860
 RE5  H11  H  HCH3   0   0.247  17.5181  23.5723  169.6033
 RE5  H12  H  HCH2   0   0.268  15.5430  21.2713  171.7759
 RE5  H13  H  HCH2   0   0.275  16.4527  21.5761  173.2500
 RE5  H15  H  HCR5   0   0.282  15.9744  23.8223  174.5128
 RE5  H16  H  HNH1   0   0.344  18.3117  26.8076  173.1469
 RE5  H17  H  HNH2   0   0.376  10.7379  26.3512  172.3986
 RE5  H18  H  HNH2   0   0.426  12.0606  26.6848  173.4676
 RE5  N24  N  NH2    0  -0.857  11.5347  25.9939  172.9011
 RE5  H14  H  HCR6   0   0.241  11.6609  22.8372  169.9042

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    1.520  0.020  1.520
 RE5  C21  N22  aromatic  1.329  0.020  1.329
 RE5  C21  N20  aromatic  1.321  0.020  1.321
 RE5  O01  P02  deloc     1.510  0.020  1.510
 RE5  O06  C05  deloc     1.247  0.020  1.247
 RE5  N22  C23  aromatic  1.342  0.020  1.342
 RE5  N20  C19  aromatic  1.333  0.020  1.333
 RE5  O07  C05  deloc     1.250  0.020  1.250
 RE5  C05  C04  single    1.547  0.020  1.547
 RE5  C15  O14  single    1.404  0.020  1.404
 RE5  C15  C17  single    1.528  0.020  1.528
 RE5  O28  P02  deloc     1.511  0.020  1.511
 RE5  P02  N03  single    1.698  0.020  1.698
 RE5  P02  C13  single    1.860  0.020  1.860
 RE5  C23  N24  single    1.336  0.020  1.336
 RE5  C23  C25  aromatic  1.410  0.020  1.410
 RE5  C19  C25  aromatic  1.389  0.020  1.389
 RE5  C19  N18  aromatic  1.363  0.020  1.363
 RE5  O14  C13  single    1.416  0.020  1.416
 RE5  C25  N26  aromatic  1.372  0.020  1.372
 RE5  C17  N18  single    1.447  0.020  1.447
 RE5  N03  C04  single    1.454  0.020  1.454
 RE5  N18  C27  aromatic  1.365  0.020  1.365
 RE5  C04  C08  single    1.532  0.020  1.532
 RE5  N26  C27  aromatic  1.301  0.020  1.301
 RE5  C08  C09  single    1.525  0.020  1.525
 RE5  C09  C10  single    1.535  0.020  1.535
 RE5  O11  C10  deloc     1.261  0.020  1.261
 RE5  C10  O12  deloc     1.243  0.020  1.243
 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

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  111.84  3.000
 RE5  H1   C04  C08  107.11  3.000
 RE5  N03  C04  C08  108.01  3.000
 RE5  H1   C04  C05  107.65  3.000
 RE5  C08  C04  C05  109.37  3.000
 RE5  N03  C04  C05  112.70  3.000
 RE5  O07  C05  O06  126.36  3.000
 RE5  O07  C05  C04  116.22  3.000
 RE5  O06  C05  C04  117.32  3.000
 RE5  H3   C08  H2   106.38  3.000
 RE5  H3   C08  C09  110.05  3.000
 RE5  H2   C08  C09  108.95  3.000
 RE5  H3   C08  C04  108.94  3.000
 RE5  H2   C08  C04  107.85  3.000
 RE5  C09  C08  C04  114.34  3.000
 RE5  H5   C09  H4   106.16  3.000
 RE5  H5   C09  C10  110.45  3.000
 RE5  H4   C09  C10  107.73  3.000
 RE5  H5   C09  C08  109.64  3.000
 RE5  H4   C09  C08  109.43  3.000
 RE5  C10  C09  C08  113.18  3.000
 RE5  O12  C10  O11  125.01  3.000
 RE5  O12  C10  C09  117.32  3.000
 RE5  O11  C10  C09  117.65  3.000
 RE5  H7   C13  H6   106.15  3.000
 RE5  H7   C13  P02  107.53  3.000
 RE5  H6   C13  P02  109.07  3.000
 RE5  H7   C13  O14  107.02  3.000
 RE5  H6   C13  O14  111.21  3.000
 RE5  P02  C13  O14  115.38  3.000
 RE5  H8   C15  O14  110.26  3.000
 RE5  H8   C15  C17  105.82  3.000
 RE5  O14  C15  C17  106.32  3.000
 RE5  H8   C15  C16  108.35  3.000
 RE5  C17  C15  C16  112.91  3.000
 RE5  O14  C15  C16  112.95  3.000
 RE5  H11  C16  H10  107.26  3.000
 RE5  H11  C16  H9   108.46  3.000
 RE5  H10  C16  H9   108.41  3.000
 RE5  H11  C16  C15  110.60  3.000
 RE5  H10  C16  C15  111.63  3.000
 RE5  H9   C16  C15  110.36  3.000
 RE5  H13  C17  H12  107.58  3.000
 RE5  H13  C17  N18  108.15  3.000
 RE5  H12  C17  N18  108.30  3.000
 RE5  H13  C17  C15  109.96  3.000
 RE5  H12  C17  C15  110.08  3.000
 RE5  N18  C17  C15  112.61  3.000
 RE5  N20  C19  N18  128.03  3.000
 RE5  N18  C19  C25  105.46  3.000
 RE5  N20  C19  C25  126.50  3.000
 RE5  H14  C21  N22  115.40  3.000
 RE5  H14  C21  N20  116.10  3.000
 RE5  N22  C21  N20  128.49  3.000
 RE5  N24  C23  N22  119.22  3.000
 RE5  N24  C23  C25  123.34  3.000
 RE5  N22  C23  C25  117.44  3.000
 RE5  N26  C25  C23  133.13  3.000
 RE5  N26  C25  C19  110.49  3.000
 RE5  C23  C25  C19  116.37  3.000
 RE5  H15  C27  N26  125.21  3.000
 RE5  H15  C27  N18  121.06  3.000
 RE5  N26  C27  N18  113.72  3.000
 RE5  H16  N03  P02  113.51  3.000
 RE5  H16  N03  C04  112.76  3.000
 RE5  P02  N03  C04  123.63  3.000
 RE5  C27  N18  C19  106.04  3.000
 RE5  C27  N18  C17  126.30  3.000
 RE5  C19  N18  C17  127.40  3.000
 RE5  C21  N20  C19  111.60  3.000
 RE5  C23  N22  C21  119.46  3.000
 RE5  C27  N26  C25  104.28  3.000
 RE5  C15  O14  C13  117.81  3.000
 RE5  O28  P02  O01  120.06  3.000
 RE5  O28  P02  N03  108.13  3.000
 RE5  O01  P02  N03  108.45  3.000
 RE5  N03  P02  C13  105.25  3.000
 RE5  O28  P02  C13  104.03  3.000
 RE5  O01  P02  C13  109.94  3.000
 RE5  H18  N24  H17  115.93  3.000
 RE5  H18  N24  C23  121.65  3.000
 RE5  H17  N24  C23  115.95  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  Var_01    C19  N18  C17  C15    93.56  30.0  2
 RE5  Var_02    O01  P02  N03  C04    30.93  30.0  2
 RE5  Var_03    C10  C09  C08  C04   169.65  30.0  3
 RE5  Var_04    O11  C10  C09  C08  -134.43  30.0  3
 RE5  Var_05    P02  C13  O14  C15   108.39  30.0  3
 RE5  Var_06    O14  C13  P02  N03    44.02  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

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  H15  0.020
 RE5  plan-1  N24  0.020
 RE5  plan-1  H14  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-4  C09  0.020
 RE5  plan-4  C10  0.020
 RE5  plan-4  O11  0.020
 RE5  plan-4  O12  0.020

