# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 00:52:20 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-(propylamino)hexanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN[C@@H](CC[C@H](N)C(O)=O)C[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
 0UM  0UM  '(2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-(propylamino)hexanoic acid (non-preferred name)'  ligand  58  30  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0UM
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
 0UM  C4   C  CR56   0   0.491   3.8893   0.3572  -0.2559
 0UM  C5   C  CR56   0  -0.011   3.8619   1.7329  -0.0882
 0UM  C6   C  CR6    0   0.457   5.0235   2.4315  -0.4649
 0UM  C8   C  CR15   0   0.113   1.9829   1.0363   0.5711
 0UM  N1   N  N      0  -0.474   6.0500   1.7241  -0.9498
 0UM  N3   N  N      0  -0.456   4.9019  -0.3598  -0.7374
 0UM  C    C  C      0   0.381  -5.1636   3.2053  -0.4204
 0UM  CA   C  CH1    0  -0.209  -4.5187   2.2173   0.5825
 0UM  N    N  NH2    0  -0.787  -5.4545   1.4449   1.3874
 0UM  CB   C  CH2    0  -0.417  -3.5848   1.2702  -0.1754
 0UM  CAM  C  CH2    0  -0.424  -2.7575   0.3721   0.7338
 0UM  CAY  C  CH1    0  -0.074  -1.7781  -0.5325  -0.0147
 0UM  NAR  N  NH1    0  -0.604  -2.4435  -1.2893  -1.0645
 0UM  CAK  C  CH2    0  -0.262  -3.4210  -2.2704  -0.6349
 0UM  CAJ  C  CH2    0  -0.441  -4.1056  -2.9130  -1.8314
 0UM  CAA  C  CH3    0  -0.666  -5.1393  -3.9496  -1.4158
 0UM  CBB  C  CH1    0  -0.029   0.0445  -2.3001   0.3739
 0UM  OAS  O  O2     0  -0.494   0.9749  -1.5543  -0.4298
 0UM  CAZ  C  CH1    0  -0.002   0.9044  -3.0190   1.4032
 0UM  OAF  O  OH1    0  -0.671   1.4297  -4.1850   0.8220
 0UM  CBA  C  CH1    0  -0.059   2.0056  -1.9832   1.6315
 0UM  OAG  O  OH1    0  -0.654   3.2093  -2.4918   2.1243
 0UM  CBC  C  CH1    0   0.216   2.2117  -1.4497   0.2116
 0UM  N9   N  NR5    0  -0.539   2.6696  -0.0798   0.1749
 0UM  N7   N  N      0  -0.449   2.6579   2.1372   0.4280
 0UM  C2   C  CR16   0   0.045   5.9328   0.4031  -1.0568
 0UM  N6   N  NH2    0  -0.816   5.1392   3.7553  -0.3456
 0UM  H1   H  HCR5   0   0.290   0.9756   0.9788   0.9571
 0UM  H3   H  HCH1   0   0.202  -3.9022   2.8081   1.2719
 0UM  H5   H  HNH2   0   0.321  -6.0826   0.9610   0.7552
 0UM  H7   H  HCH2   0   0.215  -4.1785   0.6539  -0.8593
 0UM  H8   H  HCH2   0   0.212  -2.9137   1.8633  -0.8018
 0UM  H9   H  HCH2   0   0.217  -2.1775   0.9987   1.4209
 0UM  H10  H  HCH2   0   0.217  -3.4191  -0.2241   1.3676
 0UM  H11  H  HCH1   0   0.223  -1.0630   0.1194  -0.5297
 0UM  H12  H  HNH1   0   0.341  -1.7541  -1.7361  -1.6569
 0UM  H14  H  HCH2   0   0.189  -2.9961  -3.0654  -0.0004
 0UM  H15  H  HCH2   0   0.219  -4.1755  -1.7661  -0.0241
 0UM  H16  H  HCH2   0   0.218  -4.5771  -2.1319  -2.4334
 0UM  H17  H  HCH2   0   0.214  -3.3512  -3.3849  -2.4696
 0UM  H18  H  HCH3   0   0.218  -4.6842  -4.7503  -0.8300
 0UM  H19  H  HCH3   0   0.218  -5.9244  -3.5013  -0.8041
 0UM  H20  H  HCH3   0   0.230  -5.6168  -4.4053  -2.2835
 0UM  H23  H  HCH1   0   0.253  -0.4497  -3.0250  -0.2815
 0UM  H24  H  HCH1   0   0.247   0.3452  -3.2369   2.3222
 0UM  H25  H  HOH1   0   0.449   2.2091  -4.4462   1.3263
 0UM  H26  H  HCH1   0   0.252   1.6161  -1.1829   2.2730
 0UM  H27  H  HOH1   0   0.469   3.1502  -2.5514   3.0830
 0UM  H28  H  HCH1   0   0.261   2.9795  -2.0363  -0.3040
 0UM  H29  H  HCR6   0   0.252   6.7997  -0.1100  -1.4592
 0UM  H30  H  HNH2   0   0.411   4.3579   4.3184  -0.0587
 0UM  H31  H  HNH2   0   0.403   5.9588   4.2234  -0.6918
 0UM  O    O  O     -1  -0.610  -6.3773   3.0668  -0.6722
 0UM  OXT  O  OC     0  -0.626  -4.3973   4.0591  -0.9159
 0UM  CAN  C  CH2    0  -0.477  -0.9950  -1.3838   0.9982
 0UM  H4   H  HNH2   0   0.332  -6.0550   2.0861   1.8920
 0UM  H21  H  HCH2   0   0.233  -0.5221  -0.7181   1.7280
 0UM  H22  H  HCH2   0   0.244  -1.6870  -2.0052   1.5750

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
 0UM  CAA  CAJ  single    1.522  0.020  1.522
 0UM  CAJ  CAK  single    1.521  0.020  1.521
 0UM  OAF  CAZ  single    1.405  0.020  1.405
 0UM  CAK  NAR  single    1.450  0.020  1.450
 0UM  CAZ  CBB  single    1.522  0.020  1.522
 0UM  CAZ  CBA  single    1.529  0.020  1.529
 0UM  NAR  CAY  single    1.455  0.020  1.455
 0UM  CAN  CBB  single    1.520  0.020  1.520
 0UM  CAN  CAY  single    1.537  0.020  1.537
 0UM  CBB  OAS  single    1.438  0.020  1.438
 0UM  CBA  OAG  single    1.397  0.020  1.397
 0UM  CBA  CBC  single    1.531  0.020  1.531
 0UM  CAY  CAM  single    1.529  0.020  1.529
 0UM  C8   N7   aromatic  1.299  0.020  1.299
 0UM  C8   N9   aromatic  1.369  0.020  1.369
 0UM  N7   C5   aromatic  1.371  0.020  1.371
 0UM  OAS  CBC  single    1.397  0.020  1.397
 0UM  CBC  N9   single    1.445  0.020  1.445
 0UM  N9   C4   aromatic  1.365  0.020  1.365
 0UM  CAM  CB   single    1.522  0.020  1.522
 0UM  C5   C4   aromatic  1.386  0.020  1.386
 0UM  C5   C6   aromatic  1.407  0.020  1.407
 0UM  C4   N3   aromatic  1.331  0.020  1.331
 0UM  N6   C6   single    1.334  0.020  1.334
 0UM  C6   N1   aromatic  1.338  0.020  1.338
 0UM  N3   C2   aromatic  1.322  0.020  1.322
 0UM  N1   C2   aromatic  1.330  0.020  1.330
 0UM  CB   CA   single    1.531  0.020  1.531
 0UM  CA   N    single    1.456  0.020  1.456
 0UM  CA   C    single    1.548  0.020  1.548
 0UM  O    C    deloc     1.247  0.020  1.247
 0UM  C    OXT  deloc     1.250  0.020  1.250
 0UM  C8   H1   single    0.930  0.020  1.080
 0UM  CA   H3   single    0.970  0.020  1.090
 0UM  N    H4   single    0.890  0.020  1.040
 0UM  N    H5   single    0.890  0.020  1.040
 0UM  CB   H7   single    0.970  0.020  1.090
 0UM  CB   H8   single    0.970  0.020  1.090
 0UM  CAM  H9   single    0.970  0.020  1.090
 0UM  CAM  H10  single    0.970  0.020  1.090
 0UM  CAY  H11  single    0.970  0.020  1.090
 0UM  NAR  H12  single    0.890  0.020  1.040
 0UM  CAK  H14  single    0.970  0.020  1.090
 0UM  CAK  H15  single    0.970  0.020  1.090
 0UM  CAJ  H16  single    0.970  0.020  1.090
 0UM  CAJ  H17  single    0.970  0.020  1.090
 0UM  CAA  H18  single    0.970  0.020  1.090
 0UM  CAA  H19  single    0.970  0.020  1.090
 0UM  CAA  H20  single    0.970  0.020  1.090
 0UM  CAN  H21  single    0.970  0.020  1.090
 0UM  CAN  H22  single    0.970  0.020  1.090
 0UM  CBB  H23  single    0.970  0.020  1.090
 0UM  CAZ  H24  single    0.970  0.020  1.090
 0UM  OAF  H25  single    0.850  0.020  0.980
 0UM  CBA  H26  single    0.970  0.020  1.090
 0UM  OAG  H27  single    0.850  0.020  0.980
 0UM  CBC  H28  single    0.970  0.020  1.090
 0UM  C2   H29  single    0.930  0.020  1.080
 0UM  N6   H30  single    0.860  0.020  1.020
 0UM  N6   H31  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
 0UM  N9   C4   N3   128.42  3.000
 0UM  N3   C4   C5   126.40  3.000
 0UM  N9   C4   C5   105.18  3.000
 0UM  N7   C5   C6   132.80  3.000
 0UM  C6   C5   C4   116.37  3.000
 0UM  N7   C5   C4   110.83  3.000
 0UM  N6   C6   N1   119.38  3.000
 0UM  N1   C6   C5   117.91  3.000
 0UM  N6   C6   C5   122.71  3.000
 0UM  H1   C8   N7   124.68  3.000
 0UM  H1   C8   N9   121.85  3.000
 0UM  N7   C8   N9   113.47  3.000
 0UM  C2   N1   C6   119.12  3.000
 0UM  C2   N3   C4   111.71  3.000
 0UM  O    C    CA   117.72  3.000
 0UM  O    C    OXT  126.34  3.000
 0UM  CA   C    OXT  115.93  3.000
 0UM  H3   CA   CB   107.54  3.000
 0UM  H3   CA   N    107.41  3.000
 0UM  CB   CA   N    109.73  3.000
 0UM  H3   CA   C    107.30  3.000
 0UM  N    CA   C    115.40  3.000
 0UM  CB   CA   C    109.16  3.000
 0UM  H5   N    H4   104.20  3.000
 0UM  H5   N    CA   107.85  3.000
 0UM  H4   N    CA   108.70  3.000
 0UM  H8   CB   H7   106.28  3.000
 0UM  H8   CB   CAM  109.19  3.000
 0UM  H7   CB   CAM  109.60  3.000
 0UM  H8   CB   CA   108.82  3.000
 0UM  H7   CB   CA   109.06  3.000
 0UM  CAM  CB   CA   113.63  3.000
 0UM  H10  CAM  H9   105.59  3.000
 0UM  H10  CAM  CAY  110.42  3.000
 0UM  H9   CAM  CAY  107.83  3.000
 0UM  H10  CAM  CB   109.82  3.000
 0UM  H9   CAM  CB   108.95  3.000
 0UM  CAY  CAM  CB   113.88  3.000
 0UM  H11  CAY  CAN  107.85  3.000
 0UM  H11  CAY  NAR  105.59  3.000
 0UM  CAN  CAY  NAR  114.84  3.000
 0UM  H11  CAY  CAM  107.22  3.000
 0UM  CAN  CAY  CAM  109.35  3.000
 0UM  NAR  CAY  CAM  111.59  3.000
 0UM  H12  NAR  CAK  109.50  3.000
 0UM  H12  NAR  CAY  109.88  3.000
 0UM  CAK  NAR  CAY  116.51  3.000
 0UM  H15  CAK  H14  106.07  3.000
 0UM  H15  CAK  CAJ  108.88  3.000
 0UM  H14  CAK  CAJ  108.76  3.000
 0UM  H15  CAK  NAR  108.57  3.000
 0UM  H14  CAK  NAR  113.50  3.000
 0UM  CAJ  CAK  NAR  110.87  3.000
 0UM  H17  CAJ  H16  106.51  3.000
 0UM  H17  CAJ  CAA  109.49  3.000
 0UM  H16  CAJ  CAA  110.12  3.000
 0UM  H17  CAJ  CAK  109.30  3.000
 0UM  H16  CAJ  CAK  109.00  3.000
 0UM  CAA  CAJ  CAK  112.26  3.000
 0UM  H20  CAA  H19  107.62  3.000
 0UM  H20  CAA  H18  107.65  3.000
 0UM  H19  CAA  H18  107.48  3.000
 0UM  H20  CAA  CAJ  111.40  3.000
 0UM  H19  CAA  CAJ  111.21  3.000
 0UM  H18  CAA  CAJ  111.28  3.000
 0UM  H23  CBB  CAZ  110.31  3.000
 0UM  H23  CBB  OAS  107.51  3.000
 0UM  CAZ  CBB  OAS  104.92  3.000
 0UM  H23  CBB  CAN  109.65  3.000
 0UM  OAS  CBB  CAN  111.06  3.000
 0UM  CAZ  CBB  CAN  113.17  3.000
 0UM  CBC  OAS  CBB  110.80  3.000
 0UM  H24  CAZ  CBA  112.11  3.000
 0UM  H24  CAZ  OAF  111.85  3.000
 0UM  CBA  CAZ  OAF  110.78  3.000
 0UM  H24  CAZ  CBB  111.86  3.000
 0UM  CBA  CAZ  CBB  100.83  3.000
 0UM  OAF  CAZ  CBB  108.88  3.000
 0UM  H25  OAF  CAZ  108.10  3.000
 0UM  H26  CBA  CBC  109.63  3.000
 0UM  H26  CBA  OAG  111.43  3.000
 0UM  CBC  CBA  OAG  109.76  3.000
 0UM  H26  CBA  CAZ  109.02  3.000
 0UM  CBC  CBA  CAZ  101.22  3.000
 0UM  OAG  CBA  CAZ  115.26  3.000
 0UM  H27  OAG  CBA  108.73  3.000
 0UM  H28  CBC  N9   105.89  3.000
 0UM  H28  CBC  CBA  110.15  3.000
 0UM  N9   CBC  CBA  113.37  3.000
 0UM  H28  CBC  OAS  111.37  3.000
 0UM  N9   CBC  OAS  109.87  3.000
 0UM  CBA  CBC  OAS  106.29  3.000
 0UM  CBC  N9   C8   127.35  3.000
 0UM  CBC  N9   C4   126.48  3.000
 0UM  C8   N9   C4   106.17  3.000
 0UM  C8   N7   C5   104.36  3.000
 0UM  H29  C2   N3   116.11  3.000
 0UM  H29  C2   N1   115.40  3.000
 0UM  N3   C2   N1   128.49  3.000
 0UM  H31  N6   H30  118.11  3.000
 0UM  H31  N6   C6   120.13  3.000
 0UM  H30  N6   C6   120.93  3.000
 0UM  H22  CAN  H21  105.48  3.000
 0UM  H22  CAN  CBB  107.86  3.000
 0UM  H21  CAN  CBB  110.18  3.000
 0UM  H22  CAN  CAY  109.85  3.000
 0UM  H21  CAN  CAY  108.80  3.000
 0UM  CBB  CAN  CAY  114.30  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
 0UM  CONST_01  N7   C8   N9   C4      0.00   0.0  0
 0UM  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 0UM  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 0UM  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 0UM  CONST_05  N9   C8   N7   C5      0.00   0.0  0
 0UM  CONST_06  C8   N9   C4   C5      0.00   0.0  0
 0UM  CONST_07  C2   N3   C4   C5      0.00   0.0  0
 0UM  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 0UM  CONST_09  C8   N7   C5   C6    180.00   0.0  0
 0UM  CONST_10  N9   C4   C5   C6    180.00   0.0  0
 0UM  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 0UM  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 0UM  CONST_13  N3   C4   N9   C8    180.00   0.0  0
 0UM  CONST_14  N7   C5   C6   N1    180.00   0.0  0
 0UM  CONST_15  N7   C5   C4   N3    180.00   0.0  0
 0UM  CONST_16  N7   C5   C4   N9      0.00   0.0  0
 0UM  CONST_17  C2   N3   C4   N9    180.00   0.0  0
 0UM  CONST_18  CBC  N9   C4   C5    180.00   0.0  0
 0UM  CONST_19  CBC  N9   C4   N3      0.00   0.0  0
 0UM  CONST_20  N7   C8   N9   CBC   180.00   0.0  0
 0UM  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 0UM  CONST_22  N6   C6   C5   N7      0.00   0.0  0
 0UM  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 0UM  CONST_24  H1   C8   N9   C4    180.00   0.0  0
 0UM  CONST_25  H29  C2   N3   C4    180.00   0.0  0
 0UM  CONST_26  H30  N6   C6   C5      0.00   0.0  0
 0UM  CONST_27  H31  N6   C6   C5    180.00   0.0  0
 0UM  Var_01    CAY  CAM  CB   CA   -177.44  30.0  1
 0UM  Var_02    CAJ  CAK  NAR  CAY   175.97  30.0  1
 0UM  Var_03    CAA  CAJ  CAK  NAR   180.00  30.0  1
 0UM  Var_04    H18  CAA  CAJ  CAK   -59.52  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
 0UM  chir_01  CA   CB   N    C    positiv
 0UM  chir_02  CAY  NAR  CAN  CAM  positiv
 0UM  chir_03  CBB  OAS  CAN  CAZ  positiv
 0UM  chir_04  CAZ  OAF  CBB  CBA  positiv
 0UM  chir_05  CBA  OAG  CAZ  CBC  positiv
 0UM  chir_06  CBC  OAS  N9   CBA  negativ

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
 0UM  plan-1  C4   0.020
 0UM  plan-1  C5   0.020
 0UM  plan-1  C6   0.020
 0UM  plan-1  C8   0.020
 0UM  plan-1  N1   0.020
 0UM  plan-1  N3   0.020
 0UM  plan-1  CBC  0.020
 0UM  plan-1  N9   0.020
 0UM  plan-1  N7   0.020
 0UM  plan-1  C2   0.020
 0UM  plan-1  N6   0.020
 0UM  plan-1  H1   0.020
 0UM  plan-1  H29  0.020
 0UM  plan-2  C6   0.020
 0UM  plan-2  N6   0.020
 0UM  plan-2  H30  0.020
 0UM  plan-2  H31  0.020
 0UM  plan-3  C    0.020
 0UM  plan-3  CA   0.020
 0UM  plan-3  O    0.020
 0UM  plan-3  OXT  0.020

