# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 22:28:23 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: N-cyclopentyladenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(NC4CCCC4)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
 3GU  3GU  'N-cyclopentyladenosine   '  ligand  45  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3GU
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
 3GU  C1    C  CH1   0  -0.056   4.6957   0.3780  -0.1501
 3GU  N1    N  N     0  -0.489   2.5116  -1.2979  -0.8062
 3GU  C2    C  CR16  0   0.044   1.4787  -2.0828  -1.1036
 3GU  N3    N  N     0  -0.458   0.1901  -1.8479  -0.9328
 3GU  C4    C  CR56  0   0.488  -0.0232  -0.6493  -0.3924
 3GU  C5    C  CR56  0  -0.021   0.9433   0.2758  -0.0351
 3GU  C6    C  CR6   0   0.514   2.2833  -0.0938  -0.2703
 3GU  N6    N  NH1   0  -0.667   3.3027   0.7222   0.0102
 3GU  N7    N  N     0  -0.452   0.3672   1.4074   0.4812
 3GU  C8    C  CR15  0   0.108  -0.9103   1.1689   0.4388
 3GU  N9    N  NR5   0  -0.537  -1.2151  -0.0608  -0.0792
 3GU  C1'   C  CH1   0   0.207  -2.5277  -0.6246  -0.2806
 3GU  C2'   C  CH1   0  -0.017  -3.2677  -0.9480   1.0192
 3GU  O2'   O  OH1   0  -0.653  -2.8544  -2.1858   1.4989
 3GU  C21   C  CH2   0  -0.462   5.5854   1.6189  -0.2673
 3GU  C22   C  CH2   0  -0.445   6.9873   1.1527   0.1746
 3GU  C23   C  CH2   0  -0.459   6.8088  -0.2820   0.7150
 3GU  C24   C  CH2   0  -0.439   5.3174  -0.4029   1.0083
 3GU  C3'   C  CH1   0  -0.036  -4.7224  -0.8311   0.5659
 3GU  O3'   O  OH1   0  -0.667  -5.0521  -2.0078  -0.1230
 3GU  C4'   C  CH1   0  -0.054  -4.6246   0.3815  -0.3604
 3GU  O4'   O  O2    0  -0.490  -3.3289   0.2971  -0.9624
 3GU  C5'   C  CH2   0  -0.155  -4.7981   1.6921   0.3827
 3GU  O5'   O  OH1   0  -0.667  -4.5923   2.7493  -0.5190
 3GU  H1    H  HCH1  0   0.247   4.7861  -0.2239  -1.0574
 3GU  HN6   H  HNH1  0   0.397   3.0812   1.5850   0.4827
 3GU  H8    H  HCR5  0   0.296  -1.6772   1.8591   0.7585
 3GU  H1'   H  HCH1  0   0.262  -2.3777  -1.5387  -0.8655
 3GU  H2'   H  HCH1  0   0.242  -3.0792  -0.1487   1.7494
 3GU  HO2'  H  HOH1  0   0.464  -3.1819  -2.2954   2.3971
 3GU  H21   H  HCH2  0   0.246   5.5717   2.0369  -1.2743
 3GU  H21A  H  HCH2  0   0.231   5.2152   2.3981   0.4054
 3GU  H22   H  HCH2  0   0.233   7.6998   1.1779  -0.6497
 3GU  H22A  H  HCH2  0   0.232   7.3803   1.8120   0.9488
 3GU  H23   H  HCH2  0   0.226   7.0880  -1.0083  -0.0523
 3GU  H23A  H  HCH2  0   0.236   7.4324  -0.4838   1.5861
 3GU  H24   H  HCH2  0   0.219   5.0636   0.0864   1.9538
 3GU  H24A  H  HCH2  0   0.239   4.9639  -1.4334   1.0583
 3GU  H3'   H  HCH1  0   0.254  -5.4070  -0.6453   1.4034
 3GU  HO3'  H  HOH1  0   0.457  -5.9453  -1.9175  -0.4699
 3GU  H4'   H  HCH1  0   0.261  -5.3709   0.3294  -1.1599
 3GU  H5'   H  HCH2  0   0.216  -5.8103   1.7021   0.8082
 3GU  H5'A  H  HCH2  0   0.196  -4.1006   1.7414   1.2304
 3GU  HO5'  H  HOH1  0   0.459  -4.6718   3.5755  -0.0343
 3GU  H2    H  HCR6  0   0.249   1.7351  -3.0422  -1.5404

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
 3GU  C1   N6    single    1.444  0.020  1.444
 3GU  C1   C21   single    1.531  0.020  1.531
 3GU  C1   C24   single    1.529  0.020  1.529
 3GU  N1   C2    aromatic  1.331  0.020  1.331
 3GU  N1   C6    aromatic  1.338  0.020  1.338
 3GU  C2   N3    aromatic  1.321  0.020  1.321
 3GU  N3   C4    aromatic  1.332  0.020  1.332
 3GU  C4   C5    aromatic  1.385  0.020  1.385
 3GU  C4   N9    aromatic  1.366  0.020  1.366
 3GU  C5   C6    aromatic  1.410  0.020  1.410
 3GU  C5   N7    aromatic  1.371  0.020  1.371
 3GU  C6   N6    single    1.336  0.020  1.336
 3GU  N7   C8    aromatic  1.300  0.020  1.300
 3GU  C8   N9    aromatic  1.369  0.020  1.369
 3GU  N9   C1'   single    1.443  0.020  1.443
 3GU  C1'  C2'   single    1.530  0.020  1.530
 3GU  C1'  O4'   single    1.399  0.020  1.399
 3GU  C2'  O2'   single    1.390  0.020  1.390
 3GU  C2'  C3'   single    1.528  0.020  1.528
 3GU  C21  C22   single    1.542  0.020  1.542
 3GU  C22  C23   single    1.543  0.020  1.543
 3GU  C23  C24   single    1.525  0.020  1.525
 3GU  C3'  O3'   single    1.403  0.020  1.403
 3GU  C3'  C4'   single    1.529  0.020  1.529
 3GU  C4'  O4'   single    1.431  0.020  1.431
 3GU  C4'  C5'   single    1.517  0.020  1.517
 3GU  C5'  O5'   single    1.405  0.020  1.405
 3GU  C1   H1    single    0.970  0.020  1.090
 3GU  C2   H2    single    0.930  0.020  1.080
 3GU  N6   HN6   single    0.860  0.020  1.020
 3GU  C8   H8    single    0.930  0.020  1.080
 3GU  C1'  H1'   single    0.970  0.020  1.090
 3GU  C2'  H2'   single    0.970  0.020  1.090
 3GU  O2'  HO2'  single    0.850  0.020  0.980
 3GU  C21  H21   single    0.970  0.020  1.090
 3GU  C21  H21A  single    0.970  0.020  1.090
 3GU  C22  H22   single    0.970  0.020  1.090
 3GU  C22  H22A  single    0.970  0.020  1.090
 3GU  C23  H23   single    0.970  0.020  1.090
 3GU  C23  H23A  single    0.970  0.020  1.090
 3GU  C24  H24   single    0.970  0.020  1.090
 3GU  C24  H24A  single    0.970  0.020  1.090
 3GU  C3'  H3'   single    0.970  0.020  1.090
 3GU  O3'  HO3'  single    0.850  0.020  0.980
 3GU  C4'  H4'   single    0.970  0.020  1.090
 3GU  C5'  H5'   single    0.970  0.020  1.090
 3GU  C5'  H5'A  single    0.970  0.020  1.090
 3GU  O5'  HO5'  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
 3GU  H1    C1   C24  108.31  3.000
 3GU  H1    C1   C21  109.56  3.000
 3GU  C24   C1   C21  103.62  3.000
 3GU  H1    C1   N6   107.66  3.000
 3GU  C24   C1   N6   115.46  3.000
 3GU  C21   C1   N6   112.07  3.000
 3GU  C6    N1   C2   119.20  3.000
 3GU  H2    C2   N3   116.10  3.000
 3GU  H2    C2   N1   115.35  3.000
 3GU  N3    C2   N1   128.56  3.000
 3GU  C4    N3   C2   111.64  3.000
 3GU  N9    C4   C5   105.19  3.000
 3GU  N9    C4   N3   128.36  3.000
 3GU  C5    C4   N3   126.44  3.000
 3GU  N7    C5   C6   132.75  3.000
 3GU  N7    C5   C4   110.81  3.000
 3GU  C6    C5   C4   116.43  3.000
 3GU  N6    C6   C5   122.02  3.000
 3GU  N6    C6   N1   120.26  3.000
 3GU  C5    C6   N1   117.72  3.000
 3GU  HN6   N6   C6   116.97  3.000
 3GU  HN6   N6   C1   117.91  3.000
 3GU  C6    N6   C1   124.57  3.000
 3GU  C8    N7   C5   104.43  3.000
 3GU  H8    C8   N9   121.86  3.000
 3GU  H8    C8   N7   124.80  3.000
 3GU  N9    C8   N7   113.33  3.000
 3GU  C1'   N9   C8   127.34  3.000
 3GU  C1'   N9   C4   126.41  3.000
 3GU  C8    N9   C4   106.23  3.000
 3GU  H1'   C1'  O4'  111.60  3.000
 3GU  H1'   C1'  C2'  110.08  3.000
 3GU  O4'   C1'  C2'  106.04  3.000
 3GU  H1'   C1'  N9   106.02  3.000
 3GU  O4'   C1'  N9   109.37  3.000
 3GU  C2'   C1'  N9   113.83  3.000
 3GU  H2'   C2'  C3'  107.74  3.000
 3GU  H2'   C2'  O2'  111.55  3.000
 3GU  C3'   C2'  O2'  116.97  3.000
 3GU  H2'   C2'  C1'  109.13  3.000
 3GU  C3'   C2'  C1'  101.08  3.000
 3GU  O2'   C2'  C1'  109.72  3.000
 3GU  HO2'  O2'  C2'  108.80  3.000
 3GU  H21A  C21  H21  106.89  3.000
 3GU  H21A  C21  C22  110.29  3.000
 3GU  H21   C21  C22  113.08  3.000
 3GU  H21A  C21  C1   109.48  3.000
 3GU  H21   C21  C1   111.97  3.000
 3GU  C22   C21  C1   105.15  3.000
 3GU  H22A  C22  H22  106.71  3.000
 3GU  H22A  C22  C23  110.80  3.000
 3GU  H22   C22  C23  111.22  3.000
 3GU  H22A  C22  C21  110.39  3.000
 3GU  H22   C22  C21  111.75  3.000
 3GU  C23   C22  C21  106.04  3.000
 3GU  H23A  C23  H23  106.97  3.000
 3GU  H23A  C23  C24  113.02  3.000
 3GU  H23   C23  C24  109.40  3.000
 3GU  H23A  C23  C22  112.69  3.000
 3GU  H23   C23  C22  110.03  3.000
 3GU  C24   C23  C22  104.72  3.000
 3GU  H24A  C24  H24  107.91  3.000
 3GU  H24A  C24  C23  113.62  3.000
 3GU  H24   C24  C23  110.95  3.000
 3GU  H24A  C24  C1   112.67  3.000
 3GU  H24   C24  C1   109.39  3.000
 3GU  C23   C24  C1   102.21  3.000
 3GU  H3'   C3'  C4'  111.59  3.000
 3GU  H3'   C3'  O3'  111.72  3.000
 3GU  C4'   C3'  O3'  112.50  3.000
 3GU  H3'   C3'  C2'  112.36  3.000
 3GU  C4'   C3'  C2'  100.34  3.000
 3GU  O3'   C3'  C2'  107.77  3.000
 3GU  HO3'  O3'  C3'  108.44  3.000
 3GU  H4'   C4'  C5'  108.72  3.000
 3GU  H4'   C4'  O4'  107.89  3.000
 3GU  C5'   C4'  O4'  111.14  3.000
 3GU  H4'   C4'  C3'  111.16  3.000
 3GU  C5'   C4'  C3'  112.40  3.000
 3GU  O4'   C4'  C3'  105.42  3.000
 3GU  C4'   O4'  C1'  110.63  3.000
 3GU  H5'A  C5'  H5'  106.61  3.000
 3GU  H5'A  C5'  O5'  111.62  3.000
 3GU  H5'   C5'  O5'  112.15  3.000
 3GU  H5'A  C5'  C4'  110.13  3.000
 3GU  H5'   C5'  C4'  107.65  3.000
 3GU  O5'   C5'  C4'  108.61  3.000
 3GU  HO5'  O5'  C5'  108.12  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
 3GU  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 3GU  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 3GU  CONST_03  N7   C5   C6   N1   180.00   0.0  0
 3GU  CONST_04  C5   C6   N1   C2     0.00   0.0  0
 3GU  CONST_05  C5   C4   N3   C2     0.00   0.0  0
 3GU  CONST_06  N9   C4   N3   C2   180.00   0.0  0
 3GU  CONST_07  C6   N1   C2   N3     0.00   0.0  0
 3GU  CONST_08  C6   C5   C4   N3     0.00   0.0  0
 3GU  CONST_09  N7   C5   C4   N3   180.00   0.0  0
 3GU  CONST_10  C8   N9   C4   N3   180.00   0.0  0
 3GU  CONST_11  C8   N7   C5   C4     0.00   0.0  0
 3GU  CONST_12  N7   C8   N9   C4     0.00   0.0  0
 3GU  CONST_13  C8   N9   C4   C5     0.00   0.0  0
 3GU  CONST_14  N9   C8   N7   C5     0.00   0.0  0
 3GU  CONST_15  N9   C4   C5   C6   180.00   0.0  0
 3GU  CONST_16  C8   N7   C5   C6   180.00   0.0  0
 3GU  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 3GU  CONST_18  C1'  N9   C4   N3     0.00   0.0  0
 3GU  CONST_19  C1'  N9   C4   C5   180.00   0.0  0
 3GU  CONST_20  C1'  N9   C8   N7   180.00   0.0  0
 3GU  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 3GU  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 3GU  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 3GU  CONST_24  N1   C6   N6   C1     0.00   0.0  0
 3GU  CONST_25  C5   C6   N6   C1   180.00   0.0  0
 3GU  CONST_26  H2   C2   N3   C4   180.00   0.0  0
 3GU  CONST_27  H8   C8   N9   C4   180.00   0.0  0
 3GU  CONST_28  HN6  N6   C6   N1   180.00   0.0  0
 3GU  Var_01    C23  C22  C21  C1    -7.69  30.0  1
 3GU  Var_02    C22  C23  C24  C1    37.82  30.0  1
 3GU  Var_03    C24  C23  C22  C21  -18.72  30.0  1

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
 3GU  chir_01  C1   N6   C21  C24  negativ
 3GU  chir_02  C1'  N9   C2'  O4'  negativ
 3GU  chir_03  C2'  O2'  C3'  C1'  positiv
 3GU  chir_04  C3'  O3'  C4'  C2'  positiv
 3GU  chir_05  C4'  O4'  C3'  C5'  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
 3GU  plan-1  N1   0.020
 3GU  plan-1  C2   0.020
 3GU  plan-1  N3   0.020
 3GU  plan-1  C4   0.020
 3GU  plan-1  C5   0.020
 3GU  plan-1  C6   0.020
 3GU  plan-1  N6   0.020
 3GU  plan-1  N7   0.020
 3GU  plan-1  C8   0.020
 3GU  plan-1  N9   0.020
 3GU  plan-1  C1'  0.020
 3GU  plan-1  H8   0.020
 3GU  plan-1  H2   0.020
 3GU  plan-2  C1   0.020
 3GU  plan-2  C6   0.020
 3GU  plan-2  N6   0.020
 3GU  plan-2  HN6  0.020

