# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 22:42:09 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 9-alpha-L-lyxofuranosyl-N-(2-phenylethyl)-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(NCCc4ccccc4)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
 GUB  GUB  9-alpha-L-lyxofuranosyl-N-(2-phenylethyl)-9H-purin-6-amine  ligand  48  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GUB
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
 GUB  C2    C  CH2   0  -0.538   4.7964   1.0937   0.3213
 GUB  C3    C  CH2   0  -0.254   3.8321  -0.0906   0.3203
 GUB  C5    C  CR6   0   0.518   1.3801  -0.1701   0.0287
 GUB  O18   O  OH1   0  -0.669  -6.2638   2.8191  -0.9245
 GUB  C17   C  CH2   0  -0.169  -6.5083   1.4628  -0.6368
 GUB  C16   C  CR15  0   0.003  -5.4551   0.9789   0.3286
 GUB  C19   C  CR15  0  -0.066  -5.6604  -0.4505   0.8349
 GUB  O20   O  OH1   0  -0.664  -6.0884  -1.3471  -0.1565
 GUB  O15   O  O     0  -0.498  -4.1659   0.9872  -0.3005
 GUB  C14   C  CR15  0   0.205  -3.4602  -0.1741   0.0312
 GUB  C21   C  CR15  0  -0.017  -4.2206  -0.8025   1.1994
 GUB  O22   O  OH1   0  -0.652  -3.8996  -2.1510   1.2974
 GUB  N13   N  NR5   0  -0.538  -2.0934   0.1579   0.3493
 GUB  C12   C  CR15  0   0.109  -1.6548   1.0443   1.2955
 GUB  N11   N  N     0  -0.452  -0.3592   1.1169   1.3724
 GUB  C10   C  CR56  0  -0.023   0.0889   0.2288   0.4291
 GUB  C9    C  CR56  0   0.488  -0.9734  -0.3759  -0.2216
 GUB  N6    N  N     0  -0.489   1.4744  -1.0811  -0.9449
 GUB  C7    C  CR16  0   0.048   0.3623  -1.5672  -1.4915
 GUB  N8    N  N     0  -0.457  -0.8925  -1.2820  -1.1941
 GUB  N4    N  NH1   0  -0.662   2.4800   0.3413   0.5913
 GUB  C1    C  CR6   0   0.121   6.2113   0.6306   0.1142
 GUB  C23   C  CR16  0  -0.305   6.7414   0.5076  -1.1682
 GUB  C24   C  CR16  0  -0.241   8.0328   0.0355  -1.3619
 GUB  C25   C  CR16  0  -0.271   8.8147  -0.3250  -0.2719
 GUB  C26   C  CR16  0  -0.240   8.2967  -0.2070   1.0114
 GUB  C27   C  CR16  0  -0.306   7.0050   0.2665   1.1999
 GUB  H2    H  HCH2  0   0.255   4.5063   1.7952  -0.4637
 GUB  H2A   H  HCH2  0   0.252   4.7177   1.6266   1.2731
 GUB  H3    H  HCH2  0   0.257   3.8477  -0.5873  -0.6480
 GUB  H3A   H  HCH2  0   0.241   4.1523  -0.8283   1.0639
 GUB  HO18  H  HOH1  0   0.458  -6.8851   3.0953  -1.6040
 GUB  H17   H  HCH2  0   0.205  -7.4913   1.3201  -0.1658
 GUB  H17A  H  HCH2  0   0.208  -6.4876   0.8460  -1.5427
 GUB  H16   H  HCR5  0   0.238  -5.4333   1.6547   1.1940
 GUB  H19   H  HCR5  0   0.263  -6.3242  -0.4592   1.7070
 GUB  HO20  H  HOH1  0   0.462  -7.0361  -1.2447  -0.2841
 GUB  H14   H  HCR5  0   0.262  -3.4123  -0.8739  -0.8106
 GUB  H21   H  HCR5  0   0.245  -3.9715  -0.2560   2.1202
 GUB  HO22  H  HOH1  0   0.464  -4.2617  -2.4980   2.1186
 GUB  H12   H  HCR5  0   0.298  -2.3413   1.6201   1.8982
 GUB  H7    H  HCR6  0   0.251   0.5119  -2.2962  -2.2807
 GUB  HN4   H  HNH1  0   0.403   2.3413   0.9546   1.3798
 GUB  H23   H  HCR6  0   0.248   6.1405   0.7893  -2.0255
 GUB  H24   H  HCR6  0   0.254   8.4287  -0.0513  -2.3657
 GUB  H25   H  HCR6  0   0.254   9.8216  -0.6925  -0.4225
 GUB  H26   H  HCR6  0   0.254   8.8994  -0.4804   1.8683
 GUB  H27   H  HCR6  0   0.248   6.6095   0.3598   2.2049

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
 GUB  C2   C3    single    1.527  0.020  1.527
 GUB  C2   C1    single    1.503  0.020  1.503
 GUB  C3   N4    single    1.445  0.020  1.445
 GUB  C5   C10   aromatic  1.409  0.020  1.409
 GUB  C5   N6    aromatic  1.337  0.020  1.337
 GUB  C5   N4    single    1.337  0.020  1.337
 GUB  O18  C17   single    1.408  0.020  1.408
 GUB  C17  C16   single    1.509  0.020  1.509
 GUB  C16  C19   single    1.530  0.020  1.530
 GUB  C16  O15   single    1.435  0.020  1.435
 GUB  C19  O20   single    1.404  0.020  1.404
 GUB  C19  C21   single    1.526  0.020  1.526
 GUB  O15  C14   single    1.399  0.020  1.399
 GUB  C14  C21   single    1.529  0.020  1.529
 GUB  C14  N13   single    1.442  0.020  1.442
 GUB  C21  O22   single    1.390  0.020  1.390
 GUB  N13  C12   aromatic  1.369  0.020  1.369
 GUB  N13  C9    aromatic  1.366  0.020  1.366
 GUB  C12  N11   aromatic  1.300  0.020  1.300
 GUB  N11  C10   aromatic  1.371  0.020  1.371
 GUB  C10  C9    aromatic  1.385  0.020  1.385
 GUB  C9   N8    aromatic  1.332  0.020  1.332
 GUB  N6   C7    aromatic  1.331  0.020  1.331
 GUB  C7   N8    aromatic  1.321  0.020  1.321
 GUB  C1   C23   aromatic  1.393  0.020  1.393
 GUB  C1   C27   aromatic  1.393  0.020  1.393
 GUB  C23  C24   aromatic  1.389  0.020  1.389
 GUB  C24  C25   aromatic  1.389  0.020  1.389
 GUB  C25  C26   aromatic  1.389  0.020  1.389
 GUB  C26  C27   aromatic  1.389  0.020  1.389
 GUB  C2   H2    single    0.970  0.020  1.090
 GUB  C2   H2A   single    0.970  0.020  1.090
 GUB  C3   H3    single    0.970  0.020  1.090
 GUB  C3   H3A   single    0.970  0.020  1.090
 GUB  O18  HO18  single    0.850  0.020  0.980
 GUB  C17  H17   single    0.970  0.020  1.090
 GUB  C17  H17A  single    0.970  0.020  1.090
 GUB  C16  H16   single    0.970  0.020  1.090
 GUB  C19  H19   single    0.970  0.020  1.090
 GUB  O20  HO20  single    0.850  0.020  0.980
 GUB  C14  H14   single    0.970  0.020  1.090
 GUB  C21  H21   single    0.970  0.020  1.090
 GUB  O22  HO22  single    0.850  0.020  0.980
 GUB  C12  H12   single    0.930  0.020  1.080
 GUB  C7   H7    single    0.930  0.020  1.080
 GUB  N4   HN4   single    0.860  0.020  1.020
 GUB  C23  H23   single    0.930  0.020  1.080
 GUB  C24  H24   single    0.930  0.020  1.080
 GUB  C25  H25   single    0.930  0.020  1.080
 GUB  C26  H26   single    0.930  0.020  1.080
 GUB  C27  H27   single    0.930  0.020  1.080

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
 GUB  H2A   C2   H2   107.06  3.000
 GUB  H2A   C2   C1   109.74  3.000
 GUB  H2    C2   C1   110.43  3.000
 GUB  H2A   C2   C3   109.45  3.000
 GUB  H2    C2   C3   109.26  3.000
 GUB  C1    C2   C3   110.82  3.000
 GUB  H3A   C3   H3   107.01  3.000
 GUB  H3A   C3   N4   110.33  3.000
 GUB  H3    C3   N4   108.47  3.000
 GUB  H3A   C3   C2   109.71  3.000
 GUB  H3    C3   C2   110.20  3.000
 GUB  N4    C3   C2   111.03  3.000
 GUB  N4    C5   N6   120.60  3.000
 GUB  N4    C5   C10  121.73  3.000
 GUB  N6    C5   C10  117.67  3.000
 GUB  HO18  O18  C17  107.99  3.000
 GUB  H17A  C17  H17  107.34  3.000
 GUB  H17A  C17  C16  109.58  3.000
 GUB  H17   C17  C16  107.97  3.000
 GUB  H17A  C17  O18  111.71  3.000
 GUB  H17   C17  O18  111.59  3.000
 GUB  C16   C17  O18  108.57  3.000
 GUB  H16   C16  O15  108.92  3.000
 GUB  H16   C16  C19  108.46  3.000
 GUB  O15   C16  C19  105.73  3.000
 GUB  H16   C16  C17  108.71  3.000
 GUB  O15   C16  C17  110.18  3.000
 GUB  C19   C16  C17  114.69  3.000
 GUB  H19   C19  C21  112.30  3.000
 GUB  H19   C19  O20  111.86  3.000
 GUB  C21   C19  O20  108.00  3.000
 GUB  H19   C19  C16  110.61  3.000
 GUB  C21   C19  C16   99.66  3.000
 GUB  O20   C19  C16  113.82  3.000
 GUB  HO20  O20  C19  109.04  3.000
 GUB  C14   O15  C16  110.16  3.000
 GUB  H14   C14  N13  105.97  3.000
 GUB  H14   C14  C21  110.26  3.000
 GUB  N13   C14  C21  113.42  3.000
 GUB  H14   C14  O15  111.72  3.000
 GUB  N13   C14  O15  109.83  3.000
 GUB  C21   C14  O15  105.75  3.000
 GUB  H21   C21  O22  111.78  3.000
 GUB  H21   C21  C14  108.84  3.000
 GUB  O22   C21  C14  109.74  3.000
 GUB  H21   C21  C19  107.40  3.000
 GUB  O22   C21  C19  117.29  3.000
 GUB  C14   C21  C19  101.06  3.000
 GUB  HO22  O22  C21  108.85  3.000
 GUB  C9    N13  C12  106.21  3.000
 GUB  C9    N13  C14  126.52  3.000
 GUB  C12   N13  C14  127.25  3.000
 GUB  H12   C12  N11  124.81  3.000
 GUB  H12   C12  N13  121.83  3.000
 GUB  N11   C12  N13  113.36  3.000
 GUB  C10   N11  C12  104.41  3.000
 GUB  C9    C10  N11  110.83  3.000
 GUB  C9    C10  C5   116.47  3.000
 GUB  N11   C10  C5   132.70  3.000
 GUB  N8    C9   C10  126.42  3.000
 GUB  N8    C9   N13  128.39  3.000
 GUB  C10   C9   N13  105.19  3.000
 GUB  C7    N6   C5   119.28  3.000
 GUB  H7    C7   N8   116.10  3.000
 GUB  H7    C7   N6   115.40  3.000
 GUB  N8    C7   N6   128.50  3.000
 GUB  C7    N8   C9   111.65  3.000
 GUB  HN4   N4   C5   116.64  3.000
 GUB  HN4   N4   C3   117.20  3.000
 GUB  C5    N4   C3   125.20  3.000
 GUB  C27   C1   C23  118.52  3.000
 GUB  C27   C1   C2   120.63  3.000
 GUB  C23   C1   C2   120.81  3.000
 GUB  H23   C23  C24  119.57  3.000
 GUB  H23   C23  C1   119.61  3.000
 GUB  C24   C23  C1   120.81  3.000
 GUB  H24   C24  C25  120.07  3.000
 GUB  H24   C24  C23  119.78  3.000
 GUB  C25   C24  C23  120.15  3.000
 GUB  H25   C25  C26  120.29  3.000
 GUB  H25   C25  C24  120.17  3.000
 GUB  C26   C25  C24  119.54  3.000
 GUB  H26   C26  C27  119.77  3.000
 GUB  H26   C26  C25  120.14  3.000
 GUB  C27   C26  C25  120.08  3.000
 GUB  H27   C27  C26  119.64  3.000
 GUB  H27   C27  C1   119.47  3.000
 GUB  C26   C27  C1   120.88  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
 GUB  CONST_01  C12  N11  C10  C5   180.00   0.0  0
 GUB  CONST_02  N13  C9   C10  C5   180.00   0.0  0
 GUB  CONST_03  N8   C9   C10  C5     0.00   0.0  0
 GUB  CONST_04  N8   C7   N6   C5     0.00   0.0  0
 GUB  CONST_05  C10  N11  C12  N13    0.00   0.0  0
 GUB  CONST_06  N11  C10  C9   N13    0.00   0.0  0
 GUB  CONST_07  C7   N8   C9   N13  180.00   0.0  0
 GUB  CONST_08  C10  C9   N13  C12    0.00   0.0  0
 GUB  CONST_09  N8   C9   N13  C12  180.00   0.0  0
 GUB  CONST_10  C9   C10  N11  C12    0.00   0.0  0
 GUB  CONST_11  C9   N13  C12  N11    0.00   0.0  0
 GUB  CONST_12  N6   C5   C10  N11  180.00   0.0  0
 GUB  CONST_13  N8   C9   C10  N11  180.00   0.0  0
 GUB  CONST_14  C7   N6   C5   C10    0.00   0.0  0
 GUB  CONST_15  C7   N8   C9   C10    0.00   0.0  0
 GUB  CONST_16  N6   C5   C10  C9     0.00   0.0  0
 GUB  CONST_17  N6   C7   N8   C9     0.00   0.0  0
 GUB  CONST_18  C25  C24  C23  C1     0.00   0.0  0
 GUB  CONST_19  C25  C26  C27  C1     0.00   0.0  0
 GUB  CONST_20  C26  C27  C1   C23    0.00   0.0  0
 GUB  CONST_21  C26  C25  C24  C23    0.00   0.0  0
 GUB  CONST_22  C27  C1   C23  C24    0.00   0.0  0
 GUB  CONST_23  C27  C26  C25  C24    0.00   0.0  0
 GUB  CONST_24  N11  C12  N13  C14  180.00   0.0  0
 GUB  CONST_25  C10  C9   N13  C14  180.00   0.0  0
 GUB  CONST_26  N8   C9   N13  C14    0.00   0.0  0
 GUB  CONST_27  C24  C23  C1   C2   180.00   0.0  0
 GUB  CONST_28  C26  C27  C1   C2   180.00   0.0  0
 GUB  CONST_29  N4   C5   C10  N11    0.00   0.0  0
 GUB  CONST_30  N4   C5   C10  C9   180.00   0.0  0
 GUB  CONST_31  N4   C5   N6   C7   180.00   0.0  0
 GUB  CONST_32  H7   C7   N6   C5   180.00   0.0  0
 GUB  CONST_33  H12  C12  N13  C14    0.00   0.0  0
 GUB  CONST_34  H24  C24  C23  C1   180.00   0.0  0
 GUB  CONST_35  H26  C26  C27  C1   180.00   0.0  0
 GUB  CONST_36  H27  C27  C1   C23  180.00   0.0  0
 GUB  CONST_37  H25  C25  C24  C23  180.00   0.0  0
 GUB  CONST_38  H23  C23  C24  C25  180.00   0.0  0
 GUB  CONST_39  C10  C5   N4   C3   180.00   0.0  0
 GUB  CONST_40  N6   C5   N4   C3     0.00   0.0  0
 GUB  CONST_41  HN4  N4   C5   C10    0.00   0.0  0
 GUB  Var_01    C23  C1   C2   C3    89.23  30.0  2
 GUB  Var_02    C5   N4   C3   C2   143.03  30.0  3
 GUB  Var_03    C1   C2   C3   N4   176.88  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
 GUB  chir_01  C16  C17  C19  O15  negativ
 GUB  chir_02  C19  O20  C21  C16  negativ
 GUB  chir_03  C14  O15  N13  C21  negativ
 GUB  chir_04  C21  O22  C14  C19  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
 GUB  plan-1  C2   0.020
 GUB  plan-1  C1   0.020
 GUB  plan-1  C23  0.020
 GUB  plan-1  C24  0.020
 GUB  plan-1  C25  0.020
 GUB  plan-1  C26  0.020
 GUB  plan-1  C27  0.020
 GUB  plan-1  H23  0.020
 GUB  plan-1  H24  0.020
 GUB  plan-1  H25  0.020
 GUB  plan-1  H26  0.020
 GUB  plan-1  H27  0.020
 GUB  plan-2  C5   0.020
 GUB  plan-2  C14  0.020
 GUB  plan-2  N13  0.020
 GUB  plan-2  C12  0.020
 GUB  plan-2  N11  0.020
 GUB  plan-2  C10  0.020
 GUB  plan-2  C9   0.020
 GUB  plan-2  N6   0.020
 GUB  plan-2  C7   0.020
 GUB  plan-2  N8   0.020
 GUB  plan-2  N4   0.020
 GUB  plan-2  H12  0.020
 GUB  plan-2  H7   0.020
 GUB  plan-3  C3   0.020
 GUB  plan-3  C5   0.020
 GUB  plan-3  N4   0.020
 GUB  plan-3  HN4  0.020

