# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 07:06:41 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 5'-O-(benzylcarbamoyl)guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](COC(=O)NCc4ccccc4)[C@@H](O)[C@H]3O
#
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
 KBD  KBD  5'-O-(benzylcarbamoyl)guanosine  ligand  50  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KBD
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
 KBD  N1   N  NR16  0  -0.727  -2.2206  -3.2549  -1.0114
 KBD  N3   N  N     0  -0.514  -2.3289  -0.9156  -1.2221
 KBD  C4   C  CR56  0   0.510  -1.5477  -0.9211  -0.1351
 KBD  C5   C  CR56  0  -0.086  -1.0710  -2.0066   0.5733
 KBD  C6   C  CR6   0   0.511  -1.3979  -3.3157   0.1206
 KBD  C7   C  CH2   0  -0.398   4.6845   0.2500   0.3741
 KBD  C8   C  CR15  0   0.109  -0.2852  -0.3027   1.5464
 KBD  C15  C  CR6   0   0.127   4.0698  -0.9539  -0.2974
 KBD  C17  C  CR16  0  -0.243   3.9825  -2.4969  -2.1569
 KBD  C20  C  CR16  0  -0.288   2.9963  -1.6244   0.2853
 KBD  C1   C  C     0   0.766   2.9743   1.9184   0.9263
 KBD  C16  C  CR16  0  -0.303   4.5551  -1.4010  -1.5231
 KBD  C18  C  CR16  0  -0.270   2.9154  -3.1606  -1.5666
 KBD  C19  C  CR16  0  -0.238   2.4239  -2.7214  -0.3433
 KBD  O2   O  O     0  -0.512   2.6172   1.3872   1.9578
 KBD  C2   C  CR6   0   0.691  -2.6509  -2.1177  -1.6324
 KBD  N2   N  NH2   0  -0.831  -3.4622  -2.2696  -2.6882
 KBD  N4   N  NH1   0  -0.644   3.9570   1.4764   0.1258
 KBD  C1'  C  CH1   0   0.215  -1.2165   1.5406   0.0992
 KBD  C2'  C  CH1   0  -0.050  -1.6962   2.4730   1.2086
 KBD  C3'  C  CH1   0  -0.041  -1.1984   3.8260   0.6889
 KBD  C4'  C  CH1   0  -0.018   0.1365   3.4331   0.0660
 KBD  C5'  C  CH2   0  -0.197   1.2907   3.5968   1.0387
 KBD  N7   N  N     0  -0.446  -0.2833  -1.5958   1.6187
 KBD  N9   N  NR5   0  -0.545  -1.0461   0.1735   0.5041
 KBD  O2'  O  OH1   0  -0.653  -3.0801   2.3715   1.3534
 KBD  O3'  O  OH1   0  -0.667  -2.0404   4.3167  -0.3210
 KBD  O4'  O  O2    0  -0.488   0.0153   2.0643  -0.3220
 KBD  O5'  O  O2    0  -0.487   2.4704   3.0695   0.4524
 KBD  O6   O  O     0  -0.477  -1.0503  -4.3916   0.5793
 KBD  H2   H  HCH2  0   0.266   4.7488   0.0947   1.4505
 KBD  H3   H  HCH2  0   0.271   5.7032   0.3953   0.0140
 KBD  H4   H  HCR5  0   0.290   0.2610   0.3575   2.2013
 KBD  H5   H  HCR6  0   0.254   4.3722  -2.8326  -3.1094
 KBD  H6   H  HCR6  0   0.250   2.6040  -1.2912   1.2373
 KBD  H7   H  HCR6  0   0.250   5.3912  -0.8901  -1.9873
 KBD  H8   H  HCR6  0   0.253   2.4712  -4.0178  -2.0564
 KBD  H9   H  HCR6  0   0.250   1.5971  -3.2373   0.1275
 KBD  H10  H  HNH2  0   0.415  -3.5571  -3.1605  -3.1453
 KBD  H11  H  HNH2  0   0.413  -3.6564  -1.4564  -3.2478
 KBD  H12  H  HNH1  0   0.402   4.1161   1.9479  -0.7502
 KBD  H13  H  HCH1  0   0.261  -1.9447   1.5274  -0.7191
 KBD  H14  H  HCH1  0   0.251  -1.1753   2.2369   2.1448
 KBD  H15  H  HCH1  0   0.256  -1.0735   4.5543   1.5014
 KBD  H16  H  HCH1  0   0.266   0.3337   4.0333  -0.8277
 KBD  H17  H  HCH2  0   0.259   1.4614   4.6596   1.2177
 KBD  H18  H  HCH2  0   0.242   1.0842   3.1240   2.0005
 KBD  H19  H  HOH1  0   0.471  -3.3288   2.7019   2.2225
 KBD  H20  H  HOH1  0   0.451  -2.9493   4.2616  -0.0030
 KBD  H21  H  HNR6  0   0.426  -2.5014  -4.1478  -1.3970

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
 KBD  O6   C6   double    1.220  0.020  1.220
 KBD  N1   C6   single    1.401  0.020  1.401
 KBD  N1   C2   single    1.365  0.020  1.365
 KBD  C6   C5   single    1.423  0.020  1.423
 KBD  N2   C2   single    1.340  0.020  1.340
 KBD  C2   N3   double    1.310  0.020  1.310
 KBD  C5   N7   aromatic  1.372  0.020  1.372
 KBD  C5   C4   aromatic  1.381  0.020  1.381
 KBD  N7   C8   aromatic  1.295  0.020  1.295
 KBD  N3   C4   single    1.339  0.020  1.339
 KBD  C4   N9   aromatic  1.363  0.020  1.363
 KBD  C8   N9   aromatic  1.376  0.020  1.376
 KBD  N9   C1'  single    1.436  0.020  1.436
 KBD  C1'  C2'  single    1.527  0.020  1.527
 KBD  C1'  O4'  single    1.403  0.020  1.403
 KBD  O2'  C2'  single    1.395  0.020  1.395
 KBD  C2'  C3'  single    1.532  0.020  1.532
 KBD  O4'  C4'  single    1.428  0.020  1.428
 KBD  C3'  C4'  single    1.525  0.020  1.525
 KBD  C3'  O3'  single    1.403  0.020  1.403
 KBD  C4'  C5'  single    1.518  0.020  1.518
 KBD  C5'  O5'  single    1.419  0.020  1.419
 KBD  C19  C20  aromatic  1.388  0.020  1.388
 KBD  C19  C18  aromatic  1.390  0.020  1.390
 KBD  C20  C15  aromatic  1.393  0.020  1.393
 KBD  O5'  C1   single    1.343  0.020  1.343
 KBD  C18  C17  aromatic  1.388  0.020  1.388
 KBD  O2   C1   double    1.214  0.020  1.214
 KBD  C1   N4   single    1.342  0.020  1.342
 KBD  C15  C7   single    1.509  0.020  1.509
 KBD  C15  C16  aromatic  1.392  0.020  1.392
 KBD  C7   N4   single    1.447  0.020  1.447
 KBD  C17  C16  aromatic  1.389  0.020  1.389
 KBD  C7   H2   single    0.970  0.020  1.090
 KBD  C7   H3   single    0.970  0.020  1.090
 KBD  C8   H4   single    0.930  0.020  1.080
 KBD  C17  H5   single    0.930  0.020  1.080
 KBD  C20  H6   single    0.930  0.020  1.080
 KBD  C16  H7   single    0.930  0.020  1.080
 KBD  C18  H8   single    0.930  0.020  1.080
 KBD  C19  H9   single    0.930  0.020  1.080
 KBD  N2   H10  single    0.890  0.020  1.040
 KBD  N2   H11  single    0.890  0.020  1.040
 KBD  N4   H12  single    0.860  0.020  1.020
 KBD  C1'  H13  single    0.970  0.020  1.090
 KBD  C2'  H14  single    0.970  0.020  1.090
 KBD  C3'  H15  single    0.970  0.020  1.090
 KBD  C4'  H16  single    0.970  0.020  1.090
 KBD  C5'  H17  single    0.970  0.020  1.090
 KBD  C5'  H18  single    0.970  0.020  1.090
 KBD  O2'  H19  single    0.850  0.020  0.980
 KBD  O3'  H20  single    0.850  0.020  0.980
 KBD  N1   H21  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
 KBD  H21  N1   C2   118.29  3.000
 KBD  H21  N1   C6   115.63  3.000
 KBD  C2   N1   C6   126.07  3.000
 KBD  C2   N3   C4   113.20  3.000
 KBD  N9   C4   C5   105.29  3.000
 KBD  N9   C4   N3   126.31  3.000
 KBD  C5   C4   N3   128.40  3.000
 KBD  N7   C5   C6   130.51  3.000
 KBD  N7   C5   C4   110.72  3.000
 KBD  C6   C5   C4   118.72  3.000
 KBD  O6   C6   C5   128.76  3.000
 KBD  C5   C6   N1   110.61  3.000
 KBD  O6   C6   N1   120.62  3.000
 KBD  H3   C7   H2   106.87  3.000
 KBD  H3   C7   N4   107.46  3.000
 KBD  H2   C7   N4   108.67  3.000
 KBD  H3   C7   C15  109.87  3.000
 KBD  H2   C7   C15  110.48  3.000
 KBD  N4   C7   C15  113.25  3.000
 KBD  H4   C8   N9   121.90  3.000
 KBD  H4   C8   N7   125.20  3.000
 KBD  N9   C8   N7   112.88  3.000
 KBD  C16  C15  C20  118.84  3.000
 KBD  C16  C15  C7   120.39  3.000
 KBD  C20  C15  C7   120.77  3.000
 KBD  H5   C17  C18  120.17  3.000
 KBD  H5   C17  C16  119.84  3.000
 KBD  C18  C17  C16  119.99  3.000
 KBD  H6   C20  C19  119.49  3.000
 KBD  H6   C20  C15  119.93  3.000
 KBD  C19  C20  C15  120.58  3.000
 KBD  O5'  C1   N4   110.27  3.000
 KBD  N4   C1   O2   125.31  3.000
 KBD  O5'  C1   O2   124.37  3.000
 KBD  H7   C16  C17  119.62  3.000
 KBD  H7   C16  C15  119.63  3.000
 KBD  C17  C16  C15  120.75  3.000
 KBD  H8   C18  C19  120.23  3.000
 KBD  H8   C18  C17  120.09  3.000
 KBD  C19  C18  C17  119.68  3.000
 KBD  H9   C19  C18  120.17  3.000
 KBD  H9   C19  C20  119.66  3.000
 KBD  C18  C19  C20  120.17  3.000
 KBD  N2   C2   N3   119.96  3.000
 KBD  N3   C2   N1   122.97  3.000
 KBD  N2   C2   N1   117.05  3.000
 KBD  H11  N2   H10  116.43  3.000
 KBD  H11  N2   C2   117.61  3.000
 KBD  H10  N2   C2   121.03  3.000
 KBD  H12  N4   C1   118.69  3.000
 KBD  H12  N4   C7   117.80  3.000
 KBD  C1   N4   C7   123.00  3.000
 KBD  H13  C1'  O4'  111.33  3.000
 KBD  H13  C1'  N9   106.14  3.000
 KBD  O4'  C1'  N9   109.63  3.000
 KBD  H13  C1'  C2'  109.95  3.000
 KBD  O4'  C1'  C2'  105.43  3.000
 KBD  N9   C1'  C2'  114.45  3.000
 KBD  H14  C2'  O2'  111.52  3.000
 KBD  H14  C2'  C3'  108.97  3.000
 KBD  O2'  C2'  C3'  114.94  3.000
 KBD  H14  C2'  C1'  109.85  3.000
 KBD  C3'  C2'  C1'  101.00  3.000
 KBD  O2'  C2'  C1'  110.04  3.000
 KBD  H15  C3'  O3'  111.64  3.000
 KBD  H15  C3'  C4'  111.93  3.000
 KBD  O3'  C3'  C4'  108.75  3.000
 KBD  H15  C3'  C2'  111.81  3.000
 KBD  O3'  C3'  C2'  110.97  3.000
 KBD  C4'  C3'  C2'  101.27  3.000
 KBD  H16  C4'  O4'  108.60  3.000
 KBD  H16  C4'  C5'  109.09  3.000
 KBD  O4'  C4'  C5'  110.00  3.000
 KBD  H16  C4'  C3'  110.50  3.000
 KBD  C5'  C4'  C3'  112.10  3.000
 KBD  O4'  C4'  C3'  106.49  3.000
 KBD  H18  C5'  H17  107.87  3.000
 KBD  H18  C5'  O5'  111.13  3.000
 KBD  H17  C5'  O5'  107.44  3.000
 KBD  H18  C5'  C4'  111.96  3.000
 KBD  H17  C5'  C4'  109.21  3.000
 KBD  O5'  C5'  C4'  109.10  3.000
 KBD  C8   N7   C5   104.80  3.000
 KBD  C1'  N9   C8   127.51  3.000
 KBD  C1'  N9   C4   126.06  3.000
 KBD  C8   N9   C4   106.31  3.000
 KBD  H19  O2'  C2'  108.97  3.000
 KBD  H20  O3'  C3'  107.94  3.000
 KBD  C4'  O4'  C1'  110.53  3.000
 KBD  C5'  O5'  C1   118.99  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
 KBD  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 KBD  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 KBD  CONST_03  N9   C8   N7   C5      0.00   0.0  0
 KBD  CONST_04  C8   N9   C4   C5      0.00   0.0  0
 KBD  CONST_05  C18  C19  C20  C15     0.00   0.0  0
 KBD  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 KBD  CONST_07  C20  C19  C18  C17     0.00   0.0  0
 KBD  CONST_08  C20  C15  C16  C17     0.00   0.0  0
 KBD  CONST_09  C19  C20  C15  C16     0.00   0.0  0
 KBD  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 KBD  CONST_11  N9   C4   C5   N7      0.00   0.0  0
 KBD  CONST_12  C1'  N9   C4   N3      0.00   0.0  0
 KBD  CONST_13  C1'  N9   C4   C5    180.00   0.0  0
 KBD  CONST_14  N7   C8   N9   C1'   180.00   0.0  0
 KBD  CONST_15  C4   N3   C2   N1      0.00   0.0  0
 KBD  CONST_16  C6   N1   C2   N3      0.00   0.0  0
 KBD  CONST_17  C2   N1   C6   C5      0.00   0.0  0
 KBD  CONST_18  C19  C20  C15  C7    180.00   0.0  0
 KBD  CONST_19  C17  C16  C15  C7    180.00   0.0  0
 KBD  CONST_20  N2   C2   N3   C4    180.00   0.0  0
 KBD  CONST_21  N2   C2   N1   C6    180.00   0.0  0
 KBD  CONST_22  O6   C6   N1   C2    180.00   0.0  0
 KBD  CONST_23  H4   C8   N9   C4    180.00   0.0  0
 KBD  CONST_24  H9   C19  C20  C15   180.00   0.0  0
 KBD  CONST_25  H5   C17  C16  C15   180.00   0.0  0
 KBD  CONST_26  H8   C18  C19  C20   180.00   0.0  0
 KBD  CONST_27  H7   C16  C15  C20   180.00   0.0  0
 KBD  CONST_28  H6   C20  C15  C16   180.00   0.0  0
 KBD  CONST_29  H21  N1   C2   N3    180.00   0.0  0
 KBD  CONST_31  H11  N2   C2   N1    180.00   0.0  0
 KBD  Var_01    N4   C7   C15  C20   -82.01  30.0  2
 KBD  Var_02    C1   N4   C7   C15    91.10  30.0  3
 KBD  Var_03    C4'  C5'  O5'  C1   -108.36  30.0  1
 KBD  Var_04    O5'  C1   N4   C7   -179.51  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
 KBD  chir_01  C1'  N9   C2'  O4'  negativ
 KBD  chir_02  C2'  O2'  C3'  C1'  positiv
 KBD  chir_03  C3'  O3'  C4'  C2'  positiv
 KBD  chir_04  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
 KBD  plan-1  C7   0.020
 KBD  plan-1  C15  0.020
 KBD  plan-1  C17  0.020
 KBD  plan-1  C20  0.020
 KBD  plan-1  C16  0.020
 KBD  plan-1  C18  0.020
 KBD  plan-1  C19  0.020
 KBD  plan-1  H5   0.020
 KBD  plan-1  H6   0.020
 KBD  plan-1  H7   0.020
 KBD  plan-1  H8   0.020
 KBD  plan-1  H9   0.020
 KBD  plan-2  N1   0.020
 KBD  plan-2  N3   0.020
 KBD  plan-2  C4   0.020
 KBD  plan-2  C5   0.020
 KBD  plan-2  C6   0.020
 KBD  plan-2  C8   0.020
 KBD  plan-2  C2   0.020
 KBD  plan-2  N2   0.020
 KBD  plan-2  C1'  0.020
 KBD  plan-2  N7   0.020
 KBD  plan-2  N9   0.020
 KBD  plan-2  O6   0.020
 KBD  plan-2  H4   0.020
 KBD  plan-2  H10  0.020
 KBD  plan-2  H11  0.020
 KBD  plan-2  H21  0.020
 KBD  plan-3  C1   0.020
 KBD  plan-3  O2   0.020
 KBD  plan-3  N4   0.020
 KBD  plan-3  O5'  0.020

