# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 02:22:34 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 5'-O-[(2-phenylethyl)carbamoyl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](COC(=O)NCCc4ccccc4)[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
 KBJ  KBJ  5'-O-[(2-phenylethyl)carbamoyl]guanosine  ligand  53  31  .  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_KBJ
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
 KBJ  C1   C  C     0   0.761   -2.6297   1.2553  -0.6156
 KBJ  C2   C  CR6   0   0.698    5.6328  -1.1752   1.4099
 KBJ  C3   C  CR6   0   0.122   -6.7103  -1.1035   0.7739
 KBJ  C4   C  CR56  0   0.512    3.8724  -0.6605   0.1749
 KBJ  C5   C  CR56  0  -0.098    3.7433  -1.9115  -0.3984
 KBJ  C6   C  CR6   0   0.507    4.6709  -2.9296  -0.0333
 KBJ  C8   C  CR15  0   0.098    2.1803  -0.7463  -1.2145
 KBJ  C10  C  CR16  0  -0.304   -6.9113  -2.3620   0.2109
 KBJ  C11  C  CR16  0  -0.240   -8.1862  -2.7933  -0.1299
 KBJ  C12  C  CR16  0  -0.271   -9.2825  -1.9686   0.0884
 KBJ  O6   O  O     0  -0.472    4.7310  -4.0845  -0.4196
 KBJ  N1   N  NR16  0  -0.729    5.5957  -2.4410   0.8985
 KBJ  N2   N  NH2   0  -0.833    6.6134  -0.8976   2.2758
 KBJ  N3   N  N     0  -0.515    4.7769  -0.2428   1.0681
 KBJ  N7   N  N     0  -0.441    2.6765  -1.9419  -1.2612
 KBJ  N9   N  NR5   0  -0.540    2.8668   0.0848  -0.3609
 KBJ  C1'  C  CH1   0   0.212    2.5705   1.4585  -0.0584
 KBJ  O4'  O  O2    0  -0.487    1.2717   1.5500   0.4606
 KBJ  C2'  C  CH1   0  -0.049    2.5901   2.3799  -1.2751
 KBJ  O2'  O  OH1   0  -0.652    3.9000   2.7640  -1.5614
 KBJ  C3'  C  CH1   0  -0.036    1.6711   3.5086  -0.8017
 KBJ  O3'  O  OH1   0  -0.666    2.3427   4.3638   0.0848
 KBJ  C4'  C  CH1   0  -0.044    0.6193   2.7273  -0.0199
 KBJ  C5'  C  CH2   0  -0.164   -0.5710   2.3658  -0.8822
 KBJ  O5'  O  O2    0  -0.484   -1.4399   1.5738  -0.0867
 KBJ  O2   O  O     0  -0.522   -2.9974   1.6120  -1.7172
 KBJ  N4   N  NH1   0  -0.673   -3.3512   0.5074   0.2312
 KBJ  C7   C  CH2   0  -0.231   -4.6717   0.0248  -0.1118
 KBJ  C9   C  CH2   0  -0.559   -5.3251  -0.6223   1.1045
 KBJ  C13  C  CR16  0  -0.240   -9.0939  -0.7116   0.6475
 KBJ  C14  C  CR16  0  -0.306   -7.8166  -0.2839   0.9854
 KBJ  H2   H  HCR6  0   0.248   -6.0615  -3.0138   0.0428
 KBJ  H3   H  HCR6  0   0.254   -8.3246  -3.7755  -0.5639
 KBJ  H4   H  HCR6  0   0.255  -10.2775  -2.3058  -0.1713
 KBJ  H5   H  HNH2  0   0.415    6.5930  -0.0142   2.7555
 KBJ  H6   H  HNH2  0   0.417    7.1907  -1.6204   2.6690
 KBJ  H8   H  HCH1  0   0.262    3.3217   1.7793   0.6713
 KBJ  H9   H  HCH1  0   0.250    2.1216   1.8729  -2.1288
 KBJ  H10  H  HOH1  0   0.471    3.9396   3.0866  -2.4673
 KBJ  H11  H  HCH1  0   0.257    1.2322   4.0598  -1.6438
 KBJ  H12  H  HOH1  0   0.451    3.1942   4.5905  -0.3073
 KBJ  H13  H  HCH1  0   0.269    0.2709   3.3104   0.8385
 KBJ  H14  H  HCH2  0   0.250   -1.0619   3.2875  -1.2044
 KBJ  H15  H  HCH2  0   0.230   -0.2662   1.8187  -1.7802
 KBJ  H16  H  HNH1  0   0.403   -2.9329   0.2069   1.0973
 KBJ  H17  H  HCH2  0   0.243   -5.2887   0.8573  -0.4575
 KBJ  H18  H  HCH2  0   0.238   -4.6207  -0.7010  -0.9289
 KBJ  H19  H  HCH2  0   0.259   -5.3651   0.1012   1.9222
 KBJ  H20  H  HCH2  0   0.258   -4.7111  -1.4608   1.4447
 KBJ  H21  H  HCR6  0   0.254   -9.9428  -0.0635   0.8245
 KBJ  H22  H  HCR6  0   0.248   -7.6785   0.6975   1.4248
 KBJ  H23  H  HNR6  0   0.426    6.2947  -3.1037   1.2092
 KBJ  H1   H  HCR5  0   0.287    1.3154  -0.4085  -1.7660

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
 KBJ  O6   C6   double    1.219  0.020  1.219
 KBJ  C6   N1   single    1.401  0.020  1.401
 KBJ  C6   C5   single    1.425  0.020  1.425
 KBJ  N1   C2   single    1.366  0.020  1.366
 KBJ  N2   C2   single    1.337  0.020  1.337
 KBJ  C2   N3   double    1.311  0.020  1.311
 KBJ  C5   N7   aromatic  1.372  0.020  1.372
 KBJ  C5   C4   aromatic  1.382  0.020  1.382
 KBJ  N7   C8   aromatic  1.295  0.020  1.295
 KBJ  N3   C4   single    1.338  0.020  1.338
 KBJ  C4   N9   aromatic  1.362  0.020  1.362
 KBJ  C8   N9   aromatic  1.375  0.020  1.375
 KBJ  N9   C1'  single    1.437  0.020  1.437
 KBJ  C1'  C2'  single    1.526  0.020  1.526
 KBJ  C1'  O4'  single    1.402  0.020  1.402
 KBJ  O2'  C2'  single    1.395  0.020  1.395
 KBJ  C2'  C3'  single    1.531  0.020  1.531
 KBJ  O4'  C4'  single    1.429  0.020  1.429
 KBJ  C12  C11  aromatic  1.389  0.020  1.389
 KBJ  C12  C13  aromatic  1.389  0.020  1.389
 KBJ  C3'  C4'  single    1.526  0.020  1.526
 KBJ  C3'  O3'  single    1.403  0.020  1.403
 KBJ  C11  C10  aromatic  1.388  0.020  1.388
 KBJ  C4'  C5'  single    1.514  0.020  1.514
 KBJ  C13  C14  aromatic  1.389  0.020  1.389
 KBJ  C5'  O5'  single    1.419  0.020  1.419
 KBJ  C10  C3   aromatic  1.393  0.020  1.393
 KBJ  C14  C3   aromatic  1.393  0.020  1.393
 KBJ  O5'  C1   single    1.340  0.020  1.340
 KBJ  C3   C9   single    1.503  0.020  1.503
 KBJ  O2   C1   double    1.215  0.020  1.215
 KBJ  C1   N4   single    1.340  0.020  1.340
 KBJ  C9   C7   single    1.525  0.020  1.525
 KBJ  N4   C7   single    1.447  0.020  1.447
 KBJ  C8   H1   single    0.930  0.020  1.080
 KBJ  C10  H2   single    0.930  0.020  1.080
 KBJ  C11  H3   single    0.930  0.020  1.080
 KBJ  C12  H4   single    0.930  0.020  1.080
 KBJ  N2   H5   single    0.860  0.020  1.020
 KBJ  N2   H6   single    0.860  0.020  1.020
 KBJ  C1'  H8   single    0.970  0.020  1.090
 KBJ  C2'  H9   single    0.970  0.020  1.090
 KBJ  O2'  H10  single    0.850  0.020  0.980
 KBJ  C3'  H11  single    0.970  0.020  1.090
 KBJ  O3'  H12  single    0.850  0.020  0.980
 KBJ  C4'  H13  single    0.970  0.020  1.090
 KBJ  C5'  H14  single    0.970  0.020  1.090
 KBJ  C5'  H15  single    0.970  0.020  1.090
 KBJ  N4   H16  single    0.860  0.020  1.020
 KBJ  C7   H17  single    0.970  0.020  1.090
 KBJ  C7   H18  single    0.970  0.020  1.090
 KBJ  C9   H19  single    0.970  0.020  1.090
 KBJ  C9   H20  single    0.970  0.020  1.090
 KBJ  C13  H21  single    0.930  0.020  1.080
 KBJ  C14  H22  single    0.930  0.020  1.080
 KBJ  N1   H23  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
 KBJ  N4   C1   O2   125.01  3.000
 KBJ  N4   C1   O5'  111.17  3.000
 KBJ  O2   C1   O5'  123.82  3.000
 KBJ  N3   C2   N2   119.99  3.000
 KBJ  N3   C2   N1   122.94  3.000
 KBJ  N2   C2   N1   117.05  3.000
 KBJ  C14  C3   C9   120.68  3.000
 KBJ  C9   C3   C10  120.73  3.000
 KBJ  C14  C3   C10  118.57  3.000
 KBJ  N9   C4   N3   126.23  3.000
 KBJ  N9   C4   C5   105.27  3.000
 KBJ  N3   C4   C5   128.50  3.000
 KBJ  N7   C5   C6   130.65  3.000
 KBJ  N7   C5   C4   110.69  3.000
 KBJ  C6   C5   C4   118.66  3.000
 KBJ  N1   C6   O6   120.57  3.000
 KBJ  N1   C6   C5   110.55  3.000
 KBJ  O6   C6   C5   128.88  3.000
 KBJ  H1   C8   N9   121.86  3.000
 KBJ  H1   C8   N7   125.25  3.000
 KBJ  N9   C8   N7   112.89  3.000
 KBJ  H2   C10  C11  119.67  3.000
 KBJ  H2   C10  C3   119.51  3.000
 KBJ  C11  C10  C3   120.82  3.000
 KBJ  H3   C11  C12  120.04  3.000
 KBJ  H3   C11  C10  119.85  3.000
 KBJ  C12  C11  C10  120.11  3.000
 KBJ  H4   C12  C13  120.23  3.000
 KBJ  H4   C12  C11  120.19  3.000
 KBJ  C13  C12  C11  119.57  3.000
 KBJ  H23  N1   C6   115.58  3.000
 KBJ  H23  N1   C2   118.24  3.000
 KBJ  C6   N1   C2   126.18  3.000
 KBJ  H6   N2   H5   117.18  3.000
 KBJ  H6   N2   C2   121.68  3.000
 KBJ  H5   N2   C2   118.45  3.000
 KBJ  C4   N3   C2   113.16  3.000
 KBJ  C8   N7   C5   104.76  3.000
 KBJ  C1'  N9   C8   127.26  3.000
 KBJ  C1'  N9   C4   126.34  3.000
 KBJ  C8   N9   C4   106.39  3.000
 KBJ  H8   C1'  C2'  110.21  3.000
 KBJ  H8   C1'  O4'  111.69  3.000
 KBJ  C2'  C1'  O4'  105.52  3.000
 KBJ  H8   C1'  N9   106.19  3.000
 KBJ  O4'  C1'  N9   109.35  3.000
 KBJ  C2'  C1'  N9   113.98  3.000
 KBJ  C4'  O4'  C1'  110.63  3.000
 KBJ  H9   C2'  C3'  108.96  3.000
 KBJ  H9   C2'  O2'  111.61  3.000
 KBJ  C3'  C2'  O2'  115.11  3.000
 KBJ  H9   C2'  C1'  109.61  3.000
 KBJ  C3'  C2'  C1'  101.01  3.000
 KBJ  O2'  C2'  C1'  109.99  3.000
 KBJ  H10  O2'  C2'  108.91  3.000
 KBJ  H11  C3'  C4'  111.99  3.000
 KBJ  H11  C3'  O3'  111.71  3.000
 KBJ  C4'  C3'  O3'  108.56  3.000
 KBJ  H11  C3'  C2'  111.90  3.000
 KBJ  O3'  C3'  C2'  110.95  3.000
 KBJ  C4'  C3'  C2'  101.23  3.000
 KBJ  H12  O3'  C3'  108.00  3.000
 KBJ  H13  C4'  C5'  108.88  3.000
 KBJ  H13  C4'  C3'  110.39  3.000
 KBJ  C5'  C4'  C3'  111.87  3.000
 KBJ  H13  C4'  O4'  108.69  3.000
 KBJ  C5'  C4'  O4'  110.72  3.000
 KBJ  C3'  C4'  O4'  106.23  3.000
 KBJ  H15  C5'  H14  107.74  3.000
 KBJ  H15  C5'  O5'  110.56  3.000
 KBJ  H14  C5'  O5'  111.15  3.000
 KBJ  H15  C5'  C4'  111.57  3.000
 KBJ  H14  C5'  C4'  108.65  3.000
 KBJ  O5'  C5'  C4'  107.18  3.000
 KBJ  C5'  O5'  C1   117.05  3.000
 KBJ  H16  N4   C7   118.88  3.000
 KBJ  H16  N4   C1   119.08  3.000
 KBJ  C7   N4   C1   121.84  3.000
 KBJ  H18  C7   H17  107.18  3.000
 KBJ  H18  C7   C9   109.52  3.000
 KBJ  H17  C7   C9   109.50  3.000
 KBJ  H18  C7   N4   110.84  3.000
 KBJ  H17  C7   N4   109.65  3.000
 KBJ  C9   C7   N4   110.09  3.000
 KBJ  H20  C9   H19  107.19  3.000
 KBJ  H20  C9   C7   109.45  3.000
 KBJ  H19  C9   C7   109.37  3.000
 KBJ  H20  C9   C3   109.90  3.000
 KBJ  H19  C9   C3   110.05  3.000
 KBJ  C7   C9   C3   110.81  3.000
 KBJ  H21  C13  C14  119.81  3.000
 KBJ  H21  C13  C12  120.08  3.000
 KBJ  C14  C13  C12  120.11  3.000
 KBJ  H22  C14  C13  119.64  3.000
 KBJ  H22  C14  C3   119.54  3.000
 KBJ  C13  C14  C3   120.82  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
 KBJ  CONST_01  C12  C11  C10  C3      0.00   0.0  0
 KBJ  CONST_02  C12  C13  C14  C3      0.00   0.0  0
 KBJ  CONST_03  C8   N7   C5   C4      0.00   0.0  0
 KBJ  CONST_04  N7   C8   N9   C4      0.00   0.0  0
 KBJ  CONST_05  N9   C8   N7   C5      0.00   0.0  0
 KBJ  CONST_06  C8   N9   C4   C5      0.00   0.0  0
 KBJ  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 KBJ  CONST_08  C13  C14  C3   C10     0.00   0.0  0
 KBJ  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 KBJ  CONST_10  C14  C3   C10  C11     0.00   0.0  0
 KBJ  CONST_11  N9   C4   C5   N7      0.00   0.0  0
 KBJ  CONST_12  C1'  N9   C4   C5    180.00   0.0  0
 KBJ  CONST_13  C1'  N9   C4   N3      0.00   0.0  0
 KBJ  CONST_14  C1'  N9   C8   N7    180.00   0.0  0
 KBJ  CONST_15  C5   C6   N1   C2      0.00   0.0  0
 KBJ  CONST_16  N1   C2   N3   C4      0.00   0.0  0
 KBJ  CONST_17  N3   C2   N1   C6      0.00   0.0  0
 KBJ  CONST_18  C9   C3   C10  C11   180.00   0.0  0
 KBJ  CONST_19  C13  C14  C3   C9    180.00   0.0  0
 KBJ  CONST_20  O6   C6   N1   C2    180.00   0.0  0
 KBJ  CONST_21  N2   C2   N3   C4    180.00   0.0  0
 KBJ  CONST_22  N2   C2   N1   C6    180.00   0.0  0
 KBJ  CONST_23  H3   C11  C10  C3    180.00   0.0  0
 KBJ  CONST_24  H21  C13  C14  C3    180.00   0.0  0
 KBJ  CONST_25  H1   C8   N9   C4    180.00   0.0  0
 KBJ  CONST_26  H4   C12  C11  C10   180.00   0.0  0
 KBJ  CONST_27  H22  C14  C3   C10   180.00   0.0  0
 KBJ  CONST_28  H2   C10  C11  C12   180.00   0.0  0
 KBJ  CONST_29  H23  N1   C6   C5    180.00   0.0  0
 KBJ  CONST_30  H5   N2   C2   N1    180.00   0.0  0
 KBJ  CONST_31  H6   N2   C2   N1      0.00   0.0  0
 KBJ  Var_01    C7   C9   C3   C10    85.81  30.0  2
 KBJ  Var_02    C4'  C5'  O5'  C1    173.40  30.0  1
 KBJ  Var_03    N4   C7   C9   C3    178.79  30.0  3
 KBJ  Var_04    C9   C7   N4   C1   -172.00  30.0  3
 KBJ  Var_05    O2   C1   O5'  C5'    -0.52  30.0  3
 KBJ  Var_06    C7   N4   C1   O5'  -179.49  30.0  2

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
 KBJ  chir_01  C1'  N9   C2'  O4'  negativ
 KBJ  chir_02  C2'  O2'  C3'  C1'  positiv
 KBJ  chir_03  C3'  O3'  C4'  C2'  positiv
 KBJ  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
 KBJ  plan-1  C3   0.020
 KBJ  plan-1  C10  0.020
 KBJ  plan-1  C11  0.020
 KBJ  plan-1  C12  0.020
 KBJ  plan-1  C9   0.020
 KBJ  plan-1  C13  0.020
 KBJ  plan-1  C14  0.020
 KBJ  plan-1  H2   0.020
 KBJ  plan-1  H3   0.020
 KBJ  plan-1  H4   0.020
 KBJ  plan-1  H21  0.020
 KBJ  plan-1  H22  0.020
 KBJ  plan-2  C2   0.020
 KBJ  plan-2  C4   0.020
 KBJ  plan-2  C5   0.020
 KBJ  plan-2  C6   0.020
 KBJ  plan-2  C8   0.020
 KBJ  plan-2  O6   0.020
 KBJ  plan-2  N1   0.020
 KBJ  plan-2  N2   0.020
 KBJ  plan-2  N3   0.020
 KBJ  plan-2  N7   0.020
 KBJ  plan-2  N9   0.020
 KBJ  plan-2  C1'  0.020
 KBJ  plan-2  H5   0.020
 KBJ  plan-2  H6   0.020
 KBJ  plan-2  H23  0.020
 KBJ  plan-2  H1   0.020
 KBJ  plan-3  C1   0.020
 KBJ  plan-3  O5'  0.020
 KBJ  plan-3  O2   0.020
 KBJ  plan-3  N4   0.020

