# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 23:50:57 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5'-O-(ethylcarbamoyl)guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N
#
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
 KB7  KB7  5'-O-(ethylcarbamoyl)guanosine  ligand  43  25  .  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_KB7
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
 KB7  N1   N  NR16  0  -0.729  -4.3522  -1.7025  -0.8773
 KB7  C2   C  CR6   0   0.698  -4.1350  -0.4366  -1.3412
 KB7  O2   O  O     0  -0.521   4.8318  -0.1149   1.4108
 KB7  N3   N  N     0  -0.514  -3.0870   0.2761  -1.0067
 KB7  C4   C  CR56  0   0.512  -2.2541  -0.3684  -0.1810
 KB7  N4   N  NH1   0  -0.659   4.8379  -1.1072  -0.6315
 KB7  C5   C  CR56  0  -0.098  -2.3741  -1.6433   0.3383
 KB7  C6   C  CR6   0   0.507  -3.5156  -2.4205  -0.0127
 KB7  C1'  C  CR15  0   0.210  -0.5018   1.3977   0.0353
 KB7  C2'  C  CR15  0  -0.051  -0.2163   2.2493   1.2713
 KB7  O2'  O  OH1   0  -0.653  -1.3722   2.9322   1.6510
 KB7  C3'  C  CR15  0  -0.031   0.9230   3.1360   0.7600
 KB7  O3'  O  OH1   0  -0.667   0.4316   4.1594  -0.0641
 KB7  C4'  C  CR15  0  -0.049   1.6982   2.1481  -0.1043
 KB7  O4'  O  O     0  -0.487   0.7365   1.2133  -0.5958
 KB7  C5'  C  CH2   0  -0.162   2.7796   1.4349   0.6801
 KB7  O6   O  O     0  -0.472  -3.8071  -3.5522   0.3348
 KB7  N2   N  NH2   0  -0.832  -5.0352   0.0606  -2.1971
 KB7  N7   N  N     0  -0.440  -1.3002  -1.9446   1.1375
 KB7  C8   C  CR15  0   0.098  -0.5574  -0.8838   1.1055
 KB7  N9   N  NR5   0  -0.540  -1.0865   0.1170   0.3251
 KB7  O5'  O  O2    0  -0.486   3.3660   0.4830  -0.1943
 KB7  C1   C  C     0   0.758   4.3901  -0.2385   0.2860
 KB7  C7   C  CH2   0  -0.263   5.9984  -1.9451  -0.4038
 KB7  C9   C  CH3   0  -0.696   6.0780  -3.0270  -1.4639
 KB7  H2   H  HNH1  0   0.399   4.4587  -1.0628  -1.5645
 KB7  H3   H  HCR5  0   0.264  -1.2111   1.9143  -0.6198
 KB7  H4   H  HCR5  0   0.250   0.1635   1.6177   2.0846
 KB7  H5   H  HOH1  0   0.471  -1.2775   3.2224   2.5639
 KB7  H6   H  HCR5  0   0.257   1.5350   3.5319   1.5812
 KB7  H7   H  HOH1  0   0.451  -0.3069   4.5797   0.3922
 KB7  H8   H  HCR5  0   0.270   2.1551   2.6605  -0.9566
 KB7  H9   H  HCH2  0   0.250   3.5182   2.1679   1.0147
 KB7  H10  H  HCH2  0   0.228   2.3719   0.9422   1.5692
 KB7  H11  H  HNH2  0   0.417  -5.9263  -0.3820  -2.3407
 KB7  H12  H  HNH2  0   0.414  -4.9604   1.0298  -2.4546
 KB7  H13  H  HCR5  0   0.286   0.3853  -0.7692   1.6198
 KB7  H14  H  HCH2  0   0.232   6.9145  -1.3468  -0.4115
 KB7  H15  H  HCH2  0   0.239   5.9236  -2.3999   0.5843
 KB7  H16  H  HCH3  0   0.235   5.2002  -3.6725  -1.4359
 KB7  H17  H  HCH3  0   0.233   6.1562  -2.5995  -2.4647
 KB7  H18  H  HCH3  0   0.245   6.9588  -3.6459  -1.3001
 KB7  H19  H  HNR6  0   0.426  -5.1824  -2.1908  -1.1892

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
 KB7  O6   C6   double    1.219  0.020  1.219
 KB7  N1   C6   single    1.401  0.020  1.401
 KB7  N1   C2   single    1.366  0.020  1.366
 KB7  C6   C5   single    1.425  0.020  1.425
 KB7  N2   C2   single    1.338  0.020  1.338
 KB7  C2   N3   double    1.311  0.020  1.311
 KB7  C5   N7   aromatic  1.372  0.020  1.372
 KB7  C5   C4   aromatic  1.382  0.020  1.382
 KB7  N7   C8   aromatic  1.295  0.020  1.295
 KB7  N3   C4   single    1.338  0.020  1.338
 KB7  C4   N9   aromatic  1.362  0.020  1.362
 KB7  C8   N9   aromatic  1.375  0.020  1.375
 KB7  N9   C1'  single    1.437  0.020  1.437
 KB7  C1'  C2'  single    1.528  0.020  1.528
 KB7  C1'  O4'  single    1.402  0.020  1.402
 KB7  O2'  C2'  single    1.395  0.020  1.395
 KB7  C2'  C3'  single    1.531  0.020  1.531
 KB7  O4'  C4'  single    1.428  0.020  1.428
 KB7  C3'  C4'  single    1.524  0.020  1.524
 KB7  C3'  O3'  single    1.403  0.020  1.403
 KB7  C4'  C5'  single    1.514  0.020  1.514
 KB7  C5'  O5'  single    1.419  0.020  1.419
 KB7  O5'  C1   single    1.342  0.020  1.342
 KB7  O2   C1   double    1.215  0.020  1.215
 KB7  C1   N4   single    1.341  0.020  1.341
 KB7  C9   C7   single    1.517  0.020  1.517
 KB7  C7   N4   single    1.449  0.020  1.449
 KB7  N4   H2   single    0.860  0.020  1.020
 KB7  C1'  H3   single    0.970  0.020  1.090
 KB7  C2'  H4   single    0.970  0.020  1.090
 KB7  O2'  H5   single    0.850  0.020  0.980
 KB7  C3'  H6   single    0.970  0.020  1.090
 KB7  O3'  H7   single    0.850  0.020  0.980
 KB7  C4'  H8   single    0.970  0.020  1.090
 KB7  C5'  H9   single    0.970  0.020  1.090
 KB7  C5'  H10  single    0.970  0.020  1.090
 KB7  N2   H11  single    0.890  0.020  1.040
 KB7  N2   H12  single    0.890  0.020  1.040
 KB7  C8   H13  single    0.930  0.020  1.080
 KB7  C7   H14  single    0.970  0.020  1.090
 KB7  C7   H15  single    0.970  0.020  1.090
 KB7  C9   H16  single    0.970  0.020  1.090
 KB7  C9   H17  single    0.970  0.020  1.090
 KB7  C9   H18  single    0.970  0.020  1.090
 KB7  N1   H19  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
 KB7  H19  N1   C6   115.64  3.000
 KB7  H19  N1   C2   118.22  3.000
 KB7  C6   N1   C2   126.14  3.000
 KB7  N2   C2   N3   119.94  3.000
 KB7  N3   C2   N1   122.99  3.000
 KB7  N2   C2   N1   117.05  3.000
 KB7  C4   N3   C2   113.15  3.000
 KB7  N9   C4   C5   105.28  3.000
 KB7  N9   C4   N3   126.24  3.000
 KB7  C5   C4   N3   128.48  3.000
 KB7  H2   N4   C7   118.17  3.000
 KB7  H2   N4   C1   118.64  3.000
 KB7  C7   N4   C1   122.31  3.000
 KB7  N7   C5   C6   130.60  3.000
 KB7  N7   C5   C4   110.71  3.000
 KB7  C6   C5   C4   118.69  3.000
 KB7  O6   C6   C5   128.87  3.000
 KB7  C5   C6   N1   110.54  3.000
 KB7  O6   C6   N1   120.58  3.000
 KB7  H3   C1'  N9   106.10  3.000
 KB7  H3   C1'  O4'  111.40  3.000
 KB7  N9   C1'  O4'  109.44  3.000
 KB7  H3   C1'  C2'  110.00  3.000
 KB7  O4'  C1'  C2'  105.81  3.000
 KB7  N9   C1'  C2'  114.18  3.000
 KB7  H4   C2'  C3'  108.85  3.000
 KB7  H4   C2'  O2'  111.51  3.000
 KB7  C3'  C2'  O2'  115.08  3.000
 KB7  H4   C2'  C1'  110.08  3.000
 KB7  C3'  C2'  C1'  101.05  3.000
 KB7  O2'  C2'  C1'  109.76  3.000
 KB7  H5   O2'  C2'  108.92  3.000
 KB7  H6   C3'  C4'  111.97  3.000
 KB7  H6   C3'  O3'  111.81  3.000
 KB7  C4'  C3'  O3'  108.53  3.000
 KB7  H6   C3'  C2'  111.95  3.000
 KB7  O3'  C3'  C2'  110.97  3.000
 KB7  C4'  C3'  C2'  101.09  3.000
 KB7  H7   O3'  C3'  107.95  3.000
 KB7  H8   C4'  C5'  109.01  3.000
 KB7  H8   C4'  O4'  108.63  3.000
 KB7  C5'  C4'  O4'  110.54  3.000
 KB7  H8   C4'  C3'  110.51  3.000
 KB7  C5'  C4'  C3'  112.01  3.000
 KB7  O4'  C4'  C3'  106.07  3.000
 KB7  C4'  O4'  C1'  110.71  3.000
 KB7  H10  C5'  H9   107.75  3.000
 KB7  H10  C5'  O5'  110.62  3.000
 KB7  H9   C5'  O5'  111.05  3.000
 KB7  H10  C5'  C4'  111.50  3.000
 KB7  H9   C5'  C4'  108.98  3.000
 KB7  O5'  C5'  C4'  106.96  3.000
 KB7  H12  N2   H11  116.98  3.000
 KB7  H12  N2   C2   118.16  3.000
 KB7  H11  N2   C2   121.61  3.000
 KB7  C8   N7   C5   104.75  3.000
 KB7  H13  C8   N9   121.93  3.000
 KB7  H13  C8   N7   125.15  3.000
 KB7  N9   C8   N7   112.92  3.000
 KB7  C8   N9   C1'  127.33  3.000
 KB7  C1'  N9   C4   126.25  3.000
 KB7  C8   N9   C4   106.34  3.000
 KB7  C1   O5'  C5'  117.09  3.000
 KB7  O5'  C1   N4   111.00  3.000
 KB7  N4   C1   O2   125.33  3.000
 KB7  O5'  C1   O2   123.66  3.000
 KB7  H15  C7   H14  106.97  3.000
 KB7  H15  C7   C9   109.84  3.000
 KB7  H14  C7   C9   109.95  3.000
 KB7  H15  C7   N4   109.18  3.000
 KB7  H14  C7   N4   110.69  3.000
 KB7  C9   C7   N4   110.16  3.000
 KB7  H18  C9   H17  107.62  3.000
 KB7  H18  C9   H16  108.12  3.000
 KB7  H17  C9   H16  108.26  3.000
 KB7  H18  C9   C7   110.05  3.000
 KB7  H17  C9   C7   111.43  3.000
 KB7  H16  C9   C7   111.24  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
 KB7  CONST_01  C8   N7   C5   C4     0.00   0.0  0
 KB7  CONST_02  N7   C8   N9   C4     0.00   0.0  0
 KB7  CONST_03  N9   C8   N7   C5     0.00   0.0  0
 KB7  CONST_04  C8   N9   C4   C5     0.00   0.0  0
 KB7  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 KB7  CONST_06  C1'  N9   C4   N3     0.00   0.0  0
 KB7  CONST_07  C1'  N9   C4   C5   180.00   0.0  0
 KB7  CONST_08  N7   C8   N9   C1'  180.00   0.0  0
 KB7  CONST_09  C4   N3   C2   N1     0.00   0.0  0
 KB7  CONST_10  C5   C6   N1   C2     0.00   0.0  0
 KB7  CONST_11  C6   N1   C2   N3     0.00   0.0  0
 KB7  CONST_12  O6   C6   N1   C2   180.00   0.0  0
 KB7  CONST_13  N2   C2   N3   C4   180.00   0.0  0
 KB7  CONST_14  N2   C2   N1   C6   180.00   0.0  0
 KB7  CONST_15  H13  C8   N9   C4   180.00   0.0  0
 KB7  CONST_16  H19  N1   C2   N3   180.00   0.0  0
 KB7  CONST_17  H11  N2   C2   N1     0.00   0.0  0
 KB7  CONST_18  H12  N2   C2   N1   180.00   0.0  0
 KB7  Var_01    C7   N4   C1   O2    -4.97  30.0  2
 KB7  Var_02    C9   C7   N4   C1   167.29  30.0  1
 KB7  Var_03    H16  C9   C7   N4   -61.07  30.0  3
 KB7  Var_04    H9   C5'  O5'  C1    58.97  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
 KB7  chir_01  C1'  N9   C2'  O4'  negativ
 KB7  chir_02  C2'  O2'  C3'  C1'  positiv
 KB7  chir_03  C3'  O3'  C4'  C2'  positiv
 KB7  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
 KB7  plan-1  N1   0.020
 KB7  plan-1  C2   0.020
 KB7  plan-1  N3   0.020
 KB7  plan-1  C4   0.020
 KB7  plan-1  C5   0.020
 KB7  plan-1  C6   0.020
 KB7  plan-1  C1'  0.020
 KB7  plan-1  O6   0.020
 KB7  plan-1  N2   0.020
 KB7  plan-1  N7   0.020
 KB7  plan-1  C8   0.020
 KB7  plan-1  N9   0.020
 KB7  plan-1  H11  0.020
 KB7  plan-1  H12  0.020
 KB7  plan-1  H13  0.020
 KB7  plan-1  H19  0.020
 KB7  plan-2  O2   0.020
 KB7  plan-2  N4   0.020
 KB7  plan-2  O5'  0.020
 KB7  plan-2  C1   0.020

