# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 19:39:10 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 5'-O-(2-amino-4-oxo-1,4-dihydropteridine-6-carbonyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2nc(cnc2N1)C(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45
#
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
 7C5  7C5  5'-O-(2-amino-4-oxo-1,4-dihydropteridine-6-carbonyl)adenosine  ligand  49  33  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7C5
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
 7C5  N1   N  NH2   0  -0.808  -7.0199   3.1422  -0.8617
 7C5  N3   N  N     0  -0.457   4.6560   1.1206  -1.3471
 7C5  C4   C  CR6   0   0.437  -4.1261   1.2581  -1.6096
 7C5  C5   C  CR16  0  -0.037  -3.8126  -0.6451   2.0612
 7C5  C6   C  CR6   0   0.011  -2.8867  -0.8992   1.0452
 7C5  C7   C  CH2   0  -0.181   0.1291  -2.8691   0.3606
 7C5  C8   C  CH1   0   0.211   2.8278  -1.2360  -0.7353
 7C5  C10  C  CH1   0  -0.032   2.2474  -3.5235  -0.8302
 7C5  C13  C  CR16  0   0.047   5.3474   2.2468  -1.3136
 7C5  C15  C  CR15  0   0.114   2.6523   0.1695   1.3483
 7C5  C17  C  C     0   0.595  -1.7877  -1.8720   1.2846
 7C5  C1   C  CR6   0   0.702  -6.0019   2.3040  -0.7196
 7C5  C2   C  CR66  0   0.561  -4.8818   0.7985   0.7168
 7C5  C3   C  CR66  0  -0.047  -3.9638   0.5521  -0.3110
 7C5  C9   C  CH1   0  -0.048   3.2307  -2.5799  -0.1314
 7C5  O2   O  OH1   0  -0.665   2.6465  -3.7805  -2.1497
 7C5  O3   O  OH1   0  -0.651   4.5775  -2.8313  -0.3892
 7C5  C11  C  CR56  0   0.493   3.9623   0.9366  -0.2271
 7C5  C12  C  CR56  0  -0.012   3.9287   1.7811   0.8706
 7C5  C14  C  CR6   0   0.462   4.7115   2.9474   0.7839
 7C5  N2   N  NR5   0  -0.540   3.1376  -0.1034   0.0967
 7C5  N4   N  N     0  -0.474   5.4142   3.1473  -0.3371
 7C5  N5   N  NH2   0  -0.816   4.7776   3.8469   1.7654
 7C5  N6   N  N     0  -0.447   3.1005   1.2829   1.8438
 7C5  N7   N  N     0  -0.523  -5.1754   2.1115  -1.7174
 7C5  N8   N  NR16  0  -0.727  -5.8888   1.6814   0.4900
 7C5  N9   N  N     0  -0.389  -4.8073   0.2050   1.8982
 7C5  N10  N  N     0  -0.341  -2.9735  -0.2959  -0.1280
 7C5  C16  C  CH1   0  -0.048   0.9907  -2.6612  -0.8664
 7C5  O4   O  O2    0  -0.486   1.4416  -1.3070  -0.9290
 7C5  O5   O  O2    0  -0.444  -0.9580  -1.9502   0.2643
 7C5  O6   O  O     0  -0.431  -1.6852  -2.5062   2.3051
 7C5  H1   H  HNH2  0   0.426  -7.6658   3.3480  -0.1189
 7C5  H2   H  HNH2  0   0.424  -7.1253   3.6364  -1.7313
 7C5  H3   H  HCR6  0   0.298  -3.7414  -1.1400   3.0211
 7C5  H4   H  HCH2  0   0.267  -0.2463  -3.8951   0.3794
 7C5  H5   H  HCH2  0   0.241   0.6931  -2.7014   1.2823
 7C5  H6   H  HCH1  0   0.265   3.3574  -1.0715  -1.6798
 7C5  H7   H  HCH1  0   0.259   2.0970  -4.4511  -0.2621
 7C5  H9   H  HCR5  0   0.290   1.9592  -0.4897   1.8496
 7C5  H10  H  HCH1  0   0.249   3.0198  -2.5798   0.9466
 7C5  H11  H  HOH1  0   0.452   3.5758  -4.0382  -2.1350
 7C5  H12  H  HOH1  0   0.471   4.8901  -3.5089   0.2189
 7C5  H13  H  HNH2  0   0.412   4.2553   3.7293   2.6154
 7C5  H14  H  HNH2  0   0.404   5.3328   4.6779   1.6560
 7C5  H16  H  HCH1  0   0.277   0.4000  -2.8754  -1.7619
 7C5  H15  H  HNR6  0   0.437  -6.5503   1.8615   1.2346
 7C5  O1   O  O     0  -0.454  -3.3453   1.0660  -2.5250
 7C5  H8   H  HCR6  0   0.253   5.9395   2.4696  -2.1947

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
 7C5  N5   C14  single    1.333  0.020  1.333
 7C5  O1   C4   double    1.218  0.020  1.218
 7C5  N6   C12  aromatic  1.372  0.020  1.372
 7C5  N6   C15  aromatic  1.298  0.020  1.298
 7C5  C14  C12  aromatic  1.407  0.020  1.407
 7C5  C14  N4   aromatic  1.338  0.020  1.338
 7C5  C4   N7   single    1.357  0.020  1.357
 7C5  C4   C3   single    1.487  0.020  1.487
 7C5  C12  C11  aromatic  1.385  0.020  1.385
 7C5  N7   C1   double    1.310  0.020  1.310
 7C5  C15  N2   aromatic  1.370  0.020  1.370
 7C5  N4   C13  aromatic  1.330  0.020  1.330
 7C5  O6   C17  double    1.206  0.020  1.206
 7C5  N10  C3   aromatic  1.317  0.020  1.317
 7C5  N10  C6   aromatic  1.322  0.020  1.322
 7C5  C3   C2   aromatic  1.400  0.020  1.400
 7C5  C11  N2   aromatic  1.366  0.020  1.366
 7C5  C11  N3   aromatic  1.330  0.020  1.330
 7C5  N2   C8   single    1.439  0.020  1.439
 7C5  C1   N1   single    1.326  0.020  1.326
 7C5  C1   N8   single    1.365  0.020  1.365
 7C5  C13  N3   aromatic  1.322  0.020  1.322
 7C5  C17  C6   single    1.487  0.020  1.487
 7C5  C17  O5   single    1.317  0.020  1.317
 7C5  C6   C5   aromatic  1.398  0.020  1.398
 7C5  C2   N8   single    1.358  0.020  1.358
 7C5  C2   N9   aromatic  1.324  0.020  1.324
 7C5  O4   C8   single    1.402  0.020  1.402
 7C5  O4   C16  single    1.429  0.020  1.429
 7C5  C8   C9   single    1.527  0.020  1.527
 7C5  C7   O5   single    1.427  0.020  1.427
 7C5  C7   C16  single    1.514  0.020  1.514
 7C5  C9   C10  single    1.532  0.020  1.532
 7C5  C9   O3   single    1.394  0.020  1.394
 7C5  C5   N9   aromatic  1.319  0.020  1.319
 7C5  C16  C10  single    1.524  0.020  1.524
 7C5  C10  O2   single    1.402  0.020  1.402
 7C5  N1   H1   single    0.860  0.020  1.020
 7C5  N1   H2   single    0.860  0.020  1.020
 7C5  C5   H3   single    0.930  0.020  1.080
 7C5  C7   H4   single    0.970  0.020  1.090
 7C5  C7   H5   single    0.970  0.020  1.090
 7C5  C8   H6   single    0.970  0.020  1.090
 7C5  C10  H7   single    0.970  0.020  1.090
 7C5  C13  H8   single    0.930  0.020  1.080
 7C5  C15  H9   single    0.930  0.020  1.080
 7C5  C9   H10  single    0.970  0.020  1.090
 7C5  O2   H11  single    0.850  0.020  0.980
 7C5  O3   H12  single    0.850  0.020  0.980
 7C5  N5   H13  single    0.860  0.020  1.020
 7C5  N5   H14  single    0.860  0.020  1.020
 7C5  C16  H16  single    0.970  0.020  1.090
 7C5  N8   H15  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
 7C5  H2   N1   H1   118.08  3.000
 7C5  H2   N1   C1   118.93  3.000
 7C5  H1   N1   C1   122.90  3.000
 7C5  C11  N3   C13  111.67  3.000
 7C5  N7   C4   O1   122.35  3.000
 7C5  N7   C4   C3   116.90  3.000
 7C5  O1   C4   C3   120.76  3.000
 7C5  H3   C5   N9   117.01  3.000
 7C5  H3   C5   C6   121.19  3.000
 7C5  N9   C5   C6   121.81  3.000
 7C5  N10  C6   C17  119.33  3.000
 7C5  C17  C6   C5   119.43  3.000
 7C5  N10  C6   C5   121.23  3.000
 7C5  H5   C7   H4   107.86  3.000
 7C5  H5   C7   O5   110.56  3.000
 7C5  H4   C7   O5   110.13  3.000
 7C5  H5   C7   C16  111.62  3.000
 7C5  H4   C7   C16  109.78  3.000
 7C5  O5   C7   C16  106.89  3.000
 7C5  H6   C8   O4   111.51  3.000
 7C5  H6   C8   N2   106.04  3.000
 7C5  O4   C8   N2   109.43  3.000
 7C5  H6   C8   C9   110.22  3.000
 7C5  O4   C8   C9   105.72  3.000
 7C5  N2   C8   C9   114.03  3.000
 7C5  H7   C10  C16  112.16  3.000
 7C5  H7   C10  O2   111.78  3.000
 7C5  C16  C10  O2   108.42  3.000
 7C5  H7   C10  C9   111.86  3.000
 7C5  O2   C10  C9   111.07  3.000
 7C5  C16  C10  C9   101.04  3.000
 7C5  H8   C13  N4   115.46  3.000
 7C5  H8   C13  N3   116.10  3.000
 7C5  N4   C13  N3   128.44  3.000
 7C5  H9   C15  N6   124.60  3.000
 7C5  H9   C15  N2   122.00  3.000
 7C5  N6   C15  N2   113.40  3.000
 7C5  O6   C17  O5   124.80  3.000
 7C5  O5   C17  C6   112.31  3.000
 7C5  O6   C17  C6   122.89  3.000
 7C5  N8   C1   N7   123.75  3.000
 7C5  N8   C1   N1   116.54  3.000
 7C5  N7   C1   N1   119.71  3.000
 7C5  N9   C2   N8   118.82  3.000
 7C5  N9   C2   C3   122.63  3.000
 7C5  N8   C2   C3   118.55  3.000
 7C5  N10  C3   C2   120.30  3.000
 7C5  C2   C3   C4   119.08  3.000
 7C5  N10  C3   C4   120.62  3.000
 7C5  H10  C9   O3   111.53  3.000
 7C5  H10  C9   C10  108.94  3.000
 7C5  O3   C9   C10  115.14  3.000
 7C5  H10  C9   C8   109.71  3.000
 7C5  O3   C9   C8   109.90  3.000
 7C5  C10  C9   C8   101.09  3.000
 7C5  H11  O2   C10  108.00  3.000
 7C5  H12  O3   C9   108.89  3.000
 7C5  N2   C11  C12  105.17  3.000
 7C5  N2   C11  N3   128.29  3.000
 7C5  C12  C11  N3   126.55  3.000
 7C5  N6   C12  C14  132.89  3.000
 7C5  C14  C12  C11  116.29  3.000
 7C5  N6   C12  C11  110.82  3.000
 7C5  N5   C14  N4   119.34  3.000
 7C5  N4   C14  C12  117.88  3.000
 7C5  N5   C14  C12  122.79  3.000
 7C5  C11  N2   C15  106.18  3.000
 7C5  C11  N2   C8   126.30  3.000
 7C5  C15  N2   C8   127.50  3.000
 7C5  C14  N4   C13  119.18  3.000
 7C5  H14  N5   H13  118.42  3.000
 7C5  H14  N5   C14  120.34  3.000
 7C5  H13  N5   C14  121.21  3.000
 7C5  C12  N6   C15  104.43  3.000
 7C5  C1   N7   C4   121.33  3.000
 7C5  H15  N8   C2   118.51  3.000
 7C5  H15  N8   C1   121.10  3.000
 7C5  C2   N8   C1   120.39  3.000
 7C5  C2   N9   C5   116.21  3.000
 7C5  C3   N10  C6   117.82  3.000
 7C5  H16  C16  O4   108.68  3.000
 7C5  H16  C16  C10  110.72  3.000
 7C5  O4   C16  C10  106.09  3.000
 7C5  H16  C16  C7   109.22  3.000
 7C5  C10  C16  C7   111.85  3.000
 7C5  O4   C16  C7   110.20  3.000
 7C5  C16  O4   C8   110.74  3.000
 7C5  C17  O5   C7   117.77  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
 7C5  CONST_01  N6   C12  C11  N3    180.00   0.0  0
 7C5  CONST_02  C14  C12  C11  N3      0.00   0.0  0
 7C5  CONST_03  C15  N2   C11  N3    180.00   0.0  0
 7C5  CONST_04  C14  N4   C13  N3      0.00   0.0  0
 7C5  CONST_05  C3   N10  C6   C5      0.00   0.0  0
 7C5  CONST_06  C3   C2   N9   C5      0.00   0.0  0
 7C5  CONST_07  C2   C3   N10  C6      0.00   0.0  0
 7C5  CONST_08  C2   N9   C5   C6      0.00   0.0  0
 7C5  CONST_09  C12  C14  N4   C13     0.00   0.0  0
 7C5  CONST_10  C12  C11  N3   C13     0.00   0.0  0
 7C5  CONST_11  N2   C11  N3   C13   180.00   0.0  0
 7C5  CONST_12  C14  C12  N6   C15   180.00   0.0  0
 7C5  CONST_13  C11  C12  N6   C15     0.00   0.0  0
 7C5  CONST_14  C12  C11  N2   C15     0.00   0.0  0
 7C5  CONST_15  N4   C14  C12  C11     0.00   0.0  0
 7C5  CONST_16  N6   C15  N2   C11     0.00   0.0  0
 7C5  CONST_17  N4   C13  N3   C11     0.00   0.0  0
 7C5  CONST_18  N2   C15  N6   C12     0.00   0.0  0
 7C5  CONST_19  N2   C11  C12  C14   180.00   0.0  0
 7C5  CONST_20  N6   C12  C11  N2      0.00   0.0  0
 7C5  CONST_21  N6   C12  C14  N4    180.00   0.0  0
 7C5  CONST_22  N10  C3   C2   N9      0.00   0.0  0
 7C5  CONST_23  N10  C6   C5   N9      0.00   0.0  0
 7C5  CONST_24  C8   N2   C11  N3      0.00   0.0  0
 7C5  CONST_25  N6   C15  N2   C8    180.00   0.0  0
 7C5  CONST_26  C12  C11  N2   C8    180.00   0.0  0
 7C5  CONST_27  N8   C1   N7   C4      0.00   0.0  0
 7C5  CONST_28  N7   C1   N8   C2      0.00   0.0  0
 7C5  CONST_29  N5   C14  N4   C13   180.00   0.0  0
 7C5  CONST_30  C3   N10  C6   C17   180.00   0.0  0
 7C5  CONST_31  N9   C5   C6   C17   180.00   0.0  0
 7C5  CONST_32  N5   C14  C12  C11   180.00   0.0  0
 7C5  CONST_33  N6   C12  C14  N5      0.00   0.0  0
 7C5  CONST_34  C4   N7   C1   N1    180.00   0.0  0
 7C5  CONST_35  C2   N8   C1   N1    180.00   0.0  0
 7C5  CONST_36  H9   C15  N2   C8      0.00   0.0  0
 7C5  CONST_37  H3   C5   N9   C2    180.00   0.0  0
 7C5  CONST_38  H8   C13  N3   C11   180.00   0.0  0
 7C5  CONST_39  H15  N8   C1   N7    180.00   0.0  0
 7C5  CONST_40  H13  N5   C14  C12     0.00   0.0  0
 7C5  CONST_41  H14  N5   C14  C12   180.00   0.0  0
 7C5  CONST_42  H1   N1   C1   N7    180.00   0.0  0
 7C5  CONST_43  H2   N1   C1   N7      0.00   0.0  0
 7C5  Var_01    O6   C17  C6   C5      3.34  30.0  2
 7C5  Var_02    C16  C7   O5   C17  -174.51  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
 7C5  chir_01  C8   N2  O4  C9   positiv
 7C5  chir_02  C10  O2  C9  C16  negativ
 7C5  chir_03  C9   O3  C8  C10  negativ
 7C5  chir_04  C16  O4  C7  C10  positiv

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
 7C5  plan-1  C6   0.020
 7C5  plan-1  C17  0.020
 7C5  plan-1  O5   0.020
 7C5  plan-1  O6   0.020
 7C5  plan-2  N3   0.020
 7C5  plan-2  C8   0.020
 7C5  plan-2  C13  0.020
 7C5  plan-2  C15  0.020
 7C5  plan-2  C11  0.020
 7C5  plan-2  C12  0.020
 7C5  plan-2  C14  0.020
 7C5  plan-2  N2   0.020
 7C5  plan-2  N4   0.020
 7C5  plan-2  N5   0.020
 7C5  plan-2  N6   0.020
 7C5  plan-2  H9   0.020
 7C5  plan-2  H8   0.020
 7C5  plan-3  N1   0.020
 7C5  plan-3  C4   0.020
 7C5  plan-3  C5   0.020
 7C5  plan-3  C6   0.020
 7C5  plan-3  C17  0.020
 7C5  plan-3  C1   0.020
 7C5  plan-3  C2   0.020
 7C5  plan-3  C3   0.020
 7C5  plan-3  N7   0.020
 7C5  plan-3  N8   0.020
 7C5  plan-3  N9   0.020
 7C5  plan-3  N10  0.020
 7C5  plan-3  H1   0.020
 7C5  plan-3  H2   0.020
 7C5  plan-3  H3   0.020
 7C5  plan-3  H15  0.020
 7C5  plan-3  O1   0.020
 7C5  plan-4  C14  0.020
 7C5  plan-4  N5   0.020
 7C5  plan-4  H13  0.020
 7C5  plan-4  H14  0.020

