# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:25:20 2021
#   Inital geometry file: a 90 line input string
#   Ligand name: [(2Z,3aS,4R,6Z,10aR)-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)OC[C@@H]1NC(=N)N2CCC[C@@]23NC(=N)N[C@@H]13
#
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
 U5A  U5A  '[(2Z,3aS,4R,6Z,10aR)-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate'  ligand  36  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U5A
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
 U5A  N    N  NH2   0  -0.828  -27.0406  -29.8673  70.8682
 U5A  C    C  C     0   0.714  -28.2163  -29.7096  70.2418
 U5A  O    O  O     0  -0.517  -29.1114  -30.5301  70.2142
 U5A  C5   C  CH2   0  -0.519  -30.1243  -24.7010  65.5974
 U5A  N4   N  NR15  0  -0.657  -30.2343  -27.5581  64.5227
 U5A  N3   N  NR5   0  -0.501  -28.9007  -26.5882  66.2800
 U5A  C2   C  CH1   0  -0.166  -29.4806  -28.8713  67.5194
 U5A  O1   O  O2    0  -0.480  -28.2739  -28.5195  69.6264
 U5A  C6   C  CH2   0  -0.433  -31.0503  -25.8108  66.0907
 U5A  C7   C  C     0   0.310  -30.2068  -27.0682  65.8890
 U5A  C8   C  CR5   0   0.565  -30.9204  -28.7391  64.4044
 U5A  C9   C  CR15  0  -0.044  -30.6465  -28.3193  66.6942
 U5A  C1   C  CH2   0  -0.181  -29.4523  -28.2024  68.8968
 U5A  C3   C  C     0   0.574  -27.8467  -27.4394  66.4458
 U5A  C4   C  CH2   0  -0.237  -28.7208  -25.1739  66.0000
 U5A  N1   N  NH1   0  -0.651  -28.2547  -28.7167  66.7645
 U5A  N2   N  N     0  -0.711  -26.6415  -27.0300  66.3074
 U5A  N5   N  N     0  -0.722  -31.2921  -29.2307  63.2838
 U5A  N6   N  NR15  0  -0.679  -31.0672  -29.2308  65.6660
 U5A  H1   H  HNH2  0   0.409  -26.8977  -30.6798  71.4422
 U5A  H2   H  HNH2  0   0.407  -26.3814  -29.1129  70.9548
 U5A  H4   H  HCH2  0   0.243  -30.1957  -24.5969  64.5128
 U5A  H5   H  HCH1  0   0.285  -29.6431  -29.9409  67.6562
 U5A  H6   H  HCH2  0   0.247  -31.2631  -25.6861  67.1551
 U5A  H7   H  HCH2  0   0.257  -32.0004  -25.8626  65.5597
 U5A  H8   H  HCR5  0   0.274  -31.4789  -28.0734  67.3617
 U5A  H9   H  HCH2  0   0.257  -29.4365  -27.1168  68.8014
 U5A  H10  H  HCH2  0   0.251  -30.3487  -28.4792  69.4560
 U5A  H11  H  HCH2  0   0.235  -27.9913  -25.0077  65.2053
 U5A  H12  H  HCH2  0   0.234  -28.3546  -24.6600  66.8915
 U5A  H13  H  H     0   0.318  -25.9860  -27.7618  66.5589
 U5A  H15  H  H     0   0.318  -31.7633  -30.1165  63.4242
 U5A  H17  H  HNR5  0   0.397  -31.6499  -30.0255  65.8644
 U5A  H18  H  HNR5  0   0.385  -30.2971  -26.9028  63.7591
 U5A  H19  H  HNH1  0   0.386  -27.5087  -29.3492  67.0078
 U5A  H3   H  HCH2  0   0.262  -30.3709  -23.7312  66.0261

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
 U5A  N5  C8   double  1.279  0.020  1.279
 U5A  C8  N4   single  1.371  0.020  1.371
 U5A  C8  N6   single  1.362  0.020  1.362
 U5A  N4  C7   single  1.452  0.020  1.452
 U5A  C5  C4   single  1.535  0.020  1.535
 U5A  C5  C6   single  1.527  0.020  1.527
 U5A  N6  C9   single  1.437  0.020  1.437
 U5A  C4  N3   single  1.453  0.020  1.453
 U5A  C7  C6   single  1.527  0.020  1.527
 U5A  C7  N3   single  1.445  0.020  1.445
 U5A  C7  C9   single  1.551  0.020  1.551
 U5A  N2  C3   double  1.280  0.020  1.280
 U5A  N3  C3   single  1.365  0.020  1.365
 U5A  C3  N1   single  1.378  0.020  1.378
 U5A  C9  C2   single  1.531  0.020  1.531
 U5A  N1  C2   single  1.448  0.020  1.448
 U5A  C2  C1   single  1.531  0.020  1.531
 U5A  C1  O1   single  1.422  0.020  1.422
 U5A  O1  C    single  1.341  0.020  1.341
 U5A  C   O    double  1.215  0.020  1.215
 U5A  C   N    single  1.342  0.020  1.342
 U5A  N   H1   single  0.860  0.020  1.020
 U5A  N   H2   single  0.860  0.020  1.020
 U5A  C5  H3   single  0.970  0.020  1.090
 U5A  C5  H4   single  0.970  0.020  1.090
 U5A  C2  H5   single  0.970  0.020  1.090
 U5A  C6  H6   single  0.970  0.020  1.090
 U5A  C6  H7   single  0.970  0.020  1.090
 U5A  C9  H8   single  0.970  0.020  1.090
 U5A  C1  H9   single  0.970  0.020  1.090
 U5A  C1  H10  single  0.970  0.020  1.090
 U5A  C4  H11  single  0.970  0.020  1.090
 U5A  C4  H12  single  0.970  0.020  1.090
 U5A  N2  H13  single  0.890  0.020  1.040
 U5A  N5  H15  single  0.890  0.020  1.040
 U5A  N6  H17  single  0.860  0.020  1.020
 U5A  N4  H18  single  0.890  0.020  1.040
 U5A  N1  H19  single  0.890  0.020  1.040

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
 U5A  H2   N   H1   117.66  3.000
 U5A  H2   N   C    121.77  3.000
 U5A  H1   N   C    119.10  3.000
 U5A  O1   C   O    123.88  3.000
 U5A  O    C   N    125.24  3.000
 U5A  O1   C   N    110.87  3.000
 U5A  H4   C5  H3   106.95  3.000
 U5A  H4   C5  C4   110.47  3.000
 U5A  H3   C5  C4   112.23  3.000
 U5A  H4   C5  C6   110.51  3.000
 U5A  H3   C5  C6   112.51  3.000
 U5A  C4   C5  C6   104.22  3.000
 U5A  H18  N4  C8   117.61  3.000
 U5A  H18  N4  C7   119.65  3.000
 U5A  C8   N4  C7   112.42  3.000
 U5A  C4   N3  C3   122.33  3.000
 U5A  C3   N3  C7   121.57  3.000
 U5A  C4   N3  C7   112.52  3.000
 U5A  H5   C2  N1   107.23  3.000
 U5A  H5   C2  C1   108.57  3.000
 U5A  N1   C2  C1   113.99  3.000
 U5A  H5   C2  C9   107.92  3.000
 U5A  C1   C2  C9   109.96  3.000
 U5A  N1   C2  C9   108.97  3.000
 U5A  C1   O1  C    117.97  3.000
 U5A  H7   C6  H6   108.08  3.000
 U5A  H7   C6  C7   112.21  3.000
 U5A  H6   C6  C7   109.28  3.000
 U5A  H7   C6  C5   113.94  3.000
 U5A  H6   C6  C5   110.48  3.000
 U5A  C7   C6  C5   102.75  3.000
 U5A  C9   C7  C6   116.03  3.000
 U5A  C9   C7  N3   112.55  3.000
 U5A  C6   C7  N3   100.94  3.000
 U5A  C9   C7  N4   102.18  3.000
 U5A  N3   C7  N4   112.57  3.000
 U5A  C6   C7  N4   113.06  3.000
 U5A  N6   C8  N5   129.91  3.000
 U5A  N6   C8  N4   106.56  3.000
 U5A  N5   C8  N4   123.51  3.000
 U5A  H8   C9  N6   110.86  3.000
 U5A  H8   C9  C7   110.53  3.000
 U5A  N6   C9  C7   102.89  3.000
 U5A  H8   C9  C2   109.34  3.000
 U5A  C7   C9  C2   110.77  3.000
 U5A  N6   C9  C2   112.32  3.000
 U5A  H10  C1  H9   108.01  3.000
 U5A  H10  C1  O1   111.16  3.000
 U5A  H9   C1  O1   104.78  3.000
 U5A  H10  C1  C2   109.55  3.000
 U5A  H9   C1  C2   110.89  3.000
 U5A  O1   C1  C2   112.30  3.000
 U5A  N2   C3  N1   126.87  3.000
 U5A  N1   C3  N3   112.17  3.000
 U5A  N2   C3  N3   120.96  3.000
 U5A  H12  C4  H11  107.37  3.000
 U5A  H12  C4  N3   110.01  3.000
 U5A  H11  C4  N3   111.80  3.000
 U5A  H12  C4  C5   112.07  3.000
 U5A  H11  C4  C5   111.91  3.000
 U5A  N3   C4  C5   103.73  3.000
 U5A  H19  N1  C3   114.73  3.000
 U5A  H19  N1  C2   115.71  3.000
 U5A  C3   N1  C2   118.04  3.000
 U5A  H13  N2  C3   110.54  3.000
 U5A  H15  N5  C8   110.48  3.000
 U5A  H17  N6  C9   122.00  3.000
 U5A  H17  N6  C8   122.05  3.000
 U5A  C9   N6  C8   113.72  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
 U5A  CONST_01  C9   N6  C8  N4    0.00   0.0  0
 U5A  CONST_03  N6   C8  N4  C7    0.00   0.0  0
 U5A  CONST_05  N1   C3  N3  C4  180.00   0.0  0
 U5A  CONST_07  N5   C8  N4  C7  180.00   0.0  0
 U5A  CONST_09  N5   C8  N6  C9  180.00   0.0  0
 U5A  CONST_10  N2   C3  N3  C4    0.00   0.0  0
 U5A  CONST_11  H17  N6  C8  N4  180.00   0.0  0
 U5A  CONST_12  H19  N1  C3  N3  180.00   0.0  0
 U5A  CONST_14  H15  N5  C8  N4  180.00   0.0  0
 U5A  CONST_15  H13  N2  C3  N3  180.00   0.0  0
 U5A  Var_01    C7   N3  C4  C5    9.19  30.0  1
 U5A  Var_02    C6   C5  C4  N3   16.47  30.0  1
 U5A  Var_03    C4   C5  C6  C7  -34.60  30.0  1
 U5A  Var_04    C2   C1  O1  C   -79.27  30.0  1
 U5A  Var_05    H1   N   C   O    -6.46  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
 U5A  chir_01  C2  C9  N1  C1  negativ
 U5A  chir_02  C7  N4  C9  C6  positiv
 U5A  chir_03  C9  N6  C2  C7  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
 U5A  plan-1  N    0.020
 U5A  plan-1  C    0.020
 U5A  plan-1  O    0.020
 U5A  plan-1  O1   0.020
 U5A  plan-2  N4   0.020
 U5A  plan-2  C7   0.020
 U5A  plan-2  C8   0.020
 U5A  plan-2  C9   0.020
 U5A  plan-2  N5   0.020
 U5A  plan-2  N6   0.020
 U5A  plan-2  H15  0.020
 U5A  plan-2  H17  0.020
 U5A  plan-2  H18  0.020
 U5A  plan-3  N3   0.020
 U5A  plan-3  C2   0.020
 U5A  plan-3  C7   0.020
 U5A  plan-3  C3   0.020
 U5A  plan-3  C4   0.020
 U5A  plan-3  N1   0.020
 U5A  plan-3  N2   0.020
 U5A  plan-3  H13  0.020
 U5A  plan-3  H19  0.020

