# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:56:58 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,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]1N=C(N)N2CCC(O)(O)[C@@]23N=C(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
 9SL  9SL  '[(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate'  ligand  38  21  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9SL
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
 9SL  C10  C  CR5   0   0.228   1.2908  -0.4048  -0.0492
 9SL  C20  C  CH2   0  -0.257   0.7690  -1.2118  -2.2553
 9SL  O01  O  O     0  -0.524  -4.3163  -0.9824   0.8348
 9SL  C02  C  C     0   0.711  -4.1866   0.2209   0.7231
 9SL  O03  O  O2    0  -0.475  -3.0132   0.8540   0.7717
 9SL  C04  C  CH2   0  -0.139  -1.8447   0.0576   0.9544
 9SL  C05  C  CH1   0  -0.198  -0.6430   0.9933   0.8609
 9SL  N06  N  N     0  -0.491  -0.5964   1.6707  -0.4135
 9SL  C07  C  C     0   0.597  -0.1753   0.9541  -1.3970
 9SL  N08  N  NH2   0  -0.840  -0.4077   1.3422  -2.6891
 9SL  N09  N  NT    0  -0.503   0.4559  -0.2379  -1.2228
 9SL  N11  N  N     0  -0.479   2.5590   0.2635  -0.2254
 9SL  C12  C  CR5   0   0.606   2.6756   1.1103   0.7328
 9SL  N13  N  NR15  0  -0.665   1.6989   1.0813   1.6926
 9SL  C14  C  CR15  0  -0.084   0.6367   0.2147   1.2140
 9SL  N15  N  NH2   0  -0.844   3.6793   2.0172   0.8428
 9SL  C16  C  CT    0   0.468   1.4700  -1.9335  -0.0575
 9SL  O17  O  OH1   0  -0.662   2.5231  -2.2811   0.7738
 9SL  O18  O  OH1   0  -0.661   0.2590  -2.4840   0.3774
 9SL  C19  C  CH2   0  -0.555   1.6943  -2.2086  -1.5456
 9SL  N21  N  NH2   0  -0.832  -5.1941   1.0867   0.5128
 9SL  H1   H  HCH2  0   0.243  -0.1456  -1.6845  -2.6175
 9SL  H2   H  HCH2  0   0.231   1.2800  -0.7778  -3.1188
 9SL  H3   H  HCH2  0   0.225  -1.8712  -0.4229   1.9368
 9SL  H4   H  HCH2  0   0.235  -1.7898  -0.7260   0.1978
 9SL  H5   H  HCH1  0   0.239  -0.7762   1.7530   1.6409
 9SL  H6   H  HNH2  0   0.381  -0.8097   2.2629  -2.7685
 9SL  H7   H  HNH2  0   0.381   0.3230   1.1756  -3.3633
 9SL  H9   H  HCR5  0   0.256   0.4155  -0.5447   1.9686
 9SL  H10  H  HNH2  0   0.390   4.4936   1.8320   0.2805
 9SL  H11  H  HNH2  0   0.391   3.8939   2.3579   1.7656
 9SL  H12  H  HOH1  0   0.454   2.7384  -3.2121   0.6469
 9SL  H13  H  HOH1  0   0.455   0.1758  -3.3864   0.0493
 9SL  H14  H  HCH2  0   0.263   1.4813  -3.2433  -1.8239
 9SL  H15  H  HCH2  0   0.258   2.7341  -2.0036  -1.7982
 9SL  H16  H  HNH2  0   0.405  -6.1414   0.7561   0.5671
 9SL  H17  H  HNH2  0   0.403  -5.0464   2.0808   0.5375
 9SL  H8   H  HNR5  0   0.386   1.4494   1.9397   2.1620

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
 9SL  N13  C12  single  1.370  0.020  1.370
 9SL  N13  C14  single  1.452  0.020  1.452
 9SL  N15  C12  single  1.357  0.020  1.357
 9SL  C04  C05  single  1.526  0.020  1.526
 9SL  C04  O03  single  1.426  0.020  1.426
 9SL  C12  N11  double  1.284  0.020  1.284
 9SL  C14  C05  single  1.539  0.020  1.539
 9SL  C14  C10  single  1.551  0.020  1.551
 9SL  O01  C02  double  1.215  0.020  1.215
 9SL  C05  N06  single  1.444  0.020  1.444
 9SL  O03  C02  single  1.334  0.020  1.334
 9SL  C02  N21  single  1.345  0.020  1.345
 9SL  O17  C16  single  1.386  0.020  1.386
 9SL  N11  C10  single  1.444  0.020  1.444
 9SL  C10  C16  single  1.539  0.020  1.539
 9SL  C10  N09  single  1.450  0.020  1.450
 9SL  N06  C07  double  1.288  0.020  1.288
 9SL  O18  C16  single  1.399  0.020  1.399
 9SL  C16  C19  single  1.530  0.020  1.530
 9SL  N09  C07  single  1.360  0.020  1.360
 9SL  N09  C20  single  1.453  0.020  1.453
 9SL  C07  N08  single  1.369  0.020  1.369
 9SL  C19  C20  single  1.534  0.020  1.534
 9SL  C20  H1   single  0.970  0.020  1.090
 9SL  C20  H2   single  0.970  0.020  1.090
 9SL  C04  H3   single  0.970  0.020  1.090
 9SL  C04  H4   single  0.970  0.020  1.090
 9SL  C05  H5   single  0.970  0.020  1.090
 9SL  N08  H6   single  0.890  0.020  1.040
 9SL  N08  H7   single  0.890  0.020  1.040
 9SL  C14  H9   single  0.970  0.020  1.090
 9SL  N15  H10  single  0.890  0.020  1.040
 9SL  N15  H11  single  0.890  0.020  1.040
 9SL  O17  H12  single  0.850  0.020  0.980
 9SL  O18  H13  single  0.850  0.020  0.980
 9SL  C19  H14  single  0.970  0.020  1.090
 9SL  C19  H15  single  0.970  0.020  1.090
 9SL  N21  H16  single  0.860  0.020  1.020
 9SL  N21  H17  single  0.860  0.020  1.020
 9SL  N13  H8   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
 9SL  C16  C10  C14  116.74  3.000
 9SL  C16  C10  N11  110.89  3.000
 9SL  C14  C10  N11  106.54  3.000
 9SL  C16  C10  N09  100.19  3.000
 9SL  N11  C10  N09  110.71  3.000
 9SL  C14  C10  N09  111.74  3.000
 9SL  H2   C20  H1   107.55  3.000
 9SL  H2   C20  C19  109.97  3.000
 9SL  H1   C20  C19  112.18  3.000
 9SL  H2   C20  N09  113.32  3.000
 9SL  H1   C20  N09  110.20  3.000
 9SL  C19  C20  N09  103.69  3.000
 9SL  N21  C02  O03  111.04  3.000
 9SL  N21  C02  O01  124.87  3.000
 9SL  O03  C02  O01  124.08  3.000
 9SL  C04  O03  C02  117.41  3.000
 9SL  H4   C04  H3   107.98  3.000
 9SL  H4   C04  C05  111.01  3.000
 9SL  H3   C04  C05  110.09  3.000
 9SL  H4   C04  O03  110.71  3.000
 9SL  H3   C04  O03  109.91  3.000
 9SL  C05  C04  O03  107.16  3.000
 9SL  H5   C05  C14  106.76  3.000
 9SL  H5   C05  N06  107.85  3.000
 9SL  C14  C05  N06  114.39  3.000
 9SL  H5   C05  C04  106.59  3.000
 9SL  N06  C05  C04  111.54  3.000
 9SL  C14  C05  C04  109.30  3.000
 9SL  C07  N06  C05  115.06  3.000
 9SL  N09  C07  N08  116.63  3.000
 9SL  N08  C07  N06  120.51  3.000
 9SL  N09  C07  N06  122.79  3.000
 9SL  H7   N08  H6   112.80  3.000
 9SL  H7   N08  C07  117.47  3.000
 9SL  H6   N08  C07  113.65  3.000
 9SL  C07  N09  C20  126.60  3.000
 9SL  C20  N09  C10  111.95  3.000
 9SL  C07  N09  C10  118.15  3.000
 9SL  C12  N11  C10  107.09  3.000
 9SL  N15  C12  N13  118.99  3.000
 9SL  N15  C12  N11  124.63  3.000
 9SL  N13  C12  N11  116.37  3.000
 9SL  H8   N13  C14  118.68  3.000
 9SL  H8   N13  C12  118.95  3.000
 9SL  C14  N13  C12  107.65  3.000
 9SL  H9   C14  N13  109.58  3.000
 9SL  H9   C14  C05  109.97  3.000
 9SL  N13  C14  C05  112.45  3.000
 9SL  H9   C14  C10  111.71  3.000
 9SL  C05  C14  C10  111.45  3.000
 9SL  N13  C14  C10  101.44  3.000
 9SL  H11  N15  H10  113.69  3.000
 9SL  H11  N15  C12  117.26  3.000
 9SL  H10  N15  C12  115.46  3.000
 9SL  C19  C16  O18  111.01  3.000
 9SL  C19  C16  O17  115.27  3.000
 9SL  O18  C16  O17  111.87  3.000
 9SL  C19  C16  C10  101.59  3.000
 9SL  O18  C16  C10  106.75  3.000
 9SL  O17  C16  C10  109.53  3.000
 9SL  H12  O17  C16  109.45  3.000
 9SL  H13  O18  C16  109.71  3.000
 9SL  H15  C19  H14  107.78  3.000
 9SL  H15  C19  C16  109.37  3.000
 9SL  H14  C19  C16  112.92  3.000
 9SL  H15  C19  C20  110.25  3.000
 9SL  H14  C19  C20  112.34  3.000
 9SL  C16  C19  C20  104.17  3.000
 9SL  H17  N21  H16  117.55  3.000
 9SL  H17  N21  C02  121.51  3.000
 9SL  H16  N21  C02  119.08  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
 9SL  CONST_01  N13  C12  N11  C10     0.00   0.0  0
 9SL  CONST_03  N06  C07  N09  C20   180.00   0.0  0
 9SL  CONST_04  N09  C07  N06  C05     0.00   0.0  0
 9SL  CONST_05  C14  N13  C12  N11     0.00   0.0  0
 9SL  CONST_06  N15  C12  N11  C10   180.00   0.0  0
 9SL  CONST_08  N08  C07  N09  C20     0.00   0.0  0
 9SL  CONST_10  N15  C12  N13  C14   180.00   0.0  0
 9SL  CONST_12  H6   N08  C07  N06     0.00   0.0  0
 9SL  Var_01    C20  C19  C16  C10   -36.63  30.0  1
 9SL  Var_02    C19  C20  N09  C10    10.86  30.0  1
 9SL  Var_03    C16  C19  C20  N09    16.98  30.0  1
 9SL  Var_04    C05  C04  O03  C02   175.47  30.0  1
 9SL  Var_05    N21  C02  O03  C04  -178.38  30.0  3
 9SL  Var_06    H16  N21  C02  O01     8.48  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
 9SL  chir_01  C10  N11  C16  N09  positiv
 9SL  chir_02  C05  N06  C14  C04  positiv
 9SL  chir_03  C14  N13  C10  C05  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
 9SL  plan-1  C10  0.020
 9SL  plan-1  C20  0.020
 9SL  plan-1  C05  0.020
 9SL  plan-1  N06  0.020
 9SL  plan-1  C07  0.020
 9SL  plan-1  N08  0.020
 9SL  plan-1  N09  0.020
 9SL  plan-1  H6   0.020
 9SL  plan-1  H7   0.020
 9SL  plan-2  C10  0.020
 9SL  plan-2  N11  0.020
 9SL  plan-2  C12  0.020
 9SL  plan-2  N13  0.020
 9SL  plan-2  C14  0.020
 9SL  plan-2  N15  0.020
 9SL  plan-2  H10  0.020
 9SL  plan-2  H11  0.020
 9SL  plan-2  H8   0.020
 9SL  plan-3  O01  0.020
 9SL  plan-3  C02  0.020
 9SL  plan-3  O03  0.020
 9SL  plan-3  N21  0.020

