# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:06:22 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: {(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(NC2CC2)c3ncn([C@@H]4C[C@H](CO)C=C4)c3n1
#
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
 1KX  1KX  {(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol  ligand  39  21  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1KX
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
 1KX  C     C  CH2   0  -0.515  -5.8495   1.8960   0.0888
 1KX  N     N  NH1   0  -0.664  -3.4642   1.2552   0.4206
 1KX  O     O  OH1   0  -0.672   6.6934   0.7104   0.4391
 1KX  C01   C  CR56  0   0.501  -0.2864  -0.3945  -0.0880
 1KX  N01   N  N     0  -0.515  -0.5910  -1.6884  -0.0826
 1KX  C02   C  CR56  0  -0.053  -1.1616   0.6667   0.0768
 1KX  N02   N  N     0  -0.455  -0.4951   1.8656   0.0105
 1KX  C03   C  CR15  0   0.095   0.7452   1.5309  -0.1894
 1KX  N03   N  NR5   0  -0.515   0.9386   0.1764  -0.2617
 1KX  C04   C  CH1   0  -0.134   2.1975  -0.5137  -0.4743
 1KX  N04   N  N     0  -0.520  -2.8494  -0.9649   0.2736
 1KX  C05   C  C1    0  -0.232   3.0237   0.1019  -1.5694
 1KX  N05   N  NH2   0  -0.825  -2.3236  -3.1815   0.0773
 1KX  C06   C  C1    0  -0.202   4.2999   0.2039  -1.2205
 1KX  C07   C  CH1   0  -0.308   4.5577  -0.3063   0.1704
 1KX  C08   C  CH2   0  -0.141   5.4140   0.6152   1.0208
 1KX  C09   C  CH2   0  -0.464   3.1400  -0.4814   0.7443
 1KX  C10   C  CR6   0   0.504  -2.5152   0.3202   0.2612
 1KX  C11   C  CR6   0   0.513  -1.8936  -1.8932   0.1004
 1KX  C12   C  CH1   0  -0.080  -4.8360   0.9523   0.6489
 1KX  C13   C  CH2   0  -0.479  -5.6876   0.5302  -0.5052
 1KX  H     H  HCH2  0   0.258  -6.7256   2.1022   0.6892
 1KX  HA    H  HCH2  0   0.257  -5.4891   2.7428  -0.4827
 1KX  HN    H  HNH1  0   0.401  -3.1609   2.2117   0.5093
 1KX  H03   H  HCR5  0   0.286   1.5675   2.2224  -0.2985
 1KX  H04   H  HCH1  0   0.283   1.9281  -1.5408  -0.7337
 1KX  H05   H  H     0   0.263   2.6018   0.3668  -2.5307
 1KX  HN05  H  HNH2  0   0.386  -1.6333  -3.8998   0.2148
 1KX  HN0A  H  HNH2  0   0.386  -3.2297  -3.3701   0.4702
 1KX  H06   H  H     0   0.256   5.0881   0.5708  -1.8654
 1KX  H07   H  HCH1  0   0.256   5.0621  -1.2785   0.1087
 1KX  H09   H  HCH2  0   0.248   2.8902   0.3791   1.3721
 1KX  H09A  H  HCH2  0   0.261   3.0425  -1.3690   1.3677
 1KX  H12   H  HCH1  0   0.262  -5.0606   0.5054   1.6129
 1KX  H13   H  HCH2  0   0.253  -6.4543  -0.2113  -0.3233
 1KX  H13A  H  HCH2  0   0.253  -5.2074   0.4552  -1.4720
 1KX  H16   H  HOH1  0   0.455   7.2068   1.3516   0.9379
 1KX  H08   H  HCH2  0   0.206   5.4636   0.2153   2.0428
 1KX  H18   H  HCH2  0   0.191   4.9220   1.5956   1.0857

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
 1KX  C    H     single    0.970  0.020  1.090
 1KX  C    HA    single    0.970  0.020  1.090
 1KX  N    HN    single    0.860  0.020  1.020
 1KX  C01  C02   aromatic  1.385  0.020  1.385
 1KX  N01  C01   aromatic  1.329  0.020  1.329
 1KX  N01  C11   aromatic  1.331  0.020  1.331
 1KX  C02  C10   aromatic  1.409  0.020  1.409
 1KX  C02  N02   aromatic  1.373  0.020  1.373
 1KX  C03  N02   aromatic  1.300  0.020  1.300
 1KX  C03  H03   single    0.930  0.020  1.080
 1KX  N03  C01   aromatic  1.363  0.020  1.363
 1KX  N03  C03   aromatic  1.370  0.020  1.370
 1KX  C04  N03   single    1.451  0.020  1.451
 1KX  C04  C09   single    1.541  0.020  1.541
 1KX  C04  H04   single    0.970  0.020  1.090
 1KX  N04  C10   aromatic  1.328  0.020  1.328
 1KX  C05  C04   single    1.504  0.020  1.504
 1KX  C05  C06   double    1.327  0.020  1.327
 1KX  C05  H05   single    0.930  0.020  1.080
 1KX  N05  C11   single    1.358  0.020  1.358
 1KX  N05  HN05  single    0.890  0.020  1.040
 1KX  N05  HN0A  single    0.890  0.020  1.040
 1KX  C06  C07   single    1.504  0.020  1.504
 1KX  C06  H06   single    0.930  0.020  1.080
 1KX  C07  C08   single    1.518  0.020  1.518
 1KX  C07  H07   single    0.970  0.020  1.090
 1KX  O    C08   single    1.409  0.020  1.409
 1KX  C09  C07   single    1.539  0.020  1.539
 1KX  C09  H09   single    0.970  0.020  1.090
 1KX  C09  H09A  single    0.970  0.020  1.090
 1KX  C10  N     single    1.342  0.020  1.342
 1KX  C11  N04   aromatic  1.344  0.020  1.344
 1KX  C12  C     single    1.494  0.020  1.494
 1KX  C12  N     single    1.423  0.020  1.423
 1KX  C12  C13   single    1.495  0.020  1.495
 1KX  C12  H12   single    0.970  0.020  1.090
 1KX  C13  C     single    1.498  0.020  1.498
 1KX  C13  H13   single    0.970  0.020  1.090
 1KX  C13  H13A  single    0.970  0.020  1.090
 1KX  O    H16   single    0.850  0.020  0.980
 1KX  C08  H08   single    0.970  0.020  1.090
 1KX  C08  H18   single    0.970  0.020  1.090

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
 1KX  HA    C    H     114.41  3.000
 1KX  HA    C    C13   117.87  3.000
 1KX  H     C    C13   118.77  3.000
 1KX  C13   C    C12    59.96  3.000
 1KX  HA    C    C12   117.77  3.000
 1KX  H     C    C12   117.50  3.000
 1KX  HN    N    C12   118.56  3.000
 1KX  C12   N    C10   123.54  3.000
 1KX  HN    N    C10   117.34  3.000
 1KX  H16   O    C08   108.42  3.000
 1KX  N03   C01  C02   105.20  3.000
 1KX  N03   C01  N01   127.90  3.000
 1KX  C02   C01  N01   126.90  3.000
 1KX  C11   N01  C01   111.99  3.000
 1KX  C10   C02  N02   133.40  3.000
 1KX  N02   C02  C01   110.88  3.000
 1KX  C10   C02  C01   115.72  3.000
 1KX  C03   N02  C02   104.22  3.000
 1KX  H03   C03  N03   121.34  3.000
 1KX  N03   C03  N02   113.41  3.000
 1KX  H03   C03  N02   125.25  3.000
 1KX  C04   N03  C03   126.89  3.000
 1KX  C04   N03  C01   126.82  3.000
 1KX  C03   N03  C01   106.29  3.000
 1KX  H04   C04  C09   110.99  3.000
 1KX  H04   C04  C05   110.32  3.000
 1KX  C09   C04  C05   103.38  3.000
 1KX  C05   C04  N03   112.87  3.000
 1KX  H04   C04  N03   105.53  3.000
 1KX  C09   C04  N03   113.88  3.000
 1KX  C11   N04  C10   119.23  3.000
 1KX  H05   C05  C06   126.11  3.000
 1KX  H05   C05  C04   122.19  3.000
 1KX  C06   C05  C04   111.62  3.000
 1KX  HN0A  N05  HN05  115.55  3.000
 1KX  HN0A  N05  C11   117.16  3.000
 1KX  HN05  N05  C11   117.24  3.000
 1KX  H06   C06  C07   122.76  3.000
 1KX  H06   C06  C05   124.73  3.000
 1KX  C07   C06  C05   112.46  3.000
 1KX  H07   C07  C09   110.10  3.000
 1KX  C09   C07  C08   112.31  3.000
 1KX  H07   C07  C08   108.06  3.000
 1KX  C09   C07  C06   103.03  3.000
 1KX  H07   C07  C06   109.12  3.000
 1KX  C08   C07  C06   114.13  3.000
 1KX  H18   C08  H08   106.87  3.000
 1KX  H18   C08  C07   108.78  3.000
 1KX  H08   C08  C07   109.00  3.000
 1KX  H18   C08  O     111.76  3.000
 1KX  H08   C08  O     111.58  3.000
 1KX  C07   C08  O     108.78  3.000
 1KX  H09A  C09  H09   106.98  3.000
 1KX  H09A  C09  C07   112.86  3.000
 1KX  H09   C09  C07   109.56  3.000
 1KX  H09A  C09  C04   112.39  3.000
 1KX  H09   C09  C04   109.31  3.000
 1KX  C07   C09  C04   105.72  3.000
 1KX  N04   C10  C02   118.74  3.000
 1KX  N04   C10  N     119.69  3.000
 1KX  C02   C10  N     121.57  3.000
 1KX  N05   C11  N04   115.61  3.000
 1KX  N04   C11  N01   127.41  3.000
 1KX  N05   C11  N01   116.96  3.000
 1KX  H12   C12  C13   116.82  3.000
 1KX  H12   C12  N     115.42  3.000
 1KX  C13   C12  N     119.03  3.000
 1KX  H12   C12  C     116.90  3.000
 1KX  C13   C12  C      60.17  3.000
 1KX  N     C12  C     117.35  3.000
 1KX  H13A  C13  H13   114.66  3.000
 1KX  H13A  C13  C12   117.15  3.000
 1KX  H13   C13  C12   117.86  3.000
 1KX  H13A  C13  C     117.74  3.000
 1KX  H13   C13  C     118.78  3.000
 1KX  C12   C13  C      59.87  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
 1KX  CONST_01  N04  C10  C02  C01     0.00   0.0  0
 1KX  CONST_02  C03  N02  C02  C01     0.00   0.0  0
 1KX  CONST_03  N04  C11  N01  C01     0.00   0.0  0
 1KX  CONST_04  N02  C03  N03  C01     0.00   0.0  0
 1KX  CONST_05  C10  C02  C01  N01     0.00   0.0  0
 1KX  CONST_06  N02  C02  C01  N01   180.00   0.0  0
 1KX  CONST_07  C03  N03  C01  N01   180.00   0.0  0
 1KX  CONST_08  C10  N04  C11  N01     0.00   0.0  0
 1KX  CONST_09  C11  N01  C01  C02     0.00   0.0  0
 1KX  CONST_10  C03  N03  C01  C02     0.00   0.0  0
 1KX  CONST_11  C11  N04  C10  C02     0.00   0.0  0
 1KX  CONST_12  N03  C03  N02  C02     0.00   0.0  0
 1KX  CONST_13  N03  C01  C02  N02     0.00   0.0  0
 1KX  CONST_14  N04  C10  C02  N02   180.00   0.0  0
 1KX  CONST_15  C10  C02  N02  C03   180.00   0.0  0
 1KX  CONST_16  C10  C02  C01  N03   180.00   0.0  0
 1KX  CONST_17  C11  N01  C01  N03   180.00   0.0  0
 1KX  CONST_18  C04  N03  C01  N01     0.00   0.0  0
 1KX  CONST_19  C04  N03  C01  C02   180.00   0.0  0
 1KX  CONST_20  C04  N03  C03  N02   180.00   0.0  0
 1KX  CONST_21  C01  C02  C10  N     180.00   0.0  0
 1KX  CONST_22  N02  C02  C10  N       0.00   0.0  0
 1KX  CONST_23  C11  N04  C10  N     180.00   0.0  0
 1KX  CONST_24  N05  C11  N01  C01   180.00   0.0  0
 1KX  CONST_25  C10  N04  C11  N05   180.00   0.0  0
 1KX  CONST_26  C12  N    C10  C02   180.00   0.0  0
 1KX  CONST_27  C12  N    C10  N04     0.00   0.0  0
 1KX  CONST_28  H03  C03  N03  C01   180.00   0.0  0
 1KX  CONST_31  HN   N    C10  C02     0.00   0.0  0
 1KX  Var_01    C07  C06  C05  C04    -0.69  30.0  1
 1KX  Var_02    C10  N    C12  C    -147.12  30.0  3
 1KX  Var_03    N    C12  C13  C    -106.70  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
 1KX  chir_01  C04  N03  C09  C05  positiv
 1KX  chir_02  C07  C06  C08  C09  negativ
 1KX  chir_03  C12  C    N    C13  both

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
 1KX  plan-1  N     0.020
 1KX  plan-1  C10   0.020
 1KX  plan-1  C12   0.020
 1KX  plan-1  HN    0.020
 1KX  plan-2  N     0.020
 1KX  plan-2  C01   0.020
 1KX  plan-2  N01   0.020
 1KX  plan-2  C02   0.020
 1KX  plan-2  N02   0.020
 1KX  plan-2  C03   0.020
 1KX  plan-2  N03   0.020
 1KX  plan-2  C04   0.020
 1KX  plan-2  N04   0.020
 1KX  plan-2  N05   0.020
 1KX  plan-2  C10   0.020
 1KX  plan-2  C11   0.020
 1KX  plan-2  H03   0.020
 1KX  plan-3  N05   0.020
 1KX  plan-3  C11   0.020
 1KX  plan-3  HN05  0.020
 1KX  plan-3  HN0A  0.020

