# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 21:27:22 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (7S)-7-(dimethylaminomethyl)-1-[3-(dimethylamino)propyl]-7,8-dihydrofuro[3,2-e]benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCn1c(N)nc2ccc3O[C@H](CN(C)C)Cc3c12
#
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
 ISI  ISI  (7S)-7-(dimethylaminomethyl)-1-[3-(dimethylamino)propyl]-7,8-dihydrofuro[3,2-e]benzimidazol-2-amine  ligand  50  23  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ISI
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
 ISI  C1    C  CR16  0  -0.382   1.8992  -2.8478  -0.7932
 ISI  NP1   N  NH2   0  -0.859  -3.6952  -2.5793   0.8487
 ISI  C2    C  CR16  0  -0.349   0.7314  -3.5971  -0.6662
 ISI  NP2   N  NT    0  -0.407  -3.6583   3.0391  -0.6250
 ISI  C3    C  CR56  0   0.124  -0.4250  -2.9824  -0.2009
 ISI  NP3   N  NT    0  -0.415   4.6872   1.8654  -0.1412
 ISI  C4    C  CR56  0   0.303  -0.4081  -1.6176   0.1483
 ISI  C5    C  CR56  0  -0.071   0.7357  -0.8546   0.0224
 ISI  C6    C  CR56  0   0.390   1.8700  -1.5027  -0.4435
 ISI  N7    N  N     0  -0.522  -1.6883  -3.5020  -0.0033
 ISI  C8    C  CR5   0   0.598  -2.3949  -2.5041   0.4535
 ISI  N9    N  NR5   0  -0.567  -1.6824  -1.3413   0.5870
 ISI  C10   C  CH2   0  -0.529   1.0969   0.5656   0.3305
 ISI  C11   C  CR15  0   0.043   2.4895   0.6765  -0.3225
 ISI  O12   O  O     0  -0.507   2.9437  -0.6767  -0.5173
 ISI  CA1   C  CH2   0  -0.344  -2.1842  -0.0623   1.0377
 ISI  CA2   C  CH2   0  -0.297   3.4553   1.4844   0.5207
 ISI  CB1   C  CH2   0  -0.462  -2.7378   0.7904  -0.0978
 ISI  CD1   C  CH3   0  -0.528  -4.9158   2.6051  -1.1962
 ISI  CE1   C  CH3   0  -0.521  -3.7682   4.3961  -0.1327
 ISI  CG1   C  CH2   0  -0.258  -3.1889   2.1487   0.4198
 ISI  CG2   C  CH3   0  -0.521   5.2849   3.0175   0.5035
 ISI  CG3   C  CH3   0  -0.527   5.6511   0.7867  -0.2323
 ISI  H1    H  HCR6  0   0.254   2.8106  -3.3041  -1.1566
 ISI  HNP1  H  HNH2  0   0.397  -4.1649  -3.4183   0.5467
 ISI  HNPA  H  HNH2  0   0.399  -4.2664  -1.7596   0.7161
 ISI  H2    H  HCR6  0   0.249   0.7256  -4.6459  -0.9339
 ISI  H10   H  HCH2  0   0.268   0.4105   1.3028  -0.0895
 ISI  H10A  H  HCH2  0   0.263   1.1448   0.7418   1.4107
 ISI  H11   H  HCR5  0   0.238   2.4007   1.1414  -1.3108
 ISI  HA1   H  HCH2  0   0.273  -2.9482  -0.2386   1.7979
 ISI  HA1A  H  HCH2  0   0.275  -1.3715   0.4564   1.5476
 ISI  HA2   H  HCH2  0   0.205   3.6311   0.9603   1.4769
 ISI  HA2A  H  HCH2  0   0.247   2.9216   2.4046   0.7748
 ISI  HB1   H  HCH2  0   0.238  -1.9693   0.9297  -0.8629
 ISI  HB1A  H  HCH2  0   0.241  -3.5634   0.2555  -0.5744
 ISI  HD1   H  HCH3  0   0.191  -5.7305   2.5565  -0.4559
 ISI  HD1A  H  HCH3  0   0.235  -5.2228   3.2962  -1.9824
 ISI  HD1B  H  HCH3  0   0.236  -4.8227   1.6198  -1.6522
 ISI  HE1   H  HCH3  0   0.190  -4.5018   4.5068   0.6821
 ISI  HE1A  H  HCH3  0   0.233  -2.8026   4.7420   0.2389
 ISI  HE1B  H  HCH3  0   0.232  -4.0730   5.0616  -0.9418
 ISI  HG1   H  HCH2  0   0.232  -2.3339   2.6282   0.9061
 ISI  HG1A  H  HCH2  0   0.193  -3.9519   2.0092   1.2070
 ISI  HG2   H  HCH3  0   0.192   5.5826   2.8307   1.5472
 ISI  HG2A  H  HCH3  0   0.233   6.1780   3.3243  -0.0426
 ISI  HG2B  H  HCH3  0   0.234   4.5891   3.8575   0.5009
 ISI  HG3   H  HCH3  0   0.242   5.2619  -0.0464  -0.8126
 ISI  HG3A  H  HCH3  0   0.229   6.5497   1.1443  -0.7371
 ISI  HG3B  H  HCH3  0   0.190   5.9553   0.3996   0.7530

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
 ISI  C1   C2    aromatic  1.393  0.020  1.393
 ISI  C1   C6    aromatic  1.390  0.020  1.390
 ISI  C2   C3    aromatic  1.390  0.020  1.390
 ISI  NP2  CD1   single    1.448  0.020  1.448
 ISI  NP2  CG1   single    1.451  0.020  1.451
 ISI  C3   N7    aromatic  1.380  0.020  1.380
 ISI  C3   C4    aromatic  1.409  0.020  1.409
 ISI  NP3  CA2   single    1.449  0.020  1.449
 ISI  NP3  CG3   single    1.449  0.020  1.449
 ISI  C4   N9    aromatic  1.376  0.020  1.376
 ISI  C5   C4    aromatic  1.381  0.020  1.381
 ISI  C5   C10   single    1.497  0.020  1.497
 ISI  C6   C5    aromatic  1.387  0.020  1.387
 ISI  N7   C8    aromatic  1.305  0.020  1.305
 ISI  C8   NP1   single    1.361  0.020  1.361
 ISI  C8   N9    aromatic  1.370  0.020  1.370
 ISI  N9   CA1   single    1.446  0.020  1.446
 ISI  C11  C10   single    1.542  0.020  1.542
 ISI  C11  CA2   single    1.515  0.020  1.515
 ISI  O12  C6    single    1.357  0.020  1.357
 ISI  O12  C11   single    1.441  0.020  1.441
 ISI  CB1  CA1   single    1.524  0.020  1.524
 ISI  CB1  CG1   single    1.522  0.020  1.522
 ISI  CE1  NP2   single    1.448  0.020  1.448
 ISI  CG2  NP3   single    1.449  0.020  1.449
 ISI  C1   H1    single    0.930  0.020  1.080
 ISI  NP1  HNP1  single    0.890  0.020  1.040
 ISI  NP1  HNPA  single    0.890  0.020  1.040
 ISI  C2   H2    single    0.930  0.020  1.080
 ISI  C10  H10   single    0.970  0.020  1.090
 ISI  C10  H10A  single    0.970  0.020  1.090
 ISI  C11  H11   single    0.970  0.020  1.090
 ISI  CA1  HA1   single    0.970  0.020  1.090
 ISI  CA1  HA1A  single    0.970  0.020  1.090
 ISI  CA2  HA2   single    0.970  0.020  1.090
 ISI  CA2  HA2A  single    0.970  0.020  1.090
 ISI  CB1  HB1   single    0.970  0.020  1.090
 ISI  CB1  HB1A  single    0.970  0.020  1.090
 ISI  CD1  HD1   single    0.970  0.020  1.090
 ISI  CD1  HD1A  single    0.970  0.020  1.090
 ISI  CD1  HD1B  single    0.970  0.020  1.090
 ISI  CE1  HE1   single    0.970  0.020  1.090
 ISI  CE1  HE1A  single    0.970  0.020  1.090
 ISI  CE1  HE1B  single    0.970  0.020  1.090
 ISI  CG1  HG1   single    0.970  0.020  1.090
 ISI  CG1  HG1A  single    0.970  0.020  1.090
 ISI  CG2  HG2   single    0.970  0.020  1.090
 ISI  CG2  HG2A  single    0.970  0.020  1.090
 ISI  CG2  HG2B  single    0.970  0.020  1.090
 ISI  CG3  HG3   single    0.970  0.020  1.090
 ISI  CG3  HG3A  single    0.970  0.020  1.090
 ISI  CG3  HG3B  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
 ISI  H1    C1   C6    120.68  3.000
 ISI  H1    C1   C2    120.65  3.000
 ISI  C6    C1   C2    118.67  3.000
 ISI  HNPA  NP1  HNP1  111.93  3.000
 ISI  HNPA  NP1  C8    117.28  3.000
 ISI  HNP1  NP1  C8    113.84  3.000
 ISI  H2    C2   C3    120.46  3.000
 ISI  H2    C2   C1    120.20  3.000
 ISI  C3    C2   C1    119.34  3.000
 ISI  CG1   NP2  CE1   110.79  3.000
 ISI  CE1   NP2  CD1   110.44  3.000
 ISI  CG1   NP2  CD1   112.41  3.000
 ISI  N7    C3   C4    109.89  3.000
 ISI  C4    C3   C2    120.10  3.000
 ISI  N7    C3   C2    130.01  3.000
 ISI  CG3   NP3  CG2   110.20  3.000
 ISI  CG2   NP3  CA2   110.87  3.000
 ISI  CG3   NP3  CA2   113.47  3.000
 ISI  N9    C4   C5    133.27  3.000
 ISI  C5    C4   C3    121.51  3.000
 ISI  N9    C4   C3    105.22  3.000
 ISI  C10   C5   C6    108.36  3.000
 ISI  C6    C5   C4    116.74  3.000
 ISI  C10   C5   C4    134.85  3.000
 ISI  O12   C6   C5    112.40  3.000
 ISI  O12   C6   C1    123.98  3.000
 ISI  C5    C6   C1    123.63  3.000
 ISI  C8    N7   C3    104.93  3.000
 ISI  N9    C8   N7    113.66  3.000
 ISI  N9    C8   NP1   121.02  3.000
 ISI  N7    C8   NP1   125.21  3.000
 ISI  CA1   N9   C8    126.90  3.000
 ISI  CA1   N9   C4    126.76  3.000
 ISI  C8    N9   C4    106.27  3.000
 ISI  H10A  C10  H10   107.36  3.000
 ISI  H10A  C10  C11   111.49  3.000
 ISI  H10   C10  C11   110.88  3.000
 ISI  H10A  C10  C5    111.46  3.000
 ISI  H10   C10  C5    114.19  3.000
 ISI  C11   C10  C5    101.47  3.000
 ISI  H11   C11  CA2   109.10  3.000
 ISI  H11   C11  O12   107.58  3.000
 ISI  CA2   C11  O12   112.03  3.000
 ISI  H11   C11  C10   109.83  3.000
 ISI  O12   C11  C10   105.93  3.000
 ISI  CA2   C11  C10   112.23  3.000
 ISI  C11   O12  C6    108.37  3.000
 ISI  HA1A  CA1  HA1   105.82  3.000
 ISI  HA1A  CA1  CB1   110.66  3.000
 ISI  HA1   CA1  CB1   110.78  3.000
 ISI  HA1A  CA1  N9    107.92  3.000
 ISI  HA1   CA1  N9    108.48  3.000
 ISI  CB1   CA1  N9    112.87  3.000
 ISI  HA2A  CA2  HA2   106.01  3.000
 ISI  HA2A  CA2  C11   105.47  3.000
 ISI  HA2   CA2  C11   109.28  3.000
 ISI  HA2A  CA2  NP3   107.44  3.000
 ISI  HA2   CA2  NP3   112.63  3.000
 ISI  C11   CA2  NP3   115.32  3.000
 ISI  HB1A  CB1  HB1   106.75  3.000
 ISI  HB1A  CB1  CG1   111.17  3.000
 ISI  HB1   CB1  CG1   109.43  3.000
 ISI  HB1A  CB1  CA1   108.99  3.000
 ISI  HB1   CB1  CA1   109.71  3.000
 ISI  CG1   CB1  CA1   110.71  3.000
 ISI  HD1B  CD1  HD1A  107.18  3.000
 ISI  HD1B  CD1  HD1   107.72  3.000
 ISI  HD1A  CD1  HD1   107.71  3.000
 ISI  HD1B  CD1  NP2   111.21  3.000
 ISI  HD1A  CD1  NP2   109.81  3.000
 ISI  HD1   CD1  NP2   112.98  3.000
 ISI  HE1B  CE1  HE1A  107.84  3.000
 ISI  HE1B  CE1  HE1   107.52  3.000
 ISI  HE1A  CE1  HE1   107.79  3.000
 ISI  HE1B  CE1  NP2   109.93  3.000
 ISI  HE1A  CE1  NP2   110.24  3.000
 ISI  HE1   CE1  NP2   113.34  3.000
 ISI  HG1A  CG1  HG1   106.15  3.000
 ISI  HG1A  CG1  CB1   109.52  3.000
 ISI  HG1   CG1  CB1   108.10  3.000
 ISI  HG1A  CG1  NP2   111.54  3.000
 ISI  HG1   CG1  NP2   107.69  3.000
 ISI  CB1   CG1  NP2   113.50  3.000
 ISI  HG2B  CG2  HG2A  107.73  3.000
 ISI  HG2B  CG2  HG2   107.78  3.000
 ISI  HG2A  CG2  HG2   107.52  3.000
 ISI  HG2B  CG2  NP3   110.37  3.000
 ISI  HG2A  CG2  NP3   109.79  3.000
 ISI  HG2   CG2  NP3   113.47  3.000
 ISI  HG3B  CG3  HG3A  107.56  3.000
 ISI  HG3B  CG3  HG3   107.87  3.000
 ISI  HG3A  CG3  HG3   107.40  3.000
 ISI  HG3B  CG3  NP3   112.89  3.000
 ISI  HG3A  CG3  NP3   109.45  3.000
 ISI  HG3   CG3  NP3   111.45  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
 ISI  CONST_01  N7    C3   C2   C1    180.00   0.0  0
 ISI  CONST_02  C4    C3   C2   C1      0.00   0.0  0
 ISI  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 ISI  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 ISI  CONST_05  C8    N7   C3   C2    180.00   0.0  0
 ISI  CONST_06  N9    C4   C3   C2    180.00   0.0  0
 ISI  CONST_07  C5    C4   C3   C2      0.00   0.0  0
 ISI  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 ISI  CONST_09  N9    C8   N7   C3      0.00   0.0  0
 ISI  CONST_10  C8    N9   C4   C3      0.00   0.0  0
 ISI  CONST_11  C6    C5   C4   C3      0.00   0.0  0
 ISI  CONST_12  C8    N7   C3   C4      0.00   0.0  0
 ISI  CONST_13  N7    C8   N9   C4      0.00   0.0  0
 ISI  CONST_14  N7    C3   C4   C5    180.00   0.0  0
 ISI  CONST_15  C8    N9   C4   C5    180.00   0.0  0
 ISI  CONST_16  N9    C4   C5   C6    180.00   0.0  0
 ISI  CONST_17  N9    C4   C3   N7      0.00   0.0  0
 ISI  CONST_18  C3    N7   C8   NP1   180.00   0.0  0
 ISI  CONST_19  C4    N9   C8   NP1   180.00   0.0  0
 ISI  CONST_20  CA1   N9   C4   C3    180.00   0.0  0
 ISI  CONST_21  CA1   N9   C4   C5      0.00   0.0  0
 ISI  CONST_22  CA1   N9   C8   N7    180.00   0.0  0
 ISI  CONST_23  H1    C1   C2   C3    180.00   0.0  0
 ISI  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 ISI  CONST_25  HNP1  NP1  C8   N7      0.00   0.0  0
 ISI  Var_01    C11   C10  C5   C4   -170.95  30.0  1
 ISI  Var_02    CB1   CA1  N9   C4     88.34  30.0  2
 ISI  Var_03    CG1   CB1  CA1  N9   -177.23  30.0  1
 ISI  Var_04    CG3   NP3  CA2  C11   -77.59  30.0  1
 ISI  Var_05    CA1   CB1  CG1  NP2   176.75  30.0  1
 ISI  Var_06    CD1   NP2  CG1  CB1    69.55  30.0  2
 ISI  Var_07    HG3   CG3  NP3  CA2    61.48  30.0  3
 ISI  Var_08    HG2   CG2  NP3  CA2    62.96  30.0  3
 ISI  Var_09    HE1   CE1  NP2  CD1    62.69  30.0  3
 ISI  Var_10    HD1   CD1  NP2  CE1   -63.90  30.0  3

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
 ISI  chir_01  C11  C10  CA2  O12  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
 ISI  plan-1  NP1   0.020
 ISI  plan-1  C8    0.020
 ISI  plan-1  HNP1  0.020
 ISI  plan-1  HNPA  0.020
 ISI  plan-2  C1    0.020
 ISI  plan-2  NP1   0.020
 ISI  plan-2  C2    0.020
 ISI  plan-2  C3    0.020
 ISI  plan-2  C4    0.020
 ISI  plan-2  C5    0.020
 ISI  plan-2  C6    0.020
 ISI  plan-2  N7    0.020
 ISI  plan-2  C8    0.020
 ISI  plan-2  N9    0.020
 ISI  plan-2  C10   0.020
 ISI  plan-2  O12   0.020
 ISI  plan-2  CA1   0.020
 ISI  plan-2  H1    0.020
 ISI  plan-2  H2    0.020

