# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 09:57:00 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (7R)-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
 ISH  ISH  (7R)-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_ISH
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
 ISH  C1    C  CR16  0  -0.382  -1.8379   2.9527  -0.3462
 ISH  C2    C  CR16  0  -0.350  -0.6470   3.5359  -0.7750
 ISH  C3    C  CR56  0   0.125   0.5604   2.9135  -0.4811
 ISH  C4    C  CR56  0   0.292   0.5747   1.7149   0.2576
 ISH  C5    C  CR56  0  -0.048  -0.5926   1.1206   0.6936
 ISH  C6    C  CR56  0   0.378  -1.7793   1.7645   0.3727
 ISH  N7    N  N     0  -0.521   1.8513   3.2795  -0.8051
 ISH  C8    C  CR5   0   0.598   2.6056   2.3428  -0.2969
 ISH  N9    N  NR5   0  -0.566   1.9039   1.3775   0.3783
 ISH  C10   C  CH2   0  -0.519  -0.9197  -0.0976   1.5040
 ISH  C11   C  CR15  0  -0.027  -2.4412  -0.1973   1.2776
 ISH  O12   O  O     0  -0.495  -2.8678   1.1063   0.8455
 ISH  CA1   C  CH2   0  -0.334   2.4078   0.1229   0.8925
 ISH  CA2   C  CH2   0  -0.273  -2.7486  -1.2292   0.2027
 ISH  CB1   C  CH2   0  -0.459   2.3629  -0.9879  -0.1498
 ISH  CD1   C  CH3   0  -0.520   3.4630  -4.5661   0.0395
 ISH  CE1   C  CH3   0  -0.529   1.4460  -3.7777  -0.9385
 ISH  CG1   C  CH2   0  -0.259   2.7670  -2.3236   0.4562
 ISH  CG2   C  CH3   0  -0.520  -4.2927  -2.0851  -1.3919
 ISH  CG3   C  CH3   0  -0.530  -5.0068  -1.7443   0.8565
 ISH  NP1   N  NH2   0  -0.856   3.9533   2.2535  -0.4579
 ISH  NP2   N  NT    0  -0.407   2.7785  -3.4116  -0.5043
 ISH  NP3   N  NT    0  -0.401  -4.1353  -1.2786  -0.2006
 ISH  H1    H  HCR6  0   0.254  -2.7902   3.4148  -0.5716
 ISH  H2    H  HCR6  0   0.248  -0.6658   4.4582  -1.3417
 ISH  H10   H  HCH2  0   0.252  -0.4113  -1.0055   1.1690
 ISH  H11   H  HCR5  0   0.258  -2.9722  -0.4206   2.2041
 ISH  HA1   H  HCH2  0   0.271   3.4229   0.2671   1.2644
 ISH  HA2   H  HCH2  0   0.236  -2.1425  -0.9945  -0.6796
 ISH  HB1   H  HCH2  0   0.232   1.3508  -1.0378  -0.5601
 ISH  HD1   H  HCH3  0   0.191   2.9719  -4.9784   0.9352
 ISH  HE1   H  HCH3  0   0.237   1.5043  -4.5820  -1.6724
 ISH  HG1   H  HCH2  0   0.234   3.7770  -2.2279   0.8649
 ISH  HG2   H  HCH3  0   0.233  -3.6844  -1.6819  -2.2029
 ISH  HG3   H  HCH3  0   0.237  -5.0062  -1.0558   1.7017
 ISH  HNP1  H  HNH2  0   0.397   4.4815   1.8301   0.2886
 ISH  H10A  H  HCH2  0   0.278  -0.6692   0.0402   2.5587
 ISH  HA1A  H  HCH2  0   0.272   1.8113  -0.1458   1.7660
 ISH  HA2A  H  HCH2  0   0.202  -2.3903  -2.2070   0.5744
 ISH  HB1A  H  HCH2  0   0.244   3.0308  -0.7428  -0.9790
 ISH  HD1A  H  HCH3  0   0.233   3.5095  -5.3601  -0.7071
 ISH  HD1B  H  HCH3  0   0.233   4.4867  -4.3046   0.3112
 ISH  HE1A  H  HCH3  0   0.191   0.8071  -4.1255  -0.1102
 ISH  HE1B  H  HCH3  0   0.234   0.9407  -2.9398  -1.4180
 ISH  HG1A  H  HCH2  0   0.190   2.1084  -2.5509   1.3146
 ISH  HG2A  H  HCH3  0   0.191  -4.0036  -3.1386  -1.2486
 ISH  HG2B  H  HCH3  0   0.233  -5.3336  -2.0698  -1.7185
 ISH  HG3A  H  HCH3  0   0.236  -6.0321  -1.7978   0.4889
 ISH  HG3B  H  HCH3  0   0.192  -4.7341  -2.7423   1.2361
 ISH  HNPA  H  HNH2  0   0.396   4.3812   3.1038  -0.7888

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
 ISH  C1    C6    aromatic  1.390  0.020  1.390
 ISH  C2    C1    aromatic  1.394  0.020  1.394
 ISH  C2    C3    aromatic  1.390  0.020  1.390
 ISH  C3    C4    aromatic  1.408  0.020  1.408
 ISH  C4    N9    aromatic  1.377  0.020  1.377
 ISH  C4    C5    aromatic  1.381  0.020  1.381
 ISH  C5    C10   single    1.499  0.020  1.499
 ISH  C6    C5    aromatic  1.388  0.020  1.388
 ISH  C6    O12   single    1.357  0.020  1.357
 ISH  N7    C3    aromatic  1.380  0.020  1.380
 ISH  N7    C8    aromatic  1.306  0.020  1.306
 ISH  C8    N9    aromatic  1.371  0.020  1.371
 ISH  N9    CA1   single    1.446  0.020  1.446
 ISH  C10   C11   single    1.541  0.020  1.541
 ISH  C10   H10A  single    0.970  0.020  1.090
 ISH  C11   CA2   single    1.521  0.020  1.521
 ISH  C11   H11   single    0.970  0.020  1.090
 ISH  O12   C11   single    1.438  0.020  1.438
 ISH  CA1   HA1   single    0.970  0.020  1.090
 ISH  CA1   HA1A  single    0.970  0.020  1.090
 ISH  CA2   NP3   single    1.445  0.020  1.445
 ISH  CA2   HA2   single    0.970  0.020  1.090
 ISH  CA2   HA2A  single    0.970  0.020  1.090
 ISH  CB1   CA1   single    1.524  0.020  1.524
 ISH  CB1   CG1   single    1.521  0.020  1.521
 ISH  CB1   HB1A  single    0.970  0.020  1.090
 ISH  CD1   HD1A  single    0.970  0.020  1.090
 ISH  CD1   HD1B  single    0.970  0.020  1.090
 ISH  CE1   NP2   single    1.448  0.020  1.448
 ISH  CE1   HE1A  single    0.970  0.020  1.090
 ISH  CE1   HE1B  single    0.970  0.020  1.090
 ISH  CG1   HG1   single    0.970  0.020  1.090
 ISH  CG1   HG1A  single    0.970  0.020  1.090
 ISH  CG2   NP3   single    1.447  0.020  1.447
 ISH  CG2   HG2A  single    0.970  0.020  1.090
 ISH  CG2   HG2B  single    0.970  0.020  1.090
 ISH  CG3   HG3   single    0.970  0.020  1.090
 ISH  CG3   HG3A  single    0.970  0.020  1.090
 ISH  CG3   HG3B  single    0.970  0.020  1.090
 ISH  NP1   C8    single    1.360  0.020  1.360
 ISH  NP1   HNPA  single    0.890  0.020  1.040
 ISH  NP2   CD1   single    1.448  0.020  1.448
 ISH  NP2   CG1   single    1.451  0.020  1.451
 ISH  NP3   CG3   single    1.447  0.020  1.447
 ISH  H1    C1    single    0.930  0.020  1.080
 ISH  H2    C2    single    0.930  0.020  1.080
 ISH  H10   C10   single    0.970  0.020  1.090
 ISH  HB1   CB1   single    0.970  0.020  1.090
 ISH  HD1   CD1   single    0.970  0.020  1.090
 ISH  HE1   CE1   single    0.970  0.020  1.090
 ISH  HG2   CG2   single    0.970  0.020  1.090
 ISH  HNP1  NP1   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
 ISH  H1    C1   C6    120.65  3.000
 ISH  H1    C1   C2    120.61  3.000
 ISH  C6    C1   C2    118.74  3.000
 ISH  H2    C2   C3    120.49  3.000
 ISH  H2    C2   C1    120.18  3.000
 ISH  C3    C2   C1    119.33  3.000
 ISH  N7    C3   C4    109.83  3.000
 ISH  N7    C3   C2    130.10  3.000
 ISH  C4    C3   C2    120.07  3.000
 ISH  N9    C4   C5    133.10  3.000
 ISH  C5    C4   C3    121.57  3.000
 ISH  N9    C4   C3    105.34  3.000
 ISH  C10   C5   C6    108.39  3.000
 ISH  C6    C5   C4    116.76  3.000
 ISH  C10   C5   C4    134.82  3.000
 ISH  O12   C6   C5    112.35  3.000
 ISH  O12   C6   C1    124.13  3.000
 ISH  C5    C6   C1    123.52  3.000
 ISH  C8    N7   C3    104.99  3.000
 ISH  NP1   C8   N9    121.27  3.000
 ISH  NP1   C8   N7    124.99  3.000
 ISH  N9    C8   N7    113.65  3.000
 ISH  CA1   N9   C8    127.40  3.000
 ISH  CA1   N9   C4    125.45  3.000
 ISH  C8    N9   C4    106.16  3.000
 ISH  H10A  C10  H10   107.09  3.000
 ISH  H10   C10  C11   111.12  3.000
 ISH  H10A  C10  C11   112.10  3.000
 ISH  H10   C10  C5    114.06  3.000
 ISH  H10A  C10  C5    111.67  3.000
 ISH  C11   C10  C5    100.86  3.000
 ISH  H11   C11  CA2   111.27  3.000
 ISH  H11   C11  O12   107.24  3.000
 ISH  CA2   C11  O12   110.03  3.000
 ISH  O12   C11  C10   106.16  3.000
 ISH  H11   C11  C10   111.65  3.000
 ISH  CA2   C11  C10   110.31  3.000
 ISH  C11   O12  C6    107.85  3.000
 ISH  HA1A  CA1  HA1   105.57  3.000
 ISH  HA1A  CA1  CB1   110.60  3.000
 ISH  HA1   CA1  CB1   110.92  3.000
 ISH  CB1   CA1  N9    112.26  3.000
 ISH  HA1A  CA1  N9    107.92  3.000
 ISH  HA1   CA1  N9    109.31  3.000
 ISH  HA2A  CA2  HA2   106.31  3.000
 ISH  HA2A  CA2  NP3   112.00  3.000
 ISH  HA2   CA2  NP3   108.26  3.000
 ISH  HA2A  CA2  C11   107.26  3.000
 ISH  HA2   CA2  C11   108.17  3.000
 ISH  NP3   CA2  C11   114.47  3.000
 ISH  HB1A  CB1  HB1   106.94  3.000
 ISH  HB1   CB1  CG1   110.81  3.000
 ISH  HB1A  CB1  CG1   109.69  3.000
 ISH  HB1   CB1  CA1   108.49  3.000
 ISH  HB1A  CB1  CA1   109.73  3.000
 ISH  CG1   CB1  CA1   111.08  3.000
 ISH  HD1B  CD1  HD1A  107.75  3.000
 ISH  HD1B  CD1  HD1   107.80  3.000
 ISH  HD1A  CD1  HD1   107.65  3.000
 ISH  HD1   CD1  NP2   113.14  3.000
 ISH  HD1B  CD1  NP2   110.24  3.000
 ISH  HD1A  CD1  NP2   110.08  3.000
 ISH  HE1B  CE1  HE1A  107.73  3.000
 ISH  HE1B  CE1  HE1   107.21  3.000
 ISH  HE1A  CE1  HE1   107.70  3.000
 ISH  HE1   CE1  NP2   109.82  3.000
 ISH  HE1B  CE1  NP2   111.35  3.000
 ISH  HE1A  CE1  NP2   112.81  3.000
 ISH  HG1A  CG1  HG1   106.14  3.000
 ISH  HG1A  CG1  NP2   111.37  3.000
 ISH  HG1   CG1  NP2   107.79  3.000
 ISH  NP2   CG1  CB1   113.37  3.000
 ISH  HG1A  CG1  CB1   109.36  3.000
 ISH  HG1   CG1  CB1   108.50  3.000
 ISH  HG2B  CG2  HG2A  107.62  3.000
 ISH  HG2B  CG2  HG2   107.72  3.000
 ISH  HG2A  CG2  HG2   107.68  3.000
 ISH  HG2   CG2  NP3   110.20  3.000
 ISH  HG2B  CG2  NP3   110.02  3.000
 ISH  HG2A  CG2  NP3   113.40  3.000
 ISH  HG3B  CG3  HG3A  107.72  3.000
 ISH  HG3B  CG3  HG3   107.74  3.000
 ISH  HG3A  CG3  HG3   107.03  3.000
 ISH  HG3B  CG3  NP3   113.21  3.000
 ISH  HG3A  CG3  NP3   109.62  3.000
 ISH  HG3   CG3  NP3   111.28  3.000
 ISH  HNPA  NP1  HNP1  112.03  3.000
 ISH  HNP1  NP1  C8    117.34  3.000
 ISH  HNPA  NP1  C8    113.84  3.000
 ISH  CG1   NP2  CE1   112.37  3.000
 ISH  CG1   NP2  CD1   110.66  3.000
 ISH  CE1   NP2  CD1   110.24  3.000
 ISH  CG3   NP3  CG2   110.89  3.000
 ISH  CG3   NP3  CA2   112.65  3.000
 ISH  CG2   NP3  CA2   110.68  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
 ISH  CONST_01  C4    C5   C6   C1      0.00   0.0  0
 ISH  CONST_02  C4    C3   C2   C1      0.00   0.0  0
 ISH  CONST_03  N7    C3   C2   C1    180.00   0.0  0
 ISH  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 ISH  CONST_05  N9    C4   C3   C2    180.00   0.0  0
 ISH  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 ISH  CONST_07  C8    N7   C3   C2    180.00   0.0  0
 ISH  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 ISH  CONST_09  C8    N9   C4   C3      0.00   0.0  0
 ISH  CONST_10  C6    C5   C4   C3      0.00   0.0  0
 ISH  CONST_11  N9    C8   N7   C3      0.00   0.0  0
 ISH  CONST_12  C8    N7   C3   C4      0.00   0.0  0
 ISH  CONST_13  N7    C8   N9   C4      0.00   0.0  0
 ISH  CONST_14  N7    C3   C4   C5    180.00   0.0  0
 ISH  CONST_15  C8    N9   C4   C5    180.00   0.0  0
 ISH  CONST_16  N9    C4   C5   C6    180.00   0.0  0
 ISH  CONST_17  N9    C4   C3   N7      0.00   0.0  0
 ISH  CONST_18  CA1   N9   C4   C3    180.00   0.0  0
 ISH  CONST_19  NP1   C8   N7   C3    180.00   0.0  0
 ISH  CONST_20  NP1   C8   N9   C4    180.00   0.0  0
 ISH  CONST_21  CA1   N9   C4   C5      0.00   0.0  0
 ISH  CONST_22  CA1   N9   C8   N7    180.00   0.0  0
 ISH  CONST_23  H1    C1   C2   C3    180.00   0.0  0
 ISH  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 ISH  Var_01    C11   C10  C5   C4   -168.76  30.0  1
 ISH  Var_02    CB1   CA1  N9   C4     80.10  30.0  2
 ISH  Var_03    CG1   CB1  CA1  N9   -174.36  30.0  1
 ISH  Var_04    CG2   NP3  CA2  C11   168.78  30.0  3
 ISH  Var_05    NP2   CG1  CB1  CA1  -178.33  30.0  3
 ISH  Var_06    CE1   NP2  CG1  CB1   -69.82  30.0  1
 ISH  Var_07    HG2A  CG2  NP3  CA2    62.55  30.0  3
 ISH  Var_08    HG3   CG3  NP3  CA2    63.91  30.0  3
 ISH  Var_09    HE1A  CE1  NP2  CD1    62.91  30.0  3
 ISH  Var_10    HD1A  CD1  NP2  CE1    57.87  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
 ISH  chir_01  C11  C10  CA2  O12  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
 ISH  plan-1  C8    0.020
 ISH  plan-1  NP1   0.020
 ISH  plan-1  HNP1  0.020
 ISH  plan-1  HNPA  0.020
 ISH  plan-2  C1    0.020
 ISH  plan-2  C2    0.020
 ISH  plan-2  C3    0.020
 ISH  plan-2  C4    0.020
 ISH  plan-2  C5    0.020
 ISH  plan-2  C6    0.020
 ISH  plan-2  N7    0.020
 ISH  plan-2  C8    0.020
 ISH  plan-2  N9    0.020
 ISH  plan-2  C10   0.020
 ISH  plan-2  O12   0.020
 ISH  plan-2  CA1   0.020
 ISH  plan-2  NP1   0.020
 ISH  plan-2  H1    0.020
 ISH  plan-2  H2    0.020

