# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 21:06:56 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-[(3~{R})-3-azanylpyrrolidin-1-yl]carbonyl-1~{H}-benzimidazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCN(C1)C(=O)c2[nH]c3cccc(C(N)=O)c3n2
#
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
 7U9  7U9  2-[(3~{R})-3-azanylpyrrolidin-1-yl]carbonyl-1~{H}-benzimidazole-4-carboxamide  ligand  35  20  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7U9
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
 7U9  CAJ  C  CH2   0  -0.251  -3.8339   0.5750  -0.1622
 7U9  CAS  C  CH1   0  -0.117  -4.4465  -0.8070  -0.3612
 7U9  NAB  N  NH2   0  -0.799  -5.8279  -0.8508   0.0753
 7U9  CAH  C  CH2   0  -0.476  -3.5276  -1.6830   0.4785
 7U9  CAI  C  CH2   0  -0.265  -2.1435  -1.1262   0.1823
 7U9  NAT  N  NT    0  -0.484  -2.4065   0.3023  -0.0295
 7U9  CAN  C  C     0   0.502  -1.5405   1.3154  -0.0725
 7U9  OAD  O  O     0  -0.501  -1.8888   2.4893  -0.1803
 7U9  CAP  C  CR5   0   0.349  -0.0814   1.0327   0.0015
 7U9  NAL  N  NR15  0  -0.685   0.7702   2.0886   0.0298
 7U9  NAK  N  N     0  -0.434   0.5345  -0.1179   0.0219
 7U9  CAR  C  CR56  0   0.162   1.8653   0.1886   0.0737
 7U9  CAQ  C  CR56  0   0.346   2.0342   1.5858   0.0701
 7U9  CAG  C  CR16  0  -0.297   3.2851   2.1955   0.1000
 7U9  CAE  C  CR16  0  -0.267   4.3787   1.3550   0.1209
 7U9  CAF  C  CR16  0  -0.294   4.2343  -0.0416   0.1104
 7U9  CAO  C  CR6   0  -0.134   2.9905  -0.6499   0.0885
 7U9  CAM  C  C     0   0.464   2.8403  -2.1346   0.1558
 7U9  OAC  O  O     0  -0.470   1.9888  -2.6575   0.8579
 7U9  NAA  N  NH2   0  -0.800   3.7114  -2.8304  -0.5912
 7U9  H1   H  HCH2  0   0.255  -4.0282   1.2537  -0.9930
 7U9  H2   H  HCH2  0   0.237  -4.2295   1.0317   0.7510
 7U9  H3   H  HCH1  0   0.219  -4.3175  -1.0892  -1.4173
 7U9  H4   H  HNH2  0   0.348  -6.3890  -0.2557  -0.5226
 7U9  H5   H  HNH2  0   0.350  -6.1887  -1.7861  -0.0697
 7U9  H7   H  HCH2  0   0.236  -3.7751  -1.5530   1.5356
 7U9  H8   H  HCH2  0   0.256  -3.6030  -2.7441   0.2396
 7U9  H9   H  HCH2  0   0.263  -1.4387  -1.2865   0.9932
 7U9  H10  H  HCH2  0   0.243  -1.7169  -1.5737  -0.7172
 7U9  H11  H  HNR5  0   0.422   0.4988   3.0596   0.0065
 7U9  H13  H  HCR6  0   0.277   3.3969   3.2714   0.1056
 7U9  H14  H  HCR6  0   0.266   5.3743   1.7771   0.1515
 7U9  H15  H  HCR6  0   0.266   5.1290  -0.6502   0.1462
 7U9  H16  H  HNH2  0   0.412   4.3486  -2.3841  -1.2279
 7U9  H17  H  HNH2  0   0.404   3.7085  -3.8375  -0.5677

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
 7U9  OAC  CAM  double    1.221  0.020  1.221
 7U9  NAA  CAM  single    1.342  0.020  1.342
 7U9  CAM  CAO  single    1.494  0.020  1.494
 7U9  CAO  CAF  aromatic  1.385  0.020  1.385
 7U9  CAO  CAR  aromatic  1.403  0.020  1.403
 7U9  CAF  CAE  aromatic  1.404  0.020  1.404
 7U9  CAH  CAI  single    1.521  0.020  1.521
 7U9  CAH  CAS  single    1.522  0.020  1.522
 7U9  CAI  NAT  single    1.468  0.020  1.468
 7U9  CAR  NAK  aromatic  1.367  0.020  1.367
 7U9  CAR  CAQ  aromatic  1.407  0.020  1.407
 7U9  NAK  CAP  aromatic  1.305  0.020  1.305
 7U9  CAE  CAG  aromatic  1.379  0.020  1.379
 7U9  CAS  NAB  single    1.449  0.020  1.449
 7U9  CAS  CAJ  single    1.525  0.020  1.525
 7U9  NAT  CAN  single    1.333  0.020  1.333
 7U9  NAT  CAJ  single    1.459  0.020  1.459
 7U9  CAQ  CAG  aromatic  1.392  0.020  1.392
 7U9  CAQ  NAL  aromatic  1.361  0.020  1.361
 7U9  CAP  CAN  single    1.488  0.020  1.488
 7U9  CAP  NAL  aromatic  1.357  0.020  1.357
 7U9  CAN  OAD  double    1.229  0.020  1.229
 7U9  CAJ  H1   single    0.970  0.020  1.090
 7U9  CAJ  H2   single    0.970  0.020  1.090
 7U9  CAS  H3   single    0.970  0.020  1.090
 7U9  NAB  H4   single    0.890  0.020  1.040
 7U9  NAB  H5   single    0.890  0.020  1.040
 7U9  CAH  H7   single    0.970  0.020  1.090
 7U9  CAH  H8   single    0.970  0.020  1.090
 7U9  CAI  H9   single    0.970  0.020  1.090
 7U9  CAI  H10  single    0.970  0.020  1.090
 7U9  NAL  H11  single    0.860  0.020  1.020
 7U9  CAG  H13  single    0.930  0.020  1.080
 7U9  CAE  H14  single    0.930  0.020  1.080
 7U9  CAF  H15  single    0.930  0.020  1.080
 7U9  NAA  H16  single    0.860  0.020  1.020
 7U9  NAA  H17  single    0.860  0.020  1.020

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
 7U9  H2   CAJ  H1   108.15  3.000
 7U9  H2   CAJ  NAT  110.82  3.000
 7U9  H1   CAJ  NAT  111.10  3.000
 7U9  H2   CAJ  CAS  109.98  3.000
 7U9  H1   CAJ  CAS  113.15  3.000
 7U9  NAT  CAJ  CAS  103.63  3.000
 7U9  H3   CAS  CAH  108.12  3.000
 7U9  H3   CAS  NAB  113.14  3.000
 7U9  CAH  CAS  NAB  113.07  3.000
 7U9  H3   CAS  CAJ  108.09  3.000
 7U9  NAB  CAS  CAJ  111.78  3.000
 7U9  CAH  CAS  CAJ  101.95  3.000
 7U9  H5   NAB  H4   105.11  3.000
 7U9  H5   NAB  CAS  108.92  3.000
 7U9  H4   NAB  CAS  109.41  3.000
 7U9  H8   CAH  H7   108.17  3.000
 7U9  H8   CAH  CAI  112.12  3.000
 7U9  H7   CAH  CAI  110.53  3.000
 7U9  H8   CAH  CAS  113.42  3.000
 7U9  H7   CAH  CAS  109.17  3.000
 7U9  CAI  CAH  CAS  103.37  3.000
 7U9  H10  CAI  H9   107.53  3.000
 7U9  H10  CAI  NAT  110.50  3.000
 7U9  H9   CAI  NAT  111.57  3.000
 7U9  H10  CAI  CAH  111.47  3.000
 7U9  H9   CAI  CAH  113.02  3.000
 7U9  NAT  CAI  CAH  102.78  3.000
 7U9  CAN  NAT  CAI  128.88  3.000
 7U9  CAN  NAT  CAJ  119.37  3.000
 7U9  CAI  NAT  CAJ  111.73  3.000
 7U9  CAP  CAN  OAD  117.62  3.000
 7U9  OAD  CAN  NAT  122.98  3.000
 7U9  CAP  CAN  NAT  119.39  3.000
 7U9  NAK  CAP  NAL  112.92  3.000
 7U9  NAL  CAP  CAN  117.94  3.000
 7U9  NAK  CAP  CAN  129.12  3.000
 7U9  H11  NAL  CAQ  127.33  3.000
 7U9  H11  NAL  CAP  125.44  3.000
 7U9  CAQ  NAL  CAP  107.22  3.000
 7U9  CAR  NAK  CAP  105.21  3.000
 7U9  CAO  CAR  CAQ  119.80  3.000
 7U9  CAQ  CAR  NAK  109.84  3.000
 7U9  CAO  CAR  NAK  130.33  3.000
 7U9  CAG  CAQ  CAR  122.86  3.000
 7U9  CAG  CAQ  NAL  132.34  3.000
 7U9  CAR  CAQ  NAL  104.80  3.000
 7U9  H13  CAG  CAE  121.60  3.000
 7U9  H13  CAG  CAQ  121.92  3.000
 7U9  CAE  CAG  CAQ  116.48  3.000
 7U9  H14  CAE  CAF  118.88  3.000
 7U9  H14  CAE  CAG  119.49  3.000
 7U9  CAF  CAE  CAG  121.63  3.000
 7U9  H15  CAF  CAO  119.73  3.000
 7U9  H15  CAF  CAE  118.29  3.000
 7U9  CAO  CAF  CAE  121.96  3.000
 7U9  CAM  CAO  CAF  121.75  3.000
 7U9  CAF  CAO  CAR  117.25  3.000
 7U9  CAM  CAO  CAR  120.91  3.000
 7U9  NAA  CAM  OAC  123.41  3.000
 7U9  NAA  CAM  CAO  115.15  3.000
 7U9  OAC  CAM  CAO  121.44  3.000
 7U9  H17  NAA  H16  117.41  3.000
 7U9  H17  NAA  CAM  120.23  3.000
 7U9  H16  NAA  CAM  122.26  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
 7U9  CONST_01  CAO  CAR  NAK  CAP  180.00   0.0  0
 7U9  CONST_02  CAQ  CAR  NAK  CAP    0.00   0.0  0
 7U9  CONST_03  CAR  CAQ  NAL  CAP    0.00   0.0  0
 7U9  CONST_04  CAG  CAQ  NAL  CAP  180.00   0.0  0
 7U9  CONST_05  CAO  CAR  CAQ  NAL  180.00   0.0  0
 7U9  CONST_06  NAK  CAR  CAQ  NAL    0.00   0.0  0
 7U9  CONST_07  CAE  CAG  CAQ  NAL  180.00   0.0  0
 7U9  CONST_08  CAR  NAK  CAP  NAL    0.00   0.0  0
 7U9  CONST_09  CAF  CAO  CAR  NAK  180.00   0.0  0
 7U9  CONST_10  CAG  CAQ  CAR  NAK  180.00   0.0  0
 7U9  CONST_11  CAQ  NAL  CAP  NAK    0.00   0.0  0
 7U9  CONST_12  CAE  CAF  CAO  CAR    0.00   0.0  0
 7U9  CONST_13  CAE  CAG  CAQ  CAR    0.00   0.0  0
 7U9  CONST_14  CAF  CAO  CAR  CAQ    0.00   0.0  0
 7U9  CONST_15  CAF  CAE  CAG  CAQ    0.00   0.0  0
 7U9  CONST_16  CAO  CAF  CAE  CAG    0.00   0.0  0
 7U9  CONST_17  CAO  CAR  CAQ  CAG    0.00   0.0  0
 7U9  CONST_18  CAR  NAK  CAP  CAN  180.00   0.0  0
 7U9  CONST_19  CAQ  NAL  CAP  CAN  180.00   0.0  0
 7U9  CONST_20  CAM  CAO  CAR  NAK    0.00   0.0  0
 7U9  CONST_21  CAM  CAO  CAR  CAQ  180.00   0.0  0
 7U9  CONST_22  CAM  CAO  CAF  CAE  180.00   0.0  0
 7U9  CONST_23  CAP  CAN  NAT  CAJ  180.00   0.0  0
 7U9  CONST_24  CAP  CAN  NAT  CAI    0.00   0.0  0
 7U9  CONST_25  H13  CAG  CAQ  NAL    0.00   0.0  0
 7U9  CONST_26  H11  NAL  CAP  NAK  180.00   0.0  0
 7U9  CONST_27  H15  CAF  CAO  CAR  180.00   0.0  0
 7U9  CONST_28  H14  CAE  CAG  CAQ  180.00   0.0  0
 7U9  CONST_29  OAD  CAN  NAT  CAJ    0.00   0.0  0
 7U9  CONST_30  OAD  CAN  NAT  CAI  180.00   0.0  0
 7U9  CONST_31  H16  NAA  CAM  CAO    0.00   0.0  0
 7U9  CONST_32  H17  NAA  CAM  CAO  180.00   0.0  0
 7U9  Var_01    CAH  CAI  NAT  CAJ  -12.06  30.0  1
 7U9  Var_02    NAT  CAI  CAH  CAS   32.63  30.0  1
 7U9  Var_03    CAI  NAT  CAJ  CAS  -13.34  30.0  1
 7U9  Var_04    NAK  CAP  CAN  NAT    4.90  30.0  2
 7U9  Var_05    OAC  CAM  CAO  CAR  -39.47  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
 7U9  chir_01  CAS  CAH  NAB  CAJ  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
 7U9  plan-1  CAN  0.020
 7U9  plan-1  CAP  0.020
 7U9  plan-1  NAL  0.020
 7U9  plan-1  NAK  0.020
 7U9  plan-1  CAR  0.020
 7U9  plan-1  CAQ  0.020
 7U9  plan-1  CAG  0.020
 7U9  plan-1  CAE  0.020
 7U9  plan-1  CAF  0.020
 7U9  plan-1  CAO  0.020
 7U9  plan-1  CAM  0.020
 7U9  plan-1  H11  0.020
 7U9  plan-1  H13  0.020
 7U9  plan-1  H14  0.020
 7U9  plan-1  H15  0.020
 7U9  plan-2  CAO  0.020
 7U9  plan-2  CAM  0.020
 7U9  plan-2  OAC  0.020
 7U9  plan-2  NAA  0.020
 7U9  plan-2  H16  0.020
 7U9  plan-2  H17  0.020
 7U9  plan-3  CAJ  0.020
 7U9  plan-3  CAI  0.020
 7U9  plan-3  NAT  0.020
 7U9  plan-3  CAN  0.020
 7U9  plan-3  OAD  0.020
 7U9  plan-3  CAP  0.020

