# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 02:52:29 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-piperazin-1-ylcarbonyl-1~{H}-benzimidazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc2[nH]c(nc12)C(=O)N3CCNCC3
#
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
 7U6  7U6  2-piperazin-1-ylcarbonyl-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_7U6
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
 7U6  CAI  C  CH2   0  -0.327   4.0004  -0.5616   0.3280
 7U6  CAG  C  CH2   0  -0.315   4.6683   0.3108  -0.7325
 7U6  NAL  N  NH1   0  -0.579   4.3961   1.7282  -0.5756
 7U6  CAH  C  CH2   0  -0.311   2.9709   1.9781  -0.4497
 7U6  CAJ  C  CH2   0  -0.347   2.2883   1.1231   0.6154
 7U6  NAT  N  NT    0  -0.461   2.5690  -0.2857   0.3611
 7U6  CAO  C  C     0   0.501   1.6981  -1.2693   0.1021
 7U6  OAC  O  O     0  -0.499   2.0349  -2.4312  -0.1142
 7U6  CAQ  C  CR5   0   0.356   0.2259  -1.0046   0.0805
 7U6  NAM  N  NR15  0  -0.681  -0.5884  -2.0868  -0.0077
 7U6  NAK  N  N     0  -0.456  -0.4381   0.1203   0.1097
 7U6  CAS  C  CR56  0   0.173  -1.7567  -0.2319   0.0484
 7U6  CAR  C  CR56  0   0.342  -1.8700  -1.6314  -0.0331
 7U6  CAF  C  CR16  0  -0.297  -3.0951  -2.2861  -0.1209
 7U6  CAD  C  CR16  0  -0.267  -4.2195  -1.4870  -0.1360
 7U6  CAE  C  CR16  0  -0.297  -4.1289  -0.0875  -0.0694
 7U6  CAP  C  CR6   0  -0.129  -2.9112   0.5659   0.0224
 7U6  CAN  C  C     0   0.466  -2.8190   2.0505   0.1561
 7U6  OAB  O  O     0  -0.470  -2.0014   2.5754   0.8964
 7U6  NAA  N  NH2   0  -0.802  -3.7033   2.7461  -0.5762
 7U6  H1   H  HCH2  0   0.269   4.1753  -1.6148   0.1292
 7U6  H2   H  HCH2  0   0.246   4.4151  -0.3294   1.3146
 7U6  H3   H  HCH2  0   0.247   5.7466   0.1458  -0.7050
 7U6  H4   H  HCH2  0   0.229   4.3190  -0.0047  -1.7207
 7U6  H5   H  HNH1  0   0.345   4.8679   2.0669   0.2553
 7U6  H7   H  HCH2  0   0.247   2.8086   3.0324  -0.2197
 7U6  H8   H  HCH2  0   0.228   2.4959   1.7805  -1.4159
 7U6  H9   H  HCH2  0   0.241   2.6950   1.3716   1.6014
 7U6  H10  H  HCH2  0   0.300   1.2201   1.3075   0.6335
 7U6  H11  H  HNR5  0   0.423  -0.2791  -3.0455  -0.0571
 7U6  H13  H  HCR6  0   0.278  -3.1653  -3.3641  -0.1734
 7U6  H14  H  HCR6  0   0.267  -5.1975  -1.9450  -0.1963
 7U6  H15  H  HCR6  0   0.266  -5.0472   0.4855  -0.0638
 7U6  H16  H  HNH2  0   0.411  -4.2943   2.3095  -1.2624
 7U6  H17  H  HNH2  0   0.404  -3.7205   3.7519  -0.5242

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
 7U6  OAB  CAN  double    1.221  0.020  1.221
 7U6  CAN  NAA  single    1.342  0.020  1.342
 7U6  CAN  CAP  single    1.493  0.020  1.493
 7U6  CAP  CAE  aromatic  1.385  0.020  1.385
 7U6  CAP  CAS  aromatic  1.404  0.020  1.404
 7U6  CAE  CAD  aromatic  1.404  0.020  1.404
 7U6  CAS  NAK  aromatic  1.366  0.020  1.366
 7U6  CAS  CAR  aromatic  1.406  0.020  1.406
 7U6  CAD  CAF  aromatic  1.380  0.020  1.380
 7U6  NAK  CAQ  aromatic  1.307  0.020  1.307
 7U6  CAR  CAF  aromatic  1.392  0.020  1.392
 7U6  CAR  NAM  aromatic  1.360  0.020  1.360
 7U6  NAL  CAG  single    1.452  0.020  1.452
 7U6  NAL  CAH  single    1.452  0.020  1.452
 7U6  CAI  NAT  single    1.458  0.020  1.458
 7U6  CAI  CAG  single    1.527  0.020  1.527
 7U6  CAQ  CAO  single    1.496  0.020  1.496
 7U6  CAQ  NAM  aromatic  1.357  0.020  1.357
 7U6  NAT  CAO  single    1.339  0.020  1.339
 7U6  NAT  CAJ  single    1.459  0.020  1.459
 7U6  CAO  OAC  double    1.229  0.020  1.229
 7U6  CAH  CAJ  single    1.527  0.020  1.527
 7U6  CAI  H1   single    0.970  0.020  1.090
 7U6  CAI  H2   single    0.970  0.020  1.090
 7U6  CAG  H3   single    0.970  0.020  1.090
 7U6  CAG  H4   single    0.970  0.020  1.090
 7U6  NAL  H5   single    0.890  0.020  1.040
 7U6  CAH  H7   single    0.970  0.020  1.090
 7U6  CAH  H8   single    0.970  0.020  1.090
 7U6  CAJ  H9   single    0.970  0.020  1.090
 7U6  CAJ  H10  single    0.970  0.020  1.090
 7U6  NAM  H11  single    0.860  0.020  1.020
 7U6  CAF  H13  single    0.930  0.020  1.080
 7U6  CAD  H14  single    0.930  0.020  1.080
 7U6  CAE  H15  single    0.930  0.020  1.080
 7U6  NAA  H16  single    0.860  0.020  1.020
 7U6  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
 7U6  H2   CAI  H1   108.03  3.000
 7U6  H2   CAI  NAT  108.13  3.000
 7U6  H1   CAI  NAT  110.22  3.000
 7U6  H2   CAI  CAG  109.81  3.000
 7U6  H1   CAI  CAG  110.89  3.000
 7U6  NAT  CAI  CAG  109.70  3.000
 7U6  H4   CAG  H3   107.13  3.000
 7U6  H4   CAG  NAL  108.61  3.000
 7U6  H3   CAG  NAL  109.28  3.000
 7U6  H4   CAG  CAI  108.83  3.000
 7U6  H3   CAG  CAI  109.17  3.000
 7U6  NAL  CAG  CAI  113.62  3.000
 7U6  H5   NAL  CAH  109.15  3.000
 7U6  H5   NAL  CAG  109.12  3.000
 7U6  CAH  NAL  CAG  111.18  3.000
 7U6  H8   CAH  H7   107.21  3.000
 7U6  H8   CAH  CAJ  108.70  3.000
 7U6  H7   CAH  CAJ  109.12  3.000
 7U6  H8   CAH  NAL  108.55  3.000
 7U6  H7   CAH  NAL  109.30  3.000
 7U6  CAJ  CAH  NAL  113.76  3.000
 7U6  H10  CAJ  H9   108.20  3.000
 7U6  H10  CAJ  NAT  110.89  3.000
 7U6  H9   CAJ  NAT  107.74  3.000
 7U6  H10  CAJ  CAH  110.91  3.000
 7U6  H9   CAJ  CAH  109.57  3.000
 7U6  NAT  CAJ  CAH  109.46  3.000
 7U6  CAO  NAT  CAJ  128.17  3.000
 7U6  CAJ  NAT  CAI  112.05  3.000
 7U6  CAO  NAT  CAI  119.68  3.000
 7U6  CAQ  CAO  OAC  115.75  3.000
 7U6  OAC  CAO  NAT  123.38  3.000
 7U6  CAQ  CAO  NAT  120.86  3.000
 7U6  NAK  CAQ  NAM  112.53  3.000
 7U6  NAM  CAQ  CAO  116.77  3.000
 7U6  NAK  CAQ  CAO  130.70  3.000
 7U6  H11  NAM  CAR  127.31  3.000
 7U6  H11  NAM  CAQ  125.25  3.000
 7U6  CAR  NAM  CAQ  107.43  3.000
 7U6  CAS  NAK  CAQ  105.51  3.000
 7U6  CAP  CAS  CAR  119.88  3.000
 7U6  CAR  CAS  NAK  109.69  3.000
 7U6  CAP  CAS  NAK  130.40  3.000
 7U6  CAF  CAR  CAS  122.86  3.000
 7U6  CAF  CAR  NAM  132.30  3.000
 7U6  CAS  CAR  NAM  104.84  3.000
 7U6  H13  CAF  CAD  121.60  3.000
 7U6  H13  CAF  CAR  121.94  3.000
 7U6  CAD  CAF  CAR  116.47  3.000
 7U6  H14  CAD  CAE  118.89  3.000
 7U6  H14  CAD  CAF  119.49  3.000
 7U6  CAE  CAD  CAF  121.62  3.000
 7U6  H15  CAE  CAP  119.72  3.000
 7U6  H15  CAE  CAD  118.24  3.000
 7U6  CAP  CAE  CAD  122.02  3.000
 7U6  CAN  CAP  CAE  121.95  3.000
 7U6  CAE  CAP  CAS  117.15  3.000
 7U6  CAN  CAP  CAS  120.84  3.000
 7U6  NAA  CAN  OAB  123.29  3.000
 7U6  NAA  CAN  CAP  115.19  3.000
 7U6  OAB  CAN  CAP  121.52  3.000
 7U6  H17  NAA  H16  117.31  3.000
 7U6  H17  NAA  CAN  120.03  3.000
 7U6  H16  NAA  CAN  122.31  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
 7U6  CONST_01  CAP  CAS  NAK  CAQ  180.00   0.0  0
 7U6  CONST_02  CAR  CAS  NAK  CAQ    0.00   0.0  0
 7U6  CONST_03  CAS  CAR  NAM  CAQ    0.00   0.0  0
 7U6  CONST_04  CAF  CAR  NAM  CAQ  180.00   0.0  0
 7U6  CONST_05  CAP  CAS  CAR  NAM  180.00   0.0  0
 7U6  CONST_06  NAK  CAS  CAR  NAM    0.00   0.0  0
 7U6  CONST_07  CAD  CAF  CAR  NAM  180.00   0.0  0
 7U6  CONST_08  CAS  NAK  CAQ  NAM    0.00   0.0  0
 7U6  CONST_09  CAE  CAP  CAS  NAK  180.00   0.0  0
 7U6  CONST_10  CAF  CAR  CAS  NAK  180.00   0.0  0
 7U6  CONST_11  CAR  NAM  CAQ  NAK    0.00   0.0  0
 7U6  CONST_12  CAD  CAE  CAP  CAS    0.00   0.0  0
 7U6  CONST_13  CAD  CAF  CAR  CAS    0.00   0.0  0
 7U6  CONST_14  CAE  CAP  CAS  CAR    0.00   0.0  0
 7U6  CONST_15  CAE  CAD  CAF  CAR    0.00   0.0  0
 7U6  CONST_16  CAP  CAE  CAD  CAF    0.00   0.0  0
 7U6  CONST_17  CAP  CAS  CAR  CAF    0.00   0.0  0
 7U6  CONST_18  CAS  NAK  CAQ  CAO  180.00   0.0  0
 7U6  CONST_19  CAR  NAM  CAQ  CAO  180.00   0.0  0
 7U6  CONST_20  CAN  CAP  CAS  NAK    0.00   0.0  0
 7U6  CONST_21  CAN  CAP  CAS  CAR  180.00   0.0  0
 7U6  CONST_22  CAN  CAP  CAE  CAD  180.00   0.0  0
 7U6  CONST_23  CAQ  CAO  NAT  CAI  180.00   0.0  0
 7U6  CONST_24  CAQ  CAO  NAT  CAJ    0.00   0.0  0
 7U6  CONST_25  H13  CAF  CAR  NAM    0.00   0.0  0
 7U6  CONST_26  H11  NAM  CAQ  NAK  180.00   0.0  0
 7U6  CONST_27  H15  CAE  CAP  CAS  180.00   0.0  0
 7U6  CONST_28  H14  CAD  CAF  CAR  180.00   0.0  0
 7U6  CONST_29  OAC  CAO  NAT  CAI    0.00   0.0  0
 7U6  CONST_30  OAC  CAO  NAT  CAJ  180.00   0.0  0
 7U6  CONST_31  H16  NAA  CAN  CAP    0.00   0.0  0
 7U6  CONST_32  H17  NAA  CAN  CAP  180.00   0.0  0
 7U6  Var_01    CAH  CAJ  NAT  CAI   57.16  30.0  1
 7U6  Var_02    CAH  NAL  CAG  CAI  -51.15  30.0  1
 7U6  Var_03    CAJ  CAH  NAL  CAG   51.35  30.0  1
 7U6  Var_04    CAJ  NAT  CAI  CAG  -57.17  30.0  1
 7U6  Var_05    NAT  CAI  CAG  NAL   54.06  30.0  1
 7U6  Var_06    NAT  CAJ  CAH  NAL  -54.25  30.0  1
 7U6  Var_07    NAK  CAQ  CAO  NAT   10.11  30.0  2
 7U6  Var_08    OAB  CAN  CAP  CAS  -36.88  30.0  3

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
 7U6  plan-1  CAO  0.020
 7U6  plan-1  CAQ  0.020
 7U6  plan-1  NAM  0.020
 7U6  plan-1  NAK  0.020
 7U6  plan-1  CAS  0.020
 7U6  plan-1  CAR  0.020
 7U6  plan-1  CAF  0.020
 7U6  plan-1  CAD  0.020
 7U6  plan-1  CAE  0.020
 7U6  plan-1  CAP  0.020
 7U6  plan-1  CAN  0.020
 7U6  plan-1  H11  0.020
 7U6  plan-1  H13  0.020
 7U6  plan-1  H14  0.020
 7U6  plan-1  H15  0.020
 7U6  plan-2  CAP  0.020
 7U6  plan-2  CAN  0.020
 7U6  plan-2  OAB  0.020
 7U6  plan-2  NAA  0.020
 7U6  plan-2  H16  0.020
 7U6  plan-2  H17  0.020
 7U6  plan-3  CAI  0.020
 7U6  plan-3  CAJ  0.020
 7U6  plan-3  NAT  0.020
 7U6  plan-3  CAO  0.020
 7U6  plan-3  OAC  0.020
 7U6  plan-3  CAQ  0.020

