# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 04:04:52 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 7-amino-2-[(2-chlorobenzyl)amino]-1-{[(1S,2S)-2-hydroxycycloheptyl]methyl}-1H-benzimidazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(N)c2n(C[C@@H]3CCCCC[C@@H]3O)c(NCc4ccccc4Cl)nc2c1
#
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
 JZL  JZL  7-amino-2-[(2-chlorobenzyl)amino]-1-{[(1S,2S)-2-hydroxycycloheptyl]methyl}-1H-benzimidazole-5-carboxamide  ligand  59  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JZL
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
 JZL  N1    N   NH2   0  -0.816   6.2002   2.9678  -0.9266
 JZL  C2    C   C     0   0.482   5.2979   2.9967   0.0692
 JZL  O3    O   O     0  -0.491   5.4250   3.7273   1.0446
 JZL  C4    C   CR6   0  -0.049   4.1220   2.0871  -0.0725
 JZL  C5    C   CR16  0  -0.405   4.1801   0.9289  -0.8583
 JZL  C6    C   CR6   0   0.250   3.0985   0.0584  -0.9967
 JZL  N7    N   NH2   0  -0.868   3.1838  -1.0570  -1.8265
 JZL  C8    C   CR56  0   0.313   1.9341   0.4166  -0.3098
 JZL  N9    N   NR5   0  -0.570   0.6721  -0.1515  -0.2179
 JZL  C10   C   CH2   0  -0.366   0.1373  -1.3109  -0.9079
 JZL  C11   C   CH1   0  -0.272   0.0162  -2.5486  -0.0057
 JZL  C12   C   CH2   0  -0.463   1.3599  -3.0278   0.5552
 JZL  C13   C   CH2   0  -0.425   1.2423  -3.5632   1.9820
 JZL  C14   C   CH2   0  -0.426   0.5111  -4.8916   2.1401
 JZL  C15   C   CH2   0  -0.450  -0.8618  -4.9934   1.4766
 JZL  C16   C   CH2   0  -0.484  -0.7874  -4.9931  -0.0506
 JZL  C17   C   CH1   0   0.085  -0.7883  -3.6256  -0.7363
 JZL  O18   O   OH1   0  -0.676  -0.2716  -3.7367  -2.0507
 JZL  C19   C   CR5   0   0.733  -0.0493   0.6640   0.6131
 JZL  N20   N   NH1   0  -0.709  -1.3408   0.4165   0.8964
 JZL  C21   C   CH2   0  -0.347  -2.1798   1.3512   1.6098
 JZL  C22   C   CR6   0   0.170  -3.5214   1.4825   0.9423
 JZL  C23   C   CR16  0  -0.314  -4.6653   0.9991   1.5692
 JZL  C24   C   CR16  0  -0.231  -5.9142   1.0920   0.9707
 JZL  C25   C   CR16  0  -0.275  -6.0338   1.6740  -0.2820
 JZL  C26   C   CR16  0  -0.199  -4.9087   2.1638  -0.9310
 JZL  C27   C   CR6   0  -0.102  -3.6715   2.0629  -0.3159
 JZL  CL28  CL  CL    0  -0.122  -2.2833   2.6982  -1.1397
 JZL  N29   N   N     0  -0.541   0.6316   1.6867   1.0663
 JZL  C30   C   CR56  0   0.166   1.8732   1.5641   0.4988
 JZL  C31   C   CR16  0  -0.402   2.9702   2.4059   0.6332
 JZL  HN1   H   HNH2  0   0.401   7.0020   3.5757  -0.8890
 JZL  HN1A  H   HNH2  0   0.409   6.0277   2.4926  -1.7948
 JZL  H5    H   HCR6  0   0.250   5.1016   0.6560  -1.3596
 JZL  HN7   H   HNH2  0   0.381   4.1219  -1.2232  -2.1602
 JZL  HN7A  H   HNH2  0   0.385   2.8229  -1.9122  -1.4313
 JZL  H10   H   HCH2  0   0.268  -0.8436  -1.0430  -1.3128
 JZL  H10A  H   HCH2  0   0.284   0.7653  -1.5060  -1.7724
 JZL  H11   H   HCH1  0   0.235  -0.5930  -2.2544   0.8563
 JZL  H12   H   HCH2  0   0.235   1.8136  -3.7736  -0.1055
 JZL  H12A  H   HCH2  0   0.232   2.0636  -2.1921   0.5947
 JZL  H13   H   HCH2  0   0.230   2.2443  -3.6729   2.4052
 JZL  H13A  H   HCH2  0   0.215   0.7430  -2.7974   2.5855
 JZL  H14   H   HCH2  0   0.211   1.1379  -5.6922   1.7333
 JZL  H14A  H   HCH2  0   0.227   0.4104  -5.1021   3.2083
 JZL  H15   H   HCH2  0   0.235  -1.3162  -5.9337   1.7970
 JZL  H15A  H   HCH2  0   0.221  -1.5317  -4.2068   1.8395
 JZL  H16   H   HCH2  0   0.223   0.1195  -5.5262  -0.3538
 JZL  H16A  H   HCH2  0   0.239  -1.6234  -5.5665  -0.4622
 JZL  H17   H   HCH1  0   0.203  -1.8275  -3.2643  -0.7774
 JZL  HO18  H   HOH1  0   0.452  -0.7636  -4.4237  -2.5115
 JZL  HN20  H   HNH1  0   0.405  -1.7673  -0.4398   0.5882
 JZL  H21   H   HCH2  0   0.264  -2.3257   1.0339   2.6456
 JZL  H21A  H   HCH2  0   0.275  -1.6660   2.3118   1.6402
 JZL  H23   H   HCR6  0   0.265  -4.5694   0.5405   2.5461
 JZL  H24   H   HCR6  0   0.264  -6.7882   0.7102   1.4809
 JZL  H25   H   HCR6  0   0.269  -7.0008   1.7538  -0.7605
 JZL  H26   H   HCR6  0   0.280  -4.9960   2.6239  -1.9060
 JZL  H31   H   HCR6  0   0.244   2.9171   3.2884   1.2562

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
 JZL  N1   C2    single    1.344  0.020  1.344
 JZL  C2   O3    double    1.225  0.020  1.225
 JZL  C2   C4    single    1.493  0.020  1.493
 JZL  C4   C5    aromatic  1.401  0.020  1.401
 JZL  C4   C31   aromatic  1.388  0.020  1.388
 JZL  C5   C6    aromatic  1.395  0.020  1.395
 JZL  C6   N7    single    1.393  0.020  1.393
 JZL  C6   C8    aromatic  1.398  0.020  1.398
 JZL  C8   N9    aromatic  1.387  0.020  1.387
 JZL  C8   C30   aromatic  1.405  0.020  1.405
 JZL  N9   C10   single    1.451  0.020  1.451
 JZL  N9   C19   aromatic  1.370  0.020  1.370
 JZL  C10  C11   single    1.536  0.020  1.536
 JZL  C11  C12   single    1.533  0.020  1.533
 JZL  C11  C17   single    1.530  0.020  1.530
 JZL  C12  C13   single    1.529  0.020  1.529
 JZL  C13  C14   single    1.525  0.020  1.525
 JZL  C14  C15   single    1.528  0.020  1.528
 JZL  C15  C16   single    1.529  0.020  1.529
 JZL  C16  C17   single    1.530  0.020  1.530
 JZL  C17  O18   single    1.417  0.020  1.417
 JZL  C19  N20   single    1.345  0.020  1.345
 JZL  C19  N29   aromatic  1.310  0.020  1.310
 JZL  N20  C21   single    1.444  0.020  1.444
 JZL  C21  C22   single    1.504  0.020  1.504
 JZL  C22  C23   aromatic  1.391  0.020  1.391
 JZL  C22  C27   aromatic  1.394  0.020  1.394
 JZL  C23  C24   aromatic  1.388  0.020  1.388
 JZL  C24  C25   aromatic  1.386  0.020  1.386
 JZL  C25  C26   aromatic  1.388  0.020  1.388
 JZL  C26  C27   aromatic  1.385  0.020  1.385
 JZL  C27  CL28  single    1.735  0.020  1.735
 JZL  N29  C30   aromatic  1.371  0.020  1.371
 JZL  C30  C31   aromatic  1.389  0.020  1.389
 JZL  N1   HN1   single    0.860  0.020  1.020
 JZL  N1   HN1A  single    0.860  0.020  1.020
 JZL  C5   H5    single    0.930  0.020  1.080
 JZL  N7   HN7   single    0.890  0.020  1.040
 JZL  N7   HN7A  single    0.890  0.020  1.040
 JZL  C10  H10   single    0.970  0.020  1.090
 JZL  C10  H10A  single    0.970  0.020  1.090
 JZL  C11  H11   single    0.970  0.020  1.090
 JZL  C12  H12   single    0.970  0.020  1.090
 JZL  C12  H12A  single    0.970  0.020  1.090
 JZL  C13  H13   single    0.970  0.020  1.090
 JZL  C13  H13A  single    0.970  0.020  1.090
 JZL  C14  H14   single    0.970  0.020  1.090
 JZL  C14  H14A  single    0.970  0.020  1.090
 JZL  C15  H15   single    0.970  0.020  1.090
 JZL  C15  H15A  single    0.970  0.020  1.090
 JZL  C16  H16   single    0.970  0.020  1.090
 JZL  C16  H16A  single    0.970  0.020  1.090
 JZL  C17  H17   single    0.970  0.020  1.090
 JZL  O18  HO18  single    0.850  0.020  0.980
 JZL  N20  HN20  single    0.860  0.020  1.020
 JZL  C21  H21   single    0.970  0.020  1.090
 JZL  C21  H21A  single    0.970  0.020  1.090
 JZL  C23  H23   single    0.930  0.020  1.080
 JZL  C24  H24   single    0.930  0.020  1.080
 JZL  C25  H25   single    0.930  0.020  1.080
 JZL  C26  H26   single    0.930  0.020  1.080
 JZL  C31  H31   single    0.930  0.020  1.080

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
 JZL  HN1A  N1   HN1  117.04  3.000
 JZL  HN1A  N1   C2   122.35  3.000
 JZL  HN1   N1   C2   119.61  3.000
 JZL  C4    C2   O3   121.36  3.000
 JZL  C4    C2   N1   116.44  3.000
 JZL  O3    C2   N1   122.20  3.000
 JZL  C31   C4   C5   120.63  3.000
 JZL  C31   C4   C2   117.73  3.000
 JZL  C5    C4   C2   121.61  3.000
 JZL  H5    C5   C6   117.14  3.000
 JZL  H5    C5   C4   120.18  3.000
 JZL  C6    C5   C4   122.64  3.000
 JZL  C8    C6   N7   123.28  3.000
 JZL  C8    C6   C5   115.91  3.000
 JZL  N7    C6   C5   120.74  3.000
 JZL  HN7A  N7   HN7  108.80  3.000
 JZL  HN7A  N7   C6   115.06  3.000
 JZL  HN7   N7   C6   112.69  3.000
 JZL  C30   C8   N9   104.89  3.000
 JZL  C30   C8   C6   121.86  3.000
 JZL  N9    C8   C6   133.25  3.000
 JZL  C19   N9   C10  124.75  3.000
 JZL  C19   N9   C8   105.99  3.000
 JZL  C10   N9   C8   129.12  3.000
 JZL  H10A  C10  H10  105.53  3.000
 JZL  H10A  C10  C11  111.60  3.000
 JZL  H10   C10  C11  110.11  3.000
 JZL  H10A  C10  N9   108.00  3.000
 JZL  H10   C10  N9   108.09  3.000
 JZL  C11   C10  N9   113.16  3.000
 JZL  H11   C11  C17  105.80  3.000
 JZL  H11   C11  C12  106.47  3.000
 JZL  C17   C11  C12  114.56  3.000
 JZL  H11   C11  C10  106.83  3.000
 JZL  C17   C11  C10  109.15  3.000
 JZL  C12   C11  C10  113.43  3.000
 JZL  H12A  C12  H12  106.02  3.000
 JZL  H12A  C12  C13  106.47  3.000
 JZL  H12   C12  C13  110.89  3.000
 JZL  H12A  C12  C11  109.79  3.000
 JZL  H12   C12  C11  110.82  3.000
 JZL  C13   C12  C11  112.56  3.000
 JZL  H13A  C13  H13  105.94  3.000
 JZL  H13A  C13  C14  109.47  3.000
 JZL  H13   C13  C14  108.19  3.000
 JZL  H13A  C13  C12  107.73  3.000
 JZL  H13   C13  C12  109.02  3.000
 JZL  C14   C13  C12  116.04  3.000
 JZL  H14A  C14  H14  105.95  3.000
 JZL  H14A  C14  C15  109.18  3.000
 JZL  H14   C14  C15  107.72  3.000
 JZL  H14A  C14  C13  108.25  3.000
 JZL  H14   C14  C13  108.90  3.000
 JZL  C15   C14  C13  116.35  3.000
 JZL  H15A  C15  H15  105.46  3.000
 JZL  H15A  C15  C16  111.14  3.000
 JZL  H15   C15  C16  108.27  3.000
 JZL  H15A  C15  C14  110.97  3.000
 JZL  H15   C15  C14  107.67  3.000
 JZL  C16   C15  C14  112.95  3.000
 JZL  H16A  C16  H16  105.87  3.000
 JZL  H16A  C16  C17  107.42  3.000
 JZL  H16   C16  C17  108.16  3.000
 JZL  H16A  C16  C15  109.78  3.000
 JZL  H16   C16  C15  108.47  3.000
 JZL  C17   C16  C15  116.60  3.000
 JZL  H17   C17  O18  109.60  3.000
 JZL  H17   C17  C16  108.10  3.000
 JZL  O18   C17  C16  110.21  3.000
 JZL  H17   C17  C11  106.45  3.000
 JZL  O18   C17  C11  107.84  3.000
 JZL  C16   C17  C11  114.51  3.000
 JZL  HO18  O18  C17  108.28  3.000
 JZL  N29   C19  N20  124.75  3.000
 JZL  N29   C19  N9   113.65  3.000
 JZL  N20   C19  N9   121.59  3.000
 JZL  HN20  N20  C21  117.15  3.000
 JZL  HN20  N20  C19  119.97  3.000
 JZL  C21   N20  C19  122.86  3.000
 JZL  H21A  C21  H21  107.00  3.000
 JZL  H21A  C21  C22  110.85  3.000
 JZL  H21   C21  C22  109.07  3.000
 JZL  H21A  C21  N20  108.08  3.000
 JZL  H21   C21  N20  110.96  3.000
 JZL  C22   C21  N20  110.82  3.000
 JZL  C27   C22  C23  117.57  3.000
 JZL  C27   C22  C21  122.21  3.000
 JZL  C23   C22  C21  120.21  3.000
 JZL  H23   C23  C24  119.79  3.000
 JZL  H23   C23  C22  118.72  3.000
 JZL  C24   C23  C22  121.49  3.000
 JZL  H24   C24  C25  120.30  3.000
 JZL  H24   C24  C23  120.01  3.000
 JZL  C25   C24  C23  119.69  3.000
 JZL  H25   C25  C26  119.44  3.000
 JZL  H25   C25  C24  120.52  3.000
 JZL  C26   C25  C24  120.04  3.000
 JZL  H26   C26  C27  120.22  3.000
 JZL  H26   C26  C25  120.41  3.000
 JZL  C27   C26  C25  119.37  3.000
 JZL  CL28  C27  C26  118.50  3.000
 JZL  CL28  C27  C22  119.67  3.000
 JZL  C26   C27  C22  121.83  3.000
 JZL  C30   N29  C19  104.94  3.000
 JZL  C31   C30  N29  128.39  3.000
 JZL  C31   C30  C8   121.09  3.000
 JZL  N29   C30  C8   110.52  3.000
 JZL  H31   C31  C30  120.76  3.000
 JZL  H31   C31  C4   121.40  3.000
 JZL  C30   C31  C4   117.83  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
 JZL  CONST_01  C8    C6   C5   C4     0.00   0.0  0
 JZL  CONST_02  C8    C30  C31  C4     0.00   0.0  0
 JZL  CONST_03  N29   C30  C31  C4   180.00   0.0  0
 JZL  CONST_04  C30   C31  C4   C5     0.00   0.0  0
 JZL  CONST_05  N9    C8   C6   C5   180.00   0.0  0
 JZL  CONST_06  C30   C8   C6   C5     0.00   0.0  0
 JZL  CONST_07  C31   C4   C5   C6     0.00   0.0  0
 JZL  CONST_08  C19   N9   C8   C6   180.00   0.0  0
 JZL  CONST_09  N29   C30  C8   C6   180.00   0.0  0
 JZL  CONST_10  C31   C30  C8   C6     0.00   0.0  0
 JZL  CONST_11  N29   C19  N9   C8     0.00   0.0  0
 JZL  CONST_12  C19   N29  C30  C8     0.00   0.0  0
 JZL  CONST_13  N29   C30  C8   N9     0.00   0.0  0
 JZL  CONST_14  C31   C30  C8   N9   180.00   0.0  0
 JZL  CONST_15  C30   N29  C19  N9     0.00   0.0  0
 JZL  CONST_16  C30   C8   N9   C19    0.00   0.0  0
 JZL  CONST_17  C31   C30  N29  C19  180.00   0.0  0
 JZL  CONST_18  C25   C24  C23  C22    0.00   0.0  0
 JZL  CONST_19  C25   C26  C27  C22    0.00   0.0  0
 JZL  CONST_20  C26   C27  C22  C23    0.00   0.0  0
 JZL  CONST_21  C26   C25  C24  C23    0.00   0.0  0
 JZL  CONST_22  C27   C22  C23  C24    0.00   0.0  0
 JZL  CONST_23  C27   C26  C25  C24    0.00   0.0  0
 JZL  CONST_24  C6    C5   C4   C2   180.00   0.0  0
 JZL  CONST_25  C30   C31  C4   C2   180.00   0.0  0
 JZL  CONST_26  N7    C6   C5   C4   180.00   0.0  0
 JZL  CONST_27  C10   N9   C8   C6     0.00   0.0  0
 JZL  CONST_28  N9    C8   C6   N7     0.00   0.0  0
 JZL  CONST_29  C30   C8   C6   N7   180.00   0.0  0
 JZL  CONST_30  N20   C19  N9   C8   180.00   0.0  0
 JZL  CONST_31  C30   C8   N9   C10  180.00   0.0  0
 JZL  CONST_32  N29   C19  N9   C10  180.00   0.0  0
 JZL  CONST_33  C30   N29  C19  N20  180.00   0.0  0
 JZL  CONST_34  C24   C23  C22  C21  180.00   0.0  0
 JZL  CONST_35  C26   C27  C22  C21  180.00   0.0  0
 JZL  CONST_36  CL28  C27  C22  C23  180.00   0.0  0
 JZL  CONST_37  CL28  C27  C26  C25  180.00   0.0  0
 JZL  CONST_38  H31   C31  C4   C5   180.00   0.0  0
 JZL  CONST_39  H5    C5   C6   C8   180.00   0.0  0
 JZL  CONST_40  H24   C24  C23  C22  180.00   0.0  0
 JZL  CONST_41  H26   C26  C27  C22  180.00   0.0  0
 JZL  CONST_42  H25   C25  C24  C23  180.00   0.0  0
 JZL  CONST_43  H23   C23  C24  C25  180.00   0.0  0
 JZL  CONST_44  C21   N20  C19  N9   180.00   0.0  0
 JZL  CONST_45  N29   C19  N20  C21    0.00   0.0  0
 JZL  CONST_46  HN7   N7   C6   C5     0.00   0.0  0
 JZL  CONST_48  HN20  N20  C19  N9     0.00   0.0  0
 JZL  CONST_49  HN1   N1   C2   C4   180.00   0.0  0
 JZL  CONST_50  HN1A  N1   C2   C4     0.00   0.0  0
 JZL  Var_01    C11   C10  N9   C8   105.64  30.0  2
 JZL  Var_02    C5    C4   C2   N1    24.38  30.0  2
 JZL  Var_03    C22   C21  N20  C19  134.88  30.0  3
 JZL  Var_04    C23   C22  C21  N20  111.54  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
 JZL  chir_01  C11  C10  C12  C17  positiv
 JZL  chir_02  C17  O18  C11  C16  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
 JZL  plan-1  C21   0.020
 JZL  plan-1  C22   0.020
 JZL  plan-1  C23   0.020
 JZL  plan-1  C24   0.020
 JZL  plan-1  C25   0.020
 JZL  plan-1  C26   0.020
 JZL  plan-1  C27   0.020
 JZL  plan-1  CL28  0.020
 JZL  plan-1  H23   0.020
 JZL  plan-1  H24   0.020
 JZL  plan-1  H25   0.020
 JZL  plan-1  H26   0.020
 JZL  plan-2  C2    0.020
 JZL  plan-2  C4    0.020
 JZL  plan-2  C5    0.020
 JZL  plan-2  C6    0.020
 JZL  plan-2  N7    0.020
 JZL  plan-2  C8    0.020
 JZL  plan-2  N9    0.020
 JZL  plan-2  C10   0.020
 JZL  plan-2  C19   0.020
 JZL  plan-2  N20   0.020
 JZL  plan-2  N29   0.020
 JZL  plan-2  C30   0.020
 JZL  plan-2  C31   0.020
 JZL  plan-2  H5    0.020
 JZL  plan-2  H31   0.020
 JZL  plan-3  C6    0.020
 JZL  plan-3  N7    0.020
 JZL  plan-3  HN7   0.020
 JZL  plan-3  HN7A  0.020
 JZL  plan-4  C19   0.020
 JZL  plan-4  N20   0.020
 JZL  plan-4  C21   0.020
 JZL  plan-4  HN20  0.020
 JZL  plan-5  N1    0.020
 JZL  plan-5  C2    0.020
 JZL  plan-5  O3    0.020
 JZL  plan-5  C4    0.020
 JZL  plan-5  HN1   0.020
 JZL  plan-5  HN1A  0.020

