# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 13:00:03 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-[1,3-dimethyl-6-[(2R)-2-methylpiperazin-1-yl]-2-oxidanylidene-benzimidazol-5-yl]-2-methoxy-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1C(=O)Nc2cc3N(C)C(=O)N(C)c3cc2N4CCNC[C@H]4C
#
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
 LF1  LF1  N-[1,3-dimethyl-6-[(2R)-2-methylpiperazin-1-yl]-2-oxidanylidene-benzimidazol-5-yl]-2-methoxy-benzamide  ligand  57  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LF1
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
 LF1  C01   C  CH3   0  -0.439   5.1602   2.4917   1.5310
 LF1  O05   O  O2    0  -0.458   4.0845   1.9644   0.7776
 LF1  C06   C  CR6   0   0.386   4.2920   0.8691   0.0334
 LF1  C07   C  CR16  0  -0.384   5.5219   0.2226  -0.0731
 LF1  C09   C  CR16  0  -0.238   5.6424  -0.9244  -0.8472
 LF1  C11   C  CR16  0  -0.272   4.5486  -1.4492  -1.5161
 LF1  C13   C  CR16  0  -0.264   3.3224  -0.8103  -1.4021
 LF1  C15   C  CR6   0  -0.170   3.1786   0.3451  -0.6418
 LF1  C16   C  C     0   0.512   1.8522   1.0347  -0.5842
 LF1  O17   O  O     0  -0.464   1.7158   2.2224  -0.8252
 LF1  N18   N  NH1   0  -0.727   0.8441   0.1948  -0.2654
 LF1  C20   C  CR6   0   0.321  -0.5334   0.4073  -0.2244
 LF1  C21   C  CR16  0  -0.420  -1.1424   1.6570  -0.3718
 LF1  C23   C  CR56  0   0.365  -2.5193   1.6962  -0.2838
 LF1  N24   N  NR5   0  -0.586  -3.3957   2.7541  -0.3686
 LF1  C25   C  CH3   0  -0.535  -3.0269   4.1263  -0.6014
 LF1  C29   C  CR5   0   0.653  -4.6886   2.3057  -0.2162
 LF1  O30   O  O     0  -0.505  -5.7026   2.9816  -0.2436
 LF1  N31   N  NR5   0  -0.586  -4.6048   0.9475  -0.0255
 LF1  C32   C  CH3   0  -0.536  -5.7285   0.0743   0.1909
 LF1  C36   C  CR56  0   0.330  -3.2851   0.5509  -0.0634
 LF1  C37   C  CR16  0  -0.338  -2.6893  -0.6850   0.0735
 LF1  C39   C  CR6   0   0.204  -1.3005  -0.7535  -0.0053
 LF1  N40   N  NT    0  -0.535  -0.5915  -1.9795   0.1168
 LF1  C41   C  CH2   0  -0.300  -0.6818  -2.8104  -1.0816
 LF1  C44   C  CH2   0  -0.323   0.3236  -3.9471  -0.9987
 LF1  N47   N  NH1   0  -0.580   0.1845  -4.7412   0.2075
 LF1  C49   C  CH2   0  -0.296   0.1776  -3.8955   1.3852
 LF1  C52   C  CH1   0  -0.084  -0.8224  -2.7377   1.3487
 LF1  C54   C  CH3   0  -0.678  -0.6424  -1.8664   2.5800
 LF1  H011  H  HCH3  0   0.232   5.5473   1.7662   2.2508
 LF1  H012  H  HCH3  0   0.233   5.9800   2.8297   0.8920
 LF1  H013  H  HCH3  0   0.262   4.7637   3.3465   2.0727
 LF1  H07   H  HCR6  0   0.287   6.3937   0.5978   0.4449
 LF1  H09   H  HCR6  0   0.267   6.6077  -1.4080  -0.9206
 LF1  H11   H  HCR6  0   0.261   4.6443  -2.3410  -2.1199
 LF1  H13   H  HCR6  0   0.266   2.4656  -1.2060  -1.9351
 LF1  H18   H  HNH1  0   0.401   1.0658  -0.7701  -0.0381
 LF1  H21   H  HCR6  0   0.291  -0.5619   2.5507  -0.5371
 LF1  H251  H  HCH3  0   0.254  -2.6583   4.2688  -1.6174
 LF1  H252  H  HCH3  0   0.268  -3.8972   4.7588  -0.4547
 LF1  H253  H  HCH3  0   0.256  -2.2533   4.4349   0.1007
 LF1  H321  H  HCH3  0   0.268  -6.6422   0.6612   0.1838
 LF1  H322  H  HCH3  0   0.254  -5.7911  -0.6781  -0.5950
 LF1  H323  H  HCH3  0   0.254  -5.6459  -0.4290   1.1541
 LF1  H37   H  HCR6  0   0.274  -3.2727  -1.5812   0.2452
 LF1  H411  H  HCH2  0   0.212  -1.6959  -3.2212  -1.2103
 LF1  H412  H  HCH2  0   0.246  -0.4753  -2.1894  -1.9565
 LF1  H52   H  HCH1  0   0.205  -1.8408  -3.1635   1.3549
 LF1  H441  H  HCH2  0   0.243   0.2244  -4.5938  -1.8722
 LF1  H442  H  HCH2  0   0.214   1.3364  -3.5289  -1.0208
 LF1  H47   H  HNH1  0   0.342  -0.6795  -5.2695   0.1649
 LF1  H491  H  HCH2  0   0.238  -0.0197  -4.5129   2.2642
 LF1  H492  H  HCH2  0   0.214   1.1817  -3.4722   1.5089
 LF1  H541  H  HCH3  0   0.243  -1.3850  -1.0721   2.6449
 LF1  H542  H  HCH3  0   0.239  -0.7327  -2.4754   3.4805
 LF1  H543  H  HCH3  0   0.224   0.3474  -1.4054   2.5855

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
 LF1  C01  O05   single    1.415  0.020  1.415
 LF1  O05  C06   single    1.340  0.020  1.340
 LF1  C06  C07   aromatic  1.394  0.020  1.394
 LF1  C06  C15   aromatic  1.404  0.020  1.404
 LF1  C07  C09   aromatic  1.389  0.020  1.389
 LF1  C09  C11   aromatic  1.385  0.020  1.385
 LF1  C11  C13   aromatic  1.387  0.020  1.387
 LF1  C13  C15   aromatic  1.391  0.020  1.391
 LF1  C15  C16   single    1.496  0.020  1.496
 LF1  C16  O17   double    1.220  0.020  1.220
 LF1  C16  N18   single    1.350  0.020  1.350
 LF1  N18  C20   single    1.394  0.020  1.394
 LF1  C20  C21   aromatic  1.398  0.020  1.398
 LF1  C20  C39   aromatic  1.409  0.020  1.409
 LF1  C21  C23   aromatic  1.380  0.020  1.380
 LF1  C23  N24   single    1.376  0.020  1.376
 LF1  C23  C36   aromatic  1.395  0.020  1.395
 LF1  N24  C25   single    1.440  0.020  1.440
 LF1  N24  C29   single    1.377  0.020  1.377
 LF1  C29  O30   double    1.219  0.020  1.219
 LF1  C29  N31   single    1.374  0.020  1.374
 LF1  N31  C32   single    1.439  0.020  1.439
 LF1  N31  C36   single    1.379  0.020  1.379
 LF1  C36  C37   aromatic  1.379  0.020  1.379
 LF1  C37  C39   aromatic  1.393  0.020  1.393
 LF1  C39  N40   single    1.422  0.020  1.422
 LF1  N40  C41   single    1.461  0.020  1.461
 LF1  N40  C52   single    1.465  0.020  1.465
 LF1  C41  C44   single    1.520  0.020  1.520
 LF1  C44  N47   single    1.451  0.020  1.451
 LF1  N47  C49   single    1.450  0.020  1.450
 LF1  C49  C52   single    1.530  0.020  1.530
 LF1  C52  C54   single    1.519  0.020  1.519
 LF1  C01  H011  single    0.970  0.020  1.090
 LF1  C01  H012  single    0.970  0.020  1.090
 LF1  C01  H013  single    0.970  0.020  1.090
 LF1  C07  H07   single    0.930  0.020  1.080
 LF1  C09  H09   single    0.930  0.020  1.080
 LF1  C11  H11   single    0.930  0.020  1.080
 LF1  C13  H13   single    0.930  0.020  1.080
 LF1  N18  H18   single    0.860  0.020  1.020
 LF1  C21  H21   single    0.930  0.020  1.080
 LF1  C25  H251  single    0.970  0.020  1.090
 LF1  C25  H252  single    0.970  0.020  1.090
 LF1  C25  H253  single    0.970  0.020  1.090
 LF1  C32  H321  single    0.970  0.020  1.090
 LF1  C32  H322  single    0.970  0.020  1.090
 LF1  C32  H323  single    0.970  0.020  1.090
 LF1  C37  H37   single    0.930  0.020  1.080
 LF1  C41  H411  single    0.970  0.020  1.090
 LF1  C41  H412  single    0.970  0.020  1.090
 LF1  C52  H52   single    0.970  0.020  1.090
 LF1  C44  H441  single    0.970  0.020  1.090
 LF1  C44  H442  single    0.970  0.020  1.090
 LF1  N47  H47   single    0.890  0.020  1.040
 LF1  C49  H491  single    0.970  0.020  1.090
 LF1  C49  H492  single    0.970  0.020  1.090
 LF1  C54  H541  single    0.970  0.020  1.090
 LF1  C54  H542  single    0.970  0.020  1.090
 LF1  C54  H543  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
 LF1  H013  C01  H012  108.77  3.000
 LF1  H013  C01  H011  108.85  3.000
 LF1  H012  C01  H011  108.95  3.000
 LF1  H013  C01  O05   106.33  3.000
 LF1  H012  C01  O05   111.97  3.000
 LF1  H011  C01  O05   111.87  3.000
 LF1  C06   O05  C01   118.84  3.000
 LF1  C15   C06  C07   119.35  3.000
 LF1  C15   C06  O05   116.70  3.000
 LF1  C07   C06  O05   123.93  3.000
 LF1  H07   C07  C09   118.92  3.000
 LF1  H07   C07  C06   120.93  3.000
 LF1  C09   C07  C06   120.15  3.000
 LF1  H09   C09  C11   120.14  3.000
 LF1  H09   C09  C07   118.96  3.000
 LF1  C11   C09  C07   120.89  3.000
 LF1  H11   C11  C13   120.26  3.000
 LF1  H11   C11  C09   120.82  3.000
 LF1  C13   C11  C09   118.92  3.000
 LF1  H13   C13  C15   119.37  3.000
 LF1  H13   C13  C11   119.35  3.000
 LF1  C15   C13  C11   121.26  3.000
 LF1  C16   C15  C13   119.72  3.000
 LF1  C16   C15  C06   120.84  3.000
 LF1  C13   C15  C06   119.42  3.000
 LF1  N18   C16  O17   124.68  3.000
 LF1  N18   C16  C15   112.60  3.000
 LF1  O17   C16  C15   122.72  3.000
 LF1  H18   N18  C20   110.72  3.000
 LF1  H18   N18  C16   118.74  3.000
 LF1  C20   N18  C16   130.51  3.000
 LF1  C39   C20  C21   121.06  3.000
 LF1  C39   C20  N18   114.64  3.000
 LF1  C21   C20  N18   124.30  3.000
 LF1  H21   C21  C23   121.55  3.000
 LF1  H21   C21  C20   121.49  3.000
 LF1  C23   C21  C20   116.95  3.000
 LF1  C36   C23  N24   106.93  3.000
 LF1  C36   C23  C21   122.30  3.000
 LF1  N24   C23  C21   130.77  3.000
 LF1  C29   N24  C25   124.67  3.000
 LF1  C29   N24  C23   109.92  3.000
 LF1  C25   N24  C23   125.40  3.000
 LF1  H253  C25  H252  108.49  3.000
 LF1  H253  C25  H251  108.88  3.000
 LF1  H252  C25  H251  108.71  3.000
 LF1  H253  C25  N24   110.34  3.000
 LF1  H252  C25  N24   109.14  3.000
 LF1  H251  C25  N24   111.21  3.000
 LF1  N31   C29  O30   127.01  3.000
 LF1  N31   C29  N24   106.26  3.000
 LF1  O30   C29  N24   126.73  3.000
 LF1  C36   N31  C32   125.23  3.000
 LF1  C36   N31  C29   109.81  3.000
 LF1  C32   N31  C29   124.95  3.000
 LF1  H323  C32  H322  108.83  3.000
 LF1  H323  C32  H321  108.61  3.000
 LF1  H322  C32  H321  108.67  3.000
 LF1  H323  C32  N31   110.72  3.000
 LF1  H322  C32  N31   110.81  3.000
 LF1  H321  C32  N31   109.15  3.000
 LF1  C37   C36  N31   131.98  3.000
 LF1  C37   C36  C23   120.95  3.000
 LF1  N31   C36  C23   107.07  3.000
 LF1  H37   C37  C39   120.36  3.000
 LF1  H37   C37  C36   121.65  3.000
 LF1  C39   C37  C36   117.99  3.000
 LF1  N40   C39  C37   122.33  3.000
 LF1  N40   C39  C20   116.91  3.000
 LF1  C37   C39  C20   120.75  3.000
 LF1  C52   N40  C41   112.69  3.000
 LF1  C52   N40  C39   116.11  3.000
 LF1  C41   N40  C39   112.91  3.000
 LF1  H412  C41  H411  107.00  3.000
 LF1  H412  C41  C44   110.11  3.000
 LF1  H411  C41  C44   109.66  3.000
 LF1  H412  C41  N40   108.78  3.000
 LF1  H411  C41  N40   111.39  3.000
 LF1  C44   C41  N40   109.86  3.000
 LF1  H442  C44  H441  107.09  3.000
 LF1  H442  C44  N47   108.32  3.000
 LF1  H441  C44  N47   109.41  3.000
 LF1  H442  C44  C41   108.96  3.000
 LF1  H441  C44  C41   109.84  3.000
 LF1  N47   C44  C41   113.03  3.000
 LF1  H47   N47  C49   109.52  3.000
 LF1  H47   N47  C44   109.40  3.000
 LF1  C49   N47  C44   110.89  3.000
 LF1  H492  C49  H491  107.03  3.000
 LF1  H492  C49  C52   108.00  3.000
 LF1  H491  C49  C52   109.20  3.000
 LF1  H492  C49  N47   108.21  3.000
 LF1  H491  C49  N47   108.96  3.000
 LF1  C52   C49  N47   115.15  3.000
 LF1  H52   C52  C54   109.03  3.000
 LF1  H52   C52  C49   108.12  3.000
 LF1  C54   C52  C49   109.70  3.000
 LF1  H52   C52  N40   110.48  3.000
 LF1  C54   C52  N40   111.47  3.000
 LF1  C49   C52  N40   107.98  3.000
 LF1  H543  C54  H542  107.85  3.000
 LF1  H543  C54  H541  108.05  3.000
 LF1  H542  C54  H541  107.54  3.000
 LF1  H543  C54  C52   110.72  3.000
 LF1  H542  C54  C52   109.82  3.000
 LF1  H541  C54  C52   112.69  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
 LF1  CONST_01  C11   C09  C07  C06     0.00   0.0  0
 LF1  CONST_02  C11   C13  C15  C06     0.00   0.0  0
 LF1  CONST_03  C13   C15  C06  C07     0.00   0.0  0
 LF1  CONST_04  C13   C11  C09  C07     0.00   0.0  0
 LF1  CONST_05  C15   C06  C07  C09     0.00   0.0  0
 LF1  CONST_06  C15   C13  C11  C09     0.00   0.0  0
 LF1  CONST_07  C36   C23  C21  C20     0.00   0.0  0
 LF1  CONST_08  C36   C37  C39  C20     0.00   0.0  0
 LF1  CONST_09  C37   C39  C20  C21     0.00   0.0  0
 LF1  CONST_10  C37   C36  C23  C21     0.00   0.0  0
 LF1  CONST_11  C39   C20  C21  C23     0.00   0.0  0
 LF1  CONST_12  C39   C37  C36  C23     0.00   0.0  0
 LF1  CONST_13  N40   C39  C20  C21   180.00   0.0  0
 LF1  CONST_14  N40   C39  C37  C36   180.00   0.0  0
 LF1  CONST_15  N31   C29  N24  C23     0.00   0.0  0
 LF1  CONST_16  C29   N31  C36  C23     0.00   0.0  0
 LF1  CONST_17  N31   C36  C23  N24     0.00   0.0  0
 LF1  CONST_18  C36   N31  C29  N24     0.00   0.0  0
 LF1  CONST_19  C36   C23  N24  C29     0.00   0.0  0
 LF1  CONST_20  C09   C07  C06  O05   180.00   0.0  0
 LF1  CONST_21  C13   C15  C06  O05   180.00   0.0  0
 LF1  CONST_22  C16   C15  C06  C07   180.00   0.0  0
 LF1  CONST_23  C16   C15  C13  C11   180.00   0.0  0
 LF1  CONST_24  C23   C21  C20  N18   180.00   0.0  0
 LF1  CONST_25  C37   C39  C20  N18   180.00   0.0  0
 LF1  CONST_26  N40   C39  C20  N18     0.00   0.0  0
 LF1  CONST_27  O30   C29  N24  C23   180.00   0.0  0
 LF1  CONST_28  C32   N31  C36  C23   180.00   0.0  0
 LF1  CONST_29  C32   N31  C29  N24   180.00   0.0  0
 LF1  CONST_30  C36   C23  N24  C25   180.00   0.0  0
 LF1  CONST_31  N31   C29  N24  C25   180.00   0.0  0
 LF1  CONST_32  C36   N31  C29  O30   180.00   0.0  0
 LF1  CONST_33  H09   C09  C07  C06   180.00   0.0  0
 LF1  CONST_34  H13   C13  C15  C06   180.00   0.0  0
 LF1  CONST_35  H11   C11  C09  C07   180.00   0.0  0
 LF1  CONST_36  H07   C07  C09  C11   180.00   0.0  0
 LF1  CONST_37  H37   C37  C39  C20   180.00   0.0  0
 LF1  CONST_38  H21   C21  C23  N24     0.00   0.0  0
 LF1  CONST_39  C20   N18  C16  C15   180.00   0.0  0
 LF1  CONST_40  C21   C20  N18  C16     0.00   0.0  0
 LF1  CONST_41  C39   C20  N18  C16   180.00   0.0  0
 LF1  CONST_42  O30   C29  N24  C25     0.00   0.0  0
 LF1  CONST_43  C32   N31  C29  O30     0.00   0.0  0
 LF1  CONST_44  H18   N18  C20  C21   180.00   0.0  0
 LF1  CONST_45  C20   N18  C16  O17     0.00   0.0  0
 LF1  Var_01    C41   N40  C39  C20  -103.99  30.0  2
 LF1  Var_02    C44   C41  N40  C39   168.01  30.0  1
 LF1  Var_03    N47   C44  C41  N40    54.90  30.0  1
 LF1  Var_04    C49   N47  C44  C41   -51.56  30.0  1
 LF1  Var_05    C52   C49  N47  C44    51.82  30.0  1
 LF1  Var_06    C07   C06  O05  C01    -1.51  30.0  2
 LF1  Var_07    O17   C16  C15  C06    50.78  30.0  2
 LF1  Var_08    H251  C25  N24  C23    69.43  30.0  3
 LF1  Var_09    H321  C32  N31  C29    -0.31  30.0  3
 LF1  Var_10    H011  C01  O05  C06   -59.60  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
 LF1  chir_01  C52  N40  C49  C54  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
 LF1  plan-1  O05  0.020
 LF1  plan-1  C06  0.020
 LF1  plan-1  C07  0.020
 LF1  plan-1  C09  0.020
 LF1  plan-1  C11  0.020
 LF1  plan-1  C13  0.020
 LF1  plan-1  C15  0.020
 LF1  plan-1  C16  0.020
 LF1  plan-1  H07  0.020
 LF1  plan-1  H09  0.020
 LF1  plan-1  H11  0.020
 LF1  plan-1  H13  0.020
 LF1  plan-2  N18  0.020
 LF1  plan-2  C20  0.020
 LF1  plan-2  C21  0.020
 LF1  plan-2  C23  0.020
 LF1  plan-2  N24  0.020
 LF1  plan-2  C25  0.020
 LF1  plan-2  C29  0.020
 LF1  plan-2  O30  0.020
 LF1  plan-2  N31  0.020
 LF1  plan-2  C32  0.020
 LF1  plan-2  C36  0.020
 LF1  plan-2  C37  0.020
 LF1  plan-2  C39  0.020
 LF1  plan-2  N40  0.020
 LF1  plan-2  H21  0.020
 LF1  plan-2  H37  0.020
 LF1  plan-3  C15  0.020
 LF1  plan-3  C16  0.020
 LF1  plan-3  O17  0.020
 LF1  plan-3  N18  0.020
 LF1  plan-3  C20  0.020
 LF1  plan-3  H18  0.020

