# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:36:33 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: 4-[(5-{[4-(3-chlorophenyl)-3-oxopiperazin-1-yl]methyl}-1H-imidazol-1-yl)methyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(c1)N2CCN(CC2=O)Cc3cncn3Cc4ccc(cc4)C#N
#
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
 778  778  4-[(5-{[4-(3-chlorophenyl)-3-oxopiperazin-1-yl]methyl}-1H-imidazol-1-yl)methyl]benzonitrile  ligand  49  29  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_778
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
 778  N1    N   NT    -1  -0.428  -0.5090   1.0604   0.9528
 778  C2    C   CH2    0  -0.322  -0.1294   0.0606   1.9243
 778  C3    C   CH2    0  -0.358  -1.7909   1.6731   1.2499
 778  C4    C   CH2    0  -0.391   0.5428   2.0423   0.8315
 778  C5    C   CH2    0  -0.275   1.0370  -0.7330   1.3828
 778  C7    C   CR5    0   0.288  -2.2853   2.5211   0.1321
 778  C8    C   C      0   0.520   1.9107   1.4500   0.5806
 778  N9    N   NT     0  -0.574   2.0887   0.1461   0.8859
 778  N11   N   NR5    0  -0.448  -2.4486   2.0777  -1.1580
 778  C12   C   CR15   0  -0.259  -2.6914   3.8257   0.1086
 778  O13   O   O      0  -0.490   2.8149   2.1476   0.1493
 778  C14   C   CR6    0   0.322   3.3480  -0.4527   0.6156
 778  C16   C   CH2    0  -0.356  -2.1445   0.7599  -1.6689
 778  C17   C   CR15   0   0.087  -2.9376   3.1139  -1.8754
 778  N18   N   N      0  -0.451  -3.0984   4.1847  -1.1445
 778  C20   C   CR16   0  -0.226   3.5252  -1.1536  -0.5695
 778  C21   C   CR16   0  -0.261   4.3775  -0.3642   1.5420
 778  C25   C   CR6    0   0.102  -2.9402  -0.3186  -0.9830
 778  C26   C   CR6    0  -0.041   4.7445  -1.7662  -0.8110
 778  C27   C   CR16   0  -0.266   5.5925  -0.9784   1.2771
 778  C28   C   CR16   0  -0.263  -4.3019  -0.1546  -0.7408
 778  C29   C   CR16   0  -0.285  -2.3159  -1.4976  -0.5922
 778  C30   C   CR16   0  -0.213   5.7863  -1.6864   0.0996
 778  CL31  CL  CL     0  -0.123   4.9681  -2.6451  -2.2874
 778  C32   C   CR16   0  -0.228  -5.0301  -1.1491  -0.1151
 778  C33   C   CR16   0  -0.230  -3.0311  -2.5051   0.0316
 778  C34   C   CR6    0  -0.008  -4.3918  -2.3273   0.2739
 778  C35   C   CSP    0   0.057  -5.1378  -3.3551   0.9247
 778  N36   N   NS     0  -0.252  -5.7423  -4.1840   1.4494
 778  H21A  H   HCH2   0   0.261  -0.9615  -0.6256   2.0906
 778  H22   H   HCH2   0   0.227   0.1315   0.5039   2.8989
 778  H31   H   HCH2   0   0.268  -2.5022   0.8679   1.4553
 778  H32A  H   HCH2   0   0.242  -1.7586   2.2982   2.1560
 778  H41   H   HCH2   0   0.283   0.3354   2.7213   0.0024
 778  H42   H   HCH2   0   0.247   0.6297   2.6725   1.7350
 778  H51   H   HCH2   0   0.242   0.7000  -1.3942   0.5798
 778  H52   H   HCH2   0   0.263   1.4540  -1.3614   2.1704
 778  H12   H   HCR5   0   0.256  -2.7066   4.5175   0.9379
 778  H161  H   HCH2   0   0.295  -2.3716   0.7621  -2.7366
 778  H162  H   HCH2   0   0.282  -1.0788   0.5644  -1.5589
 778  H17   H   HCR5   0   0.282  -3.1494   3.0257  -2.9313
 778  H20   H   HCR6   0   0.282   2.7234  -1.2164  -1.2936
 778  H21   H   HCR6   0   0.268   4.2270   0.1806   2.4647
 778  H27   H   HCR6   0   0.275   6.3998  -0.9084   1.9932
 778  H28   H   HCR6   0   0.267  -4.8039   0.7585  -1.0358
 778  H29   H   HCR6   0   0.266  -1.2579  -1.6325  -0.7765
 778  H30   H   HCR6   0   0.287   6.7328  -2.1685  -0.1034
 778  H32   H   HCR6   0   0.289  -6.0865  -1.0155   0.0732
 778  H33   H   HCR6   0   0.292  -2.5372  -3.4172   0.3374

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
 778  N1   C2    single    1.445  0.020  1.445
 778  N1   C3    single    1.451  0.020  1.451
 778  N1   C4    single    1.444  0.020  1.444
 778  C2   C5    single    1.511  0.020  1.511
 778  C2   H21A  single    0.970  0.020  1.090
 778  C2   H22   single    0.970  0.020  1.090
 778  C3   C7    single    1.488  0.020  1.488
 778  C3   H31   single    0.970  0.020  1.090
 778  C3   H32A  single    0.970  0.020  1.090
 778  C4   C8    single    1.512  0.020  1.512
 778  C4   H41   single    0.970  0.020  1.090
 778  C4   H42   single    0.970  0.020  1.090
 778  C5   N9    single    1.458  0.020  1.458
 778  C5   H51   single    0.970  0.020  1.090
 778  C5   H52   single    0.970  0.020  1.090
 778  C7   N11   aromatic  1.374  0.020  1.374
 778  C7   C12   aromatic  1.367  0.020  1.367
 778  C8   N9    single    1.351  0.020  1.351
 778  C8   O13   double    1.221  0.020  1.221
 778  N9   C14   single    1.420  0.020  1.420
 778  N11  C16   single    1.446  0.020  1.446
 778  N11  C17   aromatic  1.352  0.020  1.352
 778  C12  N18   aromatic  1.366  0.020  1.366
 778  C12  H12   single    0.930  0.020  1.080
 778  C14  C20   aromatic  1.388  0.020  1.388
 778  C14  C21   aromatic  1.388  0.020  1.388
 778  C16  C25   single    1.505  0.020  1.505
 778  C16  H161  single    0.970  0.020  1.090
 778  C16  H162  single    0.970  0.020  1.090
 778  C17  N18   aromatic  1.306  0.020  1.306
 778  C17  H17   single    0.930  0.020  1.080
 778  C20  C26   aromatic  1.386  0.020  1.386
 778  C20  H20   single    0.930  0.020  1.080
 778  C21  C27   aromatic  1.387  0.020  1.387
 778  C21  H21   single    0.930  0.020  1.080
 778  C25  C28   aromatic  1.393  0.020  1.393
 778  C25  C29   aromatic  1.390  0.020  1.390
 778  C26  C30   aromatic  1.386  0.020  1.386
 778  C26  CL31  single    1.733  0.020  1.733
 778  C27  C30   aromatic  1.388  0.020  1.388
 778  C27  H27   single    0.930  0.020  1.080
 778  C28  C32   aromatic  1.382  0.020  1.382
 778  C28  H28   single    0.930  0.020  1.080
 778  C29  C33   aromatic  1.384  0.020  1.384
 778  C29  H29   single    0.930  0.020  1.080
 778  C30  H30   single    0.930  0.020  1.080
 778  C32  C34   aromatic  1.395  0.020  1.395
 778  C32  H32   single    0.930  0.020  1.080
 778  C33  C34   aromatic  1.394  0.020  1.394
 778  C33  H33   single    0.930  0.020  1.080
 778  C34  C35   single    1.427  0.020  1.427
 778  C35  N36   triple    1.152  0.020  1.152

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
 778  C4    N1   C3    111.93  3.000
 778  C4    N1   C2    109.61  3.000
 778  C3    N1   C2    112.74  3.000
 778  H22   C2   H21A  107.38  3.000
 778  H22   C2   C5    110.21  3.000
 778  H21A  C2   C5    108.24  3.000
 778  H22   C2   N1    112.24  3.000
 778  H21A  C2   N1    109.71  3.000
 778  C5    C2   N1    108.98  3.000
 778  H32A  C3   H31   106.41  3.000
 778  H32A  C3   C7    107.72  3.000
 778  H31   C3   C7    110.15  3.000
 778  H32A  C3   N1    112.47  3.000
 778  H31   C3   N1    107.58  3.000
 778  C7    C3   N1    112.36  3.000
 778  H42   C4   H41   106.33  3.000
 778  H42   C4   C8    106.74  3.000
 778  H41   C4   C8    106.84  3.000
 778  H42   C4   N1    112.11  3.000
 778  H41   C4   N1    110.39  3.000
 778  C8    C4   N1    114.00  3.000
 778  H52   C5   H51   107.44  3.000
 778  H52   C5   N9    108.53  3.000
 778  H51   C5   N9    109.67  3.000
 778  H52   C5   C2    109.81  3.000
 778  H51   C5   C2    110.05  3.000
 778  N9    C5   C2    111.24  3.000
 778  C12   C7   N11   104.87  3.000
 778  C12   C7   C3    130.99  3.000
 778  N11   C7   C3    124.13  3.000
 778  O13   C8   N9    122.26  3.000
 778  O13   C8   C4    120.33  3.000
 778  N9    C8   C4    117.38  3.000
 778  C14   N9   C8    118.73  3.000
 778  C14   N9   C5    116.76  3.000
 778  C8    N9   C5    124.32  3.000
 778  C17   N11  C16   125.96  3.000
 778  C17   N11  C7    107.09  3.000
 778  C16   N11  C7    126.94  3.000
 778  H12   C12  N18   122.14  3.000
 778  H12   C12  C7    127.05  3.000
 778  N18   C12  C7    110.81  3.000
 778  C21   C14  C20   120.49  3.000
 778  C21   C14  N9    120.25  3.000
 778  C20   C14  N9    119.24  3.000
 778  H162  C16  H161  107.61  3.000
 778  H162  C16  C25   110.04  3.000
 778  H161  C16  C25   109.70  3.000
 778  H162  C16  N11   109.49  3.000
 778  H161  C16  N11   107.46  3.000
 778  C25   C16  N11   112.38  3.000
 778  H17   C17  N18   126.13  3.000
 778  H17   C17  N11   121.79  3.000
 778  N18   C17  N11   112.08  3.000
 778  C17   N18  C12   105.14  3.000
 778  H20   C20  C26   120.64  3.000
 778  H20   C20  C14   120.39  3.000
 778  C26   C20  C14   118.97  3.000
 778  H21   C21  C27   120.51  3.000
 778  H21   C21  C14   119.88  3.000
 778  C27   C21  C14   119.61  3.000
 778  C29   C25  C28   119.34  3.000
 778  C29   C25  C16   119.88  3.000
 778  C28   C25  C16   120.77  3.000
 778  CL31  C26  C30   119.48  3.000
 778  CL31  C26  C20   119.10  3.000
 778  C30   C26  C20   121.43  3.000
 778  H27   C27  C30   119.39  3.000
 778  H27   C27  C21   119.92  3.000
 778  C30   C27  C21   120.69  3.000
 778  H28   C28  C32   119.06  3.000
 778  H28   C28  C25   120.34  3.000
 778  C32   C28  C25   120.60  3.000
 778  H29   C29  C33   119.42  3.000
 778  H29   C29  C25   119.79  3.000
 778  C33   C29  C25   120.80  3.000
 778  H30   C30  C27   120.60  3.000
 778  H30   C30  C26   120.58  3.000
 778  C27   C30  C26   118.81  3.000
 778  H32   C32  C34   120.17  3.000
 778  H32   C32  C28   120.30  3.000
 778  C34   C32  C28   119.52  3.000
 778  H33   C33  C34   120.29  3.000
 778  H33   C33  C29   120.36  3.000
 778  C34   C33  C29   119.35  3.000
 778  C35   C34  C33   119.86  3.000
 778  C35   C34  C32   119.75  3.000
 778  C33   C34  C32   120.39  3.000
 778  N36   C35  C34   180.00  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
 778  CONST_01  N18   C17  N11  C7     0.00   0.0  0
 778  CONST_02  C17   N18  C12  C7     0.00   0.0  0
 778  CONST_03  N18   C12  C7   N11    0.00   0.0  0
 778  CONST_04  C12   N18  C17  N11    0.00   0.0  0
 778  CONST_05  C17   N11  C7   C12    0.00   0.0  0
 778  CONST_06  C30   C26  C20  C14    0.00   0.0  0
 778  CONST_07  C30   C27  C21  C14    0.00   0.0  0
 778  CONST_08  C27   C21  C14  C20    0.00   0.0  0
 778  CONST_09  C27   C30  C26  C20    0.00   0.0  0
 778  CONST_10  C26   C20  C14  C21    0.00   0.0  0
 778  CONST_11  C26   C30  C27  C21    0.00   0.0  0
 778  CONST_12  C34   C32  C28  C25    0.00   0.0  0
 778  CONST_13  C34   C33  C29  C25    0.00   0.0  0
 778  CONST_14  C33   C29  C25  C28    0.00   0.0  0
 778  CONST_15  C33   C34  C32  C28    0.00   0.0  0
 778  CONST_16  C32   C28  C25  C29    0.00   0.0  0
 778  CONST_17  C32   C34  C33  C29    0.00   0.0  0
 778  CONST_18  C26   C20  C14  N9   180.00   0.0  0
 778  CONST_19  C27   C21  C14  N9   180.00   0.0  0
 778  CONST_20  C5    N9   C8   C4     0.00   0.0  0
 778  CONST_21  C14   N9   C8   C4   180.00   0.0  0
 778  CONST_22  C17   N11  C7   C3   180.00   0.0  0
 778  CONST_23  N18   C12  C7   C3   180.00   0.0  0
 778  CONST_24  C16   N11  C7   C12  180.00   0.0  0
 778  CONST_25  CL31  C26  C20  C14  180.00   0.0  0
 778  CONST_26  N18   C17  N11  C16  180.00   0.0  0
 778  CONST_27  C32   C28  C25  C16  180.00   0.0  0
 778  CONST_28  C33   C29  C25  C16  180.00   0.0  0
 778  CONST_29  CL31  C26  C30  C27  180.00   0.0  0
 778  CONST_30  C35   C34  C32  C28  180.00   0.0  0
 778  CONST_31  C35   C34  C33  C29  180.00   0.0  0
 778  CONST_32  O13   C8   N9   C5   180.00   0.0  0
 778  CONST_33  C14   N9   C8   O13    0.00   0.0  0
 778  CONST_34  H17   C17  N11  C7   180.00   0.0  0
 778  CONST_35  H20   C20  C14  N9     0.00   0.0  0
 778  CONST_36  H21   C21  C14  N9     0.00   0.0  0
 778  CONST_37  H12   C12  C7   N11  180.00   0.0  0
 778  CONST_38  H27   C27  C21  C14  180.00   0.0  0
 778  CONST_39  H30   C30  C26  C20  180.00   0.0  0
 778  CONST_40  H32   C32  C28  C25  180.00   0.0  0
 778  CONST_41  H33   C33  C29  C25  180.00   0.0  0
 778  CONST_42  H29   C29  C25  C28  180.00   0.0  0
 778  CONST_43  H28   C28  C25  C29  180.00   0.0  0
 778  Var_01    N9    C5   C2   N1    49.31  30.0  1
 778  Var_02    N9    C8   C4   N1   -19.14  30.0  1
 778  Var_03    C8    N9   C5   C2   -18.05  30.0  1
 778  Var_04    C20   C14  N9   C5    79.55  30.0  2
 778  Var_05    N11   C7   C3   N1    55.20  30.0  2
 778  Var_06    C25   C16  N11  C7    60.61  30.0  2
 778  Var_07    C28   C25  C16  N11   44.24  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
 778  chir_01  N1  C3  C2  C4  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
 778  plan-1  C3    0.020
 778  plan-1  C7    0.020
 778  plan-1  N11   0.020
 778  plan-1  C12   0.020
 778  plan-1  C16   0.020
 778  plan-1  C17   0.020
 778  plan-1  N18   0.020
 778  plan-1  H12   0.020
 778  plan-1  H17   0.020
 778  plan-2  N9    0.020
 778  plan-2  C14   0.020
 778  plan-2  C20   0.020
 778  plan-2  C21   0.020
 778  plan-2  C26   0.020
 778  plan-2  C27   0.020
 778  plan-2  C30   0.020
 778  plan-2  CL31  0.020
 778  plan-2  H20   0.020
 778  plan-2  H21   0.020
 778  plan-2  H27   0.020
 778  plan-2  H30   0.020
 778  plan-3  C16   0.020
 778  plan-3  C25   0.020
 778  plan-3  C28   0.020
 778  plan-3  C29   0.020
 778  plan-3  C32   0.020
 778  plan-3  C33   0.020
 778  plan-3  C34   0.020
 778  plan-3  C35   0.020
 778  plan-3  N36   0.020
 778  plan-3  H28   0.020
 778  plan-3  H29   0.020
 778  plan-3  H32   0.020
 778  plan-3  H33   0.020
 778  plan-4  C4    0.020
 778  plan-4  C5    0.020
 778  plan-4  C8    0.020
 778  plan-4  N9    0.020
 778  plan-4  O13   0.020
 778  plan-4  C14   0.020

