# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 05:08:53 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(CC(=O)c2ccc(cc2)C#N)c(cc1OC)[N+]([O-])=O
#
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
 2XK  2XK  4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile  ligand  38  24  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2XK
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
 2XK  C10  C  CR16   0  -0.218  -4.6058  -0.3312   1.1683
 2XK  C15  C  CR16   0  -0.254  -3.4528   0.1089  -1.3266
 2XK  C17  C  CR6    0   0.204   1.7288   0.9314   0.0993
 2XK  C01  C  CH3    0  -0.446   3.7394  -3.5950   0.7010
 2XK  C03  C  CR6    0   0.373   3.3652  -1.2997   0.2596
 2XK  C04  C  CR16   0  -0.470   2.0065  -1.3888   0.5158
 2XK  C05  C  CR6    0   0.208   1.1537  -0.2887   0.4451
 2XK  C06  C  CH2    0  -0.703  -0.2940  -0.5158   0.7625
 2XK  C07  C  C      0   0.401  -1.1820  -0.4012  -0.4568
 2XK  C08  C  CR6    0   0.005  -2.6509  -0.2436  -0.2409
 2XK  C09  C  CR16   0  -0.281  -3.2378  -0.4597   1.0039
 2XK  C11  C  CR6    0   0.005  -5.3932   0.0321   0.0787
 2XK  C12  C  CSP    0   0.064  -6.8046   0.1768   0.2439
 2XK  N13  N  NS     0  -0.241  -7.9426   0.2938   0.3776
 2XK  C14  C  CR16   0  -0.225  -4.8173   0.2563  -1.1721
 2XK  O16  O  O      0  -0.372  -0.7314  -0.4740  -1.5759
 2XK  C18  C  CR16   0  -0.453   3.0986   1.0491  -0.1649
 2XK  C19  C  CR6    0   0.327   3.9223  -0.0493  -0.0926
 2XK  O20  O  O2     0  -0.458   5.2403  -0.0448  -0.3279
 2XK  O23  O  O      0  -0.395  -0.2587   2.0758   0.0789
 2XK  O24  O  O     -1  -0.388   1.5361   3.1923  -0.1591
 2XK  H1   H  HCR6   0   0.291  -5.0573  -0.5092   2.1344
 2XK  H2   H  HCR6   0   0.280  -3.0080   0.2792  -2.2973
 2XK  H3   H  HCH3   0   0.235   5.4679   1.5958  -1.5946
 2XK  H4   H  HCH3   0   0.235   5.7292   1.9282   0.1331
 2XK  H5   H  HCH3   0   0.267   6.9157   0.9764  -0.7799
 2XK  H6   H  HCH3   0   0.240   3.0005  -3.9765  -0.0068
 2XK  H7   H  HCH3   0   0.270   4.6015  -4.2556   0.7038
 2XK  H8   H  HCH3   0   0.240   3.3016  -3.5750   1.7013
 2XK  H9   H  HCR6   0   0.299   1.5749  -2.3420   0.7884
 2XK  H10  H  HCH2   0   0.317  -0.4126  -1.5344   1.1468
 2XK  H11  H  HCH2   0   0.303  -0.6402   0.1422   1.5597
 2XK  H12  H  HCR6   0   0.286  -2.6420  -0.7415   1.8610
 2XK  H13  H  HCR6   0   0.289  -5.4341   0.5409  -2.0133
 2XK  H14  H  HCR6   0   0.319   3.5016   2.0141  -0.4310
 2XK  N22  N  N      1   0.336   0.9500   2.1440   0.0005
 2XK  C21  C  CH3    0  -0.445   5.8565   1.1860  -0.6588
 2XK  O02  O  O2     0  -0.446   4.2205  -2.3161   0.3179

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
 2XK  C01  O02  single    1.419  0.020  1.419
 2XK  O02  C03  single    1.330  0.020  1.330
 2XK  O20  C21  single    1.416  0.020  1.416
 2XK  O20  C19  single    1.339  0.020  1.339
 2XK  C03  C19  aromatic  1.414  0.020  1.414
 2XK  C03  C04  aromatic  1.385  0.020  1.385
 2XK  C19  C18  aromatic  1.375  0.020  1.375
 2XK  C04  C05  aromatic  1.394  0.020  1.394
 2XK  C18  C17  aromatic  1.400  0.020  1.400
 2XK  C05  C17  aromatic  1.392  0.020  1.392
 2XK  C05  C06  single    1.499  0.020  1.499
 2XK  C17  N22  single    1.445  0.020  1.445
 2XK  O16  C07  double    1.209  0.020  1.209
 2XK  C06  C07  single    1.513  0.020  1.513
 2XK  C07  C08  single    1.493  0.020  1.493
 2XK  N22  O23  double    1.213  0.020  1.213
 2XK  N22  O24  single    1.212  0.020  1.212
 2XK  C15  C08  aromatic  1.395  0.020  1.395
 2XK  C15  C14  aromatic  1.381  0.020  1.381
 2XK  C08  C09  aromatic  1.393  0.020  1.393
 2XK  C14  C11  aromatic  1.395  0.020  1.395
 2XK  C09  C10  aromatic  1.384  0.020  1.384
 2XK  C11  C10  aromatic  1.393  0.020  1.393
 2XK  C11  C12  single    1.428  0.020  1.428
 2XK  C12  N13  triple    1.152  0.020  1.152
 2XK  C10  H1   single    0.930  0.020  1.080
 2XK  C15  H2   single    0.930  0.020  1.080
 2XK  C21  H3   single    0.970  0.020  1.090
 2XK  C21  H4   single    0.970  0.020  1.090
 2XK  C21  H5   single    0.970  0.020  1.090
 2XK  C01  H6   single    0.970  0.020  1.090
 2XK  C01  H7   single    0.970  0.020  1.090
 2XK  C01  H8   single    0.970  0.020  1.090
 2XK  C04  H9   single    0.930  0.020  1.080
 2XK  C06  H10  single    0.970  0.020  1.090
 2XK  C06  H11  single    0.970  0.020  1.090
 2XK  C09  H12  single    0.930  0.020  1.080
 2XK  C14  H13  single    0.930  0.020  1.080
 2XK  C18  H14  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
 2XK  H1   C10  C11  120.40  3.000
 2XK  H1   C10  C09  120.25  3.000
 2XK  C11  C10  C09  119.36  3.000
 2XK  H2   C15  C14  119.34  3.000
 2XK  H2   C15  C08  120.13  3.000
 2XK  C14  C15  C08  120.52  3.000
 2XK  N22  C17  C18  116.36  3.000
 2XK  N22  C17  C05  121.99  3.000
 2XK  C18  C17  C05  121.64  3.000
 2XK  H8   C01  H7   109.09  3.000
 2XK  H8   C01  H6   109.20  3.000
 2XK  H7   C01  H6   109.05  3.000
 2XK  H8   C01  O02  111.51  3.000
 2XK  H7   C01  O02  106.24  3.000
 2XK  H6   C01  O02  111.67  3.000
 2XK  C19  C03  C04  119.31  3.000
 2XK  C04  C03  O02  125.00  3.000
 2XK  C19  C03  O02  115.69  3.000
 2XK  H9   C04  C05  117.67  3.000
 2XK  H9   C04  C03  119.65  3.000
 2XK  C05  C04  C03  122.68  3.000
 2XK  C06  C05  C04  117.42  3.000
 2XK  C06  C05  C17  125.74  3.000
 2XK  C04  C05  C17  116.84  3.000
 2XK  H11  C06  H10  105.68  3.000
 2XK  H11  C06  C07  110.94  3.000
 2XK  H10  C06  C07  106.84  3.000
 2XK  H11  C06  C05  111.71  3.000
 2XK  H10  C06  C05  108.65  3.000
 2XK  C07  C06  C05  112.63  3.000
 2XK  O16  C07  C08  120.47  3.000
 2XK  C08  C07  C06  117.97  3.000
 2XK  O16  C07  C06  121.53  3.000
 2XK  C09  C08  C07  121.83  3.000
 2XK  C09  C08  C15  119.50  3.000
 2XK  C07  C08  C15  118.67  3.000
 2XK  H12  C09  C08  121.11  3.000
 2XK  H12  C09  C10  118.35  3.000
 2XK  C08  C09  C10  120.54  3.000
 2XK  C14  C11  C12  119.69  3.000
 2XK  C12  C11  C10  119.65  3.000
 2XK  C14  C11  C10  120.66  3.000
 2XK  N13  C12  C11  180.00  3.000
 2XK  H13  C14  C11  120.28  3.000
 2XK  H13  C14  C15  120.31  3.000
 2XK  C11  C14  C15  119.41  3.000
 2XK  H14  C18  C19  120.24  3.000
 2XK  H14  C18  C17  119.15  3.000
 2XK  C19  C18  C17  120.61  3.000
 2XK  O20  C19  C18  125.30  3.000
 2XK  C18  C19  C03  118.93  3.000
 2XK  O20  C19  C03  115.77  3.000
 2XK  C19  O20  C21  118.19  3.000
 2XK  O24  N22  O23  122.62  3.000
 2XK  O24  N22  C17  118.33  3.000
 2XK  O23  N22  C17  119.05  3.000
 2XK  H5   C21  H4   108.98  3.000
 2XK  H5   C21  H3   108.87  3.000
 2XK  H4   C21  H3   108.93  3.000
 2XK  H5   C21  O20  106.42  3.000
 2XK  H4   C21  O20  111.74  3.000
 2XK  H3   C21  O20  111.80  3.000
 2XK  C03  O02  C01  118.86  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
 2XK  CONST_01  C15  C08  C09  C10     0.00   0.0  0
 2XK  CONST_02  C15  C14  C11  C10     0.00   0.0  0
 2XK  CONST_03  C03  C19  C18  C17     0.00   0.0  0
 2XK  CONST_04  C03  C04  C05  C17     0.00   0.0  0
 2XK  CONST_05  C18  C19  C03  C04     0.00   0.0  0
 2XK  CONST_06  C18  C17  C05  C04     0.00   0.0  0
 2XK  CONST_07  C19  C03  C04  C05     0.00   0.0  0
 2XK  CONST_08  C19  C18  C17  C05     0.00   0.0  0
 2XK  CONST_09  C11  C14  C15  C08     0.00   0.0  0
 2XK  CONST_10  C11  C10  C09  C08     0.00   0.0  0
 2XK  CONST_11  C14  C15  C08  C09     0.00   0.0  0
 2XK  CONST_12  C14  C11  C10  C09     0.00   0.0  0
 2XK  CONST_13  C07  C08  C09  C10   180.00   0.0  0
 2XK  CONST_14  C12  C11  C14  C15   180.00   0.0  0
 2XK  CONST_15  O20  C19  C18  C17   180.00   0.0  0
 2XK  CONST_16  C18  C19  C03  O02   180.00   0.0  0
 2XK  CONST_17  C05  C04  C03  O02   180.00   0.0  0
 2XK  CONST_18  C06  C05  C04  C03   180.00   0.0  0
 2XK  CONST_19  O20  C19  C03  C04   180.00   0.0  0
 2XK  CONST_20  N22  C17  C05  C04   180.00   0.0  0
 2XK  CONST_21  C18  C17  C05  C06   180.00   0.0  0
 2XK  CONST_22  C14  C15  C08  C07   180.00   0.0  0
 2XK  CONST_23  C12  C11  C10  C09   180.00   0.0  0
 2XK  CONST_24  N22  C17  C18  C19   180.00   0.0  0
 2XK  CONST_25  H13  C14  C11  C10   180.00   0.0  0
 2XK  CONST_26  H12  C09  C08  C15   180.00   0.0  0
 2XK  CONST_27  H9   C04  C05  C17   180.00   0.0  0
 2XK  CONST_28  H14  C18  C19  C03   180.00   0.0  0
 2XK  CONST_29  H1   C10  C09  C08   180.00   0.0  0
 2XK  CONST_30  H2   C15  C08  C09   180.00   0.0  0
 2XK  CONST_31  O23  N22  C17  C05     0.00   0.0  0
 2XK  CONST_32  O24  N22  C17  C05   180.00   0.0  0
 2XK  CONST_33  O23  N22  C17  C18   180.00   0.0  0
 2XK  CONST_34  O24  N22  C17  C18     0.00   0.0  0
 2XK  Var_01    O16  C07  C08  C15   -13.84  30.0  2
 2XK  Var_02    C07  C06  C05  C17    70.61  30.0  2
 2XK  Var_03    C03  C19  O20  C21  -178.77  30.0  2
 2XK  Var_04    C19  C03  O02  C01   178.29  30.0  2
 2XK  Var_05    C08  C07  C06  C05  -164.12  30.0  3
 2XK  Var_06    H6   C01  O02  C03    62.57  30.0  3
 2XK  Var_07    H3   C21  O20  C19   -62.83  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
 2XK  plan-1  C10  0.020
 2XK  plan-1  C15  0.020
 2XK  plan-1  C07  0.020
 2XK  plan-1  C08  0.020
 2XK  plan-1  C09  0.020
 2XK  plan-1  C11  0.020
 2XK  plan-1  C12  0.020
 2XK  plan-1  N13  0.020
 2XK  plan-1  C14  0.020
 2XK  plan-1  H1   0.020
 2XK  plan-1  H2   0.020
 2XK  plan-1  H12  0.020
 2XK  plan-1  H13  0.020
 2XK  plan-2  C17  0.020
 2XK  plan-2  C03  0.020
 2XK  plan-2  C04  0.020
 2XK  plan-2  C05  0.020
 2XK  plan-2  C06  0.020
 2XK  plan-2  C18  0.020
 2XK  plan-2  C19  0.020
 2XK  plan-2  O20  0.020
 2XK  plan-2  H9   0.020
 2XK  plan-2  H14  0.020
 2XK  plan-2  N22  0.020
 2XK  plan-2  O02  0.020
 2XK  plan-3  C17  0.020
 2XK  plan-3  O23  0.020
 2XK  plan-3  O24  0.020
 2XK  plan-3  N22  0.020
 2XK  plan-4  C06  0.020
 2XK  plan-4  C07  0.020
 2XK  plan-4  C08  0.020
 2XK  plan-4  O16  0.020

