# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 14:29:35 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-(9-chloro-1H-phenanthro[9,10-d]imidazol-2-yl)benzene-1,3-dicarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2c3[nH]c(nc3c4ccccc4c2c1)c5c(cccc5C#N)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
 4DZ  4DZ  2-(9-chloro-1H-phenanthro[9,10-d]imidazol-2-yl)benzene-1,3-dicarbonitrile  ligand  39  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4DZ
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
 4DZ  C7   C   CR16  0  -0.214   5.6106  -0.1613   0.5944
 4DZ  C6   C   CR16  0  -0.214   5.1984   1.8679  -0.6031
 4DZ  C1   C   CSP   0  -0.011   2.9696   2.4931  -1.2935
 4DZ  C5   C   CR16  0  -0.245   6.0852   0.9930  -0.0033
 4DZ  C4   C   CR16  0  -0.259  -1.5457  -4.2848  -0.6886
 4DZ  C3   C   CR16  0  -0.238  -2.8902  -3.9204  -0.5709
 4DZ  C22  C   CR6   0  -0.028  -4.2669   1.5146   0.4404
 4DZ  C11  C   CR16  0  -0.226  -3.2782   2.4877   0.5896
 4DZ  C12  C   CR16  0  -0.304  -3.9545   0.1979   0.1965
 4DZ  C18  C   CR66  0   0.086  -2.6173  -0.2142   0.0887
 4DZ  C15  C   CR66  0   0.101  -2.2645  -1.6091  -0.1765
 4DZ  C8   C   CR16  0  -0.350  -3.2385  -2.6119  -0.3201
 4DZ  C17  C   CR66  0   0.077  -1.6138   0.7727   0.2408
 4DZ  C10  C   CR16  0  -0.314  -1.9623   2.1075   0.4879
 4DZ  C21  C   CR56  0   0.295  -0.2667   0.3304   0.1165
 4DZ  N27  N   NR15  0  -0.706   0.9112   1.0080   0.1965
 4DZ  C23  C   CR5   0   0.368   1.9045   0.1024  -0.0067
 4DZ  C19  C   CR6   0   0.193   3.3266   0.4302   0.0000
 4DZ  C14  C   CR6   0  -0.012   4.2452  -0.4400   0.6002
 4DZ  C13  C   CR6   0   0.002   3.8331   1.5866  -0.6066
 4DZ  N24  N   NS    0  -0.218   2.2974   3.2398  -1.8563
 4DZ  N26  N   N     0  -0.425   1.4354  -1.1017  -0.2173
 4DZ  C20  C   CR56  0   0.060   0.0845  -0.9777  -0.1431
 4DZ  C16  C   CR66  0  -0.001  -0.9095  -1.9939  -0.2973
 4DZ  C9   C   CR16  0  -0.302  -0.5668  -3.3284  -0.5517
 4DZ  H1   H   HCR6  0   0.305   6.2961  -0.8494   1.0693
 4DZ  H2   H   HCR6  0   0.305   5.5582   2.7675  -1.0820
 4DZ  H3   H   HCR6  0   0.297   7.1437   1.2088  -0.0034
 4DZ  H4   H   HCR6  0   0.263  -1.2770  -5.3143  -0.8848
 4DZ  H5   H   HCR6  0   0.263  -3.6651  -4.6678  -0.6754
 4DZ  H6   H   HCR6  0   0.288  -3.5411   3.5189   0.7791
 4DZ  H7   H   HCR6  0   0.279  -4.7609  -0.5126   0.0886
 4DZ  H8   H   HCR6  0   0.258  -4.2894  -2.3754  -0.2322
 4DZ  H9   H   HCR6  0   0.262  -1.1924   2.8605   0.5987
 4DZ  H10  H   HNR5  0   0.433   1.0314   1.9716   0.4704
 4DZ  H12  H   HCR6  0   0.255   0.4786  -3.5944  -0.6388
 4DZ  C2   C   CSP   0   0.025   3.8210  -1.6233   1.2812
 4DZ  CL   CL  CL    0  -0.117  -5.9296   1.9825   0.5630
 4DZ  N25  N   NS    0  -0.231   3.5659  -2.5791   1.8700

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
 4DZ  CL   C22  single    1.732  0.020  1.732
 4DZ  C11  C22  aromatic  1.395  0.020  1.395
 4DZ  C11  C10  aromatic  1.374  0.020  1.374
 4DZ  C22  C12  aromatic  1.375  0.020  1.375
 4DZ  C10  C17  aromatic  1.402  0.020  1.402
 4DZ  C12  C18  aromatic  1.403  0.020  1.403
 4DZ  C17  C18  aromatic  1.416  0.020  1.416
 4DZ  C17  C21  aromatic  1.423  0.020  1.423
 4DZ  C18  C15  aromatic  1.463  0.020  1.463
 4DZ  C21  N27  aromatic  1.361  0.020  1.361
 4DZ  C21  C20  aromatic  1.379  0.020  1.379
 4DZ  C15  C8   aromatic  1.405  0.020  1.405
 4DZ  C15  C16  aromatic  1.414  0.020  1.414
 4DZ  N27  C23  aromatic  1.359  0.020  1.359
 4DZ  C8   C3   aromatic  1.377  0.020  1.377
 4DZ  N24  C1   triple    1.152  0.020  1.152
 4DZ  C1   C13  single    1.428  0.020  1.428
 4DZ  C20  C16  aromatic  1.430  0.020  1.430
 4DZ  C20  N26  aromatic  1.359  0.020  1.359
 4DZ  C16  C9   aromatic  1.401  0.020  1.401
 4DZ  C3   C4   aromatic  1.398  0.020  1.398
 4DZ  C23  C19  single    1.459  0.020  1.459
 4DZ  C23  N26  aromatic  1.309  0.020  1.309
 4DZ  C13  C19  aromatic  1.401  0.020  1.401
 4DZ  C13  C6   aromatic  1.394  0.020  1.394
 4DZ  C19  C14  aromatic  1.400  0.020  1.400
 4DZ  C6   C5   aromatic  1.383  0.020  1.383
 4DZ  C9   C4   aromatic  1.375  0.020  1.375
 4DZ  C14  C2   single    1.430  0.020  1.430
 4DZ  C14  C7   aromatic  1.394  0.020  1.394
 4DZ  C2   N25  triple    1.151  0.020  1.151
 4DZ  C5   C7   aromatic  1.384  0.020  1.384
 4DZ  C7   H1   single    0.930  0.020  1.080
 4DZ  C6   H2   single    0.930  0.020  1.080
 4DZ  C5   H3   single    0.930  0.020  1.080
 4DZ  C4   H4   single    0.930  0.020  1.080
 4DZ  C3   H5   single    0.930  0.020  1.080
 4DZ  C11  H6   single    0.930  0.020  1.080
 4DZ  C12  H7   single    0.930  0.020  1.080
 4DZ  C8   H8   single    0.930  0.020  1.080
 4DZ  C10  H9   single    0.930  0.020  1.080
 4DZ  N27  H10  single    0.860  0.020  1.020
 4DZ  C9   H12  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
 4DZ  H1   C7   C14  119.48  3.000
 4DZ  H1   C7   C5   120.21  3.000
 4DZ  C14  C7   C5   120.31  3.000
 4DZ  H2   C6   C13  119.53  3.000
 4DZ  H2   C6   C5   120.36  3.000
 4DZ  C13  C6   C5   120.11  3.000
 4DZ  N24  C1   C13  180.00  3.000
 4DZ  H3   C5   C6   120.14  3.000
 4DZ  H3   C5   C7   120.18  3.000
 4DZ  C6   C5   C7   119.69  3.000
 4DZ  H4   C4   C9   120.19  3.000
 4DZ  H4   C4   C3   120.14  3.000
 4DZ  C9   C4   C3   119.66  3.000
 4DZ  H5   C3   C8   119.54  3.000
 4DZ  H5   C3   C4   120.05  3.000
 4DZ  C8   C3   C4   120.41  3.000
 4DZ  C12  C22  C11  121.72  3.000
 4DZ  C12  C22  CL   119.30  3.000
 4DZ  C11  C22  CL   118.97  3.000
 4DZ  H6   C11  C10  120.66  3.000
 4DZ  H6   C11  C22  120.78  3.000
 4DZ  C10  C11  C22  118.55  3.000
 4DZ  H7   C12  C18  120.70  3.000
 4DZ  H7   C12  C22  118.56  3.000
 4DZ  C18  C12  C22  120.75  3.000
 4DZ  C17  C18  C15  120.88  3.000
 4DZ  C15  C18  C12  121.57  3.000
 4DZ  C17  C18  C12  117.55  3.000
 4DZ  C16  C15  C8   117.47  3.000
 4DZ  C16  C15  C18  120.40  3.000
 4DZ  C8   C15  C18  122.12  3.000
 4DZ  H8   C8   C15  120.62  3.000
 4DZ  H8   C8   C3   117.95  3.000
 4DZ  C15  C8   C3   121.42  3.000
 4DZ  C21  C17  C10  123.14  3.000
 4DZ  C21  C17  C18  116.42  3.000
 4DZ  C10  C17  C18  120.44  3.000
 4DZ  H9   C10  C17  120.24  3.000
 4DZ  H9   C10  C11  118.77  3.000
 4DZ  C17  C10  C11  120.99  3.000
 4DZ  C20  C21  N27  105.24  3.000
 4DZ  C20  C21  C17  123.52  3.000
 4DZ  N27  C21  C17  131.24  3.000
 4DZ  H10  N27  C23  126.14  3.000
 4DZ  H10  N27  C21  126.47  3.000
 4DZ  C23  N27  C21  106.97  3.000
 4DZ  N26  C23  C19  123.81  3.000
 4DZ  N26  C23  N27  112.02  3.000
 4DZ  C19  C23  N27  124.17  3.000
 4DZ  C13  C19  C14  117.48  3.000
 4DZ  C14  C19  C23  120.10  3.000
 4DZ  C13  C19  C23  122.40  3.000
 4DZ  C19  C14  C2   121.59  3.000
 4DZ  C2   C14  C7   117.27  3.000
 4DZ  C19  C14  C7   121.11  3.000
 4DZ  C19  C13  C1   120.92  3.000
 4DZ  C19  C13  C6   121.31  3.000
 4DZ  C1   C13  C6   117.74  3.000
 4DZ  C20  N26  C23  105.28  3.000
 4DZ  C16  C20  N26  128.36  3.000
 4DZ  N26  C20  C21  110.49  3.000
 4DZ  C16  C20  C21  121.16  3.000
 4DZ  C9   C16  C20  121.77  3.000
 4DZ  C9   C16  C15  120.60  3.000
 4DZ  C20  C16  C15  117.63  3.000
 4DZ  H12  C9   C16  119.01  3.000
 4DZ  H12  C9   C4   120.57  3.000
 4DZ  C16  C9   C4   120.42  3.000
 4DZ  N25  C2   C14  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
 4DZ  CONST_01  C23  C19  C14  C7   180.00  0.0  0
 4DZ  CONST_02  C13  C19  C14  C7     0.00  0.0  0
 4DZ  CONST_03  C13  C6   C5   C7     0.00  0.0  0
 4DZ  CONST_04  C23  C19  C13  C6   180.00  0.0  0
 4DZ  CONST_05  C14  C19  C13  C6     0.00  0.0  0
 4DZ  CONST_06  C14  C7   C5   C6     0.00  0.0  0
 4DZ  CONST_07  C19  C13  C6   C5     0.00  0.0  0
 4DZ  CONST_08  C19  C14  C7   C5     0.00  0.0  0
 4DZ  CONST_09  C15  C8   C3   C4     0.00  0.0  0
 4DZ  CONST_10  C15  C16  C9   C4     0.00  0.0  0
 4DZ  CONST_11  C20  C16  C9   C4   180.00  0.0  0
 4DZ  CONST_12  C18  C15  C8   C3   180.00  0.0  0
 4DZ  CONST_13  C16  C15  C8   C3     0.00  0.0  0
 4DZ  CONST_14  C16  C9   C4   C3     0.00  0.0  0
 4DZ  CONST_15  C17  C10  C11  C22    0.00  0.0  0
 4DZ  CONST_16  C17  C18  C12  C22    0.00  0.0  0
 4DZ  CONST_17  C15  C18  C12  C22  180.00  0.0  0
 4DZ  CONST_18  C18  C12  C22  C11    0.00  0.0  0
 4DZ  CONST_19  C18  C17  C10  C11    0.00  0.0  0
 4DZ  CONST_20  C21  C17  C10  C11  180.00  0.0  0
 4DZ  CONST_21  C10  C11  C22  C12    0.00  0.0  0
 4DZ  CONST_22  C10  C17  C18  C12    0.00  0.0  0
 4DZ  CONST_23  C21  C17  C18  C12  180.00  0.0  0
 4DZ  CONST_24  C8   C15  C18  C12    0.00  0.0  0
 4DZ  CONST_25  C16  C15  C18  C12  180.00  0.0  0
 4DZ  CONST_26  N27  C21  C17  C18  180.00  0.0  0
 4DZ  CONST_27  C20  C21  C17  C18    0.00  0.0  0
 4DZ  CONST_28  C20  C16  C15  C18    0.00  0.0  0
 4DZ  CONST_29  C9   C16  C15  C18  180.00  0.0  0
 4DZ  CONST_30  C10  C17  C18  C15  180.00  0.0  0
 4DZ  CONST_31  C21  C17  C18  C15    0.00  0.0  0
 4DZ  CONST_32  C21  C20  C16  C15    0.00  0.0  0
 4DZ  CONST_33  N26  C20  C16  C15  180.00  0.0  0
 4DZ  CONST_34  C17  C18  C15  C8   180.00  0.0  0
 4DZ  CONST_35  C20  C16  C15  C8   180.00  0.0  0
 4DZ  CONST_36  C9   C16  C15  C8     0.00  0.0  0
 4DZ  CONST_37  C9   C4   C3   C8     0.00  0.0  0
 4DZ  CONST_38  C16  C15  C18  C17    0.00  0.0  0
 4DZ  CONST_39  C23  N27  C21  C17  180.00  0.0  0
 4DZ  CONST_40  C16  C20  C21  C17    0.00  0.0  0
 4DZ  CONST_41  N26  C20  C21  C17  180.00  0.0  0
 4DZ  CONST_42  N27  C21  C17  C10    0.00  0.0  0
 4DZ  CONST_43  C20  C21  C17  C10  180.00  0.0  0
 4DZ  CONST_44  C19  C23  N27  C21  180.00  0.0  0
 4DZ  CONST_45  N26  C23  N27  C21    0.00  0.0  0
 4DZ  CONST_46  C9   C16  C20  C21  180.00  0.0  0
 4DZ  CONST_47  C23  N26  C20  C21    0.00  0.0  0
 4DZ  CONST_48  C16  C20  C21  N27  180.00  0.0  0
 4DZ  CONST_49  N26  C20  C21  N27    0.00  0.0  0
 4DZ  CONST_52  C20  N26  C23  N27    0.00  0.0  0
 4DZ  CONST_53  C20  C21  N27  C23    0.00  0.0  0
 4DZ  CONST_54  C16  C20  N26  C23  180.00  0.0  0
 4DZ  CONST_55  C20  N26  C23  C19  180.00  0.0  0
 4DZ  CONST_58  C9   C16  C20  N26    0.00  0.0  0
 4DZ  CONST_59  C23  C19  C13  C1     0.00  0.0  0
 4DZ  CONST_60  C14  C19  C13  C1   180.00  0.0  0
 4DZ  CONST_61  C5   C6   C13  C1   180.00  0.0  0
 4DZ  CONST_62  C2   C14  C7   C5   180.00  0.0  0
 4DZ  CONST_63  C23  C19  C14  C2     0.00  0.0  0
 4DZ  CONST_64  C13  C19  C14  C2   180.00  0.0  0
 4DZ  CONST_65  C10  C11  C22  CL   180.00  0.0  0
 4DZ  CONST_66  C18  C12  C22  CL   180.00  0.0  0
 4DZ  CONST_67  H2   C6   C5   C7   180.00  0.0  0
 4DZ  CONST_68  H1   C7   C5   C6   180.00  0.0  0
 4DZ  CONST_69  H8   C8   C3   C4   180.00  0.0  0
 4DZ  CONST_70  H12  C9   C4   C3   180.00  0.0  0
 4DZ  CONST_71  H9   C10  C11  C22  180.00  0.0  0
 4DZ  CONST_72  H7   C12  C22  C11  180.00  0.0  0
 4DZ  CONST_73  H6   C11  C22  C12  180.00  0.0  0
 4DZ  CONST_74  H5   C3   C8   C15  180.00  0.0  0
 4DZ  CONST_75  H4   C4   C3   C8   180.00  0.0  0
 4DZ  CONST_76  H10  N27  C21  C17    0.00  0.0  0
 4DZ  CONST_77  H3   C5   C7   C14  180.00  0.0  0

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
 4DZ  plan-1  C7   0.020
 4DZ  plan-1  C6   0.020
 4DZ  plan-1  C1   0.020
 4DZ  plan-1  C5   0.020
 4DZ  plan-1  C23  0.020
 4DZ  plan-1  C19  0.020
 4DZ  plan-1  C14  0.020
 4DZ  plan-1  C13  0.020
 4DZ  plan-1  N24  0.020
 4DZ  plan-1  H1   0.020
 4DZ  plan-1  H2   0.020
 4DZ  plan-1  H3   0.020
 4DZ  plan-1  C2   0.020
 4DZ  plan-1  N25  0.020
 4DZ  plan-2  C4   0.020
 4DZ  plan-2  C3   0.020
 4DZ  plan-2  C22  0.020
 4DZ  plan-2  C11  0.020
 4DZ  plan-2  C12  0.020
 4DZ  plan-2  C18  0.020
 4DZ  plan-2  C15  0.020
 4DZ  plan-2  C8   0.020
 4DZ  plan-2  C17  0.020
 4DZ  plan-2  C10  0.020
 4DZ  plan-2  C21  0.020
 4DZ  plan-2  N27  0.020
 4DZ  plan-2  C23  0.020
 4DZ  plan-2  C19  0.020
 4DZ  plan-2  N26  0.020
 4DZ  plan-2  C20  0.020
 4DZ  plan-2  C16  0.020
 4DZ  plan-2  C9   0.020
 4DZ  plan-2  H4   0.020
 4DZ  plan-2  H5   0.020
 4DZ  plan-2  H6   0.020
 4DZ  plan-2  H7   0.020
 4DZ  plan-2  H8   0.020
 4DZ  plan-2  H9   0.020
 4DZ  plan-2  H10  0.020
 4DZ  plan-2  H12  0.020
 4DZ  plan-2  CL   0.020

