# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 12:00:26 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 5-[4-(3,4-dichlorophenyl)piperazin-1-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(N2CCN(CC2)c3ccc(Cl)c(Cl)c3)c(N)n1
#
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
 73X  73X  5-[4-(3,4-dichlorophenyl)piperazin-1-yl]pyrimidine-2,4-diamine  ligand  38  22  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_73X
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
 73X  C12  C   CR6   0   0.526   6.3591   0.4509  -0.1989
 73X  C13  C   CR6   0   0.465   4.6215  -0.7870   0.5880
 73X  C2   C   CR6   0  -0.047  -4.6923  -0.5789  -0.1628
 73X  C1   C   CR16  0  -0.201  -3.8804  -1.6367  -0.5328
 73X  C3   C   CR6   0   0.021  -4.0885   0.6135   0.2188
 73X  CL   CL  CL    0  -0.103  -5.0545   1.9688   0.6753
 73X  C4   C   CR16  0  -0.304  -2.7134   0.7458   0.2281
 73X  C5   C   CR6   0   0.396  -1.8780  -0.3199  -0.1419
 73X  C    C   CR16  0  -0.363  -2.5015  -1.5194  -0.5170
 73X  N    N   NT    0  -0.523  -0.5027  -0.1596  -0.1622
 73X  C9   C   CH2   0  -0.317   0.3139  -1.2708  -0.6123
 73X  C8   C   CH2   0  -0.293   1.7155  -0.8069  -0.9640
 73X  N1   N   NT    0  -0.517   2.3216  -0.1049   0.1538
 73X  C7   C   CH2   0  -0.295   1.5187   1.0431   0.5244
 73X  C6   C   CH2   0  -0.309   0.1265   0.5897   0.9176
 73X  C10  C   CR6   0   0.086   3.7081   0.1271   0.0062
 73X  N4   N   NH2   0  -0.815   4.1624  -1.8664   1.2428
 73X  N3   N   N     0  -0.503   5.9340  -0.6168   0.4787
 73X  N5   N   NH2   0  -0.823   7.7007   0.6363  -0.2603
 73X  N2   N   N     0  -0.488   5.5927   1.3704  -0.7847
 73X  C11  C   CR16  0  -0.057   4.2779   1.1776  -0.6712
 73X  H1   H   HCR6  0   0.285  -4.3272  -2.5770  -0.8264
 73X  H2   H   HCR6  0   0.290  -2.3008   1.7047   0.5056
 73X  H3   H   HCR6  0   0.282  -1.9254  -2.3895  -0.7938
 73X  H4   H   HCH2  0   0.223   0.3704  -2.0641   0.1476
 73X  H5   H   HCH2  0   0.258  -0.1193  -1.7055  -1.5129
 73X  H6   H   HCH2  0   0.254   2.3138  -1.6853  -1.2120
 73X  H7   H   HCH2  0   0.216   1.6767  -0.1715  -1.8628
 73X  H8   H   HCH2  0   0.254   1.9777   1.5455   1.3767
 73X  H9   H   HCH2  0   0.210   1.4308   1.7786  -0.2900
 73X  H10  H   HCH2  0   0.261  -0.4545   1.4757   1.1615
 73X  H11  H   HCH2  0   0.227   0.1841  -0.0250   1.8267
 73X  H12  H   HNH2  0   0.394   3.1881  -1.8771   1.4966
 73X  H13  H   HNH2  0   0.391   4.7986  -2.3982   1.8120
 73X  H14  H   HNH2  0   0.387   8.0504   1.2778  -0.9510
 73X  H15  H   HNH2  0   0.387   8.2939  -0.1460  -0.0439
 73X  H16  H   HCR6  0   0.259   3.6467   1.9233  -1.1465
 73X  CL1  CL  CL    0  -0.114  -6.4083  -0.7525  -0.1742

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
 73X  C6   C7   single    1.516  0.020  1.516
 73X  C6   N    single    1.457  0.020  1.457
 73X  C1   C    aromatic  1.384  0.020  1.384
 73X  C1   C2   aromatic  1.384  0.020  1.384
 73X  C    C5   aromatic  1.403  0.020  1.403
 73X  CL1  C2   single    1.725  0.020  1.725
 73X  C2   C3   aromatic  1.390  0.020  1.390
 73X  C5   N    single    1.385  0.020  1.385
 73X  C5   C4   aromatic  1.404  0.020  1.404
 73X  C7   N1   single    1.449  0.020  1.449
 73X  N    C9   single    1.451  0.020  1.451
 73X  C3   C4   aromatic  1.381  0.020  1.381
 73X  C3   CL   single    1.726  0.020  1.726
 73X  N4   C13  single    1.343  0.020  1.343
 73X  C9   C8   single    1.518  0.020  1.518
 73X  N1   C10  single    1.414  0.020  1.414
 73X  N1   C8   single    1.452  0.020  1.452
 73X  C13  C10  aromatic  1.417  0.020  1.417
 73X  C13  N3   aromatic  1.328  0.020  1.328
 73X  C10  C11  aromatic  1.374  0.020  1.374
 73X  N3   C12  aromatic  1.334  0.020  1.334
 73X  C11  N2   aromatic  1.334  0.020  1.334
 73X  C12  N2   aromatic  1.333  0.020  1.333
 73X  C12  N5   single    1.356  0.020  1.356
 73X  C1   H1   single    0.930  0.020  1.080
 73X  C4   H2   single    0.930  0.020  1.080
 73X  C    H3   single    0.930  0.020  1.080
 73X  C9   H4   single    0.970  0.020  1.090
 73X  C9   H5   single    0.970  0.020  1.090
 73X  C8   H6   single    0.970  0.020  1.090
 73X  C8   H7   single    0.970  0.020  1.090
 73X  C7   H8   single    0.970  0.020  1.090
 73X  C7   H9   single    0.970  0.020  1.090
 73X  C6   H10  single    0.970  0.020  1.090
 73X  C6   H11  single    0.970  0.020  1.090
 73X  N4   H12  single    0.890  0.020  1.040
 73X  N4   H13  single    0.890  0.020  1.040
 73X  N5   H14  single    0.890  0.020  1.040
 73X  N5   H15  single    0.890  0.020  1.040
 73X  C11  H16  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
 73X  N2   C12  N5   117.05  3.000
 73X  N5   C12  N3   116.60  3.000
 73X  N2   C12  N3   126.32  3.000
 73X  N3   C13  N4   118.74  3.000
 73X  N3   C13  C10  121.37  3.000
 73X  N4   C13  C10  119.88  3.000
 73X  C3   C2   C1   118.32  3.000
 73X  C3   C2   CL1  121.35  3.000
 73X  C1   C2   CL1  120.33  3.000
 73X  H1   C1   C    119.23  3.000
 73X  H1   C1   C2   119.65  3.000
 73X  C    C1   C2   121.11  3.000
 73X  C4   C3   CL   118.70  3.000
 73X  CL   C3   C2   120.21  3.000
 73X  C4   C3   C2   121.09  3.000
 73X  H2   C4   C5   120.95  3.000
 73X  H2   C4   C3   117.83  3.000
 73X  C5   C4   C3   121.19  3.000
 73X  N    C5   C    122.44  3.000
 73X  N    C5   C4   120.47  3.000
 73X  C    C5   C4   117.07  3.000
 73X  H3   C    C5   121.36  3.000
 73X  H3   C    C1   117.41  3.000
 73X  C5   C    C1   121.22  3.000
 73X  C6   N    C9   112.38  3.000
 73X  C9   N    C5   118.36  3.000
 73X  C6   N    C5   118.52  3.000
 73X  H5   C9   H4   107.68  3.000
 73X  H5   C9   C8   107.31  3.000
 73X  H4   C9   C8   109.46  3.000
 73X  H5   C9   N    109.77  3.000
 73X  H4   C9   N    111.53  3.000
 73X  C8   C9   N    110.95  3.000
 73X  H7   C8   H6   107.35  3.000
 73X  H7   C8   N1   111.34  3.000
 73X  H6   C8   N1   109.57  3.000
 73X  H7   C8   C9   109.45  3.000
 73X  H6   C8   C9   108.23  3.000
 73X  N1   C8   C9   110.78  3.000
 73X  C10  N1   C7   116.12  3.000
 73X  C10  N1   C8   114.10  3.000
 73X  C7   N1   C8   110.39  3.000
 73X  H9   C7   H8   107.69  3.000
 73X  H9   C7   C6   108.56  3.000
 73X  H8   C7   C6   108.76  3.000
 73X  H9   C7   N1   112.60  3.000
 73X  H8   C7   N1   109.36  3.000
 73X  C6   C7   N1   109.77  3.000
 73X  H11  C6   H10  107.35  3.000
 73X  H11  C6   C7   109.49  3.000
 73X  H10  C6   C7   107.77  3.000
 73X  H11  C6   N    110.37  3.000
 73X  H10  C6   N    110.77  3.000
 73X  C7   C6   N    110.98  3.000
 73X  C11  C10  N1   125.72  3.000
 73X  C11  C10  C13  115.37  3.000
 73X  N1   C10  C13  118.91  3.000
 73X  H13  N4   H12  117.64  3.000
 73X  H13  N4   C13  118.98  3.000
 73X  H12  N4   C13  117.52  3.000
 73X  C13  N3   C12  117.34  3.000
 73X  H15  N5   H14  116.04  3.000
 73X  H15  N5   C12  117.89  3.000
 73X  H14  N5   C12  117.55  3.000
 73X  C11  N2   C12  115.45  3.000
 73X  H16  C11  N2   115.86  3.000
 73X  H16  C11  C10  119.98  3.000
 73X  N2   C11  C10  124.16  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
 73X  CONST_01  C10  C13  N3   C12     0.00   0.0  0
 73X  CONST_02  C10  C11  N2   C12     0.00   0.0  0
 73X  CONST_03  N2   C11  C10  C13     0.00   0.0  0
 73X  CONST_04  N2   C12  N3   C13     0.00   0.0  0
 73X  CONST_05  C5   C    C1   C2      0.00   0.0  0
 73X  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 73X  CONST_07  C4   C5   C    C1      0.00   0.0  0
 73X  CONST_08  C4   C3   C2   C1      0.00   0.0  0
 73X  CONST_09  C    C1   C2   C3      0.00   0.0  0
 73X  CONST_10  C    C5   C4   C3      0.00   0.0  0
 73X  CONST_11  C11  C10  C13  N3      0.00   0.0  0
 73X  CONST_12  C11  N2   C12  N3      0.00   0.0  0
 73X  CONST_13  N    C5   C    C1    180.00   0.0  0
 73X  CONST_14  N    C5   C4   C3    180.00   0.0  0
 73X  CONST_15  N3   C13  C10  N1    180.00   0.0  0
 73X  CONST_16  N2   C11  C10  N1    180.00   0.0  0
 73X  CONST_17  N4   C13  N3   C12   180.00   0.0  0
 73X  CONST_18  N5   C12  N3   C13   180.00   0.0  0
 73X  CONST_19  C    C1   C2   CL1   180.00   0.0  0
 73X  CONST_20  C4   C3   C2   CL1   180.00   0.0  0
 73X  CONST_21  CL   C3   C2   C1    180.00   0.0  0
 73X  CONST_22  C5   C4   C3   CL    180.00   0.0  0
 73X  CONST_23  N4   C13  C10  N1      0.00   0.0  0
 73X  CONST_24  C11  C10  C13  N4    180.00   0.0  0
 73X  CONST_25  C11  N2   C12  N5    180.00   0.0  0
 73X  CONST_26  H16  C11  N2   C12   180.00   0.0  0
 73X  CONST_27  H3   C    C1   C2    180.00   0.0  0
 73X  CONST_28  H2   C4   C3   C2    180.00   0.0  0
 73X  CONST_29  H1   C1   C2   C3    180.00   0.0  0
 73X  CONST_30  H12  N4   C13  C10     0.00   0.0  0
 73X  CONST_31  H13  N4   C13  C10   180.00   0.0  0
 73X  Var_01    C7   N1   C10  C13   134.43  30.0  3
 73X  Var_02    C6   N    C5   C4     41.08  30.0  2
 73X  Var_03    C7   C6   N    C5   -161.84  30.0  1
 73X  Var_04    C8   C9   N    C5    163.05  30.0  1
 73X  Var_05    N1   C7   C6   N     -56.98  30.0  1
 73X  Var_06    N1   C8   C9   N      54.99  30.0  1
 73X  Var_07    C6   C7   N1   C8     59.63  30.0  1

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
 73X  plan-1  C12  0.020
 73X  plan-1  C13  0.020
 73X  plan-1  N1   0.020
 73X  plan-1  C10  0.020
 73X  plan-1  N4   0.020
 73X  plan-1  N3   0.020
 73X  plan-1  N5   0.020
 73X  plan-1  N2   0.020
 73X  plan-1  C11  0.020
 73X  plan-1  H16  0.020
 73X  plan-2  C2   0.020
 73X  plan-2  C1   0.020
 73X  plan-2  C3   0.020
 73X  plan-2  CL   0.020
 73X  plan-2  C4   0.020
 73X  plan-2  C5   0.020
 73X  plan-2  C    0.020
 73X  plan-2  N    0.020
 73X  plan-2  H1   0.020
 73X  plan-2  H2   0.020
 73X  plan-2  H3   0.020
 73X  plan-2  CL1  0.020
 73X  plan-3  C13  0.020
 73X  plan-3  N4   0.020
 73X  plan-3  H12  0.020
 73X  plan-3  H13  0.020
 73X  plan-4  C12  0.020
 73X  plan-4  N5   0.020
 73X  plan-4  H14  0.020
 73X  plan-4  H15  0.020

