# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 23:43:56 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 6-(2,3-dichlorophenyl)-N~4~-methylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(nc(N)n1)c2cccc(Cl)c2Cl
#
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
 2GD  2GD  6-(2,3-dichlorophenyl)-N~4~-methylpyrimidine-2,4-diamine  ligand  27  17  .  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_2GD
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
 2GD  C13  C   CR16  0  -0.455   1.8521  -0.9213   0.2398
 2GD  N01  N   NH2   0  -0.831   2.6111   2.7558  -1.1889
 2GD  C02  C   CR6   0   0.535   2.3591   1.5248  -0.7105
 2GD  N03  N   N     0  -0.487   1.0950   1.0941  -0.7951
 2GD  C04  C   CR6   0   0.246   0.8741  -0.1242  -0.3131
 2GD  C05  C   CR6   0   0.122  -0.5125  -0.6433  -0.4251
 2GD  C06  C   CR16  0  -0.294  -0.7471  -1.7846  -1.1844
 2GD  C07  C   CR16  0  -0.239  -2.0283  -2.2915  -1.3334
 2GD  C08  C   CR16  0  -0.230  -3.0974  -1.6652  -0.7164
 2GD  C09  C   CR6   0   0.019  -2.8750  -0.5348   0.0552
 2GD  CL1  CL  CL    0  -0.095  -4.2131   0.2212   0.8354
 2GD  C11  C   CR6   0  -0.069  -1.5898  -0.0212   0.2039
 2GD  CL2  CL  CL    0  -0.094  -1.3337   1.3501   1.2118
 2GD  C14  C   CR6   0   0.534   3.1506  -0.3701   0.2718
 2GD  N15  N   NH1   0  -0.644   4.1934  -1.0383   0.7836
 2GD  C16  C   CH3   0  -0.529   4.1270  -2.3791   1.3047
 2GD  N17  N   N     0  -0.516   3.3908   0.8517  -0.2047
 2GD  H1   H   HCR6  0   0.272   1.6252  -1.9030   0.6271
 2GD  H2   H   HNH2  0   0.395   1.8687   3.3163  -1.5657
 2GD  H3   H   HNH2  0   0.394   3.5409   3.1325  -1.1653
 2GD  H4   H   HCR6  0   0.270   0.0871  -2.2696  -1.6737
 2GD  H5   H   HCR6  0   0.276  -2.1970  -3.1754  -1.9327
 2GD  H6   H   HCR6  0   0.290  -4.1013  -2.0511  -0.8265
 2GD  H13  H   HNH1  0   0.391   5.0906  -0.5863   0.7262
 2GD  H14  H   HCH3  0   0.236   3.8185  -3.1029   0.5467
 2GD  H15  H   HCH3  0   0.266   5.1164  -2.6605   1.6533
 2GD  H16  H   HCH3  0   0.238   3.4394  -2.4549   2.1492

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
 2GD  C13  C04  aromatic  1.378  0.020  1.378
 2GD  C13  C14  aromatic  1.411  0.020  1.411
 2GD  N01  C02  single    1.344  0.020  1.344
 2GD  C02  N03  aromatic  1.338  0.020  1.338
 2GD  C02  N17  aromatic  1.332  0.020  1.332
 2GD  N03  C04  aromatic  1.329  0.020  1.329
 2GD  C04  C05  single    1.485  0.020  1.485
 2GD  C05  C06  aromatic  1.391  0.020  1.391
 2GD  C05  C11  aromatic  1.394  0.020  1.394
 2GD  C06  C07  aromatic  1.386  0.020  1.386
 2GD  C07  C08  aromatic  1.384  0.020  1.384
 2GD  C08  C09  aromatic  1.387  0.020  1.387
 2GD  C09  C11  aromatic  1.392  0.020  1.392
 2GD  C11  CL2  single    1.721  0.020  1.721
 2GD  C14  N15  single    1.340  0.020  1.340
 2GD  C14  N17  aromatic  1.333  0.020  1.333
 2GD  N15  C16  single    1.440  0.020  1.440
 2GD  C09  CL1  single    1.724  0.020  1.724
 2GD  C13  H1   single    0.930  0.020  1.080
 2GD  N01  H2   single    0.860  0.020  1.020
 2GD  N01  H3   single    0.860  0.020  1.020
 2GD  C06  H4   single    0.930  0.020  1.080
 2GD  C07  H5   single    0.930  0.020  1.080
 2GD  C08  H6   single    0.930  0.020  1.080
 2GD  N15  H13  single    0.860  0.020  1.020
 2GD  C16  H14  single    0.970  0.020  1.090
 2GD  C16  H15  single    0.970  0.020  1.090
 2GD  C16  H16  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
 2GD  H1   C13  C14  122.73  3.000
 2GD  H1   C13  C04  121.40  3.000
 2GD  C14  C13  C04  115.87  3.000
 2GD  H3   N01  H2   118.98  3.000
 2GD  H3   N01  C02  120.60  3.000
 2GD  H2   N01  C02  120.42  3.000
 2GD  N17  C02  N03  126.38  3.000
 2GD  N17  C02  N01  116.92  3.000
 2GD  N03  C02  N01  116.70  3.000
 2GD  C04  N03  C02  115.42  3.000
 2GD  C05  C04  N03  116.65  3.000
 2GD  C05  C04  C13  119.40  3.000
 2GD  N03  C04  C13  123.93  3.000
 2GD  C11  C05  C06  118.83  3.000
 2GD  C11  C05  C04  122.12  3.000
 2GD  C06  C05  C04  119.05  3.000
 2GD  H4   C06  C07  120.01  3.000
 2GD  H4   C06  C05  119.00  3.000
 2GD  C07  C06  C05  120.99  3.000
 2GD  H5   C07  C08  119.76  3.000
 2GD  H5   C07  C06  120.19  3.000
 2GD  C08  C07  C06  120.05  3.000
 2GD  H6   C08  C09  119.77  3.000
 2GD  H6   C08  C07  120.69  3.000
 2GD  C09  C08  C07  119.53  3.000
 2GD  C11  C09  CL1  120.44  3.000
 2GD  CL1  C09  C08  119.01  3.000
 2GD  C11  C09  C08  120.56  3.000
 2GD  CL2  C11  C09  119.60  3.000
 2GD  CL2  C11  C05  120.32  3.000
 2GD  C09  C11  C05  120.04  3.000
 2GD  N17  C14  N15  116.95  3.000
 2GD  N17  C14  C13  121.04  3.000
 2GD  N15  C14  C13  122.00  3.000
 2GD  H13  N15  C16  118.68  3.000
 2GD  H13  N15  C14  116.62  3.000
 2GD  C16  N15  C14  124.51  3.000
 2GD  H16  C16  H15  107.91  3.000
 2GD  H16  C16  H14  108.23  3.000
 2GD  H15  C16  H14  107.96  3.000
 2GD  H16  C16  N15  111.93  3.000
 2GD  H15  C16  N15  108.38  3.000
 2GD  H14  C16  N15  112.26  3.000
 2GD  C14  N17  C02  117.35  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
 2GD  CONST_01  C02  N03  C04  C13    0.00   0.0  0
 2GD  CONST_04  C02  N17  C14  C13    0.00   0.0  0
 2GD  CONST_05  C05  C04  N03  C02  180.00   0.0  0
 2GD  CONST_06  C14  N17  C02  N03    0.00   0.0  0
 2GD  CONST_07  C14  C13  C04  N03    0.00   0.0  0
 2GD  CONST_10  N17  C14  C13  C04    0.00   0.0  0
 2GD  CONST_11  N17  C02  N03  C04    0.00   0.0  0
 2GD  CONST_12  C07  C06  C05  C04  180.00   0.0  0
 2GD  CONST_13  C09  C11  C05  C04  180.00   0.0  0
 2GD  CONST_14  C14  C13  C04  C05  180.00   0.0  0
 2GD  CONST_15  C08  C07  C06  C05    0.00   0.0  0
 2GD  CONST_16  C08  C09  C11  C05    0.00   0.0  0
 2GD  CONST_17  C09  C11  C05  C06    0.00   0.0  0
 2GD  CONST_18  C09  C08  C07  C06    0.00   0.0  0
 2GD  CONST_19  C11  C05  C06  C07    0.00   0.0  0
 2GD  CONST_20  C11  C09  C08  C07    0.00   0.0  0
 2GD  CONST_21  C04  N03  C02  N01  180.00   0.0  0
 2GD  CONST_22  C14  N17  C02  N01  180.00   0.0  0
 2GD  CONST_23  N15  C14  N17  C02  180.00   0.0  0
 2GD  CONST_24  N15  C14  C13  C04  180.00   0.0  0
 2GD  CONST_25  CL2  C11  C05  C04    0.00   0.0  0
 2GD  CONST_26  CL1  C09  C11  C05  180.00   0.0  0
 2GD  CONST_27  CL2  C11  C05  C06  180.00   0.0  0
 2GD  CONST_28  CL1  C09  C08  C07  180.00   0.0  0
 2GD  CONST_29  CL2  C11  C09  C08  180.00   0.0  0
 2GD  CONST_30  H1   C13  C04  N03  180.00   0.0  0
 2GD  CONST_31  H4   C06  C05  C04    0.00   0.0  0
 2GD  CONST_32  H5   C07  C06  C05  180.00   0.0  0
 2GD  CONST_33  H6   C08  C07  C06  180.00   0.0  0
 2GD  CONST_34  C16  N15  C14  C13    0.00   0.0  0
 2GD  CONST_35  N17  C14  N15  C16  180.00   0.0  0
 2GD  CONST_36  H13  N15  C14  C13  180.00   0.0  0
 2GD  CONST_37  H2   N01  C02  N03    0.00   0.0  0
 2GD  CONST_38  H3   N01  C02  N03  180.00   0.0  0
 2GD  Var_01    H14  C16  N15  C14   61.06  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
 2GD  plan-1  C13  0.020
 2GD  plan-1  N01  0.020
 2GD  plan-1  C02  0.020
 2GD  plan-1  N03  0.020
 2GD  plan-1  C04  0.020
 2GD  plan-1  C05  0.020
 2GD  plan-1  C14  0.020
 2GD  plan-1  N15  0.020
 2GD  plan-1  N17  0.020
 2GD  plan-1  H1   0.020
 2GD  plan-2  C04  0.020
 2GD  plan-2  C05  0.020
 2GD  plan-2  C06  0.020
 2GD  plan-2  C07  0.020
 2GD  plan-2  C08  0.020
 2GD  plan-2  C09  0.020
 2GD  plan-2  CL1  0.020
 2GD  plan-2  C11  0.020
 2GD  plan-2  CL2  0.020
 2GD  plan-2  H4   0.020
 2GD  plan-2  H5   0.020
 2GD  plan-2  H6   0.020
 2GD  plan-3  N01  0.020
 2GD  plan-3  C02  0.020
 2GD  plan-3  H2   0.020
 2GD  plan-3  H3   0.020
 2GD  plan-4  C14  0.020
 2GD  plan-4  N15  0.020
 2GD  plan-4  C16  0.020
 2GD  plan-4  H13  0.020

