# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 01:10:52 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: N~4~-cyclopropyl-6-(2,3-dichlorophenyl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(NC2CC2)cc(n1)c3cccc(Cl)c3Cl
#
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
 2GE  2GE  N~4~-cyclopropyl-6-(2,3-dichlorophenyl)pyrimidine-2,4-diamine  ligand  31  19  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2GE
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
 2GE  C13  C   CR16  0  -0.441  -1.7095   0.2816   0.2317
 2GE  C17  C   CH2   0  -0.483  -4.4522   2.1267  -0.1348
 2GE  N01  N   NH2   0  -0.826  -1.1367  -3.6156  -0.5904
 2GE  C02  C   CR6   0   0.524  -1.3334  -2.3009  -0.3399
 2GE  N03  N   N     0  -0.482  -0.2571  -1.5118  -0.3829
 2GE  C04  C   CR6   0   0.244  -0.4729  -0.2329  -0.0890
 2GE  C05  C   CR6   0   0.122   0.6990   0.6758  -0.1482
 2GE  C06  C   CR16  0  -0.294   0.6821   1.7419  -1.0412
 2GE  C07  C   CR16  0  -0.239   1.7605   2.6066  -1.1397
 2GE  C08  C   CR16  0  -0.230   2.8729   2.4219  -0.3370
 2GE  C09  C   CR6   0   0.018   2.8960   1.3718   0.5684
 2GE  CL1  CL  CL    0  -0.095   4.2789   1.1669   1.5762
 2GE  C11  C   CR6   0  -0.069   1.8168   0.4981   0.6659
 2GE  CL2  CL  CL    0  -0.094   1.8488  -0.7643   1.8355
 2GE  C14  C   CR6   0   0.531  -2.7767  -0.6385   0.2327
 2GE  N15  N   NH1   0  -0.653  -4.0408  -0.2702   0.5108
 2GE  C16  C   CH1   0  -0.104  -4.4207   1.0433   0.9024
 2GE  C18  C   CH2   0  -0.510  -5.7291   1.5600   0.4011
 2GE  N19  N   N     0  -0.512  -2.5764  -1.9248  -0.0471
 2GE  H1   H   HCR6  0   0.277  -1.8451   1.3248   0.4730
 2GE  H3   H   HCH2  0   0.259  -4.1647   1.8570  -1.1428
 2GE  H4   H   HNH2  0   0.390  -1.9396  -4.1813  -0.8052
 2GE  H5   H   HNH2  0   0.390  -0.2715  -3.8865  -1.0247
 2GE  H6   H   HCR6  0   0.269  -0.1847   1.8827  -1.6735
 2GE  H7   H   HCR6  0   0.277   1.7386   3.4263  -1.8443
 2GE  H8   H   HCR6  0   0.291   3.7207   3.0895  -0.4056
 2GE  H9   H   HNH1  0   0.389  -4.7174  -1.0134   0.5903
 2GE  H10  H   HCH1  0   0.268  -4.1282   1.3385   1.9070
 2GE  H11  H   HCH2  0   0.261  -6.3217   2.1609   1.0774
 2GE  H12  H   HCH2  0   0.260  -6.3049   0.9123  -0.2477
 2GE  H2   H   HCH2  0   0.258  -4.1571   3.1218   0.1712

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
 2GE  C07  C06  aromatic  1.386  0.020  1.386
 2GE  C07  C08  aromatic  1.384  0.020  1.384
 2GE  C06  C05  aromatic  1.391  0.020  1.391
 2GE  N01  C02  single    1.353  0.020  1.353
 2GE  C08  C09  aromatic  1.387  0.020  1.387
 2GE  N03  C02  aromatic  1.335  0.020  1.335
 2GE  N03  C04  aromatic  1.330  0.020  1.330
 2GE  C02  N19  aromatic  1.331  0.020  1.331
 2GE  C05  C04  single    1.484  0.020  1.484
 2GE  C05  C11  aromatic  1.394  0.020  1.394
 2GE  C04  C13  aromatic  1.377  0.020  1.377
 2GE  C09  C11  aromatic  1.392  0.020  1.392
 2GE  C09  CL1  single    1.723  0.020  1.723
 2GE  N19  C14  aromatic  1.332  0.020  1.332
 2GE  C11  CL2  single    1.721  0.020  1.721
 2GE  C13  C14  aromatic  1.409  0.020  1.409
 2GE  C14  N15  single    1.346  0.020  1.346
 2GE  N15  C16  single    1.422  0.020  1.422
 2GE  C16  C18  single    1.493  0.020  1.493
 2GE  C16  C17  single    1.500  0.020  1.500
 2GE  C18  C17  single    1.496  0.020  1.496
 2GE  C13  H1   single    0.930  0.020  1.080
 2GE  C17  H2   single    0.970  0.020  1.090
 2GE  C17  H3   single    0.970  0.020  1.090
 2GE  N01  H4   single    0.890  0.020  1.040
 2GE  N01  H5   single    0.890  0.020  1.040
 2GE  C06  H6   single    0.930  0.020  1.080
 2GE  C07  H7   single    0.930  0.020  1.080
 2GE  C08  H8   single    0.930  0.020  1.080
 2GE  N15  H9   single    0.860  0.020  1.020
 2GE  C16  H10  single    0.970  0.020  1.090
 2GE  C18  H11  single    0.970  0.020  1.090
 2GE  C18  H12  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
 2GE  H1   C13  C14  122.40  3.000
 2GE  H1   C13  C04  121.73  3.000
 2GE  C14  C13  C04  115.87  3.000
 2GE  H3   C17  H2   114.84  3.000
 2GE  H3   C17  C18  117.76  3.000
 2GE  H2   C17  C18  118.67  3.000
 2GE  H3   C17  C16  117.28  3.000
 2GE  H2   C17  C16  117.58  3.000
 2GE  C18  C17  C16   59.79  3.000
 2GE  H5   N01  H4   116.32  3.000
 2GE  H5   N01  C02  117.84  3.000
 2GE  H4   N01  C02  118.05  3.000
 2GE  N19  C02  N03  126.35  3.000
 2GE  N19  C02  N01  116.81  3.000
 2GE  N03  C02  N01  116.82  3.000
 2GE  C04  N03  C02  115.49  3.000
 2GE  C05  C04  N03  116.86  3.000
 2GE  C05  C04  C13  119.31  3.000
 2GE  N03  C04  C13  123.81  3.000
 2GE  C11  C05  C06  118.84  3.000
 2GE  C11  C05  C04  122.12  3.000
 2GE  C06  C05  C04  119.04  3.000
 2GE  H6   C06  C07  120.04  3.000
 2GE  H6   C06  C05  118.99  3.000
 2GE  C07  C06  C05  120.96  3.000
 2GE  H7   C07  C08  119.70  3.000
 2GE  H7   C07  C06  120.25  3.000
 2GE  C08  C07  C06  120.06  3.000
 2GE  H8   C08  C09  119.72  3.000
 2GE  H8   C08  C07  120.73  3.000
 2GE  C09  C08  C07  119.55  3.000
 2GE  C11  C09  CL1  120.43  3.000
 2GE  CL1  C09  C08  119.03  3.000
 2GE  C11  C09  C08  120.54  3.000
 2GE  CL2  C11  C09  119.57  3.000
 2GE  CL2  C11  C05  120.34  3.000
 2GE  C09  C11  C05  120.05  3.000
 2GE  N19  C14  N15  116.68  3.000
 2GE  N15  C14  C13  122.20  3.000
 2GE  N19  C14  C13  121.11  3.000
 2GE  H9   N15  C16  118.67  3.000
 2GE  H9   N15  C14  116.42  3.000
 2GE  C16  N15  C14  124.09  3.000
 2GE  H10  C16  C18  116.87  3.000
 2GE  H10  C16  N15  115.68  3.000
 2GE  C18  C16  N15  117.46  3.000
 2GE  H10  C16  C17  116.64  3.000
 2GE  C18  C16  C17   59.98  3.000
 2GE  N15  C16  C17  118.83  3.000
 2GE  H12  C18  H11  114.56  3.000
 2GE  H12  C18  C16  117.40  3.000
 2GE  H11  C18  C16  117.54  3.000
 2GE  H12  C18  C17  117.77  3.000
 2GE  H11  C18  C17  118.76  3.000
 2GE  C16  C18  C17   60.24  3.000
 2GE  C14  N19  C02  117.36  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
 2GE  CONST_01  C02  N03  C04  C13     0.00   0.0  0
 2GE  CONST_04  C02  N19  C14  C13     0.00   0.0  0
 2GE  CONST_05  C05  C04  N03  C02   180.00   0.0  0
 2GE  CONST_06  C14  N19  C02  N03     0.00   0.0  0
 2GE  CONST_09  C14  C13  C04  N03     0.00   0.0  0
 2GE  CONST_10  N19  C02  N03  C04     0.00   0.0  0
 2GE  CONST_11  C07  C06  C05  C04   180.00   0.0  0
 2GE  CONST_12  C09  C11  C05  C04   180.00   0.0  0
 2GE  CONST_13  N19  C14  C13  C04     0.00   0.0  0
 2GE  CONST_14  C08  C07  C06  C05     0.00   0.0  0
 2GE  CONST_15  C14  C13  C04  C05   180.00   0.0  0
 2GE  CONST_16  C08  C09  C11  C05     0.00   0.0  0
 2GE  CONST_17  C09  C08  C07  C06     0.00   0.0  0
 2GE  CONST_18  C09  C11  C05  C06     0.00   0.0  0
 2GE  CONST_19  C11  C05  C06  C07     0.00   0.0  0
 2GE  CONST_20  C11  C09  C08  C07     0.00   0.0  0
 2GE  CONST_21  C04  N03  C02  N01   180.00   0.0  0
 2GE  CONST_22  C14  N19  C02  N01   180.00   0.0  0
 2GE  CONST_23  N15  C14  N19  C02   180.00   0.0  0
 2GE  CONST_24  CL2  C11  C05  C04     0.00   0.0  0
 2GE  CONST_25  N15  C14  C13  C04   180.00   0.0  0
 2GE  CONST_26  CL1  C09  C11  C05   180.00   0.0  0
 2GE  CONST_27  CL2  C11  C05  C06   180.00   0.0  0
 2GE  CONST_28  CL1  C09  C08  C07   180.00   0.0  0
 2GE  CONST_29  CL2  C11  C09  C08   180.00   0.0  0
 2GE  CONST_30  C16  N15  C14  C13     0.00   0.0  0
 2GE  CONST_31  N19  C14  N15  C16   180.00   0.0  0
 2GE  CONST_32  H1   C13  C04  N03   180.00   0.0  0
 2GE  CONST_33  H6   C06  C05  C04     0.00   0.0  0
 2GE  CONST_34  H7   C07  C06  C05   180.00   0.0  0
 2GE  CONST_35  H8   C08  C07  C06   180.00   0.0  0
 2GE  CONST_36  H9   N15  C14  C13   180.00   0.0  0
 2GE  Var_01    C14  N15  C16  C17    74.34  30.0  1
 2GE  Var_02    N15  C16  C18  C17  -109.11  30.0  1
 2GE  Var_03    H2   C17  C18  C16  -106.99  30.0  1

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
 2GE  chir_01  C16  N15  C18  C17  both

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
 2GE  plan-1  C13  0.020
 2GE  plan-1  N01  0.020
 2GE  plan-1  C02  0.020
 2GE  plan-1  N03  0.020
 2GE  plan-1  C04  0.020
 2GE  plan-1  C05  0.020
 2GE  plan-1  C14  0.020
 2GE  plan-1  N15  0.020
 2GE  plan-1  N19  0.020
 2GE  plan-1  H1   0.020
 2GE  plan-2  C04  0.020
 2GE  plan-2  C05  0.020
 2GE  plan-2  C06  0.020
 2GE  plan-2  C07  0.020
 2GE  plan-2  C08  0.020
 2GE  plan-2  C09  0.020
 2GE  plan-2  CL1  0.020
 2GE  plan-2  C11  0.020
 2GE  plan-2  CL2  0.020
 2GE  plan-2  H6   0.020
 2GE  plan-2  H7   0.020
 2GE  plan-2  H8   0.020
 2GE  plan-3  N01  0.020
 2GE  plan-3  C02  0.020
 2GE  plan-3  H4   0.020
 2GE  plan-3  H5   0.020
 2GE  plan-4  C14  0.020
 2GE  plan-4  N15  0.020
 2GE  plan-4  C16  0.020
 2GE  plan-4  H9   0.020

