# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 22:42:00 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 6-chloro-N~4~-cyclopropyl-N~4~-[(thiophen-2-yl)methyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Cl)cc(n1)N(Cc2sccc2)C3CC3
#
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
 LRI  LRI  6-chloro-N~4~-cyclopropyl-N~4~-[(thiophen-2-yl)methyl]pyrimidine-2,4-diamine  ligand  31  18  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LRI
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
 LRI  CAL  C   CR15  0  -0.233  -1.7298   2.3517  -0.0515
 LRI  CAM  C   CR15  0  -0.183  -2.3998   2.9471   1.0534
 LRI  CAN  C   CR15  0  -0.464  -3.1937   2.0649   1.7177
 LRI  SAO  S   S2    0   0.205  -3.1391   0.5087   1.0009
 LRI  CAK  C   CR5   0  -0.129  -2.0271   1.0311  -0.2110
 LRI  CAJ  C   CH2   0  -0.427  -1.5022   0.0799  -1.2420
 LRI  NAI  N   NT    0  -0.486  -0.6390  -0.9547  -0.6949
 LRI  CAP  C   CH1   0  -0.100  -1.2665  -2.1286  -0.1607
 LRI  CAQ  C   CH2   0  -0.512  -2.2067  -2.8972  -1.0362
 LRI  CAR  C   CH2   0  -0.463  -0.8722  -3.4709  -0.6770
 LRI  C4   C   CR6   0   0.578   0.6255  -0.6558  -0.2960
 LRI  N3   N   N     0  -0.500   1.2408  -1.5411   0.4815
 LRI  C5   C   CR16  0  -0.386   1.2776   0.5331  -0.6910
 LRI  C6   C   CR6   0   0.190   2.5603   0.6671  -0.2219
 LRI  CL6  CL  CL    0  -0.112   3.4496   2.0948  -0.6549
 LRI  N1   N   N     0  -0.475   3.1981  -0.1894   0.5403
 LRI  C2   C   CR6   0   0.548   2.4882  -1.2807   0.8611
 LRI  NAA  N   NH2   0  -0.820   3.0855  -2.1753   1.6674
 LRI  H1   H   HCR5  0   0.265  -1.0561   2.8884  -0.7053
 LRI  H2   H   HCR5  0   0.268  -2.2909   3.9836   1.3387
 LRI  H3   H   HCR5  0   0.295  -3.8065   2.2434   2.5878
 LRI  H4   H   HCH2  0   0.295  -2.3228  -0.4187  -1.7555
 LRI  H5   H   HCH2  0   0.287  -0.9788   0.6456  -2.0130
 LRI  H6   H   HCH1  0   0.262  -1.5178  -2.0778   0.8957
 LRI  H7   H   HCH2  0   0.261  -3.0972  -3.3011  -0.5731
 LRI  H8   H   HCH2  0   0.259  -2.3487  -2.5651  -2.0573
 LRI  H9   H   HCH2  0   0.254  -0.1187  -3.5022  -1.4528
 LRI  H10  H   HCH2  0   0.252  -0.8210  -4.2844   0.0344
 LRI  H11  H   HCR6  0   0.276   0.8320   1.2846  -1.3199
 LRI  H12  H   HNH2  0   0.398   4.0709  -2.0945   1.8466
 LRI  H13  H   HNH2  0   0.398   2.6620  -3.0775   1.7949

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
 LRI  CAN  CAM  aromatic  1.360  0.020  1.360
 LRI  CAN  SAO  aromatic  1.714  0.020  1.714
 LRI  CAM  CAL  aromatic  1.423  0.020  1.423
 LRI  CL6  C6   single    1.737  0.020  1.737
 LRI  CAL  CAK  aromatic  1.363  0.020  1.363
 LRI  SAO  CAK  aromatic  1.726  0.020  1.726
 LRI  C6   C5   aromatic  1.372  0.020  1.372
 LRI  C6   N1   aromatic  1.312  0.020  1.312
 LRI  CAK  CAJ  single    1.498  0.020  1.498
 LRI  C5   C4   aromatic  1.412  0.020  1.412
 LRI  N1   C2   aromatic  1.341  0.020  1.341
 LRI  CAP  CAR  single    1.491  0.020  1.491
 LRI  CAP  NAI  single    1.434  0.020  1.434
 LRI  CAP  CAQ  single    1.497  0.020  1.497
 LRI  C2   NAA  single    1.344  0.020  1.344
 LRI  C2   N3   aromatic  1.330  0.020  1.330
 LRI  C4   NAI  single    1.359  0.020  1.359
 LRI  C4   N3   aromatic  1.329  0.020  1.329
 LRI  CAR  CAQ  single    1.496  0.020  1.496
 LRI  NAI  CAJ  single    1.454  0.020  1.454
 LRI  CAL  H1   single    0.930  0.020  1.080
 LRI  CAM  H2   single    0.930  0.020  1.080
 LRI  CAN  H3   single    0.930  0.020  1.080
 LRI  CAJ  H4   single    0.970  0.020  1.090
 LRI  CAJ  H5   single    0.970  0.020  1.090
 LRI  CAP  H6   single    0.970  0.020  1.090
 LRI  CAQ  H7   single    0.970  0.020  1.090
 LRI  CAQ  H8   single    0.970  0.020  1.090
 LRI  CAR  H9   single    0.970  0.020  1.090
 LRI  CAR  H10  single    0.970  0.020  1.090
 LRI  C5   H11  single    0.930  0.020  1.080
 LRI  NAA  H12  single    0.890  0.020  1.040
 LRI  NAA  H13  single    0.890  0.020  1.040

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
 LRI  H1   CAL  CAK  123.09  3.000
 LRI  H1   CAL  CAM  123.73  3.000
 LRI  CAK  CAL  CAM  113.18  3.000
 LRI  H2   CAM  CAN  123.50  3.000
 LRI  H2   CAM  CAL  123.99  3.000
 LRI  CAN  CAM  CAL  112.51  3.000
 LRI  H3   CAN  SAO  120.36  3.000
 LRI  H3   CAN  CAM  128.18  3.000
 LRI  SAO  CAN  CAM  111.47  3.000
 LRI  CAK  SAO  CAN   92.25  3.000
 LRI  CAJ  CAK  SAO  121.13  3.000
 LRI  CAJ  CAK  CAL  128.28  3.000
 LRI  SAO  CAK  CAL  110.59  3.000
 LRI  H5   CAJ  H4   105.42  3.000
 LRI  H5   CAJ  NAI  110.50  3.000
 LRI  H4   CAJ  NAI  107.39  3.000
 LRI  H5   CAJ  CAK  109.00  3.000
 LRI  H4   CAJ  CAK  110.57  3.000
 LRI  NAI  CAJ  CAK  113.63  3.000
 LRI  C4   NAI  CAP  118.54  3.000
 LRI  C4   NAI  CAJ  120.41  3.000
 LRI  CAP  NAI  CAJ  117.57  3.000
 LRI  H6   CAP  CAR  116.08  3.000
 LRI  H6   CAP  CAQ  116.56  3.000
 LRI  CAR  CAP  CAQ   60.10  3.000
 LRI  H6   CAP  NAI  115.14  3.000
 LRI  CAQ  CAP  NAI  118.50  3.000
 LRI  CAR  CAP  NAI  119.48  3.000
 LRI  H8   CAQ  H7   114.21  3.000
 LRI  H8   CAQ  CAR  117.43  3.000
 LRI  H7   CAQ  CAR  119.22  3.000
 LRI  H8   CAQ  CAP  118.44  3.000
 LRI  H7   CAQ  CAP  117.28  3.000
 LRI  CAR  CAQ  CAP   59.76  3.000
 LRI  H10  CAR  H9   114.63  3.000
 LRI  H10  CAR  CAQ  119.23  3.000
 LRI  H9   CAR  CAQ  117.40  3.000
 LRI  H10  CAR  CAP  117.49  3.000
 LRI  H9   CAR  CAP  117.29  3.000
 LRI  CAQ  CAR  CAP   60.15  3.000
 LRI  C5   C4   N3   120.70  3.000
 LRI  N3   C4   NAI  117.12  3.000
 LRI  C5   C4   NAI  122.18  3.000
 LRI  C2   N3   C4   118.09  3.000
 LRI  H11  C5   C6   121.23  3.000
 LRI  H11  C5   C4   124.05  3.000
 LRI  C6   C5   C4   114.72  3.000
 LRI  N1   C6   CL6  115.63  3.000
 LRI  N1   C6   C5   126.10  3.000
 LRI  CL6  C6   C5   118.27  3.000
 LRI  C2   N1   C6   114.39  3.000
 LRI  NAA  C2   N1   116.74  3.000
 LRI  NAA  C2   N3   117.24  3.000
 LRI  N1   C2   N3   126.00  3.000
 LRI  H13  NAA  H12  117.57  3.000
 LRI  H13  NAA  C2   119.11  3.000
 LRI  H12  NAA  C2   119.29  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
 LRI  CONST_01  SAO  CAN  CAM  CAL     0.00   0.0  0
 LRI  CONST_02  CAN  SAO  CAK  CAL     0.00   0.0  0
 LRI  CONST_03  CAK  SAO  CAN  CAM     0.00   0.0  0
 LRI  CONST_04  SAO  CAK  CAL  CAM     0.00   0.0  0
 LRI  CONST_05  CAK  CAL  CAM  CAN     0.00   0.0  0
 LRI  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 LRI  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 LRI  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 LRI  CONST_09  C6   C5   C4   N3      0.00   0.0  0
 LRI  CONST_10  C2   N1   C6   C5      0.00   0.0  0
 LRI  CONST_11  C2   N3   C4   C5      0.00   0.0  0
 LRI  CONST_12  CAJ  CAK  CAL  CAM   180.00   0.0  0
 LRI  CONST_13  CAJ  CAK  SAO  CAN   180.00   0.0  0
 LRI  CONST_14  C6   C5   C4   NAI   180.00   0.0  0
 LRI  CONST_15  C2   N3   C4   NAI   180.00   0.0  0
 LRI  CONST_16  CL6  C6   C5   C4    180.00   0.0  0
 LRI  CONST_17  NAA  C2   N3   C4    180.00   0.0  0
 LRI  CONST_18  NAA  C2   N1   C6    180.00   0.0  0
 LRI  CONST_19  C2   N1   C6   CL6   180.00   0.0  0
 LRI  CONST_20  C5   C4   NAI  CAP   180.00   0.0  0
 LRI  CONST_21  N3   C4   NAI  CAP     0.00   0.0  0
 LRI  CONST_22  H3   CAN  CAM  CAL   180.00   0.0  0
 LRI  CONST_23  H1   CAL  CAM  CAN   180.00   0.0  0
 LRI  CONST_24  H2   CAM  CAN  SAO   180.00   0.0  0
 LRI  CONST_25  H11  C5   C4   N3    180.00   0.0  0
 LRI  CONST_28  H12  NAA  C2   N3    180.00   0.0  0
 LRI  CONST_29  H13  NAA  C2   N3      0.00   0.0  0
 LRI  Var_01    CAQ  CAR  CAP  NAI  -107.89  30.0  1
 LRI  Var_02    C4   NAI  CAP  CAQ  -146.11  30.0  3
 LRI  Var_03    H7   CAQ  CAR  CAP  -106.36  30.0  1
 LRI  Var_04    NAI  CAJ  CAK  CAL   111.84  30.0  2
 LRI  Var_05    CAP  NAI  CAJ  CAK    84.67  30.0  2

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
 LRI  chir_01  CAP  CAR  NAI  CAQ  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
 LRI  plan-1  CAL  0.020
 LRI  plan-1  CAM  0.020
 LRI  plan-1  CAN  0.020
 LRI  plan-1  SAO  0.020
 LRI  plan-1  CAK  0.020
 LRI  plan-1  CAJ  0.020
 LRI  plan-1  H1   0.020
 LRI  plan-1  H2   0.020
 LRI  plan-1  H3   0.020
 LRI  plan-2  NAI  0.020
 LRI  plan-2  C4   0.020
 LRI  plan-2  N3   0.020
 LRI  plan-2  C5   0.020
 LRI  plan-2  C6   0.020
 LRI  plan-2  CL6  0.020
 LRI  plan-2  N1   0.020
 LRI  plan-2  C2   0.020
 LRI  plan-2  NAA  0.020
 LRI  plan-2  H11  0.020
 LRI  plan-3  CAJ  0.020
 LRI  plan-3  NAI  0.020
 LRI  plan-3  CAP  0.020
 LRI  plan-3  C4   0.020
 LRI  plan-4  C2   0.020
 LRI  plan-4  NAA  0.020
 LRI  plan-4  H12  0.020
 LRI  plan-4  H13  0.020

