# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 08:03:18 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 6-methyl-5-[3-[2,4,5-tris(chloranyl)phenoxy]propoxy]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)nc(N)c1OCCCOc2cc(Cl)c(Cl)cc2Cl
#
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
 P65  P65  6-methyl-5-[3-[2,4,5-tris(chloranyl)phenoxy]propoxy]pyrimidine-2,4-diamine  ligand  38  23  .  2021-08-19  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P65
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
 P65  NH2  N   NH2   0  -0.823   4.6572  -0.3408   2.3667
 P65  C5   C   CR6   0   0.437   5.2340  -0.0421   1.1842
 P65  N4   N   N     0  -0.501   6.3912   0.6100   1.1978
 P65  C3   C   CR6   0   0.519   6.9283   0.9145   0.0169
 P65  NH1  N   NH2   0  -0.826   8.0757   1.6382   0.0384
 P65  N2   N   N     0  -0.501   6.4350   0.6020  -1.1797
 P65  C6   C   CR6   0   0.127   4.6140  -0.3900  -0.0322
 P65  C1   C   CR6   0   0.204   5.2694  -0.0518  -1.1972
 P65  CM1  C   CH3   0  -0.736   4.6998  -0.4087  -2.5349
 P65  O7   O   O2    0  -0.498   3.4214  -1.0589  -0.0264
 P65  C8   C   CH2   0  -0.153   2.2798  -0.2064  -0.0486
 P65  C9   C   CH2   0  -0.502   1.0414  -1.0782   0.0066
 P65  C10  C   CH2   0  -0.189  -0.2074  -0.2214  -0.0073
 P65  O11  O   O2    0  -0.452  -1.3269  -1.0981   0.0284
 P65  C12  C   CR6   0   0.482  -2.5561  -0.5840   0.0238
 P65  C17  C   CR16  0  -0.352  -2.8473   0.7750  -0.0069
 P65  C16  C   CR6   0   0.025  -4.1649   1.2116  -0.0096
 P65  CL3  CL  CL    0  -0.085  -4.4755   2.9030  -0.0469
 P65  C15  C   CR6   0  -0.044  -5.2114   0.3032   0.0178
 P65  CL2  CL  CL    0  -0.093  -6.8499   0.8296   0.0133
 P65  C14  C   CR16  0  -0.161  -4.9310  -1.0559   0.0486
 P65  C13  C   CR6   0  -0.165  -3.6228  -1.4910   0.0523
 P65  CL1  CL  CL    0  -0.089  -3.2825  -3.1791   0.0911
 P65  H1   H   HNH2  0   0.397   3.9435  -1.0484   2.3977
 P65  H2   H   HNH2  0   0.392   5.2186  -0.2469   3.1965
 P65  H3   H   HNH2  0   0.386   8.6210   1.6685  -0.8057
 P65  H4   H   HNH2  0   0.387   8.5953   1.6686   0.8987
 P65  H5   H   HCH3  0   0.252   4.3230  -1.4306  -2.5535
 P65  H6   H   HCH3  0   0.255   3.8626   0.2449  -2.7892
 P65  H7   H   HCH3  0   0.254   5.4562  -0.2964  -3.3083
 P65  H8   H   HCH2  0   0.223   2.3026   0.4838   0.8029
 P65  H9   H   HCH2  0   0.225   2.2784   0.4010  -0.9610
 P65  H10  H   HCH2  0   0.251   1.0322  -1.7548  -0.8514
 P65  H11  H   HCH2  0   0.250   1.0597  -1.6864   0.9145
 P65  H12  H   HCH2  0   0.239  -0.2244   0.4484   0.8590
 P65  H13  H   HCH2  0   0.239  -0.2409   0.3951  -0.9122
 P65  H14  H   HCR6  0   0.318  -2.0587   1.5133  -0.0282
 P65  H15  H   HCR6  0   0.310  -5.7389  -1.7738   0.0700

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
 P65  NH1  C3   single    1.357  0.020  1.357
 P65  C3   N2   aromatic  1.331  0.020  1.331
 P65  C3   N4   aromatic  1.333  0.020  1.333
 P65  N2   C1   aromatic  1.337  0.020  1.337
 P65  N4   C5   aromatic  1.328  0.020  1.328
 P65  C1   CM1  single    1.497  0.020  1.497
 P65  C1   C6   aromatic  1.379  0.020  1.379
 P65  C5   C6   aromatic  1.409  0.020  1.409
 P65  C5   NH2  single    1.349  0.020  1.349
 P65  C6   O7   single    1.367  0.020  1.367
 P65  O7   C8   single    1.425  0.020  1.425
 P65  C8   C9   single    1.515  0.020  1.515
 P65  CL1  C13  single    1.722  0.020  1.722
 P65  C13  C14  aromatic  1.379  0.020  1.379
 P65  C13  C12  aromatic  1.401  0.020  1.401
 P65  C14  C15  aromatic  1.388  0.020  1.388
 P65  C9   C10  single    1.514  0.020  1.514
 P65  O11  C12  single    1.332  0.020  1.332
 P65  O11  C10  single    1.422  0.020  1.422
 P65  C12  C17  aromatic  1.390  0.020  1.390
 P65  C15  CL2  single    1.721  0.020  1.721
 P65  C15  C16  aromatic  1.386  0.020  1.386
 P65  C17  C16  aromatic  1.388  0.020  1.388
 P65  C16  CL3  single    1.720  0.020  1.720
 P65  NH2  H1   single    0.890  0.020  1.040
 P65  NH2  H2   single    0.890  0.020  1.040
 P65  NH1  H3   single    0.890  0.020  1.040
 P65  NH1  H4   single    0.890  0.020  1.040
 P65  CM1  H5   single    0.970  0.020  1.090
 P65  CM1  H6   single    0.970  0.020  1.090
 P65  CM1  H7   single    0.970  0.020  1.090
 P65  C8   H8   single    0.970  0.020  1.090
 P65  C8   H9   single    0.970  0.020  1.090
 P65  C9   H10  single    0.970  0.020  1.090
 P65  C9   H11  single    0.970  0.020  1.090
 P65  C10  H12  single    0.970  0.020  1.090
 P65  C10  H13  single    0.970  0.020  1.090
 P65  C17  H14  single    0.930  0.020  1.080
 P65  C14  H15  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
 P65  H2   NH2  H1   115.87  3.000
 P65  H2   NH2  C5   117.62  3.000
 P65  H1   NH2  C5   119.09  3.000
 P65  C6   C5   N4   120.89  3.000
 P65  C6   C5   NH2  120.93  3.000
 P65  N4   C5   NH2  118.17  3.000
 P65  C3   N4   C5   117.01  3.000
 P65  N2   C3   NH1  116.93  3.000
 P65  N2   C3   N4   126.40  3.000
 P65  NH1  C3   N4   116.66  3.000
 P65  H4   NH1  H3   115.93  3.000
 P65  H4   NH1  C3   117.82  3.000
 P65  H3   NH1  C3   117.48  3.000
 P65  C1   N2   C3   116.73  3.000
 P65  O7   C6   C1   122.55  3.000
 P65  O7   C6   C5   120.06  3.000
 P65  C1   C6   C5   117.37  3.000
 P65  CM1  C1   C6   121.04  3.000
 P65  C6   C1   N2   121.56  3.000
 P65  CM1  C1   N2   117.40  3.000
 P65  H7   CM1  H6   107.80  3.000
 P65  H7   CM1  H5   108.99  3.000
 P65  H6   CM1  H5   107.00  3.000
 P65  H7   CM1  C1   110.25  3.000
 P65  H6   CM1  C1   110.92  3.000
 P65  H5   CM1  C1   111.75  3.000
 P65  C8   O7   C6   113.95  3.000
 P65  H9   C8   H8   107.33  3.000
 P65  H9   C8   C9   110.36  3.000
 P65  H8   C8   C9   110.54  3.000
 P65  H9   C8   O7   110.21  3.000
 P65  H8   C8   O7   110.36  3.000
 P65  C9   C8   O7   108.05  3.000
 P65  H11  C9   H10  107.93  3.000
 P65  H11  C9   C10  109.65  3.000
 P65  H10  C9   C10  109.64  3.000
 P65  H11  C9   C8   109.67  3.000
 P65  H10  C9   C8   109.54  3.000
 P65  C10  C9   C8   110.37  3.000
 P65  H13  C10  H12  107.98  3.000
 P65  H13  C10  O11  110.09  3.000
 P65  H12  C10  O11  110.18  3.000
 P65  H13  C10  C9   110.56  3.000
 P65  H12  C10  C9   110.58  3.000
 P65  O11  C10  C9   107.46  3.000
 P65  C12  O11  C10  119.22  3.000
 P65  C13  C12  C17  118.30  3.000
 P65  C17  C12  O11  124.79  3.000
 P65  C13  C12  O11  116.92  3.000
 P65  H14  C17  C16  118.54  3.000
 P65  H14  C17  C12  121.03  3.000
 P65  C16  C17  C12  120.42  3.000
 P65  C15  C16  CL3  120.57  3.000
 P65  CL3  C16  C17  118.74  3.000
 P65  C15  C16  C17  120.70  3.000
 P65  C14  C15  CL2  119.46  3.000
 P65  CL2  C15  C16  121.22  3.000
 P65  C14  C15  C16  119.32  3.000
 P65  H15  C14  C13  119.97  3.000
 P65  H15  C14  C15  119.98  3.000
 P65  C13  C14  C15  120.05  3.000
 P65  CL1  C13  C14  119.79  3.000
 P65  C14  C13  C12  121.22  3.000
 P65  CL1  C13  C12  118.99  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
 P65  CONST_01  N2   C3   N4   C5      0.00   0.0  0
 P65  CONST_02  N2   C1   C6   C5      0.00   0.0  0
 P65  CONST_03  C1   N2   C3   N4      0.00   0.0  0
 P65  CONST_04  C1   C6   C5   N4      0.00   0.0  0
 P65  CONST_05  C6   C1   N2   C3      0.00   0.0  0
 P65  CONST_06  C6   C5   N4   C3      0.00   0.0  0
 P65  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 P65  CONST_08  C15  C16  C17  C12     0.00   0.0  0
 P65  CONST_09  C14  C13  C12  C17     0.00   0.0  0
 P65  CONST_10  C14  C15  C16  C17     0.00   0.0  0
 P65  CONST_11  C13  C14  C15  C16     0.00   0.0  0
 P65  CONST_12  C13  C12  C17  C16     0.00   0.0  0
 P65  CONST_13  C3   N4   C5   NH2   180.00   0.0  0
 P65  CONST_14  C1   C6   C5   NH2   180.00   0.0  0
 P65  CONST_15  NH1  C3   N4   C5    180.00   0.0  0
 P65  CONST_16  CM1  C1   C6   C5    180.00   0.0  0
 P65  CONST_17  O7   C6   C5   N4    180.00   0.0  0
 P65  CONST_18  CM1  C1   N2   C3    180.00   0.0  0
 P65  CONST_19  C1   N2   C3   NH1   180.00   0.0  0
 P65  CONST_20  O7   C6   C1   N2    180.00   0.0  0
 P65  CONST_21  C14  C13  C12  O11   180.00   0.0  0
 P65  CONST_22  C16  C17  C12  O11   180.00   0.0  0
 P65  CONST_23  CL3  C16  C17  C12   180.00   0.0  0
 P65  CONST_24  CL1  C13  C12  C17   180.00   0.0  0
 P65  CONST_25  CL2  C15  C16  C17   180.00   0.0  0
 P65  CONST_26  C14  C15  C16  CL3   180.00   0.0  0
 P65  CONST_27  CL1  C13  C14  C15   180.00   0.0  0
 P65  CONST_28  C13  C14  C15  CL2   180.00   0.0  0
 P65  CONST_29  H15  C14  C13  C12   180.00   0.0  0
 P65  CONST_30  H14  C17  C16  C15   180.00   0.0  0
 P65  CONST_34  H2   NH2  C5   N4      0.00   0.0  0
 P65  Var_01    C13  C12  O11  C10   179.65  30.0  2
 P65  Var_02    H5   CM1  C1   N2    135.71  30.0  2
 P65  Var_03    C9   C8   O7   C6   -178.18  30.0  3
 P65  Var_04    H12  C10  O11  C12    59.49  30.0  3
 P65  Var_05    C10  C9   C8   O7    179.72  30.0  3
 P65  Var_06    O11  C10  C9   C8    179.25  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
 P65  plan-1  NH2  0.020
 P65  plan-1  C5   0.020
 P65  plan-1  N4   0.020
 P65  plan-1  C3   0.020
 P65  plan-1  NH1  0.020
 P65  plan-1  N2   0.020
 P65  plan-1  C6   0.020
 P65  plan-1  C1   0.020
 P65  plan-1  CM1  0.020
 P65  plan-1  O7   0.020
 P65  plan-2  O11  0.020
 P65  plan-2  C12  0.020
 P65  plan-2  C17  0.020
 P65  plan-2  C16  0.020
 P65  plan-2  CL3  0.020
 P65  plan-2  C15  0.020
 P65  plan-2  CL2  0.020
 P65  plan-2  C14  0.020
 P65  plan-2  C13  0.020
 P65  plan-2  CL1  0.020
 P65  plan-2  H14  0.020
 P65  plan-2  H15  0.020
 P65  plan-3  NH2  0.020
 P65  plan-3  C5   0.020
 P65  plan-3  H1   0.020
 P65  plan-3  H2   0.020
 P65  plan-4  C3   0.020
 P65  plan-4  NH1  0.020
 P65  plan-4  H3   0.020
 P65  plan-4  H4   0.020

