# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:03:30 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)N=C(N)N=C(N)N1c2ccc(Cl)cc2
#
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
 1CY  1CY  1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine  ligand  31  17  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1CY
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
 1CY  N1    N   N     0  -0.479  -3.0250   0.8391   0.7287
 1CY  C2    C   C     0   0.469  -3.5437  -0.2842   0.3752
 1CY  N3    N   N     0  -0.565  -2.9570  -1.2754  -0.3662
 1CY  C4    C   C     0   0.665  -1.6599  -1.1715  -0.4996
 1CY  N5    N   NT    0  -0.575  -0.9671  -0.0844  -0.0925
 1CY  C6    C   CT    0   0.210  -1.7426   1.1652   0.1731
 1CY  N7    N   NH2   0  -0.826  -4.8000  -0.6071   0.8092
 1CY  N8    N   NH2   0  -0.831  -0.9790  -2.2173  -1.0030
 1CY  C9    C   CH3   0  -0.665  -0.9857   2.0252   1.1776
 1CY  C10   C   CH3   0  -0.634  -1.9258   1.9381  -1.1378
 1CY  C11   C   CR6   0   0.238   0.4496  -0.0723  -0.1285
 1CY  C12   C   CR16  0  -0.245   1.1670  -0.4911   0.9870
 1CY  C13   C   CR16  0  -0.218   2.5521  -0.4772   0.9811
 1CY  C14   C   CR6   0  -0.034   3.2179  -0.0430  -0.1555
 1CY  C15   C   CR16  0  -0.213   2.5222   0.3673  -1.2811
 1CY  C16   C   CR16  0  -0.258   1.1353   0.3479  -1.2632
 1CY  CL17  CL  CL    0  -0.121   4.9490  -0.0193  -0.1698
 1CY  HN7   H   HNH2  0   0.373  -5.3953   0.1625   1.0671
 1CY  HN7A  H   HNH2  0   0.376  -5.2647  -1.3427   0.3043
 1CY  HN8   H   HNH2  0   0.401  -1.5308  -2.9787  -1.3604
 1CY  HN8A  H   HNH2  0   0.411  -0.0697  -2.0987  -1.4167
 1CY  H9    H   HCH3  0   0.228  -0.0250   2.3701   0.7957
 1CY  H9A   H   HCH3  0   0.244  -1.5875   2.9056   1.4014
 1CY  H9B   H   HCH3  0   0.234  -0.8169   1.4864   2.1103
 1CY  H10   H   HCH3  0   0.230  -2.4246   1.3229  -1.8887
 1CY  H10A  H   HCH3  0   0.234  -2.5437   2.8187  -0.9591
 1CY  H10B  H   HCH3  0   0.221  -0.9742   2.2806  -1.5473
 1CY  H12   H   HCR6  0   0.276   0.6389  -0.8312   1.8678
 1CY  H13   H   HCR6  0   0.286   3.1029  -0.8029   1.8528
 1CY  H15   H   HCR6  0   0.287   3.0486   0.6967  -2.1662
 1CY  H16   H   HCR6  0   0.278   0.5917   0.6572  -2.1457

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
 1CY  C6    N1    single    1.435  0.020  1.435
 1CY  C2    N1    double    1.287  0.020  1.287
 1CY  N3    C2    single    1.370  0.020  1.370
 1CY  C2    N7    single    1.368  0.020  1.368
 1CY  C4    N3    double    1.308  0.020  1.308
 1CY  N8    C4    single    1.346  0.020  1.346
 1CY  C4    N5    single    1.352  0.020  1.352
 1CY  C11   N5    single    1.417  0.020  1.417
 1CY  N5    C6    single    1.494  0.020  1.494
 1CY  C6    C10   single    1.533  0.020  1.533
 1CY  C6    C9    single    1.524  0.020  1.524
 1CY  N7    HN7   single    0.890  0.020  1.040
 1CY  N7    HN7A  single    0.890  0.020  1.040
 1CY  N8    HN8   single    0.890  0.020  1.040
 1CY  N8    HN8A  single    0.890  0.020  1.040
 1CY  C9    H9    single    0.970  0.020  1.090
 1CY  C9    H9A   single    0.970  0.020  1.090
 1CY  C9    H9B   single    0.970  0.020  1.090
 1CY  C10   H10   single    0.970  0.020  1.090
 1CY  C10   H10A  single    0.970  0.020  1.090
 1CY  C10   H10B  single    0.970  0.020  1.090
 1CY  C16   C11   aromatic  1.391  0.020  1.391
 1CY  C12   C11   aromatic  1.391  0.020  1.391
 1CY  C13   C12   aromatic  1.385  0.020  1.385
 1CY  C12   H12   single    0.930  0.020  1.080
 1CY  C14   C13   aromatic  1.387  0.020  1.387
 1CY  C13   H13   single    0.930  0.020  1.080
 1CY  CL17  C14   single    1.731  0.020  1.731
 1CY  C14   C15   aromatic  1.385  0.020  1.385
 1CY  C15   C16   aromatic  1.387  0.020  1.387
 1CY  C15   H15   single    0.930  0.020  1.080
 1CY  C16   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
 1CY  C6    N1   C2    116.88  3.000
 1CY  N7    C2   N3    113.22  3.000
 1CY  N7    C2   N1    119.29  3.000
 1CY  N3    C2   N1    127.43  3.000
 1CY  C4    N3   C2    114.99  3.000
 1CY  N8    C4   N5    118.58  3.000
 1CY  N5    C4   N3    122.78  3.000
 1CY  N8    C4   N3    118.56  3.000
 1CY  C11   N5   C6    121.07  3.000
 1CY  C6    N5   C4    117.39  3.000
 1CY  C11   N5   C4    120.77  3.000
 1CY  C10   C6   C9    109.79  3.000
 1CY  C9    C6   N5    109.35  3.000
 1CY  C10   C6   N5    109.37  3.000
 1CY  C9    C6   N1    108.47  3.000
 1CY  C10   C6   N1    109.81  3.000
 1CY  N5    C6   N1    110.03  3.000
 1CY  HN7A  N7   HN7   114.49  3.000
 1CY  HN7A  N7   C2    115.96  3.000
 1CY  HN7   N7   C2    116.36  3.000
 1CY  HN8A  N8   HN8   116.04  3.000
 1CY  HN8A  N8   C4    121.30  3.000
 1CY  HN8   N8   C4    116.33  3.000
 1CY  H9B   C9   H9A   108.01  3.000
 1CY  H9B   C9   H9    108.64  3.000
 1CY  H9A   C9   H9    107.64  3.000
 1CY  H9B   C9   C6    111.22  3.000
 1CY  H9A   C9   C6    108.49  3.000
 1CY  H9    C9   C6    112.67  3.000
 1CY  H10B  C10  H10A  107.59  3.000
 1CY  H10B  C10  H10   108.50  3.000
 1CY  H10A  C10  H10   107.99  3.000
 1CY  H10B  C10  C6    112.03  3.000
 1CY  H10A  C10  C6    109.56  3.000
 1CY  H10   C10  C6    111.03  3.000
 1CY  C16   C11  C12   119.41  3.000
 1CY  C12   C11  N5    119.52  3.000
 1CY  C16   C11  N5    121.07  3.000
 1CY  H12   C12  C13   119.65  3.000
 1CY  H12   C12  C11   119.73  3.000
 1CY  C13   C12  C11   120.62  3.000
 1CY  H13   C13  C14   120.69  3.000
 1CY  H13   C13  C12   120.19  3.000
 1CY  C14   C13  C12   119.12  3.000
 1CY  CL17  C14  C15   119.42  3.000
 1CY  C15   C14  C13   121.17  3.000
 1CY  CL17  C14  C13   119.41  3.000
 1CY  H15   C15  C16   120.11  3.000
 1CY  H15   C15  C14   120.73  3.000
 1CY  C16   C15  C14   119.17  3.000
 1CY  H16   C16  C15   119.20  3.000
 1CY  H16   C16  C11   120.28  3.000
 1CY  C15   C16  C11   120.51  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
 1CY  CONST_01  C14   C15  C16  C11     0.00   0.0  0
 1CY  CONST_02  C14   C13  C12  C11     0.00   0.0  0
 1CY  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 1CY  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 1CY  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 1CY  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 1CY  CONST_07  C15   C16  C11  N5    180.00   0.0  0
 1CY  CONST_08  C13   C12  C11  N5    180.00   0.0  0
 1CY  CONST_09  C4    N3   C2   N1      0.00   0.0  0
 1CY  CONST_10  N5    C4   N3   C2      0.00   0.0  0
 1CY  CONST_11  C6    N1   C2   N3      0.00   0.0  0
 1CY  CONST_12  C11   N5   C4   N3    180.00   0.0  0
 1CY  CONST_14  CL17  C14  C13  C12   180.00   0.0  0
 1CY  CONST_15  CL17  C14  C15  C16   180.00   0.0  0
 1CY  CONST_16  N8    C4   N3   C2    180.00   0.0  0
 1CY  CONST_18  N7    C2   N1   C6    180.00   0.0  0
 1CY  CONST_19  N8    C4   N5   C6    180.00   0.0  0
 1CY  CONST_20  C11   N5   C4   N8      0.00   0.0  0
 1CY  CONST_21  H16   C16  C11  N5      0.00   0.0  0
 1CY  CONST_22  H12   C12  C11  N5      0.00   0.0  0
 1CY  CONST_23  H15   C15  C16  C11   180.00   0.0  0
 1CY  CONST_24  H13   C13  C12  C11   180.00   0.0  0
 1CY  CONST_27  HN8   N8   C4   N3      0.00   0.0  0
 1CY  Var_01    C16   C11  N5   C4     88.90  30.0  2
 1CY  Var_02    C10   C6   N1   C2     90.26  30.0  1
 1CY  Var_03    H10   C10  C6   N1    -63.51  30.0  3
 1CY  Var_04    H9    C9   C6   N1   -176.08  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
 1CY  plan-1  N5    0.020
 1CY  plan-1  C11   0.020
 1CY  plan-1  C12   0.020
 1CY  plan-1  C13   0.020
 1CY  plan-1  C14   0.020
 1CY  plan-1  C15   0.020
 1CY  plan-1  C16   0.020
 1CY  plan-1  CL17  0.020
 1CY  plan-1  H12   0.020
 1CY  plan-1  H13   0.020
 1CY  plan-1  H15   0.020
 1CY  plan-1  H16   0.020
 1CY  plan-2  N1    0.020
 1CY  plan-2  C2    0.020
 1CY  plan-2  N3    0.020
 1CY  plan-2  C4    0.020
 1CY  plan-2  N5    0.020
 1CY  plan-2  C6    0.020
 1CY  plan-2  N7    0.020
 1CY  plan-2  N8    0.020
 1CY  plan-2  C11   0.020
 1CY  plan-2  HN7   0.020
 1CY  plan-2  HN7A  0.020
 1CY  plan-2  HN8   0.020
 1CY  plan-2  HN8A  0.020

