# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 16:07:29 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 6-[[(2,5-dichlorophenyl)amino]methyl]pyrido[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2cc(CNc3cc(Cl)ccc3Cl)cnc2n1
#
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
 OAG  OAG  6-[[(2,5-dichlorophenyl)amino]methyl]pyrido[2,3-d]pyrimidine-2,4-diamine  ligand  34  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OAG
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
 OAG  C1    C   CH2   0  -0.355  -0.5227   1.0464   0.3495
 OAG  N1    N   NH1   0  -0.680  -1.2184  -0.2224   0.2770
 OAG  CL2   CL  CL    0  -0.121  -2.2433  -2.9499  -0.3303
 OAG  CL5   CL  CL    0  -0.126  -5.7314   2.1502   0.2723
 OAG  C9    C   CR16  0  -0.208   1.7969   0.7465  -0.5832
 OAG  C1'   C   CR6   0   0.455  -2.5698  -0.2928   0.1135
 OAG  N1'   N   N     0  -0.501   4.9116   0.0145   1.2035
 OAG  C10   C   CR6   0  -0.024   0.9484   0.8051   0.4990
 OAG  C11   C   CR6   0  -0.136  -3.2083  -1.5167  -0.1618
 OAG  C12   C   CR16  0  -0.268  -5.3827  -0.4864  -0.1643
 OAG  C2'   C   CR6   0   0.545   5.7262  -0.0438   0.1637
 OAG  N2'   N   NH2   0  -0.815   7.0291  -0.2670   0.4035
 OAG  C3'   C   CR16  0  -0.216  -4.5780  -1.6098  -0.2982
 OAG  N3'   N   N     0  -0.508   5.3998   0.1161  -1.1354
 OAG  C4'   C   CR6   0   0.493   4.1432   0.3699  -1.4261
 OAG  N4'   N   NH2   0  -0.824   3.8178   0.5305  -2.7085
 OAG  C4A   C   CR66  0  -0.141   3.1512   0.4743  -0.3845
 OAG  C5'   C   CR6   0  -0.023  -4.7639   0.7213   0.1037
 OAG  C6'   C   CR16  0  -0.313  -3.3909   0.8366   0.2362
 OAG  C7'   C   CR16  0  -0.078   1.5156   0.5805   1.7633
 OAG  N8'   N   N     0  -0.428   2.7829   0.3313   1.9862
 OAG  C8A   C   CR66  0   0.364   3.6230   0.2716   0.9331
 OAG  H1    H   HCH2  0   0.252  -0.7117   1.6654  -0.5363
 OAG  H1A   H   HCH2  0   0.259  -0.8884   1.6100   1.2116
 OAG  HN1   H   HNH1  0   0.387  -0.6845  -0.9824  -0.1150
 OAG  H9    H   HCR6  0   0.264   1.3971   0.9201  -1.5759
 OAG  H12   H   HCR6  0   0.280  -6.4552  -0.5632  -0.2668
 OAG  HN2'  H   HNH2  0   0.396   7.3244  -0.5263   1.3280
 OAG  HN2A  H   HNH2  0   0.397   7.6458  -0.4719  -0.3625
 OAG  H3'   H   HCR6  0   0.286  -5.0305  -2.5687  -0.5118
 OAG  HN4'  H   HNH2  0   0.407   4.5235   0.4111  -3.4154
 OAG  HN4A  H   HNH2  0   0.419   2.8749   0.6760  -3.0201
 OAG  H6'   H   HCR6  0   0.298  -2.9572   1.8056   0.4390
 OAG  H7'   H   HCR6  0   0.266   0.8734   0.6201   2.6397

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
 OAG  C10  C1    single    1.498  0.020  1.498
 OAG  C1   N1    single    1.449  0.020  1.449
 OAG  C1   H1    single    0.970  0.020  1.090
 OAG  C1   H1A   single    0.970  0.020  1.090
 OAG  N1   C1'   single    1.363  0.020  1.363
 OAG  N1   HN1   single    0.890  0.020  1.040
 OAG  C11  CL2   single    1.736  0.020  1.736
 OAG  CL5  C5'   single    1.734  0.020  1.734
 OAG  C4A  C9    aromatic  1.396  0.020  1.396
 OAG  C9   C10   aromatic  1.376  0.020  1.376
 OAG  C9   H9    single    0.930  0.020  1.080
 OAG  C6'  C1'   aromatic  1.402  0.020  1.402
 OAG  C1'  C11   aromatic  1.408  0.020  1.408
 OAG  C2'  N1'   aromatic  1.322  0.020  1.322
 OAG  N1'  C8A   aromatic  1.342  0.020  1.342
 OAG  C7'  C10   aromatic  1.404  0.020  1.404
 OAG  C11  C3'   aromatic  1.380  0.020  1.380
 OAG  C5'  C12   aromatic  1.383  0.020  1.383
 OAG  C12  C3'   aromatic  1.388  0.020  1.388
 OAG  C12  H12   single    0.930  0.020  1.080
 OAG  N2'  C2'   single    1.344  0.020  1.344
 OAG  C2'  N3'   aromatic  1.349  0.020  1.349
 OAG  N2'  HN2'  single    0.860  0.020  1.020
 OAG  N2'  HN2A  single    0.860  0.020  1.020
 OAG  C3'  H3'   single    0.930  0.020  1.080
 OAG  N3'  C4'   aromatic  1.315  0.020  1.315
 OAG  C4'  C4A   aromatic  1.442  0.020  1.442
 OAG  C4'  N4'   single    1.333  0.020  1.333
 OAG  N4'  HN4'  single    0.860  0.020  1.020
 OAG  N4'  HN4A  single    0.860  0.020  1.020
 OAG  C8A  C4A   aromatic  1.414  0.020  1.414
 OAG  C6'  C5'   aromatic  1.384  0.020  1.384
 OAG  C6'  H6'   single    0.930  0.020  1.080
 OAG  N8'  C7'   aromatic  1.311  0.020  1.311
 OAG  C7'  H7'   single    0.930  0.020  1.080
 OAG  C8A  N8'   aromatic  1.348  0.020  1.348

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
 OAG  H1A   C1   H1    106.75  3.000
 OAG  H1A   C1   C10   109.44  3.000
 OAG  H1    C1   C10   109.91  3.000
 OAG  H1A   C1   N1    109.29  3.000
 OAG  H1    C1   N1    111.78  3.000
 OAG  C10   C1   N1    109.60  3.000
 OAG  HN1   N1   C1'   116.07  3.000
 OAG  HN1   N1   C1    115.17  3.000
 OAG  C1'   N1   C1    121.82  3.000
 OAG  H9    C9   C4A   121.30  3.000
 OAG  H9    C9   C10   119.06  3.000
 OAG  C4A   C9   C10   119.64  3.000
 OAG  C6'   C1'  C11   116.87  3.000
 OAG  C11   C1'  N1    121.20  3.000
 OAG  C6'   C1'  N1    121.91  3.000
 OAG  C8A   N1'  C2'   116.21  3.000
 OAG  C7'   C10  C9    116.89  3.000
 OAG  C7'   C10  C1    120.82  3.000
 OAG  C9    C10  C1    122.25  3.000
 OAG  C3'   C11  C1'   121.89  3.000
 OAG  C3'   C11  CL2   119.12  3.000
 OAG  C1'   C11  CL2   118.99  3.000
 OAG  H12   C12  C5'   121.65  3.000
 OAG  H12   C12  C3'   120.59  3.000
 OAG  C5'   C12  C3'   117.77  3.000
 OAG  N3'   C2'  N2'   115.23  3.000
 OAG  N3'   C2'  N1'   127.09  3.000
 OAG  N2'   C2'  N1'   117.67  3.000
 OAG  HN2A  N2'  HN2'  117.95  3.000
 OAG  HN2A  N2'  C2'   119.54  3.000
 OAG  HN2'  N2'  C2'   119.49  3.000
 OAG  H3'   C3'  C12   119.60  3.000
 OAG  H3'   C3'  C11   119.65  3.000
 OAG  C12   C3'  C11   120.75  3.000
 OAG  C4'   N3'  C2'   117.85  3.000
 OAG  C4A   C4'  N4'   121.22  3.000
 OAG  N4'   C4'  N3'   118.00  3.000
 OAG  C4A   C4'  N3'   120.78  3.000
 OAG  HN4A  N4'  HN4'  117.26  3.000
 OAG  HN4A  N4'  C4'   123.06  3.000
 OAG  HN4'  N4'  C4'   119.38  3.000
 OAG  C8A   C4A  C4'   115.66  3.000
 OAG  C8A   C4A  C9    118.97  3.000
 OAG  C4'   C4A  C9    125.36  3.000
 OAG  C6'   C5'  C12   122.35  3.000
 OAG  C6'   C5'  CL5   118.39  3.000
 OAG  C12   C5'  CL5   119.26  3.000
 OAG  H6'   C6'  C5'   119.38  3.000
 OAG  H6'   C6'  C1'   120.25  3.000
 OAG  C5'   C6'  C1'   120.37  3.000
 OAG  H7'   C7'  N8'   116.17  3.000
 OAG  H7'   C7'  C10   118.79  3.000
 OAG  N8'   C7'  C10   125.05  3.000
 OAG  C8A   N8'  C7'   118.56  3.000
 OAG  N8'   C8A  C4A   120.89  3.000
 OAG  N8'   C8A  N1'   116.71  3.000
 OAG  C4A   C8A  N1'   122.40  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
 OAG  CONST_01  N3'   C4'  C4A  C9    180.00   0.0  0
 OAG  CONST_02  N1'   C8A  C4A  C9    180.00   0.0  0
 OAG  CONST_03  N8'   C8A  C4A  C9      0.00   0.0  0
 OAG  CONST_04  N8'   C7'  C10  C9      0.00   0.0  0
 OAG  CONST_05  C12   C5'  C6'  C1'     0.00   0.0  0
 OAG  CONST_06  C12   C3'  C11  C1'     0.00   0.0  0
 OAG  CONST_07  C4'   N3'  C2'  N1'     0.00   0.0  0
 OAG  CONST_08  C4'   C4A  C8A  N1'     0.00   0.0  0
 OAG  CONST_09  C7'   N8'  C8A  N1'   180.00   0.0  0
 OAG  CONST_10  C4'   C4A  C9   C10   180.00   0.0  0
 OAG  CONST_11  C8A   C4A  C9   C10     0.00   0.0  0
 OAG  CONST_12  C8A   N8'  C7'  C10     0.00   0.0  0
 OAG  CONST_13  C5'   C6'  C1'  C11     0.00   0.0  0
 OAG  CONST_14  C5'   C12  C3'  C11     0.00   0.0  0
 OAG  CONST_15  C4A   C8A  N1'  C2'     0.00   0.0  0
 OAG  CONST_16  N8'   C8A  N1'  C2'   180.00   0.0  0
 OAG  CONST_17  C4A   C4'  N3'  C2'     0.00   0.0  0
 OAG  CONST_18  C6'   C1'  C11  C3'     0.00   0.0  0
 OAG  CONST_19  C6'   C5'  C12  C3'     0.00   0.0  0
 OAG  CONST_20  C8A   N1'  C2'  N3'     0.00   0.0  0
 OAG  CONST_21  C8A   C4A  C4'  N3'     0.00   0.0  0
 OAG  CONST_22  N8'   C8A  C4A  C4'   180.00   0.0  0
 OAG  CONST_23  C7'   C10  C9   C4A     0.00   0.0  0
 OAG  CONST_24  C7'   N8'  C8A  C4A     0.00   0.0  0
 OAG  CONST_25  C4A   C9   C10  C1    180.00   0.0  0
 OAG  CONST_26  N8'   C7'  C10  C1    180.00   0.0  0
 OAG  CONST_27  C5'   C6'  C1'  N1    180.00   0.0  0
 OAG  CONST_28  C3'   C11  C1'  N1    180.00   0.0  0
 OAG  CONST_29  C6'   C1'  C11  CL2   180.00   0.0  0
 OAG  CONST_30  C12   C3'  C11  CL2   180.00   0.0  0
 OAG  CONST_31  C3'   C12  C5'  CL5   180.00   0.0  0
 OAG  CONST_32  C1'   C6'  C5'  CL5   180.00   0.0  0
 OAG  CONST_33  N4'   C4'  C4A  C9      0.00   0.0  0
 OAG  CONST_34  N4'   C4'  N3'  C2'   180.00   0.0  0
 OAG  CONST_35  C8A   N1'  C2'  N2'   180.00   0.0  0
 OAG  CONST_36  C4'   N3'  C2'  N2'   180.00   0.0  0
 OAG  CONST_37  C8A   C4A  C4'  N4'   180.00   0.0  0
 OAG  CONST_38  H7'   C7'  C10  C9    180.00   0.0  0
 OAG  CONST_39  H3'   C3'  C11  C1'   180.00   0.0  0
 OAG  CONST_40  H6'   C6'  C1'  C11   180.00   0.0  0
 OAG  CONST_41  H12   C12  C3'  C11   180.00   0.0  0
 OAG  CONST_42  H9    C9   C4A  C4'     0.00   0.0  0
 OAG  CONST_43  C6'   C1'  N1   C1      0.00   0.0  0
 OAG  CONST_44  C11   C1'  N1   C1    180.00   0.0  0
 OAG  CONST_45  HN2'  N2'  C2'  N1'     0.00   0.0  0
 OAG  CONST_46  HN2A  N2'  C2'  N1'   180.00   0.0  0
 OAG  CONST_48  HN4'  N4'  C4'  N3'     0.00   0.0  0
 OAG  CONST_49  HN4A  N4'  C4'  N3'   180.00   0.0  0
 OAG  Var_01    C9    C10  C1   N1     92.90  30.0  2
 OAG  Var_02    C10   C1   N1   C1'  -178.73  30.0  1

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
 OAG  plan-1  N1    0.020
 OAG  plan-1  CL2   0.020
 OAG  plan-1  CL5   0.020
 OAG  plan-1  C1'   0.020
 OAG  plan-1  C11   0.020
 OAG  plan-1  C12   0.020
 OAG  plan-1  C3'   0.020
 OAG  plan-1  C5'   0.020
 OAG  plan-1  C6'   0.020
 OAG  plan-1  H12   0.020
 OAG  plan-1  H3'   0.020
 OAG  plan-1  H6'   0.020
 OAG  plan-2  C1    0.020
 OAG  plan-2  C9    0.020
 OAG  plan-2  N1'   0.020
 OAG  plan-2  C10   0.020
 OAG  plan-2  C2'   0.020
 OAG  plan-2  N2'   0.020
 OAG  plan-2  N3'   0.020
 OAG  plan-2  C4'   0.020
 OAG  plan-2  N4'   0.020
 OAG  plan-2  C4A   0.020
 OAG  plan-2  C7'   0.020
 OAG  plan-2  N8'   0.020
 OAG  plan-2  C8A   0.020
 OAG  plan-2  H9    0.020
 OAG  plan-2  H7'   0.020
 OAG  plan-3  C1    0.020
 OAG  plan-3  N1    0.020
 OAG  plan-3  C1'   0.020
 OAG  plan-3  HN1   0.020
 OAG  plan-4  C2'   0.020
 OAG  plan-4  N2'   0.020
 OAG  plan-4  HN2'  0.020
 OAG  plan-4  HN2A  0.020
 OAG  plan-5  C4'   0.020
 OAG  plan-5  N4'   0.020
 OAG  plan-5  HN4'  0.020
 OAG  plan-5  HN4A  0.020

