# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 07:07:29 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 5-{4-[(3,5-difluorobenzyl)amino]phenyl}-6-ethylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1c2ccc(NCc3cc(F)cc(F)c3)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
 7IG  7IG  5-{4-[(3,5-difluorobenzyl)amino]phenyl}-6-ethylpyrimidine-2,4-diamine  ligand  45  26  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7IG
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
 7IG  C1    C  CR6   0   0.482   4.3617  -1.4112  -0.1549
 7IG  N1    N  N     0  -0.512   5.6874  -1.4773  -0.2389
 7IG  C2    C  CR6   0   0.515   6.3490  -0.3219  -0.2294
 7IG  N2    N  N     0  -0.509   5.8123   0.8913  -0.1492
 7IG  C3    C  CR6   0   0.275   4.4787   0.9536  -0.0695
 7IG  C4    C  CR6   0  -0.151   3.6756  -0.1737  -0.0664
 7IG  N3    N  NH2   0  -0.829   3.6940  -2.5761  -0.1385
 7IG  N4    N  NH2   0  -0.825   7.7031  -0.3962  -0.2731
 7IG  C5    C  CH2   0  -0.502   3.9110   2.3391   0.0412
 7IG  C6    C  CH3   0  -0.663   4.1507   2.9350   1.4272
 7IG  C7    C  CR16  0  -0.330   0.1623   0.1842   1.2930
 7IG  C8    C  CR16  0  -0.269   1.5406   0.1339   1.2188
 7IG  C9    C  CR6   0  -0.024   2.1989  -0.1304   0.0156
 7IG  C10   C  CR16  0  -0.278   1.4075  -0.3509  -1.1084
 7IG  C11   C  CR16  0  -0.335   0.0216  -0.3011  -1.0530
 7IG  C12   C  CR6   0   0.361  -0.6304  -0.0377   0.1569
 7IG  N5    N  NH1   0  -0.692  -2.0034  -0.0191   0.2770
 7IG  C13   C  CR6   0   0.562  -6.5492   0.7865  -0.6080
 7IG  C14   C  CR16  0  -0.481  -5.2155   0.9377  -0.9404
 7IG  C15   C  CR6   0   0.111  -4.3028  -0.0130  -0.5005
 7IG  C16   C  CR16  0  -0.456  -4.7354  -1.0891   0.2710
 7IG  C17   C  CR6   0   0.563  -6.0768  -1.1895   0.5754
 7IG  C18   C  CR16  0  -0.569  -7.0162  -0.2673   0.1505
 7IG  C19   C  CH2   0  -0.331  -2.8524   0.1037  -0.8836
 7IG  F2    F  F     0  -0.309  -6.4973  -2.2261   1.3121
 7IG  HN31  H  HNH2  0   0.392   4.1917  -3.4370  -0.2828
 7IG  HN32  H  HNH2  0   0.404   2.6904  -2.6032  -0.1531
 7IG  HN41  H  HNH2  0   0.385   8.2043   0.4401  -0.5191
 7IG  HN42  H  HNH2  0   0.385   8.1136  -1.2600  -0.5837
 7IG  H51   H  HCH2  0   0.241   2.8438   2.3361  -0.1795
 7IG  H52   H  HCH2  0   0.243   4.3952   2.9682  -0.7093
 7IG  H61   H  HCH3  0   0.224   3.6425   2.3562   2.1993
 7IG  H62   H  HCH3  0   0.228   5.2137   2.9530   1.6672
 7IG  H63   H  HCH3  0   0.234   3.7770   3.9577   1.4770
 7IG  H7    H  HCR6  0   0.256  -0.3154   0.3966   2.2427
 7IG  H8    H  HCR6  0   0.243   2.1213   0.3097   2.1165
 7IG  H10   H  HCR6  0   0.248   1.8812  -0.5524  -2.0622
 7IG  H11   H  HCR6  0   0.265  -0.5401  -0.4653  -1.9630
 7IG  HN5   H  HNH1  0   0.381  -2.3364   0.4935   1.0799
 7IG  H14   H  HCR6  0   0.283  -4.8943   1.7873  -1.5294
 7IG  H16   H  HCR6  0   0.280  -4.0371  -1.8366   0.6244
 7IG  H18   H  HCR6  0   0.304  -8.0639  -0.3668   0.4019
 7IG  H191  H  HCH2  0   0.247  -2.6895   1.0427  -1.4277
 7IG  H192  H  HCH2  0   0.262  -2.6228  -0.7041  -1.5835
 7IG  F1    F  F     0  -0.309  -7.4278   1.7031  -1.0333

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
 7IG  C1   N1    aromatic  1.330  0.020  1.330
 7IG  C1   C4    aromatic  1.418  0.020  1.418
 7IG  C1   N3    single    1.343  0.020  1.343
 7IG  N1   C2    aromatic  1.331  0.020  1.331
 7IG  C2   N2    aromatic  1.329  0.020  1.329
 7IG  C2   N4    single    1.357  0.020  1.357
 7IG  N2   C3    aromatic  1.337  0.020  1.337
 7IG  C3   C4    aromatic  1.384  0.020  1.384
 7IG  C3   C5    single    1.501  0.020  1.501
 7IG  C4   C9    single    1.480  0.020  1.480
 7IG  N3   HN31  single    0.860  0.020  1.020
 7IG  N3   HN32  single    0.860  0.020  1.020
 7IG  N4   HN41  single    0.890  0.020  1.040
 7IG  N4   HN42  single    0.890  0.020  1.040
 7IG  C5   C6    single    1.528  0.020  1.528
 7IG  C5   H51   single    0.970  0.020  1.090
 7IG  C5   H52   single    0.970  0.020  1.090
 7IG  C6   H61   single    0.970  0.020  1.090
 7IG  C6   H62   single    0.970  0.020  1.090
 7IG  C6   H63   single    0.970  0.020  1.090
 7IG  C7   C8    aromatic  1.381  0.020  1.381
 7IG  C7   C12   aromatic  1.403  0.020  1.403
 7IG  C7   H7    single    0.930  0.020  1.080
 7IG  C8   C9    aromatic  1.397  0.020  1.397
 7IG  C8   H8    single    0.930  0.020  1.080
 7IG  C9   C10   aromatic  1.392  0.020  1.392
 7IG  C10  C11   aromatic  1.388  0.020  1.388
 7IG  C10  H10   single    0.930  0.020  1.080
 7IG  C11  C12   aromatic  1.399  0.020  1.399
 7IG  C11  H11   single    0.930  0.020  1.080
 7IG  C12  N5    single    1.378  0.020  1.378
 7IG  N5   C19   single    1.443  0.020  1.443
 7IG  N5   HN5   single    0.890  0.020  1.040
 7IG  C13  C14   aromatic  1.383  0.020  1.383
 7IG  C13  C18   aromatic  1.380  0.020  1.380
 7IG  C13  F1    single    1.339  0.020  1.339
 7IG  C14  C15   aromatic  1.389  0.020  1.389
 7IG  C14  H14   single    0.930  0.020  1.080
 7IG  C15  C16   aromatic  1.393  0.020  1.393
 7IG  C15  C19   single    1.505  0.020  1.505
 7IG  C16  C17   aromatic  1.379  0.020  1.379
 7IG  C16  H16   single    0.930  0.020  1.080
 7IG  C17  C18   aromatic  1.383  0.020  1.383
 7IG  C17  F2    single    1.339  0.020  1.339
 7IG  C18  H18   single    0.930  0.020  1.080
 7IG  C19  H191  single    0.970  0.020  1.090
 7IG  C19  H192  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
 7IG  N3    C1   C4    121.05  3.000
 7IG  N3    C1   N1    116.96  3.000
 7IG  C4    C1   N1    121.99  3.000
 7IG  C2    N1   C1    116.85  3.000
 7IG  N4    C2   N2    117.06  3.000
 7IG  N4    C2   N1    116.62  3.000
 7IG  N2    C2   N1    126.29  3.000
 7IG  C3    N2   C2    116.67  3.000
 7IG  C5    C3   C4    122.15  3.000
 7IG  C5    C3   N2    115.11  3.000
 7IG  C4    C3   N2    122.73  3.000
 7IG  C9    C4   C3    123.73  3.000
 7IG  C9    C4   C1    120.80  3.000
 7IG  C3    C4   C1    115.47  3.000
 7IG  HN32  N3   HN31  118.03  3.000
 7IG  HN32  N3   C1    121.35  3.000
 7IG  HN31  N3   C1    119.68  3.000
 7IG  HN42  N4   HN41  115.81  3.000
 7IG  HN42  N4   C2    117.68  3.000
 7IG  HN41  N4   C2    117.38  3.000
 7IG  H52   C5   H51   107.25  3.000
 7IG  H52   C5   C6    109.22  3.000
 7IG  H51   C5   C6    109.78  3.000
 7IG  H52   C5   C3    108.25  3.000
 7IG  H51   C5   C3    110.66  3.000
 7IG  C6    C5   C3    111.56  3.000
 7IG  H63   C6   H62   107.98  3.000
 7IG  H63   C6   H61   107.81  3.000
 7IG  H62   C6   H61   107.91  3.000
 7IG  H63   C6   C5    110.71  3.000
 7IG  H62   C6   C5    111.06  3.000
 7IG  H61   C6   C5    111.23  3.000
 7IG  H7    C7   C12   119.44  3.000
 7IG  H7    C7   C8    119.60  3.000
 7IG  C12   C7   C8    120.97  3.000
 7IG  H8    C8   C9    119.46  3.000
 7IG  H8    C8   C7    118.97  3.000
 7IG  C9    C8   C7    121.57  3.000
 7IG  C10   C9   C8    117.23  3.000
 7IG  C10   C9   C4    121.19  3.000
 7IG  C8    C9   C4    121.58  3.000
 7IG  H10   C10  C11   118.57  3.000
 7IG  H10   C10  C9    119.44  3.000
 7IG  C11   C10  C9    121.98  3.000
 7IG  H11   C11  C12   120.92  3.000
 7IG  H11   C11  C10   118.65  3.000
 7IG  C12   C11  C10   120.44  3.000
 7IG  N5    C12  C11   122.82  3.000
 7IG  N5    C12  C7    119.34  3.000
 7IG  C11   C12  C7    117.82  3.000
 7IG  HN5   N5   C19   113.73  3.000
 7IG  HN5   N5   C12   113.89  3.000
 7IG  C19   N5   C12   121.13  3.000
 7IG  F1    C13  C18   118.38  3.000
 7IG  F1    C13  C14   118.79  3.000
 7IG  C18   C13  C14   122.83  3.000
 7IG  H14   C14  C15   120.95  3.000
 7IG  H14   C14  C13   120.19  3.000
 7IG  C15   C14  C13   118.86  3.000
 7IG  C19   C15  C16   120.02  3.000
 7IG  C19   C15  C14   119.97  3.000
 7IG  C16   C15  C14   119.99  3.000
 7IG  H16   C16  C17   120.34  3.000
 7IG  H16   C16  C15   120.93  3.000
 7IG  C17   C16  C15   118.72  3.000
 7IG  F2    C17  C18   118.14  3.000
 7IG  F2    C17  C16   118.89  3.000
 7IG  C18   C17  C16   122.97  3.000
 7IG  H18   C18  C17   121.67  3.000
 7IG  H18   C18  C13   121.71  3.000
 7IG  C17   C18  C13   116.62  3.000
 7IG  H192  C19  H191  106.48  3.000
 7IG  H192  C19  C15   107.94  3.000
 7IG  H191  C19  C15   109.62  3.000
 7IG  H192  C19  N5    109.17  3.000
 7IG  H191  C19  N5    112.60  3.000
 7IG  C15   C19  N5    110.83  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
 7IG  CONST_01  N2    C2   N1   C1     0.00   0.0  0
 7IG  CONST_02  N2    C3   C4   C1     0.00   0.0  0
 7IG  CONST_05  C3    C4   C1   N1     0.00   0.0  0
 7IG  CONST_06  C9    C4   C1   N1   180.00   0.0  0
 7IG  CONST_07  C3    N2   C2   N1     0.00   0.0  0
 7IG  CONST_08  C4    C1   N1   C2     0.00   0.0  0
 7IG  CONST_09  C4    C3   N2   C2     0.00   0.0  0
 7IG  CONST_10  C9    C4   C3   N2   180.00   0.0  0
 7IG  CONST_13  C7    C8   C9   C4   180.00   0.0  0
 7IG  CONST_14  C11   C10  C9   C4   180.00   0.0  0
 7IG  CONST_15  C10   C9   C8   C7     0.00   0.0  0
 7IG  CONST_16  C10   C11  C12  C7     0.00   0.0  0
 7IG  CONST_17  C11   C12  C7   C8     0.00   0.0  0
 7IG  CONST_18  C11   C10  C9   C8     0.00   0.0  0
 7IG  CONST_19  C12   C7   C8   C9     0.00   0.0  0
 7IG  CONST_20  C12   C11  C10  C9     0.00   0.0  0
 7IG  CONST_21  C16   C15  C14  C13    0.00   0.0  0
 7IG  CONST_22  C16   C17  C18  C13    0.00   0.0  0
 7IG  CONST_23  C17   C18  C13  C14    0.00   0.0  0
 7IG  CONST_24  C17   C16  C15  C14    0.00   0.0  0
 7IG  CONST_25  C18   C13  C14  C15    0.00   0.0  0
 7IG  CONST_26  C18   C17  C16  C15    0.00   0.0  0
 7IG  CONST_27  N4    C2   N1   C1   180.00   0.0  0
 7IG  CONST_28  C5    C3   C4   C1   180.00   0.0  0
 7IG  CONST_29  N3    C1   N1   C2   180.00   0.0  0
 7IG  CONST_30  C5    C3   N2   C2   180.00   0.0  0
 7IG  CONST_31  N4    C2   N2   C3   180.00   0.0  0
 7IG  CONST_32  N3    C1   C4   C3   180.00   0.0  0
 7IG  CONST_33  C9    C4   C1   N3     0.00   0.0  0
 7IG  CONST_34  C9    C4   C3   C5     0.00   0.0  0
 7IG  CONST_35  N5    C12  C7   C8   180.00   0.0  0
 7IG  CONST_36  N5    C12  C11  C10  180.00   0.0  0
 7IG  CONST_37  C19   C15  C14  C13  180.00   0.0  0
 7IG  CONST_38  F2    C17  C18  C13  180.00   0.0  0
 7IG  CONST_39  F1    C13  C14  C15  180.00   0.0  0
 7IG  CONST_40  F2    C17  C16  C15  180.00   0.0  0
 7IG  CONST_41  C19   C15  C16  C17  180.00   0.0  0
 7IG  CONST_42  F1    C13  C18  C17  180.00   0.0  0
 7IG  CONST_43  H8    C8   C9   C4     0.00   0.0  0
 7IG  CONST_44  H10   C10  C9   C4     0.00   0.0  0
 7IG  CONST_45  H11   C11  C12  C7   180.00   0.0  0
 7IG  CONST_46  H7    C7   C8   C9   180.00   0.0  0
 7IG  CONST_47  H18   C18  C13  C14  180.00   0.0  0
 7IG  CONST_48  H16   C16  C15  C14  180.00   0.0  0
 7IG  CONST_49  H14   C14  C15  C16  180.00   0.0  0
 7IG  CONST_52  HN31  N3   C1   N1     0.00   0.0  0
 7IG  CONST_53  HN32  N3   C1   N1   180.00   0.0  0
 7IG  Var_01    C6    C5   C3   N2   -73.43  30.0  2
 7IG  Var_02    C15   C19  N5   C12  175.40  30.0  3
 7IG  Var_03    C14   C15  C19  N5   130.11  30.0  2
 7IG  Var_04    H61   C6   C5   C3   -62.93  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
 7IG  plan-1  C1    0.020
 7IG  plan-1  N1    0.020
 7IG  plan-1  C2    0.020
 7IG  plan-1  N2    0.020
 7IG  plan-1  C3    0.020
 7IG  plan-1  C4    0.020
 7IG  plan-1  N3    0.020
 7IG  plan-1  N4    0.020
 7IG  plan-1  C5    0.020
 7IG  plan-1  C9    0.020
 7IG  plan-2  C4    0.020
 7IG  plan-2  C7    0.020
 7IG  plan-2  C8    0.020
 7IG  plan-2  C9    0.020
 7IG  plan-2  C10   0.020
 7IG  plan-2  C11   0.020
 7IG  plan-2  C12   0.020
 7IG  plan-2  N5    0.020
 7IG  plan-2  H7    0.020
 7IG  plan-2  H8    0.020
 7IG  plan-2  H10   0.020
 7IG  plan-2  H11   0.020
 7IG  plan-3  C13   0.020
 7IG  plan-3  C14   0.020
 7IG  plan-3  C15   0.020
 7IG  plan-3  C16   0.020
 7IG  plan-3  C17   0.020
 7IG  plan-3  C18   0.020
 7IG  plan-3  C19   0.020
 7IG  plan-3  F2    0.020
 7IG  plan-3  H14   0.020
 7IG  plan-3  H16   0.020
 7IG  plan-3  H18   0.020
 7IG  plan-3  F1    0.020
 7IG  plan-4  C1    0.020
 7IG  plan-4  N3    0.020
 7IG  plan-4  HN31  0.020
 7IG  plan-4  HN32  0.020
 7IG  plan-5  C2    0.020
 7IG  plan-5  N4    0.020
 7IG  plan-5  HN41  0.020
 7IG  plan-5  HN42  0.020
 7IG  plan-6  C12   0.020
 7IG  plan-6  N5    0.020
 7IG  plan-6  C19   0.020
 7IG  plan-6  HN5   0.020

