# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 08:16:58 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: N-{2-[6-(2,4-diamino-6-ethylpyrimidin-5-yl)-2,2-dimethyl-3-oxo-2,3-dihydro-4H-1,4-benzoxazin-4-yl]ethyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1c2ccc3OC(C)(C)C(=O)N(CCNC(C)=O)c3c2
#
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
 3IG  3IG  N-{2-[6-(2,4-diamino-6-ethylpyrimidin-5-yl)-2,2-dimethyl-3-oxo-2,3-dihydro-4H-1,4-benzoxazin-4-yl]ethyl}acetamide  ligand  55  29  .  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_3IG
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
 3IG  C1    C  CR6   0   0.480  -3.3747  -0.5514   1.4182
 3IG  N1    N  N     0  -0.511  -4.6005  -0.0508   1.3066
 3IG  C2    C  CR6   0   0.520  -5.0010   0.2962   0.0848
 3IG  N2    N  N     0  -0.507  -4.2891   0.1950  -1.0338
 3IG  C3    C  CR6   0   0.282  -3.0567  -0.3076  -0.9188
 3IG  C4    C  CR6   0  -0.150  -2.5254  -0.7081   0.2962
 3IG  N3    N  NH2   0  -0.826  -2.9787  -0.9245   2.6499
 3IG  N4    N  NH2   0  -0.825  -6.2675   0.7633  -0.0304
 3IG  C5    C  CH2   0  -0.505  -2.2790  -0.3923  -2.2007
 3IG  C6    C  CH3   0  -0.675  -1.8339   0.9865  -2.6836
 3IG  C7    C  CR16  0  -0.292  -0.9751  -2.6321   0.6555
 3IG  C8    C  CR16  0  -0.347   0.3041  -3.1597   0.7514
 3IG  C9    C  CR6   0   0.333   1.4030  -2.3250   0.6577
 3IG  C10   C  CR6   0   0.322   1.2363  -0.9527   0.4703
 3IG  C11   C  CR16  0  -0.368  -0.0494  -0.4355   0.3662
 3IG  C12   C  CR6   0  -0.009  -1.1642  -1.2692   0.4451
 3IG  O3    O  O2    0  -0.479   2.6497  -2.8323   0.7705
 3IG  C14   C  CT    0   0.035   3.6343  -2.2127  -0.0598
 3IG  C15   C  C     0   0.571   3.6074  -0.6991   0.1529
 3IG  N5    N  NT    0  -0.576   2.3898  -0.1536   0.4245
 3IG  C16   C  CH2   0  -0.351   2.2908   1.2898   0.5799
 3IG  C17   C  CH2   0  -0.302   2.0814   1.9992  -0.7587
 3IG  N6    N  NH1   0  -0.623   1.8827   3.4168  -0.5904
 3IG  C13   C  C     0   0.529   0.7014   3.9507  -0.2354
 3IG  C19   C  CH3   0  -0.774   0.6759   5.4526  -0.1106
 3IG  C21   C  CH3   0  -0.660   4.9678  -2.7866   0.3817
 3IG  C20   C  CH3   0  -0.662   3.3638  -2.5098  -1.5339
 3IG  O4    O  O     0  -0.459   4.6131  -0.0249   0.0430
 3IG  O1    O  O     0  -0.495  -0.2952   3.2682  -0.0286
 3IG  HN31  H  HNH2  0   0.392  -3.5439  -0.6536   3.4364
 3IG  HN32  H  HNH2  0   0.401  -2.0119  -1.1267   2.8346
 3IG  HN41  H  HNH2  0   0.387  -6.5087   1.2577  -0.8719
 3IG  HN42  H  HNH2  0   0.387  -6.7410   1.0544   0.8074
 3IG  H51   H  HCH2  0   0.246  -2.9204  -0.8498  -2.9576
 3IG  H52   H  HCH2  0   0.241  -1.4124  -1.0429  -2.0836
 3IG  H61   H  HCH3  0   0.232  -1.2900   0.9054  -3.6249
 3IG  H62   H  HCH3  0   0.227  -2.6921   1.6379  -2.8492
 3IG  H63   H  HCH3  0   0.235  -1.1817   1.4733  -1.9570
 3IG  H8    H  HCR6  0   0.270   0.4550  -4.2216   0.8980
 3IG  H11   H  HCR6  0   0.281  -0.2101   0.6248   0.2186
 3IG  H161  H  HCH2  0   0.274   1.4736   1.5057   1.2663
 3IG  H162  H  HCH2  0   0.282   3.2039   1.6506   1.0496
 3IG  H171  H  HCH2  0   0.270   2.9561   1.8578  -1.3919
 3IG  H172  H  HCH2  0   0.254   1.2298   1.5736  -1.2918
 3IG  HN6   H  HNH1  0   0.407   2.6727   4.0250  -0.7255
 3IG  H191  H  HCH3  0   0.267  -0.1018   5.8549  -0.7592
 3IG  H192  H  HCH3  0   0.267   0.4188   5.7262   0.9126
 3IG  H193  H  HCH3  0   0.250   1.6206   5.9275  -0.3683
 3IG  H211  H  HCH3  0   0.249   4.9697  -3.8667   0.2346
 3IG  H212  H  HCH3  0   0.245   5.7811  -2.3672  -0.2054
 3IG  H213  H  HCH3  0   0.248   5.1616  -2.5808   1.4344
 3IG  H201  H  HCH3  0   0.247   2.4011  -2.1216  -1.8702
 3IG  H202  H  HCH3  0   0.255   4.1393  -2.0626  -2.1549
 3IG  H203  H  HCH3  0   0.258   3.3752  -3.5872  -1.7014
 3IG  H7    H  HCR6  0   0.254  -1.8299  -3.2935   0.7124

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
 3IG  C1   N1    aromatic  1.329  0.020  1.329
 3IG  C1   C4    aromatic  1.416  0.020  1.416
 3IG  C1   N3    single    1.346  0.020  1.346
 3IG  N1   C2    aromatic  1.332  0.020  1.332
 3IG  C2   N2    aromatic  1.330  0.020  1.330
 3IG  C2   N4    single    1.355  0.020  1.355
 3IG  N2   C3    aromatic  1.336  0.020  1.336
 3IG  C3   C4    aromatic  1.385  0.020  1.385
 3IG  C3   C5    single    1.502  0.020  1.502
 3IG  C4   C12   single    1.480  0.020  1.480
 3IG  N3   HN31  single    0.890  0.020  1.040
 3IG  N3   HN32  single    0.890  0.020  1.040
 3IG  N4   HN41  single    0.890  0.020  1.040
 3IG  N4   HN42  single    0.890  0.020  1.040
 3IG  C5   C6    single    1.527  0.020  1.527
 3IG  C5   H51   single    0.970  0.020  1.090
 3IG  C5   H52   single    0.970  0.020  1.090
 3IG  C6   H61   single    0.970  0.020  1.090
 3IG  C6   H62   single    0.970  0.020  1.090
 3IG  C6   H63   single    0.970  0.020  1.090
 3IG  C7   C8    aromatic  1.387  0.020  1.387
 3IG  C7   C12   aromatic  1.392  0.020  1.392
 3IG  C7   H7    single    0.930  0.020  1.080
 3IG  C8   C9    aromatic  1.383  0.020  1.383
 3IG  C8   H8    single    0.930  0.020  1.080
 3IG  C9   C10   aromatic  1.395  0.020  1.395
 3IG  C9   O3    single    1.351  0.020  1.351
 3IG  C10  C11   aromatic  1.390  0.020  1.390
 3IG  C10  N5    single    1.404  0.020  1.404
 3IG  C11  C12   aromatic  1.394  0.020  1.394
 3IG  C11  H11   single    0.930  0.020  1.080
 3IG  O3   C14   single    1.429  0.020  1.429
 3IG  C14  C15   single    1.529  0.020  1.529
 3IG  C14  C21   single    1.517  0.020  1.517
 3IG  C14  C20   single    1.528  0.020  1.528
 3IG  C15  N5    single    1.362  0.020  1.362
 3IG  C15  O4    double    1.216  0.020  1.216
 3IG  N5   C16   single    1.455  0.020  1.455
 3IG  C16  C17   single    1.529  0.020  1.529
 3IG  C16  H161  single    0.970  0.020  1.090
 3IG  C16  H162  single    0.970  0.020  1.090
 3IG  C17  N6    single    1.441  0.020  1.441
 3IG  C17  H171  single    0.970  0.020  1.090
 3IG  C17  H172  single    0.970  0.020  1.090
 3IG  N6   C13   single    1.344  0.020  1.344
 3IG  N6   HN6   single    0.860  0.020  1.020
 3IG  C13  C19   single    1.507  0.020  1.507
 3IG  C13  O1    double    1.225  0.020  1.225
 3IG  C19  H191  single    0.970  0.020  1.090
 3IG  C19  H192  single    0.970  0.020  1.090
 3IG  C19  H193  single    0.970  0.020  1.090
 3IG  C21  H211  single    0.970  0.020  1.090
 3IG  C21  H212  single    0.970  0.020  1.090
 3IG  C21  H213  single    0.970  0.020  1.090
 3IG  C20  H201  single    0.970  0.020  1.090
 3IG  C20  H202  single    0.970  0.020  1.090
 3IG  C20  H203  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
 3IG  N3    C1   C4    121.18  3.000
 3IG  N3    C1   N1    116.91  3.000
 3IG  C4    C1   N1    121.91  3.000
 3IG  C2    N1   C1    116.91  3.000
 3IG  N4    C2   N2    117.08  3.000
 3IG  N4    C2   N1    116.68  3.000
 3IG  N2    C2   N1    126.22  3.000
 3IG  C3    N2   C2    116.75  3.000
 3IG  C5    C3   C4    122.26  3.000
 3IG  C5    C3   N2    115.18  3.000
 3IG  C4    C3   N2    122.56  3.000
 3IG  C12   C4   C3    123.41  3.000
 3IG  C12   C4   C1    120.93  3.000
 3IG  C3    C4   C1    115.66  3.000
 3IG  HN32  N3   HN31  116.81  3.000
 3IG  HN32  N3   C1    120.46  3.000
 3IG  HN31  N3   C1    118.39  3.000
 3IG  HN42  N4   HN41  116.23  3.000
 3IG  HN42  N4   C2    117.99  3.000
 3IG  HN41  N4   C2    117.71  3.000
 3IG  H52   C5   H51   106.93  3.000
 3IG  H52   C5   C6    109.95  3.000
 3IG  H51   C5   C6    109.27  3.000
 3IG  H52   C5   C3    110.71  3.000
 3IG  H51   C5   C3    108.12  3.000
 3IG  C6    C5   C3    111.71  3.000
 3IG  H63   C6   H62   107.77  3.000
 3IG  H63   C6   H61   108.06  3.000
 3IG  H62   C6   H61   107.82  3.000
 3IG  H63   C6   C5    111.50  3.000
 3IG  H62   C6   C5    110.98  3.000
 3IG  H61   C6   C5    110.56  3.000
 3IG  H7    C7   C12   119.93  3.000
 3IG  H7    C7   C8    119.49  3.000
 3IG  C12   C7   C8    120.55  3.000
 3IG  H8    C8   C9    119.37  3.000
 3IG  H8    C8   C7    120.73  3.000
 3IG  C9    C8   C7    119.90  3.000
 3IG  O3    C9   C10   119.41  3.000
 3IG  O3    C9   C8    120.06  3.000
 3IG  C10   C9   C8    120.52  3.000
 3IG  N5    C10  C11   123.08  3.000
 3IG  N5    C10  C9    117.78  3.000
 3IG  C11   C10  C9    119.13  3.000
 3IG  H11   C11  C12   118.34  3.000
 3IG  H11   C11  C10   120.80  3.000
 3IG  C12   C11  C10   120.86  3.000
 3IG  C11   C12  C7    119.03  3.000
 3IG  C11   C12  C4    120.20  3.000
 3IG  C7    C12  C4    120.76  3.000
 3IG  C14   O3   C9    115.12  3.000
 3IG  C20   C14  C21   111.27  3.000
 3IG  C20   C14  C15   108.88  3.000
 3IG  C21   C14  C15   110.45  3.000
 3IG  C20   C14  O3    110.75  3.000
 3IG  C21   C14  O3    105.81  3.000
 3IG  C15   C14  O3    109.65  3.000
 3IG  O4    C15  N5    122.39  3.000
 3IG  O4    C15  C14   121.46  3.000
 3IG  N5    C15  C14   116.11  3.000
 3IG  C16   N5   C15   118.66  3.000
 3IG  C16   N5   C10   120.34  3.000
 3IG  C15   N5   C10   120.88  3.000
 3IG  H162  C16  H161  106.96  3.000
 3IG  H162  C16  C17   109.81  3.000
 3IG  H161  C16  C17   110.92  3.000
 3IG  H162  C16  N5    108.53  3.000
 3IG  H161  C16  N5    108.36  3.000
 3IG  C17   C16  N5    112.08  3.000
 3IG  H172  C17  H171  106.99  3.000
 3IG  H172  C17  N6    109.45  3.000
 3IG  H171  C17  N6    107.84  3.000
 3IG  H172  C17  C16   110.71  3.000
 3IG  H171  C17  C16   109.80  3.000
 3IG  N6    C17  C16   111.90  3.000
 3IG  HN6   N6   C13   119.04  3.000
 3IG  HN6   N6   C17   118.07  3.000
 3IG  C13   N6   C17   122.87  3.000
 3IG  O1    C13  C19   121.82  3.000
 3IG  O1    C13  N6    122.55  3.000
 3IG  C19   C13  N6    115.63  3.000
 3IG  H193  C19  H192  108.52  3.000
 3IG  H193  C19  H191  108.51  3.000
 3IG  H192  C19  H191  107.33  3.000
 3IG  H193  C19  C13   113.61  3.000
 3IG  H192  C19  C13   109.38  3.000
 3IG  H191  C19  C13   109.31  3.000
 3IG  H213  C21  H212  108.40  3.000
 3IG  H213  C21  H211  108.49  3.000
 3IG  H212  C21  H211  107.94  3.000
 3IG  H213  C21  C14   111.46  3.000
 3IG  H212  C21  C14   110.75  3.000
 3IG  H211  C21  C14   109.70  3.000
 3IG  H203  C20  H202  108.09  3.000
 3IG  H203  C20  H201  108.27  3.000
 3IG  H202  C20  H201  107.84  3.000
 3IG  H203  C20  C14   109.78  3.000
 3IG  H202  C20  C14   110.12  3.000
 3IG  H201  C20  C14   112.61  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
 3IG  CONST_01  N2    C2   N1   C1      0.00   0.0  0
 3IG  CONST_02  N2    C3   C4   C1      0.00   0.0  0
 3IG  CONST_05  C3    C4   C1   N1      0.00   0.0  0
 3IG  CONST_06  C12   C4   C1   N1    180.00   0.0  0
 3IG  CONST_07  C3    N2   C2   N1      0.00   0.0  0
 3IG  CONST_08  C4    C1   N1   C2      0.00   0.0  0
 3IG  CONST_09  C4    C3   N2   C2      0.00   0.0  0
 3IG  CONST_10  C12   C4   C3   N2    180.00   0.0  0
 3IG  CONST_13  C8    C7   C12  C4    180.00   0.0  0
 3IG  CONST_14  C10   C11  C12  C4    180.00   0.0  0
 3IG  CONST_15  C10   C9   C8   C7      0.00   0.0  0
 3IG  CONST_16  C10   C11  C12  C7      0.00   0.0  0
 3IG  CONST_17  C11   C12  C7   C8      0.00   0.0  0
 3IG  CONST_18  C11   C10  C9   C8      0.00   0.0  0
 3IG  CONST_19  C12   C7   C8   C9      0.00   0.0  0
 3IG  CONST_20  C12   C11  C10  C9      0.00   0.0  0
 3IG  CONST_21  C14   C15  N5   C10     0.00   0.0  0
 3IG  CONST_22  N4    C2   N1   C1    180.00   0.0  0
 3IG  CONST_23  C5    C3   C4   C1    180.00   0.0  0
 3IG  CONST_24  N3    C1   N1   C2    180.00   0.0  0
 3IG  CONST_25  C5    C3   N2   C2    180.00   0.0  0
 3IG  CONST_26  N4    C2   N2   C3    180.00   0.0  0
 3IG  CONST_27  N3    C1   C4   C3    180.00   0.0  0
 3IG  CONST_28  C12   C4   C1   N3      0.00   0.0  0
 3IG  CONST_29  C12   C4   C3   C5      0.00   0.0  0
 3IG  CONST_30  O4    C15  N5   C10   180.00   0.0  0
 3IG  CONST_31  C16   N5   C15  C14   180.00   0.0  0
 3IG  CONST_32  H7    C7   C12  C4      0.00   0.0  0
 3IG  CONST_33  H11   C11  C12  C4      0.00   0.0  0
 3IG  CONST_34  H8    C8   C9   C10   180.00   0.0  0
 3IG  CONST_35  O4    C15  N5   C16     0.00   0.0  0
 3IG  CONST_36  HN31  N3   C1   N1      0.00   0.0  0
 3IG  CONST_37  HN32  N3   C1   N1    180.00   0.0  0
 3IG  CONST_40  C19   C13  N6   C17   180.00   0.0  0
 3IG  CONST_41  O1    C13  N6   C17     0.00   0.0  0
 3IG  CONST_42  HN6   N6   C13  C19     0.00   0.0  0
 3IG  Var_01    C15   N5   C10  C9     20.04  30.0  1
 3IG  Var_02    C15   C14  O3   C9     52.48  30.0  1
 3IG  Var_03    N5    C15  C14  O3    -33.36  30.0  1
 3IG  Var_04    C6    C5   C3   N2     72.32  30.0  2
 3IG  Var_05    C17   C16  N5   C10   -89.30  30.0  3
 3IG  Var_06    H211  C21  C14  O3     60.82  30.0  3
 3IG  Var_07    H201  C20  C14  O3     61.59  30.0  3
 3IG  Var_08    N6    C17  C16  N5    175.61  30.0  3
 3IG  Var_09    H61   C6   C5   C3   -178.80  30.0  3
 3IG  Var_10    C13   N6   C17  C16   -80.47  30.0  3
 3IG  Var_11    H191  C19  C13  N6    123.82  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
 3IG  plan-1  C1    0.020
 3IG  plan-1  N1    0.020
 3IG  plan-1  C2    0.020
 3IG  plan-1  N2    0.020
 3IG  plan-1  C3    0.020
 3IG  plan-1  C4    0.020
 3IG  plan-1  N3    0.020
 3IG  plan-1  N4    0.020
 3IG  plan-1  C5    0.020
 3IG  plan-1  C12   0.020
 3IG  plan-2  C4    0.020
 3IG  plan-2  C7    0.020
 3IG  plan-2  C8    0.020
 3IG  plan-2  C9    0.020
 3IG  plan-2  C10   0.020
 3IG  plan-2  C11   0.020
 3IG  plan-2  C12   0.020
 3IG  plan-2  O3    0.020
 3IG  plan-2  N5    0.020
 3IG  plan-2  H8    0.020
 3IG  plan-2  H11   0.020
 3IG  plan-2  H7    0.020
 3IG  plan-3  C17   0.020
 3IG  plan-3  N6    0.020
 3IG  plan-3  C13   0.020
 3IG  plan-3  C19   0.020
 3IG  plan-3  O1    0.020
 3IG  plan-3  HN6   0.020
 3IG  plan-4  C1    0.020
 3IG  plan-4  N3    0.020
 3IG  plan-4  HN31  0.020
 3IG  plan-4  HN32  0.020
 3IG  plan-5  C2    0.020
 3IG  plan-5  N4    0.020
 3IG  plan-5  HN41  0.020
 3IG  plan-5  HN42  0.020
 3IG  plan-6  C10   0.020
 3IG  plan-6  C14   0.020
 3IG  plan-6  C15   0.020
 3IG  plan-6  N5    0.020
 3IG  plan-6  C16   0.020
 3IG  plan-6  O4    0.020

