# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 03:37:08 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 6-(2,4-diamino-6-ethylpyrimidin-5-yl)-4-(3-methoxypropyl)-2,2-dimethyl-2H-1,4-benzoxazin-3(4H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1c2ccc3OC(C)(C)C(=O)N(CCCOC)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
 5IG  5IG  6-(2,4-diamino-6-ethylpyrimidin-5-yl)-4-(3-methoxypropyl)-2,2-dimethyl-2H-1,4-benzoxazin-3(4H)-one  ligand  55  28  .  2022-07-23  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_5IG
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
 5IG  C1    C  CR6   0   0.481  -3.2297  -0.3802   1.5237
 5IG  N1    N  N     0  -0.509  -4.4799   0.0675   1.4581
 5IG  C2    C  CR6   0   0.523  -5.0384   0.1195   0.2505
 5IG  N2    N  N     0  -0.507  -4.4665  -0.2364  -0.8981
 5IG  C3    C  CR6   0   0.273  -3.2101  -0.6828  -0.8276
 5IG  C4    C  CR6   0  -0.155  -2.5210  -0.7836   0.3688
 5IG  N3    N  NH2   0  -0.827  -2.6707  -0.4622   2.7456
 5IG  N4    N  NH2   0  -0.824  -6.2960   0.6179   0.1821
 5IG  C6    C  CH2   0  -0.508  -2.5637  -1.0195  -2.1406
 5IG  C7    C  CR16  0  -0.288  -0.8355  -2.6253   0.5565
 5IG  C8    C  CR16  0  -0.349   0.4801  -3.0639   0.5915
 5IG  C9    C  CR6   0   0.333   1.5150  -2.1465   0.5578
 5IG  C10   C  CR6   0   0.327   1.2479  -0.7788   0.4903
 5IG  C11   C  CR16  0  -0.357  -0.0736  -0.3535   0.4346
 5IG  C12   C  CR6   0  -0.002  -1.1250  -1.2679   0.4583
 5IG  O3    O  O2    0  -0.478   2.7967  -2.5677   0.6147
 5IG  C14   C  CT    0   0.035   3.7200  -1.8032  -0.1643
 5IG  C15   C  C     0   0.571   3.5872  -0.3218   0.1894
 5IG  N5    N  NT    0  -0.574   2.3354   0.1062   0.5085
 5IG  C16   C  CH2   0  -0.343   2.1288   1.5208   0.7875
 5IG  C17   C  CH2   0  -0.485   1.8594   2.3450  -0.4669
 5IG  C18   C  CH2   0  -0.123   1.5983   3.7935  -0.1026
 5IG  O1    O  O2    0  -0.485   1.3413   4.5263  -1.2733
 5IG  C19   C  CH3   0  -0.398   1.0799   5.8815  -1.0127
 5IG  C21   C  CH3   0  -0.661   5.0977  -2.3172   0.2090
 5IG  C20   C  CH3   0  -0.663   3.4468  -1.9823  -1.6570
 5IG  O4    O  O     0  -0.460   4.5423   0.4293   0.1454
 5IG  C5    C  CH3   0  -0.664  -1.9423   0.2199  -2.7856
 5IG  HN31  H  HNH2  0   0.392  -3.1409  -0.0267   3.5204
 5IG  HN32  H  HNH2  0   0.401  -1.6829  -0.6195   2.8436
 5IG  HN41  H  HNH2  0   0.387  -6.8201   0.4516  -0.6594
 5IG  HN42  H  HNH2  0   0.387  -6.8285   0.6766   1.0329
 5IG  H61   H  HCH2  0   0.245  -3.3256  -1.4325  -2.8038
 5IG  H62   H  HCH2  0   0.244  -1.7978  -1.7842  -2.0084
 5IG  H8    H  HCR6  0   0.270   0.7090  -4.1204   0.6511
 5IG  H11   H  HCR6  0   0.271  -0.3104   0.6994   0.3630
 5IG  H161  H  HCH2  0   0.265   1.3045   1.6080   1.4959
 5IG  H162  H  HCH2  0   0.280   3.0143   1.8953   1.2990
 5IG  H171  H  HCH2  0   0.249   2.7183   2.2783  -1.1381
 5IG  H172  H  HCH2  0   0.237   0.9968   1.9444  -1.0065
 5IG  H181  H  HCH2  0   0.199   0.7438   3.8570   0.5880
 5IG  H182  H  HCH2  0   0.199   2.4659   4.2070   0.4328
 5IG  H191  H  HCH3  0   0.233   0.8611   6.3722  -1.9605
 5IG  H192  H  HCH3  0   0.203   0.2177   6.0133  -0.3477
 5IG  H193  H  HCH3  0   0.204   1.9379   6.3863  -0.5526
 5IG  H211  H  HCH3  0   0.249   5.1673  -3.3802  -0.0223
 5IG  H212  H  HCH3  0   0.245   5.8691  -1.8007  -0.3567
 5IG  H213  H  HCH3  0   0.248   5.3009  -2.1804   1.2712
 5IG  H201  H  HCH3  0   0.247   2.4446  -1.6572  -1.9404
 5IG  H202  H  HCH3  0   0.255   4.1624  -1.4051  -2.2416
 5IG  H203  H  HCH3  0   0.258   3.5547  -3.0326  -1.9305
 5IG  H51   H  HCH3  0   0.227  -1.1145   0.6036  -2.1877
 5IG  H52   H  HCH3  0   0.237  -1.5532  -0.0161  -3.7759
 5IG  H53   H  HCH3  0   0.229  -2.6777   1.0173  -2.8942
 5IG  H7    H  HCR6  0   0.254  -1.6415  -3.3470   0.5784

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
 5IG  C1   N1    aromatic  1.330  0.020  1.330
 5IG  C1   C4    aromatic  1.414  0.020  1.414
 5IG  C1   N3    single    1.346  0.020  1.346
 5IG  N1   C2    aromatic  1.332  0.020  1.332
 5IG  C2   N2    aromatic  1.332  0.020  1.332
 5IG  C2   N4    single    1.354  0.020  1.354
 5IG  N2   C3    aromatic  1.335  0.020  1.335
 5IG  C3   C4    aromatic  1.384  0.020  1.384
 5IG  C3   C6    single    1.502  0.020  1.502
 5IG  C4   C12   single    1.480  0.020  1.480
 5IG  N3   HN31  single    0.890  0.020  1.040
 5IG  N3   HN32  single    0.890  0.020  1.040
 5IG  N4   HN41  single    0.890  0.020  1.040
 5IG  N4   HN42  single    0.890  0.020  1.040
 5IG  C6   C5    single    1.529  0.020  1.529
 5IG  C6   H61   single    0.970  0.020  1.090
 5IG  C6   H62   single    0.970  0.020  1.090
 5IG  C7   C8    aromatic  1.387  0.020  1.387
 5IG  C7   C12   aromatic  1.391  0.020  1.391
 5IG  C7   H7    single    0.930  0.020  1.080
 5IG  C8   C9    aromatic  1.383  0.020  1.383
 5IG  C8   H8    single    0.930  0.020  1.080
 5IG  C9   C10   aromatic  1.395  0.020  1.395
 5IG  C9   O3    single    1.350  0.020  1.350
 5IG  C10  C11   aromatic  1.389  0.020  1.389
 5IG  C10  N5    single    1.402  0.020  1.402
 5IG  C11  C12   aromatic  1.394  0.020  1.394
 5IG  C11  H11   single    0.930  0.020  1.080
 5IG  O3   C14   single    1.430  0.020  1.430
 5IG  C14  C15   single    1.529  0.020  1.529
 5IG  C14  C21   single    1.517  0.020  1.517
 5IG  C14  C20   single    1.528  0.020  1.528
 5IG  C15  N5    single    1.361  0.020  1.361
 5IG  C15  O4    double    1.216  0.020  1.216
 5IG  N5   C16   single    1.457  0.020  1.457
 5IG  C16  C17   single    1.525  0.020  1.525
 5IG  C16  H161  single    0.970  0.020  1.090
 5IG  C16  H162  single    0.970  0.020  1.090
 5IG  C17  C18   single    1.516  0.020  1.516
 5IG  C17  H171  single    0.970  0.020  1.090
 5IG  C17  H172  single    0.970  0.020  1.090
 5IG  C18  O1    single    1.405  0.020  1.405
 5IG  C18  H181  single    0.970  0.020  1.090
 5IG  C18  H182  single    0.970  0.020  1.090
 5IG  O1   C19   single    1.405  0.020  1.405
 5IG  C19  H191  single    0.970  0.020  1.090
 5IG  C19  H192  single    0.970  0.020  1.090
 5IG  C19  H193  single    0.970  0.020  1.090
 5IG  C21  H211  single    0.970  0.020  1.090
 5IG  C21  H212  single    0.970  0.020  1.090
 5IG  C21  H213  single    0.970  0.020  1.090
 5IG  C20  H201  single    0.970  0.020  1.090
 5IG  C20  H202  single    0.970  0.020  1.090
 5IG  C20  H203  single    0.970  0.020  1.090
 5IG  C5   H51   single    0.970  0.020  1.090
 5IG  C5   H52   single    0.970  0.020  1.090
 5IG  C5   H53   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
 5IG  N3    C1   C4    121.06  3.000
 5IG  N3    C1   N1    117.11  3.000
 5IG  C4    C1   N1    121.81  3.000
 5IG  C2    N1   C1    116.89  3.000
 5IG  N4    C2   N2    116.97  3.000
 5IG  N4    C2   N1    116.72  3.000
 5IG  N2    C2   N1    126.28  3.000
 5IG  C3    N2   C2    116.62  3.000
 5IG  C6    C3   C4    121.67  3.000
 5IG  C6    C3   N2    115.71  3.000
 5IG  C4    C3   N2    122.57  3.000
 5IG  C12   C4   C3    123.06  3.000
 5IG  C12   C4   C1    121.11  3.000
 5IG  C3    C4   C1    115.83  3.000
 5IG  HN32  N3   HN31  116.89  3.000
 5IG  HN32  N3   C1    120.41  3.000
 5IG  HN31  N3   C1    118.61  3.000
 5IG  HN42  N4   HN41  116.23  3.000
 5IG  HN42  N4   C2    118.07  3.000
 5IG  HN41  N4   C2    117.74  3.000
 5IG  H62   C6   H61   107.38  3.000
 5IG  H62   C6   C5    109.52  3.000
 5IG  H61   C6   C5    109.52  3.000
 5IG  H62   C6   C3    110.71  3.000
 5IG  H61   C6   C3    108.40  3.000
 5IG  C5    C6   C3    111.22  3.000
 5IG  H7    C7   C12   119.80  3.000
 5IG  H7    C7   C8    119.67  3.000
 5IG  C12   C7   C8    120.50  3.000
 5IG  H8    C8   C9    119.36  3.000
 5IG  H8    C8   C7    120.69  3.000
 5IG  C9    C8   C7    119.94  3.000
 5IG  O3    C9   C10   119.31  3.000
 5IG  O3    C9   C8    120.14  3.000
 5IG  C10   C9   C8    120.53  3.000
 5IG  N5    C10  C11   123.03  3.000
 5IG  N5    C10  C9    118.01  3.000
 5IG  C11   C10  C9    118.95  3.000
 5IG  H11   C11  C12   118.34  3.000
 5IG  H11   C11  C10   120.59  3.000
 5IG  C12   C11  C10   121.07  3.000
 5IG  C11   C12  C7    118.96  3.000
 5IG  C11   C12  C4    119.73  3.000
 5IG  C7    C12  C4    121.31  3.000
 5IG  C14   O3   C9    115.04  3.000
 5IG  C20   C14  C21   111.29  3.000
 5IG  C20   C14  C15   108.91  3.000
 5IG  C21   C14  C15   110.50  3.000
 5IG  C20   C14  O3    110.74  3.000
 5IG  C21   C14  O3    105.74  3.000
 5IG  C15   C14  O3    109.63  3.000
 5IG  O4    C15  N5    122.46  3.000
 5IG  O4    C15  C14   121.47  3.000
 5IG  N5    C15  C14   116.03  3.000
 5IG  C16   N5   C15   118.74  3.000
 5IG  C16   N5   C10   120.36  3.000
 5IG  C15   N5   C10   120.79  3.000
 5IG  H162  C16  H161  106.38  3.000
 5IG  H162  C16  C17   110.13  3.000
 5IG  H161  C16  C17   110.95  3.000
 5IG  H162  C16  N5    107.98  3.000
 5IG  H161  C16  N5    108.02  3.000
 5IG  C17   C16  N5    113.10  3.000
 5IG  H172  C17  H171  107.14  3.000
 5IG  H172  C17  C18   109.43  3.000
 5IG  H171  C17  C18   109.96  3.000
 5IG  H172  C17  C16   110.32  3.000
 5IG  H171  C17  C16   109.49  3.000
 5IG  C18   C17  C16   110.44  3.000
 5IG  H182  C18  H181  106.56  3.000
 5IG  H182  C18  O1    110.72  3.000
 5IG  H181  C18  O1    110.54  3.000
 5IG  H182  C18  C17   109.89  3.000
 5IG  H181  C18  C17   109.85  3.000
 5IG  O1    C18  C17   109.25  3.000
 5IG  C19   O1   C18   112.51  3.000
 5IG  H193  C19  H192  107.78  3.000
 5IG  H193  C19  H191  108.34  3.000
 5IG  H192  C19  H191  108.39  3.000
 5IG  H193  C19  O1    112.11  3.000
 5IG  H192  C19  O1    112.01  3.000
 5IG  H191  C19  O1    108.09  3.000
 5IG  H213  C21  H212  108.37  3.000
 5IG  H213  C21  H211  108.49  3.000
 5IG  H212  C21  H211  107.92  3.000
 5IG  H213  C21  C14   111.50  3.000
 5IG  H212  C21  C14   110.82  3.000
 5IG  H211  C21  C14   109.64  3.000
 5IG  H203  C20  H202  108.10  3.000
 5IG  H203  C20  H201  108.22  3.000
 5IG  H202  C20  H201  107.82  3.000
 5IG  H203  C20  C14   109.89  3.000
 5IG  H202  C20  C14   110.16  3.000
 5IG  H201  C20  C14   112.53  3.000
 5IG  H53   C5   H52   107.98  3.000
 5IG  H53   C5   H51   108.02  3.000
 5IG  H52   C5   H51   107.65  3.000
 5IG  H53   C5   C6    111.15  3.000
 5IG  H52   C5   C6    110.65  3.000
 5IG  H51   C5   C6    111.24  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
 5IG  CONST_01  N2    C2   N1   C1      0.00   0.0  0
 5IG  CONST_02  N2    C3   C4   C1      0.00   0.0  0
 5IG  CONST_05  C3    C4   C1   N1      0.00   0.0  0
 5IG  CONST_06  C12   C4   C1   N1    180.00   0.0  0
 5IG  CONST_07  C3    N2   C2   N1      0.00   0.0  0
 5IG  CONST_08  C4    C1   N1   C2      0.00   0.0  0
 5IG  CONST_09  C4    C3   N2   C2      0.00   0.0  0
 5IG  CONST_10  C12   C4   C3   N2    180.00   0.0  0
 5IG  CONST_13  C8    C7   C12  C4    180.00   0.0  0
 5IG  CONST_14  C10   C11  C12  C4    180.00   0.0  0
 5IG  CONST_15  C10   C9   C8   C7      0.00   0.0  0
 5IG  CONST_16  C10   C11  C12  C7      0.00   0.0  0
 5IG  CONST_17  C11   C12  C7   C8      0.00   0.0  0
 5IG  CONST_18  C11   C10  C9   C8      0.00   0.0  0
 5IG  CONST_19  C12   C7   C8   C9      0.00   0.0  0
 5IG  CONST_20  C12   C11  C10  C9      0.00   0.0  0
 5IG  CONST_21  C14   C15  N5   C10     0.00   0.0  0
 5IG  CONST_22  N4    C2   N1   C1    180.00   0.0  0
 5IG  CONST_23  C6    C3   C4   C1    180.00   0.0  0
 5IG  CONST_24  N3    C1   N1   C2    180.00   0.0  0
 5IG  CONST_25  C6    C3   N2   C2    180.00   0.0  0
 5IG  CONST_26  N4    C2   N2   C3    180.00   0.0  0
 5IG  CONST_27  N3    C1   C4   C3    180.00   0.0  0
 5IG  CONST_28  C12   C4   C1   N3      0.00   0.0  0
 5IG  CONST_29  C12   C4   C3   C6      0.00   0.0  0
 5IG  CONST_30  O4    C15  N5   C10   180.00   0.0  0
 5IG  CONST_31  C16   N5   C15  C14   180.00   0.0  0
 5IG  CONST_32  H7    C7   C12  C4      0.00   0.0  0
 5IG  CONST_33  H11   C11  C12  C4      0.00   0.0  0
 5IG  CONST_34  H8    C8   C9   C10   180.00   0.0  0
 5IG  CONST_35  O4    C15  N5   C16     0.00   0.0  0
 5IG  CONST_36  HN31  N3   C1   N1      0.00   0.0  0
 5IG  CONST_37  HN32  N3   C1   N1    180.00   0.0  0
 5IG  Var_01    C15   N5   C10  C9     19.84  30.0  1
 5IG  Var_02    C15   C14  O3   C9     52.69  30.0  1
 5IG  Var_03    N5    C15  C14  O3    -34.06  30.0  1
 5IG  Var_04    C5    C6   C3   N2     85.36  30.0  2
 5IG  Var_05    C17   C16  N5   C10   -89.65  30.0  3
 5IG  Var_06    H211  C21  C14  O3     59.81  30.0  3
 5IG  Var_07    H201  C20  C14  O3     60.30  30.0  3
 5IG  Var_08    C18   C17  C16  N5    177.71  30.0  3
 5IG  Var_09    H51   C5   C6   C3     65.34  30.0  3
 5IG  Var_10    O1    C18  C17  C16  -179.46  30.0  3
 5IG  Var_11    H191  C19  O1   C18  -178.26  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
 5IG  plan-1  C1    0.020
 5IG  plan-1  N1    0.020
 5IG  plan-1  C2    0.020
 5IG  plan-1  N2    0.020
 5IG  plan-1  C3    0.020
 5IG  plan-1  C4    0.020
 5IG  plan-1  N3    0.020
 5IG  plan-1  N4    0.020
 5IG  plan-1  C6    0.020
 5IG  plan-1  C12   0.020
 5IG  plan-2  C4    0.020
 5IG  plan-2  C7    0.020
 5IG  plan-2  C8    0.020
 5IG  plan-2  C9    0.020
 5IG  plan-2  C10   0.020
 5IG  plan-2  C11   0.020
 5IG  plan-2  C12   0.020
 5IG  plan-2  O3    0.020
 5IG  plan-2  N5    0.020
 5IG  plan-2  H8    0.020
 5IG  plan-2  H11   0.020
 5IG  plan-2  H7    0.020
 5IG  plan-3  C1    0.020
 5IG  plan-3  N3    0.020
 5IG  plan-3  HN31  0.020
 5IG  plan-3  HN32  0.020
 5IG  plan-4  C2    0.020
 5IG  plan-4  N4    0.020
 5IG  plan-4  HN41  0.020
 5IG  plan-4  HN42  0.020
 5IG  plan-5  C10   0.020
 5IG  plan-5  C14   0.020
 5IG  plan-5  C15   0.020
 5IG  plan-5  N5    0.020
 5IG  plan-5  C16   0.020
 5IG  plan-5  O4    0.020

