# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 01:21:24 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (2S)-6-(2,4-diamino-6-ethylpyrimidin-5-yl)-2-(3,5-difluorophenyl)-4-(3-methoxypropyl)-2H-1,4-benzoxazin-3(4H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1c2ccc3O[C@H](C(=O)N(CCCOC)c3c2)c4cc(F)cc(F)c4
#
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
 4IG  4IG  (2S)-6-(2,4-diamino-6-ethylpyrimidin-5-yl)-2-(3,5-difluorophenyl)-4-(3-methoxypropyl)-2H-1,4-benzoxazin-3(4H)-one  ligand  59  34  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4IG
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
 4IG  C1    C  CR6   0   0.487  -4.1738   0.5329  -1.4033
 4IG  N1    N  N     0  -0.510  -5.4167   0.4915  -0.9339
 4IG  C2    C  CR6   0   0.523  -5.5814   0.7555   0.3610
 4IG  N2    N  N     0  -0.507  -4.6213   1.0591   1.2312
 4IG  C3    C  CR6   0   0.276  -3.3745   1.1057   0.7554
 4IG  C4    C  CR6   0  -0.157  -3.0735   0.8507  -0.5715
 4IG  N3    N  NH2   0  -0.828  -3.9997   0.2282  -2.7013
 4IG  N4    N  NH2   0  -0.824  -6.8536   0.7504   0.8259
 4IG  C5    C  CH2   0  -0.505  -2.3076   1.4233   1.7635
 4IG  C6    C  CH3   0  -0.664  -1.9074   0.1898   2.5711
 4IG  C7    C  CR16  0  -0.293  -1.2135   1.9744  -1.8096
 4IG  C8    C  CR16  0  -0.335   0.0811   1.9806  -2.3075
 4IG  C9    C  CR6   0   0.322   0.8891   0.8740  -2.1316
 4IG  C10   C  CR6   0   0.360   0.4209  -0.2549  -1.4591
 4IG  C11   C  CR16  0  -0.353  -0.8722  -0.2409  -0.9522
 4IG  C12   C  CR6   0  -0.001  -1.6968   0.8697  -1.1143
 4IG  O3    O  O2    0  -0.473   2.1509   0.8719  -2.6360
 4IG  C14   C  CH1   0  -0.134   3.0734   0.1752  -1.8290
 4IG  C15   C  C     0   0.515   2.5953  -1.2471  -1.5752
 4IG  N5    N  NT    0  -0.562   1.2606  -1.3763  -1.3759
 4IG  C16   C  CH2   0  -0.348   0.7286  -2.6835  -1.0122
 4IG  C17   C  CH2   0  -0.486   0.7928  -2.9398   0.4891
 4IG  C18   C  CH2   0  -0.121   0.1785  -4.2820   0.8344
 4IG  O1    O  O2    0  -0.484   0.2787  -4.4862   2.2202
 4IG  C19   C  CH3   0  -0.398  -0.2683  -5.7141   2.6268
 4IG  O4    O  O     0  -0.456   3.3776  -2.1763  -1.5262
 4IG  C20   C  CR6   0   0.578   4.0336   0.9373   1.7592
 4IG  C21   C  CR16  0  -0.463   3.7598   0.2205   0.6103
 4IG  C22   C  CR6   0   0.072   3.3545   0.9103  -0.5274
 4IG  C23   C  CR16  0  -0.451   3.2447   2.2970  -0.4980
 4IG  C24   C  CR6   0   0.566   3.5302   2.9596   0.6786
 4IG  C25   C  CR16  0  -0.567   3.9268   2.3111   1.8318
 4IG  F1    F  F     0  -0.306   3.4191   4.2928   0.7076
 4IG  HN31  H  HNH2  0   0.393  -4.8077   0.1313  -3.2914
 4IG  HN32  H  HNH2  0   0.403  -3.1147   0.3765  -3.1530
 4IG  HN41  H  HNH2  0   0.387  -6.9871   0.7105   1.8216
 4IG  HN42  H  HNH2  0   0.387  -7.5595   0.3063   0.2645
 4IG  H51   H  HCH2  0   0.246  -2.6959   2.1858   2.4412
 4IG  H52   H  HCH2  0   0.243  -1.4287   1.8421   1.2729
 4IG  H61   H  HCH3  0   0.238  -1.2050   0.4589   3.3598
 4IG  H62   H  HCH3  0   0.231  -2.7759  -0.2754   3.0368
 4IG  H63   H  HCH3  0   0.223  -1.4252  -0.5584   1.9405
 4IG  H7    H  HCR6  0   0.259  -1.8428   2.8447  -1.9434
 4IG  H8    H  HCR6  0   0.276   0.4670   2.8430  -2.8361
 4IG  H11   H  HCR6  0   0.267  -1.2685  -1.1005  -0.4294
 4IG  H14   H  HCH1  0   0.325   3.9945   0.1119  -2.4116
 4IG  H161  H  HCH2  0   0.271  -0.2953  -2.7509  -1.3809
 4IG  H162  H  HCH2  0   0.284   1.2979  -3.4409  -1.5492
 4IG  H171  H  HCH2  0   0.249   1.8347  -2.9170   0.8180
 4IG  H172  H  HCH2  0   0.237   0.2683  -2.1488   1.0323
 4IG  H181  H  HCH2  0   0.200  -0.8733  -4.3060   0.5124
 4IG  H182  H  HCH2  0   0.200   0.6936  -5.0838   0.2846
 4IG  H191  H  HCH3  0   0.204   0.2371  -6.5663   2.1567
 4IG  H192  H  HCH3  0   0.234  -0.1477  -5.7959   3.7064
 4IG  H193  H  HCH3  0   0.204  -1.3372  -5.7873   2.3924
 4IG  H21   H  HCR6  0   0.282   3.8781  -0.8545   0.6214
 4IG  H23   H  HCR6  0   0.285   2.9474   2.8629  -1.3701
 4IG  H25   H  HCR6  0   0.308   4.1450   2.8517   2.7434
 4IG  F2    F  F     0  -0.306   4.4180   0.2703   2.8533

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
 4IG  C1   N1    aromatic  1.329  0.020  1.329
 4IG  C1   C4    aromatic  1.415  0.020  1.415
 4IG  C1   N3    single    1.345  0.020  1.345
 4IG  N1   C2    aromatic  1.332  0.020  1.332
 4IG  C2   N2    aromatic  1.331  0.020  1.331
 4IG  C2   N4    single    1.354  0.020  1.354
 4IG  N2   C3    aromatic  1.335  0.020  1.335
 4IG  C3   C4    aromatic  1.384  0.020  1.384
 4IG  C3   C5    single    1.502  0.020  1.502
 4IG  C4   C12   single    1.480  0.020  1.480
 4IG  N3   HN31  single    0.860  0.020  1.020
 4IG  N3   HN32  single    0.860  0.020  1.020
 4IG  N4   HN41  single    0.890  0.020  1.040
 4IG  N4   HN42  single    0.890  0.020  1.040
 4IG  C5   C6    single    1.528  0.020  1.528
 4IG  C5   H51   single    0.970  0.020  1.090
 4IG  C5   H52   single    0.970  0.020  1.090
 4IG  C6   H61   single    0.970  0.020  1.090
 4IG  C6   H62   single    0.970  0.020  1.090
 4IG  C6   H63   single    0.970  0.020  1.090
 4IG  C7   C8    aromatic  1.387  0.020  1.387
 4IG  C7   C12   aromatic  1.392  0.020  1.392
 4IG  C7   H7    single    0.930  0.020  1.080
 4IG  C8   C9    aromatic  1.381  0.020  1.381
 4IG  C8   H8    single    0.930  0.020  1.080
 4IG  C9   C10   aromatic  1.395  0.020  1.395
 4IG  C9   O3    single    1.359  0.020  1.359
 4IG  C10  C11   aromatic  1.389  0.020  1.389
 4IG  C10  N5    single    1.403  0.020  1.403
 4IG  C11  C12   aromatic  1.393  0.020  1.393
 4IG  C11  H11   single    0.930  0.020  1.080
 4IG  O3   C14   single    1.410  0.020  1.410
 4IG  C14  C15   single    1.522  0.020  1.522
 4IG  C14  C22   single    1.521  0.020  1.521
 4IG  C14  H14   single    0.970  0.020  1.090
 4IG  C15  N5    single    1.356  0.020  1.356
 4IG  C15  O4    double    1.216  0.020  1.216
 4IG  N5   C16   single    1.458  0.020  1.458
 4IG  C16  C17   single    1.524  0.020  1.524
 4IG  C16  H161  single    0.970  0.020  1.090
 4IG  C16  H162  single    0.970  0.020  1.090
 4IG  C17  C18   single    1.516  0.020  1.516
 4IG  C17  H171  single    0.970  0.020  1.090
 4IG  C17  H172  single    0.970  0.020  1.090
 4IG  C18  O1    single    1.404  0.020  1.404
 4IG  C18  H181  single    0.970  0.020  1.090
 4IG  C18  H182  single    0.970  0.020  1.090
 4IG  O1   C19   single    1.404  0.020  1.404
 4IG  C19  H191  single    0.970  0.020  1.090
 4IG  C19  H192  single    0.970  0.020  1.090
 4IG  C19  H193  single    0.970  0.020  1.090
 4IG  C20  C21   aromatic  1.382  0.020  1.382
 4IG  C20  C25   aromatic  1.380  0.020  1.380
 4IG  C20  F2    single    1.338  0.020  1.338
 4IG  C21  C22   aromatic  1.391  0.020  1.391
 4IG  C21  H21   single    0.930  0.020  1.080
 4IG  C22  C23   aromatic  1.391  0.020  1.391
 4IG  C23  C24   aromatic  1.380  0.020  1.380
 4IG  C23  H23   single    0.930  0.020  1.080
 4IG  C24  C25   aromatic  1.381  0.020  1.381
 4IG  C24  F1    single    1.338  0.020  1.338
 4IG  C25  H25   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
 4IG  N3    C1   C4    121.16  3.000
 4IG  N3    C1   N1    117.06  3.000
 4IG  C4    C1   N1    121.76  3.000
 4IG  C2    N1   C1    116.92  3.000
 4IG  N4    C2   N2    116.99  3.000
 4IG  N4    C2   N1    116.69  3.000
 4IG  N2    C2   N1    126.29  3.000
 4IG  C3    N2   C2    116.65  3.000
 4IG  C5    C3   C4    121.86  3.000
 4IG  C5    C3   N2    115.56  3.000
 4IG  C4    C3   N2    122.56  3.000
 4IG  C12   C4   C3    123.47  3.000
 4IG  C12   C4   C1    120.69  3.000
 4IG  C3    C4   C1    115.82  3.000
 4IG  HN32  N3   HN31  117.28  3.000
 4IG  HN32  N3   C1    120.98  3.000
 4IG  HN31  N3   C1    118.97  3.000
 4IG  HN42  N4   HN41  116.25  3.000
 4IG  HN42  N4   C2    118.00  3.000
 4IG  HN41  N4   C2    117.70  3.000
 4IG  H52   C5   H51   107.33  3.000
 4IG  H52   C5   C6    109.68  3.000
 4IG  H51   C5   C6    109.21  3.000
 4IG  H52   C5   C3    110.60  3.000
 4IG  H51   C5   C3    108.17  3.000
 4IG  C6    C5   C3    111.73  3.000
 4IG  H63   C6   H62   107.85  3.000
 4IG  H63   C6   H61   107.63  3.000
 4IG  H62   C6   H61   108.04  3.000
 4IG  H63   C6   C5    111.35  3.000
 4IG  H62   C6   C5    111.21  3.000
 4IG  H61   C6   C5    110.61  3.000
 4IG  H7    C7   C12   119.87  3.000
 4IG  H7    C7   C8    119.66  3.000
 4IG  C12   C7   C8    120.46  3.000
 4IG  H8    C8   C9    119.46  3.000
 4IG  H8    C8   C7    120.76  3.000
 4IG  C9    C8   C7    119.78  3.000
 4IG  O3    C9   C10   119.30  3.000
 4IG  O3    C9   C8    119.81  3.000
 4IG  C10   C9   C8    120.89  3.000
 4IG  N5    C10  C11   122.92  3.000
 4IG  N5    C10  C9    118.32  3.000
 4IG  C11   C10  C9    118.71  3.000
 4IG  H11   C11  C12   118.24  3.000
 4IG  H11   C11  C10   120.64  3.000
 4IG  C12   C11  C10   121.11  3.000
 4IG  C11   C12  C7    119.04  3.000
 4IG  C11   C12  C4    119.85  3.000
 4IG  C7    C12  C4    121.09  3.000
 4IG  C14   O3   C9    113.32  3.000
 4IG  H14   C14  C22   109.20  3.000
 4IG  H14   C14  C15   107.45  3.000
 4IG  C22   C14  C15   111.53  3.000
 4IG  H14   C14  O3    105.97  3.000
 4IG  C22   C14  O3    111.84  3.000
 4IG  C15   C14  O3    110.60  3.000
 4IG  O4    C15  N5    123.70  3.000
 4IG  O4    C15  C14   121.26  3.000
 4IG  N5    C15  C14   115.01  3.000
 4IG  C16   N5   C15   118.79  3.000
 4IG  C16   N5   C10   120.87  3.000
 4IG  C15   N5   C10   120.28  3.000
 4IG  H162  C16  H161  106.33  3.000
 4IG  H162  C16  C17   110.28  3.000
 4IG  H161  C16  C17   111.24  3.000
 4IG  H162  C16  N5    108.05  3.000
 4IG  H161  C16  N5    108.29  3.000
 4IG  C17   C16  N5    112.41  3.000
 4IG  H172  C17  H171  107.02  3.000
 4IG  H172  C17  C18   109.44  3.000
 4IG  H171  C17  C18   109.65  3.000
 4IG  H172  C17  C16   110.33  3.000
 4IG  H171  C17  C16   109.46  3.000
 4IG  C18   C17  C16   110.86  3.000
 4IG  H182  C18  H181  106.58  3.000
 4IG  H182  C18  O1    110.71  3.000
 4IG  H181  C18  O1    110.72  3.000
 4IG  H182  C18  C17   109.98  3.000
 4IG  H181  C18  C17   109.89  3.000
 4IG  O1    C18  C17   108.94  3.000
 4IG  C19   O1   C18   112.65  3.000
 4IG  H193  C19  H192  108.34  3.000
 4IG  H193  C19  H191  107.80  3.000
 4IG  H192  C19  H191  108.39  3.000
 4IG  H193  C19  O1    112.09  3.000
 4IG  H192  C19  O1    108.03  3.000
 4IG  H191  C19  O1    112.08  3.000
 4IG  F2    C20  C25   118.40  3.000
 4IG  F2    C20  C21   118.58  3.000
 4IG  C25   C20  C21   123.02  3.000
 4IG  H21   C21  C22   122.22  3.000
 4IG  H21   C21  C20   119.05  3.000
 4IG  C22   C21  C20   118.73  3.000
 4IG  C23   C22  C21   120.00  3.000
 4IG  C23   C22  C14   119.03  3.000
 4IG  C21   C22  C14   120.94  3.000
 4IG  H23   C23  C24   119.55  3.000
 4IG  H23   C23  C22   121.75  3.000
 4IG  C24   C23  C22   118.70  3.000
 4IG  F1    C24  C25   118.27  3.000
 4IG  F1    C24  C23   118.66  3.000
 4IG  C25   C24  C23   123.07  3.000
 4IG  H25   C25  C24   121.78  3.000
 4IG  H25   C25  C20   121.74  3.000
 4IG  C24   C25  C20   116.47  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
 4IG  CONST_01  N2    C2   N1   C1      0.00   0.0  0
 4IG  CONST_02  N2    C3   C4   C1      0.00   0.0  0
 4IG  CONST_05  C3    C4   C1   N1      0.00   0.0  0
 4IG  CONST_06  C12   C4   C1   N1    180.00   0.0  0
 4IG  CONST_07  C3    N2   C2   N1      0.00   0.0  0
 4IG  CONST_08  C4    C1   N1   C2      0.00   0.0  0
 4IG  CONST_09  C4    C3   N2   C2      0.00   0.0  0
 4IG  CONST_10  C12   C4   C3   N2    180.00   0.0  0
 4IG  CONST_13  C8    C7   C12  C4    180.00   0.0  0
 4IG  CONST_14  C10   C11  C12  C4    180.00   0.0  0
 4IG  CONST_15  C10   C9   C8   C7      0.00   0.0  0
 4IG  CONST_16  C10   C11  C12  C7      0.00   0.0  0
 4IG  CONST_17  C11   C12  C7   C8      0.00   0.0  0
 4IG  CONST_18  C11   C10  C9   C8      0.00   0.0  0
 4IG  CONST_19  C12   C7   C8   C9      0.00   0.0  0
 4IG  CONST_20  C12   C11  C10  C9      0.00   0.0  0
 4IG  CONST_21  C23   C22  C21  C20     0.00   0.0  0
 4IG  CONST_22  C23   C24  C25  C20     0.00   0.0  0
 4IG  CONST_23  C24   C25  C20  C21     0.00   0.0  0
 4IG  CONST_24  C24   C23  C22  C21     0.00   0.0  0
 4IG  CONST_25  C25   C20  C21  C22     0.00   0.0  0
 4IG  CONST_26  C25   C24  C23  C22     0.00   0.0  0
 4IG  CONST_27  C20   C21  C22  C14   180.00   0.0  0
 4IG  CONST_28  C24   C23  C22  C14   180.00   0.0  0
 4IG  CONST_29  C14   C15  N5   C10     0.00   0.0  0
 4IG  CONST_30  N4    C2   N1   C1    180.00   0.0  0
 4IG  CONST_31  C5    C3   C4   C1    180.00   0.0  0
 4IG  CONST_32  N3    C1   N1   C2    180.00   0.0  0
 4IG  CONST_33  C5    C3   N2   C2    180.00   0.0  0
 4IG  CONST_34  N4    C2   N2   C3    180.00   0.0  0
 4IG  CONST_35  N3    C1   C4   C3    180.00   0.0  0
 4IG  CONST_36  C12   C4   C1   N3      0.00   0.0  0
 4IG  CONST_37  C12   C4   C3   C5      0.00   0.0  0
 4IG  CONST_38  F1    C24  C25  C20   180.00   0.0  0
 4IG  CONST_39  F2    C20  C21  C22   180.00   0.0  0
 4IG  CONST_40  F1    C24  C23  C22   180.00   0.0  0
 4IG  CONST_41  F2    C20  C25  C24   180.00   0.0  0
 4IG  CONST_42  O4    C15  N5   C10   180.00   0.0  0
 4IG  CONST_43  C16   N5   C15  C14   180.00   0.0  0
 4IG  CONST_44  H7    C7   C12  C4      0.00   0.0  0
 4IG  CONST_45  H11   C11  C12  C4      0.00   0.0  0
 4IG  CONST_46  H8    C8   C9   C10   180.00   0.0  0
 4IG  CONST_47  H21   C21  C22  C14     0.00   0.0  0
 4IG  CONST_48  H23   C23  C22  C14     0.00   0.0  0
 4IG  CONST_49  H25   C25  C20  C21   180.00   0.0  0
 4IG  CONST_50  O4    C15  N5   C16     0.00   0.0  0
 4IG  CONST_51  HN31  N3   C1   N1      0.00   0.0  0
 4IG  CONST_52  HN32  N3   C1   N1    180.00   0.0  0
 4IG  Var_01    C15   N5   C10  C9     19.26  30.0  1
 4IG  Var_02    C6    C5   C3   N2     80.96  30.0  2
 4IG  Var_03    C17   C16  N5   C10   -91.62  30.0  3
 4IG  Var_04    C18   C17  C16  N5    177.61  30.0  3
 4IG  Var_05    H61   C6   C5   C3   -174.51  30.0  3
 4IG  Var_06    O1    C18  C17  C16   179.03  30.0  3
 4IG  Var_07    H191  C19  O1   C18    60.45  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 4IG  chir_01  C14  O3  C15  C22  positiv

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
 4IG  plan-1  C1    0.020
 4IG  plan-1  N1    0.020
 4IG  plan-1  C2    0.020
 4IG  plan-1  N2    0.020
 4IG  plan-1  C3    0.020
 4IG  plan-1  C4    0.020
 4IG  plan-1  N3    0.020
 4IG  plan-1  N4    0.020
 4IG  plan-1  C5    0.020
 4IG  plan-1  C12   0.020
 4IG  plan-2  C14   0.020
 4IG  plan-2  C20   0.020
 4IG  plan-2  C21   0.020
 4IG  plan-2  C22   0.020
 4IG  plan-2  C23   0.020
 4IG  plan-2  C24   0.020
 4IG  plan-2  C25   0.020
 4IG  plan-2  F1    0.020
 4IG  plan-2  H21   0.020
 4IG  plan-2  H23   0.020
 4IG  plan-2  H25   0.020
 4IG  plan-2  F2    0.020
 4IG  plan-3  C4    0.020
 4IG  plan-3  C7    0.020
 4IG  plan-3  C8    0.020
 4IG  plan-3  C9    0.020
 4IG  plan-3  C10   0.020
 4IG  plan-3  C11   0.020
 4IG  plan-3  C12   0.020
 4IG  plan-3  O3    0.020
 4IG  plan-3  N5    0.020
 4IG  plan-3  H7    0.020
 4IG  plan-3  H8    0.020
 4IG  plan-3  H11   0.020
 4IG  plan-4  C1    0.020
 4IG  plan-4  N3    0.020
 4IG  plan-4  HN31  0.020
 4IG  plan-4  HN32  0.020
 4IG  plan-5  C2    0.020
 4IG  plan-5  N4    0.020
 4IG  plan-5  HN41  0.020
 4IG  plan-5  HN42  0.020
 4IG  plan-6  C10   0.020
 4IG  plan-6  C14   0.020
 4IG  plan-6  C15   0.020
 4IG  plan-6  N5    0.020
 4IG  plan-6  C16   0.020
 4IG  plan-6  O4    0.020

