# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 22:12:54 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 3-[[4-methoxy-5-[(4-methoxyphenyl)methoxy]pyridin-2-yl]methoxy]-5-(1-methylpyrazol-4-yl)pyrazin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(COc2cnc(COc3nc(cnc3N)c4cnn(C)c4)cc2OC)cc1
#
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
 LC0  LC0  3-[[4-methoxy-5-[(4-methoxyphenyl)methoxy]pyridin-2-yl]methoxy]-5-(1-methylpyrazol-4-yl)pyrazin-2-amine  ligand  57  33  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LC0
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
 LC0  C4    C  CR16  0  -0.268   -6.3346  -0.7765  -0.9923
 LC0  C5    C  CR16  0  -0.289   -6.6556  -0.8667   1.3715
 LC0  C6    C  CR16  0  -0.329   -7.6744  -0.4993  -1.1709
 LC0  C7    C  CR16  0  -0.372   -8.0107  -0.5953   1.2120
 LC0  C8    C  CR16  0  -0.438   -0.2155   0.9656  -0.4031
 LC0  C10   C  CR16  0  -0.216   -1.5172  -1.2105   0.5608
 LC0  C15   C  CR6   0   0.071   -5.8018  -0.9663   0.2843
 LC0  C17   C  CR6   0   0.192    0.4509  -0.1535   0.0981
 LC0  C20   C  CR6   0   0.259   -2.2777  -0.1523   0.0994
 LC0  C21   C  CR6   0   0.157    5.9213   0.4426   0.2946
 LC0  C22   C  CR6   0   0.355    4.2579   2.5147   0.7932
 LC0  C1    C  CH3   0  -0.508    7.6312  -4.0992  -0.7688
 LC0  C2    C  CH3   0  -0.438  -10.7364  -0.0976   0.7414
 LC0  C3    C  CH3   0  -0.442   -1.7302   3.1266  -1.3756
 LC0  C9    C  CR15  0  -0.114    8.2026  -0.7641   0.0568
 LC0  C11   C  CR16  0  -0.160    6.3811   1.7067   0.5896
 LC0  C12   C  CR15  0   0.042    6.4076  -1.9742  -0.2998
 LC0  C16   C  CR6   0   0.376   -8.5279  -0.4083  -0.0662
 LC0  C18   C  CR6   0   0.398   -1.5983   0.9780  -0.4019
 LC0  C19   C  CR5   0  -0.152    6.7955  -0.6900   0.0332
 LC0  C23   C  CR6   0   0.439    3.7857   1.2021   0.4884
 LC0  N25   N  N     0  -0.430   -0.1816  -1.2103   0.5677
 LC0  N26   N  N     0  -0.410    5.5525   2.7296   0.8305
 LC0  N27   N  N     0  -0.278    8.6271  -1.9785  -0.2347
 LC0  N28   N  N     0  -0.447    4.5907   0.2192   0.2463
 LC0  N29   N  NR5   0  -0.263    7.5289  -2.6957  -0.4497
 LC0  O30   O  O2    0  -0.469   -9.8190  -0.1431  -0.3336
 LC0  O31   O  O2    0  -0.450   -2.3641   1.9759  -0.8424
 LC0  O32   O  O2    0  -0.458   -3.6188  -0.0931   0.0852
 LC0  O33   O  O2    0  -0.481    2.4601   1.0418   0.4676
 LC0  H4    H  HCR6  0   0.255   -5.6932  -0.8525  -1.8623
 LC0  H5    H  HCR6  0   0.258   -6.2687  -1.0068   2.3739
 LC0  H6    H  HCR6  0   0.264   -8.0756  -0.3554  -2.1665
 LC0  H7    H  HCR6  0   0.281   -8.6377  -0.5313   2.0907
 LC0  H8    H  HCR6  0   0.289    0.3495   1.8012  -0.7916
 LC0  H10   H  HCR6  0   0.283   -1.9895  -2.1020   0.9556
 LC0  H13   H  HCH2  0   0.245   -4.1370  -1.5177   1.5082
 LC0  H13A  H  HCH2  0   0.242   -4.0364  -2.1049  -0.1564
 LC0  H1    H  HCH3  0   0.262    8.2999  -4.2417  -1.6147
 LC0  H1A   H  HCH3  0   0.260    8.0085  -4.6604   0.0845
 LC0  H1B   H  HCH3  0   0.260    6.6464  -4.4750  -1.0305
 LC0  H2    H  HCH3  0   0.260  -11.7143   0.0903   0.3056
 LC0  H2A   H  HCH3  0   0.229  -10.7709  -1.0441   1.2871
 LC0  H2B   H  HCH3  0   0.229  -10.5040   0.7063   1.4448
 LC0  H3    H  HCH3  0   0.237   -1.1227   2.8837  -2.2504
 LC0  H3A   H  HCH3  0   0.267   -2.5262   3.8029  -1.6745
 LC0  H3B   H  HCH3  0   0.234   -1.1025   3.6229  -0.6317
 LC0  H9    H  HCR5  0   0.256    8.9146   0.0185   0.2730
 LC0  H11   H  HCR6  0   0.254    7.4412   1.9261   0.6351
 LC0  H12   H  HCR5  0   0.290    5.4288  -2.4027  -0.4395
 LC0  H14   H  HCH2  0   0.252    2.2842  -1.0096   0.7744
 LC0  H14A  H  HCH2  0   0.251    2.3163  -0.4929  -0.9121
 LC0  HN24  H  HNH2  0   0.392    2.4461   3.4485   0.7482
 LC0  HN2A  H  HNH2  0   0.390    3.7692   4.4516   1.0611
 LC0  C13   C  CH2   0  -0.267   -4.3461  -1.2571   0.4653
 LC0  C14   C  CH2   0  -0.226    1.9511  -0.2302   0.0861
 LC0  N24   N  NH2   0  -0.826    3.3897   3.5188   1.0903

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
 LC0  C4   C6    aromatic  1.380  0.020  1.380
 LC0  C4   C15   aromatic  1.396  0.020  1.396
 LC0  C5   C7    aromatic  1.391  0.020  1.391
 LC0  C5   C15   aromatic  1.386  0.020  1.386
 LC0  C6   C16   aromatic  1.399  0.020  1.399
 LC0  C7   C16   aromatic  1.392  0.020  1.392
 LC0  C8   C17   aromatic  1.396  0.020  1.396
 LC0  C8   C18   aromatic  1.383  0.020  1.383
 LC0  C10  C20   aromatic  1.382  0.020  1.382
 LC0  C10  N25   aromatic  1.336  0.020  1.336
 LC0  C13  C15   single    1.495  0.020  1.495
 LC0  C13  O32   single    1.424  0.020  1.424
 LC0  C17  C14   single    1.502  0.020  1.502
 LC0  C17  N25   aromatic  1.318  0.020  1.318
 LC0  C20  C18   aromatic  1.411  0.020  1.411
 LC0  C20  O32   single    1.342  0.020  1.342
 LC0  C21  C11   aromatic  1.377  0.020  1.377
 LC0  C21  C19   single    1.454  0.020  1.454
 LC0  C21  N28   aromatic  1.350  0.020  1.350
 LC0  C22  C23   aromatic  1.428  0.020  1.428
 LC0  C22  N24   single    1.360  0.020  1.360
 LC0  C22  N26   aromatic  1.313  0.020  1.313
 LC0  C1   N29   single    1.443  0.020  1.443
 LC0  C2   O30   single    1.414  0.020  1.414
 LC0  C3   O31   single    1.418  0.020  1.418
 LC0  C9   C19   aromatic  1.409  0.020  1.409
 LC0  C9   N27   aromatic  1.319  0.020  1.319
 LC0  C11  N26   aromatic  1.338  0.020  1.338
 LC0  C12  C19   aromatic  1.382  0.020  1.382
 LC0  C12  N29   aromatic  1.342  0.020  1.342
 LC0  C14  O33   single    1.422  0.020  1.422
 LC0  C16  O30   single    1.345  0.020  1.345
 LC0  C18  O31   single    1.333  0.020  1.333
 LC0  C23  N28   aromatic  1.293  0.020  1.293
 LC0  C23  O33   single    1.335  0.020  1.335
 LC0  N27  N29   aromatic  1.329  0.020  1.329
 LC0  C4   H4    single    0.930  0.020  1.080
 LC0  C5   H5    single    0.930  0.020  1.080
 LC0  C6   H6    single    0.930  0.020  1.080
 LC0  C7   H7    single    0.930  0.020  1.080
 LC0  C8   H8    single    0.930  0.020  1.080
 LC0  C10  H10   single    0.930  0.020  1.080
 LC0  C13  H13   single    0.970  0.020  1.090
 LC0  C13  H13A  single    0.970  0.020  1.090
 LC0  C1   H1    single    0.970  0.020  1.090
 LC0  C1   H1A   single    0.970  0.020  1.090
 LC0  C1   H1B   single    0.970  0.020  1.090
 LC0  C2   H2    single    0.970  0.020  1.090
 LC0  C2   H2A   single    0.970  0.020  1.090
 LC0  C2   H2B   single    0.970  0.020  1.090
 LC0  C3   H3    single    0.970  0.020  1.090
 LC0  C3   H3A   single    0.970  0.020  1.090
 LC0  C3   H3B   single    0.970  0.020  1.090
 LC0  C9   H9    single    0.930  0.020  1.080
 LC0  C11  H11   single    0.930  0.020  1.080
 LC0  C12  H12   single    0.930  0.020  1.080
 LC0  C14  H14   single    0.970  0.020  1.090
 LC0  C14  H14A  single    0.970  0.020  1.090
 LC0  N24  HN24  single    0.890  0.020  1.040
 LC0  N24  HN2A  single    0.890  0.020  1.040

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
 LC0  H4    C4   C15   119.92  3.000
 LC0  H4    C4   C6    119.00  3.000
 LC0  C15   C4   C6    121.08  3.000
 LC0  H5    C5   C15   119.77  3.000
 LC0  H5    C5   C7    118.62  3.000
 LC0  C15   C5   C7    121.61  3.000
 LC0  H6    C6   C16   119.42  3.000
 LC0  H6    C6   C4    120.36  3.000
 LC0  C16   C6   C4    120.21  3.000
 LC0  H7    C7   C16   121.53  3.000
 LC0  H7    C7   C5    118.90  3.000
 LC0  C16   C7   C5    119.57  3.000
 LC0  H8    C8   C18   121.07  3.000
 LC0  H8    C8   C17   119.96  3.000
 LC0  C18   C8   C17   118.98  3.000
 LC0  H10   C10  N25   115.73  3.000
 LC0  H10   C10  C20   120.78  3.000
 LC0  N25   C10  C20   123.49  3.000
 LC0  C13   C15  C5    121.24  3.000
 LC0  C13   C15  C4    120.57  3.000
 LC0  C5    C15  C4    118.19  3.000
 LC0  N25   C17  C14   116.17  3.000
 LC0  N25   C17  C8    122.80  3.000
 LC0  C14   C17  C8    121.00  3.000
 LC0  O32   C20  C18   116.22  3.000
 LC0  O32   C20  C10   125.94  3.000
 LC0  C18   C20  C10   117.84  3.000
 LC0  N28   C21  C19   117.20  3.000
 LC0  N28   C21  C11   119.25  3.000
 LC0  C19   C21  C11   123.55  3.000
 LC0  N26   C22  N24   120.16  3.000
 LC0  N26   C22  C23   118.85  3.000
 LC0  N24   C22  C23   120.94  3.000
 LC0  H1B   C1   H1A   108.95  3.000
 LC0  H1B   C1   H1    108.96  3.000
 LC0  H1A   C1   H1    109.20  3.000
 LC0  H1B   C1   N29   109.00  3.000
 LC0  H1A   C1   N29   110.64  3.000
 LC0  H1    C1   N29   110.06  3.000
 LC0  H2B   C2   H2A   108.80  3.000
 LC0  H2B   C2   H2    108.79  3.000
 LC0  H2A   C2   H2    108.75  3.000
 LC0  H2B   C2   O30   112.02  3.000
 LC0  H2A   C2   O30   111.86  3.000
 LC0  H2    C2   O30   106.52  3.000
 LC0  H3B   C3   H3A   109.00  3.000
 LC0  H3B   C3   H3    109.07  3.000
 LC0  H3A   C3   H3    109.00  3.000
 LC0  H3B   C3   O31   111.68  3.000
 LC0  H3A   C3   O31   106.32  3.000
 LC0  H3    C3   O31   111.68  3.000
 LC0  H9    C9   N27   119.96  3.000
 LC0  H9    C9   C19   128.57  3.000
 LC0  N27   C9   C19   111.47  3.000
 LC0  H11   C11  N26   116.32  3.000
 LC0  H11   C11  C21   121.44  3.000
 LC0  N26   C11  C21   122.24  3.000
 LC0  H12   C12  N29   122.06  3.000
 LC0  H12   C12  C19   130.96  3.000
 LC0  N29   C12  C19   106.98  3.000
 LC0  O30   C16  C7    124.47  3.000
 LC0  O30   C16  C6    116.20  3.000
 LC0  C7    C16  C6    119.33  3.000
 LC0  O31   C18  C20   116.15  3.000
 LC0  O31   C18  C8    125.52  3.000
 LC0  C20   C18  C8    118.33  3.000
 LC0  C12   C19  C9    103.61  3.000
 LC0  C12   C19  C21   126.74  3.000
 LC0  C9    C19  C21   129.65  3.000
 LC0  O33   C23  N28   121.58  3.000
 LC0  O33   C23  C22   116.23  3.000
 LC0  N28   C23  C22   122.20  3.000
 LC0  C17   N25  C10   118.56  3.000
 LC0  C11   N26  C22   118.71  3.000
 LC0  N29   N27  C9    105.47  3.000
 LC0  C23   N28  C21   118.74  3.000
 LC0  N27   N29  C12   112.47  3.000
 LC0  N27   N29  C1    120.14  3.000
 LC0  C12   N29  C1    127.37  3.000
 LC0  C16   O30  C2    118.55  3.000
 LC0  C18   O31  C3    118.37  3.000
 LC0  C20   O32  C13   118.11  3.000
 LC0  C23   O33  C14   117.83  3.000
 LC0  H13A  C13  H13   107.59  3.000
 LC0  H13A  C13  O32   109.67  3.000
 LC0  H13   C13  O32   110.56  3.000
 LC0  H13A  C13  C15   110.90  3.000
 LC0  H13   C13  C15   110.33  3.000
 LC0  O32   C13  C15   107.81  3.000
 LC0  H14A  C14  H14   107.55  3.000
 LC0  H14A  C14  O33   109.87  3.000
 LC0  H14   C14  O33   111.11  3.000
 LC0  H14A  C14  C17   110.65  3.000
 LC0  H14   C14  C17   109.64  3.000
 LC0  O33   C14  C17   108.04  3.000
 LC0  HN2A  N24  HN24  114.09  3.000
 LC0  HN2A  N24  C22   115.89  3.000
 LC0  HN24  N24  C22   118.21  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
 LC0  CONST_01  C7   C16  C6   C4      0.00   0.0  0
 LC0  CONST_02  C7   C5   C15  C4      0.00   0.0  0
 LC0  CONST_03  C6   C16  C7   C5      0.00   0.0  0
 LC0  CONST_04  C6   C4   C15  C5      0.00   0.0  0
 LC0  CONST_05  C10  N25  C17  C8      0.00   0.0  0
 LC0  CONST_06  C10  C20  C18  C8      0.00   0.0  0
 LC0  CONST_07  C16  C6   C4   C15     0.00   0.0  0
 LC0  CONST_08  C16  C7   C5   C15     0.00   0.0  0
 LC0  CONST_09  C20  C18  C8   C17     0.00   0.0  0
 LC0  CONST_10  C20  C10  N25  C17     0.00   0.0  0
 LC0  CONST_11  C22  N26  C11  C21     0.00   0.0  0
 LC0  CONST_12  N27  C9   C19  C21   180.00   0.0  0
 LC0  CONST_13  N29  C12  C19  C21   180.00   0.0  0
 LC0  CONST_14  C22  C23  N28  C21     0.00   0.0  0
 LC0  CONST_15  C11  C21  C19  C9      0.00   0.0  0
 LC0  CONST_16  N28  C21  C19  C9    180.00   0.0  0
 LC0  CONST_17  N29  C12  C19  C9      0.00   0.0  0
 LC0  CONST_18  C12  N29  N27  C9      0.00   0.0  0
 LC0  CONST_19  C12  C19  C21  C11   180.00   0.0  0
 LC0  CONST_20  C23  N28  C21  C11     0.00   0.0  0
 LC0  CONST_21  C23  C22  N26  C11     0.00   0.0  0
 LC0  CONST_22  N28  C21  C19  C12     0.00   0.0  0
 LC0  CONST_23  N27  C9   C19  C12     0.00   0.0  0
 LC0  CONST_24  N25  C17  C8   C18     0.00   0.0  0
 LC0  CONST_25  N25  C10  C20  C18     0.00   0.0  0
 LC0  CONST_26  N26  C11  C21  C19   180.00   0.0  0
 LC0  CONST_27  C23  N28  C21  C19   180.00   0.0  0
 LC0  CONST_28  N29  N27  C9   C19     0.00   0.0  0
 LC0  CONST_29  N27  N29  C12  C19     0.00   0.0  0
 LC0  CONST_30  N28  C23  C22  N26     0.00   0.0  0
 LC0  CONST_31  N28  C21  C11  N26     0.00   0.0  0
 LC0  CONST_32  O30  C16  C6   C4    180.00   0.0  0
 LC0  CONST_33  O30  C16  C7   C5    180.00   0.0  0
 LC0  CONST_34  C13  C15  C4   C6    180.00   0.0  0
 LC0  CONST_35  C13  C15  C5   C7    180.00   0.0  0
 LC0  CONST_36  O32  C20  C18  C8    180.00   0.0  0
 LC0  CONST_37  O31  C18  C20  C10   180.00   0.0  0
 LC0  CONST_38  C14  C17  N25  C10   180.00   0.0  0
 LC0  CONST_39  O31  C18  C8   C17   180.00   0.0  0
 LC0  CONST_40  O33  C23  N28  C21   180.00   0.0  0
 LC0  CONST_41  C19  C12  N29  C1    180.00   0.0  0
 LC0  CONST_42  C9   N27  N29  C1    180.00   0.0  0
 LC0  CONST_43  N24  C22  N26  C11   180.00   0.0  0
 LC0  CONST_44  C18  C8   C17  C14   180.00   0.0  0
 LC0  CONST_45  N28  C23  C22  N24   180.00   0.0  0
 LC0  CONST_46  O32  C20  C10  N25   180.00   0.0  0
 LC0  CONST_47  O33  C23  C22  N26   180.00   0.0  0
 LC0  CONST_48  H5   C5   C15  C4    180.00   0.0  0
 LC0  CONST_49  H4   C4   C15  C5    180.00   0.0  0
 LC0  CONST_50  H7   C7   C16  C6    180.00   0.0  0
 LC0  CONST_51  H6   C6   C16  C7    180.00   0.0  0
 LC0  CONST_52  H10  C10  N25  C17   180.00   0.0  0
 LC0  CONST_53  H8   C8   C18  C20   180.00   0.0  0
 LC0  CONST_54  H9   C9   C19  C21     0.00   0.0  0
 LC0  CONST_55  H12  C12  C19  C21     0.00   0.0  0
 LC0  CONST_56  H11  C11  N26  C22   180.00   0.0  0
 LC0  Var_01    O32  C13  C15  C4     67.35  30.0  2
 LC0  Var_02    O33  C14  C17  C8     41.62  30.0  2
 LC0  Var_03    C18  C20  O32  C13   174.29  30.0  1
 LC0  Var_04    N28  C23  O33  C14    -3.92  30.0  2
 LC0  Var_05    H1   C1   N29  C12   128.33  30.0  2
 LC0  Var_06    H2   C2   O30  C16  -177.89  30.0  3
 LC0  Var_07    H3   C3   O31  C18    60.97  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
 LC0  plan-1  C21   0.020
 LC0  plan-1  C1    0.020
 LC0  plan-1  C9    0.020
 LC0  plan-1  C12   0.020
 LC0  plan-1  C19   0.020
 LC0  plan-1  N27   0.020
 LC0  plan-1  N29   0.020
 LC0  plan-1  H9    0.020
 LC0  plan-1  H12   0.020
 LC0  plan-2  C4    0.020
 LC0  plan-2  C5    0.020
 LC0  plan-2  C6    0.020
 LC0  plan-2  C7    0.020
 LC0  plan-2  C15   0.020
 LC0  plan-2  C16   0.020
 LC0  plan-2  O30   0.020
 LC0  plan-2  H4    0.020
 LC0  plan-2  H5    0.020
 LC0  plan-2  H6    0.020
 LC0  plan-2  H7    0.020
 LC0  plan-2  C13   0.020
 LC0  plan-3  C8    0.020
 LC0  plan-3  C10   0.020
 LC0  plan-3  C17   0.020
 LC0  plan-3  C20   0.020
 LC0  plan-3  C18   0.020
 LC0  plan-3  N25   0.020
 LC0  plan-3  O31   0.020
 LC0  plan-3  O32   0.020
 LC0  plan-3  H8    0.020
 LC0  plan-3  H10   0.020
 LC0  plan-3  C14   0.020
 LC0  plan-4  C21   0.020
 LC0  plan-4  C22   0.020
 LC0  plan-4  C11   0.020
 LC0  plan-4  C19   0.020
 LC0  plan-4  C23   0.020
 LC0  plan-4  N26   0.020
 LC0  plan-4  N28   0.020
 LC0  plan-4  O33   0.020
 LC0  plan-4  H11   0.020
 LC0  plan-4  N24   0.020
 LC0  plan-5  C22   0.020
 LC0  plan-5  HN24  0.020
 LC0  plan-5  HN2A  0.020
 LC0  plan-5  N24   0.020

