# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 10:55:12 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: [3-(5-amino-4-methylpyridin-2-yl)-1H-pyrazol-5-yl]{(3R)-3-[(2-chloro-6-methoxyphenyl)methyl]morpholin-4-yl}methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(Cl)c1C[C@@H]2COCCN2C(=O)c3[nH]nc(c3)c4cc(C)c(N)cn4
#
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
 O5D  O5D  '[3-(5-amino-4-methylpyridin-2-yl)-1H-pyrazol-5-yl]{(3R)-3-[(2-chloro-6-methoxyphenyl)methyl]morpholin-4-yl}methanone'  ligand  55  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O5D
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
 O5D  C3    C   CR5   0   0.269  -1.3294   0.0342  -0.0979
 O5D  C11   C   CR16  0  -0.165  -6.6468   0.2808  -1.6148
 O5D  C12   C   CR6   0   0.199  -7.6473   0.2779  -0.6377
 O5D  C13   C   CR6   0   0.150  -7.2387   0.2122   0.7057
 O5D  C14   C   CR16  0  -0.354  -5.8802   0.1561   0.9639
 O5D  C15   C   CH2   0  -0.376   0.6064  -2.0574   0.5083
 O5D  C16   C   CH2   0  -0.170   1.0308  -3.0270  -0.5852
 O5D  C18   C   CH2   0  -0.149   2.7756  -1.5986  -1.2516
 O5D  C19   C   CH1   0  -0.109   2.4084  -0.6171  -0.1437
 O5D  C20   C   CH2   0  -0.529   2.9640   0.7971  -0.3508
 O5D  C21   C   CR6   0   0.096   4.4380   0.8469  -0.0511
 O5D  C22   C   CR6   0   0.360   4.8760   0.8937   1.2873
 O5D  C23   C   CR16  0  -0.371   6.2300   0.9440   1.6019
 O5D  C24   C   CR16  0  -0.262   7.1706   0.9514   0.5813
 O5D  C25   C   CR16  0  -0.234   6.7799   0.9107  -0.7431
 O5D  C26   C   CR6   0  -0.118   5.4216   0.8607  -1.0322
 O5D  C28   C   CH3   0  -0.747  -8.2530   0.1957   1.8059
 O5D  C31   C   CH3   0  -0.438   4.2507   0.9283   3.5804
 O5D  C4    C   CR15  0  -0.485  -2.4953   0.1213  -0.8206
 O5D  C5    C   CR5   0   0.230  -3.5160   0.1041   0.1489
 O5D  C6    C   C     0   0.520   0.0736   0.0765  -0.5760
 O5D  C9    C   CR6   0   0.154  -4.9603   0.1621  -0.0827
 O5D  N1    N   N     0  -0.280  -3.0021   0.0299   1.3697
 O5D  N10   N   N     0  -0.425  -5.3538   0.2226  -1.3508
 O5D  N2    N   NR15  0  -0.471  -1.6941  -0.0207   1.2002
 O5D  N7    N   NT    0  -0.485   0.9627  -0.6961   0.1025
 O5D  O17   O   O2    0  -0.481   2.3993  -2.9127  -0.8969
 O5D  O30   O   O2    0  -0.467   3.9004   0.8858   2.2110
 O5D  O8    O   O     0  -0.452   0.3586   0.8252  -1.4945
 O5D  CL27  CL  CL    0  -0.127   4.9734   0.8112  -2.7126
 O5D  H34   H   HCR6  0   0.256  -6.9273   0.3317  -2.6633
 O5D  H35   H   HCR6  0   0.256  -5.5320   0.1031   1.9879
 O5D  H36   H   HCH2  0   0.284  -0.4635  -2.1617   0.6736
 O5D  H37   H   HCH2  0   0.265   1.1098  -2.2875   1.4497
 O5D  H39   H   HCH2  0   0.249   0.8578  -4.0527  -0.2554
 O5D  H38   H   HCH2  0   0.209   0.4088  -2.8527  -1.4753
 O5D  H40   H   HCH2  0   0.213   2.3034  -1.2892  -2.1942
 O5D  H41   H   HCH2  0   0.241   3.8552  -1.6160  -1.4062
 O5D  H42   H   HCH1  0   0.274   2.8524  -0.9996   0.7809
 O5D  H44   H   HCH2  0   0.266   2.7749   1.1495  -1.3606
 O5D  H43   H   HCH2  0   0.272   2.4430   1.4819   0.3201
 O5D  H45   H   HCR6  0   0.286   6.5666   0.9800   2.6288
 O5D  H46   H   HCR6  0   0.269   8.2235   0.9901   0.8269
 O5D  H47   H   HCR6  0   0.275   7.5106   0.9182  -1.5391
 O5D  H50   H   HCH3  0   0.253  -8.9501  -0.6363   1.6868
 O5D  H49   H   HCH3  0   0.261  -7.7794   0.1021   2.7810
 O5D  H48   H   HCH3  0   0.251  -8.8485   1.1122   1.8157
 O5D  H55   H   HCH3  0   0.262   3.3166   0.9107   4.1358
 O5D  H53   H   HCH3  0   0.232   4.8520   0.0644   3.8741
 O5D  H54   H   HCH3  0   0.232   4.7942   1.8420   3.8334
 O5D  H33   H   HCR5  0   0.270  -2.5980   0.1734  -1.8909
 O5D  H32   H   HNR5  0   0.426  -1.0871  -0.0343   2.0061
 O5D  H51   H   HNH2  0   0.384  -9.1823   0.5675  -1.9281
 O5D  H52   H   HNH2  0   0.387  -9.6146   0.6963  -0.3253
 O5D  N29   N   NH2   0  -0.857  -8.9776   0.2787  -0.9845

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
 O5D  N29  C12   single    1.375  0.020  1.375
 O5D  C12  C11   aromatic  1.398  0.020  1.398
 O5D  C12  C13   aromatic  1.406  0.020  1.406
 O5D  C11  N10   aromatic  1.321  0.020  1.321
 O5D  C28  C13   single    1.497  0.020  1.497
 O5D  C13  C14   aromatic  1.384  0.020  1.384
 O5D  N10  C9    aromatic  1.329  0.020  1.329
 O5D  C14  C9    aromatic  1.393  0.020  1.393
 O5D  C9   C5    single    1.464  0.020  1.464
 O5D  C5   C4    aromatic  1.408  0.020  1.408
 O5D  C5   N1    aromatic  1.327  0.020  1.327
 O5D  C4   C3    aromatic  1.375  0.020  1.375
 O5D  N1   N2    aromatic  1.320  0.020  1.320
 O5D  C3   N2    aromatic  1.349  0.020  1.349
 O5D  C3   C6    single    1.483  0.020  1.483
 O5D  O8   C6    double    1.219  0.020  1.219
 O5D  C6   N7    single    1.359  0.020  1.359
 O5D  C31  O30   single    1.414  0.020  1.414
 O5D  C23  C24   aromatic  1.388  0.020  1.388
 O5D  C23  C22   aromatic  1.391  0.020  1.391
 O5D  C24  C25   aromatic  1.381  0.020  1.381
 O5D  O30  C22   single    1.344  0.020  1.344
 O5D  C22  C21   aromatic  1.409  0.020  1.409
 O5D  C25  C26   aromatic  1.390  0.020  1.390
 O5D  N7   C15   single    1.464  0.020  1.464
 O5D  N7   C19   single    1.469  0.020  1.469
 O5D  C21  C26   aromatic  1.389  0.020  1.389
 O5D  C21  C20   single    1.505  0.020  1.505
 O5D  C26  CL27  single    1.740  0.020  1.740
 O5D  C15  C16   single    1.522  0.020  1.522
 O5D  C19  C18   single    1.525  0.020  1.525
 O5D  C19  C20   single    1.533  0.020  1.533
 O5D  C18  O17   single    1.412  0.020  1.412
 O5D  C16  O17   single    1.408  0.020  1.408
 O5D  C11  H34   single    0.930  0.020  1.080
 O5D  C14  H35   single    0.930  0.020  1.080
 O5D  C15  H36   single    0.970  0.020  1.090
 O5D  C15  H37   single    0.970  0.020  1.090
 O5D  C16  H39   single    0.970  0.020  1.090
 O5D  C16  H38   single    0.970  0.020  1.090
 O5D  C18  H40   single    0.970  0.020  1.090
 O5D  C18  H41   single    0.970  0.020  1.090
 O5D  C19  H42   single    0.970  0.020  1.090
 O5D  C20  H44   single    0.970  0.020  1.090
 O5D  C20  H43   single    0.970  0.020  1.090
 O5D  C23  H45   single    0.930  0.020  1.080
 O5D  C24  H46   single    0.930  0.020  1.080
 O5D  C25  H47   single    0.930  0.020  1.080
 O5D  C28  H50   single    0.970  0.020  1.090
 O5D  C28  H49   single    0.970  0.020  1.090
 O5D  C28  H48   single    0.970  0.020  1.090
 O5D  C31  H55   single    0.970  0.020  1.090
 O5D  C31  H53   single    0.970  0.020  1.090
 O5D  C31  H54   single    0.970  0.020  1.090
 O5D  C4   H33   single    0.930  0.020  1.080
 O5D  N2   H32   single    0.860  0.020  1.020
 O5D  N29  H51   single    0.890  0.020  1.040
 O5D  N29  H52   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
 O5D  N2    C3   C6   124.54  3.000
 O5D  C6    C3   C4   129.14  3.000
 O5D  N2    C3   C4   106.21  3.000
 O5D  H34   C11  N10  116.59  3.000
 O5D  H34   C11  C12  119.31  3.000
 O5D  N10   C11  C12  124.10  3.000
 O5D  N29   C12  C13  121.49  3.000
 O5D  C13   C12  C11  117.38  3.000
 O5D  N29   C12  C11  121.07  3.000
 O5D  C28   C13  C14  121.85  3.000
 O5D  C14   C13  C12  117.74  3.000
 O5D  C28   C13  C12  120.40  3.000
 O5D  H35   C14  C9   119.88  3.000
 O5D  H35   C14  C13  119.61  3.000
 O5D  C9    C14  C13  120.51  3.000
 O5D  H37   C15  H36  107.59  3.000
 O5D  H37   C15  N7   108.82  3.000
 O5D  H36   C15  N7   111.76  3.000
 O5D  H37   C15  C16  110.89  3.000
 O5D  H36   C15  C16  108.81  3.000
 O5D  N7    C15  C16  108.98  3.000
 O5D  H38   C16  H39  107.69  3.000
 O5D  H38   C16  O17  110.95  3.000
 O5D  H39   C16  O17  107.29  3.000
 O5D  H38   C16  C15  108.84  3.000
 O5D  H39   C16  C15  109.72  3.000
 O5D  O17   C16  C15  112.23  3.000
 O5D  H41   C18  H40  107.95  3.000
 O5D  H41   C18  O17  106.53  3.000
 O5D  H40   C18  O17  111.29  3.000
 O5D  H41   C18  C19  110.58  3.000
 O5D  H40   C18  C19  109.79  3.000
 O5D  O17   C18  C19  110.63  3.000
 O5D  H42   C19  N7   103.82  3.000
 O5D  H42   C19  C20  106.82  3.000
 O5D  N7    C19  C20  115.39  3.000
 O5D  H42   C19  C18  106.93  3.000
 O5D  C20   C19  C18  114.09  3.000
 O5D  N7    C19  C18  108.92  3.000
 O5D  H43   C20  H44  106.55  3.000
 O5D  H43   C20  C21  108.93  3.000
 O5D  H44   C20  C21  110.18  3.000
 O5D  H43   C20  C19  108.84  3.000
 O5D  H44   C20  C19  111.21  3.000
 O5D  C21   C20  C19  111.00  3.000
 O5D  C26   C21  C22  116.77  3.000
 O5D  C26   C21  C20  123.58  3.000
 O5D  C22   C21  C20  119.65  3.000
 O5D  O30   C22  C23  123.47  3.000
 O5D  O30   C22  C21  115.28  3.000
 O5D  C23   C22  C21  121.24  3.000
 O5D  H45   C23  C24  119.16  3.000
 O5D  H45   C23  C22  121.27  3.000
 O5D  C24   C23  C22  119.57  3.000
 O5D  H46   C24  C25  119.61  3.000
 O5D  H46   C24  C23  119.52  3.000
 O5D  C25   C24  C23  120.87  3.000
 O5D  H47   C25  C26  120.53  3.000
 O5D  H47   C25  C24  120.98  3.000
 O5D  C26   C25  C24  118.49  3.000
 O5D  CL27  C26  C25  116.98  3.000
 O5D  CL27  C26  C21  119.96  3.000
 O5D  C25   C26  C21  123.05  3.000
 O5D  H48   C28  H49  107.54  3.000
 O5D  H48   C28  H50  106.98  3.000
 O5D  H49   C28  H50  108.06  3.000
 O5D  H48   C28  C13  111.51  3.000
 O5D  H49   C28  C13  111.39  3.000
 O5D  H50   C28  C13  111.15  3.000
 O5D  H54   C31  H53  108.97  3.000
 O5D  H54   C31  H55  108.82  3.000
 O5D  H53   C31  H55  108.83  3.000
 O5D  H54   C31  O30  111.87  3.000
 O5D  H53   C31  O30  111.89  3.000
 O5D  H55   C31  O30  106.35  3.000
 O5D  H33   C4   C5   128.03  3.000
 O5D  H33   C4   C3   127.36  3.000
 O5D  C5    C4   C3   104.60  3.000
 O5D  N1    C5   C9   122.00  3.000
 O5D  N1    C5   C4   110.70  3.000
 O5D  C9    C5   C4   127.29  3.000
 O5D  O8    C6   N7   124.92  3.000
 O5D  N7    C6   C3   116.21  3.000
 O5D  O8    C6   C3   118.80  3.000
 O5D  N10   C9   C5   116.41  3.000
 O5D  C5    C9   C14  122.16  3.000
 O5D  N10   C9   C14  121.42  3.000
 O5D  N2    N1   C5   105.54  3.000
 O5D  C9    N10  C11  118.85  3.000
 O5D  H32   N2   N1   119.61  3.000
 O5D  H32   N2   C3   127.32  3.000
 O5D  N1    N2   C3   112.94  3.000
 O5D  C6    N7   C19  121.98  3.000
 O5D  C19   N7   C15  109.63  3.000
 O5D  C6    N7   C15  120.50  3.000
 O5D  C18   O17  C16  112.96  3.000
 O5D  C31   O30  C22  119.06  3.000
 O5D  H52   N29  H51  111.44  3.000
 O5D  H52   N29  C12  116.55  3.000
 O5D  H51   N29  C12  115.65  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
 O5D  CONST_01  C9    C5   C4   C3    180.00   0.0  0
 O5D  CONST_02  N1    C5   C4   C3      0.00   0.0  0
 O5D  CONST_03  C5    N1   N2   C3      0.00   0.0  0
 O5D  CONST_04  C14   C13  C12  C11     0.00   0.0  0
 O5D  CONST_05  C14   C9   N10  C11     0.00   0.0  0
 O5D  CONST_06  C5    C9   N10  C11   180.00   0.0  0
 O5D  CONST_07  C9    N10  C11  C12     0.00   0.0  0
 O5D  CONST_08  C9    C14  C13  C12     0.00   0.0  0
 O5D  CONST_09  N10   C11  C12  C13     0.00   0.0  0
 O5D  CONST_10  N10   C9   C14  C13     0.00   0.0  0
 O5D  CONST_11  C5    C9   C14  C13   180.00   0.0  0
 O5D  CONST_12  C4    C5   C9   C14   180.00   0.0  0
 O5D  CONST_13  N1    C5   C9   C14     0.00   0.0  0
 O5D  CONST_14  C24   C23  C22  C21     0.00   0.0  0
 O5D  CONST_15  C24   C25  C26  C21     0.00   0.0  0
 O5D  CONST_16  C25   C24  C23  C22     0.00   0.0  0
 O5D  CONST_17  C25   C26  C21  C22     0.00   0.0  0
 O5D  CONST_18  C26   C25  C24  C23     0.00   0.0  0
 O5D  CONST_19  C26   C21  C22  C23     0.00   0.0  0
 O5D  CONST_20  N10   C9   C5   C4      0.00   0.0  0
 O5D  CONST_21  N2    N1   C5   C4      0.00   0.0  0
 O5D  CONST_22  N1    N2   C3   C4      0.00   0.0  0
 O5D  CONST_23  N2    C3   C4   C5      0.00   0.0  0
 O5D  CONST_24  N2    N1   C5   C9    180.00   0.0  0
 O5D  CONST_25  N10   C9   C5   N1    180.00   0.0  0
 O5D  CONST_26  C28   C13  C12  C11   180.00   0.0  0
 O5D  CONST_27  N29   C12  C13  C14   180.00   0.0  0
 O5D  CONST_28  C23   C22  C21  C20   180.00   0.0  0
 O5D  CONST_29  C25   C26  C21  C20   180.00   0.0  0
 O5D  CONST_30  CL27  C26  C21  C22   180.00   0.0  0
 O5D  CONST_31  O30   C22  C23  C24   180.00   0.0  0
 O5D  CONST_32  CL27  C26  C25  C24   180.00   0.0  0
 O5D  CONST_33  O30   C22  C21  C26   180.00   0.0  0
 O5D  CONST_34  C9    C14  C13  C28   180.00   0.0  0
 O5D  CONST_35  C6    C3   C4   C5    180.00   0.0  0
 O5D  CONST_36  N1    N2   C3   C6    180.00   0.0  0
 O5D  CONST_37  N29   C12  C11  N10   180.00   0.0  0
 O5D  CONST_39  C19   N7   C6   C3    180.00   0.0  0
 O5D  CONST_40  H35   C14  C13  C12   180.00   0.0  0
 O5D  CONST_41  H34   C11  C12  C13   180.00   0.0  0
 O5D  CONST_42  H45   C23  C22  C21   180.00   0.0  0
 O5D  CONST_43  H47   C25  C26  C21   180.00   0.0  0
 O5D  CONST_44  H46   C24  C23  C22   180.00   0.0  0
 O5D  CONST_45  H32   N2   C3   C4    180.00   0.0  0
 O5D  CONST_46  H33   C4   C5   C9      0.00   0.0  0
 O5D  CONST_48  O8    C6   N7   C19     0.00   0.0  0
 O5D  Var_01    C19   N7   C15  C16   -58.15  30.0  1
 O5D  Var_02    C19   C18  O17  C16    56.15  30.0  1
 O5D  Var_03    O17   C16  C15  N7     55.46  30.0  1
 O5D  Var_04    C22   C21  C20  C19   -78.45  30.0  2
 O5D  Var_05    N7    C6   C3   C4   -145.65  30.0  2
 O5D  Var_06    H39   C16  O17  C18  -175.87  30.0  1
 O5D  Var_07    H50   C28  C13  C12    57.11  30.0  2
 O5D  Var_08    H55   C31  O30  C22  -179.87  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
 O5D  chir_01  C19  N7  C18  C20  negativ

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
 O5D  plan-1  C3    0.020
 O5D  plan-1  C4    0.020
 O5D  plan-1  C5    0.020
 O5D  plan-1  C6    0.020
 O5D  plan-1  C9    0.020
 O5D  plan-1  N1    0.020
 O5D  plan-1  N2    0.020
 O5D  plan-1  H33   0.020
 O5D  plan-1  H32   0.020
 O5D  plan-2  C11   0.020
 O5D  plan-2  C12   0.020
 O5D  plan-2  C13   0.020
 O5D  plan-2  C14   0.020
 O5D  plan-2  C28   0.020
 O5D  plan-2  C5    0.020
 O5D  plan-2  C9    0.020
 O5D  plan-2  N10   0.020
 O5D  plan-2  H34   0.020
 O5D  plan-2  H35   0.020
 O5D  plan-2  N29   0.020
 O5D  plan-3  C20   0.020
 O5D  plan-3  C21   0.020
 O5D  plan-3  C22   0.020
 O5D  plan-3  C23   0.020
 O5D  plan-3  C24   0.020
 O5D  plan-3  C25   0.020
 O5D  plan-3  C26   0.020
 O5D  plan-3  O30   0.020
 O5D  plan-3  CL27  0.020
 O5D  plan-3  H45   0.020
 O5D  plan-3  H46   0.020
 O5D  plan-3  H47   0.020
 O5D  plan-4  C3    0.020
 O5D  plan-4  C15   0.020
 O5D  plan-4  C19   0.020
 O5D  plan-4  C6    0.020
 O5D  plan-4  N7    0.020
 O5D  plan-4  O8    0.020
 O5D  plan-5  C12   0.020
 O5D  plan-5  H51   0.020
 O5D  plan-5  H52   0.020
 O5D  plan-5  N29   0.020

