# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 10:25:00 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: methyl (3S)-3-[2-(1,3-benzodioxol-5-ylmethylamino)-2-oxo-ethyl]-4-(2-imidazol-1-ylpyrimidin-4-yl)piperazine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N1CCN([C@H](C1)CC(=O)NCc2ccc3OCOc3c2)c4ccnc(n4)n5ccnc5
#
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
 1PM  1PM  'methyl (3S)-3-[2-(1,3-benzodioxol-5-ylmethylamino)-2-oxo-ethyl]-4-(2-imidazol-1-ylpyrimidin-4-yl)piperazine-1-carboxylate'  ligand  60  35  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1PM
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
 1PM  N3    N  NR5   0  -0.523  -1.9610  -3.7408   0.5861
 1PM  C4    C  CR15  0  -0.095  -2.2116  -5.0788   0.7835
 1PM  C5    C  CR15  0  -0.213  -1.3342  -5.4682   1.7449
 1PM  NFE   N  N     0  -0.447  -0.5497  -4.4115   2.1375
 1PM  C2    C  CR15  0   0.104  -0.9469  -3.3947   1.4305
 1PM  C11   C  CR6   0   0.637  -2.6086  -2.8873  -0.3168
 1PM  N12   N  N     0  -0.516  -2.2725  -1.6223  -0.2250
 1PM  C13   C  CR6   0   0.606  -2.8421  -0.7595  -1.0699
 1PM  C14   C  CR16  0  -0.429  -3.7611  -1.2405  -2.0305
 1PM  C15   C  CR16  0  -0.021  -4.0296  -2.5855  -2.0034
 1PM  N16   N  N     0  -0.469  -3.4619  -3.4439  -1.1487
 1PM  N21   N  NT    0  -0.505  -2.5015   0.5414  -0.9565
 1PM  C22   C  CH2   0  -0.292  -2.9629   1.4870  -1.9646
 1PM  C23   C  CH2   0  -0.368  -2.6296   2.9106  -1.5457
 1PM  N24   N  NT    0  -0.475  -2.7759   3.0292  -0.1128
 1PM  C25   C  CH2   0  -0.309  -1.7159   2.3411   0.5815
 1PM  C26   C  CH1   0  -0.121  -1.4746   0.9194   0.0062
 1PM  C27   C  C     0   0.759  -3.9485   3.3003   0.5107
 1PM  O28   O  O     0  -0.516  -4.1316   3.2140   1.7077
 1PM  O29   O  O2    0  -0.475  -4.8811   3.7099  -0.3474
 1PM  C30   C  CH3   0  -0.413  -6.1425   4.0805   0.2006
 1PM  C31   C  CH2   0  -0.581  -0.0675   0.7582  -0.5825
 1PM  C32   C  C     0   0.565   0.9779   0.7671   0.5136
 1PM  O33   O  O     0  -0.496   0.9360  -0.0411   1.4335
 1PM  N34   N  NH1   0  -0.617   1.9195   1.7177   0.4075
 1PM  C36   C  CH2   0  -0.396   3.0363   1.8657   1.3177
 1PM  C41   C  CR6   0   0.108   4.3024   1.2372   0.7926
 1PM  C42   C  CR16  0  -0.323   5.3662   2.0308   0.3922
 1PM  C43   C  CR16  0  -0.333   6.5530   1.4823  -0.1147
 1PM  C44   C  CR56  0   0.291   6.6126   0.1157  -0.2014
 1PM  C45   C  CR56  0   0.316   5.5519  -0.6869   0.1960
 1PM  C46   C  CR16  0  -0.382   4.3887  -0.1634   0.6958
 1PM  O47   O  O     0  -0.486   7.6153  -0.6663  -0.6713
 1PM  C48   C  CH2   0   0.068   7.2500  -2.0042  -0.3608
 1PM  O49   O  O     0  -0.486   5.8718  -1.9873  -0.0150
 1PM  H4    H  HCR5  0   0.297  -2.9716  -5.6093   0.2385
 1PM  H5    H  HCR5  0   0.259  -1.2257  -6.4498   2.1792
 1PM  H2    H  HCR5  0   0.294  -0.5444  -2.3935   1.4640
 1PM  H14   H  HCR6  0   0.288  -4.2425  -0.6087  -2.7596
 1PM  H15   H  HCR6  0   0.278  -4.7348  -3.0087  -2.7089
 1PM  H22   H  HCH2  0   0.261  -2.5275   1.2696  -2.9449
 1PM  H23   H  HCH2  0   0.267  -1.5972   3.1661  -1.7946
 1PM  H25   H  HCH2  0   0.256  -0.8011   2.9352   0.4922
 1PM  H301  H  HCH3  0   0.249  -6.7486   4.3975  -0.6433
 1PM  H302  H  HCH3  0   0.236  -6.6290   3.2399   0.6947
 1PM  H303  H  HCH3  0   0.236  -6.0489   4.9075   0.9040
 1PM  H311  H  HCH2  0   0.287   0.0004  -0.2133  -1.0771
 1PM  H312  H  HCH2  0   0.260   0.1295   1.5191  -1.3414
 1PM  H35   H  HNH1  0   0.403   1.9071   2.3147  -0.4035
 1PM  H361  H  HCH2  0   0.273   3.1937   2.9305   1.4907
 1PM  H362  H  HCH2  0   0.267   2.7578   1.4252   2.2741
 1PM  H42   H  HCR6  0   0.256   5.2855   3.1076   0.4746
 1PM  H43   H  HCR6  0   0.272   7.3756   2.1117  -0.4259
 1PM  H46   H  HCR6  0   0.269   3.5689  -0.7986   1.0070
 1PM  H481  H  HCH2  0   0.246   7.4048  -2.6409  -1.2316
 1PM  H482  H  HCH2  0   0.233   7.8422  -2.3636   0.4878
 1PM  H221  H  HCH2  0   0.261  -4.0467   1.3993  -2.0600
 1PM  H231  H  HCH2  0   0.297  -3.2594   3.6126  -2.0840
 1PM  H24   H  HCH2  0   0.284  -1.9505   2.2782   1.6398
 1PM  H251  H  HCH1  0   0.302  -1.5579   0.2139   0.8288

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
 1PM  N3   C4    aromatic  1.375  0.020  1.375
 1PM  N3   C2    aromatic  1.364  0.020  1.364
 1PM  N3   C11   single    1.401  0.020  1.401
 1PM  C4   C5    aromatic  1.359  0.020  1.359
 1PM  C4   H4    single    0.930  0.020  1.080
 1PM  C5   NFE   aromatic  1.373  0.020  1.373
 1PM  C5   H5    single    0.930  0.020  1.080
 1PM  NFE  C2    aromatic  1.301  0.020  1.301
 1PM  C2   H2    single    0.930  0.020  1.080
 1PM  C11  N12   aromatic  1.312  0.020  1.312
 1PM  C11  N16   aromatic  1.315  0.020  1.315
 1PM  N12  C13   aromatic  1.335  0.020  1.335
 1PM  C13  C14   aromatic  1.414  0.020  1.414
 1PM  C13  N21   single    1.350  0.020  1.350
 1PM  C14  C15   aromatic  1.372  0.020  1.372
 1PM  C14  H14   single    0.930  0.020  1.080
 1PM  C15  N16   aromatic  1.338  0.020  1.338
 1PM  C15  H15   single    0.930  0.020  1.080
 1PM  N21  C22   single    1.457  0.020  1.457
 1PM  N21  C26   single    1.458  0.020  1.458
 1PM  C22  C23   single    1.521  0.020  1.521
 1PM  C22  H22   single    0.970  0.020  1.090
 1PM  C23  N24   single    1.445  0.020  1.445
 1PM  C23  H23   single    0.970  0.020  1.090
 1PM  N24  C25   single    1.442  0.020  1.442
 1PM  N24  C27   single    1.355  0.020  1.355
 1PM  C25  C26   single    1.553  0.020  1.553
 1PM  C25  H25   single    0.970  0.020  1.090
 1PM  C26  C31   single    1.534  0.020  1.534
 1PM  C27  O28   double    1.214  0.020  1.214
 1PM  C27  O29   single    1.332  0.020  1.332
 1PM  O29  C30   single    1.424  0.020  1.424
 1PM  C30  H301  single    0.970  0.020  1.090
 1PM  C30  H302  single    0.970  0.020  1.090
 1PM  C30  H303  single    0.970  0.020  1.090
 1PM  C31  C32   single    1.515  0.020  1.515
 1PM  C31  H311  single    0.970  0.020  1.090
 1PM  C31  H312  single    0.970  0.020  1.090
 1PM  C32  O33   double    1.225  0.020  1.225
 1PM  C32  N34   single    1.342  0.020  1.342
 1PM  N34  C36   single    1.448  0.020  1.448
 1PM  N34  H35   single    0.860  0.020  1.020
 1PM  C36  C41   single    1.508  0.020  1.508
 1PM  C36  H361  single    0.970  0.020  1.090
 1PM  C36  H362  single    0.970  0.020  1.090
 1PM  C41  C42   aromatic  1.386  0.020  1.386
 1PM  C41  C46   aromatic  1.407  0.020  1.407
 1PM  C42  C43   aromatic  1.402  0.020  1.402
 1PM  C42  H42   single    0.930  0.020  1.080
 1PM  C43  C44   aromatic  1.371  0.020  1.371
 1PM  C43  H43   single    0.930  0.020  1.080
 1PM  C44  C45   aromatic  1.388  0.020  1.388
 1PM  C44  O47   single    1.356  0.020  1.356
 1PM  C45  C46   aromatic  1.370  0.020  1.370
 1PM  C45  O49   single    1.356  0.020  1.356
 1PM  C46  H46   single    0.930  0.020  1.080
 1PM  O47  C48   single    1.421  0.020  1.421
 1PM  C48  O49   single    1.421  0.020  1.421
 1PM  C48  H481  single    0.970  0.020  1.090
 1PM  C48  H482  single    0.970  0.020  1.090
 1PM  C22  H221  single    0.970  0.020  1.090
 1PM  C23  H231  single    0.970  0.020  1.090
 1PM  C25  H24   single    0.970  0.020  1.090
 1PM  C26  H251  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
 1PM  C11   N3   C2    126.01  3.000
 1PM  C11   N3   C4    126.93  3.000
 1PM  C2    N3   C4    107.06  3.000
 1PM  H4    C4   C5    132.35  3.000
 1PM  H4    C4   N3    122.41  3.000
 1PM  C5    C4   N3    105.23  3.000
 1PM  H5    C5   NFE   121.84  3.000
 1PM  H5    C5   C4    127.64  3.000
 1PM  NFE   C5   C4    110.52  3.000
 1PM  C2    NFE  C5    105.77  3.000
 1PM  H2    C2   NFE   126.46  3.000
 1PM  H2    C2   N3    122.12  3.000
 1PM  NFE   C2   N3    111.42  3.000
 1PM  N16   C11  N12   128.21  3.000
 1PM  N16   C11  N3    116.72  3.000
 1PM  N12   C11  N3    115.08  3.000
 1PM  C13   N12  C11   118.00  3.000
 1PM  N21   C13  C14   123.31  3.000
 1PM  N21   C13  N12   117.52  3.000
 1PM  C14   C13  N12   119.17  3.000
 1PM  H14   C14  C15   120.03  3.000
 1PM  H14   C14  C13   123.39  3.000
 1PM  C15   C14  C13   116.58  3.000
 1PM  H15   C15  N16   116.21  3.000
 1PM  H15   C15  C14   119.83  3.000
 1PM  N16   C15  C14   123.96  3.000
 1PM  C15   N16  C11   114.07  3.000
 1PM  C26   N21  C22   120.78  3.000
 1PM  C26   N21  C13   118.90  3.000
 1PM  C22   N21  C13   119.18  3.000
 1PM  H221  C22  H22   107.50  3.000
 1PM  H221  C22  C23   108.47  3.000
 1PM  H22   C22  C23   110.20  3.000
 1PM  H221  C22  N21   108.83  3.000
 1PM  H22   C22  N21   111.40  3.000
 1PM  C23   C22  N21   110.33  3.000
 1PM  H231  C23  H23   106.50  3.000
 1PM  H231  C23  N24   112.32  3.000
 1PM  H23   C23  N24   107.61  3.000
 1PM  H231  C23  C22   109.96  3.000
 1PM  H23   C23  C22   111.30  3.000
 1PM  N24   C23  C22   109.13  3.000
 1PM  C27   N24  C25   120.65  3.000
 1PM  C27   N24  C23   124.07  3.000
 1PM  C25   N24  C23   111.33  3.000
 1PM  H24   C25  H25   106.95  3.000
 1PM  H24   C25  C26   109.98  3.000
 1PM  H25   C25  C26   109.70  3.000
 1PM  H24   C25  N24   109.76  3.000
 1PM  H25   C25  N24   108.42  3.000
 1PM  C26   C25  N24   111.89  3.000
 1PM  H251  C26  C31   107.01  3.000
 1PM  H251  C26  C25   107.58  3.000
 1PM  C31   C26  C25   112.40  3.000
 1PM  H251  C26  N21   106.12  3.000
 1PM  C31   C26  N21   111.44  3.000
 1PM  C25   C26  N21   111.88  3.000
 1PM  O29   C27  O28   123.47  3.000
 1PM  O29   C27  N24   111.77  3.000
 1PM  O28   C27  N24   124.74  3.000
 1PM  C30   O29  C27   116.89  3.000
 1PM  H303  C30  H302  109.34  3.000
 1PM  H303  C30  H301  109.15  3.000
 1PM  H302  C30  H301  109.17  3.000
 1PM  H303  C30  O29   111.70  3.000
 1PM  H302  C30  O29   111.66  3.000
 1PM  H301  C30  O29   105.73  3.000
 1PM  H312  C31  H311  107.08  3.000
 1PM  H312  C31  C32   111.97  3.000
 1PM  H311  C31  C32   106.86  3.000
 1PM  H312  C31  C26   111.03  3.000
 1PM  H311  C31  C26   108.92  3.000
 1PM  C32   C31  C26   110.78  3.000
 1PM  N34   C32  O33   123.40  3.000
 1PM  N34   C32  C31   115.54  3.000
 1PM  O33   C32  C31   121.06  3.000
 1PM  H35   N34  C36   117.06  3.000
 1PM  H35   N34  C32   118.35  3.000
 1PM  C36   N34  C32   124.31  3.000
 1PM  H362  C36  H361  107.02  3.000
 1PM  H362  C36  C41   110.60  3.000
 1PM  H361  C36  C41   109.95  3.000
 1PM  H362  C36  N34   108.26  3.000
 1PM  H361  C36  N34   108.11  3.000
 1PM  C41   C36  N34   112.71  3.000
 1PM  C46   C41  C42   120.21  3.000
 1PM  C46   C41  C36   119.37  3.000
 1PM  C42   C41  C36   120.42  3.000
 1PM  H42   C42  C43   118.65  3.000
 1PM  H42   C42  C41   119.34  3.000
 1PM  C43   C42  C41   122.00  3.000
 1PM  H43   C43  C44   121.94  3.000
 1PM  H43   C43  C42   121.34  3.000
 1PM  C44   C43  C42   116.72  3.000
 1PM  O47   C44  C45   109.32  3.000
 1PM  O47   C44  C43   128.99  3.000
 1PM  C45   C44  C43   121.68  3.000
 1PM  O49   C45  C46   128.58  3.000
 1PM  O49   C45  C44   109.25  3.000
 1PM  C46   C45  C44   122.16  3.000
 1PM  H46   C46  C45   121.57  3.000
 1PM  H46   C46  C41   121.20  3.000
 1PM  C45   C46  C41   117.23  3.000
 1PM  C48   O47  C44   106.09  3.000
 1PM  H482  C48  H481  110.52  3.000
 1PM  H482  C48  O49   109.86  3.000
 1PM  H481  C48  O49   109.83  3.000
 1PM  H482  C48  O47   109.82  3.000
 1PM  H481  C48  O47   109.81  3.000
 1PM  O49   C48  O47   106.93  3.000
 1PM  C48   O49  C45   106.15  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
 1PM  CONST_01  NFE   C5   C4   N3     0.00   0.0  0
 1PM  CONST_02  C5    NFE  C2   N3     0.00   0.0  0
 1PM  CONST_03  C13   N12  C11  N3   180.00   0.0  0
 1PM  CONST_04  C15   N16  C11  N3   180.00   0.0  0
 1PM  CONST_05  NFE   C2   N3   C4     0.00   0.0  0
 1PM  CONST_06  N12   C11  N3   C4   180.00   0.0  0
 1PM  CONST_07  N16   C11  N3   C4     0.00   0.0  0
 1PM  CONST_08  C2    NFE  C5   C4     0.00   0.0  0
 1PM  CONST_09  C2    N3   C4   C5     0.00   0.0  0
 1PM  CONST_10  C11   N3   C4   C5   180.00   0.0  0
 1PM  CONST_11  C11   N3   C2   NFE  180.00   0.0  0
 1PM  CONST_12  N12   C11  N3   C2     0.00   0.0  0
 1PM  CONST_13  N16   C11  N3   C2   180.00   0.0  0
 1PM  CONST_14  C14   C13  N12  C11    0.00   0.0  0
 1PM  CONST_15  C14   C15  N16  C11    0.00   0.0  0
 1PM  CONST_16  C15   N16  C11  N12    0.00   0.0  0
 1PM  CONST_17  C15   C14  C13  N12    0.00   0.0  0
 1PM  CONST_18  N16   C11  N12  C13    0.00   0.0  0
 1PM  CONST_19  N16   C15  C14  C13    0.00   0.0  0
 1PM  CONST_20  C44   C43  C42  C41    0.00   0.0  0
 1PM  CONST_21  C44   C45  C46  C41    0.00   0.0  0
 1PM  CONST_22  C45   C46  C41  C42    0.00   0.0  0
 1PM  CONST_23  C45   C44  C43  C42    0.00   0.0  0
 1PM  CONST_24  C46   C41  C42  C43    0.00   0.0  0
 1PM  CONST_25  C46   C45  C44  C43    0.00   0.0  0
 1PM  CONST_26  N21   C13  N12  C11  180.00   0.0  0
 1PM  CONST_27  N21   C13  C14  C15  180.00   0.0  0
 1PM  CONST_28  C43   C42  C41  C36  180.00   0.0  0
 1PM  CONST_29  C45   C46  C41  C36  180.00   0.0  0
 1PM  CONST_30  H5    C5   C4   N3   180.00   0.0  0
 1PM  CONST_31  H2    C2   N3   C4   180.00   0.0  0
 1PM  CONST_32  H4    C4   C5   NFE  180.00   0.0  0
 1PM  CONST_33  H15   C15  N16  C11  180.00   0.0  0
 1PM  CONST_34  H14   C14  C13  N12  180.00   0.0  0
 1PM  CONST_35  H43   C43  C42  C41  180.00   0.0  0
 1PM  CONST_36  H46   C46  C41  C42  180.00   0.0  0
 1PM  CONST_37  H42   C42  C43  C44  180.00   0.0  0
 1PM  CONST_38  C36   N34  C32  C31  180.00   0.0  0
 1PM  CONST_39  C36   N34  C32  O33    0.00   0.0  0
 1PM  CONST_40  H35   N34  C32  C31    0.00   0.0  0
 1PM  Var_01    C22   N21  C13  N12  172.09  30.0  2
 1PM  Var_02    C23   C22  N21  C13  172.31  30.0  1
 1PM  Var_03    N24   C23  C22  N21  -36.25  30.0  1
 1PM  Var_04    C25   N24  C23  C22   71.98  30.0  1
 1PM  Var_05    C26   C25  N24  C23  -46.60  30.0  1
 1PM  Var_06    O49   C48  O47  C44   14.63  30.0  1
 1PM  Var_07    O47   C48  O49  C45  -14.57  30.0  1
 1PM  Var_08    O28   C27  N24  C23  168.83  30.0  2
 1PM  Var_09    C42   C41  C36  N34  110.09  30.0  2
 1PM  Var_10    O33   C32  C31  C26   57.26  30.0  3
 1PM  Var_11    C41   C36  N34  C32   97.83  30.0  3
 1PM  Var_12    H301  C30  O29  C27  178.97  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
 1PM  chir_01  C26  N21  C25  C31  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
 1PM  plan-1  N3   0.020
 1PM  plan-1  C4   0.020
 1PM  plan-1  C5   0.020
 1PM  plan-1  NFE  0.020
 1PM  plan-1  C2   0.020
 1PM  plan-1  C11  0.020
 1PM  plan-1  H4   0.020
 1PM  plan-1  H5   0.020
 1PM  plan-1  H2   0.020
 1PM  plan-2  N3   0.020
 1PM  plan-2  C11  0.020
 1PM  plan-2  N12  0.020
 1PM  plan-2  C13  0.020
 1PM  plan-2  C14  0.020
 1PM  plan-2  C15  0.020
 1PM  plan-2  N16  0.020
 1PM  plan-2  N21  0.020
 1PM  plan-2  H14  0.020
 1PM  plan-2  H15  0.020
 1PM  plan-3  C36  0.020
 1PM  plan-3  C41  0.020
 1PM  plan-3  C42  0.020
 1PM  plan-3  C43  0.020
 1PM  plan-3  C44  0.020
 1PM  plan-3  C45  0.020
 1PM  plan-3  C46  0.020
 1PM  plan-3  O47  0.020
 1PM  plan-3  O49  0.020
 1PM  plan-3  H42  0.020
 1PM  plan-3  H43  0.020
 1PM  plan-3  H46  0.020
 1PM  plan-4  C31  0.020
 1PM  plan-4  C32  0.020
 1PM  plan-4  O33  0.020
 1PM  plan-4  N34  0.020
 1PM  plan-4  C36  0.020
 1PM  plan-4  H35  0.020
 1PM  plan-5  N24  0.020
 1PM  plan-5  C27  0.020
 1PM  plan-5  O28  0.020
 1PM  plan-5  O29  0.020

