# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:32:14 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: 2-[[2-[[(2S)-3-(3H-imidazol-4-yl)-1-methoxy-1-oxo-propan-2-yl]amino]-2-oxo-ethyl]-(phenylmethyl)amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](Cc1[nH]cnc1)NC(=O)CN(CC(O)=O)Cc2ccccc2
#
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
 I41  I41  '2-[[2-[[(2S)-3-(3H-imidazol-4-yl)-1-methoxy-1-oxo-propan-2-yl]amino]-2-oxo-ethyl]-(phenylmethyl)amino]ethanoic acid'  ligand  48  27  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I41
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
 I41  O04   O  O      0  -0.434   1.8300   2.2886   0.5310
 I41  C03   C  C      0   0.589   2.5342   1.4569   1.0383
 I41  O02   O  O2     0  -0.450   3.2265   1.6370   2.1499
 I41  C01   C  CH3    0  -0.424   3.1475   2.9200   2.7742
 I41  C05   C  CH1    0  -0.165   2.8017   0.0783   0.4471
 I41  C06   C  CH2    0  -0.568   4.0847   0.1405  -0.4015
 I41  C07   C  CR5    0   0.309   4.4051  -1.1606  -1.0424
 I41  C08   C  CR15   0  -0.264   4.3866  -1.5558  -2.3515
 I41  N09   N  N      0  -0.441   4.7288  -2.8743  -2.4634
 I41  C10   C  CR15   0   0.084   4.9497  -3.2781  -1.2400
 I41  N11   N  NR15   0  -0.610   4.7666  -2.2824  -0.3491
 I41  N12   N  NH1    0  -0.636   1.6946  -0.3455  -0.3586
 I41  C13   C  C      0   0.547   0.4799  -0.5497   0.1835
 I41  O14   O  O      0  -0.485   0.2830  -0.4291   1.3820
 I41  C15   C  CH2    0  -0.397  -0.6029  -0.9770  -0.7987
 I41  N16   N  NT     0  -0.400  -1.8351  -0.3115  -0.5047
 I41  C17   C  CH2    0  -0.454  -1.8675   1.0849  -0.8630
 I41  C18   C  C      0   0.401  -1.9173   1.4476  -2.3658
 I41  O19   O  OC    -1  -0.626  -1.9688   2.6717  -2.6050
 I41  O20   O  O      0  -0.599  -1.9004   0.5250  -3.2025
 I41  C21   C  CH2    0  -0.315  -3.0611  -1.0288  -0.7397
 I41  C22   C  CR6    0   0.088  -4.1200  -0.6917   0.2860
 I41  C23   C  CR16   0  -0.317  -5.4680  -0.6890  -0.0589
 I41  C24   C  CR16   0  -0.243  -6.4467  -0.4269   0.8923
 I41  C25   C  CR16   0  -0.273  -6.0855  -0.1541   2.2045
 I41  C26   C  CR16   0  -0.244  -4.7407  -0.1473   2.5564
 I41  C27   C  CR16   0  -0.287  -3.7668  -0.4135   1.6046
 I41  H05   H  HCH1   0   0.286   2.9538  -0.6269   1.2693
 I41  H011  H  HCH3   0   0.241   3.5199   3.7041   2.1158
 I41  H012  H  HCH3   0   0.242   2.1257   3.1532   3.0711
 I41  H013  H  HCH3   0   0.254   3.7760   2.8611   3.6573
 I41  H061  H  HCH2   0   0.284   3.9696   0.8929  -1.1849
 I41  H062  H  HCH2   0   0.292   4.9079   0.4725   0.2346
 I41  H12   H  HNH1   0   0.401   1.8004  -0.3716  -1.3604
 I41  H08   H  HCR5   0   0.257   4.1473  -0.9494  -3.2126
 I41  H11   H  HNR5   0   0.419   4.8902  -2.3586   0.6481
 I41  H10   H  HCR5   0   0.278   5.2460  -4.2709  -0.9393
 I41  H151  H  HCH2   0   0.224  -0.2578  -0.8391  -1.8322
 I41  H152  H  HCH2   0   0.266  -0.7300  -2.0551  -0.6615
 I41  H171  H  HCH2   0   0.236  -2.7297   1.5498  -0.3722
 I41  H172  H  HCH2   0   0.237  -0.9953   1.5864  -0.4262
 I41  H211  H  HCH2   0   0.218  -3.4670  -0.8714  -1.7470
 I41  H212  H  HCH2   0   0.243  -2.8524  -2.1005  -0.6670
 I41  H23   H  HCR6   0   0.242  -5.7585  -0.8936  -1.0835
 I41  H27   H  HCR6   0   0.248  -2.7159  -0.3955   1.8685
 I41  H24   H  HCR6   0   0.250  -7.4910  -0.4284   0.6061
 I41  H25   H  HCR6   0   0.250  -6.8451   0.0561   2.9466
 I41  H26   H  HCR6   0   0.248  -4.4507   0.0695   3.5769

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
 I41  O04  C03   double    1.202  0.020  1.202
 I41  C03  O02   single    1.322  0.020  1.322
 I41  C03  C05   single    1.524  0.020  1.524
 I41  O02  C01   single    1.429  0.020  1.429
 I41  C05  C06   single    1.539  0.020  1.539
 I41  C05  N12   single    1.433  0.020  1.433
 I41  C06  C07   single    1.485  0.020  1.485
 I41  C07  C08   aromatic  1.368  0.020  1.368
 I41  C07  N11   aromatic  1.367  0.020  1.367
 I41  C08  N09   aromatic  1.367  0.020  1.367
 I41  N09  C10   aromatic  1.307  0.020  1.307
 I41  C10  N11   aromatic  1.349  0.020  1.349
 I41  N12  C13   single    1.346  0.020  1.346
 I41  C13  O14   double    1.221  0.020  1.221
 I41  C13  C15   single    1.523  0.020  1.523
 I41  C15  N16   single    1.431  0.020  1.431
 I41  N16  C17   single    1.442  0.020  1.442
 I41  N16  C21   single    1.440  0.020  1.440
 I41  C17  C18   single    1.547  0.020  1.547
 I41  C18  O19   deloc     1.248  0.020  1.248
 I41  C18  O20   deloc     1.246  0.020  1.246
 I41  C21  C22   single    1.512  0.020  1.512
 I41  C22  C23   aromatic  1.391  0.020  1.391
 I41  C22  C27   aromatic  1.393  0.020  1.393
 I41  C23  C24   aromatic  1.390  0.020  1.390
 I41  C24  C25   aromatic  1.388  0.020  1.388
 I41  C25  C26   aromatic  1.390  0.020  1.390
 I41  C26  C27   aromatic  1.388  0.020  1.388
 I41  C05  H05   single    0.970  0.020  1.090
 I41  C01  H011  single    0.970  0.020  1.090
 I41  C01  H012  single    0.970  0.020  1.090
 I41  C01  H013  single    0.970  0.020  1.090
 I41  C06  H061  single    0.970  0.020  1.090
 I41  C06  H062  single    0.970  0.020  1.090
 I41  N12  H12   single    0.860  0.020  1.020
 I41  C08  H08   single    0.930  0.020  1.080
 I41  N11  H11   single    0.860  0.020  1.020
 I41  C10  H10   single    0.930  0.020  1.080
 I41  C15  H151  single    0.970  0.020  1.090
 I41  C15  H152  single    0.970  0.020  1.090
 I41  C17  H171  single    0.970  0.020  1.090
 I41  C17  H172  single    0.970  0.020  1.090
 I41  C21  H211  single    0.970  0.020  1.090
 I41  C21  H212  single    0.970  0.020  1.090
 I41  C23  H23   single    0.930  0.020  1.080
 I41  C27  H27   single    0.930  0.020  1.080
 I41  C24  H24   single    0.930  0.020  1.080
 I41  C25  H25   single    0.930  0.020  1.080
 I41  C26  H26   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
 I41  C05   C03  O02   110.96  3.000
 I41  C05   C03  O04   124.41  3.000
 I41  O02   C03  O04   124.57  3.000
 I41  C01   O02  C03   117.44  3.000
 I41  H013  C01  H012  109.45  3.000
 I41  H013  C01  H011  109.43  3.000
 I41  H012  C01  H011  109.35  3.000
 I41  H013  C01  O02   105.94  3.000
 I41  H012  C01  O02   111.29  3.000
 I41  H011  C01  O02   111.30  3.000
 I41  H05   C05  N12   109.84  3.000
 I41  H05   C05  C06   108.94  3.000
 I41  N12   C05  C06   110.23  3.000
 I41  H05   C05  C03   108.42  3.000
 I41  N12   C05  C03   110.49  3.000
 I41  C06   C05  C03   108.88  3.000
 I41  H062  C06  H061  106.72  3.000
 I41  H062  C06  C07   110.80  3.000
 I41  H061  C06  C07   108.46  3.000
 I41  H062  C06  C05   108.63  3.000
 I41  H061  C06  C05   109.59  3.000
 I41  C07   C06  C05   112.47  3.000
 I41  N11   C07  C08   104.59  3.000
 I41  N11   C07  C06   123.84  3.000
 I41  C08   C07  C06   131.55  3.000
 I41  H08   C08  N09   122.13  3.000
 I41  H08   C08  C07   127.15  3.000
 I41  N09   C08  C07   110.72  3.000
 I41  C10   N09  C08   105.29  3.000
 I41  H10   C10  N11   122.18  3.000
 I41  H10   C10  N09   126.27  3.000
 I41  N11   C10  N09   111.55  3.000
 I41  H11   N11  C10   125.54  3.000
 I41  H11   N11  C07   126.60  3.000
 I41  C10   N11  C07   107.85  3.000
 I41  H12   N12  C13   119.43  3.000
 I41  H12   N12  C05   119.04  3.000
 I41  C13   N12  C05   121.04  3.000
 I41  C15   C13  O14   123.12  3.000
 I41  C15   C13  N12   115.12  3.000
 I41  O14   C13  N12   121.74  3.000
 I41  H152  C15  H151  106.16  3.000
 I41  H152  C15  N16   109.41  3.000
 I41  H151  C15  N16   113.92  3.000
 I41  H152  C15  C13   106.15  3.000
 I41  H151  C15  C13   110.38  3.000
 I41  N16   C15  C13   110.44  3.000
 I41  C21   N16  C17   115.01  3.000
 I41  C21   N16  C15   117.91  3.000
 I41  C17   N16  C15   114.75  3.000
 I41  H172  C17  H171  104.68  3.000
 I41  H172  C17  C18   107.77  3.000
 I41  H171  C17  C18   108.08  3.000
 I41  H172  C17  N16   109.03  3.000
 I41  H171  C17  N16   108.50  3.000
 I41  C18   C17  N16   117.98  3.000
 I41  O20   C18  O19   126.74  3.000
 I41  O20   C18  C17   118.59  3.000
 I41  O19   C18  C17   114.67  3.000
 I41  H212  C21  H211  105.78  3.000
 I41  H212  C21  C22   107.86  3.000
 I41  H211  C21  C22   109.37  3.000
 I41  H212  C21  N16   108.34  3.000
 I41  H211  C21  N16   113.16  3.000
 I41  C22   C21  N16   112.00  3.000
 I41  C27   C22  C23   118.68  3.000
 I41  C27   C22  C21   120.59  3.000
 I41  C23   C22  C21   120.71  3.000
 I41  H23   C23  C24   119.58  3.000
 I41  H23   C23  C22   119.56  3.000
 I41  C24   C23  C22   120.86  3.000
 I41  H24   C24  C25   120.07  3.000
 I41  H24   C24  C23   119.87  3.000
 I41  C25   C24  C23   120.06  3.000
 I41  H25   C25  C26   120.29  3.000
 I41  H25   C25  C24   120.24  3.000
 I41  C26   C25  C24   119.47  3.000
 I41  H26   C26  C27   119.79  3.000
 I41  H26   C26  C25   119.91  3.000
 I41  C27   C26  C25   120.30  3.000
 I41  H27   C27  C26   120.69  3.000
 I41  H27   C27  C22   118.67  3.000
 I41  C26   C27  C22   120.64  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
 I41  CONST_01  C10   N09  C08  C07     0.00   0.0  0
 I41  CONST_02  N09   C10  N11  C07     0.00   0.0  0
 I41  CONST_03  C10   N11  C07  C08     0.00   0.0  0
 I41  CONST_04  N11   C10  N09  C08     0.00   0.0  0
 I41  CONST_05  N11   C07  C08  N09     0.00   0.0  0
 I41  CONST_06  C25   C24  C23  C22     0.00   0.0  0
 I41  CONST_07  C25   C26  C27  C22     0.00   0.0  0
 I41  CONST_08  C26   C27  C22  C23     0.00   0.0  0
 I41  CONST_09  C26   C25  C24  C23     0.00   0.0  0
 I41  CONST_10  C27   C22  C23  C24     0.00   0.0  0
 I41  CONST_11  C27   C26  C25  C24     0.00   0.0  0
 I41  CONST_12  N09   C08  C07  C06   180.00   0.0  0
 I41  CONST_13  C10   N11  C07  C06   180.00   0.0  0
 I41  CONST_14  C24   C23  C22  C21   180.00   0.0  0
 I41  CONST_15  C26   C27  C22  C21   180.00   0.0  0
 I41  CONST_16  H10   C10  N11  C07   180.00   0.0  0
 I41  CONST_17  H11   N11  C07  C08   180.00   0.0  0
 I41  CONST_18  H08   C08  N09  C10   180.00   0.0  0
 I41  CONST_19  H24   C24  C23  C22   180.00   0.0  0
 I41  CONST_20  H26   C26  C27  C22   180.00   0.0  0
 I41  CONST_21  H27   C27  C22  C23   180.00   0.0  0
 I41  CONST_22  H25   C25  C24  C23   180.00   0.0  0
 I41  CONST_23  H23   C23  C24  C25   180.00   0.0  0
 I41  CONST_24  O14   C13  N12  C05     0.00   0.0  0
 I41  CONST_25  C15   C13  N12  C05   180.00   0.0  0
 I41  CONST_26  H12   N12  C13  O14   180.00   0.0  0
 I41  Var_01    C08   C07  C06  C05   111.29  30.0  2
 I41  Var_02    C23   C22  C21  N16   147.61  30.0  2
 I41  Var_03    C22   C21  N16  C15   144.94  30.0  3
 I41  Var_04    C05   C03  O02  C01   175.96  30.0  1
 I41  Var_05    N16   C15  C13  N12  -139.09  30.0  3
 I41  Var_06    C17   N16  C15  C13    73.50  30.0  3
 I41  Var_07    C18   C17  N16  C15    71.14  30.0  3
 I41  Var_08    O19   C18  C17  N16   178.72  30.0  3
 I41  Var_09    H011  C01  O02  C03   -61.19  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
 I41  chir_01  C05  C03  C06  N12  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
 I41  plan-1  C06  0.020
 I41  plan-1  C07  0.020
 I41  plan-1  C08  0.020
 I41  plan-1  N09  0.020
 I41  plan-1  C10  0.020
 I41  plan-1  N11  0.020
 I41  plan-1  H08  0.020
 I41  plan-1  H11  0.020
 I41  plan-1  H10  0.020
 I41  plan-2  C21  0.020
 I41  plan-2  C22  0.020
 I41  plan-2  C23  0.020
 I41  plan-2  C24  0.020
 I41  plan-2  C25  0.020
 I41  plan-2  C26  0.020
 I41  plan-2  C27  0.020
 I41  plan-2  H23  0.020
 I41  plan-2  H27  0.020
 I41  plan-2  H24  0.020
 I41  plan-2  H25  0.020
 I41  plan-2  H26  0.020
 I41  plan-3  C05  0.020
 I41  plan-3  N12  0.020
 I41  plan-3  C13  0.020
 I41  plan-3  O14  0.020
 I41  plan-3  C15  0.020
 I41  plan-3  H12  0.020
 I41  plan-4  C17  0.020
 I41  plan-4  C18  0.020
 I41  plan-4  O19  0.020
 I41  plan-4  O20  0.020
 I41  plan-5  O04  0.020
 I41  plan-5  C03  0.020
 I41  plan-5  O02  0.020
 I41  plan-5  C05  0.020

