# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 12:02:02 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: N-(4-carbamimidoylbenzoyl)-beta-alanyl-N-[(S)-carboxy(phenyl)methyl]-L-alpha-asparagine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(cc1)C(=O)NCCC(=O)N[C@@H](CC(O)=O)C(=O)N[C@H](C(O)=O)c2ccccc2
#
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
 4M3  4M3  N-(4-carbamimidoylbenzoyl)-beta-alanyl-N-[(S)-carboxy(phenyl)methyl]-L-alpha-asparagine  ligand  58  35  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4M3
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
 4M3  C28   C  CR16   0  -0.275   -5.8200  -0.0789   0.7010
 4M3  C12   C  C      0   0.572    3.2310   0.6905  -0.1750
 4M3  C14   C  CH1    0  -0.213    2.4634   1.2312  -1.3887
 4M3  C20   C  C      0   0.564    0.3032   0.0983  -1.2863
 4M3  C31   C  CR16   0  -0.262   -8.0563  -1.4305  -0.2161
 4M3  C15   C  CH2    0  -0.621    2.9068   2.6241  -1.8252
 4M3  C32   C  CR16   0  -0.257   -6.9030  -1.4064  -0.9778
 4M3  C22   C  CH2    0  -0.621   -1.0731   0.1691  -0.6579
 4M3  C27   C  CR6    0  -0.041   -5.7664  -0.7417  -0.5213
 4M3  C01   C  CR16   0  -0.309    5.8233  -1.7748   2.0181
 4M3  C02   C  CR16   0  -0.248    5.9990  -3.1515   2.0440
 4M3  C03   C  CR6    0   0.159    5.5797  -1.1092   0.8205
 4M3  C04   C  CR16   0  -0.275    5.9385  -3.8848   0.8655
 4M3  C05   C  CH1    0  -0.266    5.4531   0.3955   0.8045
 4M3  C06   C  CR16   0  -0.245    5.6982  -3.2279  -0.3344
 4M3  C07   C  C      0   0.422    6.8686   1.0104   0.5780
 4M3  C08   C  CR16   0  -0.300    5.5211  -1.8503  -0.3560
 4M3  O09   O  O      0  -0.587    7.0372   1.6515  -0.4756
 4M3  O10   O  OC    -1  -0.586    7.6938   0.7828   1.4744
 4M3  N11   N  NH1    0  -0.655    4.5564   0.8752  -0.2115
 4M3  O17   O  O      0  -0.602    2.1806   3.4087   0.3033
 4M3  O18   O  OC    -1  -0.610    3.3825   4.7839  -0.9735
 4M3  N19   N  NH1    0  -0.619    1.0511   1.1999  -1.1202
 4M3  O21   O  O      0  -0.505    0.6828  -0.8917  -1.8976
 4M3  C23   C  CH2    0  -0.244   -2.0977  -0.6427  -1.4343
 4M3  N24   N  NH1    0  -0.654   -3.3733  -0.6271  -0.7507
 4M3  C25   C  C      0   0.529   -4.5486  -0.7418  -1.3896
 4M3  O26   O  O      0  -0.488   -4.6447  -0.8433  -2.6057
 4M3  C29   C  CR16   0  -0.277   -6.9843  -0.0855   1.4545
 4M3  C30   C  CR6    0   0.047   -8.1151  -0.7627   1.0060
 4M3  C33   C  C      0   0.338   -9.3752  -0.8006   1.8005
 4M3  N34   N  N      0  -0.648  -10.1634  -1.7920   1.6371
 4M3  N35   N  NH2    0  -0.822   -9.5396   0.2282   2.6820
 4M3  H1    H  HCR6   0   0.263   -4.9657   0.4717   1.0742
 4M3  H2    H  HCH1   0   0.281    2.6586   0.5369  -2.2108
 4M3  H3    H  HCR6   0   0.260   -8.9275  -1.9631  -0.5719
 4M3  H5    H  HCH2   0   0.241    3.9201   2.5928  -2.2342
 4M3  H4    H  HCH2   0   0.264    2.2811   2.9333  -2.6689
 4M3  H6    H  HCR6   0   0.262   -6.8820  -1.9163  -1.9318
 4M3  H7    H  HCH2   0   0.277   -0.9778  -0.2212   0.3615
 4M3  H8    H  HCH2   0   0.267   -1.4046   1.2051  -0.5624
 4M3  H9    H  HCR6   0   0.239    5.8657  -1.2095   2.9413
 4M3  H10   H  HCR6   0   0.249    6.1817  -3.6533   2.9859
 4M3  H11   H  HCR6   0   0.249    6.0717  -4.9588   0.8825
 4M3  H12   H  HCH1   0   0.254    5.1055   0.7229   1.7902
 4M3  H13   H  HCR6   0   0.249    5.6480  -3.7903  -1.2584
 4M3  H14   H  HCR6   0   0.240    5.3263  -1.3534  -1.2985
 4M3  H16   H  HNH1   0   0.388    5.0034   1.4025  -0.9476
 4M3  H18   H  HNH1   0   0.391    0.7325   1.9182  -0.4856
 4M3  H19   H  HCH2   0   0.253   -2.2354  -0.2211  -2.4290
 4M3  H20   H  HCH2   0   0.245   -1.7459  -1.6685  -1.5641
 4M3  H21   H  HNH1   0   0.405   -3.3553  -0.7332   0.2512
 4M3  H22   H  HCR6   0   0.265   -6.9914   0.4345   2.4034
 4M3  H23   H  H      0   0.326  -10.9981  -1.6976   2.2097
 4M3  H25   H  HNH2   0   0.397   -9.1100   1.1141   2.4712
 4M3  H352  H  HNH2   0   0.393  -10.4376   0.3128   3.1318
 4M3  C16   C  C      0   0.434    2.8223   3.7010  -0.7297
 4M3  O13   O  O      0  -0.495    2.6716   0.0807   0.7234

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
 4M3  O09  C07   deloc     1.245  0.020  1.245
 4M3  C02  C01   aromatic  1.388  0.020  1.388
 4M3  C02  C04   aromatic  1.389  0.020  1.389
 4M3  C01  C03   aromatic  1.392  0.020  1.392
 4M3  C07  O10   deloc     1.239  0.020  1.239
 4M3  C07  C05   single    1.560  0.020  1.560
 4M3  C04  C06   aromatic  1.389  0.020  1.389
 4M3  C03  C05   single    1.510  0.020  1.510
 4M3  C03  C08   aromatic  1.392  0.020  1.392
 4M3  C05  N11   single    1.438  0.020  1.438
 4M3  C06  C08   aromatic  1.389  0.020  1.389
 4M3  N11  C12   single    1.339  0.020  1.339
 4M3  O13  C12   double    1.221  0.020  1.221
 4M3  C12  C14   single    1.534  0.020  1.534
 4M3  C23  N24   single    1.447  0.020  1.447
 4M3  C23  C22   single    1.520  0.020  1.520
 4M3  N24  C25   single    1.343  0.020  1.343
 4M3  O21  C20   double    1.224  0.020  1.224
 4M3  C14  N19   single    1.438  0.020  1.438
 4M3  C14  C15   single    1.526  0.020  1.526
 4M3  O17  C16   deloc     1.251  0.020  1.251
 4M3  C20  N19   single    1.342  0.020  1.342
 4M3  C20  C22   single    1.515  0.020  1.515
 4M3  N34  C33   double    1.277  0.020  1.277
 4M3  C32  C31   aromatic  1.382  0.020  1.382
 4M3  C32  C27   aromatic  1.394  0.020  1.394
 4M3  C16  C15   single    1.538  0.020  1.538
 4M3  C16  O18   deloc     1.243  0.020  1.243
 4M3  C31  C30   aromatic  1.394  0.020  1.394
 4M3  C25  C27   single    1.496  0.020  1.496
 4M3  C25  O26   double    1.224  0.020  1.224
 4M3  C27  C28   aromatic  1.391  0.020  1.391
 4M3  C30  C33   single    1.490  0.020  1.490
 4M3  C30  C29   aromatic  1.392  0.020  1.392
 4M3  C33  N35   single    1.365  0.020  1.365
 4M3  C28  C29   aromatic  1.387  0.020  1.387
 4M3  C28  H1    single    0.930  0.020  1.080
 4M3  C14  H2    single    0.970  0.020  1.090
 4M3  C31  H3    single    0.930  0.020  1.080
 4M3  C15  H5    single    0.970  0.020  1.090
 4M3  C15  H4    single    0.970  0.020  1.090
 4M3  C32  H6    single    0.930  0.020  1.080
 4M3  C22  H7    single    0.970  0.020  1.090
 4M3  C22  H8    single    0.970  0.020  1.090
 4M3  C01  H9    single    0.930  0.020  1.080
 4M3  C02  H10   single    0.930  0.020  1.080
 4M3  C04  H11   single    0.930  0.020  1.080
 4M3  C05  H12   single    0.970  0.020  1.090
 4M3  C06  H13   single    0.930  0.020  1.080
 4M3  C08  H14   single    0.930  0.020  1.080
 4M3  N11  H16   single    0.860  0.020  1.020
 4M3  N19  H18   single    0.890  0.020  1.040
 4M3  C23  H19   single    0.970  0.020  1.090
 4M3  C23  H20   single    0.970  0.020  1.090
 4M3  N24  H21   single    0.860  0.020  1.020
 4M3  C29  H22   single    0.930  0.020  1.080
 4M3  N34  H23   single    0.890  0.020  1.040
 4M3  N35  H25   single    0.890  0.020  1.040
 4M3  N35  H352  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
 4M3  H1    C28  C29  118.52  3.000
 4M3  H1    C28  C27  120.98  3.000
 4M3  C29   C28  C27  120.49  3.000
 4M3  O13   C12  N11  122.84  3.000
 4M3  O13   C12  C14  121.91  3.000
 4M3  N11   C12  C14  115.15  3.000
 4M3  H2    C14  N19  107.56  3.000
 4M3  H2    C14  C15  108.22  3.000
 4M3  N19   C14  C15  111.03  3.000
 4M3  H2    C14  C12  106.36  3.000
 4M3  C15   C14  C12  113.75  3.000
 4M3  N19   C14  C12  109.63  3.000
 4M3  O21   C20  N19  123.58  3.000
 4M3  N19   C20  C22  114.63  3.000
 4M3  O21   C20  C22  121.79  3.000
 4M3  H3    C31  C30  119.37  3.000
 4M3  H3    C31  C32  119.97  3.000
 4M3  C30   C31  C32  120.66  3.000
 4M3  H4    C15  H5   104.45  3.000
 4M3  H4    C15  C16  108.64  3.000
 4M3  H5    C15  C16  109.72  3.000
 4M3  H4    C15  C14  108.19  3.000
 4M3  H5    C15  C14  110.51  3.000
 4M3  C16   C15  C14  114.79  3.000
 4M3  H6    C32  C27  119.86  3.000
 4M3  H6    C32  C31  119.59  3.000
 4M3  C27   C32  C31  120.55  3.000
 4M3  H8    C22  H7   106.44  3.000
 4M3  H8    C22  C23  110.29  3.000
 4M3  H7    C22  C23  110.09  3.000
 4M3  H8    C22  C20  110.88  3.000
 4M3  H7    C22  C20  106.87  3.000
 4M3  C23   C22  C20  112.06  3.000
 4M3  C25   C27  C32  118.28  3.000
 4M3  C25   C27  C28  122.78  3.000
 4M3  C32   C27  C28  118.92  3.000
 4M3  H9    C01  C03  119.38  3.000
 4M3  H9    C01  C02  119.78  3.000
 4M3  C03   C01  C02  120.83  3.000
 4M3  H10   C02  C04  120.04  3.000
 4M3  H10   C02  C01  119.81  3.000
 4M3  C04   C02  C01  120.14  3.000
 4M3  C08   C03  C05  121.21  3.000
 4M3  C08   C03  C01  118.70  3.000
 4M3  C05   C03  C01  120.02  3.000
 4M3  H11   C04  C06  120.28  3.000
 4M3  H11   C04  C02  120.33  3.000
 4M3  C06   C04  C02  119.38  3.000
 4M3  H12   C05  N11  109.78  3.000
 4M3  H12   C05  C07  107.51  3.000
 4M3  N11   C05  C07  109.38  3.000
 4M3  H12   C05  C03  108.35  3.000
 4M3  N11   C05  C03  113.10  3.000
 4M3  C07   C05  C03  108.55  3.000
 4M3  H13   C06  C08  119.73  3.000
 4M3  H13   C06  C04  119.97  3.000
 4M3  C08   C06  C04  120.31  3.000
 4M3  O10   C07  O09  128.07  3.000
 4M3  O10   C07  C05  115.26  3.000
 4M3  O09   C07  C05  116.67  3.000
 4M3  H14   C08  C06  119.44  3.000
 4M3  H14   C08  C03  119.93  3.000
 4M3  C06   C08  C03  120.63  3.000
 4M3  H16   N11  C05  114.41  3.000
 4M3  H16   N11  C12  122.02  3.000
 4M3  C05   N11  C12  123.52  3.000
 4M3  H18   N19  C20  119.06  3.000
 4M3  H18   N19  C14  114.31  3.000
 4M3  C20   N19  C14  122.84  3.000
 4M3  H20   C23  H19  107.21  3.000
 4M3  H20   C23  N24  110.50  3.000
 4M3  H19   C23  N24  108.41  3.000
 4M3  H20   C23  C22  110.19  3.000
 4M3  H19   C23  C22  110.17  3.000
 4M3  N24   C23  C22  110.30  3.000
 4M3  H21   N24  C25  118.67  3.000
 4M3  H21   N24  C23  116.92  3.000
 4M3  C25   N24  C23  123.08  3.000
 4M3  O26   C25  N24  123.27  3.000
 4M3  O26   C25  C27  120.86  3.000
 4M3  N24   C25  C27  115.88  3.000
 4M3  H22   C29  C30  120.73  3.000
 4M3  H22   C29  C28  118.66  3.000
 4M3  C30   C29  C28  120.60  3.000
 4M3  C33   C30  C29  121.83  3.000
 4M3  C29   C30  C31  118.76  3.000
 4M3  C33   C30  C31  119.40  3.000
 4M3  N35   C33  N34  126.40  3.000
 4M3  N35   C33  C30  115.28  3.000
 4M3  N34   C33  C30  118.26  3.000
 4M3  H23   N34  C33  111.26  3.000
 4M3  H352  N35  H25  113.56  3.000
 4M3  H352  N35  C33  117.32  3.000
 4M3  H25   N35  C33  118.46  3.000
 4M3  O18   C16  O17  126.63  3.000
 4M3  O18   C16  C15  116.44  3.000
 4M3  O17   C16  C15  116.92  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
 4M3  CONST_01  C31   C32  C27  C28    0.00   0.0  0
 4M3  CONST_02  C31   C30  C29  C28    0.00   0.0  0
 4M3  CONST_03  C29   C30  C31  C32    0.00   0.0  0
 4M3  CONST_04  C29   C28  C27  C32    0.00   0.0  0
 4M3  CONST_05  C30   C31  C32  C27    0.00   0.0  0
 4M3  CONST_06  C30   C29  C28  C27    0.00   0.0  0
 4M3  CONST_07  C06   C04  C02  C01    0.00   0.0  0
 4M3  CONST_08  C06   C08  C03  C01    0.00   0.0  0
 4M3  CONST_09  C08   C03  C01  C02    0.00   0.0  0
 4M3  CONST_10  C08   C06  C04  C02    0.00   0.0  0
 4M3  CONST_11  C04   C02  C01  C03    0.00   0.0  0
 4M3  CONST_12  C04   C06  C08  C03    0.00   0.0  0
 4M3  CONST_13  C33   C30  C29  C28  180.00   0.0  0
 4M3  CONST_14  C25   C27  C32  C31  180.00   0.0  0
 4M3  CONST_15  C33   C30  C31  C32  180.00   0.0  0
 4M3  CONST_16  C05   C03  C01  C02  180.00   0.0  0
 4M3  CONST_17  C06   C08  C03  C05  180.00   0.0  0
 4M3  CONST_18  C29   C28  C27  C25  180.00   0.0  0
 4M3  CONST_19  H6    C32  C27  C28  180.00   0.0  0
 4M3  CONST_20  H22   C29  C30  C31  180.00   0.0  0
 4M3  CONST_21  H1    C28  C27  C32  180.00   0.0  0
 4M3  CONST_22  H3    C31  C32  C27  180.00   0.0  0
 4M3  CONST_23  H11   C04  C02  C01  180.00   0.0  0
 4M3  CONST_24  H14   C08  C03  C01  180.00   0.0  0
 4M3  CONST_25  H13   C06  C04  C02  180.00   0.0  0
 4M3  CONST_26  H10   C02  C01  C03  180.00   0.0  0
 4M3  CONST_27  H9    C01  C02  C04  180.00   0.0  0
 4M3  CONST_28  C23   N24  C25  C27  180.00   0.0  0
 4M3  CONST_29  H21   N24  C25  C27    0.00   0.0  0
 4M3  CONST_30  H23   N34  C33  C30  180.00   0.0  0
 4M3  CONST_32  H352  N35  C33  C30  180.00   0.0  0
 4M3  CONST_33  C05   N11  C12  C14  180.00   0.0  0
 4M3  CONST_34  O21   C20  N19  C14    0.00   0.0  0
 4M3  CONST_35  C22   C20  N19  C14  180.00   0.0  0
 4M3  CONST_36  O13   C12  N11  C05    0.00   0.0  0
 4M3  CONST_37  O26   C25  N24  C23    0.00   0.0  0
 4M3  CONST_38  H16   N11  C12  C14    0.00   0.0  0
 4M3  CONST_39  H18   N19  C20  C22    0.00   0.0  0
 4M3  Var_01    N24   C25  C27  C28   29.06  30.0  2
 4M3  Var_02    N34   C33  C30  C31   25.86  30.0  2
 4M3  Var_03    O17   C16  C15  C14  -13.00  30.0  2
 4M3  Var_04    N24   C23  C22  C20  175.92  30.0  2
 4M3  Var_05    C25   N24  C23  C22  151.27  30.0  3
 4M3  Var_06    C23   C22  C20  N19  148.81  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
 4M3  chir_01  C14  C12  N19  C15  negativ
 4M3  chir_02  C05  N11  C07  C03  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
 4M3  plan-1  C28   0.020
 4M3  plan-1  C31   0.020
 4M3  plan-1  C32   0.020
 4M3  plan-1  C27   0.020
 4M3  plan-1  C25   0.020
 4M3  plan-1  C29   0.020
 4M3  plan-1  C30   0.020
 4M3  plan-1  C33   0.020
 4M3  plan-1  H1    0.020
 4M3  plan-1  H3    0.020
 4M3  plan-1  H6    0.020
 4M3  plan-1  H22   0.020
 4M3  plan-2  C05   0.020
 4M3  plan-2  C07   0.020
 4M3  plan-2  O09   0.020
 4M3  plan-2  O10   0.020
 4M3  plan-3  C15   0.020
 4M3  plan-3  O17   0.020
 4M3  plan-3  O18   0.020
 4M3  plan-3  C16   0.020
 4M3  plan-4  C01   0.020
 4M3  plan-4  C02   0.020
 4M3  plan-4  C03   0.020
 4M3  plan-4  C04   0.020
 4M3  plan-4  C05   0.020
 4M3  plan-4  C06   0.020
 4M3  plan-4  C08   0.020
 4M3  plan-4  H9    0.020
 4M3  plan-4  H10   0.020
 4M3  plan-4  H11   0.020
 4M3  plan-4  H13   0.020
 4M3  plan-4  H14   0.020
 4M3  plan-5  C12   0.020
 4M3  plan-5  C14   0.020
 4M3  plan-5  C05   0.020
 4M3  plan-5  N11   0.020
 4M3  plan-5  H16   0.020
 4M3  plan-5  O13   0.020
 4M3  plan-6  C14   0.020
 4M3  plan-6  C20   0.020
 4M3  plan-6  C22   0.020
 4M3  plan-6  N19   0.020
 4M3  plan-6  O21   0.020
 4M3  plan-6  H18   0.020
 4M3  plan-7  C27   0.020
 4M3  plan-7  C23   0.020
 4M3  plan-7  N24   0.020
 4M3  plan-7  C25   0.020
 4M3  plan-7  O26   0.020
 4M3  plan-7  H21   0.020
 4M3  plan-8  C30   0.020
 4M3  plan-8  C33   0.020
 4M3  plan-8  N34   0.020
 4M3  plan-8  N35   0.020
 4M3  plan-8  H23   0.020
 4M3  plan-8  H25   0.020
 4M3  plan-8  H352  0.020

