# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:11:14 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  60  35  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.277   -6.2946   0.0434   0.8378
 4M3  C12   C  C     0   0.584    3.0402  -0.2135   0.3613
 4M3  C14   C  CH1   0  -0.217    2.1643  -0.3189  -0.8849
 4M3  C20   C  C     0   0.579   -0.2369  -0.5735  -1.2291
 4M3  C31   C  CR16  0  -0.262   -8.7572  -0.4672  -0.3216
 4M3  C15   C  CH2   0  -0.592    2.6455   0.6051  -2.0069
 4M3  C32   C  CR16  0  -0.258   -7.6004  -0.9212  -0.9279
 4M3  C22   C  CH2   0  -0.636   -1.5993  -0.1805  -0.7004
 4M3  C27   C  CR6   0  -0.040   -6.3542  -0.6588  -0.3619
 4M3  C01   C  CR16  0  -0.310    7.2961  -1.9211   1.4209
 4M3  C02   C  CR16  0  -0.239    8.5544  -2.3344   1.0035
 4M3  C03   C  CR6   0   0.080    6.6533  -0.8706   0.7770
 4M3  C04   C  CR16  0  -0.258    9.1768  -1.7002  -0.0627
 4M3  C05   C  CH1   0  -0.214    5.2844  -0.4232   1.2380
 4M3  C06   C  CR16  0  -0.237    8.5384  -0.6489  -0.7086
 4M3  C07   C  C     0   0.547    5.3989   1.0038   1.7640
 4M3  C08   C  CR16  0  -0.281    7.2835  -0.2322  -0.2893
 4M3  O09   O  O     0  -0.420    5.1968   1.9883   1.1060
 4M3  O10   O  OH1   0  -0.585    5.8107   1.0083   3.0217
 4M3  N11   N  NH1   0  -0.651    4.3401  -0.4813   0.1542
 4M3  O13   O  O     0  -0.473    2.6035   0.0772   1.4603
 4M3  O17   O  O     0  -0.429    2.2757   2.5019  -0.5754
 4M3  O18   O  OH1   0  -0.595    3.2583   2.7985  -2.5566
 4M3  N19   N  NH1   0  -0.637    0.7952  -0.0922  -0.5159
 4M3  O21   O  O     0  -0.496   -0.0867  -1.2610  -2.2287
 4M3  C23   C  CH2   0  -0.232   -2.7273  -0.9231  -1.3942
 4M3  N24   N  NH1   0  -0.661   -3.9929  -0.5183  -0.8182
 4M3  C25   C  C     0   0.538   -5.1342  -1.1849  -1.0490
 4M3  O26   O  O     0  -0.489   -5.1908  -2.1707  -1.7722
 4M3  C29   C  CR16  0  -0.276   -7.4563   0.4814   1.4555
 4M3  C30   C  CR6   0   0.048   -8.7005   0.2331   0.8820
 4M3  C33   C  C     0   0.339   -9.9635   0.7085   1.5144
 4M3  N34   N  N     0  -0.648  -10.9739   0.9234   0.7633
 4M3  N35   N  NH2   0  -0.822   -9.8957   0.9239   2.8596
 4M3  H1    H  HCR6  0   0.262   -5.3469   0.2392   1.3234
 4M3  H2    H  HCH1  0   0.315    2.2586  -1.3441  -1.2569
 4M3  H3    H  HCR6  0   0.260   -9.7183  -0.6635  -0.7764
 4M3  H5    H  HCH2  0   0.289    3.6239   0.2946  -2.3807
 4M3  H4    H  HCH2  0   0.314    1.9726   0.5024  -2.8627
 4M3  H6    H  HCR6  0   0.261   -7.6652  -1.4801  -1.8519
 4M3  H7    H  HCH2  0   0.281   -1.6377  -0.3575   0.3778
 4M3  H8    H  HCH2  0   0.286   -1.7159   0.8997  -0.8377
 4M3  H9    H  HCR6  0   0.262    6.8115  -2.4232   2.2493
 4M3  H10   H  HCR6  0   0.263    9.0465  -3.1536   1.5110
 4M3  H11   H  HCR6  0   0.263   10.1569  -2.0222  -0.3892
 4M3  H12   H  HCH1  0   0.306    4.9594  -1.0687   2.0587
 4M3  H13   H  HCR6  0   0.263    9.0207  -0.1476  -1.5374
 4M3  H14   H  HCR6  0   0.264    6.8029   0.5966  -0.7959
 4M3  H15   H  HOH1  0   0.485    5.9471   1.9181   3.3266
 4M3  H16   H  HNH1  0   0.415    4.6550  -0.8246  -0.7389
 4M3  H17   H  HOH1  0   0.481    3.2628   3.7296  -2.2876
 4M3  H18   H  HNH1  0   0.404    0.6192   0.4819   0.2940
 4M3  H19   H  HCH2  0   0.245   -2.7110  -0.7245  -2.4684
 4M3  H20   H  HCH2  0   0.249   -2.6078  -1.9991  -1.2644
 4M3  H21   H  HNH1  0   0.409   -4.0338   0.3745  -0.3538
 4M3  H22   H  HCR6  0   0.265   -7.3753   1.0310   2.3841
 4M3  H23   H  H     0   0.326  -11.7799   1.2202   1.3071
 4M3  H25   H  HNH2  0   0.397   -9.2414   0.3861   3.4037
 4M3  H352  H  HNH2  0   0.393  -10.7571   1.1230   3.3430
 4M3  C16   C  C     0   0.560    2.6974   2.0551  -1.6106

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   double    1.201  0.020  1.201
 4M3  C02  C01   aromatic  1.389  0.020  1.389
 4M3  C02  C04   aromatic  1.388  0.020  1.388
 4M3  C01  C03   aromatic  1.390  0.020  1.390
 4M3  C07  O10   single    1.323  0.020  1.323
 4M3  C07  C05   single    1.525  0.020  1.525
 4M3  C04  C06   aromatic  1.389  0.020  1.389
 4M3  C03  C05   single    1.512  0.020  1.512
 4M3  C03  C08   aromatic  1.393  0.020  1.393
 4M3  C05  N11   single    1.439  0.020  1.439
 4M3  C06  C08   aromatic  1.387  0.020  1.387
 4M3  N11  C12   single    1.343  0.020  1.343
 4M3  O13  C12   double    1.218  0.020  1.218
 4M3  C12  C14   single    1.527  0.020  1.527
 4M3  C23  N24   single    1.448  0.020  1.448
 4M3  C23  C22   single    1.518  0.020  1.518
 4M3  N24  C25   single    1.342  0.020  1.342
 4M3  O21  C20   double    1.222  0.020  1.222
 4M3  C14  N19   single    1.436  0.020  1.436
 4M3  C14  C15   single    1.531  0.020  1.531
 4M3  O17  C16   double    1.204  0.020  1.204
 4M3  C20  N19   single    1.344  0.020  1.344
 4M3  C20  C22   single    1.513  0.020  1.513
 4M3  N34  C33   double    1.277  0.020  1.277
 4M3  C32  C31   aromatic  1.383  0.020  1.383
 4M3  C32  C27   aromatic  1.394  0.020  1.394
 4M3  C16  C15   single    1.504  0.020  1.504
 4M3  C16  O18   single    1.327  0.020  1.327
 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    1.364  0.020  1.364
 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  O10  H15   single    0.850  0.020  0.980
 4M3  N11  H16   single    0.860  0.020  1.020
 4M3  O18  H17   single    0.850  0.020  0.980
 4M3  N19  H18   single    0.860  0.020  1.020
 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  118.45  3.000
 4M3  H1    C28  C27  121.02  3.000
 4M3  C29   C28  C27  120.50  3.000
 4M3  O13   C12  N11  122.26  3.000
 4M3  O13   C12  C14  123.18  3.000
 4M3  N11   C12  C14  114.55  3.000
 4M3  H2    C14  N19  108.50  3.000
 4M3  H2    C14  C15  106.81  3.000
 4M3  N19   C14  C15  113.12  3.000
 4M3  H2    C14  C12  107.01  3.000
 4M3  C15   C14  C12  112.09  3.000
 4M3  N19   C14  C12  109.04  3.000
 4M3  O21   C20  N19  122.76  3.000
 4M3  N19   C20  C22  114.40  3.000
 4M3  O21   C20  C22  122.84  3.000
 4M3  H3    C31  C30  119.38  3.000
 4M3  H3    C31  C32  119.98  3.000
 4M3  C30   C31  C32  120.64  3.000
 4M3  H4    C15  H5   104.87  3.000
 4M3  H4    C15  C16  108.54  3.000
 4M3  H5    C15  C16  109.47  3.000
 4M3  H4    C15  C14  108.87  3.000
 4M3  H5    C15  C14  111.14  3.000
 4M3  C16   C15  C14  113.55  3.000
 4M3  H6    C32  C27  119.85  3.000
 4M3  H6    C32  C31  119.61  3.000
 4M3  C27   C32  C31  120.55  3.000
 4M3  H8    C22  H7   106.23  3.000
 4M3  H8    C22  C23  110.25  3.000
 4M3  H7    C22  C23  110.21  3.000
 4M3  H8    C22  C20  107.95  3.000
 4M3  H7    C22  C20  109.52  3.000
 4M3  C23   C22  C20  112.47  3.000
 4M3  C25   C27  C32  118.47  3.000
 4M3  C25   C27  C28  122.59  3.000
 4M3  C32   C27  C28  118.91  3.000
 4M3  H9    C01  C03  119.86  3.000
 4M3  H9    C01  C02  119.82  3.000
 4M3  C03   C01  C02  120.32  3.000
 4M3  H10   C02  C04  120.15  3.000
 4M3  H10   C02  C01  119.76  3.000
 4M3  C04   C02  C01  120.09  3.000
 4M3  C08   C03  C05  120.47  3.000
 4M3  C08   C03  C01  119.45  3.000
 4M3  C05   C03  C01  120.08  3.000
 4M3  H11   C04  C06  120.08  3.000
 4M3  H11   C04  C02  120.13  3.000
 4M3  C06   C04  C02  119.79  3.000
 4M3  H12   C05  N11  110.28  3.000
 4M3  H12   C05  C07  108.41  3.000
 4M3  N11   C05  C07  110.30  3.000
 4M3  H12   C05  C03  108.85  3.000
 4M3  N11   C05  C03  110.64  3.000
 4M3  C07   C05  C03  108.30  3.000
 4M3  H13   C06  C08  119.71  3.000
 4M3  H13   C06  C04  120.12  3.000
 4M3  C08   C06  C04  120.17  3.000
 4M3  O10   C07  O09  124.76  3.000
 4M3  O10   C07  C05  110.75  3.000
 4M3  O09   C07  C05  124.42  3.000
 4M3  H14   C08  C06  119.31  3.000
 4M3  H14   C08  C03  120.50  3.000
 4M3  C06   C08  C03  120.19  3.000
 4M3  H15   O10  C07  110.24  3.000
 4M3  H16   N11  C05  118.46  3.000
 4M3  H16   N11  C12  120.48  3.000
 4M3  C05   N11  C12  120.73  3.000
 4M3  H17   O18  C16  110.01  3.000
 4M3  H18   N19  C20  119.75  3.000
 4M3  H18   N19  C14  117.56  3.000
 4M3  C20   N19  C14  122.64  3.000
 4M3  H20   C23  H19  107.15  3.000
 4M3  H20   C23  N24  108.92  3.000
 4M3  H19   C23  N24  110.69  3.000
 4M3  H20   C23  C22  110.30  3.000
 4M3  H19   C23  C22  110.44  3.000
 4M3  N24   C23  C22  109.32  3.000
 4M3  H21   N24  C25  119.02  3.000
 4M3  H21   N24  C23  117.82  3.000
 4M3  C25   N24  C23  122.42  3.000
 4M3  O26   C25  N24  122.76  3.000
 4M3  O26   C25  C27  121.13  3.000
 4M3  N24   C25  C27  116.11  3.000
 4M3  H22   C29  C30  120.72  3.000
 4M3  H22   C29  C28  118.68  3.000
 4M3  C30   C29  C28  120.59  3.000
 4M3  C33   C30  C29  121.71  3.000
 4M3  C29   C30  C31  118.79  3.000
 4M3  C33   C30  C31  119.49  3.000
 4M3  N35   C33  N34  126.35  3.000
 4M3  N35   C33  C30  115.26  3.000
 4M3  N34   C33  C30  118.33  3.000
 4M3  H23   N34  C33  111.20  3.000
 4M3  H352  N35  H25  113.69  3.000
 4M3  H352  N35  C33  117.51  3.000
 4M3  H25   N35  C33  118.75  3.000
 4M3  O18   C16  O17  123.57  3.000
 4M3  O18   C16  C15  111.51  3.000
 4M3  O17   C16  C15  124.91  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  CONST_40  H17   O18  C16  C15   180.00   0.0  0
 4M3  CONST_41  H15   O10  C07  C05   180.00   0.0  0
 4M3  Var_01    N24   C25  C27  C28   -27.27  30.0  2
 4M3  Var_02    N34   C33  C30  C31   -25.91  30.0  2
 4M3  Var_03    O17   C16  C15  C14    -7.69  30.0  1
 4M3  Var_04    N24   C23  C22  C20   178.78  30.0  1
 4M3  Var_05    C25   N24  C23  C22  -167.00  30.0  3
 4M3  Var_06    C23   C22  C20  N19  -170.70  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-2  H15   0.020
 4M3  plan-3  C15   0.020
 4M3  plan-3  O17   0.020
 4M3  plan-3  O18   0.020
 4M3  plan-3  H17   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  O13   0.020
 4M3  plan-5  H16   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

