# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:09:25 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: (2S)-N-(4-carbamimidoylbenzyl)-1-[(2R)-2-cyclohexyl-2-{[2-(methylamino)-2-oxoethyl]amino}acetyl]azetidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)CN[C@H](C1CCCCC1)C(=O)N2CC[C@H]2C(=O)NCc3ccc(cc3)C(N)=N
#
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
 M6S  M6S  (2S)-N-(4-carbamimidoylbenzyl)-1-[(2R)-2-cyclohexyl-2-{[2-(methylamino)-2-oxoethyl]amino}acetyl]azetidine-2-carboxamide  ligand  66  32  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M6S
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
 M6S  C1    C  CH1   0  -0.257  -4.0231   1.8030   0.1982
 M6S  C2    C  CH2   0  -0.429  -3.4266   3.0301   0.8891
 M6S  C3    C  CH2   0  -0.426  -4.2849   4.2693   0.6546
 M6S  C4    C  CH2   0  -0.429  -4.4827   4.5315  -0.8343
 M6S  C5    C  CH2   0  -0.429  -5.0634   3.3061  -1.5327
 M6S  C6    C  CH2   0  -0.430  -4.2025   2.0680  -1.2960
 M6S  N7    N  NH1   0  -0.607  -3.7240  -0.7030  -0.1135
 M6S  C8    C  CH1   0  -0.166  -3.2417   0.5068   0.5228
 M6S  C9    C  C     0   0.526  -1.7714   0.6322   0.1559
 M6S  O0    O  O     0  -0.494  -1.3707   0.5120  -0.9961
 M6S  N11   N  N     0  -0.451  -0.9220   0.9052   1.1494
 M6S  C12   C  C     0  -0.189   0.5198   0.9665   1.0661
 M6S  C13   C  C     0   0.582   1.1262  -0.3167   0.5230
 M6S  O14   O  O     0  -0.488   0.6784  -1.4060   0.8434
 M6S  N15   N  NH1   0  -0.638   2.1964  -0.1388  -0.2649
 M6S  C16   C  CH2   0  -0.339   2.9703  -1.2126  -0.8420
 M6S  C17   C  CR6   0   0.086   4.4491  -1.0235  -0.6269
 M6S  C18   C  CR16  0  -0.273   4.9578  -0.7163   0.6342
 M6S  C19   C  CR16  0  -0.259   6.3194  -0.5757   0.8319
 M6S  C20   C  CR6   0   0.034   7.2133  -0.7262  -0.2283
 M6S  C21   C  CR16  0  -0.275   6.7062  -1.0321  -1.4879
 M6S  C22   C  CR16  0  -0.296   5.3391  -1.1780  -1.6816
 M6S  C23   C  C     0   0.332   8.6744  -0.5771   0.0176
 M6S  N24   N  N     0  -0.651   9.1223  -0.8089   1.1916
 M6S  N25   N  NH2   0  -0.822   9.4203  -0.2502  -1.0789
 M6S  C26   C  C     0  -0.522   0.5517   1.0617   2.6144
 M6S  C27   C  C     0  -0.255  -0.9805   0.8970   2.6063
 M6S  C28   C  CH2   0  -0.391  -5.1034  -1.0253   0.1615
 M6S  C29   C  C     0   0.533  -5.4913  -2.2886  -0.5849
 M6S  O30   O  O     0  -0.502  -5.0517  -2.5335  -1.7009
 M6S  C10   C  CH3   0  -0.514  -6.9034  -4.2788  -0.5644
 M6S  N2    N  NH1   0  -0.625  -6.3733  -3.0779   0.0376
 M6S  H1    H  HCH1  0   0.229  -5.0249   1.6608   0.6261
 M6S  H21C  H  HCH2  0   0.229  -3.3295   2.8473   1.9634
 M6S  H22C  H  HCH2  0   0.216  -2.4165   3.2213   0.5092
 M6S  H61C  H  HCH2  0   0.220  -3.2264   2.2149  -1.7668
 M6S  H62C  H  HCH2  0   0.222  -4.6598   1.2048  -1.7888
 M6S  H8    H  HCH1  0   0.260  -3.3247   0.3578   1.6061
 M6S  H31C  H  HCH2  0   0.210  -5.2618   4.1253   1.1292
 M6S  H32C  H  HCH2  0   0.227  -3.8290   5.1364   1.1383
 M6S  H41C  H  HCH2  0   0.225  -5.1331   5.3971  -0.9836
 M6S  H42C  H  HCH2  0   0.208  -3.5179   4.7826  -1.2889
 M6S  H51C  H  HCH2  0   0.209  -6.0768   3.1225  -1.1587
 M6S  H52C  H  HCH2  0   0.227  -5.1587   3.4918  -2.6054
 M6S  H7    H  HNH1  0   0.350  -3.5705  -0.6598  -1.1128
 M6S  H281  H  HCH2  0   0.253  -5.2382  -1.1551   1.2386
 M6S  H282  H  HCH2  0   0.239  -5.8227  -0.2484  -0.1440
 M6S  H12   H  H     0   0.279   0.8963   1.8511   0.5461
 M6S  H271  H  H     0   0.255  -1.5451   1.7241   3.0368
 M6S  H272  H  H     0   0.254  -1.3430  -0.0429   3.0249
 M6S  H261  H  H     0   0.269   1.0988   0.2686   3.1180
 M6S  H262  H  H     0   0.274   0.8959   2.0262   2.9779
 M6S  H15   H  HNH1  0   0.405   2.4511   0.8019  -0.5214
 M6S  H161  H  HCH2  0   0.273   2.6421  -2.1450  -0.3820
 M6S  H162  H  HCH2  0   0.266   2.7608  -1.2982  -1.9113
 M6S  H18   H  HCR6  0   0.251   4.2844  -0.5856   1.4726
 M6S  H22   H  HCR6  0   0.258   4.9664  -1.4196  -2.6697
 M6S  H19   H  HCR6  0   0.255   6.6997  -0.3397   1.8165
 M6S  H21   H  HCR6  0   0.259   7.3700  -1.1771  -2.3306
 M6S  H24   H  H     0   0.324  10.1246  -0.6465   1.2424
 M6S  H251  H  HNH2  0   0.395   8.9839   0.2878  -1.8092
 M6S  H252  H  HNH2  0   0.391  10.3859  -0.0065  -0.9248
 M6S  H2    H  HNH1  0   0.406  -6.6575  -2.8508   0.9753
 M6S  H101  H  HCH3  0   0.238  -6.1346  -5.0416  -0.6957
 M6S  H102  H  HCH3  0   0.251  -7.6742  -4.6790   0.0877
 M6S  H103  H  HCH3  0   0.240  -7.3497  -4.0721  -1.5367

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
 M6S  C1   C2    single    1.529  0.020  1.529
 M6S  C1   C6    single    1.528  0.020  1.528
 M6S  C1   C8    single    1.548  0.020  1.548
 M6S  C2   C3    single    1.526  0.020  1.526
 M6S  C3   C4    single    1.525  0.020  1.525
 M6S  C4   C5    single    1.525  0.020  1.525
 M6S  C5   C6    single    1.526  0.020  1.526
 M6S  N7   C8    single    1.449  0.020  1.449
 M6S  N7   C28   single    1.443  0.020  1.443
 M6S  C8   C9    single    1.521  0.020  1.521
 M6S  C9   O0    double    1.226  0.020  1.226
 M6S  C9   N11   single    1.335  0.020  1.335
 M6S  N11  C12   single    1.446  0.020  1.446
 M6S  N11  C27   single    1.458  0.020  1.458
 M6S  C12  C13   single    1.520  0.020  1.520
 M6S  C12  C26   single    1.552  0.020  1.552
 M6S  C13  O14   double    1.220  0.020  1.220
 M6S  C13  N15   single    1.341  0.020  1.341
 M6S  N15  C16   single    1.444  0.020  1.444
 M6S  C16  C17   single    1.506  0.020  1.506
 M6S  C17  C18   aromatic  1.394  0.020  1.394
 M6S  C17  C22   aromatic  1.389  0.020  1.389
 M6S  C18  C19   aromatic  1.383  0.020  1.383
 M6S  C19  C20   aromatic  1.395  0.020  1.395
 M6S  C20  C21   aromatic  1.392  0.020  1.392
 M6S  C20  C23   single    1.489  0.020  1.489
 M6S  C21  C22   aromatic  1.388  0.020  1.388
 M6S  C23  N24   double    1.278  0.020  1.278
 M6S  C23  N25   single    1.366  0.020  1.366
 M6S  C26  C27   single    1.541  0.020  1.541
 M6S  C28  C29   single    1.518  0.020  1.518
 M6S  C29  O30   double    1.224  0.020  1.224
 M6S  C29  N2    single    1.337  0.020  1.337
 M6S  C10  N2    single    1.444  0.020  1.444
 M6S  C1   H1    single    0.970  0.020  1.090
 M6S  C2   H21C  single    0.970  0.020  1.090
 M6S  C2   H22C  single    0.970  0.020  1.090
 M6S  C6   H61C  single    0.970  0.020  1.090
 M6S  C6   H62C  single    0.970  0.020  1.090
 M6S  C8   H8    single    0.970  0.020  1.090
 M6S  C3   H31C  single    0.970  0.020  1.090
 M6S  C3   H32C  single    0.970  0.020  1.090
 M6S  C4   H41C  single    0.970  0.020  1.090
 M6S  C4   H42C  single    0.970  0.020  1.090
 M6S  C5   H51C  single    0.970  0.020  1.090
 M6S  C5   H52C  single    0.970  0.020  1.090
 M6S  N7   H7    single    0.890  0.020  1.040
 M6S  C28  H281  single    0.970  0.020  1.090
 M6S  C28  H282  single    0.970  0.020  1.090
 M6S  C12  H12   single    0.970  0.020  1.090
 M6S  C27  H271  single    0.970  0.020  1.090
 M6S  C27  H272  single    0.970  0.020  1.090
 M6S  C26  H261  single    0.970  0.020  1.090
 M6S  C26  H262  single    0.970  0.020  1.090
 M6S  N15  H15   single    0.860  0.020  1.020
 M6S  C16  H161  single    0.970  0.020  1.090
 M6S  C16  H162  single    0.970  0.020  1.090
 M6S  C18  H18   single    0.930  0.020  1.080
 M6S  C22  H22   single    0.930  0.020  1.080
 M6S  C19  H19   single    0.930  0.020  1.080
 M6S  C21  H21   single    0.930  0.020  1.080
 M6S  N24  H24   single    0.890  0.020  1.040
 M6S  N25  H251  single    0.890  0.020  1.040
 M6S  N25  H252  single    0.890  0.020  1.040
 M6S  N2   H2    single    0.860  0.020  1.020
 M6S  C10  H101  single    0.970  0.020  1.090
 M6S  C10  H102  single    0.970  0.020  1.090
 M6S  C10  H103  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
 M6S  H1    C1   C8    105.69  3.000
 M6S  H1    C1   C6    107.23  3.000
 M6S  C8    C1   C6    114.18  3.000
 M6S  H1    C1   C2    106.47  3.000
 M6S  C8    C1   C2    112.35  3.000
 M6S  C6    C1   C2    110.38  3.000
 M6S  H22C  C2   H21C  106.72  3.000
 M6S  H22C  C2   C3    108.87  3.000
 M6S  H21C  C2   C3    109.67  3.000
 M6S  H22C  C2   C1    110.06  3.000
 M6S  H21C  C2   C1    110.13  3.000
 M6S  C3    C2   C1    111.28  3.000
 M6S  H32C  C3   H31C  106.54  3.000
 M6S  H32C  C3   C4    110.49  3.000
 M6S  H31C  C3   C4    109.27  3.000
 M6S  H32C  C3   C2    109.99  3.000
 M6S  H31C  C3   C2    109.16  3.000
 M6S  C4    C3   C2    111.27  3.000
 M6S  H42C  C4   H41C  106.61  3.000
 M6S  H42C  C4   C5    109.22  3.000
 M6S  H41C  C4   C5    110.31  3.000
 M6S  H42C  C4   C3    109.29  3.000
 M6S  H41C  C4   C3    110.29  3.000
 M6S  C5    C4   C3    111.00  3.000
 M6S  H52C  C5   H51C  106.43  3.000
 M6S  H52C  C5   C6    109.83  3.000
 M6S  H51C  C5   C6    109.43  3.000
 M6S  H52C  C5   C4    110.25  3.000
 M6S  H51C  C5   C4    109.30  3.000
 M6S  C6    C5   C4    111.46  3.000
 M6S  H62C  C6   H61C  106.57  3.000
 M6S  H62C  C6   C5    109.53  3.000
 M6S  H61C  C6   C5    109.13  3.000
 M6S  H62C  C6   C1    110.65  3.000
 M6S  H61C  C6   C1    109.84  3.000
 M6S  C5    C6   C1    111.01  3.000
 M6S  H7    N7   C28   110.04  3.000
 M6S  H7    N7   C8    110.33  3.000
 M6S  C28   N7   C8    114.89  3.000
 M6S  H8    C8   C9    108.83  3.000
 M6S  H8    C8   N7    107.16  3.000
 M6S  C9    C8   N7    106.54  3.000
 M6S  H8    C8   C1    106.42  3.000
 M6S  C9    C8   C1    111.62  3.000
 M6S  N7    C8   C1    116.03  3.000
 M6S  N11   C9   O0    120.75  3.000
 M6S  N11   C9   C8    116.90  3.000
 M6S  O0    C9   C8    122.34  3.000
 M6S  C27   N11  C12    95.61  3.000
 M6S  C27   N11  C9    135.79  3.000
 M6S  C12   N11  C9    126.89  3.000
 M6S  H12   C12  C26   114.71  3.000
 M6S  H12   C12  C13   112.08  3.000
 M6S  C26   C12  C13   113.59  3.000
 M6S  H12   C12  N11   113.91  3.000
 M6S  C26   C12  N11    88.03  3.000
 M6S  C13   C12  N11   112.51  3.000
 M6S  N15   C13  O14   124.44  3.000
 M6S  N15   C13  C12   114.61  3.000
 M6S  O14   C13  C12   120.89  3.000
 M6S  H15   N15  C16   117.20  3.000
 M6S  H15   N15  C13   118.37  3.000
 M6S  C16   N15  C13   124.33  3.000
 M6S  H162  C16  H161  106.75  3.000
 M6S  H162  C16  C17   109.74  3.000
 M6S  H161  C16  C17   110.04  3.000
 M6S  H162  C16  N15   110.27  3.000
 M6S  H161  C16  N15   107.82  3.000
 M6S  C17   C16  N15   112.07  3.000
 M6S  C22   C17  C18   118.54  3.000
 M6S  C22   C17  C16   120.45  3.000
 M6S  C18   C17  C16   121.00  3.000
 M6S  H18   C18  C19   119.28  3.000
 M6S  H18   C18  C17   119.99  3.000
 M6S  C19   C18  C17   120.73  3.000
 M6S  H19   C19  C20   119.35  3.000
 M6S  H19   C19  C18   119.90  3.000
 M6S  C20   C19  C18   120.75  3.000
 M6S  C23   C20  C21   121.93  3.000
 M6S  C23   C20  C19   119.50  3.000
 M6S  C21   C20  C19   118.56  3.000
 M6S  H21   C21  C22   118.76  3.000
 M6S  H21   C21  C20   120.70  3.000
 M6S  C22   C21  C20   120.53  3.000
 M6S  H22   C22  C21   119.30  3.000
 M6S  H22   C22  C17   119.81  3.000
 M6S  C21   C22  C17   120.89  3.000
 M6S  N25   C23  N24   126.13  3.000
 M6S  N25   C23  C20   115.29  3.000
 M6S  N24   C23  C20   118.52  3.000
 M6S  H24   N24  C23   111.26  3.000
 M6S  H252  N25  H251  113.40  3.000
 M6S  H252  N25  C23   117.28  3.000
 M6S  H251  N25  C23   118.26  3.000
 M6S  H262  C26  H261  109.46  3.000
 M6S  H262  C26  C27   114.30  3.000
 M6S  H261  C26  C27   115.14  3.000
 M6S  H262  C26  C12   113.25  3.000
 M6S  H261  C26  C12   115.33  3.000
 M6S  C27   C26  C12    88.15  3.000
 M6S  H272  C27  H271  109.27  3.000
 M6S  H272  C27  C26   114.86  3.000
 M6S  H271  C27  C26   115.59  3.000
 M6S  H272  C27  N11   113.67  3.000
 M6S  H271  C27  N11   114.27  3.000
 M6S  C26   C27  N11    87.98  3.000
 M6S  H282  C28  H281  106.04  3.000
 M6S  H282  C28  C29   106.48  3.000
 M6S  H281  C28  C29   110.75  3.000
 M6S  H282  C28  N7    114.44  3.000
 M6S  H281  C28  N7    109.40  3.000
 M6S  C29   C28  N7    109.67  3.000
 M6S  N2    C29  O30   122.90  3.000
 M6S  N2    C29  C28   115.52  3.000
 M6S  O30   C29  C28   121.54  3.000
 M6S  H103  C10  H102  108.36  3.000
 M6S  H103  C10  H101  108.29  3.000
 M6S  H102  C10  H101  108.35  3.000
 M6S  H103  C10  N2    111.38  3.000
 M6S  H102  C10  N2    108.46  3.000
 M6S  H101  C10  N2    111.90  3.000
 M6S  H2    N2   C10   118.21  3.000
 M6S  H2    N2   C29   119.15  3.000
 M6S  C10   N2   C29   122.60  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
 M6S  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 M6S  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 M6S  CONST_03  C21   C22  C17  C18     0.00   0.0  0
 M6S  CONST_04  C21   C20  C19  C18     0.00   0.0  0
 M6S  CONST_05  C22   C17  C18  C19     0.00   0.0  0
 M6S  CONST_06  C22   C21  C20  C19     0.00   0.0  0
 M6S  CONST_07  C19   C18  C17  C16   180.00   0.0  0
 M6S  CONST_08  C21   C22  C17  C16   180.00   0.0  0
 M6S  CONST_09  C23   C20  C19  C18   180.00   0.0  0
 M6S  CONST_10  C23   C20  C21  C22   180.00   0.0  0
 M6S  CONST_11  H19   C19  C18  C17   180.00   0.0  0
 M6S  CONST_12  H21   C21  C22  C17   180.00   0.0  0
 M6S  CONST_13  H22   C22  C17  C18   180.00   0.0  0
 M6S  CONST_14  H18   C18  C19  C20   180.00   0.0  0
 M6S  CONST_15  C12   N11  C9   C8    180.00   0.0  0
 M6S  CONST_16  C27   N11  C9   C8      0.00   0.0  0
 M6S  CONST_17  C12   N11  C9   O0      0.00   0.0  0
 M6S  CONST_18  C27   N11  C9   O0    180.00   0.0  0
 M6S  CONST_19  C16   N15  C13  C12   180.00   0.0  0
 M6S  CONST_20  H15   N15  C13  C12     0.00   0.0  0
 M6S  CONST_21  H24   N24  C23  C20   180.00   0.0  0
 M6S  CONST_23  H252  N25  C23  C20   180.00   0.0  0
 M6S  CONST_24  C16   N15  C13  O14     0.00   0.0  0
 M6S  CONST_25  C10   N2   C29  C28   180.00   0.0  0
 M6S  CONST_26  C10   N2   C29  O30     0.00   0.0  0
 M6S  CONST_27  H2    N2   C29  C28     0.00   0.0  0
 M6S  Var_01    C4    C3   C2   C1    -56.02  30.0  1
 M6S  Var_02    C4    C5   C6   C1     56.12  30.0  1
 M6S  Var_03    C5    C4   C3   C2     55.08  30.0  1
 M6S  Var_04    C6    C5   C4   C3    -55.25  30.0  1
 M6S  Var_05    C12   C26  C27  N11    -3.45  30.0  1
 M6S  Var_06    C18   C17  C16  N15    48.79  30.0  2
 M6S  Var_07    N24   C23  C20  C19    25.66  30.0  2
 M6S  Var_08    C17   C16  N15  C13  -131.24  30.0  3
 M6S  Var_09    O30   C29  C28  N7    -36.12  30.0  3
 M6S  Var_10    C29   C28  N7   C8    178.69  30.0  3
 M6S  Var_11    H101  C10  N2   C29    66.71  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
 M6S  chir_01  C1   C2   C6   C8   negativ
 M6S  chir_02  C8   N7   C1   C9   positiv
 M6S  chir_03  C12  N11  C13  C26  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
 M6S  plan-1  C8    0.020
 M6S  plan-1  C9    0.020
 M6S  plan-1  O0    0.020
 M6S  plan-1  N11   0.020
 M6S  plan-1  C12   0.020
 M6S  plan-1  C27   0.020
 M6S  plan-2  C16   0.020
 M6S  plan-2  C17   0.020
 M6S  plan-2  C18   0.020
 M6S  plan-2  C19   0.020
 M6S  plan-2  C20   0.020
 M6S  plan-2  C21   0.020
 M6S  plan-2  C22   0.020
 M6S  plan-2  C23   0.020
 M6S  plan-2  H18   0.020
 M6S  plan-2  H22   0.020
 M6S  plan-2  H19   0.020
 M6S  plan-2  H21   0.020
 M6S  plan-3  C28   0.020
 M6S  plan-3  C29   0.020
 M6S  plan-3  O30   0.020
 M6S  plan-3  C10   0.020
 M6S  plan-3  N2    0.020
 M6S  plan-3  H2    0.020
 M6S  plan-4  C12   0.020
 M6S  plan-4  C13   0.020
 M6S  plan-4  O14   0.020
 M6S  plan-4  N15   0.020
 M6S  plan-4  C16   0.020
 M6S  plan-4  H15   0.020
 M6S  plan-5  C20   0.020
 M6S  plan-5  C23   0.020
 M6S  plan-5  N24   0.020
 M6S  plan-5  N25   0.020
 M6S  plan-5  H24   0.020
 M6S  plan-5  H251  0.020
 M6S  plan-5  H252  0.020

