# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 18:33:00 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (2S)-1-{(2R)-2-[(2-amino-2-oxoethyl)amino]-2-cyclohexylacetyl}-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=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
 MVF  MVF  (2S)-1-{(2R)-2-[(2-amino-2-oxoethyl)amino]-2-cyclohexylacetyl}-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide  ligand  63  31  .  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_MVF
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
 MVF  C1    C  CH1   0  -0.252  -4.1332   1.4042   0.1636
 MVF  C2    C  CH2   0  -0.428  -3.7292   2.8462   0.4702
 MVF  C3    C  CH2   0  -0.426  -4.9007   3.8040   0.2712
 MVF  C4    C  CH2   0  -0.430  -5.4781   3.6859  -1.1349
 MVF  C5    C  CH2   0  -0.429  -5.8679   2.2467  -1.4525
 MVF  C6    C  CH2   0  -0.429  -4.6914   1.2942  -1.2545
 MVF  N7    N  NH1   0  -0.603  -3.3374  -1.0051   0.3170
 MVF  C8    C  CH1   0  -0.173  -3.0051   0.3965   0.4873
 MVF  C9    C  C     0   0.532  -1.7601   0.6551  -0.3460
 MVF  O0    O  O     0  -0.494  -1.6590   0.2742  -1.5060
 MVF  N11   N  N     0  -0.452  -0.7769   1.3466   0.2373
 MVF  C12   C  C     0  -0.186   0.5435   1.5958  -0.2960
 MVF  C13   C  C     0   0.587   1.2681   0.3162  -0.6777
 MVF  O14   O  O     0  -0.483   1.1244  -0.7097  -0.0327
 MVF  N15   N  NH1   0  -0.631   2.0923   0.4238  -1.7274
 MVF  C16   C  CH2   0  -0.390   2.9578  -0.6574  -2.1503
 MVF  C17   C  CR6   0   0.121   4.1500  -0.8305  -1.2431
 MVF  C22   C  CR16  0  -0.282   5.1863   0.1015  -1.2563
 MVF  C21   C  CR16  0  -0.263   6.2771  -0.0385  -0.4165
 MVF  C20   C  CR6   0   0.034   6.3566  -1.1117   0.4706
 MVF  C19   C  CR16  0  -0.281   5.3250  -2.0468   0.4806
 MVF  C18   C  CR16  0  -0.276   4.2348  -1.9046  -0.3675
 MVF  C23   C  C     0   0.332   7.5436  -1.2441   1.3600
 MVF  N25   N  NH2   0  -0.821   7.3403  -1.9729   2.4966
 MVF  N24   N  N     0  -0.652   8.6497  -0.7246   0.9857
 MVF  C26   C  C     0  -0.521   0.9484   2.1344   1.1020
 MVF  C27   C  C     0  -0.256  -0.4489   1.7254   1.6066
 MVF  C28   C  CH2   0  -0.393  -4.4484  -1.4576   1.1166
 MVF  C29   C  C     0   0.502  -4.6814  -2.9438   0.9135
 MVF  O30   O  O     0  -0.492  -4.3973  -3.5027  -0.1358
 MVF  N30   N  NH2   0  -0.802  -5.2585  -3.5680   1.9487
 MVF  H1    H  HCH1  0   0.229  -4.9514   1.1598   0.8546
 MVF  H21C  H  HCH2  0   0.228  -3.3608   2.9232   1.4976
 MVF  H22C  H  HCH2  0   0.216  -2.9034   3.1548  -0.1807
 MVF  H61C  H  HCH2  0   0.220  -3.9122   1.5270  -1.9858
 MVF  H62C  H  HCH2  0   0.220  -5.0122   0.2700  -1.4659
 MVF  H8    H  HCH1  0   0.260  -2.7588   0.5411   1.5464
 MVF  H31C  H  HCH2  0   0.210  -5.6798   3.5821   1.0086
 MVF  H32C  H  HCH2  0   0.227  -4.5787   4.8305   0.4633
 MVF  H41C  H  HCH2  0   0.226  -6.3393   4.3487  -1.2490
 MVF  H42C  H  HCH2  0   0.208  -4.7265   4.0227  -1.8572
 MVF  H51C  H  HCH2  0   0.209  -6.6954   1.9397  -0.8032
 MVF  H52C  H  HCH2  0   0.226  -6.2376   2.1723  -2.4781
 MVF  H7    H  HNH1  0   0.348  -3.4969  -1.2155  -0.6596
 MVF  H281  H  HCH2  0   0.255  -4.2428  -1.2462   2.1694
 MVF  H282  H  HCH2  0   0.243  -5.4061  -0.9614   0.8921
 MVF  H12   H  H     0   0.279   0.5671   2.3354  -1.1000
 MVF  H271  H  H     0   0.254  -1.0580   2.5347   2.0081
 MVF  H272  H  H     0   0.254  -0.4582   0.8867   2.3039
 MVF  H261  H  H     0   0.268   1.7829   1.6245   1.5769
 MVF  H262  H  H     0   0.273   1.1282   3.2063   1.1128
 MVF  H15   H  HNH1  0   0.407   2.1584   1.3039  -2.2117
 MVF  H161  H  HCH2  0   0.265   2.3853  -1.5840  -2.1993
 MVF  H162  H  HCH2  0   0.278   3.2862  -0.4267  -3.1632
 MVF  H18   H  HCR6  0   0.252   3.4448  -2.6441  -0.3459
 MVF  H22   H  HCR6  0   0.254   5.1443   0.9456  -1.9350
 MVF  H19   H  HCR6  0   0.257   5.3654  -2.9080   1.1350
 MVF  H21   H  HCR6  0   0.254   7.0765   0.6895  -0.4417
 MVF  H24   H  H     0   0.323   9.3746  -0.8570   1.6861
 MVF  H25A  H  HNH2  0   0.395   6.4156  -1.9932   2.8940
 MVF  H25B  H  HNH2  0   0.391   8.0761  -1.9724   3.1848
 MVF  H301  H  HNH2  0   0.408  -5.4795  -3.0870   2.8034
 MVF  H302  H  HNH2  0   0.401  -5.5390  -4.5324   1.8737

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
 MVF  C1   C2    single    1.529  0.020  1.529
 MVF  C1   C6    single    1.528  0.020  1.528
 MVF  C1   C8    single    1.547  0.020  1.547
 MVF  C2   C3    single    1.526  0.020  1.526
 MVF  C3   C4    single    1.525  0.020  1.525
 MVF  C4   C5    single    1.524  0.020  1.524
 MVF  C5   C6    single    1.527  0.020  1.527
 MVF  N7   C8    single    1.450  0.020  1.450
 MVF  N7   C28   single    1.442  0.020  1.442
 MVF  C8   C9    single    1.520  0.020  1.520
 MVF  C9   O0    double    1.225  0.020  1.225
 MVF  C9   N11   single    1.336  0.020  1.336
 MVF  N11  C12   single    1.446  0.020  1.446
 MVF  N11  C27   single    1.458  0.020  1.458
 MVF  C12  C13   single    1.519  0.020  1.519
 MVF  C12  C26   single    1.552  0.020  1.552
 MVF  C13  O14   double    1.220  0.020  1.220
 MVF  C13  N15   single    1.339  0.020  1.339
 MVF  N15  C16   single    1.448  0.020  1.448
 MVF  C16  C17   single    1.508  0.020  1.508
 MVF  C17  C18   aromatic  1.388  0.020  1.388
 MVF  C17  C22   aromatic  1.394  0.020  1.394
 MVF  C18  C19   aromatic  1.389  0.020  1.389
 MVF  C19  C20   aromatic  1.392  0.020  1.392
 MVF  C20  C21   aromatic  1.395  0.020  1.395
 MVF  C20  C23   single    1.489  0.020  1.489
 MVF  C21  C22   aromatic  1.384  0.020  1.384
 MVF  C23  N24   double    1.278  0.020  1.278
 MVF  C23  N25   single    1.365  0.020  1.365
 MVF  C26  C27   single    1.541  0.020  1.541
 MVF  C28  C29   single    1.518  0.020  1.518
 MVF  C29  O30   double    1.222  0.020  1.222
 MVF  C29  N30   single    1.339  0.020  1.339
 MVF  C1   H1    single    0.970  0.020  1.090
 MVF  C2   H21C  single    0.970  0.020  1.090
 MVF  C2   H22C  single    0.970  0.020  1.090
 MVF  C6   H61C  single    0.970  0.020  1.090
 MVF  C6   H62C  single    0.970  0.020  1.090
 MVF  C8   H8    single    0.970  0.020  1.090
 MVF  C3   H31C  single    0.970  0.020  1.090
 MVF  C3   H32C  single    0.970  0.020  1.090
 MVF  C4   H41C  single    0.970  0.020  1.090
 MVF  C4   H42C  single    0.970  0.020  1.090
 MVF  C5   H51C  single    0.970  0.020  1.090
 MVF  C5   H52C  single    0.970  0.020  1.090
 MVF  N7   H7    single    0.890  0.020  1.040
 MVF  C28  H281  single    0.970  0.020  1.090
 MVF  C28  H282  single    0.970  0.020  1.090
 MVF  C12  H12   single    0.970  0.020  1.090
 MVF  C27  H271  single    0.970  0.020  1.090
 MVF  C27  H272  single    0.970  0.020  1.090
 MVF  C26  H261  single    0.970  0.020  1.090
 MVF  C26  H262  single    0.970  0.020  1.090
 MVF  N15  H15   single    0.860  0.020  1.020
 MVF  C16  H161  single    0.970  0.020  1.090
 MVF  C16  H162  single    0.970  0.020  1.090
 MVF  C18  H18   single    0.930  0.020  1.080
 MVF  C22  H22   single    0.930  0.020  1.080
 MVF  C19  H19   single    0.930  0.020  1.080
 MVF  C21  H21   single    0.930  0.020  1.080
 MVF  N24  H24   single    0.890  0.020  1.040
 MVF  N25  H25A  single    0.890  0.020  1.040
 MVF  N25  H25B  single    0.890  0.020  1.040
 MVF  N30  H301  single    0.860  0.020  1.020
 MVF  N30  H302  single    0.860  0.020  1.020

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
 MVF  H1    C1   C8    105.46  3.000
 MVF  H1    C1   C6    107.19  3.000
 MVF  C8    C1   C6    114.44  3.000
 MVF  H1    C1   C2    106.29  3.000
 MVF  C8    C1   C2    112.33  3.000
 MVF  C6    C1   C2    110.52  3.000
 MVF  H22C  C2   H21C  106.50  3.000
 MVF  H22C  C2   C3    108.92  3.000
 MVF  H21C  C2   C3    109.68  3.000
 MVF  H22C  C2   C1    110.22  3.000
 MVF  H21C  C2   C1    110.10  3.000
 MVF  C3    C2   C1    111.29  3.000
 MVF  H32C  C3   H31C  106.35  3.000
 MVF  H32C  C3   C4    110.27  3.000
 MVF  H31C  C3   C4    109.62  3.000
 MVF  H32C  C3   C2    109.90  3.000
 MVF  H31C  C3   C2    109.33  3.000
 MVF  C4    C3   C2    111.24  3.000
 MVF  H42C  C4   H41C  106.58  3.000
 MVF  H42C  C4   C5    109.16  3.000
 MVF  H41C  C4   C5    110.45  3.000
 MVF  H42C  C4   C3    108.93  3.000
 MVF  H41C  C4   C3    110.35  3.000
 MVF  C5    C4   C3    111.23  3.000
 MVF  H52C  C5   H51C  106.35  3.000
 MVF  H52C  C5   C6    109.87  3.000
 MVF  H51C  C5   C6    109.29  3.000
 MVF  H52C  C5   C4    110.26  3.000
 MVF  H51C  C5   C4    109.52  3.000
 MVF  C6    C5   C4    111.41  3.000
 MVF  H62C  C6   H61C  106.20  3.000
 MVF  H62C  C6   C5    109.46  3.000
 MVF  H61C  C6   C5    109.24  3.000
 MVF  H62C  C6   C1    110.73  3.000
 MVF  H61C  C6   C1    110.18  3.000
 MVF  C5    C6   C1    110.92  3.000
 MVF  H7    N7   C28   110.40  3.000
 MVF  H7    N7   C8    110.51  3.000
 MVF  C28   N7   C8    114.51  3.000
 MVF  H8    C8   C9    108.84  3.000
 MVF  H8    C8   N7    106.99  3.000
 MVF  C9    C8   N7    106.72  3.000
 MVF  H8    C8   C1    106.26  3.000
 MVF  C9    C8   C1    111.82  3.000
 MVF  N7    C8   C1    115.97  3.000
 MVF  N11   C9   O0    120.90  3.000
 MVF  N11   C9   C8    116.83  3.000
 MVF  O0    C9   C8    122.26  3.000
 MVF  C27   N11  C12    95.52  3.000
 MVF  C27   N11  C9    135.23  3.000
 MVF  C12   N11  C9    126.89  3.000
 MVF  H12   C12  C26   114.97  3.000
 MVF  H12   C12  C13   112.03  3.000
 MVF  C26   C12  C13   113.21  3.000
 MVF  H12   C12  N11   114.07  3.000
 MVF  C26   C12  N11    88.04  3.000
 MVF  C13   C12  N11   112.53  3.000
 MVF  N15   C13  O14   123.68  3.000
 MVF  N15   C13  C12   115.01  3.000
 MVF  O14   C13  C12   121.27  3.000
 MVF  H15   N15  C16   118.23  3.000
 MVF  H15   N15  C13   119.20  3.000
 MVF  C16   N15  C13   122.47  3.000
 MVF  H162  C16  H161  107.25  3.000
 MVF  H162  C16  C17   110.20  3.000
 MVF  H161  C16  C17   110.15  3.000
 MVF  H162  C16  N15   107.08  3.000
 MVF  H161  C16  N15   109.50  3.000
 MVF  C17   C16  N15   112.49  3.000
 MVF  C18   C17  C22   118.55  3.000
 MVF  C22   C17  C16   120.35  3.000
 MVF  C18   C17  C16   121.10  3.000
 MVF  H22   C22  C21   119.30  3.000
 MVF  H22   C22  C17   119.86  3.000
 MVF  C21   C22  C17   120.84  3.000
 MVF  H21   C21  C20   119.38  3.000
 MVF  H21   C21  C22   120.03  3.000
 MVF  C20   C21  C22   120.59  3.000
 MVF  C23   C20  C19   121.78  3.000
 MVF  C23   C20  C21   119.59  3.000
 MVF  C19   C20  C21   118.63  3.000
 MVF  H19   C19  C18   118.69  3.000
 MVF  H19   C19  C20   120.73  3.000
 MVF  C18   C19  C20   120.57  3.000
 MVF  H18   C18  C19   119.40  3.000
 MVF  H18   C18  C17   119.78  3.000
 MVF  C19   C18  C17   120.83  3.000
 MVF  N24   C23  N25   126.13  3.000
 MVF  N25   C23  C20   115.21  3.000
 MVF  N24   C23  C20   118.61  3.000
 MVF  H25B  N25  H25A  113.66  3.000
 MVF  H25B  N25  C23   117.36  3.000
 MVF  H25A  N25  C23   118.43  3.000
 MVF  H24   N24  C23   111.25  3.000
 MVF  H262  C26  H261  109.34  3.000
 MVF  H262  C26  C27   114.11  3.000
 MVF  H261  C26  C27   115.38  3.000
 MVF  H262  C26  C12   113.23  3.000
 MVF  H261  C26  C12   115.53  3.000
 MVF  C27   C26  C12    88.07  3.000
 MVF  H272  C27  H271  109.32  3.000
 MVF  H272  C27  C26   114.91  3.000
 MVF  H271  C27  C26   115.50  3.000
 MVF  H272  C27  N11   113.49  3.000
 MVF  H271  C27  N11   114.41  3.000
 MVF  C26   C27  N11    88.02  3.000
 MVF  H282  C28  H281  105.82  3.000
 MVF  H282  C28  C29   106.28  3.000
 MVF  H281  C28  C29   110.30  3.000
 MVF  H282  C28  N7    114.55  3.000
 MVF  H281  C28  N7    109.17  3.000
 MVF  C29   C28  N7    110.58  3.000
 MVF  N30   C29  O30   123.40  3.000
 MVF  N30   C29  C28   114.77  3.000
 MVF  O30   C29  C28   121.79  3.000
 MVF  H302  N30  H301  117.40  3.000
 MVF  H302  N30  C29   120.57  3.000
 MVF  H301  N30  C29   121.93  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
 MVF  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 MVF  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 MVF  CONST_03  C19   C18  C17  C22     0.00   0.0  0
 MVF  CONST_04  C19   C20  C21  C22     0.00   0.0  0
 MVF  CONST_05  C18   C19  C20  C21     0.00   0.0  0
 MVF  CONST_06  C18   C17  C22  C21     0.00   0.0  0
 MVF  CONST_07  C19   C18  C17  C16   180.00   0.0  0
 MVF  CONST_08  C21   C22  C17  C16   180.00   0.0  0
 MVF  CONST_09  C23   C20  C21  C22   180.00   0.0  0
 MVF  CONST_10  C23   C20  C19  C18   180.00   0.0  0
 MVF  CONST_11  H19   C19  C18  C17   180.00   0.0  0
 MVF  CONST_12  H21   C21  C22  C17   180.00   0.0  0
 MVF  CONST_13  H18   C18  C17  C22   180.00   0.0  0
 MVF  CONST_14  H22   C22  C21  C20   180.00   0.0  0
 MVF  CONST_15  C12   N11  C9   C8    180.00   0.0  0
 MVF  CONST_17  C12   N11  C9   O0      0.00   0.0  0
 MVF  CONST_18  C27   N11  C9   O0    180.00   0.0  0
 MVF  CONST_19  C16   N15  C13  C12   180.00   0.0  0
 MVF  CONST_20  H15   N15  C13  C12     0.00   0.0  0
 MVF  CONST_21  H24   N24  C23  C20   180.00   0.0  0
 MVF  CONST_23  H25B  N25  C23  C20   180.00   0.0  0
 MVF  CONST_24  C16   N15  C13  O14     0.00   0.0  0
 MVF  CONST_25  H301  N30  C29  C28     0.00   0.0  0
 MVF  CONST_26  H302  N30  C29  C28   180.00   0.0  0
 MVF  Var_01    C4    C3   C2   C1    -55.68  30.0  1
 MVF  Var_02    C4    C5   C6   C1     56.10  30.0  1
 MVF  Var_03    C5    C4   C3   C2     54.84  30.0  1
 MVF  Var_04    C6    C5   C4   C3    -55.20  30.0  1
 MVF  Var_05    C12   C26  C27  N11    -4.33  30.0  1
 MVF  Var_06    C18   C17  C16  N15   107.08  30.0  2
 MVF  Var_07    N24   C23  C20  C21   -26.01  30.0  2
 MVF  Var_08    C17   C16  N15  C13   -75.16  30.0  3
 MVF  Var_09    O30   C29  C28  N7    -28.88  30.0  3
 MVF  Var_10    C29   C28  N7   C8   -177.64  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
 MVF  chir_01  C1   C2   C6   C8   negativ
 MVF  chir_02  C8   N7   C1   C9   positiv
 MVF  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
 MVF  plan-1  C8    0.020
 MVF  plan-1  C9    0.020
 MVF  plan-1  O0    0.020
 MVF  plan-1  N11   0.020
 MVF  plan-1  C12   0.020
 MVF  plan-1  C27   0.020
 MVF  plan-2  C16   0.020
 MVF  plan-2  C17   0.020
 MVF  plan-2  C22   0.020
 MVF  plan-2  C21   0.020
 MVF  plan-2  C20   0.020
 MVF  plan-2  C19   0.020
 MVF  plan-2  C18   0.020
 MVF  plan-2  C23   0.020
 MVF  plan-2  H18   0.020
 MVF  plan-2  H22   0.020
 MVF  plan-2  H19   0.020
 MVF  plan-2  H21   0.020
 MVF  plan-3  C28   0.020
 MVF  plan-3  C29   0.020
 MVF  plan-3  O30   0.020
 MVF  plan-3  N30   0.020
 MVF  plan-3  H301  0.020
 MVF  plan-3  H302  0.020
 MVF  plan-4  C12   0.020
 MVF  plan-4  C13   0.020
 MVF  plan-4  O14   0.020
 MVF  plan-4  N15   0.020
 MVF  plan-4  C16   0.020
 MVF  plan-4  H15   0.020
 MVF  plan-5  C20   0.020
 MVF  plan-5  C23   0.020
 MVF  plan-5  N25   0.020
 MVF  plan-5  N24   0.020
 MVF  plan-5  H24   0.020
 MVF  plan-5  H25A  0.020
 MVF  plan-5  H25B  0.020

