FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: RQR18

Calculation Name: 2BDZ-A-Xray547

Preferred Name:

Target Type:

Ligand Name: n-[n-[1-hydroxycarboxyethyl-carbonyl]leucylamino-butyl]-guanidine

Ligand 3-letter code: E64

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BDZ

Chain ID: A

ChEMBL ID:

UniProt ID: P84346

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 209
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2542476.180697
FMO2-HF: Nuclear repulsion 2459995.978277
FMO2-HF: Total energy -82480.202419
FMO2-MP2: Total energy -82720.741951


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:TYR)


Summations of interaction energy for fragment #1(A:1:TYR)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
66.38778.5649.616-6.375-15.414-0.037
Interaction energy analysis for fragmet #1(A:1:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / q_NPA : 0.922
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3GLU-1-0.762-0.8692.340-38.882-36.3691.923-1.722-2.714-0.023
4A4SER0-0.025-0.0204.2192.5522.772-0.001-0.002-0.2160.000
117A119ILE0-0.027-0.0141.995-5.451-4.3141.960-0.892-2.204-0.002
118A120SER00.002-0.0234.749-3.566-3.388-0.001-0.004-0.1720.000
120A122ILE0-0.021-0.0122.942-2.309-0.8352.773-0.721-3.5250.006
121A123GLN0-0.026-0.0222.512-3.126-1.4140.646-0.510-1.849-0.003
122A124ALA0-0.0050.0174.2970.0710.2530.001-0.026-0.1560.000
124A126ALA0-0.061-0.0212.440-0.4800.0900.996-0.585-0.981-0.004
125A127ASN0-0.067-0.0234.364-0.160-0.060-0.001-0.025-0.0740.000
164A166TYR0-0.080-0.0472.415-1.6841.2781.281-1.426-2.817-0.016
189A191ARG10.8040.8983.12729.69030.8190.039-0.462-0.7060.005
5A5ILE0-0.032-0.0095.713-2.354-2.3540.0000.0000.0000.000
6A6ASP-1-0.740-0.8477.763-18.076-18.0760.0000.0000.0000.000
7A7TRP00.009-0.0228.1951.7751.7750.0000.0000.0000.000
8A8ARG10.7990.87812.53818.19718.1970.0000.0000.0000.000
9A9GLU-1-0.900-0.94212.526-21.013-21.0130.0000.0000.0000.000
10A10LYS10.8950.9558.92627.55527.5550.0000.0000.0000.000
11A11GLY00.0250.02314.5520.4080.4080.0000.0000.0000.000
12A12ALA0-0.043-0.03014.3720.6730.6730.0000.0000.0000.000
13A13VAL00.006-0.00915.219-0.200-0.2000.0000.0000.0000.000
14A14THR0-0.012-0.02617.9540.3730.3730.0000.0000.0000.000
15A15PRO00.0330.00721.403-0.311-0.3110.0000.0000.0000.000
16A16VAL0-0.0420.00122.164-0.115-0.1150.0000.0000.0000.000
17A17LYS10.8110.91324.37512.10712.1070.0000.0000.0000.000
18A18ASN0-0.003-0.03426.776-0.227-0.2270.0000.0000.0000.000
19A19GLN00.0440.03127.368-0.132-0.1320.0000.0000.0000.000
20A20ASN0-0.0030.02630.2160.2300.2300.0000.0000.0000.000
21A21PRO00.006-0.01533.0060.0710.0710.0000.0000.0000.000
22A22CYS0-0.068-0.02532.506-0.258-0.2580.0000.0000.0000.000
23A23GLY00.0950.05531.141-0.304-0.3040.0000.0000.0000.000
24A24SER00.017-0.02229.817-0.188-0.1880.0000.0000.0000.000
25A25CYS0-0.074-0.01325.067-0.198-0.1980.0000.0000.0000.000
26A26TRP00.0310.02224.257-0.612-0.6120.0000.0000.0000.000
27A27ALA00.0200.01824.054-0.387-0.3870.0000.0000.0000.000
28A28PHE0-0.018-0.02023.881-0.289-0.2890.0000.0000.0000.000
29A29SER0-0.063-0.01319.476-0.544-0.5440.0000.0000.0000.000
30A30THR00.0600.01019.333-0.976-0.9760.0000.0000.0000.000
31A31VAL00.0190.02420.246-0.595-0.5950.0000.0000.0000.000
32A32ALA0-0.020-0.00218.776-0.251-0.2510.0000.0000.0000.000
33A33THR0-0.075-0.05615.567-0.811-0.8110.0000.0000.0000.000
34A34ILE00.0040.00517.232-0.497-0.4970.0000.0000.0000.000
35A35GLU-1-0.746-0.84719.985-12.892-12.8920.0000.0000.0000.000
36A36GLY00.0310.02215.843-0.028-0.0280.0000.0000.0000.000
37A37ILE0-0.002-0.01114.081-0.540-0.5400.0000.0000.0000.000
38A38ASN00.0320.00516.4610.2690.2690.0000.0000.0000.000
39A39LYS10.8300.95116.86815.61015.6100.0000.0000.0000.000
40A40ILE0-0.053-0.03511.9670.1310.1310.0000.0000.0000.000
41A41ILE0-0.0140.00815.438-0.196-0.1960.0000.0000.0000.000
42A42THR0-0.022-0.03017.9050.7540.7540.0000.0000.0000.000
43A43GLY00.0360.02719.4390.6440.6440.0000.0000.0000.000
44A44GLN0-0.043-0.02420.5550.4150.4150.0000.0000.0000.000
45A45LEU0-0.018-0.00119.303-0.287-0.2870.0000.0000.0000.000
46A46ILE0-0.002-0.00822.0520.5520.5520.0000.0000.0000.000
47A47SER0-0.015-0.00324.043-0.437-0.4370.0000.0000.0000.000
48A48LEU0-0.038-0.01123.2080.4940.4940.0000.0000.0000.000
49A49SER0-0.004-0.02926.6390.0000.0000.0000.0000.0000.000
50A50GLU-1-0.729-0.87025.222-11.483-11.4830.0000.0000.0000.000
51A51GLN0-0.043-0.03128.6780.0350.0350.0000.0000.0000.000
52A52GLU-1-0.741-0.85730.848-9.432-9.4320.0000.0000.0000.000
53A53LEU0-0.018-0.00225.8630.1290.1290.0000.0000.0000.000
54A54LEU0-0.0170.00730.5240.1560.1560.0000.0000.0000.000
55A55ASP-1-0.693-0.79332.809-8.065-8.0650.0000.0000.0000.000
56A56CYS0-0.053-0.00733.5990.2560.2560.0000.0000.0000.000
57A57GLU-1-0.742-0.82128.933-10.064-10.0640.0000.0000.0000.000
58A58ARG10.7860.88132.3887.9927.9920.0000.0000.0000.000
59A59ARG10.8690.95429.44510.19110.1910.0000.0000.0000.000
60A60SER0-0.011-0.01729.402-0.098-0.0980.0000.0000.0000.000
61A61HIS10.8370.89831.7659.3579.3570.0000.0000.0000.000
62A62GLY00.0720.03733.3800.1880.1880.0000.0000.0000.000
63A64ASP-1-0.867-0.91734.108-8.294-8.2940.0000.0000.0000.000
64A65GLY00.0120.00730.202-0.093-0.0930.0000.0000.0000.000
65A66GLY0-0.002-0.03629.0240.2820.2820.0000.0000.0000.000
66A67TYR00.0100.01925.992-0.200-0.2000.0000.0000.0000.000
67A68GLN00.0250.02818.9090.4150.4150.0000.0000.0000.000
68A69THR00.0310.02822.2230.0050.0050.0000.0000.0000.000
69A70THR00.005-0.02623.644-0.041-0.0410.0000.0000.0000.000
70A71SER0-0.006-0.00624.6980.1070.1070.0000.0000.0000.000
71A72LEU00.007-0.00819.0740.0500.0500.0000.0000.0000.000
72A73GLN0-0.038-0.03523.067-0.260-0.2600.0000.0000.0000.000
73A74TYR0-0.068-0.04825.7460.3280.3280.0000.0000.0000.000
74A75VAL0-0.002-0.00423.9140.2620.2620.0000.0000.0000.000
75A76VAL0-0.021-0.00423.337-0.100-0.1000.0000.0000.0000.000
76A77ASP-1-0.848-0.91825.884-10.193-10.1930.0000.0000.0000.000
77A78ASN0-0.068-0.03329.3370.5570.5570.0000.0000.0000.000
78A79GLY00.0160.01327.3010.1740.1740.0000.0000.0000.000
79A80VAL0-0.081-0.04825.5300.1780.1780.0000.0000.0000.000
80A81HIS00.0030.00028.608-0.091-0.0910.0000.0000.0000.000
81A82THR00.0510.01929.029-0.204-0.2040.0000.0000.0000.000
82A83GLU-1-0.849-0.93428.704-10.115-10.1150.0000.0000.0000.000
83A84ARG10.8170.88529.28110.15910.1590.0000.0000.0000.000
84A85GLU-1-0.722-0.83533.384-8.339-8.3390.0000.0000.0000.000
85A86TYR0-0.082-0.07533.0220.3280.3280.0000.0000.0000.000
86A87PRO00.0510.04732.995-0.313-0.3130.0000.0000.0000.000
87A88TYR0-0.024-0.03231.7740.0850.0850.0000.0000.0000.000
88A89GLU-1-0.841-0.92033.901-7.622-7.6220.0000.0000.0000.000
89A90LYS10.8870.95434.5158.7498.7490.0000.0000.0000.000
90A91LYS10.9760.99335.7927.5877.5870.0000.0000.0000.000
91A92GLN00.0080.00335.9660.0720.0720.0000.0000.0000.000
92A93GLY00.0100.01037.8900.2320.2320.0000.0000.0000.000
93A94ARG10.8440.89339.7197.1147.1140.0000.0000.0000.000
94A96ARG10.7830.84437.8758.0518.0510.0000.0000.0000.000
95A97ALA00.0500.02535.0020.0470.0470.0000.0000.0000.000
96A98LYS10.9390.96136.5307.1307.1300.0000.0000.0000.000
97A99ASP-1-0.792-0.86839.501-7.131-7.1310.0000.0000.0000.000
98A100LYS10.8510.94336.1498.2768.2760.0000.0000.0000.000
99A101LYS10.8040.88138.0607.7377.7370.0000.0000.0000.000
100A102GLY00.0070.01835.6770.0140.0140.0000.0000.0000.000
101A103PRO0-0.017-0.02130.740-0.090-0.0900.0000.0000.0000.000
102A104LYS10.8670.94929.8659.5269.5260.0000.0000.0000.000
103A105VAL0-0.027-0.00323.116-0.136-0.1360.0000.0000.0000.000
104A106TYR00.0770.03125.4930.1840.1840.0000.0000.0000.000
105A107ILE0-0.079-0.03120.414-0.542-0.5420.0000.0000.0000.000
106A108THR00.0510.01721.3060.2830.2830.0000.0000.0000.000
107A109GLY00.0320.01820.8780.3480.3480.0000.0000.0000.000
108A110TYR0-0.033-0.01817.853-0.402-0.4020.0000.0000.0000.000
109A111LYS10.9590.99111.61522.52922.5290.0000.0000.0000.000
110A112TYR00.0170.00915.854-0.237-0.2370.0000.0000.0000.000
111A113VAL0-0.045-0.02910.412-1.067-1.0670.0000.0000.0000.000
112A114PRO0-0.019-0.01411.2860.9850.9850.0000.0000.0000.000
113A115ALA00.0350.03212.461-0.948-0.9480.0000.0000.0000.000
114A116ASN0-0.058-0.04814.1850.0410.0410.0000.0000.0000.000
115A117ASP-1-0.817-0.8958.183-26.000-26.0000.0000.0000.0000.000
116A118GLU-1-0.780-0.8665.455-28.870-28.8700.0000.0000.0000.000
119A121LEU0-0.0040.0017.453-0.292-0.2920.0000.0000.0000.000
123A125ILE00.008-0.0066.7360.1520.1520.0000.0000.0000.000
126A128GLN00.006-0.0017.5192.8172.8170.0000.0000.0000.000
127A129PRO0-0.021-0.00610.018-0.669-0.6690.0000.0000.0000.000
128A130VAL0-0.023-0.00210.2980.5850.5850.0000.0000.0000.000
129A131SER0-0.0080.00113.2100.6510.6510.0000.0000.0000.000
130A132VAL00.009-0.01513.876-0.571-0.5710.0000.0000.0000.000
131A133VAL00.0080.01417.1330.7620.7620.0000.0000.0000.000
132A134THR0-0.010-0.01718.592-0.493-0.4930.0000.0000.0000.000
133A135ASP-1-0.860-0.93021.015-10.571-10.5710.0000.0000.0000.000
134A136SER0-0.037-0.04123.720-0.036-0.0360.0000.0000.0000.000
135A137ARG10.8930.95125.72710.61710.6170.0000.0000.0000.000
136A138GLY00.0170.01527.2050.3970.3970.0000.0000.0000.000
137A139ARG10.9180.94128.2048.7938.7930.0000.0000.0000.000
138A140GLY00.0450.02626.7330.0120.0120.0000.0000.0000.000
139A141PHE00.0490.03220.768-0.188-0.1880.0000.0000.0000.000
140A142GLN00.015-0.00825.2130.1680.1680.0000.0000.0000.000
141A143PHE0-0.027-0.01528.3070.0660.0660.0000.0000.0000.000
142A144TYR00.0050.02919.3340.1310.1310.0000.0000.0000.000
143A145LYS10.8250.88724.66910.33410.3340.0000.0000.0000.000
144A146GLY00.0480.01321.697-0.068-0.0680.0000.0000.0000.000
145A147GLY0-0.0010.01119.1670.2760.2760.0000.0000.0000.000
146A148ILE0-0.043-0.01213.095-0.294-0.2940.0000.0000.0000.000
147A149TYR00.002-0.02916.7470.5380.5380.0000.0000.0000.000
148A150GLU-1-0.825-0.91916.804-15.204-15.2040.0000.0000.0000.000
149A151GLY0-0.0110.00718.499-0.006-0.0060.0000.0000.0000.000
150A152PRO00.0090.00721.6490.0770.0770.0000.0000.0000.000
151A153CYS0-0.089-0.03016.460-0.314-0.3140.0000.0000.0000.000
152A154GLY00.0430.04423.077-0.052-0.0520.0000.0000.0000.000
153A155THR0-0.047-0.04919.720-0.474-0.4740.0000.0000.0000.000
154A156ASN0-0.0090.00922.254-0.265-0.2650.0000.0000.0000.000
155A157THR0-0.012-0.01220.4670.1900.1900.0000.0000.0000.000
156A158ASP-1-0.827-0.90423.869-10.608-10.6080.0000.0000.0000.000
157A159HIS0-0.020-0.01324.1170.3450.3450.0000.0000.0000.000
158A160ALA00.0210.00621.702-0.567-0.5670.0000.0000.0000.000
159A161VAL00.0080.00218.1280.3240.3240.0000.0000.0000.000
160A162THR00.0260.02515.209-0.050-0.0500.0000.0000.0000.000
161A163ALA0-0.0030.00411.5900.1580.1580.0000.0000.0000.000
162A164VAL00.003-0.01512.290-0.612-0.6120.0000.0000.0000.000
163A165GLY00.0630.0189.073-0.345-0.3450.0000.0000.0000.000
165A167GLY00.0420.0217.108-0.811-0.8110.0000.0000.0000.000
166A168LYS10.8600.9125.63626.05226.0520.0000.0000.0000.000
167A169THR00.0400.0226.685-0.068-0.0680.0000.0000.0000.000
168A170TYR0-0.012-0.0018.9141.3061.3060.0000.0000.0000.000
169A171LEU00.0510.0238.582-2.440-2.4400.0000.0000.0000.000
170A172LEU0-0.046-0.02310.9071.7101.7100.0000.0000.0000.000
171A173LEU00.0090.00113.210-0.710-0.7100.0000.0000.0000.000
172A174LYS10.8590.92915.91514.39314.3930.0000.0000.0000.000
173A175ASN00.0280.02518.5570.0060.0060.0000.0000.0000.000
174A176SER00.009-0.01221.922-0.142-0.1420.0000.0000.0000.000
175A177TRP00.000-0.00125.0120.4050.4050.0000.0000.0000.000
176A178GLY00.0280.01927.0090.3770.3770.0000.0000.0000.000
177A179PRO00.002-0.01226.108-0.208-0.2080.0000.0000.0000.000
178A180ASN0-0.035-0.03427.174-0.162-0.1620.0000.0000.0000.000
179A181TRP00.0130.03221.8720.0100.0100.0000.0000.0000.000
180A182GLY00.0210.00923.589-0.374-0.3740.0000.0000.0000.000
181A183GLU-1-0.750-0.82318.543-14.357-14.3570.0000.0000.0000.000
182A184LYS10.8770.92221.92810.40710.4070.0000.0000.0000.000
183A185GLY00.0110.01223.784-0.058-0.0580.0000.0000.0000.000
184A186TYR0-0.019-0.01017.540-0.538-0.5380.0000.0000.0000.000
185A187ILE00.0250.00618.0600.6190.6190.0000.0000.0000.000
186A188ARG10.8190.89614.27915.01715.0170.0000.0000.0000.000
187A189ILE00.0350.02314.4730.9110.9110.0000.0000.0000.000
188A190LYS10.8800.93612.94114.10214.1020.0000.0000.0000.000
190A192ALA0-0.024-0.00410.3540.8600.8600.0000.0000.0000.000
191A193SER00.0290.0208.096-1.630-1.6300.0000.0000.0000.000
192A194GLY00.0360.0147.2721.3561.3560.0000.0000.0000.000
193A195ARG10.9680.9858.52018.16118.1610.0000.0000.0000.000
194A196SER00.0300.00911.9691.1731.1730.0000.0000.0000.000
195A197LYS10.9960.99513.84211.90711.9070.0000.0000.0000.000
196A198GLY00.0450.03613.459-0.214-0.2140.0000.0000.0000.000
197A199THR0-0.014-0.03714.3201.1671.1670.0000.0000.0000.000
198A201GLY00.0730.04018.3330.3160.3160.0000.0000.0000.000
199A202VAL0-0.0050.02313.491-0.177-0.1770.0000.0000.0000.000
200A203TYR0-0.048-0.0399.331-1.150-1.1500.0000.0000.0000.000
201A204THR0-0.018-0.01614.293-0.026-0.0260.0000.0000.0000.000
202A205SER0-0.017-0.03017.7430.3160.3160.0000.0000.0000.000
203A206SER00.0160.01413.9090.4750.4750.0000.0000.0000.000
204A207PHE00.0180.00715.686-0.134-0.1340.0000.0000.0000.000
205A208PHE00.0130.00411.025-0.543-0.5430.0000.0000.0000.000
206A209PRO00.0270.01714.8310.3510.3510.0000.0000.0000.000
207A210ILE0-0.018-0.01215.450-1.224-1.2240.0000.0000.0000.000
208A211LYS10.8350.91317.02814.57714.5770.0000.0000.0000.000
209A212GLY-1-0.834-0.90718.542-14.239-14.2390.0000.0000.0000.000