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: 5RMLZ

Calculation Name: 2DY0-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DY0

Chain ID: B

ChEMBL ID:

UniProt ID: P69503

Base Structure: X-ray

Registration Date: 2025-10-04

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 181
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1833164.318404
FMO2-HF: Nuclear repulsion 1766187.992513
FMO2-HF: Total energy -66976.32589
FMO2-MP2: Total energy -67178.023798


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:3:ALA)


Summations of interaction energy for fragment #1(A:3:ALA)
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.
-99.853-96.0559.458-5.131-8.124-0.042
Interaction energy analysis for fragmet #1(A:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.875 / q_NPA : 0.939
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].
3A5ALA00.0730.0253.361-2.046-0.4890.042-0.777-0.823-0.001
5A7GLN00.0200.0172.277-15.514-14.0173.640-2.344-2.793-0.024
6A8LEU00.0230.0122.3211.4801.6082.447-0.755-1.820-0.006
7A9GLU-1-0.949-0.9644.745-20.398-20.383-0.001-0.006-0.0080.000
45A47LEU0-0.080-0.0552.293-7.949-7.8383.329-1.112-2.327-0.010
46A48LEU0-0.024-0.0035.162-3.827-3.790-0.001-0.002-0.0340.000
173A175TYR0-0.042-0.0173.810-6.415-6.0690.002-0.117-0.231-0.001
175A177LEU0-0.051-0.0023.950-3.578-3.4710.000-0.018-0.0880.000
4A6GLN00.0590.0296.0160.4660.4660.0000.0000.0000.000
8A10TYR0-0.072-0.0747.3952.4152.4150.0000.0000.0000.000
9A11LEU00.0100.0065.0232.1962.1960.0000.0000.0000.000
10A12LYS10.8780.9548.41324.54724.5470.0000.0000.0000.000
11A13ASN0-0.015-0.01610.4412.2792.2790.0000.0000.0000.000
12A14SER0-0.027-0.01411.3771.3861.3860.0000.0000.0000.000
13A15ILE0-0.0290.01311.3841.0221.0220.0000.0000.0000.000
14A16LYS10.9820.99814.86514.26914.2690.0000.0000.0000.000
15A17SER0-0.004-0.00417.929-0.425-0.4250.0000.0000.0000.000
16A18ILE0-0.039-0.00820.2360.3980.3980.0000.0000.0000.000
17A19GLN00.0370.00323.952-0.405-0.4050.0000.0000.0000.000
18A20ASP-1-0.892-0.93326.137-9.838-9.8380.0000.0000.0000.000
19A21TYR00.0150.02525.9850.5320.5320.0000.0000.0000.000
20A22PRO0-0.020-0.02426.403-0.439-0.4390.0000.0000.0000.000
21A23LYS10.9500.96829.36810.59510.5950.0000.0000.0000.000
22A24PRO00.024-0.00729.636-0.306-0.3060.0000.0000.0000.000
23A25GLY0-0.0090.00228.6960.0740.0740.0000.0000.0000.000
24A26ILE0-0.063-0.01624.550-0.198-0.1980.0000.0000.0000.000
25A27LEU0-0.003-0.00321.3520.0300.0300.0000.0000.0000.000
26A28PHE0-0.0050.00821.298-0.621-0.6210.0000.0000.0000.000
27A29ARG10.8730.92116.70515.47815.4780.0000.0000.0000.000
28A30ASP-1-0.846-0.91218.700-14.047-14.0470.0000.0000.0000.000
29A31VAL00.0220.00014.811-0.578-0.5780.0000.0000.0000.000
30A32THR0-0.033-0.03516.881-0.376-0.3760.0000.0000.0000.000
31A33SER00.013-0.02716.6020.0960.0960.0000.0000.0000.000
32A34LEU0-0.037-0.00810.652-0.333-0.3330.0000.0000.0000.000
33A35LEU0-0.041-0.02814.549-0.543-0.5430.0000.0000.0000.000
34A36GLU-1-0.983-0.98016.995-13.126-13.1260.0000.0000.0000.000
35A37ASP-1-0.777-0.86913.586-19.258-19.2580.0000.0000.0000.000
36A38PRO0-0.005-0.00814.761-1.079-1.0790.0000.0000.0000.000
37A39LYS10.8740.9619.70323.97823.9780.0000.0000.0000.000
38A40ALA0-0.007-0.00710.000-2.326-2.3260.0000.0000.0000.000
39A41TYR0-0.015-0.01510.263-1.630-1.6300.0000.0000.0000.000
40A42ALA00.0320.02911.436-1.209-1.2090.0000.0000.0000.000
41A43LEU00.0070.0054.867-2.045-2.0450.0000.0000.0000.000
42A44SER0-0.058-0.0516.511-4.444-4.4440.0000.0000.0000.000
43A45ILE00.0080.0088.073-1.037-1.0370.0000.0000.0000.000
44A46ASP-1-0.872-0.9378.021-28.709-28.7090.0000.0000.0000.000
47A49VAL00.0310.0127.9210.9000.9000.0000.0000.0000.000
48A50GLU-1-0.841-0.9095.481-34.250-34.2500.0000.0000.0000.000
49A51ARG10.8230.9245.60531.34731.3470.0000.0000.0000.000
50A52TYR0-0.020-0.0267.1271.8961.8960.0000.0000.0000.000
51A53LYS10.8500.9249.14432.95532.9550.0000.0000.0000.000
52A54ASN0-0.013-0.01011.9262.0672.0670.0000.0000.0000.000
53A55ALA0-0.026-0.00412.8300.9000.9000.0000.0000.0000.000
54A56GLY00.0140.00814.6920.9410.9410.0000.0000.0000.000
55A57ILE0-0.033-0.01215.0660.7000.7000.0000.0000.0000.000
56A58THR0-0.002-0.03118.1460.0060.0060.0000.0000.0000.000
57A59LYS10.7930.87820.56812.67912.6790.0000.0000.0000.000
58A60VAL00.0100.01716.302-0.653-0.6530.0000.0000.0000.000
59A61VAL0-0.009-0.00519.0900.8500.8500.0000.0000.0000.000
60A62GLY00.0520.01818.922-1.028-1.0280.0000.0000.0000.000
61A63THR00.0210.01520.1750.6530.6530.0000.0000.0000.000
62A64GLU-1-0.834-0.87721.778-11.018-11.0180.0000.0000.0000.000
63A65ALA0-0.039-0.03123.8300.0490.0490.0000.0000.0000.000
64A66ARG10.8840.89919.01314.13714.1370.0000.0000.0000.000
65A67GLY00.1080.07117.542-0.694-0.6940.0000.0000.0000.000
66A68PHE0-0.070-0.03617.688-0.450-0.4500.0000.0000.0000.000
67A69LEU00.0020.01517.781-0.142-0.1420.0000.0000.0000.000
68A70PHE00.0620.03112.736-0.588-0.5880.0000.0000.0000.000
69A71GLY00.0480.01214.529-0.729-0.7290.0000.0000.0000.000
70A72ALA0-0.0030.00416.485-0.041-0.0410.0000.0000.0000.000
71A73PRO00.005-0.00714.7750.1160.1160.0000.0000.0000.000
72A74VAL00.0240.01611.381-0.545-0.5450.0000.0000.0000.000
73A75ALA0-0.012-0.01214.078-0.183-0.1830.0000.0000.0000.000
74A76LEU0-0.017-0.00817.5200.2700.2700.0000.0000.0000.000
75A77GLY0-0.014-0.00514.5050.3240.3240.0000.0000.0000.000
76A78LEU0-0.049-0.02412.144-0.711-0.7110.0000.0000.0000.000
77A79GLY0-0.0210.01115.5810.5810.5810.0000.0000.0000.000
78A80VAL0-0.060-0.01817.9420.8890.8890.0000.0000.0000.000
79A81GLY0-0.011-0.00420.5180.1100.1100.0000.0000.0000.000
80A82PHE00.0120.00219.369-0.355-0.3550.0000.0000.0000.000
81A83VAL0-0.027-0.01722.1110.7840.7840.0000.0000.0000.000
82A84PRO0-0.036-0.01023.248-0.362-0.3620.0000.0000.0000.000
83A85VAL00.0100.00624.3520.4520.4520.0000.0000.0000.000
84A86ARG10.8000.87025.72010.52210.5220.0000.0000.0000.000
85A87LYS10.9260.95328.51010.17410.1740.0000.0000.0000.000
86A88PRO00.0150.01131.4540.0110.0110.0000.0000.0000.000
87A89GLY0-0.0090.01034.9400.0610.0610.0000.0000.0000.000
88A90LYS10.9010.95931.5689.3939.3930.0000.0000.0000.000
89A91LEU0-0.031-0.01829.664-0.082-0.0820.0000.0000.0000.000
90A92PRO0-0.012-0.00333.8000.1780.1780.0000.0000.0000.000
91A93ARG10.9250.96332.2349.5249.5240.0000.0000.0000.000
92A94GLU-1-0.862-0.93436.380-8.269-8.2690.0000.0000.0000.000
93A95THR0-0.047-0.02533.254-0.243-0.2430.0000.0000.0000.000
94A96ILE0-0.0150.01131.5670.2770.2770.0000.0000.0000.000
95A97SER00.0240.00232.744-0.336-0.3360.0000.0000.0000.000
96A98GLU-1-0.841-0.91330.100-9.700-9.7000.0000.0000.0000.000
97A99THR0-0.021-0.01132.2470.0920.0920.0000.0000.0000.000
98A100TYR0-0.034-0.01628.160-0.206-0.2060.0000.0000.0000.000
99A101ASP-1-0.888-0.94330.976-9.381-9.3810.0000.0000.0000.000
100A102LEU0-0.059-0.04129.434-0.452-0.4520.0000.0000.0000.000
101A103GLU-1-0.928-0.95931.977-9.108-9.1080.0000.0000.0000.000
102A104TYR0-0.049-0.02733.5970.3210.3210.0000.0000.0000.000
103A105GLY0-0.002-0.00435.8080.2430.2430.0000.0000.0000.000
104A106THR0-0.045-0.01533.877-0.164-0.1640.0000.0000.0000.000
105A107ASP-1-0.807-0.87631.300-9.462-9.4620.0000.0000.0000.000
106A108GLN0-0.045-0.03932.3260.0040.0040.0000.0000.0000.000
107A109LEU0-0.038-0.02225.822-0.262-0.2620.0000.0000.0000.000
108A110GLU-1-0.835-0.92529.967-8.800-8.8000.0000.0000.0000.000
109A111ILE00.0220.00226.112-0.415-0.4150.0000.0000.0000.000
110A112HIS0-0.011-0.01229.7350.5530.5530.0000.0000.0000.000
111A113VAL00.0420.01530.998-0.358-0.3580.0000.0000.0000.000
112A114ASP-1-0.903-0.95432.569-9.108-9.1080.0000.0000.0000.000
113A115ALA0-0.062-0.02527.868-0.098-0.0980.0000.0000.0000.000
114A116ILE0-0.016-0.00324.717-0.499-0.4990.0000.0000.0000.000
115A117LYS10.8720.93228.11010.18310.1830.0000.0000.0000.000
116A118PRO00.028-0.00228.659-0.354-0.3540.0000.0000.0000.000
117A119GLY0-0.0040.01027.5560.1630.1630.0000.0000.0000.000
118A120ASP-1-0.791-0.84224.606-12.405-12.4050.0000.0000.0000.000
119A121LYS10.8720.95517.64517.02517.0250.0000.0000.0000.000
120A122VAL0-0.021-0.01920.238-0.387-0.3870.0000.0000.0000.000
121A123LEU0-0.0080.01412.805-0.370-0.3700.0000.0000.0000.000
122A124VAL0-0.008-0.01216.9900.7420.7420.0000.0000.0000.000
123A125VAL0-0.022-0.01713.156-1.317-1.3170.0000.0000.0000.000
124A126ASP-1-0.834-0.93514.991-14.218-14.2180.0000.0000.0000.000
125A127ASP-1-0.838-0.90914.428-17.343-17.3430.0000.0000.0000.000
126A128LEU0-0.033-0.02114.107-1.445-1.4450.0000.0000.0000.000
127A129LEU0-0.0170.01415.1731.0321.0320.0000.0000.0000.000
128A130ALA00.0690.01916.834-0.072-0.0720.0000.0000.0000.000
129A131THR00.0450.01820.102-0.250-0.2500.0000.0000.0000.000
130A132GLY00.0480.01220.8720.2520.2520.0000.0000.0000.000
131A133GLY0-0.0100.00421.7960.0550.0550.0000.0000.0000.000
132A134THR00.0610.02922.1230.2290.2290.0000.0000.0000.000
133A135ILE00.0220.02018.8410.1610.1610.0000.0000.0000.000
134A136GLU-1-0.801-0.87821.982-11.260-11.2600.0000.0000.0000.000
135A137ALA00.0300.00924.7060.2860.2860.0000.0000.0000.000
136A138THR00.022-0.01122.1900.2800.2800.0000.0000.0000.000
137A139VAL0-0.014-0.00621.9410.0890.0890.0000.0000.0000.000
138A140LYS10.8600.94524.53810.91210.9120.0000.0000.0000.000
139A141LEU0-0.022-0.01427.2310.2440.2440.0000.0000.0000.000
140A142ILE0-0.001-0.00122.3420.2150.2150.0000.0000.0000.000
141A143ARG10.8250.90222.77813.29613.2960.0000.0000.0000.000
142A144ARG10.8110.88728.2079.7319.7310.0000.0000.0000.000
143A145LEU0-0.0270.00629.3580.3550.3550.0000.0000.0000.000
144A146GLY0-0.020-0.01030.3130.0830.0830.0000.0000.0000.000
145A147GLY00.0110.00826.174-0.095-0.0950.0000.0000.0000.000
146A148GLU-1-0.921-0.96921.627-14.020-14.0200.0000.0000.0000.000
147A149VAL0-0.006-0.01219.624-0.387-0.3870.0000.0000.0000.000
148A150ALA00.0490.02518.5400.5610.5610.0000.0000.0000.000
149A151ASP-1-0.878-0.93713.616-22.422-22.4220.0000.0000.0000.000
150A152ALA0-0.003-0.00514.8201.0641.0640.0000.0000.0000.000
151A153ALA0-0.024-0.01510.249-1.566-1.5660.0000.0000.0000.000
152A154PHE00.0340.01110.7101.7251.7250.0000.0000.0000.000
153A155ILE00.0110.0079.632-3.224-3.2240.0000.0000.0000.000
154A156ILE0-0.010-0.01210.012-1.731-1.7310.0000.0000.0000.000
155A157ASN0-0.003-0.00712.2701.7351.7350.0000.0000.0000.000
156A158LEU00.0140.01213.871-0.417-0.4170.0000.0000.0000.000
157A159PHE00.0390.01114.1720.5110.5110.0000.0000.0000.000
158A160ASP-1-0.832-0.91217.171-14.101-14.1010.0000.0000.0000.000
159A161LEU0-0.061-0.02820.2330.7450.7450.0000.0000.0000.000
160A162GLY0-0.0020.01220.5450.3870.3870.0000.0000.0000.000
161A163GLY00.0170.00320.0960.2050.2050.0000.0000.0000.000
162A164GLU-1-0.916-0.95913.822-21.081-21.0810.0000.0000.0000.000
163A165GLN00.0470.01617.3900.7980.7980.0000.0000.0000.000
164A166ARG10.8130.90420.82812.48412.4840.0000.0000.0000.000
165A167LEU00.0140.00618.3810.4810.4810.0000.0000.0000.000
166A168GLU-1-0.858-0.92818.225-16.231-16.2310.0000.0000.0000.000
167A169LYS10.8060.89821.08013.64013.6400.0000.0000.0000.000
168A170GLN0-0.045-0.01723.2690.1820.1820.0000.0000.0000.000
169A171GLY00.0090.00822.0850.1800.1800.0000.0000.0000.000
170A172ILE0-0.074-0.03017.442-0.206-0.2060.0000.0000.0000.000
171A173THR0-0.0020.00212.970-0.058-0.0580.0000.0000.0000.000
172A174SER00.0260.00413.7480.1560.1560.0000.0000.0000.000
174A176SER00.012-0.0048.6892.6422.6420.0000.0000.0000.000
176A178VAL0-0.009-0.0056.274-1.857-1.8570.0000.0000.0000.000
177A179PRO00.0180.0258.4892.2942.2940.0000.0000.0000.000
178A180PHE0-0.029-0.04911.500-0.057-0.0570.0000.0000.0000.000
179A181PRO00.0370.03814.9810.1010.1010.0000.0000.0000.000
180A182GLY0-0.049-0.03118.397-0.036-0.0360.0000.0000.0000.000
181A183HIS-1-0.890-0.94721.081-12.976-12.9760.0000.0000.0000.000