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: 1VQ6Z

Calculation Name: 2DO8-A-Other549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DO8

Chain ID: A

ChEMBL ID:

UniProt ID: Q7VKS7

Base Structure: SolutionNMR

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1965680.675455
FMO2-HF: Nuclear repulsion 1890055.441716
FMO2-HF: Total energy -75625.233739
FMO2-MP2: Total energy -75841.917813


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-294.496-294.8519.619-10.854-8.411-0.127
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.715 / q_NPA : 0.849
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].
3A3GLY00.0120.0263.8970.9852.297-0.011-0.610-0.690-0.001
31A31HIS0-0.066-0.0374.2175.5285.716-0.001-0.037-0.1500.000
137A137HIS0-0.024-0.0102.529-28.467-26.4943.318-2.389-2.902-0.032
140A140GLU-1-0.741-0.8661.704-123.535-127.36216.313-7.818-4.669-0.094
4A4ASN00.0260.0026.1704.8094.8090.0000.0000.0000.000
5A5LEU00.0240.0096.4712.2242.2240.0000.0000.0000.000
6A6GLN00.0210.0209.5222.0942.0940.0000.0000.0000.000
7A7GLY00.0290.01412.795-0.644-0.6440.0000.0000.0000.000
8A8LYS10.8200.93010.41428.05528.0550.0000.0000.0000.000
9A9PHE00.001-0.01014.0110.6100.6100.0000.0000.0000.000
10A10ILE00.001-0.00612.528-1.271-1.2710.0000.0000.0000.000
11A11ILE0-0.014-0.00315.5711.0311.0310.0000.0000.0000.000
12A12ALA0-0.025-0.01718.292-0.201-0.2010.0000.0000.0000.000
13A13THR0-0.048-0.02719.4000.4120.4120.0000.0000.0000.000
14A14PRO00.0080.01022.8890.0060.0060.0000.0000.0000.000
15A15GLU-1-0.967-0.96624.766-11.468-11.4680.0000.0000.0000.000
16A16MET0-0.082-0.05227.9640.6090.6090.0000.0000.0000.000
17A17ASP-1-0.896-0.95526.789-12.156-12.1560.0000.0000.0000.000
18A18ASP-1-0.931-0.95628.438-10.319-10.3190.0000.0000.0000.000
19A19GLU-1-0.769-0.87528.219-10.393-10.3930.0000.0000.0000.000
20A20TYR0-0.084-0.06530.6490.2290.2290.0000.0000.0000.000
21A21PHE0-0.106-0.06431.6930.1310.1310.0000.0000.0000.000
22A22ASP-1-0.885-0.92031.391-9.876-9.8760.0000.0000.0000.000
23A23ARG10.7880.87527.27110.06010.0600.0000.0000.0000.000
24A24THR00.0590.03024.097-0.156-0.1560.0000.0000.0000.000
25A25VAL0-0.077-0.03218.763-0.461-0.4610.0000.0000.0000.000
26A26ILE00.0060.01320.3610.3600.3600.0000.0000.0000.000
27A27TYR00.011-0.01117.370-0.439-0.4390.0000.0000.0000.000
28A28ILE00.0000.00011.3320.2850.2850.0000.0000.0000.000
29A29CYS0-0.047-0.02114.7460.2240.2240.0000.0000.0000.000
30A30GLU-1-0.897-0.96012.964-19.748-19.7480.0000.0000.0000.000
32A32ASN00.0080.0029.6180.6550.6550.0000.0000.0000.000
33A33ASP-1-0.909-0.9478.905-30.238-30.2380.0000.0000.0000.000
34A34ASN0-0.016-0.0209.8210.5990.5990.0000.0000.0000.000
35A35GLY0-0.031-0.01410.6341.5071.5070.0000.0000.0000.000
36A36THR0-0.036-0.0208.729-2.555-2.5550.0000.0000.0000.000
37A37ILE00.0100.01410.9411.5501.5500.0000.0000.0000.000
38A38GLY00.011-0.00914.374-0.880-0.8800.0000.0000.0000.000
39A39VAL0-0.0190.00716.1830.7090.7090.0000.0000.0000.000
40A40ILE0-0.001-0.01915.2110.3430.3430.0000.0000.0000.000
41A41ILE0-0.036-0.00718.629-0.090-0.0900.0000.0000.0000.000
42A42ASN00.0230.00520.5090.5180.5180.0000.0000.0000.000
43A43THR00.0430.02323.9770.0140.0140.0000.0000.0000.000
44A44PRO00.0180.02527.135-0.097-0.0970.0000.0000.0000.000
45A45THR0-0.036-0.03430.3210.1270.1270.0000.0000.0000.000
46A46ASP-1-0.902-0.95233.288-8.606-8.6060.0000.0000.0000.000
47A47LEU0-0.062-0.00835.3250.2950.2950.0000.0000.0000.000
48A48SER0-0.010-0.02735.629-0.159-0.1590.0000.0000.0000.000
49A49VAL00.001-0.00534.4720.0560.0560.0000.0000.0000.000
50A50LEU00.006-0.02336.5500.1040.1040.0000.0000.0000.000
51A51GLU-1-0.840-0.89839.964-7.499-7.4990.0000.0000.0000.000
52A52LEU0-0.011-0.00234.5590.1180.1180.0000.0000.0000.000
53A53LEU0-0.020-0.00436.9640.0600.0600.0000.0000.0000.000
54A54THR0-0.093-0.07540.0460.2000.2000.0000.0000.0000.000
55A55ARG10.8530.92441.5917.8517.8510.0000.0000.0000.000
56A56MET0-0.080-0.03237.0510.0150.0150.0000.0000.0000.000
57A57ASP-1-0.912-0.95242.398-7.023-7.0230.0000.0000.0000.000
58A58PHE0-0.016-0.01038.8520.0520.0520.0000.0000.0000.000
59A59GLN00.0100.00843.3000.0900.0900.0000.0000.0000.000
60A60MET0-0.064-0.02146.3910.0890.0890.0000.0000.0000.000
61A61ALA00.0850.05642.999-0.087-0.0870.0000.0000.0000.000
62A62LYS10.9150.94242.5447.7827.7820.0000.0000.0000.000
63A63PRO00.0490.03044.320-0.038-0.0380.0000.0000.0000.000
64A64ARG10.9250.94345.3146.7336.7330.0000.0000.0000.000
65A65ILE00.0430.00648.759-0.045-0.0450.0000.0000.0000.000
66A66TYR0-0.0030.01246.3770.0720.0720.0000.0000.0000.000
67A67THR0-0.071-0.02947.1320.0030.0030.0000.0000.0000.000
68A68GLN00.0000.00942.1980.0610.0610.0000.0000.0000.000
69A69ASP-1-0.740-0.86538.967-8.316-8.3160.0000.0000.0000.000
70A70GLN0-0.049-0.03334.732-0.294-0.2940.0000.0000.0000.000
71A71MET00.0750.06233.9910.0720.0720.0000.0000.0000.000
72A72VAL0-0.029-0.00930.522-0.278-0.2780.0000.0000.0000.000
73A73LEU00.0580.04326.7100.0650.0650.0000.0000.0000.000
74A74ASN00.0000.00726.2570.0290.0290.0000.0000.0000.000
75A75GLY00.0340.01323.113-0.321-0.3210.0000.0000.0000.000
76A76GLY00.0130.00121.220-1.037-1.0370.0000.0000.0000.000
77A77PRO0-0.0180.00020.7830.5610.5610.0000.0000.0000.000
78A78VAL00.0010.00419.5130.4960.4960.0000.0000.0000.000
79A79ASN0-0.005-0.01720.9280.2920.2920.0000.0000.0000.000
80A80GLN00.021-0.01524.4000.5500.5500.0000.0000.0000.000
81A81ASP-1-0.935-0.93827.346-10.147-10.1470.0000.0000.0000.000
82A82ARG10.8850.94027.39411.44511.4450.0000.0000.0000.000
83A83GLY00.0520.04227.847-0.296-0.2960.0000.0000.0000.000
84A84PHE0-0.044-0.02424.014-0.026-0.0260.0000.0000.0000.000
85A85ILE00.0170.00826.8260.0550.0550.0000.0000.0000.000
86A86VAL00.0010.00423.551-0.267-0.2670.0000.0000.0000.000
87A87HIS10.8770.91226.35311.50311.5030.0000.0000.0000.000
88A88SER00.0580.04527.242-0.457-0.4570.0000.0000.0000.000
89A89LYS10.8490.91427.23211.59911.5990.0000.0000.0000.000
90A90THR0-0.040-0.03230.9630.1740.1740.0000.0000.0000.000
91A91ASP-1-0.869-0.91934.691-8.218-8.2180.0000.0000.0000.000
92A92HIS0-0.088-0.05434.585-0.466-0.4660.0000.0000.0000.000
93A93GLU-1-0.907-0.94035.338-8.414-8.4140.0000.0000.0000.000
94A94PHE0-0.071-0.04326.529-0.479-0.4790.0000.0000.0000.000
95A95THR0-0.042-0.01932.5400.2010.2010.0000.0000.0000.000
96A96HIS0-0.090-0.05429.914-0.355-0.3550.0000.0000.0000.000
97A97SER00.0010.01727.553-0.185-0.1850.0000.0000.0000.000
98A98TYR0-0.075-0.03517.5260.2480.2480.0000.0000.0000.000
99A99LYS10.8880.93821.14713.38413.3840.0000.0000.0000.000
100A100VAL00.0080.02118.319-0.769-0.7690.0000.0000.0000.000
101A101THR0-0.012-0.01618.217-0.840-0.8400.0000.0000.0000.000
102A102ASP-1-0.908-0.93720.295-11.982-11.9820.0000.0000.0000.000
103A103ASP-1-0.752-0.86323.427-11.326-11.3260.0000.0000.0000.000
104A104ILE0-0.042-0.00822.2780.3310.3310.0000.0000.0000.000
105A105THR00.006-0.01223.236-0.365-0.3650.0000.0000.0000.000
106A106LEU0-0.0050.01021.3330.2220.2220.0000.0000.0000.000
107A107THR00.022-0.00424.904-0.029-0.0290.0000.0000.0000.000
108A108THR0-0.039-0.03326.499-0.018-0.0180.0000.0000.0000.000
109A109SER00.0250.01029.2320.3360.3360.0000.0000.0000.000
110A110GLY00.0290.01631.5870.0940.0940.0000.0000.0000.000
111A111ASP-1-0.751-0.88132.069-9.679-9.6790.0000.0000.0000.000
112A112VAL0-0.0120.00031.5380.0750.0750.0000.0000.0000.000
113A113LEU0-0.045-0.02734.4280.1220.1220.0000.0000.0000.000
114A114ASP-1-0.958-0.95337.522-7.925-7.9250.0000.0000.0000.000
115A115SER00.000-0.00734.9300.0570.0570.0000.0000.0000.000
116A116PHE0-0.034-0.02734.9920.1680.1680.0000.0000.0000.000
117A117GLY0-0.005-0.00939.0900.1190.1190.0000.0000.0000.000
118A118THR00.0030.01440.7990.3230.3230.0000.0000.0000.000
119A119GLN0-0.063-0.05342.106-0.004-0.0040.0000.0000.0000.000
120A120THR00.0210.01738.1990.0060.0060.0000.0000.0000.000
121A121ALA0-0.0010.01137.280-0.264-0.2640.0000.0000.0000.000
122A122PRO0-0.002-0.01432.8850.0540.0540.0000.0000.0000.000
123A123GLU-1-0.882-0.90634.696-9.074-9.0740.0000.0000.0000.000
124A124LYS10.8850.93931.5059.3199.3190.0000.0000.0000.000
125A125PHE0-0.006-0.01230.210-0.196-0.1960.0000.0000.0000.000
126A126ILE00.0170.02624.8660.2070.2070.0000.0000.0000.000
127A127VAL00.001-0.00928.554-0.171-0.1710.0000.0000.0000.000
128A128CYS0-0.022-0.00825.120-0.228-0.2280.0000.0000.0000.000
129A129LEU00.0250.01427.106-0.018-0.0180.0000.0000.0000.000
130A130GLY00.0320.02724.844-0.279-0.2790.0000.0000.0000.000
131A131CYS0-0.072-0.04819.368-0.350-0.3500.0000.0000.0000.000
132A132SER0-0.003-0.01317.5810.3870.3870.0000.0000.0000.000
133A133THR0-0.031-0.02315.029-0.346-0.3460.0000.0000.0000.000
134A134TRP00.0390.01910.9880.6720.6720.0000.0000.0000.000
135A135LYS10.9510.97111.32818.89518.8950.0000.0000.0000.000
136A136PRO00.0680.0258.518-2.401-2.4010.0000.0000.0000.000
138A138GLN0-0.018-0.0045.481-2.520-2.5200.0000.0000.0000.000
139A139LEU00.0500.0238.150-0.689-0.6890.0000.0000.0000.000
141A141GLN0-0.013-0.0045.618-1.600-1.6000.0000.0000.0000.000
142A142GLU-1-0.871-0.9337.418-23.082-23.0820.0000.0000.0000.000
143A143ILE0-0.013-0.0057.8211.9501.9500.0000.0000.0000.000
144A144ALA0-0.034-0.0126.6932.0902.0900.0000.0000.0000.000
145A145GLN0-0.096-0.0598.7753.4683.4680.0000.0000.0000.000
146A146ASN0-0.104-0.04911.7372.6852.6850.0000.0000.0000.000
147A147TYR00.0230.02113.2911.7341.7340.0000.0000.0000.000
148A148TRP0-0.001-0.01012.3491.1111.1110.0000.0000.0000.000
149A149LEU00.0300.02412.862-1.908-1.9080.0000.0000.0000.000
150A150LEU0-0.028-0.0148.823-0.001-0.0010.0000.0000.0000.000
151A151SER00.0310.01212.9530.6390.6390.0000.0000.0000.000
152A152GLU-1-0.900-0.95812.787-24.273-24.2730.0000.0000.0000.000
153A153ALA00.0140.00315.5301.4021.4020.0000.0000.0000.000
154A154ASN0-0.019-0.01218.524-0.296-0.2960.0000.0000.0000.000
155A155ASN0-0.027-0.04619.9770.6760.6760.0000.0000.0000.000
156A156GLN00.0240.01422.105-0.231-0.2310.0000.0000.0000.000
157A157THR0-0.063-0.04521.8100.4590.4590.0000.0000.0000.000
158A158LEU0-0.049-0.01519.437-0.126-0.1260.0000.0000.0000.000
159A159PHE0-0.048-0.03422.6110.1680.1680.0000.0000.0000.000
160A160GLU-1-0.881-0.92226.157-10.479-10.4790.0000.0000.0000.000
161A161THR0-0.036-0.02126.0260.3580.3580.0000.0000.0000.000
162A162SER00.001-0.01027.7860.2570.2570.0000.0000.0000.000
163A163TYR0-0.112-0.06830.8410.4180.4180.0000.0000.0000.000
164A164LEU0-0.026-0.02032.9900.3250.3250.0000.0000.0000.000
165A165ASP-1-0.972-0.97834.320-9.041-9.0410.0000.0000.0000.000
166A166ARG10.7640.83629.40210.23210.2320.0000.0000.0000.000
167A167TRP00.0650.04530.1390.0230.0230.0000.0000.0000.000
168A168VAL0-0.0080.00626.8310.0900.0900.0000.0000.0000.000
169A169GLU-1-0.798-0.89725.292-12.543-12.5430.0000.0000.0000.000
170A170ALA0-0.014-0.01521.312-0.368-0.3680.0000.0000.0000.000
171A171ASN00.0290.00221.551-0.977-0.9770.0000.0000.0000.000
172A172GLU-1-0.840-0.88623.395-10.941-10.9410.0000.0000.0000.000
173A173MET0-0.0460.00418.906-0.145-0.1450.0000.0000.0000.000
174A174LEU0-0.005-0.00718.137-0.203-0.2030.0000.0000.0000.000
175A175GLY0-0.036-0.01521.6810.0450.0450.0000.0000.0000.000
176A176ILE0-0.084-0.03724.9540.4370.4370.0000.0000.0000.000
177A177SER0-0.035-0.00621.100-0.158-0.1580.0000.0000.0000.000
178A178GLY00.0460.00423.0300.3020.3020.0000.0000.0000.000
179A179ILE0-0.056-0.03521.875-0.210-0.2100.0000.0000.0000.000
180A180LEU0-0.026-0.02216.842-0.176-0.1760.0000.0000.0000.000
181A181ALA00.1060.06418.004-0.784-0.7840.0000.0000.0000.000
182A182PRO0-0.0110.01420.1530.1700.1700.0000.0000.0000.000
183A183ALA00.011-0.00122.2470.3490.3490.0000.0000.0000.000
184A184GLY00.0090.00324.3040.4140.4140.0000.0000.0000.000
185A185ARG10.7550.86323.72512.92912.9290.0000.0000.0000.000
186A186ALA0-0.003-0.00325.027-0.440-0.4400.0000.0000.0000.000
187A187LEU0-0.070-0.03926.155-0.171-0.1710.0000.0000.0000.000
188A188GLU-2-1.765-1.85326.432-22.910-22.9100.0000.0000.0000.000