Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 76K9K

Calculation Name: 3FVW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FVW

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DWD8

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1889334.89899
FMO2-HF: Nuclear repulsion 1820107.410802
FMO2-HF: Total energy -69227.488188
FMO2-MP2: Total energy -69434.450276


3D Structure
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:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-398.563-395.94740.015-21.375-21.251-0.222
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.820 / q_NPA : 0.886
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].
3A5ILE0-0.018-0.0103.328-1.9010.7560.001-1.218-1.4400.005
4A6LEU00.0280.0325.6472.1722.1720.0000.0000.0000.000
5A7PHE0-0.003-0.0198.7910.2770.2770.0000.0000.0000.000
6A8ILE00.0490.01611.9421.1331.1330.0000.0000.0000.000
7A9VAL00.0160.00815.4130.1710.1710.0000.0000.0000.000
8A10GLY00.0260.02618.4430.5050.5050.0000.0000.0000.000
9A11SER0-0.058-0.06121.6080.7360.7360.0000.0000.0000.000
10A12PHE00.0760.04422.599-0.269-0.2690.0000.0000.0000.000
11A13SER0-0.046-0.00324.9510.1340.1340.0000.0000.0000.000
12A14GLU-1-0.877-0.96423.439-12.327-12.3270.0000.0000.0000.000
13A15GLY00.0510.03524.477-0.308-0.3080.0000.0000.0000.000
14A16SER0-0.0250.00323.211-0.108-0.1080.0000.0000.0000.000
15A17PHE00.0550.01223.545-0.420-0.4200.0000.0000.0000.000
16A18ASN00.0640.02820.677-0.713-0.7130.0000.0000.0000.000
17A19ARG10.9030.94819.09312.35112.3510.0000.0000.0000.000
18A20GLN0-0.044-0.02918.893-0.616-0.6160.0000.0000.0000.000
19A21LEU0-0.016-0.00617.698-0.246-0.2460.0000.0000.0000.000
20A22ALA00.0390.01915.188-0.733-0.7330.0000.0000.0000.000
21A23LYS10.9770.99814.48013.42113.4210.0000.0000.0000.000
22A24LYS10.8760.95315.36213.08313.0830.0000.0000.0000.000
23A25ALA00.0260.02012.508-0.602-0.6020.0000.0000.0000.000
24A26GLU-1-0.808-0.89010.726-20.504-20.5040.0000.0000.0000.000
25A27THR0-0.061-0.03310.748-0.793-0.7930.0000.0000.0000.000
26A28ILE0-0.075-0.02511.724-0.287-0.2870.0000.0000.0000.000
27A29ILE0-0.017-0.0016.316-1.055-1.0550.0000.0000.0000.000
28A30GLY0-0.012-0.0048.128-1.908-1.9080.0000.0000.0000.000
29A31ASP-1-0.927-0.9617.425-28.319-28.3190.0000.0000.0000.000
30A32ARG10.7660.8734.60630.62730.774-0.001-0.012-0.1330.000
31A33ALA0-0.005-0.0172.377-13.206-10.7781.569-1.539-2.457-0.008
32A34GLN0-0.0100.0173.1925.9686.0440.0160.551-0.6430.000
33A35VAL00.0110.0105.390-0.556-0.520-0.001-0.008-0.0270.000
34A36SER00.0100.0147.9931.1631.1630.0000.0000.0000.000
35A37TYR0-0.097-0.07910.7960.0040.0040.0000.0000.0000.000
36A38LEU00.0310.02913.8260.4890.4890.0000.0000.0000.000
37A39SER0-0.044-0.02015.7190.4850.4850.0000.0000.0000.000
38A40TYR0-0.002-0.03319.3330.1390.1390.0000.0000.0000.000
39A41ASP-1-0.864-0.92821.784-11.425-11.4250.0000.0000.0000.000
40A42ARG10.7880.88324.89510.87010.8700.0000.0000.0000.000
41A43VAL00.0410.02423.359-0.234-0.2340.0000.0000.0000.000
42A44PRO00.0110.02426.6750.2510.2510.0000.0000.0000.000
43A45PHE00.002-0.00328.815-0.272-0.2720.0000.0000.0000.000
44A46PHE00.005-0.00528.2410.1560.1560.0000.0000.0000.000
45A47ASN0-0.037-0.05830.2940.2770.2770.0000.0000.0000.000
46A48GLN00.0720.03332.6780.0690.0690.0000.0000.0000.000
47A49ASP-1-0.932-0.93433.730-8.009-8.0090.0000.0000.0000.000
48A50LEU0-0.026-0.01532.5650.1100.1100.0000.0000.0000.000
49A51GLU-1-0.861-0.94829.069-10.225-10.2250.0000.0000.0000.000
50A52THR0-0.040-0.00430.101-0.194-0.1940.0000.0000.0000.000
51A53SER0-0.062-0.02631.9590.1730.1730.0000.0000.0000.000
52A54VAL0-0.013-0.01126.729-0.296-0.2960.0000.0000.0000.000
53A55HIS00.0100.00127.0140.2700.2700.0000.0000.0000.000
54A56PRO00.0000.00025.067-0.444-0.4440.0000.0000.0000.000
55A57GLU-1-0.879-0.94623.218-10.909-10.9090.0000.0000.0000.000
56A58VAL0-0.014-0.01722.143-0.513-0.5130.0000.0000.0000.000
57A59ALA0-0.041-0.02221.100-0.505-0.5050.0000.0000.0000.000
58A60HIS00.0120.01017.211-0.345-0.3450.0000.0000.0000.000
59A61ALA00.003-0.00517.274-0.773-0.7730.0000.0000.0000.000
60A62ARG10.8410.90716.23512.41712.4170.0000.0000.0000.000
61A63GLU-1-0.790-0.88015.102-14.780-14.7800.0000.0000.0000.000
62A64GLU-1-0.908-0.95112.637-19.927-19.9270.0000.0000.0000.000
63A65VAL0-0.039-0.02111.198-1.749-1.7490.0000.0000.0000.000
64A66GLN0-0.040-0.02411.332-0.848-0.8480.0000.0000.0000.000
65A67GLU-1-0.933-0.9629.208-22.309-22.3090.0000.0000.0000.000
66A68ALA0-0.065-0.0176.815-2.774-2.7740.0000.0000.0000.000
67A69ASP-1-0.811-0.8912.304-52.526-49.9373.368-3.152-2.804-0.032
68A70ALA0-0.052-0.0285.7720.9430.9430.0000.0000.0000.000
69A71ILE00.002-0.0047.2551.1891.1890.0000.0000.0000.000
70A72TRP0-0.009-0.0169.379-0.730-0.7300.0000.0000.0000.000
71A73ILE0-0.0070.00411.7050.8430.8430.0000.0000.0000.000
72A74PHE00.0460.02412.6150.6780.6780.0000.0000.0000.000
73A75SER00.0140.01517.6330.4620.4620.0000.0000.0000.000
74A76PRO0-0.0480.01321.074-0.033-0.0330.0000.0000.0000.000
75A77VAL00.0490.03824.721-0.085-0.0850.0000.0000.0000.000
76A78TYR0-0.049-0.03026.8560.3220.3220.0000.0000.0000.000
77A79ASN0-0.029-0.02030.261-0.022-0.0220.0000.0000.0000.000
78A80TYR00.008-0.00830.1950.2540.2540.0000.0000.0000.000
79A81ALA00.0170.02928.561-0.193-0.1930.0000.0000.0000.000
80A82ILE00.0210.01023.267-0.187-0.1870.0000.0000.0000.000
81A83PRO0-0.042-0.02123.8090.3950.3950.0000.0000.0000.000
82A84GLY00.0550.02625.702-0.223-0.2230.0000.0000.0000.000
83A85PRO0-0.004-0.02524.941-0.090-0.0900.0000.0000.0000.000
84A86VAL00.0140.02020.400-0.250-0.2500.0000.0000.0000.000
85A87LYS10.8490.91122.55610.50110.5010.0000.0000.0000.000
86A88ASN00.0160.00824.9760.2000.2000.0000.0000.0000.000
87A89LEU0-0.0040.00218.6050.0290.0290.0000.0000.0000.000
88A90LEU00.0310.00718.534-0.237-0.2370.0000.0000.0000.000
89A91ASP-1-0.808-0.86321.896-10.997-10.9970.0000.0000.0000.000
90A92TRP0-0.017-0.00723.5520.1490.1490.0000.0000.0000.000
91A93LEU00.007-0.00517.274-0.072-0.0720.0000.0000.0000.000
92A94SER0-0.051-0.02920.293-0.248-0.2480.0000.0000.0000.000
93A95ARG10.8240.91522.25611.48111.4810.0000.0000.0000.000
94A96SER00.005-0.00522.908-0.706-0.7060.0000.0000.0000.000
95A97LEU0-0.007-0.01618.2310.1540.1540.0000.0000.0000.000
96A98ASP-1-0.857-0.90722.891-10.333-10.3330.0000.0000.0000.000
97A99LEU0-0.024-0.01326.1430.1690.1690.0000.0000.0000.000
98A100SER0-0.125-0.07729.4120.4850.4850.0000.0000.0000.000
99A101ASP-1-0.850-0.92927.979-10.378-10.3780.0000.0000.0000.000
100A102PRO0-0.0140.00628.099-0.386-0.3860.0000.0000.0000.000
101A103THR0-0.126-0.06528.691-0.045-0.0450.0000.0000.0000.000
102A104GLY00.0270.03425.660-0.196-0.1960.0000.0000.0000.000
103A105PRO0-0.033-0.02220.111-0.023-0.0230.0000.0000.0000.000
104A106SER00.0430.03220.374-0.128-0.1280.0000.0000.0000.000
105A107VAL00.003-0.01715.528-0.470-0.4700.0000.0000.0000.000
106A108LEU0-0.035-0.03415.108-1.224-1.2240.0000.0000.0000.000
107A109GLN0-0.076-0.04616.3830.2900.2900.0000.0000.0000.000
108A110ASP-1-0.882-0.93513.842-18.778-18.7780.0000.0000.0000.000
109A111LYS10.8050.9149.40722.67822.6780.0000.0000.0000.000
110A112ILE00.0260.0276.7921.3521.3520.0000.0000.0000.000
111A113VAL0-0.010-0.00810.102-0.406-0.4060.0000.0000.0000.000
112A114THR00.0030.00410.8410.5580.5580.0000.0000.0000.000
113A115VAL00.011-0.00113.0960.1590.1590.0000.0000.0000.000
114A116SER00.0220.03115.723-0.388-0.3880.0000.0000.0000.000
115A117SER0-0.055-0.03517.6620.4280.4280.0000.0000.0000.000
116A118VAL0-0.055-0.03821.2090.0250.0250.0000.0000.0000.000
117A119ALA00.001-0.00723.8620.4040.4040.0000.0000.0000.000
118A120ASN0-0.052-0.03827.342-0.188-0.1880.0000.0000.0000.000
119A121GLY00.0780.04429.1810.2990.2990.0000.0000.0000.000
120A122ALA00.0330.02129.477-0.202-0.2020.0000.0000.0000.000
121A123SER0-0.0360.01127.604-0.479-0.4790.0000.0000.0000.000
122A124PRO0-0.060-0.04525.9350.3670.3670.0000.0000.0000.000
123A125GLU-1-0.933-0.96325.657-12.428-12.4280.0000.0000.0000.000
124A126GLU-1-0.808-0.91727.243-9.062-9.0620.0000.0000.0000.000
125A127VAL0-0.085-0.03123.694-0.007-0.0070.0000.0000.0000.000
126A128PHE0-0.012-0.02820.067-0.160-0.1600.0000.0000.0000.000
127A129GLU-1-0.882-0.92823.054-10.828-10.8280.0000.0000.0000.000
128A130ASP-1-0.838-0.93525.132-11.267-11.2670.0000.0000.0000.000
129A131TYR00.015-0.03719.798-0.163-0.1630.0000.0000.0000.000
130A132ARG10.8060.86320.31913.42213.4220.0000.0000.0000.000
131A133SER0-0.047-0.01021.779-0.093-0.0930.0000.0000.0000.000
132A134LEU00.004-0.00222.7360.0020.0020.0000.0000.0000.000
133A135LEU00.007-0.01016.564-0.049-0.0490.0000.0000.0000.000
134A136PRO00.0210.01318.914-0.425-0.4250.0000.0000.0000.000
135A137PHE0-0.050-0.00620.0170.1870.1870.0000.0000.0000.000
136A138ILE0-0.087-0.04519.7770.3630.3630.0000.0000.0000.000
137A139ARG10.9280.95919.70612.83412.8340.0000.0000.0000.000
138A140MET00.0410.07214.216-0.352-0.3520.0000.0000.0000.000
139A141HIS0-0.017-0.01611.9831.1041.1040.0000.0000.0000.000
140A142LEU0-0.006-0.00912.878-1.484-1.4840.0000.0000.0000.000
141A143VAL00.0150.0049.6040.4340.4340.0000.0000.0000.000
142A144ASP-1-0.835-0.89413.056-15.216-15.2160.0000.0000.0000.000
143A145GLN0-0.036-0.01613.7531.4671.4670.0000.0000.0000.000
144A146LEU0-0.031-0.00815.548-0.666-0.6660.0000.0000.0000.000
145A147THR00.0080.00816.3610.9440.9440.0000.0000.0000.000
146A148GLY00.0180.00318.8750.0040.0040.0000.0000.0000.000
147A149VAL0-0.051-0.04220.7030.2340.2340.0000.0000.0000.000
148A150PRO00.0450.03423.5460.1860.1860.0000.0000.0000.000
149A151ILE0-0.001-0.01426.725-0.228-0.2280.0000.0000.0000.000
150A152ASN0-0.026-0.01429.0340.0250.0250.0000.0000.0000.000
151A153SER00.048-0.01231.0340.0120.0120.0000.0000.0000.000
152A154GLU-1-0.809-0.89233.194-9.057-9.0570.0000.0000.0000.000
153A155ALA0-0.0360.00629.8710.1220.1220.0000.0000.0000.000
154A156TRP00.0080.01431.745-0.037-0.0370.0000.0000.0000.000
155A157SER0-0.019-0.00134.4260.0970.0970.0000.0000.0000.000
156A158THR0-0.036-0.03332.566-0.073-0.0730.0000.0000.0000.000
157A159GLY00.0450.02131.156-0.093-0.0930.0000.0000.0000.000
158A160ILE0-0.038-0.01826.687-0.355-0.3550.0000.0000.0000.000
159A161LEU00.0070.01022.8750.3030.3030.0000.0000.0000.000
160A162LYS10.7860.88225.6409.7249.7240.0000.0000.0000.000
161A163VAL00.0070.00321.2230.1810.1810.0000.0000.0000.000
162A164SER0-0.016-0.03124.445-0.137-0.1370.0000.0000.0000.000
163A165ALA00.0550.00523.007-0.493-0.4930.0000.0000.0000.000
164A166GLU-1-0.818-0.88722.145-12.127-12.1270.0000.0000.0000.000
165A167LYS10.8270.89821.73312.67612.6760.0000.0000.0000.000
166A168LEU0-0.045-0.01818.306-0.655-0.6550.0000.0000.0000.000
167A169ALA00.0210.01417.608-1.013-1.0130.0000.0000.0000.000
168A170GLU-1-0.817-0.88716.787-15.056-15.0560.0000.0000.0000.000
169A171LEU00.0080.00714.708-0.920-0.9200.0000.0000.0000.000
170A172SER0-0.023-0.02113.030-1.323-1.3230.0000.0000.0000.000
171A173ALA00.0520.02711.908-1.861-1.8610.0000.0000.0000.000
172A174GLN00.0020.00411.675-0.723-0.7230.0000.0000.0000.000
173A175ALA00.000-0.0139.291-1.573-1.5730.0000.0000.0000.000
174A176ASP-1-0.818-0.8937.635-33.424-33.4240.0000.0000.0000.000
175A177ALA0-0.051-0.0227.337-3.581-3.5810.0000.0000.0000.000
176A178LEU0-0.023-0.0125.559-1.251-1.2510.0000.0000.0000.000
177A179LEU00.0240.0022.764-4.668-3.7920.464-0.197-1.143-0.001
178A180SER00.003-0.0052.849-14.481-12.7480.228-0.867-1.093-0.011
179A181ALA0-0.072-0.0145.573-0.332-0.3320.0000.0000.0000.000
180A182ILE0-0.001-0.0112.029-0.1340.4142.768-0.729-2.587-0.009
181A183GLU-1-0.851-0.8821.712-156.926-165.46231.602-14.189-8.877-0.166
182A184ASN0-0.099-0.0504.4109.1979.2590.001-0.015-0.0470.000