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: MNL5Z

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 OptH
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 -1889394.972922
FMO2-HF: Nuclear repulsion 1820168.51707
FMO2-HF: Total energy -69226.455852
FMO2-MP2: Total energy -69433.523898


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.
-386.314-379.40430.339-18.089-19.161-0.183
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 : 0.860 / q_NPA : 0.908
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].
3A5ILE00.0000.0053.382-2.0910.633-0.003-1.263-1.4570.005
4A6LEU00.0290.0275.6272.0712.0710.0000.0000.0000.000
5A7PHE00.002-0.0169.3140.1850.1850.0000.0000.0000.000
6A8ILE00.0500.01711.9241.1281.1280.0000.0000.0000.000
7A9VAL00.0160.00515.3950.1420.1420.0000.0000.0000.000
8A10GLY00.0200.02118.4270.5060.5060.0000.0000.0000.000
9A11SER0-0.085-0.07721.5930.6770.6770.0000.0000.0000.000
10A12PHE00.0880.05222.581-0.250-0.2500.0000.0000.0000.000
11A13SER0-0.055-0.00924.9320.0430.0430.0000.0000.0000.000
12A14GLU-1-0.874-0.96624.040-12.131-12.1310.0000.0000.0000.000
13A15GLY00.0660.04024.462-0.328-0.3280.0000.0000.0000.000
14A16SER0-0.0270.01123.196-0.021-0.0210.0000.0000.0000.000
15A17PHE00.0700.01923.534-0.407-0.4070.0000.0000.0000.000
16A18ASN00.0640.02820.648-0.761-0.7610.0000.0000.0000.000
17A19ARG10.9210.97419.07912.39112.3910.0000.0000.0000.000
18A20GLN0-0.063-0.05018.882-0.675-0.6750.0000.0000.0000.000
19A21LEU0-0.022-0.00817.633-0.291-0.2910.0000.0000.0000.000
20A22ALA00.0410.02015.207-0.760-0.7600.0000.0000.0000.000
21A23LYS10.9790.99614.47213.41113.4110.0000.0000.0000.000
22A24LYS10.9010.95715.30213.44913.4490.0000.0000.0000.000
23A25ALA00.0360.02012.308-0.639-0.6390.0000.0000.0000.000
24A26GLU-1-0.847-0.93010.663-21.258-21.2580.0000.0000.0000.000
25A27THR0-0.032-0.01310.692-0.855-0.8550.0000.0000.0000.000
26A28ILE0-0.053-0.01311.223-0.261-0.2610.0000.0000.0000.000
27A29ILE0-0.0330.0125.765-1.310-1.3100.0000.0000.0000.000
28A30GLY0-0.022-0.0057.896-2.072-2.0720.0000.0000.0000.000
29A31ASP-1-0.923-0.9607.363-28.846-28.8460.0000.0000.0000.000
30A32ARG10.7750.8604.27931.80531.992-0.001-0.017-0.1690.000
31A33ALA0-0.002-0.0212.302-14.678-12.3072.282-1.847-2.807-0.010
32A34GLN0-0.0240.0053.1377.7427.7280.0150.702-0.704-0.001
33A35VAL0-0.0030.0065.337-0.487-0.442-0.001-0.008-0.0350.000
34A36SER00.0020.0127.9751.6211.6210.0000.0000.0000.000
35A37TYR0-0.064-0.03910.7730.0110.0110.0000.0000.0000.000
36A38LEU00.0460.03613.8040.4850.4850.0000.0000.0000.000
37A39SER0-0.042-0.03815.6950.6240.6240.0000.0000.0000.000
38A40TYR0-0.001-0.02119.3270.1410.1410.0000.0000.0000.000
39A41ASP-1-0.948-0.98221.760-11.621-11.6210.0000.0000.0000.000
40A42ARG10.8870.94224.87210.53510.5350.0000.0000.0000.000
41A43VAL00.0490.02523.365-0.237-0.2370.0000.0000.0000.000
42A44PRO0-0.0120.02226.6510.2600.2600.0000.0000.0000.000
43A45PHE00.009-0.00728.793-0.271-0.2710.0000.0000.0000.000
44A46PHE00.006-0.01528.1690.1750.1750.0000.0000.0000.000
45A47ASN0-0.008-0.03430.2740.2530.2530.0000.0000.0000.000
46A48GLN00.0840.03332.5850.0510.0510.0000.0000.0000.000
47A49ASP-1-0.955-0.95033.697-7.897-7.8970.0000.0000.0000.000
48A50LEU0-0.052-0.02932.4380.1050.1050.0000.0000.0000.000
49A51GLU-1-0.874-0.95529.376-10.066-10.0660.0000.0000.0000.000
50A52THR0-0.044-0.00430.078-0.185-0.1850.0000.0000.0000.000
51A53SER0-0.069-0.02831.9350.1780.1780.0000.0000.0000.000
52A54VAL0-0.004-0.00826.718-0.301-0.3010.0000.0000.0000.000
53A55HIS00.0020.00327.0310.2370.2370.0000.0000.0000.000
54A56PRO00.0020.00025.067-0.438-0.4380.0000.0000.0000.000
55A57GLU-1-0.868-0.94123.200-10.832-10.8320.0000.0000.0000.000
56A58VAL0-0.016-0.01522.118-0.505-0.5050.0000.0000.0000.000
57A59ALA0-0.065-0.03821.076-0.485-0.4850.0000.0000.0000.000
58A60HIS00.0540.02517.323-0.430-0.4300.0000.0000.0000.000
59A61ALA00.0010.00117.254-0.745-0.7450.0000.0000.0000.000
60A62ARG10.9460.97616.20612.11812.1180.0000.0000.0000.000
61A63GLU-1-0.921-0.95515.183-15.003-15.0030.0000.0000.0000.000
62A64GLU-1-0.916-0.95312.638-19.533-19.5330.0000.0000.0000.000
63A65VAL0-0.056-0.02711.172-1.769-1.7690.0000.0000.0000.000
64A66GLN0-0.059-0.03811.300-0.872-0.8720.0000.0000.0000.000
65A67GLU-1-0.948-0.9899.544-20.358-20.3580.0000.0000.0000.000
66A68ALA0-0.089-0.0256.787-2.783-2.7830.0000.0000.0000.000
67A69ASP-1-0.834-0.9172.464-50.185-47.0111.858-2.662-2.370-0.029
68A70ALA0-0.028-0.0185.7310.9170.9170.0000.0000.0000.000
69A71ILE00.007-0.0027.2451.2281.2280.0000.0000.0000.000
70A72TRP00.002-0.0089.380-0.811-0.8110.0000.0000.0000.000
71A73ILE0-0.0140.00611.6960.8840.8840.0000.0000.0000.000
72A74PHE00.0360.01512.6900.6460.6460.0000.0000.0000.000
73A75SER00.0180.00017.6230.4740.4740.0000.0000.0000.000
74A76PRO0-0.067-0.00421.064-0.028-0.0280.0000.0000.0000.000
75A77VAL00.0560.04524.712-0.126-0.1260.0000.0000.0000.000
76A78TYR0-0.043-0.02126.8580.3170.3170.0000.0000.0000.000
77A79ASN0-0.034-0.02130.250-0.006-0.0060.0000.0000.0000.000
78A80TYR00.000-0.01730.1670.2590.2590.0000.0000.0000.000
79A81ALA00.0450.04528.485-0.195-0.1950.0000.0000.0000.000
80A82ILE0-0.006-0.00523.150-0.187-0.1870.0000.0000.0000.000
81A83PRO0-0.030-0.02423.7750.4120.4120.0000.0000.0000.000
82A84GLY00.0530.02725.687-0.230-0.2300.0000.0000.0000.000
83A85PRO00.004-0.02225.006-0.089-0.0890.0000.0000.0000.000
84A86VAL00.0160.02120.447-0.241-0.2410.0000.0000.0000.000
85A87LYS10.8600.91622.53910.58010.5800.0000.0000.0000.000
86A88ASN00.0460.02324.9610.2430.2430.0000.0000.0000.000
87A89LEU0-0.0120.00318.4290.0390.0390.0000.0000.0000.000
88A90LEU00.023-0.00118.615-0.231-0.2310.0000.0000.0000.000
89A91ASP-1-0.820-0.87521.879-11.018-11.0180.0000.0000.0000.000
90A92TRP0-0.022-0.00323.6140.1110.1110.0000.0000.0000.000
91A93LEU0-0.002-0.01017.298-0.071-0.0710.0000.0000.0000.000
92A94SER0-0.042-0.02320.270-0.240-0.2400.0000.0000.0000.000
93A95ARG10.8440.93122.24011.38011.3800.0000.0000.0000.000
94A96SER0-0.005-0.01422.877-0.683-0.6830.0000.0000.0000.000
95A97LEU0-0.022-0.02618.2140.1390.1390.0000.0000.0000.000
96A98ASP-1-0.866-0.92822.869-10.324-10.3240.0000.0000.0000.000
97A99LEU0-0.021-0.01726.1230.1570.1570.0000.0000.0000.000
98A100SER0-0.107-0.04429.3920.4920.4920.0000.0000.0000.000
99A101ASP-1-0.882-0.95027.872-10.328-10.3280.0000.0000.0000.000
100A102PRO0-0.0070.01528.074-0.396-0.3960.0000.0000.0000.000
101A103THR0-0.093-0.04328.660-0.049-0.0490.0000.0000.0000.000
102A104GLY00.0290.03425.634-0.183-0.1830.0000.0000.0000.000
103A105PRO0-0.035-0.02320.135-0.032-0.0320.0000.0000.0000.000
104A106SER00.0510.03520.487-0.111-0.1110.0000.0000.0000.000
105A107VAL0-0.003-0.02115.565-0.432-0.4320.0000.0000.0000.000
106A108LEU0-0.040-0.03515.074-1.187-1.1870.0000.0000.0000.000
107A109GLN0-0.053-0.02216.3730.2680.2680.0000.0000.0000.000
108A110ASP-1-0.890-0.95013.857-18.789-18.7890.0000.0000.0000.000
109A111LYS10.8370.9519.97022.08022.0800.0000.0000.0000.000
110A112ILE00.0220.0216.7821.2621.2620.0000.0000.0000.000
111A113VAL0-0.025-0.01010.084-0.492-0.4920.0000.0000.0000.000
112A114THR00.0290.01910.5920.5730.5730.0000.0000.0000.000
113A115VAL00.0210.00213.0350.1910.1910.0000.0000.0000.000
114A116SER00.0130.02115.691-0.426-0.4260.0000.0000.0000.000
115A117SER0-0.046-0.02117.5570.4120.4120.0000.0000.0000.000
116A118VAL0-0.047-0.03421.0970.0150.0150.0000.0000.0000.000
117A119ALA0-0.001-0.01023.7400.4070.4070.0000.0000.0000.000
118A120ASN0-0.058-0.03927.225-0.078-0.0780.0000.0000.0000.000
119A121GLY00.0820.04529.0730.2990.2990.0000.0000.0000.000
120A122ALA00.0350.02229.384-0.203-0.2030.0000.0000.0000.000
121A123SER0-0.0460.00227.341-0.472-0.4720.0000.0000.0000.000
122A124PRO0-0.043-0.03525.5340.3540.3540.0000.0000.0000.000
123A125GLU-1-0.930-0.95925.537-12.358-12.3580.0000.0000.0000.000
124A126GLU-1-0.792-0.90827.165-9.048-9.0480.0000.0000.0000.000
125A127VAL0-0.094-0.03423.731-0.013-0.0130.0000.0000.0000.000
126A128PHE00.001-0.02419.713-0.142-0.1420.0000.0000.0000.000
127A129GLU-1-0.882-0.93222.999-10.845-10.8450.0000.0000.0000.000
128A130ASP-1-0.851-0.93525.138-11.118-11.1180.0000.0000.0000.000
129A131TYR0-0.002-0.03719.750-0.205-0.2050.0000.0000.0000.000
130A132ARG10.8520.90620.65813.14613.1460.0000.0000.0000.000
131A133SER0-0.0360.00021.746-0.109-0.1090.0000.0000.0000.000
132A134LEU00.0210.00222.6200.0260.0260.0000.0000.0000.000
133A135LEU0-0.025-0.01816.632-0.028-0.0280.0000.0000.0000.000
134A136PRO00.0270.01618.976-0.433-0.4330.0000.0000.0000.000
135A137PHE0-0.044-0.00420.0230.1980.1980.0000.0000.0000.000
136A138ILE0-0.091-0.04419.6530.3780.3780.0000.0000.0000.000
137A139ARG10.9310.96119.73712.93412.9340.0000.0000.0000.000
138A140MET00.0340.06414.026-0.333-0.3330.0000.0000.0000.000
139A141HIS0-0.021-0.01712.0211.3481.3480.0000.0000.0000.000
140A142LEU0-0.005-0.01312.886-1.480-1.4800.0000.0000.0000.000
141A143VAL0-0.001-0.0039.6860.3790.3790.0000.0000.0000.000
142A144ASP-1-0.883-0.95513.084-15.431-15.4310.0000.0000.0000.000
143A145GLN0-0.045-0.01413.6021.4851.4850.0000.0000.0000.000
144A146LEU0-0.045-0.01915.350-0.690-0.6900.0000.0000.0000.000
145A147THR00.0320.01516.3040.9960.9960.0000.0000.0000.000
146A148GLY00.001-0.00118.7790.0160.0160.0000.0000.0000.000
147A149VAL0-0.056-0.04420.6250.2270.2270.0000.0000.0000.000
148A150PRO00.0360.02923.4280.1990.1990.0000.0000.0000.000
149A151ILE00.014-0.01126.597-0.234-0.2340.0000.0000.0000.000
150A152ASN00.0300.02728.9030.0450.0450.0000.0000.0000.000
151A153SER00.054-0.00430.9010.0260.0260.0000.0000.0000.000
152A154GLU-1-0.860-0.94732.838-9.032-9.0320.0000.0000.0000.000
153A155ALA0-0.051-0.01029.8240.1180.1180.0000.0000.0000.000
154A156TRP00.0050.02231.689-0.022-0.0220.0000.0000.0000.000
155A157SER0-0.0050.00234.4190.1490.1490.0000.0000.0000.000
156A158THR0-0.059-0.03232.285-0.081-0.0810.0000.0000.0000.000
157A159GLY00.0570.02231.148-0.092-0.0920.0000.0000.0000.000
158A160ILE0-0.044-0.01926.634-0.366-0.3660.0000.0000.0000.000
159A161LEU00.0080.00822.7950.3050.3050.0000.0000.0000.000
160A162LYS10.7790.89425.4389.8969.8960.0000.0000.0000.000
161A163VAL00.0160.00721.2040.1950.1950.0000.0000.0000.000
162A164SER00.0330.02224.224-0.155-0.1550.0000.0000.0000.000
163A165ALA00.0640.00722.817-0.495-0.4950.0000.0000.0000.000
164A166GLU-1-0.904-0.95721.842-12.238-12.2380.0000.0000.0000.000
165A167LYS10.8390.90921.34812.74112.7410.0000.0000.0000.000
166A168LEU0-0.047-0.01718.094-0.631-0.6310.0000.0000.0000.000
167A169ALA00.0150.01217.416-1.046-1.0460.0000.0000.0000.000
168A170GLU-1-0.825-0.90116.401-15.654-15.6540.0000.0000.0000.000
169A171LEU0-0.0020.00214.458-0.918-0.9180.0000.0000.0000.000
170A172SER0-0.045-0.02712.809-1.485-1.4850.0000.0000.0000.000
171A173ALA00.0670.03811.500-1.907-1.9070.0000.0000.0000.000
172A174GLN00.0010.01311.376-0.816-0.8160.0000.0000.0000.000
173A175ALA00.001-0.0169.052-1.568-1.5680.0000.0000.0000.000
174A176ASP-1-0.846-0.9077.272-34.912-34.9120.0000.0000.0000.000
175A177ALA0-0.047-0.0177.095-3.634-3.6340.0000.0000.0000.000
176A178LEU0-0.022-0.0135.734-1.136-1.1360.0000.0000.0000.000
177A179LEU00.010-0.0052.804-4.752-3.7330.482-0.231-1.270-0.001
178A180SER00.007-0.0062.855-14.036-12.3490.261-0.878-1.070-0.011
179A181ALA0-0.073-0.0225.5890.0990.0990.0000.0000.0000.000
180A182ILE0-0.014-0.0192.260-0.4760.9211.675-0.597-2.475-0.007
181A183GLU-1-0.891-0.8891.756-144.931-150.67923.771-11.267-6.757-0.129
182A184ASN0-0.083-0.0394.3747.4427.5100.000-0.021-0.0470.000