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

tag_button

FMODB ID: 2NMYR

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 OptAll
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 -1895907.193125
FMO2-HF: Nuclear repulsion 1826679.10464
FMO2-HF: Total energy -69228.088485
FMO2-MP2: Total energy -69434.980236


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.
-398.494-395.99842.342-20.974-23.864-0.229
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 : 0.830 / q_NPA : 0.897
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].
3A5ILE0-0.012-0.0133.317-2.1740.1860.017-1.066-1.3120.004
4A6LEU00.0170.0265.6362.2872.2870.0000.0000.0000.000
5A7PHE00.007-0.0108.6250.6840.6840.0000.0000.0000.000
6A8ILE00.0240.00312.0071.2341.2340.0000.0000.0000.000
7A9VAL00.0140.01315.3970.3370.3370.0000.0000.0000.000
8A10GLY00.0320.02218.3720.4720.4720.0000.0000.0000.000
9A11SER0-0.023-0.03121.4920.7520.7520.0000.0000.0000.000
10A12PHE00.0680.04522.590-0.300-0.3000.0000.0000.0000.000
11A13SER0-0.0250.00324.9660.0970.0970.0000.0000.0000.000
12A14GLU-1-0.815-0.90922.417-12.932-12.9320.0000.0000.0000.000
13A15GLY00.0720.02323.925-0.403-0.4030.0000.0000.0000.000
14A16SER0-0.0140.01623.544-0.030-0.0300.0000.0000.0000.000
15A17PHE00.0420.00623.493-0.518-0.5180.0000.0000.0000.000
16A18ASN00.0530.02620.890-0.773-0.7730.0000.0000.0000.000
17A19ARG10.8770.93219.23112.40812.4080.0000.0000.0000.000
18A20GLN0-0.058-0.04219.140-0.594-0.5940.0000.0000.0000.000
19A21LEU0-0.007-0.00717.610-0.252-0.2520.0000.0000.0000.000
20A22ALA00.0360.03115.345-0.752-0.7520.0000.0000.0000.000
21A23LYS10.9060.94514.60613.36613.3660.0000.0000.0000.000
22A24LYS10.8350.93215.70413.18413.1840.0000.0000.0000.000
23A25ALA00.0280.00812.729-0.492-0.4920.0000.0000.0000.000
24A26GLU-1-0.823-0.89010.692-20.676-20.6760.0000.0000.0000.000
25A27THR0-0.062-0.04110.903-1.087-1.0870.0000.0000.0000.000
26A28ILE0-0.061-0.01711.791-0.165-0.1650.0000.0000.0000.000
27A29ILE0-0.023-0.0066.080-1.395-1.3950.0000.0000.0000.000
28A30GLY0-0.009-0.0037.998-2.061-2.0610.0000.0000.0000.000
29A31ASP-1-0.936-0.9667.323-29.498-29.4980.0000.0000.0000.000
30A32ARG10.7650.8604.76331.00031.151-0.001-0.016-0.1340.000
31A33ALA00.000-0.0092.399-14.609-12.6272.515-1.686-2.810-0.008
32A34GLN0-0.0260.0043.0666.4256.2840.0220.843-0.724-0.001
33A35VAL00.0160.0155.343-0.603-0.551-0.001-0.008-0.0420.000
34A36SER0-0.040-0.0108.0950.8720.8720.0000.0000.0000.000
35A37TYR0-0.087-0.08210.8640.0350.0350.0000.0000.0000.000
36A38LEU00.0220.02713.9540.7140.7140.0000.0000.0000.000
37A39SER0-0.036-0.01415.7340.4800.4800.0000.0000.0000.000
38A40TYR0-0.006-0.04319.3550.2640.2640.0000.0000.0000.000
39A41ASP-1-0.854-0.92321.752-11.535-11.5350.0000.0000.0000.000
40A42ARG10.7820.87224.80711.11211.1120.0000.0000.0000.000
41A43VAL00.0390.02622.875-0.333-0.3330.0000.0000.0000.000
42A44PRO00.0120.02826.2270.2470.2470.0000.0000.0000.000
43A45PHE0-0.0010.00528.406-0.288-0.2880.0000.0000.0000.000
44A46PHE00.0050.00527.8340.1470.1470.0000.0000.0000.000
45A47ASN0-0.044-0.06029.8530.2710.2710.0000.0000.0000.000
46A48GLN00.0580.03431.6720.0850.0850.0000.0000.0000.000
47A49ASP-1-0.905-0.93033.528-8.016-8.0160.0000.0000.0000.000
48A50LEU0-0.038-0.01032.1640.0840.0840.0000.0000.0000.000
49A51GLU-1-0.849-0.94429.121-10.244-10.2440.0000.0000.0000.000
50A52THR0-0.036-0.00929.853-0.179-0.1790.0000.0000.0000.000
51A53SER0-0.056-0.02031.2100.2690.2690.0000.0000.0000.000
52A54VAL0-0.025-0.01626.791-0.308-0.3080.0000.0000.0000.000
53A55HIS00.0100.00426.7410.2460.2460.0000.0000.0000.000
54A56PRO0-0.015-0.01725.008-0.442-0.4420.0000.0000.0000.000
55A57GLU-1-0.872-0.94123.143-10.980-10.9800.0000.0000.0000.000
56A58VAL00.005-0.00421.834-0.540-0.5400.0000.0000.0000.000
57A59ALA0-0.035-0.00720.970-0.511-0.5110.0000.0000.0000.000
58A60HIS00.0100.00517.405-0.578-0.5780.0000.0000.0000.000
59A61ALA0-0.002-0.00717.171-0.807-0.8070.0000.0000.0000.000
60A62ARG10.8270.87516.24312.51812.5180.0000.0000.0000.000
61A63GLU-1-0.785-0.86915.411-14.855-14.8550.0000.0000.0000.000
62A64GLU-1-0.889-0.94312.276-21.026-21.0260.0000.0000.0000.000
63A65VAL0-0.036-0.01911.130-1.791-1.7910.0000.0000.0000.000
64A66GLN0-0.014-0.00511.619-0.649-0.6490.0000.0000.0000.000
65A67GLU-1-0.891-0.9419.155-23.252-23.2520.0000.0000.0000.000
66A68ALA0-0.044-0.0146.593-2.586-2.5860.0000.0000.0000.000
67A69ASP-1-0.817-0.8922.352-53.882-50.6413.482-3.424-3.300-0.037
68A70ALA0-0.041-0.0215.5391.5941.5940.0000.0000.0000.000
69A71ILE0-0.006-0.0066.9660.9310.9310.0000.0000.0000.000
70A72TRP0-0.003-0.0179.261-0.975-0.9750.0000.0000.0000.000
71A73ILE0-0.0180.00411.6080.8880.8880.0000.0000.0000.000
72A74PHE00.0430.01412.3950.4430.4430.0000.0000.0000.000
73A75SER0-0.008-0.01517.4970.5680.5680.0000.0000.0000.000
74A76PRO0-0.0140.02521.0080.0250.0250.0000.0000.0000.000
75A77VAL00.0360.02524.440-0.171-0.1710.0000.0000.0000.000
76A78TYR0-0.064-0.03626.3630.3670.3670.0000.0000.0000.000
77A79ASN0-0.032-0.02830.036-0.015-0.0150.0000.0000.0000.000
78A80TYR00.002-0.00230.0290.2690.2690.0000.0000.0000.000
79A81ALA00.0270.03828.300-0.205-0.2050.0000.0000.0000.000
80A82ILE00.006-0.01022.760-0.164-0.1640.0000.0000.0000.000
81A83PRO0-0.058-0.02523.6250.3880.3880.0000.0000.0000.000
82A84GLY00.0470.02225.245-0.243-0.2430.0000.0000.0000.000
83A85PRO0-0.012-0.01824.710-0.065-0.0650.0000.0000.0000.000
84A86VAL00.0380.03019.926-0.196-0.1960.0000.0000.0000.000
85A87LYS10.8370.91022.17810.63110.6310.0000.0000.0000.000
86A88ASN00.015-0.00524.5680.1360.1360.0000.0000.0000.000
87A89LEU0-0.009-0.00118.1470.0100.0100.0000.0000.0000.000
88A90LEU00.0370.01317.996-0.291-0.2910.0000.0000.0000.000
89A91ASP-1-0.818-0.87321.375-11.104-11.1040.0000.0000.0000.000
90A92TRP0-0.024-0.02323.3380.0840.0840.0000.0000.0000.000
91A93LEU0-0.009-0.00716.892-0.080-0.0800.0000.0000.0000.000
92A94SER0-0.052-0.02920.024-0.184-0.1840.0000.0000.0000.000
93A95ARG10.8360.91821.89611.54311.5430.0000.0000.0000.000
94A96SER00.011-0.00122.598-0.719-0.7190.0000.0000.0000.000
95A97LEU0-0.011-0.02318.0200.1490.1490.0000.0000.0000.000
96A98ASP-1-0.866-0.90422.606-10.285-10.2850.0000.0000.0000.000
97A99LEU0-0.015-0.00826.1360.1860.1860.0000.0000.0000.000
98A100SER0-0.109-0.07429.5000.4640.4640.0000.0000.0000.000
99A101ASP-1-0.850-0.91627.892-10.366-10.3660.0000.0000.0000.000
100A102PRO0-0.028-0.00827.980-0.402-0.4020.0000.0000.0000.000
101A103THR0-0.117-0.06928.5750.0100.0100.0000.0000.0000.000
102A104GLY00.0130.02725.644-0.233-0.2330.0000.0000.0000.000
103A105PRO0-0.026-0.01719.958-0.084-0.0840.0000.0000.0000.000
104A106SER00.0480.03219.960-0.143-0.1430.0000.0000.0000.000
105A107VAL0-0.014-0.01815.676-0.501-0.5010.0000.0000.0000.000
106A108LEU0-0.013-0.02214.955-1.135-1.1350.0000.0000.0000.000
107A109GLN0-0.073-0.04915.8070.1690.1690.0000.0000.0000.000
108A110ASP-1-0.881-0.93013.893-18.624-18.6240.0000.0000.0000.000
109A111LYS10.7940.9089.44622.41522.4150.0000.0000.0000.000
110A112ILE00.0230.0216.7801.4481.4480.0000.0000.0000.000
111A113VAL0-0.013-0.0029.770-0.421-0.4210.0000.0000.0000.000
112A114THR00.0090.00610.7290.6180.6180.0000.0000.0000.000
113A115VAL00.0170.00312.8940.2310.2310.0000.0000.0000.000
114A116SER00.0090.02715.616-0.352-0.3520.0000.0000.0000.000
115A117SER0-0.046-0.03617.5370.5220.5220.0000.0000.0000.000
116A118VAL0-0.046-0.02521.1860.0470.0470.0000.0000.0000.000
117A119ALA00.017-0.00123.8810.3020.3020.0000.0000.0000.000
118A120ASN0-0.051-0.04627.283-0.065-0.0650.0000.0000.0000.000
119A121GLY00.0480.03629.9420.1680.1680.0000.0000.0000.000
120A122ALA0-0.0210.00529.977-0.112-0.1120.0000.0000.0000.000
121A123SER00.001-0.00127.306-0.560-0.5600.0000.0000.0000.000
122A124PRO0-0.057-0.03725.3490.3920.3920.0000.0000.0000.000
123A125GLU-1-0.878-0.93325.221-12.676-12.6760.0000.0000.0000.000
124A126GLU-1-0.857-0.92027.451-9.308-9.3080.0000.0000.0000.000
125A127VAL0-0.058-0.03323.727-0.108-0.1080.0000.0000.0000.000
126A128PHE00.011-0.00720.065-0.296-0.2960.0000.0000.0000.000
127A129GLU-1-0.853-0.92022.960-10.876-10.8760.0000.0000.0000.000
128A130ASP-1-0.817-0.90525.065-11.435-11.4350.0000.0000.0000.000
129A131TYR00.0290.00819.641-0.348-0.3480.0000.0000.0000.000
130A132ARG10.7870.84320.37713.36513.3650.0000.0000.0000.000
131A133SER0-0.052-0.02221.574-0.096-0.0960.0000.0000.0000.000
132A134LEU00.002-0.00622.519-0.077-0.0770.0000.0000.0000.000
133A135LEU0-0.005-0.00916.373-0.077-0.0770.0000.0000.0000.000
134A136PRO00.0450.02118.939-0.341-0.3410.0000.0000.0000.000
135A137PHE0-0.070-0.01219.9000.2110.2110.0000.0000.0000.000
136A138ILE0-0.061-0.04119.3270.3100.3100.0000.0000.0000.000
137A139ARG10.9200.96519.43512.84812.8480.0000.0000.0000.000
138A140MET00.0300.04713.569-0.396-0.3960.0000.0000.0000.000
139A141HIS00.005-0.00311.8701.0001.0000.0000.0000.0000.000
140A142LEU0-0.030-0.02212.501-1.636-1.6360.0000.0000.0000.000
141A143VAL00.0120.0039.6570.4560.4560.0000.0000.0000.000
142A144ASP-1-0.816-0.87813.103-15.334-15.3340.0000.0000.0000.000
143A145GLN0-0.046-0.02313.1311.2521.2520.0000.0000.0000.000
144A146LEU0-0.038-0.00815.638-0.454-0.4540.0000.0000.0000.000
145A147THR00.0240.00516.0371.0451.0450.0000.0000.0000.000
146A148GLY00.0270.01418.5180.0490.0490.0000.0000.0000.000
147A149VAL0-0.037-0.03020.8330.1740.1740.0000.0000.0000.000
148A150PRO00.0300.02123.6810.2130.2130.0000.0000.0000.000
149A151ILE0-0.009-0.00526.995-0.204-0.2040.0000.0000.0000.000
150A152ASN0-0.023-0.01328.6850.0260.0260.0000.0000.0000.000
151A153SER00.027-0.00930.8610.1070.1070.0000.0000.0000.000
152A154GLU-1-0.719-0.85132.436-9.392-9.3920.0000.0000.0000.000
153A155ALA0-0.0420.02729.8020.0350.0350.0000.0000.0000.000
154A156TRP0-0.006-0.01331.578-0.019-0.0190.0000.0000.0000.000
155A157SER0-0.040-0.01434.5070.1460.1460.0000.0000.0000.000
156A158THR0-0.017-0.04932.263-0.052-0.0520.0000.0000.0000.000
157A159GLY00.0340.03231.047-0.098-0.0980.0000.0000.0000.000
158A160ILE0-0.018-0.00226.632-0.380-0.3800.0000.0000.0000.000
159A161LEU00.0230.01522.6400.2820.2820.0000.0000.0000.000
160A162LYS10.7360.86025.2919.6549.6540.0000.0000.0000.000
161A163VAL00.0140.00221.2770.1800.1800.0000.0000.0000.000
162A164SER0-0.017-0.03024.468-0.026-0.0260.0000.0000.0000.000
163A165ALA00.039-0.00123.068-0.487-0.4870.0000.0000.0000.000
164A166GLU-1-0.807-0.87121.969-12.595-12.5950.0000.0000.0000.000
165A167LYS10.8270.88521.18912.60912.6090.0000.0000.0000.000
166A168LEU0-0.020-0.00517.957-0.623-0.6230.0000.0000.0000.000
167A169ALA00.0070.01017.363-1.055-1.0550.0000.0000.0000.000
168A170GLU-1-0.831-0.88716.534-15.094-15.0940.0000.0000.0000.000
169A171LEU00.0120.01414.678-0.947-0.9470.0000.0000.0000.000
170A172SER0-0.039-0.03712.888-1.436-1.4360.0000.0000.0000.000
171A173ALA00.0420.01411.748-2.009-2.0090.0000.0000.0000.000
172A174GLN00.0020.00011.817-0.418-0.4180.0000.0000.0000.000
173A175ALA00.011-0.0039.230-1.800-1.8000.0000.0000.0000.000
174A176ASP-1-0.805-0.8867.443-34.570-34.5700.0000.0000.0000.000
175A177ALA0-0.0360.0007.073-3.730-3.7300.0000.0000.0000.000
176A178LEU0-0.0100.0005.584-1.569-1.5690.0000.0000.0000.000
177A179LEU00.006-0.0102.681-4.586-3.6550.495-0.219-1.206-0.001
178A180SER0-0.017-0.0302.725-15.067-13.1810.401-0.993-1.295-0.014
179A181ALA0-0.051-0.0155.3370.4740.510-0.001-0.003-0.0310.000
180A182ILE0-0.003-0.0062.117-0.5130.1384.231-0.903-3.979-0.011
181A183GLU-1-0.823-0.8701.760-152.372-161.09031.179-13.485-8.977-0.161
182A184ASN0-0.158-0.0764.07314.79314.8580.003-0.014-0.0540.000