Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: YY252

Calculation Name: 2WD5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WD5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CU62

Base Structure: X-ray

Registration Date: 2023-06-21

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1813480.443356
FMO2-HF: Nuclear repulsion 1743583.040323
FMO2-HF: Total energy -69897.403033
FMO2-MP2: Total energy -70101.415094


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:499:ARG)


Summations of interaction energy for fragment #1(A:499:ARG)
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.
-50.635-52.54430.624-16.312-12.402-0.166
Interaction energy analysis for fragmet #1(A:499:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / q_NPA : 0.895
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].
3A501ALA0-0.024-0.0162.9784.5207.4870.042-1.177-1.8330.007
4A502GLU-1-0.839-0.9061.719-59.369-63.13618.504-8.923-5.813-0.091
5A503ILE00.0390.0204.4741.9702.152-0.001-0.017-0.1630.000
6A504MET0-0.0250.0317.0042.6482.6480.0000.0000.0000.000
7A505GLU-1-0.862-0.9307.776-19.806-19.8060.0000.0000.0000.000
8A506SER0-0.0050.0008.9251.6111.6110.0000.0000.0000.000
9A507ILE0-0.013-0.01110.6811.6081.6080.0000.0000.0000.000
10A508LYS10.8500.93312.64216.91716.9170.0000.0000.0000.000
11A509ARG10.9510.96913.12217.53617.5360.0000.0000.0000.000
12A510LEU0-0.013-0.00214.0270.9430.9430.0000.0000.0000.000
13A511TYR00.0170.01316.7571.2731.2730.0000.0000.0000.000
14A512PRO00.0620.04218.498-0.163-0.1630.0000.0000.0000.000
15A513GLY0-0.043-0.03919.377-0.369-0.3690.0000.0000.0000.000
16A514SER0-0.0130.00420.7320.4220.4220.0000.0000.0000.000
17A515VAL00.0180.00314.435-0.103-0.1030.0000.0000.0000.000
18A516TYR0-0.048-0.04717.503-0.007-0.0070.0000.0000.0000.000
19A517GLY00.0600.02913.758-0.200-0.2000.0000.0000.0000.000
20A518ARG10.7040.8107.99331.55231.5520.0000.0000.0000.000
21A519LEU00.0480.00613.0950.7040.7040.0000.0000.0000.000
22A520ILE0-0.027-0.0049.8610.9700.9700.0000.0000.0000.000
23A521ASP-1-0.846-0.95112.549-20.273-20.2730.0000.0000.0000.000
24A522LEU00.0020.02015.3500.8970.8970.0000.0000.0000.000
25A523CYS0-0.065-0.02818.2920.9750.9750.0000.0000.0000.000
26A524GLN00.0410.00118.102-1.188-1.1880.0000.0000.0000.000
27A525PRO00.0120.02120.0090.6830.6830.0000.0000.0000.000
28A526THR0-0.034-0.02123.2420.0970.0970.0000.0000.0000.000
29A527GLN00.0240.01426.433-0.034-0.0340.0000.0000.0000.000
30A528LYS10.9140.94421.59413.06213.0620.0000.0000.0000.000
31A529LYS10.9570.98324.9799.2799.2790.0000.0000.0000.000
32A530TYR00.0290.00225.894-0.052-0.0520.0000.0000.0000.000
33A531GLN0-0.019-0.00520.785-0.186-0.1860.0000.0000.0000.000
34A532ILE00.0350.02020.847-0.809-0.8090.0000.0000.0000.000
35A533ALA00.0330.02021.966-0.314-0.3140.0000.0000.0000.000
36A534VAL00.012-0.00220.269-0.200-0.2000.0000.0000.0000.000
37A535THR0-0.0040.00116.752-0.683-0.6830.0000.0000.0000.000
38A536LYS10.8450.93318.02613.56213.5620.0000.0000.0000.000
39A537VAL0-0.067-0.04120.255-0.161-0.1610.0000.0000.0000.000
40A538LEU00.0000.01217.659-0.047-0.0470.0000.0000.0000.000
41A539GLY00.0240.01216.196-0.429-0.4290.0000.0000.0000.000
42A540LYS10.9760.96510.37524.28324.2830.0000.0000.0000.000
43A541ASN00.0130.00313.685-1.580-1.5800.0000.0000.0000.000
44A542MET0-0.028-0.00113.2620.6770.6770.0000.0000.0000.000
45A543ASP-1-0.803-0.8908.207-31.355-31.3550.0000.0000.0000.000
46A544ALA0-0.040-0.00611.243-0.982-0.9820.0000.0000.0000.000
47A545ILE00.0030.00210.1051.1641.1640.0000.0000.0000.000
48A546ILE00.0110.01414.1740.8050.8050.0000.0000.0000.000
49A547VAL0-0.006-0.00216.972-0.132-0.1320.0000.0000.0000.000
50A548ASP-1-0.851-0.90019.481-11.706-11.7060.0000.0000.0000.000
51A549SER00.0470.00522.7100.3740.3740.0000.0000.0000.000
52A550GLU-1-0.785-0.88522.305-13.207-13.2070.0000.0000.0000.000
53A551LYS10.8580.92122.41012.16512.1650.0000.0000.0000.000
54A552THR00.0010.01719.621-0.595-0.5950.0000.0000.0000.000
55A553GLY00.0480.02218.371-0.931-0.9310.0000.0000.0000.000
56A554ARG10.8180.86617.88311.68611.6860.0000.0000.0000.000
57A555ASP-1-0.828-0.89518.846-14.165-14.1650.0000.0000.0000.000
58A556CYS0-0.042-0.01714.646-0.814-0.8140.0000.0000.0000.000
59A557ILE0-0.033-0.01514.113-1.528-1.5280.0000.0000.0000.000
60A558GLN0-0.080-0.05114.668-0.802-0.8020.0000.0000.0000.000
61A559TYR00.0600.00910.641-0.422-0.4220.0000.0000.0000.000
62A560ILE0-0.011-0.0129.414-1.039-1.0390.0000.0000.0000.000
63A561LYS10.9150.95611.37415.64015.6400.0000.0000.0000.000
64A562GLU-1-0.875-0.91013.491-16.861-16.8610.0000.0000.0000.000
65A563GLN0-0.042-0.0179.6181.1461.1460.0000.0000.0000.000
66A564ARG10.8910.95810.27922.47822.4780.0000.0000.0000.000
67A565GLY00.0090.0196.902-2.864-2.8640.0000.0000.0000.000
68A566GLU-1-0.912-0.9631.732-104.260-105.55112.079-6.195-4.593-0.082
69A567PRO00.000-0.0076.2611.2441.2440.0000.0000.0000.000
70A568GLU-1-0.773-0.8567.629-38.322-38.3220.0000.0000.0000.000
71A569THR0-0.093-0.04810.4451.8931.8930.0000.0000.0000.000
72A570PHE00.0570.01312.782-0.513-0.5130.0000.0000.0000.000
73A571LEU0-0.032-0.00716.5750.7580.7580.0000.0000.0000.000
74A572PRO0-0.0030.01819.802-0.110-0.1100.0000.0000.0000.000
75A573LEU00.017-0.01522.2670.5250.5250.0000.0000.0000.000
76A574ASP-1-0.790-0.89224.736-11.535-11.5350.0000.0000.0000.000
77A575TYR00.0160.01026.0470.4590.4590.0000.0000.0000.000
78A576LEU0-0.116-0.03622.8270.1190.1190.0000.0000.0000.000
79A577GLU-1-0.889-0.93726.173-9.790-9.7900.0000.0000.0000.000
80A578VAL0-0.048-0.01526.737-0.096-0.0960.0000.0000.0000.000
81A579LYS10.8800.92229.4549.8239.8230.0000.0000.0000.000
82A580PRO00.0270.00531.829-0.235-0.2350.0000.0000.0000.000
83A581THR0-0.007-0.00131.3450.0310.0310.0000.0000.0000.000
84A582ASP-1-0.837-0.91733.693-7.946-7.9460.0000.0000.0000.000
85A583GLU-1-0.847-0.92236.638-7.938-7.9380.0000.0000.0000.000
86A584LYS10.9140.94437.9937.7867.7860.0000.0000.0000.000
87A585LEU0-0.051-0.03335.4720.0460.0460.0000.0000.0000.000
88A586ARG10.7510.84333.4068.7678.7670.0000.0000.0000.000
89A587GLU-1-0.819-0.89038.279-6.944-6.9440.0000.0000.0000.000
90A588LEU0-0.069-0.03738.3330.1570.1570.0000.0000.0000.000
91A589LYS10.8620.92939.7536.9596.9590.0000.0000.0000.000
92A590GLY00.0180.00339.0540.1160.1160.0000.0000.0000.000
93A591ALA0-0.033-0.00333.962-0.168-0.1680.0000.0000.0000.000
94A592LYS10.9520.97131.9789.4869.4860.0000.0000.0000.000
95A593LEU00.0050.00031.399-0.341-0.3410.0000.0000.0000.000
96A594VAL0-0.005-0.00325.190-0.087-0.0870.0000.0000.0000.000
97A595ILE00.025-0.00226.416-0.248-0.2480.0000.0000.0000.000
98A596ASP-1-0.791-0.84027.610-9.475-9.4750.0000.0000.0000.000
99A597VAL0-0.023-0.01426.2480.1740.1740.0000.0000.0000.000
100A598ILE0-0.044-0.01222.384-0.386-0.3860.0000.0000.0000.000
101A599ARG10.8670.93923.97412.14612.1460.0000.0000.0000.000
102A600TYR0-0.022-0.02222.775-0.473-0.4730.0000.0000.0000.000
103A601GLU-1-0.924-0.94122.359-11.908-11.9080.0000.0000.0000.000
104A602PRO00.0620.02022.188-0.495-0.4950.0000.0000.0000.000
105A603PRO00.039-0.00125.397-0.251-0.2510.0000.0000.0000.000
106A604HIS00.0480.01025.5000.3920.3920.0000.0000.0000.000
107A605ILE0-0.0310.00921.174-0.027-0.0270.0000.0000.0000.000
108A606LYS10.9530.97324.2269.4149.4140.0000.0000.0000.000
109A607LYS10.8640.92226.29311.00511.0050.0000.0000.0000.000
110A608ALA00.0750.03120.744-0.070-0.0700.0000.0000.0000.000
111A609LEU0-0.007-0.00121.805-0.429-0.4290.0000.0000.0000.000
112A610GLN0-0.018-0.02923.9660.0310.0310.0000.0000.0000.000
113A611TYR00.0000.01419.6080.4010.4010.0000.0000.0000.000
114A612ALA0-0.0220.00020.769-0.127-0.1270.0000.0000.0000.000
115A613CYS0-0.102-0.03922.555-0.067-0.0670.0000.0000.0000.000
116A614GLY00.0390.02125.4040.2570.2570.0000.0000.0000.000
117A615ASN0-0.040-0.02528.655-0.069-0.0690.0000.0000.0000.000
118A616ALA0-0.0260.00027.4720.2050.2050.0000.0000.0000.000
119A617LEU00.0410.01429.4380.1470.1470.0000.0000.0000.000
120A618VAL0-0.030-0.01328.300-0.355-0.3550.0000.0000.0000.000
121A619CYS0-0.0090.02430.4670.2980.2980.0000.0000.0000.000
122A620ASP-1-0.872-0.94931.515-9.368-9.3680.0000.0000.0000.000
123A621ASN00.004-0.00932.362-0.280-0.2800.0000.0000.0000.000
124A622VAL00.021-0.00730.492-0.068-0.0680.0000.0000.0000.000
125A623GLU-1-0.910-0.95932.916-8.004-8.0040.0000.0000.0000.000
126A624ASP-1-0.838-0.92136.195-8.014-8.0140.0000.0000.0000.000
127A625ALA0-0.066-0.05331.6310.0370.0370.0000.0000.0000.000
128A626ARG10.9740.98433.7678.5218.5210.0000.0000.0000.000
129A627ARG10.9981.00135.1337.3797.3790.0000.0000.0000.000
130A628ILE00.0220.01036.1410.1850.1850.0000.0000.0000.000
131A629ALA0-0.0390.01033.478-0.062-0.0620.0000.0000.0000.000
132A630PHE0-0.061-0.07632.307-0.018-0.0180.0000.0000.0000.000
133A631GLY00.0400.04537.5660.1320.1320.0000.0000.0000.000
134A632GLY0-0.0200.00540.1670.2010.2010.0000.0000.0000.000
135A633HIS00.0580.02341.370-0.142-0.1420.0000.0000.0000.000
136A634GLN00.0050.02338.696-0.177-0.1770.0000.0000.0000.000
137A635ARG10.9340.96034.1178.8648.8640.0000.0000.0000.000
138A636HIS10.8350.89633.9788.4798.4790.0000.0000.0000.000
139A637LYS10.9080.96523.51412.76112.7610.0000.0000.0000.000
140A638THR00.005-0.00330.1420.1450.1450.0000.0000.0000.000
141A639VAL0-0.045-0.01724.711-0.255-0.2550.0000.0000.0000.000
142A640ALA00.0750.06328.1170.2960.2960.0000.0000.0000.000
143A641LEU00.008-0.01127.045-0.523-0.5230.0000.0000.0000.000
144A642ASP-1-0.852-0.89925.938-11.276-11.2760.0000.0000.0000.000
145A643GLY0-0.030-0.02623.090-0.476-0.4760.0000.0000.0000.000
146A644THR0-0.050-0.04923.442-0.376-0.3760.0000.0000.0000.000
147A645LEU0-0.078-0.04523.2700.1910.1910.0000.0000.0000.000
148A646PHE00.0370.02126.3970.0120.0120.0000.0000.0000.000
149A647GLN00.028-0.00124.426-0.102-0.1020.0000.0000.0000.000
150A648LYS11.0000.99329.07510.29110.2910.0000.0000.0000.000
151A649SER00.0260.00927.5870.3170.3170.0000.0000.0000.000
152A650GLY00.0150.02030.8260.1600.1600.0000.0000.0000.000
153A651VAL0-0.0130.00024.667-0.012-0.0120.0000.0000.0000.000
154A652ILE00.0530.02227.3920.1010.1010.0000.0000.0000.000
155A653SER0-0.044-0.01322.384-0.601-0.6010.0000.0000.0000.000
156A654GLY00.0620.02022.9910.3510.3510.0000.0000.0000.000
157A655GLY00.0610.04620.740-0.450-0.4500.0000.0000.0000.000
158A656ALA00.0430.01220.509-0.618-0.6180.0000.0000.0000.000
159A657SER00.0150.00720.2470.0510.0510.0000.0000.0000.000
160A658ASP-1-0.833-0.91815.737-17.832-17.8320.0000.0000.0000.000
161A659LEU0-0.069-0.04316.581-0.909-0.9090.0000.0000.0000.000
162A660LYS10.9470.97418.50313.34213.3420.0000.0000.0000.000
163A661ALA0-0.010-0.00515.257-0.108-0.1080.0000.0000.0000.000
164A662LYS10.9580.97312.85819.32519.3250.0000.0000.0000.000
165A663ALA00.0170.01514.892-0.534-0.5340.0000.0000.0000.000
166A664ARG10.9450.97214.38218.72218.7220.0000.0000.0000.000
167A665ARG10.9050.9439.08726.75826.7580.0000.0000.0000.000
168A666TRP0-0.022-0.02713.7910.0710.0710.0000.0000.0000.000
169A667ASP-1-0.809-0.89916.791-13.776-13.7760.0000.0000.0000.000
170A668GLU-1-0.899-0.95211.375-22.270-22.2700.0000.0000.0000.000
171A669LYS10.8850.97213.62316.16116.1610.0000.0000.0000.000
172A670ALA0-0.044-0.03015.2890.5580.5580.0000.0000.0000.000
173A671VAL00.0060.00916.9760.5410.5410.0000.0000.0000.000
174A672ASP-1-0.777-0.88213.225-18.861-18.8610.0000.0000.0000.000
175A673LYS10.8500.92116.80112.62812.6280.0000.0000.0000.000
176A674LEU0-0.038-0.00920.0420.5640.5640.0000.0000.0000.000
177A675LYS10.8430.94012.57519.08819.0880.0000.0000.0000.000