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: 4N77N

Calculation Name: 1VOL-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VOL

Chain ID: A

ChEMBL ID:

UniProt ID: P28147

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 204
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2249202.963103
FMO2-HF: Nuclear repulsion 2168497.861676
FMO2-HF: Total energy -80705.101427
FMO2-MP2: Total energy -80936.237354


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:113:ALA )


Summations of interaction energy for fragment #1(A:113:ALA )
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.
-6.504-2.0881.396-2.229-3.582-0.008
Interaction energy analysis for fragmet #1(A:113:ALA )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.004
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].
3A115MET 00.0300.0133.818-3.315-1.360-0.010-0.987-0.9570.001
4A116ASN 0-0.007-0.0432.903-1.022-0.3250.053-0.211-0.5390.000
5A117ALA 00.0610.0374.192-0.440-0.1600.001-0.081-0.2010.000
6A118PHE 00.030-0.0065.5050.2900.2900.0000.0000.0000.000
7A119LYS 10.8790.9836.113-0.680-0.6800.0000.0000.0000.000
8A120GLU -1-0.852-0.9158.528-0.421-0.4210.0000.0000.0000.000
9A121ILE 0-0.058-0.0149.6680.0660.0660.0000.0000.0000.000
10A122THR 0-0.028-0.01211.7370.0480.0480.0000.0000.0000.000
11A123THR 00.0770.04213.121-0.004-0.0040.0000.0000.0000.000
12A124MET 0-0.087-0.06211.5600.0300.0300.0000.0000.0000.000
13A125ALA 0-0.023-0.02715.7080.0240.0240.0000.0000.0000.000
14A126ASP -1-0.876-0.93817.734-0.037-0.0370.0000.0000.0000.000
15A127ARG 10.9150.96417.8260.1590.1590.0000.0000.0000.000
16A128ILE 0-0.063-0.02520.2940.0070.0070.0000.0000.0000.000
17A129ASN 0-0.027-0.01322.3530.0060.0060.0000.0000.0000.000
18A130LEU 0-0.057-0.02819.2200.0100.0100.0000.0000.0000.000
19A131PRO 00.0160.01721.5120.0050.0050.0000.0000.0000.000
20A132ARG 11.0180.98317.581-0.040-0.0400.0000.0000.0000.000
21A133ASN 00.0660.03820.2040.0000.0000.0000.0000.0000.000
22A134LYS 10.9660.98220.0210.0250.0250.0000.0000.0000.000
23A135VAL 0-0.022-0.01016.155-0.010-0.0100.0000.0000.0000.000
24A136ASP -1-0.901-0.94715.6440.1620.1620.0000.0000.0000.000
25A137ARG 10.9670.97915.728-0.010-0.0100.0000.0000.0000.000
26A138THR 0-0.061-0.03013.777-0.009-0.0090.0000.0000.0000.000
27A139ASN 00.0100.00811.470-0.063-0.0630.0000.0000.0000.000
28A140ASN 00.0100.00111.7860.0270.0270.0000.0000.0000.000
29A141LEU 0-0.0070.01413.9960.0050.0050.0000.0000.0000.000
30A142PHE 00.009-0.0124.867-0.015-0.0150.0000.0000.0000.000
31A143ARG 10.8490.9118.708-0.700-0.7000.0000.0000.0000.000
32A144GLN 00.0980.0519.9610.0360.0360.0000.0000.0000.000
33A145ALA 0-0.0160.01510.021-0.010-0.0100.0000.0000.0000.000
34A146TYR 0-0.177-0.1202.865-0.5680.0320.150-0.218-0.5310.001
35A147GLU -1-0.799-0.8998.3360.5650.5650.0000.0000.0000.000
36A148GLN 00.0760.05611.337-0.037-0.0370.0000.0000.0000.000
37A149LYS 10.8320.9267.0150.1600.1600.0000.0000.0000.000
38A150SER 00.0420.00911.522-0.021-0.0210.0000.0000.0000.000
39A151LEU 0-0.029-0.0239.765-0.023-0.0230.0000.0000.0000.000
40A152LYS 10.9220.9389.4140.0600.0600.0000.0000.0000.000
41A153GLY 00.0640.0488.796-0.069-0.0690.0000.0000.0000.000
42A154ARG 10.7990.9089.9130.2570.2570.0000.0000.0000.000
43A155ALA 00.1020.0387.925-0.106-0.1060.0000.0000.0000.000
44A156ASN 00.0760.0332.485-2.114-1.2301.202-0.732-1.354-0.010
45A157ASP -1-0.752-0.8975.846-0.702-0.7020.0000.0000.0000.000
46A158ALA 0-0.056-0.0158.3670.1740.1740.0000.0000.0000.000
47A159ILE 0-0.024-0.0246.5860.1180.1180.0000.0000.0000.000
48A160ALA 00.0420.0398.4610.1070.1070.0000.0000.0000.000
49A161SER 00.0230.01110.3030.1180.1180.0000.0000.0000.000
50A162ALA 0-0.018-0.01513.5030.0520.0520.0000.0000.0000.000
51A163CYS 00.0800.05311.8730.0610.0610.0000.0000.0000.000
52A164LEU 0-0.0090.00814.2610.0510.0510.0000.0000.0000.000
53A165TYR 0-0.088-0.04016.1960.0030.0030.0000.0000.0000.000
54A166ILE 0-0.052-0.03816.5740.0170.0170.0000.0000.0000.000
55A167ALA 00.0480.03217.5020.0170.0170.0000.0000.0000.000
56A168CYS 0-0.096-0.03719.4310.0120.0120.0000.0000.0000.000
57A169ARG 10.9400.94422.2540.0710.0710.0000.0000.0000.000
58A170GLN 0-0.0100.01620.9360.0090.0090.0000.0000.0000.000
59A171GLU -1-0.882-0.94022.4530.0260.0260.0000.0000.0000.000
60A172GLY 00.0260.03125.2220.0030.0030.0000.0000.0000.000
61A173VAL 0-0.027-0.01026.314-0.003-0.0030.0000.0000.0000.000
62A174PRO 00.0470.02924.702-0.009-0.0090.0000.0000.0000.000
63A175ARG 10.9620.94621.7350.0710.0710.0000.0000.0000.000
64A176THR 00.0120.01424.267-0.010-0.0100.0000.0000.0000.000
65A177PHE 00.007-0.01420.029-0.004-0.0040.0000.0000.0000.000
66A178LYS 10.8630.89621.8570.0770.0770.0000.0000.0000.000
67A179GLU -1-0.743-0.85123.186-0.082-0.0820.0000.0000.0000.000
68A180ILE 00.0200.02317.229-0.003-0.0030.0000.0000.0000.000
69A181CYS 0-0.031-0.02818.437-0.018-0.0180.0000.0000.0000.000
70A182ALA 0-0.0150.01519.032-0.019-0.0190.0000.0000.0000.000
71A183VAL 0-0.054-0.01117.0570.0100.0100.0000.0000.0000.000
72A184SER 0-0.064-0.03514.180-0.026-0.0260.0000.0000.0000.000
73A185ARG 11.0011.0179.8500.5130.5130.0000.0000.0000.000
74A186ILE 0-0.037-0.00811.2790.0250.0250.0000.0000.0000.000
75A187SER 00.028-0.00515.2590.0400.0400.0000.0000.0000.000
76A188LYS 11.0571.01318.3050.1090.1090.0000.0000.0000.000
77A189LYS 10.9150.95420.0990.1600.1600.0000.0000.0000.000
78A190GLU -1-0.739-0.86014.495-0.264-0.2640.0000.0000.0000.000
79A191ILE 00.0700.07415.702-0.002-0.0020.0000.0000.0000.000
80A192GLY 00.008-0.00516.9070.0230.0230.0000.0000.0000.000
81A193ARG 10.8270.90117.4820.1840.1840.0000.0000.0000.000
82A194CYS 00.033-0.00813.0610.0060.0060.0000.0000.0000.000
83A195PHE 00.0450.04215.1560.0150.0150.0000.0000.0000.000
84A196LYS 10.9160.94817.4290.1320.1320.0000.0000.0000.000
85A197LEU 0-0.057-0.03314.5730.0100.0100.0000.0000.0000.000
86A198ILE 00.0350.01212.4840.0090.0090.0000.0000.0000.000
87A199LEU 0-0.0410.00215.8960.0190.0190.0000.0000.0000.000
88A200LYS 10.9070.95119.4680.0820.0820.0000.0000.0000.000
89A201ALA 0-0.0230.00815.5110.0090.0090.0000.0000.0000.000
90A202LEU 00.0210.00514.8080.0120.0120.0000.0000.0000.000
91A203GLU -1-0.915-0.93018.1770.0360.0360.0000.0000.0000.000
92A204THR 0-0.037-0.02220.7050.0060.0060.0000.0000.0000.000
93A205SER 0-0.034-0.04322.177-0.016-0.0160.0000.0000.0000.000
94A206VAL 0-0.070-0.05822.7870.0040.0040.0000.0000.0000.000
95A207ASP -1-0.794-0.90525.625-0.014-0.0140.0000.0000.0000.000
96A208LEU 0-0.053-0.02428.398-0.001-0.0010.0000.0000.0000.000
97A209ILE 0-0.117-0.01826.188-0.006-0.0060.0000.0000.0000.000
98A210THR 00.009-0.00830.4400.0010.0010.0000.0000.0000.000
99A211THR 00.0660.00933.800-0.002-0.0020.0000.0000.0000.000
100A212GLY 0-0.0120.01035.534-0.002-0.0020.0000.0000.0000.000
101A213ASP -1-0.816-0.91730.958-0.031-0.0310.0000.0000.0000.000
102A214PHE 0-0.087-0.05428.010-0.003-0.0030.0000.0000.0000.000
103A215MET 0-0.0340.00032.314-0.002-0.0020.0000.0000.0000.000
104A216SER 00.0220.03533.3020.0000.0000.0000.0000.0000.000
105A217ARG 10.8450.90727.5110.0570.0570.0000.0000.0000.000
106A218PHE 00.0250.02029.695-0.001-0.0010.0000.0000.0000.000
107A219CYS 00.0230.01033.7140.0000.0000.0000.0000.0000.000
108A220SER 00.004-0.00433.5020.0020.0020.0000.0000.0000.000
109A221ASN 0-0.042-0.01829.5950.0030.0030.0000.0000.0000.000
110A222LEU 00.0070.00433.891-0.001-0.0010.0000.0000.0000.000
111A223CYS 0-0.0400.00137.0000.0020.0020.0000.0000.0000.000
112A224LEU 0-0.0180.00838.9240.0020.0020.0000.0000.0000.000
113A225PRO 00.0350.02040.8560.0010.0010.0000.0000.0000.000
114A226LYS 10.9940.98542.3100.0120.0120.0000.0000.0000.000
115A227GLN 0-0.012-0.01843.3270.0010.0010.0000.0000.0000.000
116A228VAL 00.0920.04942.5610.0000.0000.0000.0000.0000.000
117A229GLN 00.0340.01238.438-0.002-0.0020.0000.0000.0000.000
118A230MET 0-0.029-0.02740.773-0.001-0.0010.0000.0000.0000.000
119A231ALA 00.0600.03143.7880.0000.0000.0000.0000.0000.000
120A232ALA 00.0330.02941.383-0.001-0.0010.0000.0000.0000.000
121A233THR 0-0.065-0.06040.029-0.001-0.0010.0000.0000.0000.000
122A234HIS 0-0.026-0.01341.6500.0020.0020.0000.0000.0000.000
123A235ILE 00.0010.02844.7270.0000.0000.0000.0000.0000.000
124A236ALA 0-0.015-0.02740.1640.0000.0000.0000.0000.0000.000
125A237ARG 10.9270.96741.9100.0140.0140.0000.0000.0000.000
126A238LYS 10.9560.98242.7620.0150.0150.0000.0000.0000.000
127A239ALA 00.0050.00443.2230.0000.0000.0000.0000.0000.000
128A240VAL 0-0.056-0.03339.9240.0000.0000.0000.0000.0000.000
129A241GLU -1-0.909-0.95043.104-0.014-0.0140.0000.0000.0000.000
130A242LEU 0-0.050-0.03245.7170.0010.0010.0000.0000.0000.000
131A243ASP -1-0.916-0.96144.359-0.025-0.0250.0000.0000.0000.000
132A244LEU 0-0.0190.00745.933-0.001-0.0010.0000.0000.0000.000
133A245VAL 0-0.094-0.05941.517-0.002-0.0020.0000.0000.0000.000
134A246PRO 00.0870.04041.367-0.003-0.0030.0000.0000.0000.000
135A247GLY 00.0430.03038.9380.0000.0000.0000.0000.0000.000
136A248ARG 10.8310.92837.6050.0370.0370.0000.0000.0000.000
137A249SER 00.0180.00831.9570.0010.0010.0000.0000.0000.000
138A250PRO 00.1200.04732.2540.0000.0000.0000.0000.0000.000
139A251ILE 00.0010.01629.5630.0010.0010.0000.0000.0000.000
140A252SER 0-0.043-0.02833.5150.0000.0000.0000.0000.0000.000
141A253VAL 00.0350.03236.4200.0020.0020.0000.0000.0000.000
142A254ALA 00.0340.01235.6520.0020.0020.0000.0000.0000.000
143A255ALA 00.018-0.00135.8030.0020.0020.0000.0000.0000.000
144A256ALA 0-0.012-0.01937.7400.0020.0020.0000.0000.0000.000
145A257ALA 00.011-0.00441.1180.0020.0020.0000.0000.0000.000
146A258ILE 00.002-0.01237.1410.0020.0020.0000.0000.0000.000
147A259TYR 0-0.007-0.01841.2980.0000.0000.0000.0000.0000.000
148A260MET 0-0.0030.00043.3950.0020.0020.0000.0000.0000.000
149A261ALA 0-0.0110.00144.1600.0010.0010.0000.0000.0000.000
150A262SER 0-0.021-0.00643.5040.0010.0010.0000.0000.0000.000
151A263GLN 0-0.024-0.01645.5970.0020.0020.0000.0000.0000.000
152A264ALA 00.0350.02448.1840.0010.0010.0000.0000.0000.000
153A265SER 0-0.060-0.03847.7970.0020.0020.0000.0000.0000.000
154A266ALA 00.0580.04949.7870.0000.0000.0000.0000.0000.000
155A267GLU -1-0.899-0.99044.911-0.026-0.0260.0000.0000.0000.000
156A268LYS 10.8520.99145.5780.0220.0220.0000.0000.0000.000
157A269ARG 10.8910.93740.5330.0310.0310.0000.0000.0000.000
158A270THR 0-0.011-0.02442.1220.0000.0000.0000.0000.0000.000
159A271GLN 0-0.008-0.01140.848-0.003-0.0030.0000.0000.0000.000
160A272LYS 10.9190.96635.5970.0590.0590.0000.0000.0000.000
161A273GLU -1-0.733-0.85337.178-0.042-0.0420.0000.0000.0000.000
162A274ILE 0-0.024-0.00636.545-0.002-0.0020.0000.0000.0000.000
163A275GLY 0-0.025-0.03835.364-0.003-0.0030.0000.0000.0000.000
164A276ASP -1-0.880-0.94333.146-0.070-0.0700.0000.0000.0000.000
165A277ILE 0-0.0120.00531.584-0.005-0.0050.0000.0000.0000.000
166A278ALA 0-0.035-0.02230.875-0.003-0.0030.0000.0000.0000.000
167A279GLY 0-0.0010.01329.553-0.005-0.0050.0000.0000.0000.000
168A280VAL 0-0.102-0.06330.510-0.005-0.0050.0000.0000.0000.000
169A281ALA 00.0390.01833.287-0.001-0.0010.0000.0000.0000.000
170A282ASP -1-0.776-0.89135.933-0.052-0.0520.0000.0000.0000.000
171A283VAL 0-0.0010.00739.2670.0030.0030.0000.0000.0000.000
172A284THR 0-0.031-0.03336.1500.0020.0020.0000.0000.0000.000
173A285ILE 0-0.0090.02637.5400.0020.0020.0000.0000.0000.000
174A286ARG 10.9530.98240.0850.0400.0400.0000.0000.0000.000
175A287GLN 0-0.035-0.03341.5430.0020.0020.0000.0000.0000.000
176A288SER 00.0580.02840.1740.0020.0020.0000.0000.0000.000
177A289TYR 0-0.0120.00142.7630.0020.0020.0000.0000.0000.000
178A290ARG 10.9230.94844.9600.0350.0350.0000.0000.0000.000
179A291LEU 0-0.059-0.02343.6100.0010.0010.0000.0000.0000.000
180A292ILE 00.0180.00043.9680.0010.0010.0000.0000.0000.000
181A293TYR 00.0180.01647.7630.0010.0010.0000.0000.0000.000
182A294PRO 0-0.006-0.00950.3350.0010.0010.0000.0000.0000.000
183A295ARG 10.8980.96050.7010.0190.0190.0000.0000.0000.000
184A296ALA 0-0.003-0.01050.8870.0010.0010.0000.0000.0000.000
185A297PRO 0-0.023-0.01051.9490.0000.0000.0000.0000.0000.000
186A298ASP -1-0.824-0.91752.793-0.015-0.0150.0000.0000.0000.000
187A299LEU 0-0.070-0.01647.1910.0000.0000.0000.0000.0000.000
188A300PHE 0-0.007-0.01948.8810.0000.0000.0000.0000.0000.000
189A301PRO 0-0.045-0.02448.2930.0010.0010.0000.0000.0000.000
190A302THR 00.0370.04950.7240.0010.0010.0000.0000.0000.000
191A303ASP -1-0.896-0.94352.342-0.011-0.0110.0000.0000.0000.000
192A304PHE 0-0.080-0.06448.4780.0000.0000.0000.0000.0000.000
193A305LYS 10.8770.94149.4100.0140.0140.0000.0000.0000.000
194A306PHE 00.008-0.02552.4750.0000.0000.0000.0000.0000.000
195A307ASP -1-0.914-0.93152.820-0.018-0.0180.0000.0000.0000.000
196A308THR 0-0.026-0.01453.2560.0000.0000.0000.0000.0000.000
197A309PRO 00.0210.02554.2060.0000.0000.0000.0000.0000.000
198A310VAL 00.0860.02053.657-0.001-0.0010.0000.0000.0000.000
199A311ASP -1-0.916-0.95455.552-0.017-0.0170.0000.0000.0000.000
200A312LYS 10.9130.94056.8220.0170.0170.0000.0000.0000.000
201A313LEU 0-0.0400.00350.473-0.001-0.0010.0000.0000.0000.000
202A314PRO 0-0.015-0.00149.2220.0000.0000.0000.0000.0000.000
203A315GLN 00.0750.03451.001-0.001-0.0010.0000.0000.0000.000
204A1NME 0-0.069-0.03148.927-0.001-0.0010.0000.0000.0000.000