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: V58G1

Calculation Name: 4JU5-A-Xray372

Preferred Name: Protein disulfide-isomerase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4JU5

Chain ID: A

ChEMBL ID: CHEMBL5422

UniProt ID: P07237

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2067051.349268
FMO2-HF: Nuclear repulsion 1989544.890026
FMO2-HF: Total energy -77506.459241
FMO2-MP2: Total energy -77737.177396


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:136:ALA)


Summations of interaction energy for fragment #1(A:136: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.
-7.884-3.1621.301-2.59-3.434-0.013
Interaction energy analysis for fragmet #1(A:136:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : 0.000
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].
3A138THR0-0.056-0.0123.8051.4392.841-0.022-0.733-0.6480.002
4A139THR00.001-0.0016.411-0.728-0.7280.0000.0000.0000.000
5A140LEU0-0.0020.0008.874-0.120-0.1200.0000.0000.0000.000
6A141PRO00.0220.03212.325-0.081-0.0810.0000.0000.0000.000
7A142ASP-1-0.844-0.91315.2610.2680.2680.0000.0000.0000.000
8A143GLY00.027-0.00717.0920.0040.0040.0000.0000.0000.000
9A144ALA00.0310.01718.961-0.023-0.0230.0000.0000.0000.000
10A145ALA00.0190.01013.650-0.016-0.0160.0000.0000.0000.000
11A146ALA0-0.0020.00014.315-0.013-0.0130.0000.0000.0000.000
12A147GLU-1-0.910-0.96615.4210.0380.0380.0000.0000.0000.000
13A148SER0-0.022-0.00715.264-0.033-0.0330.0000.0000.0000.000
14A149LEU0-0.014-0.0039.389-0.022-0.0220.0000.0000.0000.000
15A150VAL0-0.023-0.02413.179-0.077-0.0770.0000.0000.0000.000
16A151GLU-1-0.921-0.96815.740-0.054-0.0540.0000.0000.0000.000
17A152SER0-0.083-0.02513.165-0.002-0.0020.0000.0000.0000.000
18A153SER0-0.049-0.02313.283-0.019-0.0190.0000.0000.0000.000
19A154GLU-1-0.919-0.94815.377-0.119-0.1190.0000.0000.0000.000
20A155VAL0-0.009-0.01214.0980.0160.0160.0000.0000.0000.000
21A156ALA00.0190.01912.232-0.054-0.0540.0000.0000.0000.000
22A157VAL00.0110.01910.2100.0620.0620.0000.0000.0000.000
23A158ILE0-0.029-0.00410.254-0.015-0.0150.0000.0000.0000.000
24A159GLY00.0240.0079.964-0.042-0.0420.0000.0000.0000.000
25A160PHE0-0.055-0.04410.8930.1480.1480.0000.0000.0000.000
26A161PHE00.0500.01510.313-0.054-0.0540.0000.0000.0000.000
27A162LYS10.9020.95613.372-0.051-0.0510.0000.0000.0000.000
28A163ASP-1-0.900-0.94314.0940.2910.2910.0000.0000.0000.000
29A164VAL00.0200.0038.006-0.046-0.0460.0000.0000.0000.000
30A165GLU-1-0.972-0.9919.2520.5080.5080.0000.0000.0000.000
31A166SER00.0190.01611.290-0.079-0.0790.0000.0000.0000.000
32A167ASP-1-0.880-0.95211.940-0.061-0.0610.0000.0000.0000.000
33A168SER00.004-0.00312.067-0.050-0.0500.0000.0000.0000.000
34A169ALA00.0210.0239.504-0.093-0.0930.0000.0000.0000.000
35A170LYS10.9040.9437.737-0.223-0.2230.0000.0000.0000.000
36A171GLN0-0.026-0.0117.504-0.236-0.2360.0000.0000.0000.000
37A172PHE00.0240.0016.632-0.217-0.2170.0000.0000.0000.000
38A173LEU0-0.020-0.0132.950-0.750-0.2480.148-0.134-0.5150.000
39A174GLN00.0290.0233.343-2.094-1.2140.034-0.448-0.466-0.004
40A175ALA0-0.056-0.0325.977-0.027-0.0270.0000.0000.0000.000
41A176ALA0-0.044-0.0233.183-0.1420.1080.022-0.077-0.1960.000
42A177GLU-1-0.954-0.9842.428-4.558-3.0271.121-1.171-1.481-0.011
43A178ALA0-0.073-0.0224.5330.4610.492-0.001-0.014-0.0160.000
44A179ILE0-0.047-0.0257.1450.3350.3350.0000.0000.0000.000
45A180ASP-1-0.881-0.9377.291-1.279-1.2790.0000.0000.0000.000
46A181ASP-1-1.004-1.0098.946-0.481-0.4810.0000.0000.0000.000
47A182ILE0-0.066-0.0359.7330.1480.1480.0000.0000.0000.000
48A183PRO0-0.0020.0197.620-0.287-0.2870.0000.0000.0000.000
49A184PHE00.0500.0195.2880.0430.169-0.001-0.013-0.1120.000
50A185GLY0-0.013-0.0076.6430.3550.3550.0000.0000.0000.000
51A186ILE00.0110.0096.225-0.234-0.2340.0000.0000.0000.000
52A187THR0-0.020-0.0358.8720.1630.1630.0000.0000.0000.000
53A188SER00.0500.01712.209-0.025-0.0250.0000.0000.0000.000
54A189ASN0-0.065-0.04614.468-0.067-0.0670.0000.0000.0000.000
55A190SER00.007-0.01617.418-0.021-0.0210.0000.0000.0000.000
56A191ASP-1-0.894-0.93820.3500.1300.1300.0000.0000.0000.000
57A192VAL0-0.028-0.02115.783-0.026-0.0260.0000.0000.0000.000
58A193PHE0-0.020-0.01715.762-0.026-0.0260.0000.0000.0000.000
59A194SER00.0190.01519.570-0.027-0.0270.0000.0000.0000.000
60A195LYS10.8190.95120.257-0.094-0.0940.0000.0000.0000.000
61A196TYR0-0.022-0.01517.981-0.022-0.0220.0000.0000.0000.000
62A197GLN0-0.026-0.00421.459-0.029-0.0290.0000.0000.0000.000
63A198LEU00.0080.02418.087-0.015-0.0150.0000.0000.0000.000
64A199ASP-1-0.906-0.95621.5630.0200.0200.0000.0000.0000.000
65A200LYS10.8830.93920.7940.0410.0410.0000.0000.0000.000
66A201ASP-1-0.821-0.93615.9350.0750.0750.0000.0000.0000.000
67A202GLY0-0.004-0.00815.432-0.016-0.0160.0000.0000.0000.000
68A203VAL0-0.0120.00711.7870.0100.0100.0000.0000.0000.000
69A204VAL0-0.0130.00814.1900.0100.0100.0000.0000.0000.000
70A205LEU0-0.0080.01214.394-0.034-0.0340.0000.0000.0000.000
71A206PHE0-0.010-0.03715.0980.0580.0580.0000.0000.0000.000
72A207LYS10.8880.94716.7030.1400.1400.0000.0000.0000.000
73A208LYS10.8660.94218.8870.1030.1030.0000.0000.0000.000
74A209PHE0-0.005-0.00319.9560.0120.0120.0000.0000.0000.000
75A210ASP-1-0.844-0.92423.991-0.135-0.1350.0000.0000.0000.000
76A211GLU-1-0.855-0.94024.005-0.126-0.1260.0000.0000.0000.000
77A212GLY0-0.0160.01822.9500.0100.0100.0000.0000.0000.000
78A213ARG10.7920.84620.1060.0510.0510.0000.0000.0000.000
79A214ASN0-0.012-0.00419.317-0.001-0.0010.0000.0000.0000.000
80A215ASN00.0560.03818.458-0.017-0.0170.0000.0000.0000.000
81A216PHE0-0.022-0.00715.844-0.008-0.0080.0000.0000.0000.000
82A217GLU-1-0.943-0.97217.930-0.073-0.0730.0000.0000.0000.000
83A218GLY0-0.016-0.01220.092-0.007-0.0070.0000.0000.0000.000
84A219GLU-1-0.913-0.93917.829-0.123-0.1230.0000.0000.0000.000
85A220VAL00.000-0.01412.347-0.034-0.0340.0000.0000.0000.000
86A221THR0-0.043-0.01514.0840.0130.0130.0000.0000.0000.000
87A222LYS11.0070.9999.3490.6400.6400.0000.0000.0000.000
88A223GLU-1-0.891-0.97311.748-0.467-0.4670.0000.0000.0000.000
89A224ASN0-0.015-0.00214.9450.0000.0000.0000.0000.0000.000
90A225LEU0-0.032-0.00410.0360.0090.0090.0000.0000.0000.000
91A226LEU0-0.027-0.01810.091-0.014-0.0140.0000.0000.0000.000
92A227ASP-1-0.885-0.93513.508-0.261-0.2610.0000.0000.0000.000
93A228PHE0-0.072-0.03014.4680.0260.0260.0000.0000.0000.000
94A229ILE0-0.002-0.01210.8580.0240.0240.0000.0000.0000.000
95A230LYS10.8580.93914.8090.4900.4900.0000.0000.0000.000
96A231HIS00.0170.01917.4770.0270.0270.0000.0000.0000.000
97A232ASN0-0.077-0.04918.4820.0520.0520.0000.0000.0000.000
98A233GLN00.0140.02514.0520.0430.0430.0000.0000.0000.000
99A234LEU0-0.009-0.00517.8190.0040.0040.0000.0000.0000.000
100A235PRO0-0.014-0.01020.9080.0110.0110.0000.0000.0000.000
101A236LEU0-0.044-0.02424.165-0.004-0.0040.0000.0000.0000.000
102A237VAL0-0.066-0.03127.3210.0030.0030.0000.0000.0000.000
103A238ILE00.0050.01322.5260.0030.0030.0000.0000.0000.000
104A239GLU-1-0.847-0.92926.425-0.099-0.0990.0000.0000.0000.000
105A240PHE0-0.019-0.03526.007-0.015-0.0150.0000.0000.0000.000
106A241THR00.0490.02424.1830.0020.0020.0000.0000.0000.000
107A242GLU-1-0.853-0.94723.510-0.145-0.1450.0000.0000.0000.000
108A243GLN0-0.032-0.01616.478-0.040-0.0400.0000.0000.0000.000
109A244THR0-0.007-0.00319.554-0.038-0.0380.0000.0000.0000.000
110A245ALA00.0080.01121.842-0.012-0.0120.0000.0000.0000.000
111A246PRO0-0.006-0.00918.5780.0040.0040.0000.0000.0000.000
112A247LYS10.9160.96215.6680.3620.3620.0000.0000.0000.000
113A248ILE00.0020.01419.6940.0040.0040.0000.0000.0000.000
114A249PHE0-0.040-0.02523.3680.0090.0090.0000.0000.0000.000
115A250GLY0-0.012-0.00120.0360.0060.0060.0000.0000.0000.000
116A251GLY00.0220.03320.956-0.012-0.0120.0000.0000.0000.000
117A252GLU-1-0.837-0.93620.474-0.261-0.2610.0000.0000.0000.000
118A253ILE0-0.026-0.01123.6980.0170.0170.0000.0000.0000.000
119A254LYS10.8700.93324.4580.2220.2220.0000.0000.0000.000
120A255THR00.0020.02328.4930.0100.0100.0000.0000.0000.000
121A256HIS00.0170.00226.3350.0060.0060.0000.0000.0000.000
122A257ILE0-0.016-0.00731.4430.0090.0090.0000.0000.0000.000
123A258LEU00.015-0.00131.950-0.004-0.0040.0000.0000.0000.000
124A259LEU0-0.035-0.02134.0640.0080.0080.0000.0000.0000.000
125A260PHE00.010-0.00334.965-0.004-0.0040.0000.0000.0000.000
126A261LEU0-0.013-0.02635.8850.0060.0060.0000.0000.0000.000
127A262PRO00.0130.01636.805-0.003-0.0030.0000.0000.0000.000
128A263LYS10.9110.94231.1230.0860.0860.0000.0000.0000.000
129A264SER0-0.047-0.01138.0310.0040.0040.0000.0000.0000.000
130A265VAL0-0.084-0.01540.7920.0040.0040.0000.0000.0000.000
131A266SER00.009-0.00142.5150.0000.0000.0000.0000.0000.000
132A267ASP-1-0.879-0.95243.457-0.047-0.0470.0000.0000.0000.000
133A268TYR00.0490.03233.504-0.002-0.0020.0000.0000.0000.000
134A269ASP-1-0.842-0.94635.696-0.062-0.0620.0000.0000.0000.000
135A270GLY00.0060.01638.237-0.002-0.0020.0000.0000.0000.000
136A271LYS10.8330.89940.4830.0480.0480.0000.0000.0000.000
137A272LEU00.0070.01032.719-0.003-0.0030.0000.0000.0000.000
138A273SER0-0.036-0.01835.771-0.006-0.0060.0000.0000.0000.000
139A274ASN00.0130.00137.447-0.001-0.0010.0000.0000.0000.000
140A275PHE0-0.0110.00032.2420.0000.0000.0000.0000.0000.000
141A276LYS10.9920.99632.0430.0720.0720.0000.0000.0000.000
142A277THR00.0040.00434.371-0.001-0.0010.0000.0000.0000.000
143A278ALA0-0.035-0.02537.2120.0000.0000.0000.0000.0000.000
144A279ALA00.0190.01031.606-0.002-0.0020.0000.0000.0000.000
145A280GLU-1-0.935-0.96632.400-0.092-0.0920.0000.0000.0000.000
146A281SER0-0.053-0.02433.9160.0000.0000.0000.0000.0000.000
147A282PHE0-0.038-0.01933.8850.0020.0020.0000.0000.0000.000
148A283LYS11.0561.05026.5420.1210.1210.0000.0000.0000.000
149A284GLY00.002-0.00327.4880.0040.0040.0000.0000.0000.000
150A285LYS10.7780.89428.4970.0990.0990.0000.0000.0000.000
151A286ILE0-0.013-0.02031.3340.0000.0000.0000.0000.0000.000
152A287LEU00.0240.02824.9820.0020.0020.0000.0000.0000.000
153A288PHE0-0.015-0.01528.8810.0070.0070.0000.0000.0000.000
154A289ILE00.0140.01527.579-0.007-0.0070.0000.0000.0000.000
155A290PHE0-0.037-0.00929.2780.0100.0100.0000.0000.0000.000
156A291ILE00.0290.01130.638-0.008-0.0080.0000.0000.0000.000
157A292ASP-1-0.794-0.90332.803-0.065-0.0650.0000.0000.0000.000
158A293SER0-0.001-0.06234.871-0.002-0.0020.0000.0000.0000.000
159A294ASP-1-0.895-0.94738.064-0.054-0.0540.0000.0000.0000.000
160A295HIS0-0.0260.00833.2980.0030.0030.0000.0000.0000.000
161A296THR0-0.012-0.02736.058-0.001-0.0010.0000.0000.0000.000
162A297ASP-1-0.967-0.97731.637-0.094-0.0940.0000.0000.0000.000
163A298ASN00.0660.02632.139-0.012-0.0120.0000.0000.0000.000
164A299GLN0-0.015-0.01634.5900.0000.0000.0000.0000.0000.000
165A300ARG10.9240.96734.9950.0810.0810.0000.0000.0000.000
166A301ILE00.0310.01630.8860.0000.0000.0000.0000.0000.000
167A302LEU00.0000.00135.4080.0000.0000.0000.0000.0000.000
168A303GLU-1-0.910-0.95638.692-0.067-0.0670.0000.0000.0000.000
169A304PHE0-0.069-0.02435.6110.0010.0010.0000.0000.0000.000
170A305PHE0-0.056-0.02834.0620.0000.0000.0000.0000.0000.000
171A306GLY0-0.040-0.01339.6140.0030.0030.0000.0000.0000.000
172A307LEU0-0.037-0.01639.8970.0030.0030.0000.0000.0000.000
173A308LYS10.8650.92342.7430.0460.0460.0000.0000.0000.000
174A309LYS10.9920.97542.0630.0520.0520.0000.0000.0000.000
175A310GLU-1-0.863-0.93243.871-0.048-0.0480.0000.0000.0000.000
176A311GLU-1-0.956-0.96145.426-0.054-0.0540.0000.0000.0000.000
177A312CYS0-0.0260.04641.478-0.004-0.0040.0000.0000.0000.000
178A313PRO0-0.004-0.02741.2970.0030.0030.0000.0000.0000.000
179A314ALA0-0.0150.01140.7340.0030.0030.0000.0000.0000.000
180A315VAL00.0210.00837.931-0.004-0.0040.0000.0000.0000.000
181A316ARG10.9080.96237.1690.0770.0770.0000.0000.0000.000
182A317LEU0-0.0050.00935.620-0.004-0.0040.0000.0000.0000.000
183A318ILE0-0.017-0.00932.3980.0040.0040.0000.0000.0000.000
184A319THR00.0160.01632.911-0.004-0.0040.0000.0000.0000.000
185A320LEU0-0.038-0.00927.2270.0030.0030.0000.0000.0000.000
186A321GLU-1-0.860-0.93330.905-0.110-0.1100.0000.0000.0000.000
187A322GLU-1-0.989-0.99028.014-0.166-0.1660.0000.0000.0000.000
188A335THR0-0.001-0.02737.438-0.002-0.0020.0000.0000.0000.000
189A336ALA00.018-0.00339.310-0.003-0.0030.0000.0000.0000.000
190A337GLU-1-0.837-0.91141.909-0.074-0.0740.0000.0000.0000.000
191A338ARG10.8280.87934.6020.0960.0960.0000.0000.0000.000
192A339ILE00.0250.01537.467-0.003-0.0030.0000.0000.0000.000
193A340THR0-0.008-0.00338.7770.0000.0000.0000.0000.0000.000
194A341GLU-1-0.846-0.89639.160-0.085-0.0850.0000.0000.0000.000
195A342PHE0-0.034-0.00232.7800.0000.0000.0000.0000.0000.000
196A343CYS0-0.009-0.01537.111-0.002-0.0020.0000.0000.0000.000
197A344HIS0-0.070-0.00639.4960.0020.0020.0000.0000.0000.000
198A345ARG10.8510.91435.3000.1080.1080.0000.0000.0000.000
199A346PHE0-0.027-0.01138.929-0.001-0.0010.0000.0000.0000.000
200A347LEU0-0.012-0.00140.1450.0000.0000.0000.0000.0000.000