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: G6L21

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2073390.035266
FMO2-HF: Nuclear repulsion 1995882.230416
FMO2-HF: Total energy -77507.804849
FMO2-MP2: Total energy -77738.609727


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.
-9.48-4.0683.858-4.079-5.192-0.027
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 : -0.004 / q_NPA : -0.003
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].
3A138THR0-0.028-0.0073.8781.3302.668-0.017-0.749-0.5730.002
4A139THR0-0.004-0.0017.012-0.546-0.5460.0000.0000.0000.000
5A140LEU0-0.0160.0008.686-0.091-0.0910.0000.0000.0000.000
6A141PRO0-0.0040.01412.111-0.078-0.0780.0000.0000.0000.000
7A142ASP-1-0.816-0.92315.0050.2420.2420.0000.0000.0000.000
8A143GLY00.0340.00016.7940.0030.0030.0000.0000.0000.000
9A144ALA00.0500.03418.915-0.021-0.0210.0000.0000.0000.000
10A145ALA0-0.025-0.00114.304-0.008-0.0080.0000.0000.0000.000
11A146ALA00.0180.00014.381-0.005-0.0050.0000.0000.0000.000
12A147GLU-1-0.850-0.92315.4580.0360.0360.0000.0000.0000.000
13A148SER0-0.051-0.03715.459-0.032-0.0320.0000.0000.0000.000
14A149LEU0-0.047-0.0189.275-0.015-0.0150.0000.0000.0000.000
15A150VAL0-0.013-0.01313.236-0.075-0.0750.0000.0000.0000.000
16A151GLU-1-0.836-0.91715.682-0.064-0.0640.0000.0000.0000.000
17A152SER0-0.087-0.02913.4060.0050.0050.0000.0000.0000.000
18A153SER0-0.048-0.04013.612-0.025-0.0250.0000.0000.0000.000
19A154GLU-1-0.877-0.93415.707-0.103-0.1030.0000.0000.0000.000
20A155VAL0-0.025-0.01514.3730.0110.0110.0000.0000.0000.000
21A156ALA00.0320.03912.205-0.043-0.0430.0000.0000.0000.000
22A157VAL00.0010.0019.9300.0490.0490.0000.0000.0000.000
23A158ILE0-0.015-0.00210.188-0.016-0.0160.0000.0000.0000.000
24A159GLY00.0280.0239.541-0.039-0.0390.0000.0000.0000.000
25A160PHE0-0.025-0.02910.4650.1300.1300.0000.0000.0000.000
26A161PHE00.0660.0129.397-0.046-0.0460.0000.0000.0000.000
27A162LYS10.7860.89313.216-0.018-0.0180.0000.0000.0000.000
28A163ASP-1-0.862-0.93113.5710.2530.2530.0000.0000.0000.000
29A164VAL00.0120.0097.524-0.052-0.0520.0000.0000.0000.000
30A165GLU-1-0.952-0.9768.5580.5350.5350.0000.0000.0000.000
31A166SER00.0070.00210.756-0.095-0.0950.0000.0000.0000.000
32A167ASP-1-0.920-0.97211.168-0.052-0.0520.0000.0000.0000.000
33A168SER00.000-0.00211.345-0.049-0.0490.0000.0000.0000.000
34A169ALA00.0210.0288.667-0.087-0.0870.0000.0000.0000.000
35A170LYS10.8730.9346.914-0.150-0.1500.0000.0000.0000.000
36A171GLN00.0120.0146.730-0.203-0.2030.0000.0000.0000.000
37A172PHE00.0300.0016.338-0.186-0.1860.0000.0000.0000.000
38A173LEU0-0.024-0.0102.524-0.824-0.4971.234-0.379-1.1830.000
39A174GLN00.0260.0043.350-1.636-0.8580.041-0.387-0.432-0.003
40A175ALA0-0.038-0.0175.7550.0880.0880.0000.0000.0000.000
41A176ALA0-0.0030.0003.339-0.1960.0600.016-0.083-0.1890.000
42A177GLU-1-0.976-1.0032.485-6.913-4.4032.582-2.430-2.662-0.026
43A178ALA0-0.069-0.0273.9800.4210.5000.003-0.038-0.0430.000
44A179ILE0-0.039-0.0236.8970.3220.3220.0000.0000.0000.000
45A180ASP-1-0.880-0.9417.890-1.106-1.1060.0000.0000.0000.000
46A181ASP-1-0.905-0.9399.178-0.414-0.4140.0000.0000.0000.000
47A182ILE0-0.033-0.0119.6660.1540.1540.0000.0000.0000.000
48A183PRO0-0.0090.0157.892-0.265-0.2650.0000.0000.0000.000
49A184PHE00.0510.0205.325-0.0580.066-0.001-0.013-0.1100.000
50A185GLY00.002-0.0046.6900.2710.2710.0000.0000.0000.000
51A186ILE0-0.008-0.0076.009-0.212-0.2120.0000.0000.0000.000
52A187THR0-0.020-0.0268.6950.1550.1550.0000.0000.0000.000
53A188SER00.029-0.00712.074-0.020-0.0200.0000.0000.0000.000
54A189ASN0-0.072-0.03014.364-0.050-0.0500.0000.0000.0000.000
55A190SER00.0580.01817.444-0.019-0.0190.0000.0000.0000.000
56A191ASP-1-0.878-0.92220.5120.1400.1400.0000.0000.0000.000
57A192VAL0-0.016-0.01015.539-0.025-0.0250.0000.0000.0000.000
58A193PHE00.0010.00115.340-0.031-0.0310.0000.0000.0000.000
59A194SER0-0.014-0.01319.087-0.026-0.0260.0000.0000.0000.000
60A195LYS10.7270.87420.175-0.085-0.0850.0000.0000.0000.000
61A196TYR00.0280.01618.227-0.005-0.0050.0000.0000.0000.000
62A197GLN0-0.058-0.02320.826-0.027-0.0270.0000.0000.0000.000
63A198LEU00.0080.02917.376-0.011-0.0110.0000.0000.0000.000
64A199ASP-1-0.821-0.88420.7970.0170.0170.0000.0000.0000.000
65A200LYS10.7990.86120.3030.0330.0330.0000.0000.0000.000
66A201ASP-1-0.770-0.89415.3540.0810.0810.0000.0000.0000.000
67A202GLY00.0120.00914.817-0.016-0.0160.0000.0000.0000.000
68A203VAL0-0.026-0.00711.1590.0070.0070.0000.0000.0000.000
69A204VAL0-0.023-0.00213.5830.0160.0160.0000.0000.0000.000
70A205LEU0-0.0020.02413.969-0.031-0.0310.0000.0000.0000.000
71A206PHE0-0.007-0.02515.1550.0580.0580.0000.0000.0000.000
72A207LYS10.8420.90616.6880.1450.1450.0000.0000.0000.000
73A208LYS10.7770.88719.1310.0880.0880.0000.0000.0000.000
74A209PHE0-0.020-0.01319.7990.0130.0130.0000.0000.0000.000
75A210ASP-1-0.820-0.91623.876-0.132-0.1320.0000.0000.0000.000
76A211GLU-1-0.814-0.89423.694-0.130-0.1300.0000.0000.0000.000
77A212GLY0-0.0050.02622.9350.0080.0080.0000.0000.0000.000
78A213ARG10.8240.88419.9560.0530.0530.0000.0000.0000.000
79A214ASN00.000-0.00318.779-0.002-0.0020.0000.0000.0000.000
80A215ASN00.0110.00817.859-0.020-0.0200.0000.0000.0000.000
81A216PHE0-0.038-0.00815.263-0.015-0.0150.0000.0000.0000.000
82A217GLU-1-0.897-0.95217.338-0.072-0.0720.0000.0000.0000.000
83A218GLY0-0.013-0.01719.0380.0000.0000.0000.0000.0000.000
84A219GLU-1-0.910-0.93717.349-0.119-0.1190.0000.0000.0000.000
85A220VAL0-0.0040.00111.734-0.030-0.0300.0000.0000.0000.000
86A221THR0-0.039-0.02612.996-0.002-0.0020.0000.0000.0000.000
87A222LYS10.8770.9189.3600.6370.6370.0000.0000.0000.000
88A223GLU-1-0.807-0.91211.431-0.533-0.5330.0000.0000.0000.000
89A224ASN0-0.022-0.01414.498-0.005-0.0050.0000.0000.0000.000
90A225LEU00.0030.0139.7840.0110.0110.0000.0000.0000.000
91A226LEU0-0.030-0.0109.837-0.021-0.0210.0000.0000.0000.000
92A227ASP-1-0.945-0.95913.227-0.250-0.2500.0000.0000.0000.000
93A228PHE0-0.008-0.00613.6830.0160.0160.0000.0000.0000.000
94A229ILE00.0040.00410.4770.0190.0190.0000.0000.0000.000
95A230LYS10.8280.90414.3880.4880.4880.0000.0000.0000.000
96A231HIS00.0280.01216.6910.0270.0270.0000.0000.0000.000
97A232ASN0-0.089-0.06017.9620.0540.0540.0000.0000.0000.000
98A233GLN0-0.0280.00413.4990.0520.0520.0000.0000.0000.000
99A234LEU0-0.014-0.00717.5650.0110.0110.0000.0000.0000.000
100A235PRO0-0.007-0.01120.8760.0110.0110.0000.0000.0000.000
101A236LEU0-0.056-0.02424.010-0.003-0.0030.0000.0000.0000.000
102A237VAL0-0.041-0.02627.0870.0050.0050.0000.0000.0000.000
103A238ILE0-0.0210.00122.3180.0020.0020.0000.0000.0000.000
104A239GLU-1-0.795-0.87726.806-0.090-0.0900.0000.0000.0000.000
105A240PHE0-0.023-0.02126.078-0.016-0.0160.0000.0000.0000.000
106A241THR00.0320.00524.0460.0070.0070.0000.0000.0000.000
107A242GLU-1-0.888-0.95623.673-0.139-0.1390.0000.0000.0000.000
108A243GLN00.0120.01217.240-0.050-0.0500.0000.0000.0000.000
109A244THR0-0.013-0.01219.820-0.031-0.0310.0000.0000.0000.000
110A245ALA00.0050.01521.827-0.015-0.0150.0000.0000.0000.000
111A246PRO00.007-0.00118.6730.0020.0020.0000.0000.0000.000
112A247LYS10.8830.93615.3890.3650.3650.0000.0000.0000.000
113A248ILE00.0030.00619.6280.0040.0040.0000.0000.0000.000
114A249PHE0-0.032-0.01623.1940.0110.0110.0000.0000.0000.000
115A250GLY00.0030.00419.6870.0040.0040.0000.0000.0000.000
116A251GLY00.0330.01320.6850.0000.0000.0000.0000.0000.000
117A252GLU-1-0.861-0.93119.874-0.255-0.2550.0000.0000.0000.000
118A253ILE0-0.011-0.00923.1800.0160.0160.0000.0000.0000.000
119A254LYS10.8570.94423.1780.2300.2300.0000.0000.0000.000
120A255THR0-0.056-0.01827.8540.0070.0070.0000.0000.0000.000
121A256HIS00.005-0.01026.0280.0050.0050.0000.0000.0000.000
122A257ILE0-0.026-0.01531.0780.0090.0090.0000.0000.0000.000
123A258LEU00.0050.00731.626-0.005-0.0050.0000.0000.0000.000
124A259LEU0-0.027-0.01134.0460.0070.0070.0000.0000.0000.000
125A260PHE00.0060.00035.145-0.003-0.0030.0000.0000.0000.000
126A261LEU00.026-0.00835.8570.0060.0060.0000.0000.0000.000
127A262PRO00.0000.00837.228-0.002-0.0020.0000.0000.0000.000
128A263LYS10.8680.90531.2360.0840.0840.0000.0000.0000.000
129A264SER0-0.049-0.01138.2780.0040.0040.0000.0000.0000.000
130A265VAL0-0.078-0.02140.9660.0040.0040.0000.0000.0000.000
131A266SER00.006-0.00342.8080.0000.0000.0000.0000.0000.000
132A267ASP-1-0.829-0.92943.098-0.046-0.0460.0000.0000.0000.000
133A268TYR00.0800.04533.464-0.001-0.0010.0000.0000.0000.000
134A269ASP-1-0.820-0.91135.538-0.064-0.0640.0000.0000.0000.000
135A270GLY00.0640.04038.191-0.002-0.0020.0000.0000.0000.000
136A271LYS10.7810.88740.4840.0440.0440.0000.0000.0000.000
137A272LEU00.0510.03232.686-0.002-0.0020.0000.0000.0000.000
138A273SER0-0.014-0.01335.770-0.005-0.0050.0000.0000.0000.000
139A274ASN0-0.079-0.03537.4130.0000.0000.0000.0000.0000.000
140A275PHE00.0110.00632.4030.0000.0000.0000.0000.0000.000
141A276LYS10.8960.93532.3340.0650.0650.0000.0000.0000.000
142A277THR0-0.030-0.02734.322-0.001-0.0010.0000.0000.0000.000
143A278ALA0-0.037-0.01937.1220.0000.0000.0000.0000.0000.000
144A279ALA00.0320.01431.488-0.001-0.0010.0000.0000.0000.000
145A280GLU-1-0.867-0.94331.813-0.095-0.0950.0000.0000.0000.000
146A281SER0-0.053-0.02033.320-0.001-0.0010.0000.0000.0000.000
147A282PHE0-0.067-0.03433.2170.0010.0010.0000.0000.0000.000
148A283LYS10.9771.00126.7710.1080.1080.0000.0000.0000.000
149A284GLY00.0150.00527.0170.0050.0050.0000.0000.0000.000
150A285LYS10.7540.87628.0450.1010.1010.0000.0000.0000.000
151A286ILE0-0.003-0.00830.7550.0020.0020.0000.0000.0000.000
152A287LEU00.0260.02524.9600.0000.0000.0000.0000.0000.000
153A288PHE00.002-0.00628.6210.0080.0080.0000.0000.0000.000
154A289ILE00.0110.01827.626-0.004-0.0040.0000.0000.0000.000
155A290PHE0-0.024-0.01829.4410.0100.0100.0000.0000.0000.000
156A291ILE00.0170.00430.721-0.007-0.0070.0000.0000.0000.000
157A292ASP-1-0.758-0.87732.987-0.062-0.0620.0000.0000.0000.000
158A293SER00.023-0.02235.050-0.002-0.0020.0000.0000.0000.000
159A294ASP-1-0.846-0.92238.151-0.049-0.0490.0000.0000.0000.000
160A295HIS0-0.0020.01932.5800.0090.0090.0000.0000.0000.000
161A296THR0-0.004-0.02036.054-0.001-0.0010.0000.0000.0000.000
162A297ASP-1-0.883-0.93832.269-0.085-0.0850.0000.0000.0000.000
163A298ASN00.0360.00032.223-0.009-0.0090.0000.0000.0000.000
164A299GLN0-0.0070.00534.5740.0000.0000.0000.0000.0000.000
165A300ARG10.8610.92235.0530.0750.0750.0000.0000.0000.000
166A301ILE00.0080.00331.227-0.001-0.0010.0000.0000.0000.000
167A302LEU0-0.012-0.00835.4330.0000.0000.0000.0000.0000.000
168A303GLU-1-0.846-0.91438.822-0.066-0.0660.0000.0000.0000.000
169A304PHE0-0.065-0.02034.9560.0010.0010.0000.0000.0000.000
170A305PHE00.000-0.00233.6570.0000.0000.0000.0000.0000.000
171A306GLY0-0.0250.00139.1990.0030.0030.0000.0000.0000.000
172A307LEU0-0.053-0.02539.8160.0020.0020.0000.0000.0000.000
173A308LYS10.8640.93142.8320.0440.0440.0000.0000.0000.000
174A309LYS10.8240.89241.4610.0520.0520.0000.0000.0000.000
175A310GLU-1-0.847-0.92544.037-0.045-0.0450.0000.0000.0000.000
176A311GLU-1-0.966-0.97745.519-0.050-0.0500.0000.0000.0000.000
177A312CYS0-0.0310.01541.586-0.004-0.0040.0000.0000.0000.000
178A313PRO0-0.021-0.02841.1650.0030.0030.0000.0000.0000.000
179A314ALA0-0.0270.00140.7180.0030.0030.0000.0000.0000.000
180A315VAL00.0120.00437.673-0.003-0.0030.0000.0000.0000.000
181A316ARG10.8300.92536.7980.0740.0740.0000.0000.0000.000
182A317LEU00.0190.00635.625-0.003-0.0030.0000.0000.0000.000
183A318ILE0-0.017-0.00632.1160.0040.0040.0000.0000.0000.000
184A319THR00.0370.02332.062-0.003-0.0030.0000.0000.0000.000
185A320LEU0-0.0240.00526.8460.0040.0040.0000.0000.0000.000
186A321GLU-1-0.819-0.89430.206-0.108-0.1080.0000.0000.0000.000
187A322GLU-1-0.992-0.98827.013-0.168-0.1680.0000.0000.0000.000
188A335THR00.013-0.01837.224-0.002-0.0020.0000.0000.0000.000
189A336ALA00.0210.00339.095-0.003-0.0030.0000.0000.0000.000
190A337GLU-1-0.830-0.88841.465-0.072-0.0720.0000.0000.0000.000
191A338ARG10.8260.88034.3740.0960.0960.0000.0000.0000.000
192A339ILE00.0280.01237.000-0.004-0.0040.0000.0000.0000.000
193A340THR0-0.021-0.01938.4080.0000.0000.0000.0000.0000.000
194A341GLU-1-0.851-0.90838.725-0.085-0.0850.0000.0000.0000.000
195A342PHE0-0.0200.00231.7740.0000.0000.0000.0000.0000.000
196A343CYS0-0.041-0.03136.777-0.002-0.0020.0000.0000.0000.000
197A344HIS0-0.027-0.01339.4100.0010.0010.0000.0000.0000.000
198A345ARG10.8010.89035.0020.1080.1080.0000.0000.0000.000
199A346PHE0-0.019-0.00838.389-0.001-0.0010.0000.0000.0000.000
200A347LEU0-0.041-0.00539.7360.0010.0010.0000.0000.0000.000