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: 172LZ

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2067700.706522
FMO2-HF: Nuclear repulsion 1990193.263157
FMO2-HF: Total energy -77507.443364
FMO2-MP2: Total energy -77738.225195


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.
-8.543-3.1721.372-2.956-3.785-0.017
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 : -0.010 / 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].
3A138THR0-0.043-0.0043.8051.4962.896-0.021-0.720-0.6580.002
4A139THR0-0.002-0.0056.347-0.693-0.6930.0000.0000.0000.000
5A140LEU0-0.011-0.0038.896-0.120-0.1200.0000.0000.0000.000
6A141PRO0-0.0050.01412.354-0.073-0.0730.0000.0000.0000.000
7A142ASP-1-0.822-0.91315.2850.2600.2600.0000.0000.0000.000
8A143GLY00.030-0.00717.1250.0040.0040.0000.0000.0000.000
9A144ALA00.0270.02018.898-0.024-0.0240.0000.0000.0000.000
10A145ALA00.0020.00513.636-0.016-0.0160.0000.0000.0000.000
11A146ALA00.0140.00514.254-0.013-0.0130.0000.0000.0000.000
12A147GLU-1-0.842-0.91615.3620.0370.0370.0000.0000.0000.000
13A148SER0-0.034-0.02515.066-0.034-0.0340.0000.0000.0000.000
14A149LEU0-0.017-0.0069.088-0.025-0.0250.0000.0000.0000.000
15A150VAL0-0.025-0.02313.125-0.075-0.0750.0000.0000.0000.000
16A151GLU-1-0.862-0.93115.690-0.068-0.0680.0000.0000.0000.000
17A152SER0-0.071-0.01413.0430.0030.0030.0000.0000.0000.000
18A153SER0-0.071-0.04113.233-0.027-0.0270.0000.0000.0000.000
19A154GLU-1-0.873-0.93315.346-0.121-0.1210.0000.0000.0000.000
20A155VAL0-0.008-0.01214.2520.0180.0180.0000.0000.0000.000
21A156ALA00.0270.03212.237-0.058-0.0580.0000.0000.0000.000
22A157VAL00.0110.01610.2060.0630.0630.0000.0000.0000.000
23A158ILE0-0.028-0.00410.254-0.017-0.0170.0000.0000.0000.000
24A159GLY00.0310.01010.019-0.039-0.0390.0000.0000.0000.000
25A160PHE0-0.052-0.04310.9500.1440.1440.0000.0000.0000.000
26A161PHE00.0510.01210.184-0.054-0.0540.0000.0000.0000.000
27A162LYS10.8560.94313.411-0.035-0.0350.0000.0000.0000.000
28A163ASP-1-0.883-0.93814.1370.2940.2940.0000.0000.0000.000
29A164VAL00.0270.0128.041-0.048-0.0480.0000.0000.0000.000
30A165GLU-1-0.961-0.9849.2750.5410.5410.0000.0000.0000.000
31A166SER00.0140.01011.305-0.085-0.0850.0000.0000.0000.000
32A167ASP-1-0.895-0.96011.942-0.035-0.0350.0000.0000.0000.000
33A168SER00.000-0.00312.077-0.044-0.0440.0000.0000.0000.000
34A169ALA00.0200.0229.596-0.087-0.0870.0000.0000.0000.000
35A170LYS10.8800.9347.757-0.188-0.1880.0000.0000.0000.000
36A171GLN0-0.0080.0017.509-0.203-0.2030.0000.0000.0000.000
37A172PHE00.0240.0016.769-0.208-0.2080.0000.0000.0000.000
38A173LEU0-0.007-0.0082.936-0.751-0.2580.149-0.136-0.5060.000
39A174GLN00.0140.0113.367-1.944-1.0970.032-0.437-0.442-0.003
40A175ALA0-0.047-0.0265.986-0.045-0.0450.0000.0000.0000.000
41A176ALA0-0.028-0.0173.314-0.1490.0710.013-0.067-0.1660.000
42A177GLU-1-0.967-0.9852.420-5.559-3.3081.201-1.568-1.883-0.016
43A178ALA0-0.075-0.0264.5500.4120.442-0.001-0.013-0.0160.000
44A179ILE0-0.044-0.0227.1700.3090.3090.0000.0000.0000.000
45A180ASP-1-0.881-0.9407.299-1.216-1.2160.0000.0000.0000.000
46A181ASP-1-0.927-0.9498.947-0.468-0.4680.0000.0000.0000.000
47A182ILE0-0.037-0.0259.7560.1420.1420.0000.0000.0000.000
48A183PRO0-0.0040.0197.593-0.285-0.2850.0000.0000.0000.000
49A184PHE00.0440.0175.2860.0720.202-0.001-0.015-0.1140.000
50A185GLY0-0.011-0.0056.6430.3120.3120.0000.0000.0000.000
51A186ILE00.0060.0056.221-0.206-0.2060.0000.0000.0000.000
52A187THR0-0.015-0.0268.9200.1600.1600.0000.0000.0000.000
53A188SER00.0350.00312.250-0.021-0.0210.0000.0000.0000.000
54A189ASN0-0.065-0.02914.504-0.064-0.0640.0000.0000.0000.000
55A190SER00.0370.00617.453-0.020-0.0200.0000.0000.0000.000
56A191ASP-1-0.892-0.94220.3910.1440.1440.0000.0000.0000.000
57A192VAL0-0.018-0.02115.864-0.027-0.0270.0000.0000.0000.000
58A193PHE00.0040.00415.820-0.032-0.0320.0000.0000.0000.000
59A194SER00.0080.00819.619-0.027-0.0270.0000.0000.0000.000
60A195LYS10.7460.89220.484-0.090-0.0900.0000.0000.0000.000
61A196TYR00.0090.00518.239-0.006-0.0060.0000.0000.0000.000
62A197GLN0-0.051-0.01821.519-0.027-0.0270.0000.0000.0000.000
63A198LEU00.0170.02818.190-0.015-0.0150.0000.0000.0000.000
64A199ASP-1-0.835-0.89721.6180.0240.0240.0000.0000.0000.000
65A200LYS10.7920.86020.7980.0250.0250.0000.0000.0000.000
66A201ASP-1-0.812-0.92915.8970.0990.0990.0000.0000.0000.000
67A202GLY00.0170.00615.479-0.016-0.0160.0000.0000.0000.000
68A203VAL0-0.0130.00511.9140.0120.0120.0000.0000.0000.000
69A204VAL0-0.0230.00514.2500.0080.0080.0000.0000.0000.000
70A205LEU0-0.0130.01314.462-0.033-0.0330.0000.0000.0000.000
71A206PHE0-0.013-0.03815.1710.0560.0560.0000.0000.0000.000
72A207LYS10.8390.90116.7140.1400.1400.0000.0000.0000.000
73A208LYS10.7730.89218.6070.0980.0980.0000.0000.0000.000
74A209PHE0-0.014-0.00819.7480.0110.0110.0000.0000.0000.000
75A210ASP-1-0.834-0.92224.002-0.134-0.1340.0000.0000.0000.000
76A211GLU-1-0.832-0.91124.072-0.128-0.1280.0000.0000.0000.000
77A212GLY0-0.0090.02222.9610.0110.0110.0000.0000.0000.000
78A213ARG10.8170.87620.2780.0460.0460.0000.0000.0000.000
79A214ASN0-0.006-0.00219.367-0.003-0.0030.0000.0000.0000.000
80A215ASN00.0530.02918.525-0.018-0.0180.0000.0000.0000.000
81A216PHE0-0.028-0.00815.884-0.009-0.0090.0000.0000.0000.000
82A217GLU-1-0.937-0.96917.991-0.065-0.0650.0000.0000.0000.000
83A218GLY0-0.014-0.01220.153-0.007-0.0070.0000.0000.0000.000
84A219GLU-1-0.914-0.94317.844-0.105-0.1050.0000.0000.0000.000
85A220VAL00.004-0.00612.354-0.032-0.0320.0000.0000.0000.000
86A221THR0-0.051-0.02114.0930.0140.0140.0000.0000.0000.000
87A222LYS10.9140.9349.7350.5610.5610.0000.0000.0000.000
88A223GLU-1-0.815-0.91811.777-0.492-0.4920.0000.0000.0000.000
89A224ASN0-0.031-0.02114.9770.0010.0010.0000.0000.0000.000
90A225LEU0-0.0070.01010.1200.0090.0090.0000.0000.0000.000
91A226LEU0-0.027-0.01710.121-0.010-0.0100.0000.0000.0000.000
92A227ASP-1-0.931-0.95113.556-0.243-0.2430.0000.0000.0000.000
93A228PHE0-0.014-0.00714.3850.0230.0230.0000.0000.0000.000
94A229ILE00.0110.00411.0080.0250.0250.0000.0000.0000.000
95A230LYS10.8780.94214.5980.4930.4930.0000.0000.0000.000
96A231HIS00.0260.02617.4950.0250.0250.0000.0000.0000.000
97A232ASN0-0.106-0.07418.4850.0520.0520.0000.0000.0000.000
98A233GLN0-0.0270.00614.1020.0280.0280.0000.0000.0000.000
99A234LEU0-0.018-0.00717.8330.0030.0030.0000.0000.0000.000
100A235PRO00.004-0.00720.9200.0110.0110.0000.0000.0000.000
101A236LEU0-0.059-0.02924.176-0.004-0.0040.0000.0000.0000.000
102A237VAL0-0.058-0.03227.3340.0030.0030.0000.0000.0000.000
103A238ILE00.0000.01422.2370.0020.0020.0000.0000.0000.000
104A239GLU-1-0.814-0.89526.432-0.095-0.0950.0000.0000.0000.000
105A240PHE0-0.007-0.02926.010-0.015-0.0150.0000.0000.0000.000
106A241THR00.0230.00924.1110.0030.0030.0000.0000.0000.000
107A242GLU-1-0.854-0.94323.610-0.148-0.1480.0000.0000.0000.000
108A243GLN0-0.009-0.00416.802-0.047-0.0470.0000.0000.0000.000
109A244THR00.0010.00119.555-0.037-0.0370.0000.0000.0000.000
110A245ALA0-0.0020.01021.844-0.011-0.0110.0000.0000.0000.000
111A246PRO0-0.007-0.01218.6340.0040.0040.0000.0000.0000.000
112A247LYS10.8480.91315.3760.3860.3860.0000.0000.0000.000
113A248ILE00.0020.01219.7020.0050.0050.0000.0000.0000.000
114A249PHE0-0.039-0.02323.3910.0090.0090.0000.0000.0000.000
115A250GLY0-0.012-0.00320.0460.0070.0070.0000.0000.0000.000
116A251GLY00.0240.03420.970-0.011-0.0110.0000.0000.0000.000
117A252GLU-1-0.863-0.94420.403-0.255-0.2550.0000.0000.0000.000
118A253ILE0-0.012-0.00523.7160.0160.0160.0000.0000.0000.000
119A254LYS10.8780.93824.2620.2210.2210.0000.0000.0000.000
120A255THR0-0.0250.00728.5070.0070.0070.0000.0000.0000.000
121A256HIS00.016-0.00726.2700.0060.0060.0000.0000.0000.000
122A257ILE0-0.016-0.00431.4550.0090.0090.0000.0000.0000.000
123A258LEU00.015-0.00131.770-0.004-0.0040.0000.0000.0000.000
124A259LEU0-0.028-0.02034.0770.0080.0080.0000.0000.0000.000
125A260PHE0-0.003-0.00734.970-0.004-0.0040.0000.0000.0000.000
126A261LEU00.013-0.01135.8980.0060.0060.0000.0000.0000.000
127A262PRO00.0120.01236.808-0.003-0.0030.0000.0000.0000.000
128A263LYS10.8500.90130.9770.0910.0910.0000.0000.0000.000
129A264SER0-0.0210.00638.0310.0040.0040.0000.0000.0000.000
130A265VAL0-0.086-0.02440.7190.0040.0040.0000.0000.0000.000
131A266SER00.0180.00442.5170.0000.0000.0000.0000.0000.000
132A267ASP-1-0.834-0.92343.404-0.047-0.0470.0000.0000.0000.000
133A268TYR00.0770.04933.439-0.002-0.0020.0000.0000.0000.000
134A269ASP-1-0.798-0.92335.578-0.068-0.0680.0000.0000.0000.000
135A270GLY0-0.0050.01338.242-0.002-0.0020.0000.0000.0000.000
136A271LYS10.7910.86340.5380.0480.0480.0000.0000.0000.000
137A272LEU00.0090.00832.665-0.002-0.0020.0000.0000.0000.000
138A273SER0-0.041-0.01635.780-0.005-0.0050.0000.0000.0000.000
139A274ASN00.0060.00037.458-0.001-0.0010.0000.0000.0000.000
140A275PHE0-0.0030.00032.3910.0000.0000.0000.0000.0000.000
141A276LYS10.9390.97132.3290.0690.0690.0000.0000.0000.000
142A277THR0-0.010-0.00634.382-0.001-0.0010.0000.0000.0000.000
143A278ALA0-0.040-0.02437.2260.0000.0000.0000.0000.0000.000
144A279ALA00.0290.01231.641-0.002-0.0020.0000.0000.0000.000
145A280GLU-1-0.903-0.95032.415-0.093-0.0930.0000.0000.0000.000
146A281SER0-0.061-0.02733.9330.0000.0000.0000.0000.0000.000
147A282PHE0-0.045-0.02433.9020.0020.0020.0000.0000.0000.000
148A283LYS11.0231.03826.8660.1150.1150.0000.0000.0000.000
149A284GLY00.0160.00427.5070.0040.0040.0000.0000.0000.000
150A285LYS10.7720.89128.5280.0970.0970.0000.0000.0000.000
151A286ILE0-0.017-0.02131.3620.0000.0000.0000.0000.0000.000
152A287LEU00.0350.03325.0850.0020.0020.0000.0000.0000.000
153A288PHE0-0.011-0.01328.8950.0070.0070.0000.0000.0000.000
154A289ILE00.0090.01427.647-0.007-0.0070.0000.0000.0000.000
155A290PHE0-0.032-0.01029.3360.0100.0100.0000.0000.0000.000
156A291ILE00.0210.01130.643-0.008-0.0080.0000.0000.0000.000
157A292ASP-1-0.769-0.89232.806-0.067-0.0670.0000.0000.0000.000
158A293SER00.031-0.01634.872-0.002-0.0020.0000.0000.0000.000
159A294ASP-1-0.882-0.94638.065-0.054-0.0540.0000.0000.0000.000
160A295HIS0-0.0050.01132.1280.0090.0090.0000.0000.0000.000
161A296THR00.0310.00636.200-0.001-0.0010.0000.0000.0000.000
162A297ASP-1-0.947-0.97431.958-0.094-0.0940.0000.0000.0000.000
163A298ASN00.0430.01532.122-0.012-0.0120.0000.0000.0000.000
164A299GLN0-0.013-0.01434.5890.0000.0000.0000.0000.0000.000
165A300ARG10.8670.92235.0000.0810.0810.0000.0000.0000.000
166A301ILE00.0270.01331.0010.0010.0010.0000.0000.0000.000
167A302LEU00.0110.00535.4100.0010.0010.0000.0000.0000.000
168A303GLU-1-0.855-0.91138.694-0.069-0.0690.0000.0000.0000.000
169A304PHE0-0.061-0.02135.3000.0020.0020.0000.0000.0000.000
170A305PHE0-0.032-0.01434.0320.0000.0000.0000.0000.0000.000
171A306GLY0-0.039-0.01739.6180.0030.0030.0000.0000.0000.000
172A307LEU0-0.045-0.02139.8930.0030.0030.0000.0000.0000.000
173A308LYS10.8370.91642.7440.0460.0460.0000.0000.0000.000
174A309LYS10.8640.91941.3380.0570.0570.0000.0000.0000.000
175A310GLU-1-0.847-0.92743.871-0.048-0.0480.0000.0000.0000.000
176A311GLU-1-0.944-0.96245.503-0.053-0.0530.0000.0000.0000.000
177A312CYS0-0.0550.00741.462-0.004-0.0040.0000.0000.0000.000
178A313PRO0-0.012-0.02741.2630.0030.0030.0000.0000.0000.000
179A314ALA0-0.0110.01140.7400.0030.0030.0000.0000.0000.000
180A315VAL00.0210.00737.814-0.004-0.0040.0000.0000.0000.000
181A316ARG10.8730.94337.2450.0770.0770.0000.0000.0000.000
182A317LEU00.0060.01935.620-0.004-0.0040.0000.0000.0000.000
183A318ILE0-0.020-0.01532.3790.0040.0040.0000.0000.0000.000
184A319THR00.0190.01732.904-0.005-0.0050.0000.0000.0000.000
185A320LEU0-0.025-0.00127.4050.0040.0040.0000.0000.0000.000
186A321GLU-1-0.837-0.90630.919-0.107-0.1070.0000.0000.0000.000
187A322GLU-1-0.981-0.98427.709-0.169-0.1690.0000.0000.0000.000
188A335THR00.004-0.02337.445-0.002-0.0020.0000.0000.0000.000
189A336ALA00.011-0.00539.316-0.003-0.0030.0000.0000.0000.000
190A337GLU-1-0.827-0.90741.848-0.073-0.0730.0000.0000.0000.000
191A338ARG10.8240.88034.6750.0950.0950.0000.0000.0000.000
192A339ILE00.0300.01737.402-0.003-0.0030.0000.0000.0000.000
193A340THR0-0.010-0.00638.7860.0000.0000.0000.0000.0000.000
194A341GLU-1-0.847-0.89739.172-0.084-0.0840.0000.0000.0000.000
195A342PHE0-0.033-0.00232.3150.0000.0000.0000.0000.0000.000
196A343CYS0-0.023-0.02237.122-0.002-0.0020.0000.0000.0000.000
197A344HIS0-0.056-0.00339.5070.0010.0010.0000.0000.0000.000
198A345ARG10.8110.87835.4160.1060.1060.0000.0000.0000.000
199A346PHE0-0.031-0.01138.943-0.001-0.0010.0000.0000.0000.000
200A347LEU0-0.0090.00240.2190.0000.0000.0000.0000.0000.000