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: 2NNGR

Calculation Name: 5C5S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5C5S

Chain ID: A

ChEMBL ID:

UniProt ID: Q13459

Base Structure: X-ray

Registration Date: 2023-09-21

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2452110.118475
FMO2-HF: Nuclear repulsion 2368187.004304
FMO2-HF: Total energy -83923.11417
FMO2-MP2: Total energy -84164.584492


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:109:PHE)


Summations of interaction energy for fragment #1(A:109:PHE)
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.
-7.999-3.8251.488-1.853-3.81-0.002
Interaction energy analysis for fragmet #1(A:109:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.009
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].
3A111GLY0-0.013-0.0053.896-1.467-0.270-0.011-0.497-0.6890.002
4A112VAL0-0.041-0.0082.3650.1810.8831.318-0.554-1.466-0.002
5A113GLU-1-0.906-0.9503.118-5.394-4.2940.066-0.490-0.677-0.005
6A114PRO0-0.041-0.0213.183-0.6510.4430.116-0.301-0.9090.003
7A115GLY0-0.0140.0124.9100.3760.457-0.001-0.011-0.0690.000
8A116HIS00.005-0.0248.373-0.097-0.0970.0000.0000.0000.000
9A117PHE0-0.051-0.03111.0120.0750.0750.0000.0000.0000.000
10A118GLY00.0100.01010.2780.0190.0190.0000.0000.0000.000
11A119VAL00.0070.0076.2000.0510.0510.0000.0000.0000.000
12A120CYS0-0.018-0.0217.8920.0670.0670.0000.0000.0000.000
13A121VAL00.0490.0299.819-0.106-0.1060.0000.0000.0000.000
14A122ASP-1-0.865-0.93611.280-0.519-0.5190.0000.0000.0000.000
15A123SER0-0.055-0.0316.974-0.079-0.0790.0000.0000.0000.000
16A124LEU0-0.058-0.0239.040-0.134-0.1340.0000.0000.0000.000
17A125THR0-0.055-0.03211.4910.1010.1010.0000.0000.0000.000
18A126SER0-0.007-0.01413.281-0.054-0.0540.0000.0000.0000.000
19A127ASP-1-0.857-0.93315.780-0.334-0.3340.0000.0000.0000.000
20A128LYS10.8680.92918.1230.4090.4090.0000.0000.0000.000
21A129ALA0-0.042-0.02216.5710.0080.0080.0000.0000.0000.000
22A130SER00.0750.05117.253-0.042-0.0420.0000.0000.0000.000
23A131VAL0-0.0030.00818.9480.0060.0060.0000.0000.0000.000
24A132PRO00.0170.01314.575-0.021-0.0210.0000.0000.0000.000
25A133ILE00.0380.01315.1700.0440.0440.0000.0000.0000.000
26A134VAL0-0.013-0.01314.7370.0420.0420.0000.0000.0000.000
27A135LEU0-0.0140.00617.4640.0390.0390.0000.0000.0000.000
28A136GLU-1-0.765-0.87019.739-0.217-0.2170.0000.0000.0000.000
29A137LYS10.8160.91420.1690.3330.3330.0000.0000.0000.000
30A138LEU0-0.037-0.02020.1960.0250.0250.0000.0000.0000.000
31A139LEU0-0.029-0.01423.4260.0230.0230.0000.0000.0000.000
32A140GLU-1-0.874-0.93825.310-0.186-0.1860.0000.0000.0000.000
33A141HIS00.0800.03826.2920.0100.0100.0000.0000.0000.000
34A142VAL0-0.049-0.03927.4230.0160.0160.0000.0000.0000.000
35A143GLU-1-0.795-0.87628.822-0.163-0.1630.0000.0000.0000.000
36A144MET0-0.0250.00430.8530.0160.0160.0000.0000.0000.000
37A145HIS0-0.043-0.01830.4350.0130.0130.0000.0000.0000.000
38A146GLY0-0.007-0.00432.6080.0050.0050.0000.0000.0000.000
39A147LEU00.0170.02232.7040.0070.0070.0000.0000.0000.000
40A148TYR00.0430.02335.3930.0040.0040.0000.0000.0000.000
41A149THR0-0.078-0.04635.2780.0050.0050.0000.0000.0000.000
42A150GLU-1-0.830-0.91337.051-0.077-0.0770.0000.0000.0000.000
43A151GLY0-0.022-0.03236.726-0.002-0.0020.0000.0000.0000.000
44A152LEU00.0010.00931.598-0.003-0.0030.0000.0000.0000.000
45A153TYR00.027-0.01726.346-0.001-0.0010.0000.0000.0000.000
46A154ARG10.9600.99830.3810.0770.0770.0000.0000.0000.000
47A155LYS10.8180.91333.0830.0890.0890.0000.0000.0000.000
48A156SER0-0.002-0.01329.990-0.006-0.0060.0000.0000.0000.000
49A157GLY0-0.0060.00229.5810.0060.0060.0000.0000.0000.000
50A158ALA00.0240.01229.9830.0030.0030.0000.0000.0000.000
51A159ALA00.0610.03226.324-0.011-0.0110.0000.0000.0000.000
52A160ASN0-0.040-0.03124.943-0.005-0.0050.0000.0000.0000.000
53A161ARG10.8990.94324.3800.1530.1530.0000.0000.0000.000
54A162THR0-0.002-0.01323.305-0.014-0.0140.0000.0000.0000.000
55A163ARG10.8920.95220.0310.1280.1280.0000.0000.0000.000
56A164GLU-1-0.825-0.90719.920-0.172-0.1720.0000.0000.0000.000
57A165LEU00.0070.01820.754-0.023-0.0230.0000.0000.0000.000
58A166ARG10.8380.90314.2140.2120.2120.0000.0000.0000.000
59A167GLN0-0.039-0.03116.091-0.014-0.0140.0000.0000.0000.000
60A168ALA00.0060.00915.966-0.046-0.0460.0000.0000.0000.000
61A169LEU00.020-0.00916.847-0.040-0.0400.0000.0000.0000.000
62A170GLN00.0200.02310.882-0.104-0.1040.0000.0000.0000.000
63A171THR0-0.028-0.00111.933-0.087-0.0870.0000.0000.0000.000
64A172ASP-1-0.741-0.87713.089-0.589-0.5890.0000.0000.0000.000
65A173PRO0-0.0150.00514.5250.0780.0780.0000.0000.0000.000
66A174ALA0-0.012-0.00517.5590.0550.0550.0000.0000.0000.000
67A175ALA0-0.009-0.01319.5130.0490.0490.0000.0000.0000.000
68A176VAL0-0.036-0.01519.5490.0390.0390.0000.0000.0000.000
69A177LYS10.9090.96922.3120.2550.2550.0000.0000.0000.000
70A178LEU00.0640.02423.1430.0110.0110.0000.0000.0000.000
71A179GLU-1-0.797-0.90426.602-0.181-0.1810.0000.0000.0000.000
72A180ASN0-0.118-0.04528.1740.0200.0200.0000.0000.0000.000
73A181PHE0-0.029-0.02323.9660.0010.0010.0000.0000.0000.000
74A182PRO00.0210.02428.8760.0030.0030.0000.0000.0000.000
75A183ILE00.1170.04729.585-0.007-0.0070.0000.0000.0000.000
76A184HIS00.0360.00929.493-0.011-0.0110.0000.0000.0000.000
77A185ALA0-0.015-0.00726.5910.0030.0030.0000.0000.0000.000
78A186ILE00.0060.02125.086-0.012-0.0120.0000.0000.0000.000
79A187THR00.0150.00424.928-0.009-0.0090.0000.0000.0000.000
80A188GLY0-0.024-0.01725.6350.0000.0000.0000.0000.0000.000
81A189VAL00.018-0.00619.7510.0010.0010.0000.0000.0000.000
82A190LEU0-0.0050.02220.477-0.014-0.0140.0000.0000.0000.000
83A191LYS10.8490.90521.2010.1240.1240.0000.0000.0000.000
84A192GLN0-0.122-0.06418.4300.0060.0060.0000.0000.0000.000
85A193TRP00.0370.00013.8560.0350.0350.0000.0000.0000.000
86A194LEU00.0230.01316.411-0.009-0.0090.0000.0000.0000.000
87A195ARG10.8780.92718.0860.1430.1430.0000.0000.0000.000
88A196GLU-1-0.799-0.87514.217-0.210-0.2100.0000.0000.0000.000
89A197LEU00.0230.03713.025-0.024-0.0240.0000.0000.0000.000
90A198PRO00.000-0.0019.5100.0480.0480.0000.0000.0000.000
91A199GLU-1-0.851-0.91212.549-0.157-0.1570.0000.0000.0000.000
92A200PRO0-0.076-0.02315.514-0.019-0.0190.0000.0000.0000.000
93A201LEU00.0520.01917.564-0.003-0.0030.0000.0000.0000.000
94A202MET0-0.046-0.01019.176-0.006-0.0060.0000.0000.0000.000
95A203THR00.0060.00418.5690.0210.0210.0000.0000.0000.000
96A204PHE0-0.003-0.03716.2590.0120.0120.0000.0000.0000.000
97A205ALA0-0.035-0.00920.4530.0160.0160.0000.0000.0000.000
98A206GLN00.017-0.00122.2970.0010.0010.0000.0000.0000.000
99A207TYR0-0.042-0.03424.0200.0040.0040.0000.0000.0000.000
100A208GLY0-0.011-0.01025.7390.0060.0060.0000.0000.0000.000
101A209ASP-1-0.792-0.89927.368-0.071-0.0710.0000.0000.0000.000
102A210PHE00.036-0.01324.8340.0050.0050.0000.0000.0000.000
103A211LEU0-0.052-0.02129.6740.0030.0030.0000.0000.0000.000
104A212ARG10.8080.88931.1380.0500.0500.0000.0000.0000.000
105A213ALA00.0070.01032.9860.0030.0030.0000.0000.0000.000
106A214VAL0-0.041-0.03034.0010.0010.0010.0000.0000.0000.000
107A215GLU-1-0.856-0.90135.697-0.038-0.0380.0000.0000.0000.000
108A216LEU0-0.0370.00237.9750.0040.0040.0000.0000.0000.000
109A217PRO0-0.004-0.00340.467-0.001-0.0010.0000.0000.0000.000
110A218GLU-1-0.833-0.88843.631-0.044-0.0440.0000.0000.0000.000
111A219LYS10.9470.96841.6780.0580.0580.0000.0000.0000.000
112A220GLN0-0.064-0.06040.997-0.004-0.0040.0000.0000.0000.000
113A221GLU-1-0.822-0.91440.772-0.046-0.0460.0000.0000.0000.000
114A222GLN0-0.012-0.00538.039-0.006-0.0060.0000.0000.0000.000
115A223LEU0-0.034-0.02736.472-0.005-0.0050.0000.0000.0000.000
116A224ALA0-0.013-0.00435.861-0.005-0.0050.0000.0000.0000.000
117A225ALA00.0190.01735.114-0.003-0.0030.0000.0000.0000.000
118A226ILE00.009-0.01231.177-0.004-0.0040.0000.0000.0000.000
119A227TYR0-0.030-0.04130.929-0.004-0.0040.0000.0000.0000.000
120A228ALA0-0.0010.00131.039-0.005-0.0050.0000.0000.0000.000
121A229VAL0-0.029-0.00827.4550.0000.0000.0000.0000.0000.000
122A230LEU0-0.022-0.02226.586-0.007-0.0070.0000.0000.0000.000
123A231GLU-1-0.907-0.94525.899-0.136-0.1360.0000.0000.0000.000
124A232HIS0-0.066-0.02125.3850.0000.0000.0000.0000.0000.000
125A233LEU0-0.053-0.00421.578-0.005-0.0050.0000.0000.0000.000
126A234PRO00.001-0.00417.277-0.001-0.0010.0000.0000.0000.000
127A235GLU-1-0.890-0.93718.609-0.258-0.2580.0000.0000.0000.000
128A236ALA00.0640.04115.4400.0050.0050.0000.0000.0000.000
129A237ASN0-0.044-0.03516.445-0.026-0.0260.0000.0000.0000.000
130A238HIS0-0.023-0.00118.6790.0000.0000.0000.0000.0000.000
131A239ASN00.0790.03020.460-0.005-0.0050.0000.0000.0000.000
132A240SER0-0.039-0.04218.078-0.005-0.0050.0000.0000.0000.000
133A241LEU0-0.021-0.01320.5830.0120.0120.0000.0000.0000.000
134A242GLU-1-0.921-0.95423.277-0.166-0.1660.0000.0000.0000.000
135A243ARG10.7660.84723.1890.2270.2270.0000.0000.0000.000
136A244LEU00.0000.00322.9400.0090.0090.0000.0000.0000.000
137A245ILE0-0.008-0.01625.4150.0140.0140.0000.0000.0000.000
138A246PHE00.0240.00428.4350.0130.0130.0000.0000.0000.000
139A247HIS00.0020.00627.6820.0130.0130.0000.0000.0000.000
140A248LEU00.003-0.01427.5790.0110.0110.0000.0000.0000.000
141A249VAL0-0.018-0.01031.0380.0100.0100.0000.0000.0000.000
142A250LYS10.8560.92931.3460.1590.1590.0000.0000.0000.000
143A251VAL0-0.0160.00331.8060.0050.0050.0000.0000.0000.000
144A252ALA00.0090.01434.8100.0070.0070.0000.0000.0000.000
145A253LEU0-0.051-0.04336.8670.0070.0070.0000.0000.0000.000
146A254LEU00.0030.01037.7590.0040.0040.0000.0000.0000.000
147A255GLU-1-0.832-0.89439.950-0.072-0.0720.0000.0000.0000.000
148A256ASP-1-0.956-0.98940.803-0.067-0.0670.0000.0000.0000.000
149A257VAL0-0.058-0.01741.4870.0020.0020.0000.0000.0000.000
150A258ASN0-0.008-0.01937.2660.0040.0040.0000.0000.0000.000
151A259ARG10.8360.90138.8980.0700.0700.0000.0000.0000.000
152A260MET0-0.103-0.02933.7360.0040.0040.0000.0000.0000.000
153A261SER00.0830.05536.998-0.004-0.0040.0000.0000.0000.000
154A262PRO0-0.003-0.02135.357-0.003-0.0030.0000.0000.0000.000
155A263GLY00.0620.05634.649-0.004-0.0040.0000.0000.0000.000
156A264ALA0-0.038-0.02935.1750.0000.0000.0000.0000.0000.000
157A265LEU0-0.009-0.00731.491-0.003-0.0030.0000.0000.0000.000
158A266ALA00.0390.01830.786-0.006-0.0060.0000.0000.0000.000
159A267ILE0-0.006-0.00330.697-0.001-0.0010.0000.0000.0000.000
160A268ILE0-0.074-0.02228.0980.0000.0000.0000.0000.0000.000
161A269PHE00.031-0.00524.756-0.005-0.0050.0000.0000.0000.000
162A270ALA00.0380.03025.761-0.008-0.0080.0000.0000.0000.000
163A271PRO00.0130.00325.880-0.004-0.0040.0000.0000.0000.000
164A272CYS0-0.118-0.05222.522-0.001-0.0010.0000.0000.0000.000
165A273LEU0-0.0060.00521.295-0.018-0.0180.0000.0000.0000.000
166A274LEU00.0000.00722.401-0.004-0.0040.0000.0000.0000.000
167A275ARG10.8370.92115.9410.1740.1740.0000.0000.0000.000
168A276CYS00.0110.00422.720-0.003-0.0030.0000.0000.0000.000
169A277PRO00.0390.01721.470-0.002-0.0020.0000.0000.0000.000
170A278ASP-1-0.934-0.94819.810-0.012-0.0120.0000.0000.0000.000
171A279ASN0-0.017-0.00722.4230.0010.0010.0000.0000.0000.000
172A280SER0-0.044-0.02524.8490.0020.0020.0000.0000.0000.000
173A281ASP-1-0.807-0.91227.415-0.005-0.0050.0000.0000.0000.000
174A282PRO00.0430.02229.686-0.006-0.0060.0000.0000.0000.000
175A283LEU0-0.015-0.00131.160-0.003-0.0030.0000.0000.0000.000
176A284THR0-0.086-0.04732.207-0.003-0.0030.0000.0000.0000.000
177A285SER00.005-0.01830.258-0.005-0.0050.0000.0000.0000.000
178A286MET0-0.014-0.01331.909-0.004-0.0040.0000.0000.0000.000
179A287LYS10.9420.96435.1330.0270.0270.0000.0000.0000.000
180A288ASP-1-0.740-0.84130.654-0.049-0.0490.0000.0000.0000.000
181A289VAL00.0350.02130.269-0.006-0.0060.0000.0000.0000.000
182A290LEU00.0070.01132.075-0.005-0.0050.0000.0000.0000.000
183A291LYS10.8210.91833.1830.0400.0400.0000.0000.0000.000
184A292ILE00.0460.01827.557-0.003-0.0030.0000.0000.0000.000
185A293THR0-0.041-0.03030.760-0.008-0.0080.0000.0000.0000.000
186A294THR0-0.018-0.02632.673-0.002-0.0020.0000.0000.0000.000
187A295CYS0-0.0270.00630.915-0.003-0.0030.0000.0000.0000.000
188A296VAL00.0440.01628.171-0.004-0.0040.0000.0000.0000.000
189A297GLU-1-0.824-0.92031.137-0.075-0.0750.0000.0000.0000.000
190A298MET0-0.062-0.03034.6070.0000.0000.0000.0000.0000.000
191A299LEU00.0400.03528.9120.0010.0010.0000.0000.0000.000
192A300ILE00.0100.00030.658-0.002-0.0020.0000.0000.0000.000
193A301LYS10.8300.89933.7890.0740.0740.0000.0000.0000.000
194A302GLU-1-0.776-0.83136.475-0.075-0.0750.0000.0000.0000.000
195A303GLN00.0470.03631.3070.0070.0070.0000.0000.0000.000
196A304MET00.0040.00535.4760.0000.0000.0000.0000.0000.000
197A305ARG10.7860.86237.6540.0740.0740.0000.0000.0000.000
198A306LYS10.8620.91436.1550.0930.0930.0000.0000.0000.000
199A307TYR00.0170.01235.903-0.001-0.0010.0000.0000.0000.000
200A308LYS10.9270.95238.9810.0830.0830.0000.0000.0000.000
201A309VAL0-0.016-0.00142.4510.0020.0020.0000.0000.0000.000
202A310LYS10.9860.98639.3740.0900.0900.0000.0000.0000.000
203A311MET0-0.051-0.01640.011-0.001-0.0010.0000.0000.0000.000
204A312GLU-1-0.867-0.91343.127-0.067-0.0670.0000.0000.0000.000
205A313GLU-1-0.984-0.97843.776-0.074-0.0740.0000.0000.0000.000
206A314ILE0-0.058-0.03440.4300.0000.0000.0000.0000.0000.000
207A315SER0-0.082-0.04844.8980.0000.0000.0000.0000.0000.000
208A316GLN0-0.056-0.03347.6750.0050.0050.0000.0000.0000.000
209A317LEU0-0.024-0.00549.089-0.003-0.0030.0000.0000.0000.000
210A318GLU-1-0.967-0.98251.091-0.060-0.0600.0000.0000.0000.000