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: MNNZZ

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2443438.158035
FMO2-HF: Nuclear repulsion 2359516.14545
FMO2-HF: Total energy -83922.012586
FMO2-MP2: Total energy -84163.481992


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.
-4.073-1.7351.673-1.267-2.746-0.001
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 : -0.018 / q_NPA : -0.016
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].
3A111GLY0-0.0050.0003.848-1.1850.187-0.020-0.573-0.7790.002
4A112VAL0-0.045-0.0072.247-0.0740.3781.694-0.625-1.521-0.003
5A113GLU-1-0.918-0.9614.380-1.646-1.498-0.001-0.031-0.1170.000
6A114PRO0-0.034-0.0124.596-0.1240.2420.000-0.038-0.3290.000
7A115GLY0-0.0090.0146.3070.0070.0070.0000.0000.0000.000
8A116HIS00.028-0.0159.700-0.046-0.0460.0000.0000.0000.000
9A117PHE0-0.084-0.04511.5780.0340.0340.0000.0000.0000.000
10A118GLY00.0170.0139.804-0.012-0.0120.0000.0000.0000.000
11A119VAL0-0.0080.0096.017-0.117-0.1170.0000.0000.0000.000
12A120CYS0-0.013-0.0267.7950.0940.0940.0000.0000.0000.000
13A121VAL00.0510.0249.704-0.051-0.0510.0000.0000.0000.000
14A122ASP-1-0.846-0.93311.201-0.536-0.5360.0000.0000.0000.000
15A123SER0-0.079-0.0277.335-0.052-0.0520.0000.0000.0000.000
16A124LEU0-0.064-0.0339.335-0.013-0.0130.0000.0000.0000.000
17A125THR0-0.059-0.02011.9050.0890.0890.0000.0000.0000.000
18A126SER0-0.020-0.02913.706-0.041-0.0410.0000.0000.0000.000
19A127ASP-1-0.837-0.92216.086-0.258-0.2580.0000.0000.0000.000
20A128LYS10.8490.92418.5120.3140.3140.0000.0000.0000.000
21A129ALA0-0.035-0.01817.2810.0170.0170.0000.0000.0000.000
22A130SER00.0750.05317.763-0.036-0.0360.0000.0000.0000.000
23A131VAL00.0060.00818.992-0.008-0.0080.0000.0000.0000.000
24A132PRO00.0230.01515.045-0.005-0.0050.0000.0000.0000.000
25A133ILE00.0650.02716.5020.0350.0350.0000.0000.0000.000
26A134VAL0-0.006-0.01215.5000.0340.0340.0000.0000.0000.000
27A135LEU0-0.0250.00218.2720.0280.0280.0000.0000.0000.000
28A136GLU-1-0.765-0.88219.966-0.191-0.1910.0000.0000.0000.000
29A137LYS10.8690.94721.3740.2500.2500.0000.0000.0000.000
30A138LEU0-0.047-0.02820.5280.0210.0210.0000.0000.0000.000
31A139LEU0-0.035-0.02423.7000.0180.0180.0000.0000.0000.000
32A140GLU-1-0.875-0.93025.909-0.152-0.1520.0000.0000.0000.000
33A141HIS00.0730.03127.1310.0100.0100.0000.0000.0000.000
34A142VAL0-0.057-0.03927.9220.0130.0130.0000.0000.0000.000
35A143GLU-1-0.829-0.91929.369-0.153-0.1530.0000.0000.0000.000
36A144MET0-0.0250.01031.6620.0120.0120.0000.0000.0000.000
37A145HIS0-0.054-0.02031.6510.0120.0120.0000.0000.0000.000
38A146GLY0-0.023-0.02133.3160.0050.0050.0000.0000.0000.000
39A147LEU0-0.0010.01132.9860.0020.0020.0000.0000.0000.000
40A148TYR00.0430.01935.8460.0040.0040.0000.0000.0000.000
41A149THR0-0.070-0.02035.0990.0050.0050.0000.0000.0000.000
42A150GLU-1-0.912-0.95736.991-0.079-0.0790.0000.0000.0000.000
43A151GLY0-0.056-0.04036.488-0.002-0.0020.0000.0000.0000.000
44A152LEU00.0370.03331.735-0.004-0.0040.0000.0000.0000.000
45A153TYR0-0.005-0.06326.548-0.004-0.0040.0000.0000.0000.000
46A154ARG10.9630.98430.1610.0860.0860.0000.0000.0000.000
47A155LYS10.8950.94532.1930.0890.0890.0000.0000.0000.000
48A156SER00.0030.00929.276-0.006-0.0060.0000.0000.0000.000
49A157GLY00.0240.01128.8840.0070.0070.0000.0000.0000.000
50A158ALA0-0.0010.00129.2130.0010.0010.0000.0000.0000.000
51A159ALA00.0670.03025.760-0.009-0.0090.0000.0000.0000.000
52A160ASN0-0.0020.00324.654-0.015-0.0150.0000.0000.0000.000
53A161ARG10.9370.94024.6340.1300.1300.0000.0000.0000.000
54A162THR00.005-0.00922.441-0.009-0.0090.0000.0000.0000.000
55A163ARG10.9510.98419.8690.1280.1280.0000.0000.0000.000
56A164GLU-1-0.930-0.97220.168-0.155-0.1550.0000.0000.0000.000
57A165LEU00.0100.01820.932-0.012-0.0120.0000.0000.0000.000
58A166ARG10.8740.93012.4170.3340.3340.0000.0000.0000.000
59A167GLN0-0.071-0.04416.266-0.016-0.0160.0000.0000.0000.000
60A168ALA0-0.003-0.00216.219-0.024-0.0240.0000.0000.0000.000
61A169LEU0-0.001-0.01017.810-0.012-0.0120.0000.0000.0000.000
62A170GLN00.0160.02010.819-0.043-0.0430.0000.0000.0000.000
63A171THR0-0.010-0.00512.606-0.037-0.0370.0000.0000.0000.000
64A172ASP-1-0.812-0.92013.655-0.395-0.3950.0000.0000.0000.000
65A173PRO0-0.0180.00615.6700.0480.0480.0000.0000.0000.000
66A174ALA0-0.0130.00218.7230.0320.0320.0000.0000.0000.000
67A175ALA00.0080.00620.5460.0300.0300.0000.0000.0000.000
68A176VAL0-0.039-0.01520.2620.0260.0260.0000.0000.0000.000
69A177LYS10.9520.97423.0850.1650.1650.0000.0000.0000.000
70A178LEU00.0470.00924.0410.0070.0070.0000.0000.0000.000
71A179GLU-1-0.861-0.92727.507-0.135-0.1350.0000.0000.0000.000
72A180ASN0-0.044-0.00828.5340.0160.0160.0000.0000.0000.000
73A181PHE0-0.056-0.02023.9700.0030.0030.0000.0000.0000.000
74A182PRO00.0220.01329.1900.0020.0020.0000.0000.0000.000
75A183ILE00.1150.04829.541-0.009-0.0090.0000.0000.0000.000
76A184HIS00.0380.00729.575-0.011-0.0110.0000.0000.0000.000
77A185ALA0-0.034-0.02226.462-0.003-0.0030.0000.0000.0000.000
78A186ILE00.0140.01825.112-0.013-0.0130.0000.0000.0000.000
79A187THR00.0230.01424.745-0.010-0.0100.0000.0000.0000.000
80A188GLY0-0.066-0.03225.062-0.004-0.0040.0000.0000.0000.000
81A189VAL00.0420.01119.839-0.007-0.0070.0000.0000.0000.000
82A190LEU00.0120.03020.133-0.020-0.0200.0000.0000.0000.000
83A191LYS10.9070.94120.8450.1390.1390.0000.0000.0000.000
84A192GLN0-0.112-0.05517.4880.0110.0110.0000.0000.0000.000
85A193TRP00.0420.00414.1220.0100.0100.0000.0000.0000.000
86A194LEU0-0.0010.00616.163-0.023-0.0230.0000.0000.0000.000
87A195ARG10.8830.93117.5810.1850.1850.0000.0000.0000.000
88A196GLU-1-0.821-0.90013.332-0.335-0.3350.0000.0000.0000.000
89A197LEU0-0.0050.02312.475-0.057-0.0570.0000.0000.0000.000
90A198PRO0-0.032-0.0229.1610.0530.0530.0000.0000.0000.000
91A199GLU-1-0.880-0.93511.644-0.265-0.2650.0000.0000.0000.000
92A200PRO0-0.045-0.01514.883-0.012-0.0120.0000.0000.0000.000
93A201LEU00.0650.02617.605-0.003-0.0030.0000.0000.0000.000
94A202MET0-0.0370.00119.0420.0000.0000.0000.0000.0000.000
95A203THR0-0.020-0.01318.3120.0230.0230.0000.0000.0000.000
96A204PHE00.012-0.02116.2050.0170.0170.0000.0000.0000.000
97A205ALA0-0.033-0.01220.2580.0210.0210.0000.0000.0000.000
98A206GLN00.0700.04022.1150.0020.0020.0000.0000.0000.000
99A207TYR0-0.027-0.01123.7230.0080.0080.0000.0000.0000.000
100A208GLY0-0.008-0.02525.4740.0080.0080.0000.0000.0000.000
101A209ASP-1-0.842-0.92327.436-0.107-0.1070.0000.0000.0000.000
102A210PHE00.014-0.01324.7950.0080.0080.0000.0000.0000.000
103A211LEU0-0.087-0.03529.5480.0070.0070.0000.0000.0000.000
104A212ARG10.8980.93130.8930.0890.0890.0000.0000.0000.000
105A213ALA00.0070.02033.0620.0050.0050.0000.0000.0000.000
106A214VAL0-0.016-0.02433.6350.0040.0040.0000.0000.0000.000
107A215GLU-1-0.878-0.90935.334-0.070-0.0700.0000.0000.0000.000
108A216LEU0-0.0310.00738.0890.0050.0050.0000.0000.0000.000
109A217PRO00.0110.01340.398-0.001-0.0010.0000.0000.0000.000
110A218GLU-1-0.888-0.93343.816-0.053-0.0530.0000.0000.0000.000
111A219LYS10.9680.98041.5210.0700.0700.0000.0000.0000.000
112A220GLN0-0.014-0.01740.774-0.005-0.0050.0000.0000.0000.000
113A221GLU-1-0.821-0.92140.612-0.063-0.0630.0000.0000.0000.000
114A222GLN0-0.057-0.03338.100-0.006-0.0060.0000.0000.0000.000
115A223LEU0-0.036-0.02836.437-0.005-0.0050.0000.0000.0000.000
116A224ALA0-0.013-0.00435.666-0.006-0.0060.0000.0000.0000.000
117A225ALA00.0210.02035.131-0.004-0.0040.0000.0000.0000.000
118A226ILE00.012-0.00531.110-0.006-0.0060.0000.0000.0000.000
119A227TYR0-0.062-0.06330.835-0.006-0.0060.0000.0000.0000.000
120A228ALA00.0110.01531.126-0.005-0.0050.0000.0000.0000.000
121A229VAL0-0.014-0.00426.935-0.004-0.0040.0000.0000.0000.000
122A230LEU0-0.062-0.04526.654-0.011-0.0110.0000.0000.0000.000
123A231GLU-1-0.931-0.95826.150-0.143-0.1430.0000.0000.0000.000
124A232HIS0-0.057-0.01825.575-0.007-0.0070.0000.0000.0000.000
125A233LEU0-0.103-0.03121.753-0.010-0.0100.0000.0000.0000.000
126A234PRO00.0110.00717.7200.0020.0020.0000.0000.0000.000
127A235GLU-1-0.874-0.93418.624-0.276-0.2760.0000.0000.0000.000
128A236ALA00.0590.03615.5460.0090.0090.0000.0000.0000.000
129A237ASN0-0.040-0.04316.421-0.011-0.0110.0000.0000.0000.000
130A238HIS00.0100.01718.8550.0060.0060.0000.0000.0000.000
131A239ASN00.0620.02319.984-0.003-0.0030.0000.0000.0000.000
132A240SER0-0.019-0.01718.1970.0030.0030.0000.0000.0000.000
133A241LEU0-0.025-0.01620.7290.0140.0140.0000.0000.0000.000
134A242GLU-1-0.934-0.95623.374-0.162-0.1620.0000.0000.0000.000
135A243ARG10.7670.86323.3900.2080.2080.0000.0000.0000.000
136A244LEU0-0.006-0.00723.0670.0120.0120.0000.0000.0000.000
137A245ILE00.001-0.00825.5700.0140.0140.0000.0000.0000.000
138A246PHE00.0140.00528.6280.0140.0140.0000.0000.0000.000
139A247HIS00.0220.04927.8230.0100.0100.0000.0000.0000.000
140A248LEU0-0.003-0.01528.0760.0100.0100.0000.0000.0000.000
141A249VAL0-0.041-0.01531.2580.0100.0100.0000.0000.0000.000
142A250LYS10.9380.97032.1480.1380.1380.0000.0000.0000.000
143A251VAL0-0.0110.00331.7890.0060.0060.0000.0000.0000.000
144A252ALA00.0080.00934.9060.0060.0060.0000.0000.0000.000
145A253LEU0-0.053-0.02537.1320.0070.0070.0000.0000.0000.000
146A254LEU0-0.0200.00138.3190.0050.0050.0000.0000.0000.000
147A255GLU-1-0.861-0.92240.077-0.080-0.0800.0000.0000.0000.000
148A256ASP-1-0.942-0.97940.917-0.070-0.0700.0000.0000.0000.000
149A257VAL0-0.063-0.02541.7540.0030.0030.0000.0000.0000.000
150A258ASN0-0.013-0.02337.4150.0030.0030.0000.0000.0000.000
151A259ARG10.8730.92538.6230.0730.0730.0000.0000.0000.000
152A260MET0-0.081-0.01833.7740.0020.0020.0000.0000.0000.000
153A261SER00.0640.04437.489-0.004-0.0040.0000.0000.0000.000
154A262PRO00.018-0.01635.681-0.004-0.0040.0000.0000.0000.000
155A263GLY00.0840.05235.000-0.004-0.0040.0000.0000.0000.000
156A264ALA0-0.028-0.01335.294-0.002-0.0020.0000.0000.0000.000
157A265LEU0-0.002-0.01131.672-0.005-0.0050.0000.0000.0000.000
158A266ALA00.0320.02430.693-0.009-0.0090.0000.0000.0000.000
159A267ILE0-0.005-0.00230.566-0.005-0.0050.0000.0000.0000.000
160A268ILE0-0.098-0.04028.004-0.003-0.0030.0000.0000.0000.000
161A269PHE00.021-0.01725.002-0.009-0.0090.0000.0000.0000.000
162A270ALA00.0500.03525.640-0.012-0.0120.0000.0000.0000.000
163A271PRO0-0.0080.00125.575-0.008-0.0080.0000.0000.0000.000
164A272CYS0-0.130-0.06022.110-0.010-0.0100.0000.0000.0000.000
165A273LEU0-0.030-0.00521.035-0.021-0.0210.0000.0000.0000.000
166A274LEU00.0130.00322.190-0.009-0.0090.0000.0000.0000.000
167A275ARG10.9110.96715.7390.2810.2810.0000.0000.0000.000
168A276CYS0-0.006-0.00122.388-0.004-0.0040.0000.0000.0000.000
169A277PRO00.0310.01721.182-0.007-0.0070.0000.0000.0000.000
170A278ASP-1-0.921-0.95319.547-0.115-0.1150.0000.0000.0000.000
171A279ASN0-0.029-0.01522.2110.0040.0040.0000.0000.0000.000
172A280SER0-0.034-0.01124.4300.0070.0070.0000.0000.0000.000
173A281ASP-1-0.808-0.92127.215-0.047-0.0470.0000.0000.0000.000
174A282PRO00.0260.00829.278-0.004-0.0040.0000.0000.0000.000
175A283LEU0-0.007-0.00230.7250.0000.0000.0000.0000.0000.000
176A284THR0-0.082-0.03731.8410.0000.0000.0000.0000.0000.000
177A285SER00.019-0.00929.711-0.003-0.0030.0000.0000.0000.000
178A286MET0-0.039-0.01831.389-0.002-0.0020.0000.0000.0000.000
179A287LYS10.9580.96534.6440.0580.0580.0000.0000.0000.000
180A288ASP-1-0.809-0.89030.026-0.092-0.0920.0000.0000.0000.000
181A289VAL00.0570.03029.546-0.006-0.0060.0000.0000.0000.000
182A290LEU00.0030.00131.522-0.003-0.0030.0000.0000.0000.000
183A291LYS10.8440.91432.9210.0740.0740.0000.0000.0000.000
184A292ILE00.0390.02027.322-0.001-0.0010.0000.0000.0000.000
185A293THR0-0.033-0.03230.587-0.007-0.0070.0000.0000.0000.000
186A294THR0-0.002-0.00132.3880.0010.0010.0000.0000.0000.000
187A295CYS0-0.0220.00129.9960.0000.0000.0000.0000.0000.000
188A296VAL00.0240.01228.465-0.002-0.0020.0000.0000.0000.000
189A297GLU-1-0.927-0.97031.280-0.088-0.0880.0000.0000.0000.000
190A298MET0-0.064-0.03634.7590.0020.0020.0000.0000.0000.000
191A299LEU00.0300.03729.1010.0020.0020.0000.0000.0000.000
192A300ILE00.009-0.00131.3090.0010.0010.0000.0000.0000.000
193A301LYS10.9330.95534.0150.0840.0840.0000.0000.0000.000
194A302GLU-1-0.774-0.86036.414-0.082-0.0820.0000.0000.0000.000
195A303GLN00.0190.01032.2820.0070.0070.0000.0000.0000.000
196A304MET00.0210.01335.7170.0020.0020.0000.0000.0000.000
197A305ARG10.7880.88137.9460.0830.0830.0000.0000.0000.000
198A306LYS10.8790.94335.1900.1080.1080.0000.0000.0000.000
199A307TYR00.0080.01736.5230.0000.0000.0000.0000.0000.000
200A308LYS10.9620.96239.3280.0840.0840.0000.0000.0000.000
201A309VAL0-0.0230.00142.8370.0020.0020.0000.0000.0000.000
202A310LYS11.0010.98638.3050.0950.0950.0000.0000.0000.000
203A311MET0-0.055-0.01640.2600.0000.0000.0000.0000.0000.000
204A312GLU-1-0.926-0.97043.484-0.064-0.0640.0000.0000.0000.000
205A313GLU-1-0.985-0.98344.909-0.071-0.0710.0000.0000.0000.000
206A314ILE0-0.033-0.02740.4620.0000.0000.0000.0000.0000.000
207A315SER0-0.089-0.02645.1170.0010.0010.0000.0000.0000.000
208A316GLN0-0.019-0.01247.8410.0050.0050.0000.0000.0000.000
209A317LEU0-0.032-0.00549.702-0.002-0.0020.0000.0000.0000.000
210A318GLU-1-0.960-0.97451.757-0.054-0.0540.0000.0000.0000.000