FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 7233K

Calculation Name: 3EFY-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3EFY

Chain ID: A

ChEMBL ID:
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UniProt ID: Q7WRZ5

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2013199.168483
FMO2-HF: Nuclear repulsion 1937658.884786
FMO2-HF: Total energy -75540.283697
FMO2-MP2: Total energy -75753.19485


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:107:PRO)


Summations of interaction energy for fragment #1(A:107:PRO)
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.
-5.292-0.3131.347-2.367-3.958-0.008
Interaction energy analysis for fragmet #1(A:107:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.007
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].
3A109CYS00.0160.0493.391-2.671-0.5740.028-1.100-1.0260.001
4A110GLY00.0920.0306.0320.1450.1450.0000.0000.0000.000
5A111VAL0-0.027-0.0102.599-0.5210.0870.915-0.324-1.1990.000
6A112THR0-0.003-0.0142.692-2.437-0.7060.402-0.824-1.309-0.009
7A113ALA00.0300.0174.1440.4720.5920.001-0.027-0.0940.000
8A114ASN00.0280.0147.4000.1730.1730.0000.0000.0000.000
9A115ALA00.0000.0045.8840.1990.1990.0000.0000.0000.000
10A116ILE00.0100.0047.8350.1850.1850.0000.0000.0000.000
11A117MET0-0.0050.0079.8500.1450.1450.0000.0000.0000.000
12A118LYS10.8240.89710.7610.3460.3460.0000.0000.0000.000
13A119LEU0-0.031-0.0019.3510.0720.0720.0000.0000.0000.000
14A120PHE00.0410.01212.9630.0580.0580.0000.0000.0000.000
15A121LEU0-0.0210.00515.6180.0530.0530.0000.0000.0000.000
16A122ASP-1-0.784-0.88014.804-0.232-0.2320.0000.0000.0000.000
17A123LYS10.8140.89417.4050.2030.2030.0000.0000.0000.000
18A124ASP-1-0.898-0.94720.742-0.098-0.0980.0000.0000.0000.000
19A125GLY0-0.025-0.00523.4560.0010.0010.0000.0000.0000.000
20A126PHE0-0.054-0.02718.3950.0040.0040.0000.0000.0000.000
21A127SER0-0.027-0.02716.9070.0010.0010.0000.0000.0000.000
22A128TYR00.0010.00611.727-0.013-0.0130.0000.0000.0000.000
23A129CYS0-0.066-0.05613.934-0.001-0.0010.0000.0000.0000.000
24A130PHE00.004-0.00411.9190.0120.0120.0000.0000.0000.000
25A131GLU-1-0.856-0.92312.536-0.186-0.1860.0000.0000.0000.000
26A132ASN0-0.076-0.03515.7910.0340.0340.0000.0000.0000.000
27A133GLU-1-0.865-0.91916.475-0.208-0.2080.0000.0000.0000.000
28A134GLN0-0.027-0.02319.0910.0040.0040.0000.0000.0000.000
29A135THR0-0.006-0.00418.831-0.017-0.0170.0000.0000.0000.000
30A136LEU0-0.080-0.03421.3180.0190.0190.0000.0000.0000.000
31A137SER00.032-0.00522.285-0.022-0.0220.0000.0000.0000.000
32A138LEU00.0270.00123.398-0.011-0.0110.0000.0000.0000.000
33A139GLU-1-0.835-0.90025.079-0.139-0.1390.0000.0000.0000.000
34A140GLN00.0200.01626.2680.0010.0010.0000.0000.0000.000
35A141LEU0-0.021-0.00821.5050.0010.0010.0000.0000.0000.000
36A142GLN00.019-0.00525.4010.0090.0090.0000.0000.0000.000
37A143GLU-1-0.903-0.93028.072-0.123-0.1230.0000.0000.0000.000
38A144ARG10.9070.94824.9890.1950.1950.0000.0000.0000.000
39A145LEU0-0.012-0.01323.661-0.002-0.0020.0000.0000.0000.000
40A146SER0-0.014-0.01327.7410.0050.0050.0000.0000.0000.000
41A147CYS0-0.115-0.04930.8270.0090.0090.0000.0000.0000.000
42A148MET00.0060.02923.8570.0000.0000.0000.0000.0000.000
43A149PRO0-0.013-0.01029.0650.0040.0040.0000.0000.0000.000
44A150GLU-1-0.768-0.86929.326-0.149-0.1490.0000.0000.0000.000
45A151CYS0-0.050-0.02430.400-0.006-0.0060.0000.0000.0000.000
46A152LYS10.7700.85827.5100.1580.1580.0000.0000.0000.000
47A153SER00.0350.02023.1380.0080.0080.0000.0000.0000.000
48A154PHE0-0.011-0.02021.9220.0070.0070.0000.0000.0000.000
49A155VAL00.0160.01515.377-0.019-0.0190.0000.0000.0000.000
50A156LEU00.0060.00017.1780.0320.0320.0000.0000.0000.000
51A157ARG10.8740.9189.9900.6230.6230.0000.0000.0000.000
52A158VAL0-0.013-0.00513.8230.0890.0890.0000.0000.0000.000
53A159ASN00.0020.00112.926-0.178-0.1780.0000.0000.0000.000
54A160ASP-1-0.728-0.83514.666-0.324-0.3240.0000.0000.0000.000
55A161GLY00.0380.01616.137-0.027-0.0270.0000.0000.0000.000
56A162ALA00.0130.00618.0130.0090.0090.0000.0000.0000.000
57A163LEU0-0.027-0.01815.5090.0200.0200.0000.0000.0000.000
58A164GLY0-0.0130.00115.309-0.015-0.0150.0000.0000.0000.000
59A165HIS0-0.033-0.0249.523-0.120-0.1200.0000.0000.0000.000
60A166ALA0-0.021-0.0219.3730.1190.1190.0000.0000.0000.000
61A167TYR0-0.029-0.0299.275-0.259-0.2590.0000.0000.0000.000
62A168ILE0-0.014-0.00610.3030.1080.1080.0000.0000.0000.000
63A169VAL00.0090.00812.942-0.008-0.0080.0000.0000.0000.000
64A170ASP-1-0.785-0.85216.548-0.387-0.3870.0000.0000.0000.000
65A171ILE00.0400.01618.3190.0160.0160.0000.0000.0000.000
66A172PRO00.0540.02621.6380.0190.0190.0000.0000.0000.000
67A173LYS10.8660.94224.0760.1790.1790.0000.0000.0000.000
68A174GLY0-0.007-0.00627.661-0.002-0.0020.0000.0000.0000.000
69A175GLU-1-0.935-0.96830.082-0.129-0.1290.0000.0000.0000.000
70A176ASN0-0.034-0.04529.916-0.022-0.0220.0000.0000.0000.000
71A177SER0-0.046-0.01731.506-0.002-0.0020.0000.0000.0000.000
72A178CYS0-0.041-0.00530.5080.0040.0040.0000.0000.0000.000
73A179ARG10.8350.92326.3740.1940.1940.0000.0000.0000.000
74A180PRO00.005-0.00225.818-0.015-0.0150.0000.0000.0000.000
75A181ALA0-0.013-0.00121.042-0.002-0.0020.0000.0000.0000.000
76A182PHE00.0070.01317.6120.0120.0120.0000.0000.0000.000
77A183LEU00.0100.00613.538-0.010-0.0100.0000.0000.0000.000
78A184TYR0-0.054-0.04311.148-0.040-0.0400.0000.0000.0000.000
79A185GLN0-0.004-0.0068.809-0.075-0.0750.0000.0000.0000.000
80A186SER0-0.021-0.0254.0480.1870.316-0.001-0.018-0.1090.000
81A187ASP-1-0.738-0.8556.573-0.822-0.8220.0000.0000.0000.000
82A188LEU0-0.034-0.0154.026-0.2370.0570.002-0.074-0.2210.000
83A189GLY0-0.029-0.0296.9480.4100.4100.0000.0000.0000.000
84A190GLU-1-0.973-0.9829.409-0.007-0.0070.0000.0000.0000.000
85A191GLY00.0500.03112.4810.0600.0600.0000.0000.0000.000
86A192VAL0-0.0030.00614.5160.0540.0540.0000.0000.0000.000
87A193THR00.010-0.01012.5270.0800.0800.0000.0000.0000.000
88A194ARG10.7420.81913.0490.2870.2870.0000.0000.0000.000
89A195LYS10.8580.9276.030-0.279-0.2790.0000.0000.0000.000
90A196LEU0-0.0220.0047.7630.1570.1570.0000.0000.0000.000
91A197ARG10.7650.8505.446-0.535-0.5350.0000.0000.0000.000
92A198PHE00.0560.0084.8650.1250.1250.0000.0000.0000.000
93A199GLU-1-0.815-0.8836.4330.0310.0310.0000.0000.0000.000
94A200ASP-1-0.789-0.8678.776-0.360-0.3600.0000.0000.0000.000
95A201TRP00.020-0.0169.9500.0690.0690.0000.0000.0000.000
96A202MET0-0.028-0.0169.8310.0780.0780.0000.0000.0000.000
97A203THR0-0.061-0.04612.2330.0940.0940.0000.0000.0000.000
98A204HIS0-0.063-0.03314.2450.1100.1100.0000.0000.0000.000
99A205LYS10.8280.91115.8600.3830.3830.0000.0000.0000.000
100A206ALA00.0000.00513.6250.0220.0220.0000.0000.0000.000
101A207LEU0-0.0030.00115.7790.0200.0200.0000.0000.0000.000
102A208THR0-0.061-0.01718.5870.0510.0510.0000.0000.0000.000
103A209PRO0-0.039-0.00720.447-0.026-0.0260.0000.0000.0000.000
104A210ILE0-0.014-0.01319.8080.0120.0120.0000.0000.0000.000
105A211LEU00.0040.00823.3860.0070.0070.0000.0000.0000.000
106A212LEU00.017-0.00322.875-0.021-0.0210.0000.0000.0000.000
107A213ASP-1-0.838-0.93524.540-0.200-0.2000.0000.0000.0000.000
108A214ASP-1-0.883-0.94124.191-0.223-0.2230.0000.0000.0000.000
109A215ILE0-0.014-0.01218.361-0.003-0.0030.0000.0000.0000.000
110A216CYS0-0.021-0.01022.221-0.005-0.0050.0000.0000.0000.000
111A217ASN0-0.030-0.00924.4880.0100.0100.0000.0000.0000.000
112A218TYR0-0.005-0.02518.8560.0200.0200.0000.0000.0000.000
113A219PHE00.0180.00318.4320.0070.0070.0000.0000.0000.000
114A220SER0-0.0030.00623.1690.0170.0170.0000.0000.0000.000
115A221CYS0-0.043-0.02326.4230.0180.0180.0000.0000.0000.000
116A222MET00.0380.03720.9590.0270.0270.0000.0000.0000.000
117A223SER0-0.031-0.02524.6030.0150.0150.0000.0000.0000.000
118A224GLN0-0.0230.00625.6890.0270.0270.0000.0000.0000.000
119A225ASN00.002-0.00726.8830.0030.0030.0000.0000.0000.000
120A226LYS10.8230.91427.9520.1430.1430.0000.0000.0000.000
121A227THR00.005-0.00824.761-0.009-0.0090.0000.0000.0000.000
122A228ASP-1-0.842-0.90726.297-0.171-0.1710.0000.0000.0000.000
123A229LEU00.012-0.01322.940-0.020-0.0200.0000.0000.0000.000
124A230GLU-1-0.817-0.91623.046-0.183-0.1830.0000.0000.0000.000
125A231GLN0-0.025-0.00523.602-0.020-0.0200.0000.0000.0000.000
126A232ILE00.0210.00918.675-0.025-0.0250.0000.0000.0000.000
127A233ALA0-0.019-0.00819.199-0.044-0.0440.0000.0000.0000.000
128A234THR0-0.019-0.03219.786-0.022-0.0220.0000.0000.0000.000
129A235LEU0-0.0190.00318.822-0.013-0.0130.0000.0000.0000.000
130A236PHE0-0.012-0.00114.642-0.040-0.0400.0000.0000.0000.000
131A237ASP-1-0.730-0.82414.647-0.391-0.3910.0000.0000.0000.000
132A238ILE0-0.033-0.01113.1010.0110.0110.0000.0000.0000.000
133A239ASP-1-0.841-0.90115.922-0.221-0.2210.0000.0000.0000.000
134A240GLY0-0.029-0.00819.1240.0280.0280.0000.0000.0000.000
135A241ASN0-0.033-0.02620.1200.0330.0330.0000.0000.0000.000
136A242VAL00.0650.02420.583-0.011-0.0110.0000.0000.0000.000
137A243LYS10.8800.93622.3230.1050.1050.0000.0000.0000.000
138A244MET0-0.085-0.03217.3730.0270.0270.0000.0000.0000.000
139A245LEU0-0.0140.01117.599-0.026-0.0260.0000.0000.0000.000
140A246ARG10.9030.95316.6280.1400.1400.0000.0000.0000.000
141A247LYS10.9160.93120.1210.0920.0920.0000.0000.0000.000
142A248GLU-1-0.848-0.91522.226-0.118-0.1180.0000.0000.0000.000
143A249ASN0-0.060-0.03516.8230.0400.0400.0000.0000.0000.000
144A250ILE0-0.0160.01019.166-0.025-0.0250.0000.0000.0000.000
145A251GLN0-0.090-0.04118.4740.0490.0490.0000.0000.0000.000
146A252TYR0-0.036-0.02721.3380.0050.0050.0000.0000.0000.000
147A253GLN0-0.001-0.00321.4730.0020.0020.0000.0000.0000.000
148A254LYS10.9090.94725.7210.0800.0800.0000.0000.0000.000
149A255HIS00.0150.00127.398-0.001-0.0010.0000.0000.0000.000
150A256ASP-1-0.899-0.95223.642-0.150-0.1500.0000.0000.0000.000
151A257ASN0-0.016-0.00521.858-0.014-0.0140.0000.0000.0000.000
152A258PHE0-0.035-0.01018.725-0.025-0.0250.0000.0000.0000.000
153A259SER0-0.0310.00118.2130.0290.0290.0000.0000.0000.000
154A260PHE00.0270.00617.464-0.047-0.0470.0000.0000.0000.000
155A261GLN00.0210.01115.498-0.014-0.0140.0000.0000.0000.000
156A262LEU0-0.033-0.00317.780-0.035-0.0350.0000.0000.0000.000
157A263PHE0-0.019-0.00818.3800.0280.0280.0000.0000.0000.000
158A264GLU-1-0.797-0.87920.917-0.182-0.1820.0000.0000.0000.000
159A265TYR0-0.080-0.07619.6690.0040.0040.0000.0000.0000.000
160A266ASP-1-0.814-0.89221.737-0.188-0.1880.0000.0000.0000.000
161A267THR0-0.043-0.04321.604-0.024-0.0240.0000.0000.0000.000
162A268ASP-1-0.842-0.93721.471-0.174-0.1740.0000.0000.0000.000
163A269ASN0-0.061-0.03518.7370.0280.0280.0000.0000.0000.000
164A270ILE00.0300.02414.437-0.010-0.0100.0000.0000.0000.000
165A271GLU-1-0.880-0.92016.915-0.217-0.2170.0000.0000.0000.000
166A272LYS10.8330.91418.6910.1970.1970.0000.0000.0000.000
167A273ASN0-0.037-0.03014.4830.0490.0490.0000.0000.0000.000
168A274ILE00.0130.01313.995-0.021-0.0210.0000.0000.0000.000
169A275GLU-1-0.827-0.90015.083-0.172-0.1720.0000.0000.0000.000
170A276ILE0-0.0140.00214.8220.0260.0260.0000.0000.0000.000
171A277ILE00.0100.0038.0160.0290.0290.0000.0000.0000.000
172A278LYS10.8380.90712.4890.2400.2400.0000.0000.0000.000
173A279SER0-0.0310.00114.3940.0450.0450.0000.0000.0000.000
174A280LEU00.0290.01412.9780.0330.0330.0000.0000.0000.000
175A281CYS0-0.055-0.03510.6010.0400.0400.0000.0000.0000.000
176A282SER0-0.115-0.06912.8870.0500.0500.0000.0000.0000.000
177A283GLY00.0300.01416.2200.0150.0150.0000.0000.0000.000
178A284ALA00.0220.00712.5230.0200.0200.0000.0000.0000.000
179A285ALA0-0.020-0.01214.5280.0360.0360.0000.0000.0000.000
180A286ALA0-0.023-0.00116.5970.0090.0090.0000.0000.0000.000
181A287LEU0-0.050-0.02213.832-0.016-0.0160.0000.0000.0000.000
182A288GLU-1-0.964-0.96911.8100.5750.5750.0000.0000.0000.000
183A289HIS0-0.080-0.03616.363-0.011-0.0110.0000.0000.0000.000