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: MV66Z

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2005673.067544
FMO2-HF: Nuclear repulsion 1930132.992855
FMO2-HF: Total energy -75540.074689
FMO2-MP2: Total energy -75752.943535


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.
-4.621-0.2552.639-2.59-4.416-0.005
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 : 0.018 / q_NPA : -0.014
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].
3A109CYS00.0550.0483.357-2.832-0.7080.034-1.109-1.0490.002
4A110GLY00.0640.0225.9810.1830.1830.0000.0000.0000.000
5A111VAL0-0.023-0.0062.380-0.361-0.2972.302-0.634-1.7330.000
6A112THR0-0.0110.0012.641-2.019-0.4350.300-0.707-1.178-0.007
7A113ALA00.0440.0244.1690.4350.5560.001-0.026-0.0950.000
8A114ASN00.0360.0127.3320.1620.1620.0000.0000.0000.000
9A115ALA0-0.0080.0006.0000.1850.1850.0000.0000.0000.000
10A116ILE00.0280.0177.8890.1560.1560.0000.0000.0000.000
11A117MET0-0.0120.0089.9250.1330.1330.0000.0000.0000.000
12A118LYS10.8190.89910.4450.3130.3130.0000.0000.0000.000
13A119LEU0-0.035-0.0079.5850.0680.0680.0000.0000.0000.000
14A120PHE00.0280.00713.1110.0530.0530.0000.0000.0000.000
15A121LEU0-0.0180.00415.7450.0490.0490.0000.0000.0000.000
16A122ASP-1-0.804-0.87914.774-0.213-0.2130.0000.0000.0000.000
17A123LYS10.8590.92617.4770.1830.1830.0000.0000.0000.000
18A124ASP-1-0.888-0.93920.755-0.089-0.0890.0000.0000.0000.000
19A125GLY0-0.056-0.03323.509-0.002-0.0020.0000.0000.0000.000
20A126PHE0-0.042-0.01518.2740.0050.0050.0000.0000.0000.000
21A127SER0-0.036-0.02216.757-0.002-0.0020.0000.0000.0000.000
22A128TYR00.016-0.00611.537-0.016-0.0160.0000.0000.0000.000
23A129CYS0-0.048-0.03813.8470.0170.0170.0000.0000.0000.000
24A130PHE0-0.0140.00111.708-0.006-0.0060.0000.0000.0000.000
25A131GLU-1-0.879-0.95912.895-0.115-0.1150.0000.0000.0000.000
26A132ASN0-0.067-0.03415.6190.0250.0250.0000.0000.0000.000
27A133GLU-1-0.841-0.90416.490-0.190-0.1900.0000.0000.0000.000
28A134GLN0-0.059-0.03319.1500.0090.0090.0000.0000.0000.000
29A135THR0-0.013-0.01518.709-0.020-0.0200.0000.0000.0000.000
30A136LEU0-0.063-0.01921.3660.0190.0190.0000.0000.0000.000
31A137SER00.0710.03422.169-0.022-0.0220.0000.0000.0000.000
32A138LEU00.0370.00223.611-0.007-0.0070.0000.0000.0000.000
33A139GLU-1-0.931-0.95525.102-0.119-0.1190.0000.0000.0000.000
34A140GLN00.0560.01426.275-0.001-0.0010.0000.0000.0000.000
35A141LEU0-0.024-0.00521.6300.0010.0010.0000.0000.0000.000
36A142GLN00.020-0.00625.5300.0070.0070.0000.0000.0000.000
37A143GLU-1-0.896-0.93128.264-0.117-0.1170.0000.0000.0000.000
38A144ARG10.9060.94325.5700.1780.1780.0000.0000.0000.000
39A145LEU0-0.010-0.01824.006-0.001-0.0010.0000.0000.0000.000
40A146SER0-0.011-0.00128.0680.0040.0040.0000.0000.0000.000
41A147CYS0-0.116-0.04931.2900.0070.0070.0000.0000.0000.000
42A148MET0-0.0160.02124.0710.0000.0000.0000.0000.0000.000
43A149PRO0-0.005-0.00529.0880.0040.0040.0000.0000.0000.000
44A150GLU-1-0.760-0.86729.374-0.146-0.1460.0000.0000.0000.000
45A151CYS0-0.070-0.02630.419-0.006-0.0060.0000.0000.0000.000
46A152LYS10.7600.84927.2570.1510.1510.0000.0000.0000.000
47A153SER00.0260.02522.8260.0060.0060.0000.0000.0000.000
48A154PHE0-0.017-0.03021.8270.0130.0130.0000.0000.0000.000
49A155VAL00.0310.02815.185-0.022-0.0220.0000.0000.0000.000
50A156LEU0-0.003-0.00617.3580.0330.0330.0000.0000.0000.000
51A157ARG10.8650.9109.7600.5460.5460.0000.0000.0000.000
52A158VAL0-0.029-0.01313.9020.0820.0820.0000.0000.0000.000
53A159ASN00.0150.01513.019-0.168-0.1680.0000.0000.0000.000
54A160ASP-1-0.746-0.85614.521-0.307-0.3070.0000.0000.0000.000
55A161GLY00.0520.03216.013-0.024-0.0240.0000.0000.0000.000
56A162ALA0-0.002-0.00518.0210.0140.0140.0000.0000.0000.000
57A163LEU0-0.029-0.01815.7230.0200.0200.0000.0000.0000.000
58A164GLY0-0.0170.00315.286-0.009-0.0090.0000.0000.0000.000
59A165HIS0-0.047-0.0409.603-0.117-0.1170.0000.0000.0000.000
60A166ALA00.000-0.0069.3130.1150.1150.0000.0000.0000.000
61A167TYR0-0.046-0.0479.733-0.206-0.2060.0000.0000.0000.000
62A168ILE0-0.014-0.00810.4000.0980.0980.0000.0000.0000.000
63A169VAL0-0.0030.00113.086-0.005-0.0050.0000.0000.0000.000
64A170ASP-1-0.779-0.84016.601-0.372-0.3720.0000.0000.0000.000
65A171ILE00.0280.00018.2330.0150.0150.0000.0000.0000.000
66A172PRO00.0610.02921.6930.0190.0190.0000.0000.0000.000
67A173LYS10.8860.94923.9720.1740.1740.0000.0000.0000.000
68A174GLY00.003-0.00227.576-0.004-0.0040.0000.0000.0000.000
69A175GLU-1-0.938-0.96529.771-0.126-0.1260.0000.0000.0000.000
70A176ASN0-0.018-0.04530.337-0.021-0.0210.0000.0000.0000.000
71A177SER0-0.039-0.00131.8760.0010.0010.0000.0000.0000.000
72A178CYS0-0.026-0.01230.4930.0040.0040.0000.0000.0000.000
73A179ARG10.8270.92326.6030.1930.1930.0000.0000.0000.000
74A180PRO00.019-0.00425.305-0.012-0.0120.0000.0000.0000.000
75A181ALA0-0.023-0.00820.774-0.002-0.0020.0000.0000.0000.000
76A182PHE00.0010.01217.6720.0110.0110.0000.0000.0000.000
77A183LEU00.0120.01713.539-0.014-0.0140.0000.0000.0000.000
78A184TYR0-0.041-0.04211.209-0.043-0.0430.0000.0000.0000.000
79A185GLN00.011-0.0018.944-0.043-0.0430.0000.0000.0000.000
80A186SER0-0.050-0.0403.9790.0900.210-0.001-0.019-0.1000.000
81A187ASP-1-0.726-0.8526.756-0.880-0.8800.0000.0000.0000.000
82A188LEU0-0.056-0.0273.584-0.3090.0440.003-0.095-0.2610.000
83A189GLY0-0.036-0.0277.0620.3780.3780.0000.0000.0000.000
84A190GLU-1-0.983-0.9919.3640.0140.0140.0000.0000.0000.000
85A191GLY00.0350.02312.5640.0620.0620.0000.0000.0000.000
86A192VAL0-0.0040.01514.8740.0380.0380.0000.0000.0000.000
87A193THR00.027-0.00312.8460.0850.0850.0000.0000.0000.000
88A194ARG10.7640.83113.3420.3080.3080.0000.0000.0000.000
89A195LYS10.8900.9425.5850.0010.0010.0000.0000.0000.000
90A196LEU0-0.0110.0048.2510.1550.1550.0000.0000.0000.000
91A197ARG10.7700.8596.059-0.278-0.2780.0000.0000.0000.000
92A198PHE00.0520.0075.3500.1670.1670.0000.0000.0000.000
93A199GLU-1-0.825-0.8906.939-0.104-0.1040.0000.0000.0000.000
94A200ASP-1-0.801-0.8749.044-0.395-0.3950.0000.0000.0000.000
95A201TRP00.030-0.01510.3720.0750.0750.0000.0000.0000.000
96A202MET0-0.039-0.02510.2420.0800.0800.0000.0000.0000.000
97A203THR0-0.066-0.04412.6630.0950.0950.0000.0000.0000.000
98A204HIS0-0.063-0.03214.5470.1160.1160.0000.0000.0000.000
99A205LYS10.8320.90716.4010.3880.3880.0000.0000.0000.000
100A206ALA0-0.0110.00514.0860.0260.0260.0000.0000.0000.000
101A207LEU00.0110.00716.2410.0230.0230.0000.0000.0000.000
102A208THR0-0.060-0.01918.8890.0480.0480.0000.0000.0000.000
103A209PRO0-0.0300.00320.902-0.024-0.0240.0000.0000.0000.000
104A210ILE0-0.011-0.01219.6980.0150.0150.0000.0000.0000.000
105A211LEU00.0290.01423.2520.0090.0090.0000.0000.0000.000
106A212LEU00.0220.00022.773-0.017-0.0170.0000.0000.0000.000
107A213ASP-1-0.851-0.94024.618-0.191-0.1910.0000.0000.0000.000
108A214ASP-1-0.888-0.94124.822-0.212-0.2120.0000.0000.0000.000
109A215ILE0-0.053-0.02618.689-0.004-0.0040.0000.0000.0000.000
110A216CYS0-0.019-0.01222.489-0.002-0.0020.0000.0000.0000.000
111A217ASN0-0.030-0.01124.7370.0090.0090.0000.0000.0000.000
112A218TYR0-0.003-0.02318.9830.0200.0200.0000.0000.0000.000
113A219PHE00.008-0.00418.6520.0080.0080.0000.0000.0000.000
114A220SER0-0.014-0.00423.3810.0180.0180.0000.0000.0000.000
115A221CYS0-0.028-0.00926.4380.0180.0180.0000.0000.0000.000
116A222MET00.0350.03021.3590.0240.0240.0000.0000.0000.000
117A223SER0-0.040-0.02424.7250.0150.0150.0000.0000.0000.000
118A224GLN0-0.021-0.00425.9990.0260.0260.0000.0000.0000.000
119A225ASN0-0.030-0.01627.0720.0040.0040.0000.0000.0000.000
120A226LYS10.8390.92328.1330.1340.1340.0000.0000.0000.000
121A227THR0-0.021-0.00925.060-0.008-0.0080.0000.0000.0000.000
122A228ASP-1-0.792-0.90125.636-0.162-0.1620.0000.0000.0000.000
123A229LEU0-0.019-0.02923.068-0.017-0.0170.0000.0000.0000.000
124A230GLU-1-0.837-0.92223.552-0.188-0.1880.0000.0000.0000.000
125A231GLN0-0.0160.00323.890-0.020-0.0200.0000.0000.0000.000
126A232ILE00.004-0.00419.114-0.022-0.0220.0000.0000.0000.000
127A233ALA00.0040.00119.694-0.043-0.0430.0000.0000.0000.000
128A234THR0-0.009-0.02320.171-0.023-0.0230.0000.0000.0000.000
129A235LEU0-0.0020.01319.023-0.014-0.0140.0000.0000.0000.000
130A236PHE0-0.009-0.00214.697-0.036-0.0360.0000.0000.0000.000
131A237ASP-1-0.750-0.82314.967-0.416-0.4160.0000.0000.0000.000
132A238ILE0-0.034-0.01613.5450.0160.0160.0000.0000.0000.000
133A239ASP-1-0.835-0.89516.447-0.240-0.2400.0000.0000.0000.000
134A240GLY0-0.055-0.02119.4800.0300.0300.0000.0000.0000.000
135A241ASN0-0.026-0.02420.3550.0380.0380.0000.0000.0000.000
136A242VAL00.0710.02620.942-0.012-0.0120.0000.0000.0000.000
137A243LYS10.8920.94022.7800.1120.1120.0000.0000.0000.000
138A244MET0-0.082-0.03217.8300.0220.0220.0000.0000.0000.000
139A245LEU0-0.0230.01017.864-0.020-0.0200.0000.0000.0000.000
140A246ARG10.9360.97017.4420.1360.1360.0000.0000.0000.000
141A247LYS10.9160.94220.3800.0970.0970.0000.0000.0000.000
142A248GLU-1-0.880-0.95121.864-0.118-0.1180.0000.0000.0000.000
143A249ASN0-0.069-0.03617.4010.0370.0370.0000.0000.0000.000
144A250ILE00.0050.01919.405-0.020-0.0200.0000.0000.0000.000
145A251GLN0-0.110-0.05118.6580.0510.0510.0000.0000.0000.000
146A252TYR0-0.008-0.00421.7300.0020.0020.0000.0000.0000.000
147A253GLN00.0070.00521.4670.0030.0030.0000.0000.0000.000
148A254LYS10.9120.94625.7610.0720.0720.0000.0000.0000.000
149A255HIS00.017-0.00227.665-0.005-0.0050.0000.0000.0000.000
150A256ASP-1-0.925-0.95923.943-0.128-0.1280.0000.0000.0000.000
151A257ASN00.001-0.00121.854-0.008-0.0080.0000.0000.0000.000
152A258PHE0-0.039-0.00518.856-0.018-0.0180.0000.0000.0000.000
153A259SER0-0.0210.00017.8850.0270.0270.0000.0000.0000.000
154A260PHE00.0330.00817.495-0.045-0.0450.0000.0000.0000.000
155A261GLN00.0460.03815.353-0.009-0.0090.0000.0000.0000.000
156A262LEU0-0.0140.00717.987-0.034-0.0340.0000.0000.0000.000
157A263PHE0-0.015-0.00818.0690.0260.0260.0000.0000.0000.000
158A264GLU-1-0.799-0.87520.969-0.177-0.1770.0000.0000.0000.000
159A265TYR0-0.090-0.07819.7490.0050.0050.0000.0000.0000.000
160A266ASP-1-0.841-0.91621.816-0.175-0.1750.0000.0000.0000.000
161A267THR0-0.010-0.03121.805-0.022-0.0220.0000.0000.0000.000
162A268ASP-1-0.859-0.92921.839-0.168-0.1680.0000.0000.0000.000
163A269ASN0-0.065-0.04718.8270.0250.0250.0000.0000.0000.000
164A270ILE00.0170.02114.598-0.010-0.0100.0000.0000.0000.000
165A271GLU-1-0.893-0.93517.146-0.221-0.2210.0000.0000.0000.000
166A272LYS10.8590.92618.9020.1890.1890.0000.0000.0000.000
167A273ASN0-0.043-0.03914.6580.0460.0460.0000.0000.0000.000
168A274ILE00.0030.01313.788-0.022-0.0220.0000.0000.0000.000
169A275GLU-1-0.826-0.90315.120-0.188-0.1880.0000.0000.0000.000
170A276ILE0-0.0140.00114.8210.0250.0250.0000.0000.0000.000
171A277ILE00.0050.0018.1490.0260.0260.0000.0000.0000.000
172A278LYS10.8370.90912.6130.2470.2470.0000.0000.0000.000
173A279SER0-0.0100.00614.5340.0420.0420.0000.0000.0000.000
174A280LEU00.0240.01513.0220.0350.0350.0000.0000.0000.000
175A281CYS0-0.060-0.03610.5810.0320.0320.0000.0000.0000.000
176A282SER0-0.113-0.06612.8550.0500.0500.0000.0000.0000.000
177A283GLY00.0180.00516.2610.0190.0190.0000.0000.0000.000
178A284ALA00.0200.00812.6040.0210.0210.0000.0000.0000.000
179A285ALA0-0.004-0.00214.6530.0370.0370.0000.0000.0000.000
180A286ALA0-0.021-0.00616.4120.0160.0160.0000.0000.0000.000
181A287LEU0-0.061-0.03214.031-0.012-0.0120.0000.0000.0000.000
182A288GLU-1-0.977-0.97311.9940.5600.5600.0000.0000.0000.000
183A289HIS0-0.056-0.01916.490-0.009-0.0090.0000.0000.0000.000