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: 94NN2

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2004555.655882
FMO2-HF: Nuclear repulsion 1929016.617368
FMO2-HF: Total energy -75539.038514
FMO2-MP2: Total energy -75751.928544


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.
-3.4990.6653.828-3.119-4.87-0.006
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 : 0.023 / 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].
3A109CYS00.0500.0433.148-2.940-0.4690.100-1.347-1.2230.000
4A110GLY00.0550.0195.7350.2440.2440.0000.0000.0000.000
5A111VAL0-0.022-0.0072.266-0.013-0.4362.934-0.745-1.7650.000
6A112THR0-0.0040.0072.186-1.2880.1680.787-0.862-1.380-0.006
7A113ALA00.0450.0244.1000.3870.5400.002-0.043-0.1120.000
8A114ASN00.0330.0047.3080.1630.1630.0000.0000.0000.000
9A115ALA0-0.030-0.0115.9540.1790.1790.0000.0000.0000.000
10A116ILE00.0400.0237.7390.1310.1310.0000.0000.0000.000
11A117MET0-0.0140.0099.7900.1120.1120.0000.0000.0000.000
12A118LYS10.9560.9829.3980.1580.1580.0000.0000.0000.000
13A119LEU0-0.0250.0039.4320.0540.0540.0000.0000.0000.000
14A120PHE00.016-0.00312.9700.0420.0420.0000.0000.0000.000
15A121LEU0-0.027-0.00715.6060.0390.0390.0000.0000.0000.000
16A122ASP-1-0.864-0.91514.838-0.134-0.1340.0000.0000.0000.000
17A123LYS10.9260.97017.5190.1180.1180.0000.0000.0000.000
18A124ASP-1-0.873-0.92720.831-0.040-0.0400.0000.0000.0000.000
19A125GLY0-0.060-0.04123.726-0.005-0.0050.0000.0000.0000.000
20A126PHE0-0.077-0.03618.2020.0020.0020.0000.0000.0000.000
21A127SER00.0100.00516.6850.0040.0040.0000.0000.0000.000
22A128TYR0-0.011-0.01611.690-0.019-0.0190.0000.0000.0000.000
23A129CYS0-0.087-0.06013.8890.0230.0230.0000.0000.0000.000
24A130PHE0-0.010-0.00411.717-0.010-0.0100.0000.0000.0000.000
25A131GLU-1-0.898-0.96713.521-0.101-0.1010.0000.0000.0000.000
26A132ASN0-0.047-0.01415.7340.0150.0150.0000.0000.0000.000
27A133GLU-1-0.870-0.92116.721-0.146-0.1460.0000.0000.0000.000
28A134GLN0-0.045-0.02919.1890.0020.0020.0000.0000.0000.000
29A135THR0-0.033-0.02018.791-0.019-0.0190.0000.0000.0000.000
30A136LEU0-0.0330.00021.2750.0180.0180.0000.0000.0000.000
31A137SER00.0660.02822.049-0.023-0.0230.0000.0000.0000.000
32A138LEU00.0350.00123.472-0.006-0.0060.0000.0000.0000.000
33A139GLU-1-0.925-0.95624.937-0.119-0.1190.0000.0000.0000.000
34A140GLN00.0540.01826.063-0.002-0.0020.0000.0000.0000.000
35A141LEU0-0.019-0.00621.6110.0030.0030.0000.0000.0000.000
36A142GLN00.009-0.01125.3930.0080.0080.0000.0000.0000.000
37A143GLU-1-0.899-0.94028.104-0.116-0.1160.0000.0000.0000.000
38A144ARG10.8960.93925.4960.1680.1680.0000.0000.0000.000
39A145LEU0-0.009-0.01823.8410.0000.0000.0000.0000.0000.000
40A146SER0-0.0020.01027.9300.0040.0040.0000.0000.0000.000
41A147CYS0-0.108-0.04331.1710.0080.0080.0000.0000.0000.000
42A148MET0-0.0240.01924.1040.0010.0010.0000.0000.0000.000
43A149PRO0-0.018-0.01729.0280.0040.0040.0000.0000.0000.000
44A150GLU-1-0.768-0.88629.288-0.138-0.1380.0000.0000.0000.000
45A151CYS0-0.078-0.03030.338-0.006-0.0060.0000.0000.0000.000
46A152LYS10.9110.95027.1730.1320.1320.0000.0000.0000.000
47A153SER00.0130.01822.8680.0010.0010.0000.0000.0000.000
48A154PHE0-0.008-0.02421.7950.0150.0150.0000.0000.0000.000
49A155VAL00.0360.02715.163-0.022-0.0220.0000.0000.0000.000
50A156LEU0-0.003-0.00717.2590.0320.0320.0000.0000.0000.000
51A157ARG10.8680.9219.5470.5370.5370.0000.0000.0000.000
52A158VAL0-0.025-0.00913.7510.0790.0790.0000.0000.0000.000
53A159ASN00.0180.00712.737-0.196-0.1960.0000.0000.0000.000
54A160ASP-1-0.754-0.86014.313-0.346-0.3460.0000.0000.0000.000
55A161GLY00.0540.03415.789-0.033-0.0330.0000.0000.0000.000
56A162ALA00.0050.00117.8160.0080.0080.0000.0000.0000.000
57A163LEU0-0.019-0.01415.3400.0180.0180.0000.0000.0000.000
58A164GLY0-0.0180.00315.049-0.017-0.0170.0000.0000.0000.000
59A165HIS0-0.039-0.0429.278-0.117-0.1170.0000.0000.0000.000
60A166ALA00.004-0.0079.0520.1250.1250.0000.0000.0000.000
61A167TYR0-0.070-0.0639.500-0.210-0.2100.0000.0000.0000.000
62A168ILE0-0.010-0.01110.2690.1020.1020.0000.0000.0000.000
63A169VAL00.0010.00112.934-0.011-0.0110.0000.0000.0000.000
64A170ASP-1-0.780-0.83616.532-0.338-0.3380.0000.0000.0000.000
65A171ILE00.027-0.00118.1170.0120.0120.0000.0000.0000.000
66A172PRO00.0580.02921.5080.0210.0210.0000.0000.0000.000
67A173LYS10.9220.96823.8830.1540.1540.0000.0000.0000.000
68A174GLY0-0.003-0.00427.496-0.005-0.0050.0000.0000.0000.000
69A175GLU-1-0.930-0.95929.662-0.121-0.1210.0000.0000.0000.000
70A176ASN00.003-0.03030.033-0.022-0.0220.0000.0000.0000.000
71A177SER0-0.049-0.00331.7310.0000.0000.0000.0000.0000.000
72A178CYS0-0.024-0.01530.3270.0010.0010.0000.0000.0000.000
73A179ARG10.8410.93426.4370.1840.1840.0000.0000.0000.000
74A180PRO00.018-0.00225.024-0.012-0.0120.0000.0000.0000.000
75A181ALA0-0.022-0.00620.5910.0000.0000.0000.0000.0000.000
76A182PHE00.0000.01117.5300.0090.0090.0000.0000.0000.000
77A183LEU00.0280.02813.502-0.012-0.0120.0000.0000.0000.000
78A184TYR0-0.044-0.04810.975-0.037-0.0370.0000.0000.0000.000
79A185GLN00.002-0.0058.711-0.061-0.0610.0000.0000.0000.000
80A186SER0-0.059-0.0373.709-0.0770.079-0.001-0.038-0.1180.000
81A187ASP-1-0.719-0.8446.864-1.021-1.0210.0000.0000.0000.000
82A188LEU0-0.030-0.0213.367-0.465-0.1140.006-0.084-0.2720.000
83A189GLY0-0.047-0.0216.9850.3780.3780.0000.0000.0000.000
84A190GLU-1-1.003-0.9959.808-0.147-0.1470.0000.0000.0000.000
85A191GLY00.0320.02112.4510.0820.0820.0000.0000.0000.000
86A192VAL0-0.0020.01114.8110.0410.0410.0000.0000.0000.000
87A193THR00.007-0.02212.7280.1020.1020.0000.0000.0000.000
88A194ARG10.7980.87113.3200.3570.3570.0000.0000.0000.000
89A195LYS10.9270.9615.3470.5800.5800.0000.0000.0000.000
90A196LEU0-0.014-0.0028.3020.1740.1740.0000.0000.0000.000
91A197ARG10.8010.8795.789-0.175-0.1750.0000.0000.0000.000
92A198PHE00.0700.0185.0720.1960.1960.0000.0000.0000.000
93A199GLU-1-0.853-0.9016.682-0.113-0.1130.0000.0000.0000.000
94A200ASP-1-0.839-0.9108.822-0.408-0.4080.0000.0000.0000.000
95A201TRP00.028-0.01410.0430.0710.0710.0000.0000.0000.000
96A202MET0-0.041-0.03010.0900.0880.0880.0000.0000.0000.000
97A203THR0-0.071-0.03612.4700.0970.0970.0000.0000.0000.000
98A204HIS0-0.054-0.03014.2310.1110.1110.0000.0000.0000.000
99A205LYS10.8540.92716.1040.4120.4120.0000.0000.0000.000
100A206ALA0-0.0110.00413.8720.0280.0280.0000.0000.0000.000
101A207LEU00.0210.00916.0350.0260.0260.0000.0000.0000.000
102A208THR0-0.072-0.02418.7230.0490.0490.0000.0000.0000.000
103A209PRO0-0.0280.00920.707-0.026-0.0260.0000.0000.0000.000
104A210ILE0-0.003-0.01119.5310.0130.0130.0000.0000.0000.000
105A211LEU00.0210.01023.0480.0120.0120.0000.0000.0000.000
106A212LEU00.017-0.00422.496-0.018-0.0180.0000.0000.0000.000
107A213ASP-1-0.859-0.94224.427-0.190-0.1900.0000.0000.0000.000
108A214ASP-1-0.902-0.94924.742-0.218-0.2180.0000.0000.0000.000
109A215ILE0-0.056-0.02818.296-0.006-0.0060.0000.0000.0000.000
110A216CYS0-0.0030.00022.260-0.002-0.0020.0000.0000.0000.000
111A217ASN0-0.014-0.00724.5220.0070.0070.0000.0000.0000.000
112A218TYR0-0.009-0.02318.5240.0220.0220.0000.0000.0000.000
113A219PHE00.005-0.00318.5560.0070.0070.0000.0000.0000.000
114A220SER0-0.010-0.00323.1530.0160.0160.0000.0000.0000.000
115A221CYS0-0.035-0.00726.1280.0180.0180.0000.0000.0000.000
116A222MET00.0150.01221.0530.0190.0190.0000.0000.0000.000
117A223SER0-0.043-0.02324.4760.0150.0150.0000.0000.0000.000
118A224GLN0-0.065-0.04325.7730.0280.0280.0000.0000.0000.000
119A225ASN0-0.040-0.02426.8280.0020.0020.0000.0000.0000.000
120A226LYS10.8890.95527.8830.1420.1420.0000.0000.0000.000
121A227THR0-0.023-0.00924.521-0.008-0.0080.0000.0000.0000.000
122A228ASP-1-0.800-0.90425.371-0.181-0.1810.0000.0000.0000.000
123A229LEU0-0.023-0.03322.690-0.016-0.0160.0000.0000.0000.000
124A230GLU-1-0.883-0.94023.613-0.213-0.2130.0000.0000.0000.000
125A231GLN0-0.0060.01023.549-0.019-0.0190.0000.0000.0000.000
126A232ILE0-0.003-0.00618.796-0.021-0.0210.0000.0000.0000.000
127A233ALA00.0050.00219.537-0.045-0.0450.0000.0000.0000.000
128A234THR0-0.009-0.01620.222-0.023-0.0230.0000.0000.0000.000
129A235LEU0-0.0080.00418.753-0.012-0.0120.0000.0000.0000.000
130A236PHE0-0.0050.00114.301-0.036-0.0360.0000.0000.0000.000
131A237ASP-1-0.743-0.83915.004-0.487-0.4870.0000.0000.0000.000
132A238ILE0-0.044-0.02313.1460.0220.0220.0000.0000.0000.000
133A239ASP-1-0.853-0.91416.240-0.270-0.2700.0000.0000.0000.000
134A240GLY0-0.065-0.02819.4430.0330.0330.0000.0000.0000.000
135A241ASN0-0.016-0.01220.4290.0400.0400.0000.0000.0000.000
136A242VAL00.0940.03420.978-0.016-0.0160.0000.0000.0000.000
137A243LYS10.8930.93922.7910.1400.1400.0000.0000.0000.000
138A244MET0-0.088-0.04017.8100.0180.0180.0000.0000.0000.000
139A245LEU0-0.0110.01617.838-0.027-0.0270.0000.0000.0000.000
140A246ARG10.9190.96717.9780.2110.2110.0000.0000.0000.000
141A247LYS11.0050.98520.3420.1350.1350.0000.0000.0000.000
142A248GLU-1-0.950-0.98421.420-0.163-0.1630.0000.0000.0000.000
143A249ASN0-0.059-0.02917.5980.0400.0400.0000.0000.0000.000
144A250ILE00.0050.01019.403-0.023-0.0230.0000.0000.0000.000
145A251GLN0-0.099-0.04218.5690.0580.0580.0000.0000.0000.000
146A252TYR0-0.0230.00021.7100.0040.0040.0000.0000.0000.000
147A253GLN00.0070.00221.242-0.002-0.0020.0000.0000.0000.000
148A254LYS10.9080.94925.5580.0860.0860.0000.0000.0000.000
149A255HIS00.013-0.01027.452-0.004-0.0040.0000.0000.0000.000
150A256ASP-1-0.917-0.95223.717-0.137-0.1370.0000.0000.0000.000
151A257ASN00.0200.00821.660-0.014-0.0140.0000.0000.0000.000
152A258PHE0-0.038-0.00118.585-0.020-0.0200.0000.0000.0000.000
153A259SER0-0.029-0.00317.6520.0300.0300.0000.0000.0000.000
154A260PHE00.0320.00717.354-0.045-0.0450.0000.0000.0000.000
155A261GLN00.0460.03915.7560.0060.0060.0000.0000.0000.000
156A262LEU0-0.0190.00417.904-0.033-0.0330.0000.0000.0000.000
157A263PHE0-0.017-0.01217.6020.0260.0260.0000.0000.0000.000
158A264GLU-1-0.924-0.96320.942-0.163-0.1630.0000.0000.0000.000
159A265TYR0-0.116-0.09119.7270.0050.0050.0000.0000.0000.000
160A266ASP-1-0.871-0.92521.716-0.139-0.1390.0000.0000.0000.000
161A267THR00.003-0.03421.549-0.017-0.0170.0000.0000.0000.000
162A268ASP-1-0.853-0.91921.555-0.134-0.1340.0000.0000.0000.000
163A269ASN0-0.079-0.06118.7630.0300.0300.0000.0000.0000.000
164A270ILE00.0000.00814.250-0.004-0.0040.0000.0000.0000.000
165A271GLU-1-0.926-0.95816.929-0.176-0.1760.0000.0000.0000.000
166A272LYS10.8640.92618.6920.1350.1350.0000.0000.0000.000
167A273ASN0-0.042-0.03114.5340.0490.0490.0000.0000.0000.000
168A274ILE0-0.0110.00313.580-0.007-0.0070.0000.0000.0000.000
169A275GLU-1-0.848-0.93014.966-0.124-0.1240.0000.0000.0000.000
170A276ILE0-0.0110.00215.0000.0270.0270.0000.0000.0000.000
171A277ILE0-0.006-0.0068.2270.0320.0320.0000.0000.0000.000
172A278LYS10.8570.93312.7300.2020.2020.0000.0000.0000.000
173A279SER00.0050.00914.5430.0410.0410.0000.0000.0000.000
174A280LEU00.0130.01013.1590.0320.0320.0000.0000.0000.000
175A281CYS0-0.051-0.03010.6110.0460.0460.0000.0000.0000.000
176A282SER0-0.108-0.05713.0910.0420.0420.0000.0000.0000.000
177A283GLY00.0210.00916.5740.0110.0110.0000.0000.0000.000
178A284ALA00.0140.00612.5920.0180.0180.0000.0000.0000.000
179A285ALA0-0.0010.00114.6840.0370.0370.0000.0000.0000.000
180A286ALA0-0.021-0.00816.5180.0120.0120.0000.0000.0000.000
181A287LEU0-0.070-0.03914.143-0.017-0.0170.0000.0000.0000.000
182A288GLU-1-0.981-0.97412.3920.6840.6840.0000.0000.0000.000
183A289HIS0-0.042-0.01316.744-0.014-0.0140.0000.0000.0000.000