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About

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: K9KZ3

Calculation Name: 5T1J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5T1J

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JKD8

Base Structure: X-ray

Registration Date: 2023-06-22

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2117564.257688
FMO2-HF: Nuclear repulsion 2039962.932454
FMO2-HF: Total energy -77601.325235
FMO2-MP2: Total energy -77827.046227


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:136:LYS)


Summations of interaction energy for fragment #1(A:136:LYS)
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.
44.00947.8192.872-2.5-4.182-0.011
Interaction energy analysis for fragmet #1(A:136:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.942 / q_NPA : 0.970
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].
3A138ARG10.9690.9973.14731.09134.0830.028-1.374-1.6460.004
4A139VAL00.0260.0175.8002.6182.6180.0000.0000.0000.000
5A140ALA0-0.0020.0199.3480.4080.4080.0000.0000.0000.000
6A141LEU00.0610.00111.8260.3490.3490.0000.0000.0000.000
7A142SER00.0380.02715.6080.5740.5740.0000.0000.0000.000
8A143ASN00.022-0.00918.2420.2380.2380.0000.0000.0000.000
9A144HIS00.0150.02117.3100.7080.7080.0000.0000.0000.000
10A145LEU00.0820.02220.1670.2680.2680.0000.0000.0000.000
11A146LEU0-0.019-0.02023.3700.3300.3300.0000.0000.0000.000
12A147TRP00.0360.01321.2400.5290.5290.0000.0000.0000.000
13A148SER00.0240.01522.5010.1210.1210.0000.0000.0000.000
14A149LYS10.9120.96024.99210.46610.4660.0000.0000.0000.000
15A150PHE0-0.012-0.01827.6620.3390.3390.0000.0000.0000.000
16A151ASN0-0.0160.01025.0570.3440.3440.0000.0000.0000.000
17A152GLN00.007-0.00427.7260.3520.3520.0000.0000.0000.000
18A153HIS10.8060.90629.9749.5149.5140.0000.0000.0000.000
19A154GLN0-0.019-0.01030.7800.4840.4840.0000.0000.0000.000
20A155THR00.0670.03027.5170.3240.3240.0000.0000.0000.000
21A156GLU-1-0.750-0.88430.646-8.614-8.6140.0000.0000.0000.000
22A157MET0-0.0300.01127.3770.1620.1620.0000.0000.0000.000
23A158ILE00.0050.01932.3520.1010.1010.0000.0000.0000.000
24A159ILE00.0060.00333.188-0.145-0.1450.0000.0000.0000.000
25A160THR0-0.018-0.03435.6690.3500.3500.0000.0000.0000.000
26A161LYS11.0101.06837.5897.0657.0650.0000.0000.0000.000
27A162GLN00.0370.02938.360-0.041-0.0410.0000.0000.0000.000
28A163GLY00.0460.01035.420-0.170-0.1700.0000.0000.0000.000
29A164ARG10.8690.93033.9428.4338.4330.0000.0000.0000.000
30A165ARG10.9891.00329.5569.3419.3410.0000.0000.0000.000
31A166MET0-0.030-0.00124.2220.1280.1280.0000.0000.0000.000
32A167PHE0-0.0410.00628.3010.0290.0290.0000.0000.0000.000
33A168PRO00.0360.02125.4890.2830.2830.0000.0000.0000.000
34A169PHE00.019-0.00723.770-0.311-0.3110.0000.0000.0000.000
35A170LEU00.0490.05118.671-0.056-0.0560.0000.0000.0000.000
36A171SER0-0.055-0.07319.0500.2610.2610.0000.0000.0000.000
37A172PHE0-0.078-0.01313.8370.1920.1920.0000.0000.0000.000
38A173THR00.0640.03411.3580.7860.7860.0000.0000.0000.000
39A174VAL00.0220.0138.061-1.014-1.0140.0000.0000.0000.000
40A175ALA00.0360.0116.0391.4941.4940.0000.0000.0000.000
41A176GLY0-0.070-0.0452.422-2.312-2.6712.644-1.462-0.8240.004
42A177LEU0-0.0290.0152.833-9.079-8.0110.2010.340-1.608-0.019
43A178GLU-1-0.875-0.9475.555-29.514-29.5140.0000.0000.0000.000
44A179PRO0-0.025-0.0248.2900.8780.8780.0000.0000.0000.000
45A180THR00.0560.00611.6680.6460.6460.0000.0000.0000.000
46A181SER00.0500.0609.6441.3101.3100.0000.0000.0000.000
47A182HIS00.0180.00012.1940.6540.6540.0000.0000.0000.000
48A183TYR00.0160.0097.466-0.807-0.8070.0000.0000.0000.000
49A184ARG10.9520.97012.67717.02317.0230.0000.0000.0000.000
50A185MET0-0.0070.01010.862-0.907-0.9070.0000.0000.0000.000
51A186PHE00.012-0.00115.6501.4411.4410.0000.0000.0000.000
52A187VAL0-0.033-0.01217.255-1.040-1.0400.0000.0000.0000.000
53A188ASP-1-0.770-0.87419.338-15.283-15.2830.0000.0000.0000.000
54A189VAL00.0060.00820.677-0.437-0.4370.0000.0000.0000.000
55A190VAL00.0140.01020.4890.4680.4680.0000.0000.0000.000
56A191LEU0-0.045-0.02423.2910.1290.1290.0000.0000.0000.000
57A192VAL0-0.060-0.02724.367-0.091-0.0910.0000.0000.0000.000
58A193ASP-1-0.832-0.93125.922-11.111-11.1110.0000.0000.0000.000
59A194GLN0-0.037-0.02728.5490.3490.3490.0000.0000.0000.000
60A195HIS0-0.0200.01332.1060.3390.3390.0000.0000.0000.000
61A196HIS00.0240.02334.246-0.293-0.2930.0000.0000.0000.000
62A197TRP0-0.030-0.03332.260-0.154-0.1540.0000.0000.0000.000
63A198ARG10.9120.91537.4407.4887.4880.0000.0000.0000.000
64A199TYR00.0140.01438.393-0.055-0.0550.0000.0000.0000.000
65A200GLN00.0910.04141.2050.0400.0400.0000.0000.0000.000
66A201SER0-0.009-0.01942.591-0.148-0.1480.0000.0000.0000.000
67A202GLY00.0490.04941.902-0.023-0.0230.0000.0000.0000.000
68A203LYS10.9500.96738.0727.9347.9340.0000.0000.0000.000
69A204TRP0-0.0220.00335.4250.0640.0640.0000.0000.0000.000
70A205VAL0-0.036-0.02137.062-0.146-0.1460.0000.0000.0000.000
71A206GLN00.0520.02633.6460.1620.1620.0000.0000.0000.000
72A207CYS0-0.062-0.01637.8180.3620.3620.0000.0000.0000.000
73A208GLY00.0210.02239.512-0.161-0.1610.0000.0000.0000.000
74A209LYS10.9570.95938.7957.8177.8170.0000.0000.0000.000
75A210ALA00.0220.01935.0190.0180.0180.0000.0000.0000.000
76A211GLU-1-0.902-0.95035.802-8.325-8.3250.0000.0000.0000.000
77A212GLY00.0000.00133.260-0.076-0.0760.0000.0000.0000.000
78A213SER0-0.105-0.05734.064-0.084-0.0840.0000.0000.0000.000
79A214MET0-0.013-0.01627.952-0.017-0.0170.0000.0000.0000.000
80A215PRO00.0580.02425.7510.1890.1890.0000.0000.0000.000
81A216GLY0-0.047-0.01726.489-0.279-0.2790.0000.0000.0000.000
82A217ASN00.0740.01222.126-0.216-0.2160.0000.0000.0000.000
83A218ARG10.8700.93825.73710.92210.9220.0000.0000.0000.000
84A219LEU00.0530.02521.582-0.146-0.1460.0000.0000.0000.000
85A220TYR0-0.0040.00022.5810.8150.8150.0000.0000.0000.000
86A221VAL00.0160.01120.235-0.787-0.7870.0000.0000.0000.000
87A222HIS00.024-0.00318.0590.8320.8320.0000.0000.0000.000
88A223PRO0-0.053-0.03821.0410.0380.0380.0000.0000.0000.000
89A224ASP-1-0.870-0.90920.806-11.889-11.8890.0000.0000.0000.000
90A225SER0-0.032-0.00218.297-1.155-1.1550.0000.0000.0000.000
91A226PRO0-0.048-0.03917.2270.4960.4960.0000.0000.0000.000
92A227ASN00.0520.01616.4080.4360.4360.0000.0000.0000.000
93A228THR00.0410.03114.993-1.146-1.1460.0000.0000.0000.000
94A229GLY00.1070.00210.941-0.105-0.1050.0000.0000.0000.000
95A230ALA00.0170.00611.491-0.191-0.1910.0000.0000.0000.000
96A231HIS00.0030.01413.1040.8630.8630.0000.0000.0000.000
97A232TRP0-0.079-0.05111.4240.7620.7620.0000.0000.0000.000
98A233MET0-0.051-0.0398.471-0.304-0.3040.0000.0000.0000.000
99A234ARG10.8150.94211.80114.67714.6770.0000.0000.0000.000
100A235GLN0-0.001-0.00315.5560.6400.6400.0000.0000.0000.000
101A236GLU-1-0.949-0.97415.930-12.725-12.7250.0000.0000.0000.000
102A237VAL00.0060.04414.1290.1570.1570.0000.0000.0000.000
103A238SER00.015-0.01117.334-0.163-0.1630.0000.0000.0000.000
104A239PHE00.0320.01317.2390.1450.1450.0000.0000.0000.000
105A240GLY00.013-0.00622.4010.3580.3580.0000.0000.0000.000
106A241LYS10.9000.93125.64910.48910.4890.0000.0000.0000.000
107A242LEU00.0230.03923.5840.3930.3930.0000.0000.0000.000
108A243LYS10.9010.94627.1429.4069.4060.0000.0000.0000.000
109A244LEU00.004-0.00127.884-0.214-0.2140.0000.0000.0000.000
110A245THR0-0.031-0.06531.7970.4090.4090.0000.0000.0000.000
111A246ASN00.0210.01034.600-0.173-0.1730.0000.0000.0000.000
112A247ASN00.0450.01637.1830.2010.2010.0000.0000.0000.000
113A248LYS10.9670.97434.2918.8338.8330.0000.0000.0000.000
114A249GLY00.0420.02836.867-0.069-0.0690.0000.0000.0000.000
115A250ALA0-0.051-0.03135.7610.1910.1910.0000.0000.0000.000
116A251SER00.0150.00337.492-0.020-0.0200.0000.0000.0000.000
117A252ASN00.002-0.00338.609-0.133-0.1330.0000.0000.0000.000
118A253ASN0-0.021-0.00333.417-0.108-0.1080.0000.0000.0000.000
119A254VAL00.0910.04934.6110.1050.1050.0000.0000.0000.000
120A255THR0-0.034-0.01533.450-0.014-0.0140.0000.0000.0000.000
121A256GLN0-0.0010.02025.2950.0890.0890.0000.0000.0000.000
122A257MET0-0.027-0.02228.965-0.232-0.2320.0000.0000.0000.000
123A258ILE00.0100.00425.0530.1550.1550.0000.0000.0000.000
124A259VAL0-0.069-0.02529.3560.3160.3160.0000.0000.0000.000
125A260LEU0-0.030-0.03028.389-0.214-0.2140.0000.0000.0000.000
126A261GLN00.0460.03132.3390.4360.4360.0000.0000.0000.000
127A262SER00.0160.00434.114-0.214-0.2140.0000.0000.0000.000
128A263LEU00.0120.01536.0890.0050.0050.0000.0000.0000.000
129A264HIS10.8690.91431.9579.1979.1970.0000.0000.0000.000
130A265LYS10.9781.00327.94010.67510.6750.0000.0000.0000.000
131A266TYR00.0060.01726.4410.0440.0440.0000.0000.0000.000
132A267GLN00.0680.00220.007-0.295-0.2950.0000.0000.0000.000
133A268PRO0-0.068-0.00920.971-0.245-0.2450.0000.0000.0000.000
134A269ARG10.8860.92116.31716.39316.3930.0000.0000.0000.000
135A270LEU00.0080.01112.8120.8830.8830.0000.0000.0000.000
136A271HIS10.8230.91812.81817.28417.2840.0000.0000.0000.000
137A272ILE00.0040.0057.3411.6181.6180.0000.0000.0000.000
138A273VAL00.0260.03310.300-2.059-2.0590.0000.0000.0000.000
139A274GLU-1-0.848-0.9396.648-36.478-36.4780.0000.0000.0000.000
140A275VAL0-0.070-0.03011.4170.0760.0760.0000.0000.0000.000
141A276ASN0-0.006-0.00213.1250.2480.2480.0000.0000.0000.000
142A277ASP-1-0.857-0.92114.664-15.232-15.2320.0000.0000.0000.000
143A278GLY00.016-0.00117.247-0.435-0.4350.0000.0000.0000.000
144A279GLU-1-0.973-0.99918.605-14.528-14.5280.0000.0000.0000.000
145A280PRO0-0.072-0.02619.6500.4400.4400.0000.0000.0000.000
146A281GLU-1-0.880-0.92222.388-12.468-12.4680.0000.0000.0000.000
147A282ALA0-0.018-0.02819.6470.1120.1120.0000.0000.0000.000
148A283ALA0-0.060-0.04015.368-1.188-1.1880.0000.0000.0000.000
149A284CYS0-0.0320.02315.4820.6130.6130.0000.0000.0000.000
150A285SER0-0.020-0.02113.7990.5420.5420.0000.0000.0000.000
151A286ALA00.014-0.01611.031-1.767-1.7670.0000.0000.0000.000
152A287SER00.0130.02511.4071.4031.4030.0000.0000.0000.000
153A288ASN0-0.044-0.0307.302-1.771-1.7710.0000.0000.0000.000
154A289THR00.0040.0089.0253.0843.0840.0000.0000.0000.000
155A290HIS00.0200.0154.7340.4330.542-0.001-0.004-0.1040.000
156A291VAL0-0.045-0.0449.7363.2483.2480.0000.0000.0000.000
157A292PHE00.0060.0116.694-1.087-1.0870.0000.0000.0000.000
158A293THR0-0.018-0.02012.2101.7911.7910.0000.0000.0000.000
159A294PHE00.0190.01413.554-0.514-0.5140.0000.0000.0000.000
160A295GLN00.0890.07217.5480.3830.3830.0000.0000.0000.000
161A296GLU-1-0.931-0.96618.346-15.317-15.3170.0000.0000.0000.000
162A297THR0-0.062-0.06520.5000.2060.2060.0000.0000.0000.000
163A298GLN0-0.030-0.01923.060-0.194-0.1940.0000.0000.0000.000
164A299PHE0-0.029-0.02925.0440.2880.2880.0000.0000.0000.000
165A300ILE00.0320.02928.543-0.089-0.0890.0000.0000.0000.000
166A301ALA0-0.0370.00531.7730.0440.0440.0000.0000.0000.000
167A302VAL00.0230.00433.3950.2400.2400.0000.0000.0000.000
168A303THR00.009-0.01536.863-0.158-0.1580.0000.0000.0000.000
169A304ALA0-0.004-0.01339.7670.1140.1140.0000.0000.0000.000
170A305TYR0-0.052-0.02435.069-0.199-0.1990.0000.0000.0000.000
171A306GLN00.0280.03038.9500.3070.3070.0000.0000.0000.000
172A307ASN0-0.011-0.01637.5430.3530.3530.0000.0000.0000.000
173A308ALA00.0620.02939.377-0.063-0.0630.0000.0000.0000.000
174A309GLU-1-0.800-0.88135.846-8.540-8.5400.0000.0000.0000.000
175A310ILE00.0200.02332.666-0.127-0.1270.0000.0000.0000.000
176A311THR0-0.005-0.01035.796-0.069-0.0690.0000.0000.0000.000
177A312GLN00.0350.01538.2060.0160.0160.0000.0000.0000.000
178A313LEU00.0150.00431.985-0.056-0.0560.0000.0000.0000.000
179A314LYS10.7970.89832.2079.2859.2850.0000.0000.0000.000
180A315ILE00.0080.02034.496-0.102-0.1020.0000.0000.0000.000
181A316ASP-1-0.860-0.95234.296-8.630-8.6300.0000.0000.0000.000
182A317ASN0-0.075-0.05230.668-0.238-0.2380.0000.0000.0000.000
183A318ASN0-0.032-0.00831.784-0.222-0.2220.0000.0000.0000.000
184A319PRO00.0270.00331.7700.2730.2730.0000.0000.0000.000
185A320PHE0-0.056-0.03032.2640.1200.1200.0000.0000.0000.000
186A321ALA0-0.052-0.03137.0520.1980.1980.0000.0000.0000.000
187A322LYS10.8970.95535.8038.2778.2770.0000.0000.0000.000
188A323GLY00.0030.02140.4540.1240.1240.0000.0000.0000.000
189A324PHE0-0.039-0.01742.5140.1200.1200.0000.0000.0000.000
190A325ARG10.9120.93338.4037.5757.5750.0000.0000.0000.000
191A326GLU-1-0.939-0.94743.195-6.343-6.3430.0000.0000.0000.000
192A327ASN00.0110.02045.4930.1650.1650.0000.0000.0000.000