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: 49ZYN

Calculation Name: 5E1T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5E1T

Chain ID: A

ChEMBL ID:

UniProt ID: Q13077

Base Structure: X-ray

Registration Date: 2023-09-19

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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2006003.467982
FMO2-HF: Nuclear repulsion 1928165.099422
FMO2-HF: Total energy -77838.36856
FMO2-MP2: Total energy -78063.437216


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:224:LEU)


Summations of interaction energy for fragment #1(A:224:LEU)
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.
-13.306-6.7673.491-3.534-6.496-0.02
Interaction energy analysis for fragmet #1(A:224:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.019
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].
3A226ARG10.9630.9863.096-3.288-1.0700.022-0.971-1.2690.003
4A227GLU-1-0.897-0.9472.445-10.466-7.7363.156-2.143-3.743-0.025
5A228ARG10.9431.0162.623-0.3151.1580.314-0.414-1.3730.002
6A229ILE00.0250.0065.3100.1700.288-0.001-0.006-0.1110.000
7A230LEU0-0.002-0.0027.8270.0940.0940.0000.0000.0000.000
8A231SER0-0.024-0.0647.0600.0180.0180.0000.0000.0000.000
9A232LEU0-0.062-0.0399.4670.1260.1260.0000.0000.0000.000
10A233GLU-1-0.923-0.94511.481-0.039-0.0390.0000.0000.0000.000
11A234GLN00.016-0.01012.800-0.013-0.0130.0000.0000.0000.000
12A235ARG10.9780.99012.5280.3890.3890.0000.0000.0000.000
13A236VAL0-0.0160.00015.3230.0440.0440.0000.0000.0000.000
14A237VAL00.0160.02017.3190.0250.0250.0000.0000.0000.000
15A238GLU-1-0.912-0.96417.014-0.317-0.3170.0000.0000.0000.000
16A239LEU0-0.051-0.03918.0240.0240.0240.0000.0000.0000.000
17A240GLN00.0090.00521.2100.0050.0050.0000.0000.0000.000
18A241GLN00.0080.01223.0340.0040.0040.0000.0000.0000.000
19A242THR0-0.046-0.02223.0140.0120.0120.0000.0000.0000.000
20A243LEU00.008-0.00425.1510.0090.0090.0000.0000.0000.000
21A244ALA00.0490.03027.0090.0090.0090.0000.0000.0000.000
22A245GLN0-0.0140.00026.9800.0060.0060.0000.0000.0000.000
23A246LYS10.8750.92227.9530.1000.1000.0000.0000.0000.000
24A247ASP-1-0.900-0.93231.222-0.036-0.0360.0000.0000.0000.000
25A248GLN00.0150.00633.0540.0000.0000.0000.0000.0000.000
26A249ALA0-0.081-0.04134.2370.0040.0040.0000.0000.0000.000
27A250LEU00.0250.00835.4270.0020.0020.0000.0000.0000.000
28A251GLY00.1050.06337.1800.0040.0040.0000.0000.0000.000
29A252LYS10.9070.94038.7130.0600.0600.0000.0000.0000.000
30A253LEU0-0.037-0.00839.3540.0010.0010.0000.0000.0000.000
31A254GLU-1-0.827-0.89941.281-0.025-0.0250.0000.0000.0000.000
32A255GLN00.002-0.00743.2450.0030.0030.0000.0000.0000.000
33A256SER0-0.061-0.03144.4550.0020.0020.0000.0000.0000.000
34A257LEU00.0160.01345.7530.0010.0010.0000.0000.0000.000
35A258ARG10.9080.93544.3180.0270.0270.0000.0000.0000.000
36A259LEU0-0.060-0.03348.1960.0010.0010.0000.0000.0000.000
37A260MET0-0.057-0.03050.2080.0000.0000.0000.0000.0000.000
38A261GLU-1-0.973-0.97950.775-0.020-0.0200.0000.0000.0000.000
39A262GLU-1-0.968-0.99653.422-0.021-0.0210.0000.0000.0000.000
40A263ALA0-0.0430.00354.9620.0000.0000.0000.0000.0000.000
41A264SER00.005-0.02256.7410.0010.0010.0000.0000.0000.000
42A265PHE0-0.016-0.03256.398-0.002-0.0020.0000.0000.0000.000
43A266ASP-1-0.806-0.89462.114-0.019-0.0190.0000.0000.0000.000
44A267GLY00.0220.02464.3170.0000.0000.0000.0000.0000.000
45A268THR0-0.100-0.04865.5630.0010.0010.0000.0000.0000.000
46A269PHE00.0230.02957.7430.0000.0000.0000.0000.0000.000
47A270LEU0-0.030-0.02562.3510.0010.0010.0000.0000.0000.000
48A271TRP00.0280.01456.0530.0000.0000.0000.0000.0000.000
49A272LYS10.9800.99158.7660.0130.0130.0000.0000.0000.000
50A273ILE0-0.0190.00057.798-0.001-0.0010.0000.0000.0000.000
51A274THR00.0400.00355.4690.0010.0010.0000.0000.0000.000
52A275ASN0-0.029-0.01154.2020.0000.0000.0000.0000.0000.000
53A276VAL00.0300.01957.437-0.001-0.0010.0000.0000.0000.000
54A277THR00.020-0.00559.931-0.001-0.0010.0000.0000.0000.000
55A278ARG10.9230.95950.4940.0130.0130.0000.0000.0000.000
56A279ARG10.9230.95052.1880.0160.0160.0000.0000.0000.000
57A280CYS0-0.0070.00756.207-0.001-0.0010.0000.0000.0000.000
58A281HIS00.021-0.00157.141-0.001-0.0010.0000.0000.0000.000
59A282GLU-1-0.933-0.96652.176-0.016-0.0160.0000.0000.0000.000
60A283SER00.006-0.00354.8790.0000.0000.0000.0000.0000.000
61A284ALA0-0.052-0.00356.294-0.001-0.0010.0000.0000.0000.000
62A285CYS0-0.0640.00252.1750.0000.0000.0000.0000.0000.000
63A286GLY0-0.008-0.01352.744-0.001-0.0010.0000.0000.0000.000
64A287ARG10.8920.94249.9890.0130.0130.0000.0000.0000.000
65A288THR00.0270.00049.0310.0010.0010.0000.0000.0000.000
66A289VAL00.0350.02651.4590.0010.0010.0000.0000.0000.000
67A290SER0-0.040-0.01753.6480.0010.0010.0000.0000.0000.000
68A291LEU0-0.021-0.00753.049-0.001-0.0010.0000.0000.0000.000
69A292PHE00.0400.00252.1170.0000.0000.0000.0000.0000.000
70A293SER0-0.029-0.00653.5320.0000.0000.0000.0000.0000.000
71A294PRO00.0420.01953.211-0.002-0.0020.0000.0000.0000.000
72A295ALA0-0.004-0.00353.6690.0010.0010.0000.0000.0000.000
73A296PHE0-0.032-0.01255.4610.0010.0010.0000.0000.0000.000
74A297TYR00.012-0.00654.000-0.002-0.0020.0000.0000.0000.000
75A298THR00.012-0.00260.6780.0010.0010.0000.0000.0000.000
76A299ALA00.0340.01562.6850.0010.0010.0000.0000.0000.000
77A300LYS10.9380.99156.4810.0270.0270.0000.0000.0000.000
78A301TYR0-0.034-0.02057.615-0.001-0.0010.0000.0000.0000.000
79A302GLY00.0050.00460.8290.0000.0000.0000.0000.0000.000
80A303TYR0-0.007-0.03760.213-0.001-0.0010.0000.0000.0000.000
81A304LYS10.9700.99251.2670.0380.0380.0000.0000.0000.000
82A305LEU0-0.032-0.01358.2690.0000.0000.0000.0000.0000.000
83A306CYS00.0130.02554.6130.0000.0000.0000.0000.0000.000
84A307LEU00.002-0.00257.8340.0010.0010.0000.0000.0000.000
85A308ARG10.9420.97754.3160.0280.0280.0000.0000.0000.000
86A309LEU0-0.004-0.00357.6940.0010.0010.0000.0000.0000.000
87A310TYR0-0.0090.00657.278-0.001-0.0010.0000.0000.0000.000
88A311LEU00.038-0.00457.0650.0010.0010.0000.0000.0000.000
89A312ASN00.019-0.00159.7700.0010.0010.0000.0000.0000.000
90A313GLY00.0620.03861.4230.0000.0000.0000.0000.0000.000
91A314ASP-1-0.970-1.01060.039-0.024-0.0240.0000.0000.0000.000
92A315GLY00.0610.03762.3570.0010.0010.0000.0000.0000.000
93A316THR00.007-0.01964.6300.0000.0000.0000.0000.0000.000
94A317GLY00.0520.03966.6710.0010.0010.0000.0000.0000.000
95A318LYS10.9070.96059.4020.0190.0190.0000.0000.0000.000
96A319ARG10.8980.94660.4970.0170.0170.0000.0000.0000.000
97A320THR0-0.024-0.03264.9120.0010.0010.0000.0000.0000.000
98A321HIS00.0140.03766.8220.0010.0010.0000.0000.0000.000
99A322LEU0-0.0140.02862.820-0.001-0.0010.0000.0000.0000.000
100A323SER0-0.063-0.05462.9500.0000.0000.0000.0000.0000.000
101A324LEU0-0.010-0.00162.026-0.001-0.0010.0000.0000.0000.000
102A325PHE0-0.023-0.01261.1120.0000.0000.0000.0000.0000.000
103A326ILE00.0460.01761.5560.0000.0000.0000.0000.0000.000
104A327VAL0-0.006-0.02256.0410.0000.0000.0000.0000.0000.000
105A328ILE0-0.0050.01158.9780.0000.0000.0000.0000.0000.000
106A329MET0-0.025-0.02552.174-0.001-0.0010.0000.0000.0000.000
107A330ARG10.9290.97549.3120.0460.0460.0000.0000.0000.000
108A331GLY0-0.015-0.01453.711-0.001-0.0010.0000.0000.0000.000
109A332GLU-1-0.936-0.97551.013-0.044-0.0440.0000.0000.0000.000
110A333TYR00.0240.00154.5150.0000.0000.0000.0000.0000.000
111A334ASP-1-0.803-0.89657.358-0.033-0.0330.0000.0000.0000.000
112A335ALA0-0.090-0.05058.3300.0010.0010.0000.0000.0000.000
113A336LEU0-0.010-0.00660.1820.0010.0010.0000.0000.0000.000
114A337LEU0-0.0220.00661.7160.0010.0010.0000.0000.0000.000
115A338PRO00.0030.00164.711-0.001-0.0010.0000.0000.0000.000
116A339TRP0-0.0210.03260.7630.0000.0000.0000.0000.0000.000
117A340PRO00.0510.00266.0930.0000.0000.0000.0000.0000.000
118A341PHE00.0060.00764.5180.0010.0010.0000.0000.0000.000
119A342ARG10.8340.90366.6040.0230.0230.0000.0000.0000.000
120A343ASN0-0.0370.00968.4450.0000.0000.0000.0000.0000.000
121A344LYS10.9350.97170.0740.0160.0160.0000.0000.0000.000
122A345VAL00.0050.01366.8660.0000.0000.0000.0000.0000.000
123A346THR0-0.027-0.01869.6690.0010.0010.0000.0000.0000.000
124A347PHE0-0.006-0.00165.057-0.001-0.0010.0000.0000.0000.000
125A348MET00.018-0.00568.4670.0010.0010.0000.0000.0000.000
126A349LEU0-0.0160.00966.784-0.001-0.0010.0000.0000.0000.000
127A350LEU0-0.021-0.02068.0210.0010.0010.0000.0000.0000.000
128A351ASP-1-0.724-0.88669.508-0.008-0.0080.0000.0000.0000.000
129A352GLN0-0.024-0.03666.0810.0000.0000.0000.0000.0000.000
130A353ASN0-0.126-0.06971.3190.0010.0010.0000.0000.0000.000
131A354ASN00.0260.01474.6320.0000.0000.0000.0000.0000.000
132A355ARG10.8480.95175.6730.0070.0070.0000.0000.0000.000
133A356GLU-1-0.905-0.94376.632-0.010-0.0100.0000.0000.0000.000
134A357HIS00.0510.03372.8280.0000.0000.0000.0000.0000.000
135A358ALA0-0.0180.01072.0080.0000.0000.0000.0000.0000.000
136A359ILE0-0.030-0.03172.158-0.001-0.0010.0000.0000.0000.000
137A360ASP-1-0.800-0.88971.507-0.015-0.0150.0000.0000.0000.000
138A361ALA0-0.061-0.04972.0640.0000.0000.0000.0000.0000.000
139A362PHE00.0230.02566.9500.0000.0000.0000.0000.0000.000
140A363ARG10.9570.97472.0310.0170.0170.0000.0000.0000.000
141A364PRO00.0330.03068.3240.0000.0000.0000.0000.0000.000
142A365ASP-1-0.878-0.94870.285-0.022-0.0220.0000.0000.0000.000
143A366LEU00.001-0.01369.622-0.001-0.0010.0000.0000.0000.000
144A367SER0-0.0020.01069.353-0.001-0.0010.0000.0000.0000.000
145A368SER0-0.0020.01266.228-0.001-0.0010.0000.0000.0000.000
146A369ALA00.030-0.00761.9000.0000.0000.0000.0000.0000.000
147A370SER0-0.027-0.02061.812-0.001-0.0010.0000.0000.0000.000
148A371PHE0-0.025-0.02562.5810.0000.0000.0000.0000.0000.000
149A372GLN00.0140.02162.3560.0000.0000.0000.0000.0000.000
150A373ARG10.9780.99957.0370.0360.0360.0000.0000.0000.000
151A374PRO0-0.0080.00456.219-0.001-0.0010.0000.0000.0000.000
152A375GLN00.0050.00355.217-0.002-0.0020.0000.0000.0000.000
153A376SER0-0.039-0.02751.164-0.002-0.0020.0000.0000.0000.000
154A377GLU-1-0.911-0.95049.121-0.044-0.0440.0000.0000.0000.000
155A378THR0-0.028-0.03851.4370.0020.0020.0000.0000.0000.000
156A379ASN0-0.0260.01654.527-0.002-0.0020.0000.0000.0000.000
157A380VAL0-0.004-0.00457.2620.0000.0000.0000.0000.0000.000
158A381ALA00.0050.00058.9390.0010.0010.0000.0000.0000.000
159A382SER00.0130.00060.5860.0010.0010.0000.0000.0000.000
160A383GLY0-0.001-0.00464.3450.0000.0000.0000.0000.0000.000
161A384CYS0-0.0060.01666.4370.0000.0000.0000.0000.0000.000
162A385PRO00.0520.01765.9210.0000.0000.0000.0000.0000.000
163A386LEU0-0.0260.01566.9440.0000.0000.0000.0000.0000.000
164A387PHE0-0.0150.00867.4110.0010.0010.0000.0000.0000.000
165A388PHE00.0730.01968.8460.0010.0010.0000.0000.0000.000
166A389PRO0-0.0020.00468.8980.0000.0000.0000.0000.0000.000
167A390LEU00.038-0.00664.3830.0010.0010.0000.0000.0000.000
168A391SER0-0.036-0.01168.4020.0010.0010.0000.0000.0000.000
169A392LYS10.9050.94771.1800.0090.0090.0000.0000.0000.000
170A393LEU00.0290.03364.7800.0000.0000.0000.0000.0000.000
171A394GLN00.017-0.01065.0460.0000.0000.0000.0000.0000.000
172A395SER0-0.020-0.00669.5140.0010.0010.0000.0000.0000.000
173A396PRO00.0820.03073.0600.0000.0000.0000.0000.0000.000
174A397LYS10.9220.96175.0780.0060.0060.0000.0000.0000.000
175A398HIS0-0.036-0.01273.7370.0000.0000.0000.0000.0000.000
176A399ALA0-0.043-0.02371.4880.0000.0000.0000.0000.0000.000
177A400TYR0-0.0060.00168.9820.0000.0000.0000.0000.0000.000
178A401VAL0-0.034-0.00964.353-0.001-0.0010.0000.0000.0000.000
179A402LYS10.8960.95066.0490.0070.0070.0000.0000.0000.000
180A403ASP-1-0.846-0.92363.308-0.005-0.0050.0000.0000.0000.000
181A404ASP-1-0.834-0.90559.433-0.009-0.0090.0000.0000.0000.000
182A405THR0-0.048-0.03860.745-0.001-0.0010.0000.0000.0000.000
183A406MET0-0.0060.00862.1000.0000.0000.0000.0000.0000.000
184A407PHE00.001-0.00862.480-0.001-0.0010.0000.0000.0000.000
185A408LEU00.0000.00861.8580.0000.0000.0000.0000.0000.000
186A409LYS10.9800.98864.1690.0140.0140.0000.0000.0000.000
187A410CYS0-0.034-0.00364.4090.0000.0000.0000.0000.0000.000
188A411ILE00.008-0.00466.4540.0000.0000.0000.0000.0000.000
189A412VAL0-0.029-0.02865.3130.0000.0000.0000.0000.0000.000
190A413GLU-1-0.942-0.97168.396-0.018-0.0180.0000.0000.0000.000
191A414THR00.0300.01068.194-0.001-0.0010.0000.0000.0000.000
192A415SER00.0090.01170.8610.0000.0000.0000.0000.0000.000