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: YZ812

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2006028.759757
FMO2-HF: Nuclear repulsion 1928188.049049
FMO2-HF: Total energy -77840.710708
FMO2-MP2: Total energy -78065.559105


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.
-19.244-12.0368.854-7.604-8.458-0.067
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 : 0.021 / q_NPA : 0.004
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].
3A226ARG10.9520.9922.966-2.5060.1820.082-1.259-1.5120.005
4A227GLU-1-0.814-0.9172.056-18.498-15.1418.700-6.031-6.025-0.073
5A228ARG10.8230.9012.9570.4311.5940.072-0.314-0.9210.001
6A229ILE00.0370.0155.7040.4080.4080.0000.0000.0000.000
7A230LEU0-0.004-0.0037.0760.1420.1420.0000.0000.0000.000
8A231SER0-0.002-0.0166.9660.2140.2140.0000.0000.0000.000
9A232LEU0-0.042-0.0229.4870.1760.1760.0000.0000.0000.000
10A233GLU-1-0.906-0.94711.667-0.125-0.1250.0000.0000.0000.000
11A234GLN0-0.066-0.03212.610-0.025-0.0250.0000.0000.0000.000
12A235ARG10.8720.91612.0270.4670.4670.0000.0000.0000.000
13A236VAL00.0100.01315.0390.0560.0560.0000.0000.0000.000
14A237VAL00.0130.00717.4420.0360.0360.0000.0000.0000.000
15A238GLU-1-0.824-0.90615.499-0.394-0.3940.0000.0000.0000.000
16A239LEU0-0.0150.00918.2880.0310.0310.0000.0000.0000.000
17A240GLN00.0020.00321.1780.0140.0140.0000.0000.0000.000
18A241GLN0-0.0060.00122.9630.0130.0130.0000.0000.0000.000
19A242THR0-0.051-0.05122.7210.0180.0180.0000.0000.0000.000
20A243LEU00.0100.01125.1180.0110.0110.0000.0000.0000.000
21A244ALA00.0430.01926.9980.0110.0110.0000.0000.0000.000
22A245GLN00.0080.01127.8070.0060.0060.0000.0000.0000.000
23A246LYS10.8510.91427.4250.1380.1380.0000.0000.0000.000
24A247ASP-1-0.895-0.93131.296-0.062-0.0620.0000.0000.0000.000
25A248GLN0-0.007-0.00533.0720.0040.0040.0000.0000.0000.000
26A249ALA0-0.056-0.03034.1050.0050.0050.0000.0000.0000.000
27A250LEU00.0260.01635.4450.0040.0040.0000.0000.0000.000
28A251GLY00.0760.03937.2880.0040.0040.0000.0000.0000.000
29A252LYS10.9130.94938.1990.0800.0800.0000.0000.0000.000
30A253LEU0-0.011-0.00339.5580.0020.0020.0000.0000.0000.000
31A254GLU-1-0.832-0.90041.385-0.040-0.0400.0000.0000.0000.000
32A255GLN00.0270.01143.2600.0030.0030.0000.0000.0000.000
33A256SER0-0.040-0.03344.2400.0010.0010.0000.0000.0000.000
34A257LEU0-0.0310.00645.7590.0010.0010.0000.0000.0000.000
35A258ARG10.8870.92944.9210.0410.0410.0000.0000.0000.000
36A259LEU0-0.071-0.04047.4380.0020.0020.0000.0000.0000.000
37A260MET0-0.043-0.01650.3170.0000.0000.0000.0000.0000.000
38A261GLU-1-0.941-0.98050.129-0.033-0.0330.0000.0000.0000.000
39A262GLU-1-0.981-0.99953.418-0.030-0.0300.0000.0000.0000.000
40A263ALA0-0.0400.00054.6350.0010.0010.0000.0000.0000.000
41A264SER0-0.018-0.02256.5260.0010.0010.0000.0000.0000.000
42A265PHE0-0.002-0.02755.731-0.001-0.0010.0000.0000.0000.000
43A266ASP-1-0.799-0.87261.702-0.026-0.0260.0000.0000.0000.000
44A267GLY00.0170.01364.1950.0010.0010.0000.0000.0000.000
45A268THR0-0.143-0.08465.4890.0010.0010.0000.0000.0000.000
46A269PHE00.0650.03057.809-0.001-0.0010.0000.0000.0000.000
47A270LEU0-0.028-0.02362.0370.0010.0010.0000.0000.0000.000
48A271TRP00.0330.03155.7180.0000.0000.0000.0000.0000.000
49A272LYS10.9650.99159.1830.0220.0220.0000.0000.0000.000
50A273ILE0-0.0110.00057.280-0.001-0.0010.0000.0000.0000.000
51A274THR00.0550.02055.7280.0010.0010.0000.0000.0000.000
52A275ASN0-0.0080.00554.377-0.001-0.0010.0000.0000.0000.000
53A276VAL00.0430.03057.268-0.001-0.0010.0000.0000.0000.000
54A277THR0-0.001-0.02959.992-0.001-0.0010.0000.0000.0000.000
55A278ARG10.8290.89550.7020.0250.0250.0000.0000.0000.000
56A279ARG10.9200.94551.9020.0280.0280.0000.0000.0000.000
57A280CYS0-0.034-0.01656.456-0.001-0.0010.0000.0000.0000.000
58A281HIS00.0200.01356.788-0.001-0.0010.0000.0000.0000.000
59A282GLU-1-0.815-0.88351.586-0.028-0.0280.0000.0000.0000.000
60A283SER0-0.048-0.03754.250-0.001-0.0010.0000.0000.0000.000
61A284ALA0-0.029-0.00656.1690.0000.0000.0000.0000.0000.000
62A285CYS0-0.0440.01052.6480.0000.0000.0000.0000.0000.000
63A286GLY00.0220.00052.342-0.001-0.0010.0000.0000.0000.000
64A287ARG10.8470.90049.0530.0260.0260.0000.0000.0000.000
65A288THR00.007-0.01049.2240.0010.0010.0000.0000.0000.000
66A289VAL00.0290.02851.5170.0010.0010.0000.0000.0000.000
67A290SER0-0.033-0.01353.5940.0010.0010.0000.0000.0000.000
68A291LEU0-0.0200.00252.848-0.002-0.0020.0000.0000.0000.000
69A292PHE00.058-0.00452.0540.0010.0010.0000.0000.0000.000
70A293SER0-0.026-0.01753.5380.0000.0000.0000.0000.0000.000
71A294PRO00.0550.02753.026-0.002-0.0020.0000.0000.0000.000
72A295ALA0-0.0040.02153.3090.0010.0010.0000.0000.0000.000
73A296PHE0-0.029-0.01655.0390.0010.0010.0000.0000.0000.000
74A297TYR00.0300.00953.714-0.002-0.0020.0000.0000.0000.000
75A298THR0-0.018-0.02060.4800.0010.0010.0000.0000.0000.000
76A299ALA00.0400.02362.6390.0010.0010.0000.0000.0000.000
77A300LYS10.9290.96956.3240.0360.0360.0000.0000.0000.000
78A301TYR0-0.024-0.01357.860-0.002-0.0020.0000.0000.0000.000
79A302GLY00.0240.02060.8120.0000.0000.0000.0000.0000.000
80A303TYR0-0.031-0.04759.980-0.001-0.0010.0000.0000.0000.000
81A304LYS10.8640.94051.2330.0490.0490.0000.0000.0000.000
82A305LEU0-0.043-0.01057.7130.0000.0000.0000.0000.0000.000
83A306CYS0-0.002-0.00355.345-0.001-0.0010.0000.0000.0000.000
84A307LEU00.0010.00357.4230.0010.0010.0000.0000.0000.000
85A308ARG10.8840.94154.6610.0350.0350.0000.0000.0000.000
86A309LEU00.0160.00957.5460.0010.0010.0000.0000.0000.000
87A310TYR0-0.026-0.01557.294-0.002-0.0020.0000.0000.0000.000
88A311LEU00.019-0.00557.2460.0010.0010.0000.0000.0000.000
89A312ASN00.0240.00959.4000.0010.0010.0000.0000.0000.000
90A313GLY00.0570.02961.2710.0000.0000.0000.0000.0000.000
91A314ASP-1-0.867-0.94959.954-0.032-0.0320.0000.0000.0000.000
92A315GLY00.0480.02662.1090.0010.0010.0000.0000.0000.000
93A316THR00.010-0.01264.1370.0000.0000.0000.0000.0000.000
94A317GLY00.0420.03366.1920.0010.0010.0000.0000.0000.000
95A318LYS10.7790.90258.5840.0280.0280.0000.0000.0000.000
96A319ARG10.9320.96660.8800.0240.0240.0000.0000.0000.000
97A320THR0-0.015-0.01764.5200.0010.0010.0000.0000.0000.000
98A321HIS00.0090.00966.7110.0010.0010.0000.0000.0000.000
99A322LEU0-0.0030.01663.063-0.001-0.0010.0000.0000.0000.000
100A323SER0-0.061-0.03662.5480.0000.0000.0000.0000.0000.000
101A324LEU0-0.0120.00062.074-0.001-0.0010.0000.0000.0000.000
102A325PHE0-0.011-0.00960.6160.0000.0000.0000.0000.0000.000
103A326ILE00.0410.01761.0620.0000.0000.0000.0000.0000.000
104A327VAL0-0.032-0.02955.5580.0000.0000.0000.0000.0000.000
105A328ILE00.0090.01558.5480.0000.0000.0000.0000.0000.000
106A329MET0-0.020-0.00752.085-0.001-0.0010.0000.0000.0000.000
107A330ARG10.8620.91248.2540.0560.0560.0000.0000.0000.000
108A331GLY00.0290.01253.520-0.001-0.0010.0000.0000.0000.000
109A332GLU-1-0.889-0.95051.034-0.050-0.0500.0000.0000.0000.000
110A333TYR00.007-0.00454.3810.0000.0000.0000.0000.0000.000
111A334ASP-1-0.803-0.91157.611-0.040-0.0400.0000.0000.0000.000
112A335ALA0-0.090-0.04758.2260.0010.0010.0000.0000.0000.000
113A336LEU0-0.011-0.00160.1340.0010.0010.0000.0000.0000.000
114A337LEU0-0.0360.00561.3970.0010.0010.0000.0000.0000.000
115A338PRO00.0120.00564.6290.0000.0000.0000.0000.0000.000
116A339TRP0-0.0180.01160.675-0.001-0.0010.0000.0000.0000.000
117A340PRO00.016-0.00265.6270.0010.0010.0000.0000.0000.000
118A341PHE00.0110.00964.2900.0010.0010.0000.0000.0000.000
119A342ARG10.8390.90366.3720.0290.0290.0000.0000.0000.000
120A343ASN0-0.039-0.01767.9380.0000.0000.0000.0000.0000.000
121A344LYS10.8800.92869.6920.0210.0210.0000.0000.0000.000
122A345VAL00.0080.01666.5050.0000.0000.0000.0000.0000.000
123A346THR0-0.007-0.01868.9550.0010.0010.0000.0000.0000.000
124A347PHE0-0.008-0.00764.661-0.001-0.0010.0000.0000.0000.000
125A348MET00.0170.00667.9660.0010.0010.0000.0000.0000.000
126A349LEU0-0.0080.01066.469-0.001-0.0010.0000.0000.0000.000
127A350LEU0-0.001-0.00567.8920.0010.0010.0000.0000.0000.000
128A351ASP-1-0.751-0.89369.774-0.014-0.0140.0000.0000.0000.000
129A352GLN0-0.056-0.04366.3730.0000.0000.0000.0000.0000.000
130A353ASN0-0.074-0.03471.1630.0010.0010.0000.0000.0000.000
131A354ASN00.0350.01974.5930.0000.0000.0000.0000.0000.000
132A355ARG10.8430.90776.5930.0130.0130.0000.0000.0000.000
133A356GLU-1-0.875-0.92876.868-0.015-0.0150.0000.0000.0000.000
134A357HIS00.0300.03472.956-0.001-0.0010.0000.0000.0000.000
135A358ALA00.0090.02371.7900.0000.0000.0000.0000.0000.000
136A359ILE0-0.035-0.02771.835-0.001-0.0010.0000.0000.0000.000
137A360ASP-1-0.778-0.87770.963-0.021-0.0210.0000.0000.0000.000
138A361ALA0-0.057-0.04871.9840.0000.0000.0000.0000.0000.000
139A362PHE00.0280.03166.5100.0000.0000.0000.0000.0000.000
140A363ARG10.8500.88971.6370.0220.0220.0000.0000.0000.000
141A364PRO0-0.0050.01267.9900.0000.0000.0000.0000.0000.000
142A365ASP-1-0.775-0.88069.959-0.026-0.0260.0000.0000.0000.000
143A366LEU0-0.044-0.03269.464-0.001-0.0010.0000.0000.0000.000
144A367SER00.019-0.01269.242-0.001-0.0010.0000.0000.0000.000
145A368SER0-0.0270.00765.373-0.001-0.0010.0000.0000.0000.000
146A369ALA00.0600.01561.3160.0000.0000.0000.0000.0000.000
147A370SER0-0.029-0.01961.456-0.001-0.0010.0000.0000.0000.000
148A371PHE0-0.010-0.00561.9710.0000.0000.0000.0000.0000.000
149A372GLN00.0040.00662.1170.0000.0000.0000.0000.0000.000
150A373ARG10.9831.00656.5320.0430.0430.0000.0000.0000.000
151A374PRO00.0090.02555.917-0.001-0.0010.0000.0000.0000.000
152A375GLN0-0.054-0.02054.797-0.002-0.0020.0000.0000.0000.000
153A376SER0-0.010-0.01851.188-0.003-0.0030.0000.0000.0000.000
154A377GLU-1-0.799-0.89448.951-0.052-0.0520.0000.0000.0000.000
155A378THR00.0000.00151.3540.0010.0010.0000.0000.0000.000
156A379ASN0-0.024-0.00454.279-0.002-0.0020.0000.0000.0000.000
157A380VAL0-0.009-0.01056.9660.0000.0000.0000.0000.0000.000
158A381ALA00.0160.00758.1730.0010.0010.0000.0000.0000.000
159A382SER00.0040.00259.9250.0010.0010.0000.0000.0000.000
160A383GLY00.0160.00763.7130.0000.0000.0000.0000.0000.000
161A384CYS0-0.037-0.01566.0750.0000.0000.0000.0000.0000.000
162A385PRO00.0430.00765.4800.0000.0000.0000.0000.0000.000
163A386LEU0-0.0170.00066.4890.0000.0000.0000.0000.0000.000
164A387PHE0-0.0200.00766.7710.0010.0010.0000.0000.0000.000
165A388PHE00.0650.02368.6540.0010.0010.0000.0000.0000.000
166A389PRO00.0000.01768.688-0.001-0.0010.0000.0000.0000.000
167A390LEU00.0360.01264.4170.0010.0010.0000.0000.0000.000
168A391SER0-0.018-0.01268.1090.0000.0000.0000.0000.0000.000
169A392LYS10.8770.93370.9070.0150.0150.0000.0000.0000.000
170A393LEU00.0380.02964.4210.0000.0000.0000.0000.0000.000
171A394GLN00.0320.00065.3650.0000.0000.0000.0000.0000.000
172A395SER0-0.046-0.02269.7410.0010.0010.0000.0000.0000.000
173A396PRO00.0560.01773.5790.0000.0000.0000.0000.0000.000
174A397LYS10.9010.95975.1480.0110.0110.0000.0000.0000.000
175A398HIS00.0350.04073.7890.0000.0000.0000.0000.0000.000
176A399ALA0-0.025-0.01171.2870.0000.0000.0000.0000.0000.000
177A400TYR0-0.039-0.03469.2330.0000.0000.0000.0000.0000.000
178A401VAL0-0.058-0.02264.692-0.001-0.0010.0000.0000.0000.000
179A402LYS10.8780.93366.0950.0140.0140.0000.0000.0000.000
180A403ASP-1-0.844-0.92264.095-0.014-0.0140.0000.0000.0000.000
181A404ASP-1-0.809-0.87459.515-0.019-0.0190.0000.0000.0000.000
182A405THR0-0.042-0.03460.608-0.002-0.0020.0000.0000.0000.000
183A406MET00.0140.02061.9560.0010.0010.0000.0000.0000.000
184A407PHE00.024-0.00362.632-0.001-0.0010.0000.0000.0000.000
185A408LEU00.0120.01961.8970.0010.0010.0000.0000.0000.000
186A409LYS10.9360.96164.1680.0210.0210.0000.0000.0000.000
187A410CYS0-0.056-0.01864.2220.0000.0000.0000.0000.0000.000
188A411ILE00.006-0.00966.2090.0000.0000.0000.0000.0000.000
189A412VAL00.0000.01364.7930.0000.0000.0000.0000.0000.000
190A413GLU-1-0.760-0.84068.020-0.023-0.0230.0000.0000.0000.000
191A414THR00.0620.04768.017-0.001-0.0010.0000.0000.0000.000
192A415SER0-0.074-0.03570.4410.0010.0010.0000.0000.0000.000