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: 5265Z

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2006574.2676
FMO2-HF: Nuclear repulsion 1928734.319061
FMO2-HF: Total energy -77839.948539
FMO2-MP2: Total energy -78064.915681


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.
-18.848-9.1733.061-5.434-7.301-0.036
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 : 0.043 / q_NPA : 0.025
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].
3A226ARG10.9680.9923.406-5.662-3.0130.020-1.244-1.4240.007
4A227GLU-1-0.885-0.9472.486-13.363-7.6152.863-3.858-4.753-0.044
5A228ARG10.8450.9192.722-0.3300.9480.178-0.332-1.1240.001
6A229ILE00.0270.0045.5380.1590.1590.0000.0000.0000.000
7A230LEU00.0080.0077.8180.0080.0080.0000.0000.0000.000
8A231SER0-0.012-0.0206.743-0.036-0.0360.0000.0000.0000.000
9A232LEU0-0.050-0.0339.3090.0430.0430.0000.0000.0000.000
10A233GLU-1-0.921-0.94611.6890.1790.1790.0000.0000.0000.000
11A234GLN0-0.030-0.02512.272-0.025-0.0250.0000.0000.0000.000
12A235ARG10.9770.98912.6250.2710.2710.0000.0000.0000.000
13A236VAL0-0.0080.00515.2950.0130.0130.0000.0000.0000.000
14A237VAL00.0160.01117.2380.0080.0080.0000.0000.0000.000
15A238GLU-1-0.910-0.95916.260-0.201-0.2010.0000.0000.0000.000
16A239LEU0-0.043-0.03718.3200.0070.0070.0000.0000.0000.000
17A240GLN00.0010.00721.3060.0070.0070.0000.0000.0000.000
18A241GLN0-0.0010.00722.949-0.002-0.0020.0000.0000.0000.000
19A242THR0-0.024-0.01323.0830.0030.0030.0000.0000.0000.000
20A243LEU0-0.008-0.00825.2220.0020.0020.0000.0000.0000.000
21A244ALA00.0540.03127.1120.0040.0040.0000.0000.0000.000
22A245GLN0-0.033-0.01527.334-0.001-0.0010.0000.0000.0000.000
23A246LYS10.9020.93927.9220.0580.0580.0000.0000.0000.000
24A247ASP-1-0.893-0.92831.328-0.005-0.0050.0000.0000.0000.000
25A248GLN0-0.001-0.00633.064-0.002-0.0020.0000.0000.0000.000
26A249ALA0-0.070-0.03534.1810.0010.0010.0000.0000.0000.000
27A250LEU00.0270.01235.4560.0000.0000.0000.0000.0000.000
28A251GLY00.0880.04937.2770.0020.0020.0000.0000.0000.000
29A252LYS10.9060.94538.8080.0280.0280.0000.0000.0000.000
30A253LEU0-0.016-0.00339.4050.0000.0000.0000.0000.0000.000
31A254GLU-1-0.819-0.88741.407-0.005-0.0050.0000.0000.0000.000
32A255GLN00.0140.00543.2990.0010.0010.0000.0000.0000.000
33A256SER0-0.023-0.01944.4150.0000.0000.0000.0000.0000.000
34A257LEU0-0.031-0.00445.7100.0000.0000.0000.0000.0000.000
35A258ARG10.8730.91344.7690.0060.0060.0000.0000.0000.000
36A259LEU0-0.073-0.04148.2220.0010.0010.0000.0000.0000.000
37A260MET0-0.048-0.02550.043-0.001-0.0010.0000.0000.0000.000
38A261GLU-1-0.951-0.97350.659-0.008-0.0080.0000.0000.0000.000
39A262GLU-1-0.987-1.00453.522-0.005-0.0050.0000.0000.0000.000
40A263ALA0-0.0330.00854.7460.0000.0000.0000.0000.0000.000
41A264SER0-0.003-0.02256.6080.0000.0000.0000.0000.0000.000
42A265PHE0-0.009-0.02555.990-0.001-0.0010.0000.0000.0000.000
43A266ASP-1-0.797-0.87961.913-0.008-0.0080.0000.0000.0000.000
44A267GLY00.0090.01964.1190.0000.0000.0000.0000.0000.000
45A268THR0-0.123-0.07165.5300.0010.0010.0000.0000.0000.000
46A269PHE00.0470.02857.9030.0000.0000.0000.0000.0000.000
47A270LEU0-0.034-0.02262.3090.0010.0010.0000.0000.0000.000
48A271TRP00.0350.01955.9480.0000.0000.0000.0000.0000.000
49A272LYS10.9710.99059.1240.0000.0000.0000.0000.0000.000
50A273ILE00.0080.01257.4850.0000.0000.0000.0000.0000.000
51A274THR00.0520.00755.6060.0010.0010.0000.0000.0000.000
52A275ASN0-0.033-0.00554.7240.0010.0010.0000.0000.0000.000
53A276VAL00.0330.02657.5170.0000.0000.0000.0000.0000.000
54A277THR00.033-0.00759.9470.0000.0000.0000.0000.0000.000
55A278ARG10.8700.93150.779-0.008-0.0080.0000.0000.0000.000
56A279ARG10.9170.94451.953-0.002-0.0020.0000.0000.0000.000
57A280CYS0-0.032-0.00956.179-0.001-0.0010.0000.0000.0000.000
58A281HIS00.0240.00157.001-0.001-0.0010.0000.0000.0000.000
59A282GLU-1-0.847-0.90351.6620.0090.0090.0000.0000.0000.000
60A283SER0-0.009-0.00954.6940.0000.0000.0000.0000.0000.000
61A284ALA0-0.047-0.00556.0730.0000.0000.0000.0000.0000.000
62A285CYS0-0.0530.00452.8020.0010.0010.0000.0000.0000.000
63A286GLY00.004-0.01252.573-0.001-0.0010.0000.0000.0000.000
64A287ARG10.8290.89249.566-0.012-0.0120.0000.0000.0000.000
65A288THR00.015-0.00248.8460.0000.0000.0000.0000.0000.000
66A289VAL00.0410.02851.2010.0000.0000.0000.0000.0000.000
67A290SER0-0.030-0.00853.2160.0000.0000.0000.0000.0000.000
68A291LEU0-0.027-0.01252.9330.0000.0000.0000.0000.0000.000
69A292PHE00.0530.00451.6900.0000.0000.0000.0000.0000.000
70A293SER0-0.032-0.01353.3380.0000.0000.0000.0000.0000.000
71A294PRO00.0530.02453.045-0.001-0.0010.0000.0000.0000.000
72A295ALA0-0.008-0.00153.4560.0000.0000.0000.0000.0000.000
73A296PHE0-0.017-0.00855.2230.0000.0000.0000.0000.0000.000
74A297TYR00.021-0.00353.665-0.001-0.0010.0000.0000.0000.000
75A298THR00.008-0.00260.4990.0000.0000.0000.0000.0000.000
76A299ALA00.0240.01262.5150.0000.0000.0000.0000.0000.000
77A300LYS10.9320.98556.1240.0180.0180.0000.0000.0000.000
78A301TYR0-0.018-0.01557.560-0.001-0.0010.0000.0000.0000.000
79A302GLY00.0040.00360.6630.0000.0000.0000.0000.0000.000
80A303TYR0-0.019-0.03860.0580.0000.0000.0000.0000.0000.000
81A304LYS10.8790.93351.3190.0190.0190.0000.0000.0000.000
82A305LEU0-0.033-0.00858.1130.0000.0000.0000.0000.0000.000
83A306CYS00.0110.01955.4150.0000.0000.0000.0000.0000.000
84A307LEU00.0100.00857.5160.0000.0000.0000.0000.0000.000
85A308ARG10.9020.95554.1250.0040.0040.0000.0000.0000.000
86A309LEU0-0.004-0.00157.4010.0000.0000.0000.0000.0000.000
87A310TYR0-0.038-0.03056.8170.0000.0000.0000.0000.0000.000
88A311LEU00.0420.01457.0020.0000.0000.0000.0000.0000.000
89A312ASN00.0350.00659.2890.0000.0000.0000.0000.0000.000
90A313GLY00.0710.04361.1540.0000.0000.0000.0000.0000.000
91A314ASP-1-0.897-0.95359.333-0.002-0.0020.0000.0000.0000.000
92A315GLY00.0730.04161.8900.0000.0000.0000.0000.0000.000
93A316THR00.014-0.01364.1220.0000.0000.0000.0000.0000.000
94A317GLY00.0450.03566.2110.0000.0000.0000.0000.0000.000
95A318LYS10.8040.90858.807-0.002-0.0020.0000.0000.0000.000
96A319ARG10.9080.95260.626-0.005-0.0050.0000.0000.0000.000
97A320THR0-0.010-0.01364.5980.0010.0010.0000.0000.0000.000
98A321HIS00.0120.01866.4870.0000.0000.0000.0000.0000.000
99A322LEU0-0.0130.01962.9520.0000.0000.0000.0000.0000.000
100A323SER0-0.053-0.03862.4900.0000.0000.0000.0000.0000.000
101A324LEU0-0.0070.00561.9990.0000.0000.0000.0000.0000.000
102A325PHE0-0.019-0.01260.6740.0000.0000.0000.0000.0000.000
103A326ILE00.0510.02361.1910.0000.0000.0000.0000.0000.000
104A327VAL0-0.027-0.03155.6260.0000.0000.0000.0000.0000.000
105A328ILE0-0.0020.01358.6550.0000.0000.0000.0000.0000.000
106A329MET0-0.022-0.01951.9850.0000.0000.0000.0000.0000.000
107A330ARG10.9160.96248.7750.0230.0230.0000.0000.0000.000
108A331GLY00.0150.00753.5790.0000.0000.0000.0000.0000.000
109A332GLU-1-0.924-0.96551.038-0.025-0.0250.0000.0000.0000.000
110A333TYR00.014-0.00654.3780.0000.0000.0000.0000.0000.000
111A334ASP-1-0.808-0.90257.325-0.017-0.0170.0000.0000.0000.000
112A335ALA0-0.088-0.04758.2170.0010.0010.0000.0000.0000.000
113A336LEU0-0.009-0.00560.0790.0000.0000.0000.0000.0000.000
114A337LEU0-0.0370.00761.4980.0010.0010.0000.0000.0000.000
115A338PRO00.0090.00264.5890.0000.0000.0000.0000.0000.000
116A339TRP0-0.0180.01760.6940.0000.0000.0000.0000.0000.000
117A340PRO00.015-0.01865.9030.0000.0000.0000.0000.0000.000
118A341PHE00.0280.01664.3380.0000.0000.0000.0000.0000.000
119A342ARG10.8610.93166.4110.0100.0100.0000.0000.0000.000
120A343ASN0-0.062-0.02268.0650.0000.0000.0000.0000.0000.000
121A344LYS10.9610.98669.8010.0060.0060.0000.0000.0000.000
122A345VAL0-0.0110.00766.4340.0000.0000.0000.0000.0000.000
123A346THR0-0.032-0.01869.3560.0010.0010.0000.0000.0000.000
124A347PHE0-0.010-0.00564.7250.0000.0000.0000.0000.0000.000
125A348MET00.015-0.00268.2980.0000.0000.0000.0000.0000.000
126A349LEU0-0.0140.00966.6390.0000.0000.0000.0000.0000.000
127A350LEU0-0.014-0.01867.9250.0000.0000.0000.0000.0000.000
128A351ASP-1-0.733-0.88769.5490.0020.0020.0000.0000.0000.000
129A352GLN0-0.035-0.04366.3820.0000.0000.0000.0000.0000.000
130A353ASN0-0.095-0.04071.4780.0010.0010.0000.0000.0000.000
131A354ASN00.0310.02074.8160.0000.0000.0000.0000.0000.000
132A355ARG10.8520.90876.322-0.002-0.0020.0000.0000.0000.000
133A356GLU-1-0.894-0.93476.674-0.001-0.0010.0000.0000.0000.000
134A357HIS00.0470.03872.9100.0000.0000.0000.0000.0000.000
135A358ALA0-0.0010.01671.9060.0000.0000.0000.0000.0000.000
136A359ILE0-0.034-0.02772.0070.0000.0000.0000.0000.0000.000
137A360ASP-1-0.788-0.87571.151-0.003-0.0030.0000.0000.0000.000
138A361ALA0-0.055-0.04871.7380.0000.0000.0000.0000.0000.000
139A362PHE00.0280.02366.4490.0000.0000.0000.0000.0000.000
140A363ARG10.8540.91771.6620.0070.0070.0000.0000.0000.000
141A364PRO0-0.0110.01467.9720.0000.0000.0000.0000.0000.000
142A365ASP-1-0.782-0.89069.842-0.008-0.0080.0000.0000.0000.000
143A366LEU0-0.004-0.02269.2550.0000.0000.0000.0000.0000.000
144A367SER0-0.027-0.01969.042-0.001-0.0010.0000.0000.0000.000
145A368SER0-0.0060.01165.8090.0000.0000.0000.0000.0000.000
146A369ALA00.034-0.00361.5600.0000.0000.0000.0000.0000.000
147A370SER0-0.031-0.01961.429-0.001-0.0010.0000.0000.0000.000
148A371PHE0-0.019-0.02262.2440.0000.0000.0000.0000.0000.000
149A372GLN0-0.0030.00962.227-0.001-0.0010.0000.0000.0000.000
150A373ARG10.9821.00956.8260.0200.0200.0000.0000.0000.000
151A374PRO00.0010.00956.0570.0000.0000.0000.0000.0000.000
152A375GLN0-0.028-0.02055.103-0.002-0.0020.0000.0000.0000.000
153A376SER0-0.030-0.01850.910-0.001-0.0010.0000.0000.0000.000
154A377GLU-1-0.819-0.89348.734-0.021-0.0210.0000.0000.0000.000
155A378THR0-0.036-0.03151.1750.0010.0010.0000.0000.0000.000
156A379ASN0-0.0290.00254.195-0.001-0.0010.0000.0000.0000.000
157A380VAL00.009-0.00356.8430.0000.0000.0000.0000.0000.000
158A381ALA0-0.0040.00358.4400.0000.0000.0000.0000.0000.000
159A382SER00.006-0.00360.1000.0000.0000.0000.0000.0000.000
160A383GLY0-0.004-0.00763.8550.0000.0000.0000.0000.0000.000
161A384CYS0-0.023-0.00366.0180.0000.0000.0000.0000.0000.000
162A385PRO00.0350.01165.4990.0000.0000.0000.0000.0000.000
163A386LEU0-0.024-0.00866.5020.0010.0010.0000.0000.0000.000
164A387PHE0-0.0150.00866.8140.0000.0000.0000.0000.0000.000
165A388PHE00.0790.01968.6400.0000.0000.0000.0000.0000.000
166A389PRO0-0.0150.00768.6590.0000.0000.0000.0000.0000.000
167A390LEU00.0420.00064.4320.0000.0000.0000.0000.0000.000
168A391SER0-0.026-0.01068.2290.0000.0000.0000.0000.0000.000
169A392LYS10.8800.93871.051-0.004-0.0040.0000.0000.0000.000
170A393LEU00.0480.03964.6310.0000.0000.0000.0000.0000.000
171A394GLN00.016-0.01065.1430.0000.0000.0000.0000.0000.000
172A395SER0-0.028-0.00369.5560.0010.0010.0000.0000.0000.000
173A396PRO00.0820.02973.3060.0000.0000.0000.0000.0000.000
174A397LYS10.9090.95675.201-0.004-0.0040.0000.0000.0000.000
175A398HIS0-0.0010.02273.7750.0000.0000.0000.0000.0000.000
176A399ALA0-0.055-0.02571.6110.0000.0000.0000.0000.0000.000
177A400TYR0-0.017-0.01068.9650.0000.0000.0000.0000.0000.000
178A401VAL0-0.045-0.01564.3900.0000.0000.0000.0000.0000.000
179A402LYS10.8750.93066.221-0.004-0.0040.0000.0000.0000.000
180A403ASP-1-0.850-0.92563.6820.0050.0050.0000.0000.0000.000
181A404ASP-1-0.831-0.90159.8340.0070.0070.0000.0000.0000.000
182A405THR0-0.046-0.03560.9190.0000.0000.0000.0000.0000.000
183A406MET00.0080.01662.0700.0000.0000.0000.0000.0000.000
184A407PHE00.009-0.00562.6590.0000.0000.0000.0000.0000.000
185A408LEU00.0020.01161.8750.0000.0000.0000.0000.0000.000
186A409LYS10.9770.98664.1020.0040.0040.0000.0000.0000.000
187A410CYS0-0.042-0.00564.2200.0000.0000.0000.0000.0000.000
188A411ILE00.005-0.00366.2630.0000.0000.0000.0000.0000.000
189A412VAL0-0.013-0.02465.0300.0000.0000.0000.0000.0000.000
190A413GLU-1-0.840-0.91468.151-0.008-0.0080.0000.0000.0000.000
191A414THR00.0370.02068.0880.0000.0000.0000.0000.0000.000
192A415SER00.0110.01470.6910.0000.0000.0000.0000.0000.000