FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

tag_button

FMODB ID: YZQY2

Calculation Name: 5INT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5INT

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0F7

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2183938.288933
FMO2-HF: Nuclear repulsion 2106853.702637
FMO2-HF: Total energy -77084.586296
FMO2-MP2: Total energy -77307.614785


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:182:SER)


Summations of interaction energy for fragment #1(A:182:SER)
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.
-7.798-1.90.888-3.07-3.714-0.016
Interaction energy analysis for fragmet #1(A:182:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.027
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].
3A184ALA00.0280.0282.809-1.6411.9440.014-1.820-1.778-0.003
4A185LEU0-0.013-0.0024.6330.4360.569-0.001-0.013-0.1190.000
5A186GLN00.0410.0155.901-0.927-0.9270.0000.0000.0000.000
6A187GLY0-0.043-0.0148.2980.4540.4540.0000.0000.0000.000
7A188LYS10.9350.98510.7150.9000.9000.0000.0000.0000.000
8A189ARG10.9600.99612.3900.4130.4130.0000.0000.0000.000
9A190ILE00.004-0.00111.1800.0800.0800.0000.0000.0000.000
10A191LEU00.0220.01415.218-0.005-0.0050.0000.0000.0000.000
11A192ILE0-0.017-0.01114.2650.0170.0170.0000.0000.0000.000
12A193THR00.0760.05718.8150.0220.0220.0000.0000.0000.000
13A194ALA0-0.0180.03620.660-0.007-0.0070.0000.0000.0000.000
14A195GLY00.0200.01422.7900.0110.0110.0000.0000.0000.000
15A196PRO0-0.067-0.01225.733-0.001-0.0010.0000.0000.0000.000
16A197THR00.0530.03929.459-0.002-0.0020.0000.0000.0000.000
17A198ARG10.8620.91531.8170.1280.1280.0000.0000.0000.000
18A199GLU-1-0.796-0.90334.817-0.130-0.1300.0000.0000.0000.000
19A200LYS10.9400.95538.1270.1070.1070.0000.0000.0000.000
20A201ILE0-0.015-0.00141.1560.0000.0000.0000.0000.0000.000
21A202ASP-1-0.770-0.89144.548-0.065-0.0650.0000.0000.0000.000
22A203PRO0-0.030-0.02944.544-0.003-0.0030.0000.0000.0000.000
23A204VAL0-0.048-0.01844.137-0.002-0.0020.0000.0000.0000.000
24A205ARG10.8690.95443.5070.0620.0620.0000.0000.0000.000
25A206PHE00.0030.00036.640-0.003-0.0030.0000.0000.0000.000
26A207MET00.0080.02838.7500.0040.0040.0000.0000.0000.000
27A208THR0-0.017-0.02733.470-0.007-0.0070.0000.0000.0000.000
28A209ASN00.0250.02333.3340.0070.0070.0000.0000.0000.000
29A210PHE00.0400.00929.605-0.012-0.0120.0000.0000.0000.000
30A211SER00.0480.00127.023-0.005-0.0050.0000.0000.0000.000
31A212SER0-0.043-0.00525.013-0.009-0.0090.0000.0000.0000.000
32A213GLY00.0950.03823.0220.0050.0050.0000.0000.0000.000
33A214LYS10.9280.95620.7150.1300.1300.0000.0000.0000.000
34A215MET00.0130.02018.679-0.027-0.0270.0000.0000.0000.000
35A216GLY00.0660.03217.324-0.041-0.0410.0000.0000.0000.000
36A217TYR00.021-0.02616.597-0.061-0.0610.0000.0000.0000.000
37A218ALA0-0.019-0.00214.753-0.039-0.0390.0000.0000.0000.000
38A219ILE0-0.001-0.01412.798-0.074-0.0740.0000.0000.0000.000
39A220ALA00.0320.01211.738-0.159-0.1590.0000.0000.0000.000
40A221GLU-1-0.950-0.96810.462-0.487-0.4870.0000.0000.0000.000
41A222VAL0-0.061-0.0437.853-0.128-0.1280.0000.0000.0000.000
42A223ALA00.0410.0126.797-0.517-0.5170.0000.0000.0000.000
43A224VAL00.0300.0277.381-0.521-0.5210.0000.0000.0000.000
44A225ASN0-0.075-0.0374.757-0.485-0.437-0.001-0.010-0.0370.000
45A226LEU0-0.084-0.0322.692-4.412-2.3230.877-1.232-1.733-0.013
46A227GLY00.0610.0313.955-0.305-0.262-0.0010.005-0.0470.000
47A228ALA0-0.0240.0005.7110.9640.9640.0000.0000.0000.000
48A229GLU-1-0.972-0.9849.165-0.646-0.6460.0000.0000.0000.000
49A230VAL0-0.018-0.01111.0730.1360.1360.0000.0000.0000.000
50A231ILE00.0190.00813.8580.0830.0830.0000.0000.0000.000
51A232LEU0-0.034-0.01917.4850.0030.0030.0000.0000.0000.000
52A233VAL00.0180.00919.1510.0360.0360.0000.0000.0000.000
53A234SER0-0.004-0.00822.295-0.001-0.0010.0000.0000.0000.000
54A235GLY00.0370.04624.1170.0140.0140.0000.0000.0000.000
55A236PRO0-0.014-0.02026.556-0.007-0.0070.0000.0000.0000.000
56A237THR0-0.027-0.00524.5680.0040.0040.0000.0000.0000.000
57A238ALA0-0.020-0.01326.5870.0060.0060.0000.0000.0000.000
58A239LEU0-0.069-0.03321.0060.0110.0110.0000.0000.0000.000
59A240ASN00.0250.01220.948-0.004-0.0040.0000.0000.0000.000
60A241PRO0-0.013-0.00818.308-0.006-0.0060.0000.0000.0000.000
61A242PRO00.0150.02313.2200.0370.0370.0000.0000.0000.000
62A243LEU00.0440.01112.625-0.003-0.0030.0000.0000.0000.000
63A244HIS0-0.012-0.01810.408-0.133-0.1330.0000.0000.0000.000
64A245VAL0-0.0070.01913.210-0.079-0.0790.0000.0000.0000.000
65A246THR00.0040.01314.9540.1060.1060.0000.0000.0000.000
66A247THR0-0.017-0.01718.002-0.012-0.0120.0000.0000.0000.000
67A248VAL0-0.016-0.00720.6820.0290.0290.0000.0000.0000.000
68A249GLN0-0.019-0.01023.4890.0020.0020.0000.0000.0000.000
69A250VAL00.0150.01126.5320.0120.0120.0000.0000.0000.000
70A251GLU-1-0.909-0.97929.389-0.120-0.1200.0000.0000.0000.000
71A252SER00.0080.02432.107-0.002-0.0020.0000.0000.0000.000
72A253ALA00.026-0.01531.759-0.011-0.0110.0000.0000.0000.000
73A254GLN0-0.057-0.02132.152-0.005-0.0050.0000.0000.0000.000
74A255ASP-1-0.790-0.90231.749-0.152-0.1520.0000.0000.0000.000
75A256MET0-0.050-0.01726.240-0.016-0.0160.0000.0000.0000.000
76A257LEU0-0.034-0.02728.114-0.017-0.0170.0000.0000.0000.000
77A258GLU-1-0.924-0.95929.674-0.171-0.1710.0000.0000.0000.000
78A259ALA00.0160.00726.257-0.009-0.0090.0000.0000.0000.000
79A260VAL0-0.034-0.02424.382-0.023-0.0230.0000.0000.0000.000
80A261ILE00.012-0.00225.653-0.016-0.0160.0000.0000.0000.000
81A262GLN0-0.053-0.00725.9710.0110.0110.0000.0000.0000.000
82A263HIS0-0.028-0.02622.106-0.016-0.0160.0000.0000.0000.000
83A264TYR00.001-0.00123.027-0.037-0.0370.0000.0000.0000.000
84A265GLN00.0220.00423.835-0.013-0.0130.0000.0000.0000.000
85A266ASN0-0.067-0.03421.8370.0100.0100.0000.0000.0000.000
86A267VAL0-0.0130.00418.883-0.046-0.0460.0000.0000.0000.000
87A268ASP-1-0.842-0.93415.771-0.545-0.5450.0000.0000.0000.000
88A269VAL00.0020.00914.3660.0410.0410.0000.0000.0000.000
89A270VAL00.0030.01017.381-0.019-0.0190.0000.0000.0000.000
90A271ILE0-0.008-0.00714.6760.0290.0290.0000.0000.0000.000
91A272LYS10.9520.96419.2900.2200.2200.0000.0000.0000.000
92A273THR0-0.129-0.12019.3290.0210.0210.0000.0000.0000.000
93A274ALA00.013-0.00422.5240.0130.0130.0000.0000.0000.000
94A275ALA0-0.039-0.01326.3090.0030.0030.0000.0000.0000.000
95A276VAL00.0030.01228.2550.0100.0100.0000.0000.0000.000
96A277ALA0-0.025-0.00331.253-0.008-0.0080.0000.0000.0000.000
97A278ASP-1-0.844-0.92932.019-0.153-0.1530.0000.0000.0000.000
98A279TYR0-0.049-0.04535.0510.0050.0050.0000.0000.0000.000
99A280ARG10.9180.94637.4430.1110.1110.0000.0000.0000.000
100A281PRO00.0120.01340.4450.0040.0040.0000.0000.0000.000
101A282LYS10.9100.97243.5860.0720.0720.0000.0000.0000.000
102A283TYR0-0.027-0.01046.1620.0000.0000.0000.0000.0000.000
103A284VAL00.0300.01344.001-0.002-0.0020.0000.0000.0000.000
104A285HIS0-0.036-0.01946.6110.0040.0040.0000.0000.0000.000
105A297VAL00.010-0.01251.6980.0000.0000.0000.0000.0000.000
106A298ILE00.0240.01745.666-0.001-0.0010.0000.0000.0000.000
107A299GLU-1-0.917-0.94648.231-0.065-0.0650.0000.0000.0000.000
108A300LEU0-0.003-0.00142.763-0.003-0.0030.0000.0000.0000.000
109A301GLU-1-0.870-0.94142.248-0.090-0.0900.0000.0000.0000.000
110A302ARG10.8240.91835.9080.1160.1160.0000.0000.0000.000
111A303THR00.0230.01535.2300.0010.0010.0000.0000.0000.000
112A304VAL00.011-0.00434.4040.0030.0030.0000.0000.0000.000
113A305ASP-1-0.867-0.93931.604-0.168-0.1680.0000.0000.0000.000
114A306ILE00.0760.04427.572-0.002-0.0020.0000.0000.0000.000
115A307LEU00.0190.00425.152-0.006-0.0060.0000.0000.0000.000
116A308LYS10.8390.90528.4650.1290.1290.0000.0000.0000.000
117A309THR00.006-0.00731.1950.0070.0070.0000.0000.0000.000
118A310LEU0-0.003-0.00524.8260.0010.0010.0000.0000.0000.000
119A311GLY00.0230.01628.066-0.006-0.0060.0000.0000.0000.000
120A312GLU-1-0.899-0.93829.106-0.129-0.1290.0000.0000.0000.000
121A313MET0-0.052-0.01829.2900.0060.0060.0000.0000.0000.000
122A314LYS10.8070.92024.2830.2170.2170.0000.0000.0000.000
123A315ASP-1-0.969-0.97226.099-0.191-0.1910.0000.0000.0000.000
124A316LYS10.9150.95521.4380.3440.3440.0000.0000.0000.000
125A317GLN0-0.0210.00520.630-0.011-0.0110.0000.0000.0000.000
126A318LEU00.0020.00116.2960.0280.0280.0000.0000.0000.000
127A319LEU0-0.040-0.01819.905-0.027-0.0270.0000.0000.0000.000
128A320ILE00.0250.00917.2150.0200.0200.0000.0000.0000.000
129A321GLY00.0130.00420.638-0.002-0.0020.0000.0000.0000.000
130A322PHE00.0130.00818.993-0.001-0.0010.0000.0000.0000.000
131A323ALA0-0.032-0.03024.3780.0130.0130.0000.0000.0000.000
132A324ALA00.010-0.00427.083-0.004-0.0040.0000.0000.0000.000
133A325GLU-1-0.895-0.93129.414-0.109-0.1090.0000.0000.0000.000
134A326THR0-0.012-0.01732.2950.0020.0020.0000.0000.0000.000
135A327THR0-0.038-0.03134.9990.0080.0080.0000.0000.0000.000
136A328ASN0-0.040-0.01335.692-0.004-0.0040.0000.0000.0000.000
137A329VAL00.0590.02929.446-0.005-0.0050.0000.0000.0000.000
138A330GLU-1-0.882-0.93830.228-0.095-0.0950.0000.0000.0000.000
139A331GLU-1-0.817-0.88431.310-0.091-0.0910.0000.0000.0000.000
140A332TYR0-0.011-0.00630.867-0.008-0.0080.0000.0000.0000.000
141A333ALA00.0100.00127.457-0.007-0.0070.0000.0000.0000.000
142A334THR00.007-0.01528.735-0.012-0.0120.0000.0000.0000.000
143A335LYS10.8250.90130.3480.1050.1050.0000.0000.0000.000
144A336LYS10.8780.92927.9830.1780.1780.0000.0000.0000.000
145A337LEU0-0.015-0.00624.881-0.007-0.0070.0000.0000.0000.000
146A338ARG10.8330.91527.8240.1300.1300.0000.0000.0000.000
147A339GLU-1-0.850-0.91330.983-0.114-0.1140.0000.0000.0000.000
148A340LYS10.8000.90628.7010.1460.1460.0000.0000.0000.000
149A341ASN0-0.0230.00628.808-0.011-0.0110.0000.0000.0000.000
150A342ALA00.0150.01124.327-0.014-0.0140.0000.0000.0000.000
151A343ASN00.013-0.00320.7800.0120.0120.0000.0000.0000.000
152A344MET00.0450.01716.5850.0120.0120.0000.0000.0000.000
153A345ILE0-0.054-0.01221.713-0.012-0.0120.0000.0000.0000.000
154A346VAL0-0.007-0.00919.1120.0100.0100.0000.0000.0000.000
155A347ALA00.0050.00022.3230.0040.0040.0000.0000.0000.000
156A348ASN0-0.063-0.05123.009-0.003-0.0030.0000.0000.0000.000
157A349ASP-1-0.896-0.93526.052-0.117-0.1170.0000.0000.0000.000
158A361THR0-0.082-0.05622.446-0.002-0.0020.0000.0000.0000.000
159A362ASN0-0.037-0.03721.400-0.010-0.0100.0000.0000.0000.000
160A363ILE00.0760.04922.6940.0020.0020.0000.0000.0000.000
161A364VAL0-0.0100.00219.744-0.005-0.0050.0000.0000.0000.000
162A365THR00.0540.03122.2390.0090.0090.0000.0000.0000.000
163A366MET0-0.077-0.04216.207-0.029-0.0290.0000.0000.0000.000
164A367TYR00.0690.03221.6160.0100.0100.0000.0000.0000.000
165A368ARG10.9060.94617.6700.1660.1660.0000.0000.0000.000
166A369LYS10.9640.98222.4800.1950.1950.0000.0000.0000.000
167A370ASP-1-0.802-0.90322.430-0.143-0.1430.0000.0000.0000.000
168A371GLY0-0.028-0.01025.0910.0140.0140.0000.0000.0000.000
169A372GLU-1-0.943-0.95722.200-0.094-0.0940.0000.0000.0000.000
170A373VAL0-0.021-0.01723.946-0.017-0.0170.0000.0000.0000.000
171A374ILE0-0.027-0.01118.5080.0070.0070.0000.0000.0000.000
172A375GLU-1-0.910-0.95221.792-0.106-0.1060.0000.0000.0000.000
173A376LEU0-0.070-0.02817.396-0.001-0.0010.0000.0000.0000.000
174A377PRO00.0150.01120.0050.0090.0090.0000.0000.0000.000
175A378LEU0-0.024-0.01622.014-0.015-0.0150.0000.0000.0000.000
176A379LEU00.0160.02316.7100.0040.0040.0000.0000.0000.000
177A380THR0-0.033-0.02617.113-0.017-0.0170.0000.0000.0000.000
178A381LYS10.9680.96417.6820.1620.1620.0000.0000.0000.000
179A382LYS10.9991.00010.4780.2310.2310.0000.0000.0000.000
180A383GLU-1-0.842-0.91912.826-0.228-0.2280.0000.0000.0000.000
181A384VAL00.0600.03013.686-0.043-0.0430.0000.0000.0000.000
182A385ALA0-0.001-0.00312.716-0.029-0.0290.0000.0000.0000.000
183A386ARG10.9360.9686.2850.6590.6590.0000.0000.0000.000
184A387GLU-1-0.904-0.94610.350-0.347-0.3470.0000.0000.0000.000
185A388ILE0-0.008-0.01312.9580.0150.0150.0000.0000.0000.000
186A389LEU0-0.035-0.0209.0410.0110.0110.0000.0000.0000.000
187A390LYS10.9691.0039.3150.1740.1740.0000.0000.0000.000
188A391GLN00.007-0.01210.2310.0790.0790.0000.0000.0000.000
189A392ILE0-0.028-0.01812.2320.0380.0380.0000.0000.0000.000
190A393GLU-1-0.911-0.9647.162-0.581-0.5810.0000.0000.0000.000
191A394MET0-0.029-0.01010.8340.0830.0830.0000.0000.0000.000
192A395MET0-0.022-0.01713.6420.0270.0270.0000.0000.0000.000
193A396LEU0-0.037-0.01911.831-0.018-0.0180.0000.0000.0000.000
194A397GLU-1-0.988-0.98911.438-0.231-0.2310.0000.0000.0000.000
195A398ASP-1-0.996-0.98415.375-0.136-0.1360.0000.0000.0000.000
196A399ASP-1-1.032-1.00318.547-0.244-0.2440.0000.0000.0000.000