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: 52LVZ

Calculation Name: 5ILA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5ILA

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FL12

Base Structure: X-ray

Registration Date: 2023-09-20

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2094320.302565
FMO2-HF: Nuclear repulsion 2018796.193918
FMO2-HF: Total energy -75524.108648
FMO2-MP2: Total energy -75745.438536


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:124:SER)


Summations of interaction energy for fragment #1(A:124: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.
-10.722-3.4532.93-3.549-6.6520.007
Interaction energy analysis for fragmet #1(A:124:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.010
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].
3A126ASP-1-0.846-0.9153.264-2.368-0.0080.011-1.074-1.2970.001
4A127ALA00.0270.0352.9910.4260.9990.091-0.175-0.4900.000
5A128VAL0-0.0170.0054.6510.7550.897-0.001-0.030-0.1110.000
6A129VAL0-0.0060.0056.868-0.075-0.0750.0000.0000.0000.000
7A130LYS10.8230.92610.4570.0110.0110.0000.0000.0000.000
8A131VAL00.000-0.00213.955-0.022-0.0220.0000.0000.0000.000
9A132PHE0-0.019-0.01516.4790.0060.0060.0000.0000.0000.000
10A133CYS00.0230.01620.158-0.007-0.0070.0000.0000.0000.000
11A134VAL0-0.035-0.00823.0680.0010.0010.0000.0000.0000.000
12A135HIS00.0550.03225.9030.0020.0020.0000.0000.0000.000
13A136THR0-0.017-0.02027.775-0.003-0.0030.0000.0000.0000.000
14A137GLU-1-0.748-0.81830.9510.0390.0390.0000.0000.0000.000
15A138PRO00.0880.04131.203-0.003-0.0030.0000.0000.0000.000
16A139ASN00.0160.01334.035-0.003-0.0030.0000.0000.0000.000
17A140PHE0-0.003-0.01837.0380.0000.0000.0000.0000.0000.000
18A141SER00.0060.00638.4900.0000.0000.0000.0000.0000.000
19A142LEU00.0460.01839.9790.0000.0000.0000.0000.0000.000
20A143PRO0-0.011-0.00943.8070.0000.0000.0000.0000.0000.000
21A144TRP00.0340.02445.7470.0000.0000.0000.0000.0000.000
22A145GLN0-0.050-0.02342.201-0.001-0.0010.0000.0000.0000.000
23A146ARG10.9770.97838.616-0.018-0.0180.0000.0000.0000.000
24A147LYS10.8540.93435.980-0.027-0.0270.0000.0000.0000.000
25A148ARG10.8220.89333.406-0.035-0.0350.0000.0000.0000.000
26A149GLN00.010-0.00331.6680.0010.0010.0000.0000.0000.000
27A150TYR0-0.059-0.04927.602-0.001-0.0010.0000.0000.0000.000
28A151SER00.0030.00624.4980.0000.0000.0000.0000.0000.000
29A152SER0-0.007-0.00723.9000.0020.0020.0000.0000.0000.000
30A153GLY00.007-0.01120.062-0.007-0.0070.0000.0000.0000.000
31A154SER0-0.0190.00216.8450.0010.0010.0000.0000.0000.000
32A155SER0-0.017-0.00511.764-0.023-0.0230.0000.0000.0000.000
33A156GLY00.0740.04811.3040.0060.0060.0000.0000.0000.000
34A157PHE0-0.042-0.0276.1590.0610.0610.0000.0000.0000.000
35A158ILE00.0240.0236.6520.0420.0420.0000.0000.0000.000
36A159ILE00.005-0.0056.1710.2130.2130.0000.0000.0000.000
37A160GLY00.0310.0058.561-0.142-0.1420.0000.0000.0000.000
38A161GLY00.0080.00010.9190.0280.0280.0000.0000.0000.000
39A162ARG10.7910.89413.2010.0900.0900.0000.0000.0000.000
40A163ARG10.8620.92912.347-0.051-0.0510.0000.0000.0000.000
41A164VAL00.001-0.00510.437-0.012-0.0120.0000.0000.0000.000
42A165LEU00.0060.02410.747-0.022-0.0220.0000.0000.0000.000
43A166THR0-0.007-0.03211.8980.0090.0090.0000.0000.0000.000
44A167ASN0-0.024-0.01514.416-0.011-0.0110.0000.0000.0000.000
45A168ALA00.0120.02017.545-0.010-0.0100.0000.0000.0000.000
46A169HIS10.9300.92920.099-0.109-0.1090.0000.0000.0000.000
47A170SER0-0.081-0.05519.500-0.011-0.0110.0000.0000.0000.000
48A171VAL0-0.077-0.04919.079-0.008-0.0080.0000.0000.0000.000
49A172GLU-1-0.881-0.92222.2020.0560.0560.0000.0000.0000.000
50A173HIS0-0.064-0.02925.572-0.006-0.0060.0000.0000.0000.000
51A174HIS00.0290.00727.7260.0000.0000.0000.0000.0000.000
52A175THR0-0.068-0.03027.010-0.004-0.0040.0000.0000.0000.000
53A176GLN00.0370.02624.9820.0000.0000.0000.0000.0000.000
54A177VAL00.0390.01319.4180.0010.0010.0000.0000.0000.000
55A178LYS10.8700.92219.520-0.007-0.0070.0000.0000.0000.000
56A179LEU00.0100.01413.4230.0150.0150.0000.0000.0000.000
57A180LYS10.7990.92414.5430.0070.0070.0000.0000.0000.000
58A181LYS10.8890.94810.4870.2980.2980.0000.0000.0000.000
59A182ARG10.8550.9076.1990.2200.2200.0000.0000.0000.000
60A183GLY0-0.038-0.02711.2720.0560.0560.0000.0000.0000.000
61A184SER00.0340.01913.4700.0190.0190.0000.0000.0000.000
62A185ASP-1-0.914-0.95516.373-0.018-0.0180.0000.0000.0000.000
63A186THR00.0240.01617.7030.0040.0040.0000.0000.0000.000
64A187LYS10.7760.88617.336-0.009-0.0090.0000.0000.0000.000
65A188TYR00.0550.03415.8220.0000.0000.0000.0000.0000.000
66A189LEU0-0.044-0.02718.9190.0100.0100.0000.0000.0000.000
67A190ALA00.0010.00117.540-0.009-0.0090.0000.0000.0000.000
68A191THR0-0.054-0.02219.3170.0030.0030.0000.0000.0000.000
69A192VAL00.018-0.00419.5590.0040.0040.0000.0000.0000.000
70A193LEU0-0.064-0.02217.670-0.008-0.0080.0000.0000.0000.000
71A194ALA00.0120.00120.413-0.004-0.0040.0000.0000.0000.000
72A195ILE0-0.009-0.00920.5530.0110.0110.0000.0000.0000.000
73A196GLY0-0.0100.00921.851-0.006-0.0060.0000.0000.0000.000
74A197THR0-0.036-0.05423.153-0.002-0.0020.0000.0000.0000.000
75A198GLU-1-0.881-0.91824.9850.0530.0530.0000.0000.0000.000
76A199CYS0-0.048-0.01920.5340.0070.0070.0000.0000.0000.000
77A200ASP-1-0.731-0.84220.4510.1080.1080.0000.0000.0000.000
78A201ILE0-0.017-0.01315.9190.0230.0230.0000.0000.0000.000
79A202ALA00.0230.00317.172-0.025-0.0250.0000.0000.0000.000
80A203LEU0-0.0200.00114.6400.0340.0340.0000.0000.0000.000
81A204LEU0-0.006-0.00315.278-0.024-0.0240.0000.0000.0000.000
82A205THR00.035-0.01215.386-0.002-0.0020.0000.0000.0000.000
83A206VAL00.0070.00115.5190.0050.0050.0000.0000.0000.000
84A207THR00.0040.00017.696-0.009-0.0090.0000.0000.0000.000
85A208ASP-1-0.862-0.93418.540-0.087-0.0870.0000.0000.0000.000
86A209ASP-1-0.759-0.87817.433-0.097-0.0970.0000.0000.0000.000
87A210GLU-1-0.880-0.93016.076-0.117-0.1170.0000.0000.0000.000
88A211PHE0-0.051-0.03012.005-0.040-0.0400.0000.0000.0000.000
89A212TRP0-0.062-0.03810.943-0.060-0.0600.0000.0000.0000.000
90A213GLU-1-0.926-0.95311.508-0.226-0.2260.0000.0000.0000.000
91A214GLY0-0.037-0.02711.376-0.012-0.0120.0000.0000.0000.000
92A215VAL0-0.047-0.0166.083-0.098-0.0980.0000.0000.0000.000
93A216SER0-0.0130.0065.2060.2830.2830.0000.0000.0000.000
94A217PRO0-0.025-0.0124.183-1.177-0.944-0.001-0.047-0.1850.000
95A218VAL0-0.026-0.0152.644-2.837-0.7971.134-1.072-2.1020.005
96A219GLU-1-0.895-0.9363.681-1.369-1.2470.0170.030-0.1700.000
97A220PHE0-0.029-0.0275.7890.3220.3220.0000.0000.0000.000
98A221GLY00.007-0.0098.422-0.201-0.2010.0000.0000.0000.000
99A222ASP-1-0.881-0.94010.316-0.093-0.0930.0000.0000.0000.000
100A223LEU0-0.034-0.01213.1760.0250.0250.0000.0000.0000.000
101A224PRO0-0.0200.00214.111-0.018-0.0180.0000.0000.0000.000
102A225ALA0-0.004-0.00815.9460.0110.0110.0000.0000.0000.000
103A226LEU0-0.006-0.02418.6660.0030.0030.0000.0000.0000.000
104A227GLN0-0.045-0.04120.379-0.004-0.0040.0000.0000.0000.000
105A228ASP-1-0.820-0.88415.120-0.035-0.0350.0000.0000.0000.000
106A229ALA0-0.015-0.01214.4440.0160.0160.0000.0000.0000.000
107A230VAL0-0.013-0.00711.213-0.036-0.0360.0000.0000.0000.000
108A231THR0-0.058-0.0437.7180.0350.0350.0000.0000.0000.000
109A232VAL00.0230.0238.454-0.006-0.0060.0000.0000.0000.000
110A233VAL0-0.026-0.0145.268-0.026-0.0260.0000.0000.0000.000
111A234GLY00.020-0.0028.5010.0430.0430.0000.0000.0000.000
112A235TYR0-0.032-0.0359.9140.0180.0180.0000.0000.0000.000
113A236PRO00.0580.03914.010-0.007-0.0070.0000.0000.0000.000
114A237ILE00.008-0.01317.213-0.010-0.0100.0000.0000.0000.000
115A238GLY00.0120.00720.4720.0000.0000.0000.0000.0000.000
116A239GLY0-0.0050.00619.892-0.005-0.0050.0000.0000.0000.000
117A240ASP-1-0.759-0.90517.1730.0230.0230.0000.0000.0000.000
118A241THR0-0.030-0.00514.797-0.017-0.0170.0000.0000.0000.000
119A242ILE0-0.029-0.0248.208-0.004-0.0040.0000.0000.0000.000
120A243SER0-0.041-0.01211.8610.0190.0190.0000.0000.0000.000
121A244VAL00.025-0.0068.1950.0290.0290.0000.0000.0000.000
122A245THR0-0.039-0.01810.587-0.021-0.0210.0000.0000.0000.000
123A246SER00.0030.00712.0760.0030.0030.0000.0000.0000.000
124A247GLY00.0390.02413.2360.0130.0130.0000.0000.0000.000
125A248VAL0-0.041-0.01915.084-0.019-0.0190.0000.0000.0000.000
126A249VAL0-0.0040.00015.8690.0130.0130.0000.0000.0000.000
127A250SER00.0220.02018.309-0.006-0.0060.0000.0000.0000.000
128A251ARG10.7710.85821.178-0.060-0.0600.0000.0000.0000.000
129A252MET0-0.0070.00220.2560.0060.0060.0000.0000.0000.000
130A253GLU-1-0.853-0.90222.1930.0540.0540.0000.0000.0000.000
131A254ILE0-0.006-0.00423.0040.0070.0070.0000.0000.0000.000
132A255LEU00.0320.03825.236-0.004-0.0040.0000.0000.0000.000
133A256SER00.008-0.01427.193-0.003-0.0030.0000.0000.0000.000
134A257TYR0-0.040-0.03525.598-0.002-0.0020.0000.0000.0000.000
135A258VAL0-0.014-0.02131.964-0.002-0.0020.0000.0000.0000.000
136A259HIS00.0080.00830.968-0.002-0.0020.0000.0000.0000.000
137A260GLY00.0010.00833.843-0.002-0.0020.0000.0000.0000.000
138A261SER0-0.028-0.00928.935-0.001-0.0010.0000.0000.0000.000
139A262THR0-0.028-0.02226.9110.0020.0020.0000.0000.0000.000
140A263GLU-1-0.822-0.89122.1200.0620.0620.0000.0000.0000.000
141A264LEU0-0.018-0.00417.4510.0000.0000.0000.0000.0000.000
142A265LEU00.007-0.00120.2860.0120.0120.0000.0000.0000.000
143A266GLY00.022-0.01119.6850.0130.0130.0000.0000.0000.000
144A267LEU0-0.009-0.00115.164-0.013-0.0130.0000.0000.0000.000
145A268GLN00.0220.01718.7980.0100.0100.0000.0000.0000.000
146A269ILE0-0.015-0.00914.738-0.006-0.0060.0000.0000.0000.000
147A270ASP-1-0.878-0.93018.6390.0510.0510.0000.0000.0000.000
148A271ALA00.0490.01916.887-0.001-0.0010.0000.0000.0000.000
149A272ALA00.0280.01618.8540.0060.0060.0000.0000.0000.000
150A273ILE0-0.060-0.01615.0710.0090.0090.0000.0000.0000.000
151A274ASN00.0150.00117.125-0.009-0.0090.0000.0000.0000.000
152A275SER00.0390.00617.5240.0110.0110.0000.0000.0000.000
153A276GLY0-0.024-0.00917.9140.0060.0060.0000.0000.0000.000
154A277ASN0-0.028-0.00112.250-0.013-0.0130.0000.0000.0000.000
155A278SER00.0480.02613.6410.0360.0360.0000.0000.0000.000
156A279GLY0-0.047-0.00314.153-0.027-0.0270.0000.0000.0000.000
157A280GLY00.0450.01310.3470.0380.0380.0000.0000.0000.000
158A281PRO0-0.0280.0025.699-0.060-0.0600.0000.0000.0000.000
159A282ALA00.0220.0088.111-0.185-0.1850.0000.0000.0000.000
160A283PHE0-0.019-0.0232.617-2.929-1.5291.679-1.054-2.0250.002
161A284ASN00.0730.0307.037-0.120-0.1200.0000.0000.0000.000
162A285ASP-1-0.782-0.9028.160-0.477-0.4770.0000.0000.0000.000
163A286LYS10.7920.9148.9940.1410.1410.0000.0000.0000.000
164A287GLY00.0000.0094.906-0.262-0.2620.0000.0000.0000.000
165A288LYS10.8010.9043.728-0.495-0.1500.001-0.126-0.220-0.001
166A289CYS0-0.062-0.0225.060-0.158-0.104-0.001-0.001-0.0520.000
167A290VAL00.008-0.0116.411-0.217-0.2170.0000.0000.0000.000
168A291GLY00.0480.0019.577-0.089-0.0890.0000.0000.0000.000
169A292ILE0-0.053-0.0019.9650.1480.1480.0000.0000.0000.000
170A293ALA00.0330.01812.055-0.068-0.0680.0000.0000.0000.000
171A294PHE0-0.019-0.02613.699-0.004-0.0040.0000.0000.0000.000
172A295GLN00.0210.00817.385-0.005-0.0050.0000.0000.0000.000
173A296SER0-0.021-0.02120.2100.0000.0000.0000.0000.0000.000
174A297LEU00.0060.00523.499-0.002-0.0020.0000.0000.0000.000
175A298LYS10.9270.95925.912-0.045-0.0450.0000.0000.0000.000
176A299HIS0-0.046-0.01126.1330.0010.0010.0000.0000.0000.000
177A300GLU-1-0.861-0.92425.5880.0650.0650.0000.0000.0000.000
178A301ASP-1-0.923-0.97322.6000.0720.0720.0000.0000.0000.000
179A302ALA0-0.008-0.01724.5740.0020.0020.0000.0000.0000.000
180A303GLU-1-0.893-0.94426.1130.0410.0410.0000.0000.0000.000
181A304ASN0-0.128-0.05722.5980.0010.0010.0000.0000.0000.000
182A305ILE00.0000.01222.135-0.002-0.0020.0000.0000.0000.000
183A306GLY00.0250.04118.8410.0030.0030.0000.0000.0000.000
184A307TYR0-0.028-0.01918.637-0.010-0.0100.0000.0000.0000.000
185A308VAL0-0.001-0.01013.0230.0210.0210.0000.0000.0000.000
186A309ILE00.0070.01615.408-0.026-0.0260.0000.0000.0000.000
187A310PRO00.0070.01614.3610.0530.0530.0000.0000.0000.000
188A311THR00.0590.00611.592-0.005-0.0050.0000.0000.0000.000
189A312PRO0-0.0010.01014.261-0.001-0.0010.0000.0000.0000.000
190A313VAL00.0450.02618.043-0.005-0.0050.0000.0000.0000.000
191A314ILE0-0.027-0.00312.0510.0020.0020.0000.0000.0000.000
192A315VAL0-0.014-0.00615.161-0.011-0.0110.0000.0000.0000.000
193A316HIS0-0.014-0.02317.245-0.012-0.0120.0000.0000.0000.000
194A317PHE00.0040.00617.419-0.011-0.0110.0000.0000.0000.000
195A318ILE0-0.031-0.01914.188-0.008-0.0080.0000.0000.0000.000
196A319GLN00.0360.01318.783-0.026-0.0260.0000.0000.0000.000
197A320ASP-1-0.860-0.92521.5870.0440.0440.0000.0000.0000.000
198A321TYR0-0.061-0.01819.886-0.007-0.0070.0000.0000.0000.000
199A322GLU-1-0.874-0.91719.2610.0510.0510.0000.0000.0000.000
200A323LYS10.7560.88223.368-0.058-0.0580.0000.0000.0000.000