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: K91L3

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2094150.243343
FMO2-HF: Nuclear repulsion 2018627.548846
FMO2-HF: Total energy -75522.694497
FMO2-MP2: Total energy -75744.059526


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.
-11.28-6.0134.121-3.016-6.3750.003
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 : 0.036 / q_NPA : 0.007
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-1-0.899-0.9463.595-1.8010.188-0.004-0.832-1.1530.002
4A127ALA00.0240.0363.2310.1260.6440.035-0.156-0.3980.000
5A128VAL0-0.0120.0064.8460.4030.557-0.001-0.028-0.1260.000
6A129VAL0-0.0050.0027.103-0.118-0.1180.0000.0000.0000.000
7A130LYS10.8790.95210.659-0.154-0.1540.0000.0000.0000.000
8A131VAL0-0.013-0.01214.149-0.025-0.0250.0000.0000.0000.000
9A132PHE0-0.028-0.02616.711-0.003-0.0030.0000.0000.0000.000
10A133CYS00.0140.02620.366-0.010-0.0100.0000.0000.0000.000
11A134VAL0-0.029-0.01323.2520.0010.0010.0000.0000.0000.000
12A135HIS00.0520.03425.592-0.005-0.0050.0000.0000.0000.000
13A136THR0-0.018-0.03527.475-0.002-0.0020.0000.0000.0000.000
14A137GLU-1-0.761-0.82730.7210.0460.0460.0000.0000.0000.000
15A138PRO00.0620.03230.737-0.003-0.0030.0000.0000.0000.000
16A139ASN0-0.009-0.01933.431-0.004-0.0040.0000.0000.0000.000
17A140PHE0-0.027-0.01836.5490.0020.0020.0000.0000.0000.000
18A141SER0-0.0080.00237.787-0.001-0.0010.0000.0000.0000.000
19A142LEU00.0430.00639.403-0.001-0.0010.0000.0000.0000.000
20A143PRO0-0.0040.00143.0770.0000.0000.0000.0000.0000.000
21A144TRP00.0360.01945.034-0.001-0.0010.0000.0000.0000.000
22A145GLN0-0.049-0.01741.6480.0000.0000.0000.0000.0000.000
23A146ARG10.9820.98039.197-0.032-0.0320.0000.0000.0000.000
24A147LYS10.9170.98235.849-0.029-0.0290.0000.0000.0000.000
25A148ARG10.8320.90333.606-0.046-0.0460.0000.0000.0000.000
26A149GLN00.026-0.00231.446-0.001-0.0010.0000.0000.0000.000
27A150TYR0-0.063-0.04127.6210.0000.0000.0000.0000.0000.000
28A151SER0-0.031-0.01225.1450.0010.0010.0000.0000.0000.000
29A152SER00.0290.01722.9040.0040.0040.0000.0000.0000.000
30A153GLY0-0.011-0.01819.9310.0020.0020.0000.0000.0000.000
31A154SER00.0230.02816.200-0.012-0.0120.0000.0000.0000.000
32A155SER0-0.015-0.01211.4360.0210.0210.0000.0000.0000.000
33A156GLY00.0580.03811.400-0.050-0.0500.0000.0000.0000.000
34A157PHE0-0.033-0.0186.4290.1290.1290.0000.0000.0000.000
35A158ILE00.0170.0296.836-0.087-0.0870.0000.0000.0000.000
36A159ILE00.0080.0026.6300.1680.1680.0000.0000.0000.000
37A160GLY00.0230.0028.921-0.087-0.0870.0000.0000.0000.000
38A161GLY00.008-0.00511.1860.0250.0250.0000.0000.0000.000
39A162ARG10.8510.93113.1780.0340.0340.0000.0000.0000.000
40A163ARG10.8890.95312.5710.0170.0170.0000.0000.0000.000
41A164VAL0-0.017-0.01710.9080.0150.0150.0000.0000.0000.000
42A165LEU00.0150.03110.763-0.045-0.0450.0000.0000.0000.000
43A166THR0-0.002-0.02211.9480.0560.0560.0000.0000.0000.000
44A167ASN0-0.0320.02414.340-0.035-0.0350.0000.0000.0000.000
45A168ALA00.0210.00917.3180.0010.0010.0000.0000.0000.000
46A169HIS10.8820.90019.390-0.087-0.0870.0000.0000.0000.000
47A170SER0-0.091-0.07419.482-0.001-0.0010.0000.0000.0000.000
48A171VAL0-0.052-0.03819.431-0.001-0.0010.0000.0000.0000.000
49A172GLU-1-0.905-0.93122.3520.0400.0400.0000.0000.0000.000
50A173HIS0-0.034-0.02325.623-0.001-0.0010.0000.0000.0000.000
51A174HIS00.0100.00227.3800.0020.0020.0000.0000.0000.000
52A175THR0-0.062-0.03626.044-0.002-0.0020.0000.0000.0000.000
53A176GLN00.0020.00125.0920.0030.0030.0000.0000.0000.000
54A177VAL00.0590.02619.0450.0030.0030.0000.0000.0000.000
55A178LYS10.8970.94720.067-0.070-0.0700.0000.0000.0000.000
56A179LEU00.0080.01313.4990.0130.0130.0000.0000.0000.000
57A180LYS10.8830.96414.781-0.218-0.2180.0000.0000.0000.000
58A181LYS10.9390.96410.6500.0360.0360.0000.0000.0000.000
59A182ARG10.9020.9356.842-0.540-0.5400.0000.0000.0000.000
60A183GLY0-0.026-0.00311.2170.0260.0260.0000.0000.0000.000
61A184SER00.0440.05213.522-0.011-0.0110.0000.0000.0000.000
62A185ASP-1-0.824-0.94116.4370.1490.1490.0000.0000.0000.000
63A186THR0-0.076-0.03618.194-0.011-0.0110.0000.0000.0000.000
64A187LYS10.8830.93417.792-0.091-0.0910.0000.0000.0000.000
65A188TYR00.0500.02415.760-0.005-0.0050.0000.0000.0000.000
66A189LEU0-0.060-0.03419.1050.0090.0090.0000.0000.0000.000
67A190ALA00.0340.01217.709-0.005-0.0050.0000.0000.0000.000
68A191THR0-0.061-0.03019.495-0.006-0.0060.0000.0000.0000.000
69A192VAL00.007-0.01319.9210.0050.0050.0000.0000.0000.000
70A193LEU0-0.047-0.00918.396-0.007-0.0070.0000.0000.0000.000
71A194ALA00.0250.00821.017-0.008-0.0080.0000.0000.0000.000
72A195ILE0-0.004-0.00220.9360.0120.0120.0000.0000.0000.000
73A196GLY0-0.0160.00621.566-0.007-0.0070.0000.0000.0000.000
74A197THR00.003-0.01722.9650.0020.0020.0000.0000.0000.000
75A198GLU-1-0.914-0.94724.9660.0000.0000.0000.0000.0000.000
76A199CYS0-0.046-0.02520.514-0.001-0.0010.0000.0000.0000.000
77A200ASP-1-0.692-0.81219.8610.0760.0760.0000.0000.0000.000
78A201ILE0-0.005-0.00615.6580.0190.0190.0000.0000.0000.000
79A202ALA00.0310.00617.091-0.016-0.0160.0000.0000.0000.000
80A203LEU0-0.023-0.00315.2110.0240.0240.0000.0000.0000.000
81A204LEU0-0.027-0.02115.495-0.014-0.0140.0000.0000.0000.000
82A205THR00.0510.00915.634-0.002-0.0020.0000.0000.0000.000
83A206VAL00.0280.01415.4470.0070.0070.0000.0000.0000.000
84A207THR0-0.011-0.00717.875-0.010-0.0100.0000.0000.0000.000
85A208ASP-1-0.842-0.92018.7940.0150.0150.0000.0000.0000.000
86A209ASP-1-0.821-0.92317.741-0.019-0.0190.0000.0000.0000.000
87A210GLU-1-0.896-0.94316.6620.0100.0100.0000.0000.0000.000
88A211PHE0-0.104-0.05811.8610.0000.0000.0000.0000.0000.000
89A212TRP0-0.084-0.04311.142-0.013-0.0130.0000.0000.0000.000
90A213GLU-1-0.933-0.95211.774-0.070-0.0700.0000.0000.0000.000
91A214GLY0-0.041-0.01411.6330.0120.0120.0000.0000.0000.000
92A215VAL0-0.021-0.0166.510-0.015-0.0150.0000.0000.0000.000
93A216SER0-0.031-0.0134.9570.1570.1570.0000.0000.0000.000
94A217PRO0-0.029-0.0064.114-0.825-0.607-0.001-0.039-0.1770.000
95A218VAL0-0.024-0.0113.043-1.455-0.2890.170-0.401-0.9350.003
96A219GLU-1-0.914-0.9544.377-1.017-0.948-0.001-0.019-0.0500.000
97A220PHE0-0.009-0.0166.379-0.214-0.2140.0000.0000.0000.000
98A221GLY0-0.022-0.0178.845-0.120-0.1200.0000.0000.0000.000
99A222ASP-1-0.966-0.97510.434-0.315-0.3150.0000.0000.0000.000
100A223LEU0-0.043-0.02813.017-0.018-0.0180.0000.0000.0000.000
101A224PRO00.0030.01913.550-0.010-0.0100.0000.0000.0000.000
102A225ALA0-0.014-0.01315.3910.0410.0410.0000.0000.0000.000
103A226LEU0-0.001-0.02718.135-0.004-0.0040.0000.0000.0000.000
104A227GLN0-0.064-0.04920.021-0.002-0.0020.0000.0000.0000.000
105A228ASP-1-0.831-0.88314.670-0.278-0.2780.0000.0000.0000.000
106A229ALA0-0.028-0.01514.0030.0270.0270.0000.0000.0000.000
107A230VAL0-0.028-0.02910.786-0.094-0.0940.0000.0000.0000.000
108A231THR0-0.046-0.0226.4900.1590.1590.0000.0000.0000.000
109A232VAL00.0240.0128.024-0.134-0.1340.0000.0000.0000.000
110A233VAL0-0.033-0.0044.549-0.0100.067-0.001-0.009-0.0680.000
111A234GLY00.024-0.0017.8800.0550.0550.0000.0000.0000.000
112A235TYR0-0.074-0.0419.9320.0200.0200.0000.0000.0000.000
113A236PRO00.0610.04113.623-0.032-0.0320.0000.0000.0000.000
114A237ILE00.013-0.01616.7070.0020.0020.0000.0000.0000.000
115A238GLY0-0.031-0.01419.807-0.003-0.0030.0000.0000.0000.000
116A239GLY0-0.0010.01419.115-0.007-0.0070.0000.0000.0000.000
117A240ASP-1-0.909-0.97116.7530.1730.1730.0000.0000.0000.000
118A241THR0-0.050-0.02814.4030.0210.0210.0000.0000.0000.000
119A242ILE00.0250.0067.886-0.019-0.0190.0000.0000.0000.000
120A243SER0-0.055-0.02611.1520.0090.0090.0000.0000.0000.000
121A244VAL00.021-0.0097.5160.0630.0630.0000.0000.0000.000
122A245THR0-0.038-0.0049.900-0.023-0.0230.0000.0000.0000.000
123A246SER00.018-0.00511.416-0.061-0.0610.0000.0000.0000.000
124A247GLY00.0210.01513.2350.0340.0340.0000.0000.0000.000
125A248VAL00.0160.01514.660-0.054-0.0540.0000.0000.0000.000
126A249VAL0-0.030-0.00315.6440.0260.0260.0000.0000.0000.000
127A250SER00.0090.00217.9260.0040.0040.0000.0000.0000.000
128A251ARG10.8340.90720.9740.0310.0310.0000.0000.0000.000
129A252MET00.0060.00720.076-0.011-0.0110.0000.0000.0000.000
130A253GLU-1-0.940-0.94922.221-0.017-0.0170.0000.0000.0000.000
131A254ILE00.001-0.01723.118-0.006-0.0060.0000.0000.0000.000
132A255LEU00.0200.02525.3360.0060.0060.0000.0000.0000.000
133A256SER00.017-0.01327.223-0.006-0.0060.0000.0000.0000.000
134A257TYR0-0.065-0.05625.6690.0060.0060.0000.0000.0000.000
135A258VAL0-0.033-0.02832.0160.0000.0000.0000.0000.0000.000
136A259HIS00.0220.00331.3070.0000.0000.0000.0000.0000.000
137A260GLY0-0.0080.00833.680-0.001-0.0010.0000.0000.0000.000
138A261SER0-0.055-0.01928.784-0.005-0.0050.0000.0000.0000.000
139A262THR0-0.008-0.01826.4210.0010.0010.0000.0000.0000.000
140A263GLU-1-0.803-0.85822.070-0.067-0.0670.0000.0000.0000.000
141A264LEU00.002-0.00217.2910.0070.0070.0000.0000.0000.000
142A265LEU00.0170.00720.7890.0040.0040.0000.0000.0000.000
143A266GLY00.006-0.01119.5110.0110.0110.0000.0000.0000.000
144A267LEU0-0.0040.00614.910-0.014-0.0140.0000.0000.0000.000
145A268GLN00.0470.02318.5430.0200.0200.0000.0000.0000.000
146A269ILE0-0.016-0.01214.236-0.019-0.0190.0000.0000.0000.000
147A270ASP-1-0.878-0.91518.144-0.035-0.0350.0000.0000.0000.000
148A271ALA00.0430.01116.4640.0080.0080.0000.0000.0000.000
149A272ALA00.0050.01218.546-0.001-0.0010.0000.0000.0000.000
150A273ILE0-0.028-0.00614.4190.0140.0140.0000.0000.0000.000
151A274ASN00.0300.00016.898-0.012-0.0120.0000.0000.0000.000
152A275SER00.0830.02417.3320.0190.0190.0000.0000.0000.000
153A276GLY0-0.061-0.02117.5310.0010.0010.0000.0000.0000.000
154A277ASN0-0.0060.00513.3620.0320.0320.0000.0000.0000.000
155A278SER00.0210.01513.2040.0170.0170.0000.0000.0000.000
156A279GLY0-0.009-0.00813.430-0.003-0.0030.0000.0000.0000.000
157A280GLY00.0150.0069.6620.0590.0590.0000.0000.0000.000
158A281PRO0-0.0350.0045.114-0.192-0.091-0.001-0.006-0.0940.000
159A282ALA00.0500.0177.559-0.120-0.1200.0000.0000.0000.000
160A283PHE0-0.031-0.0302.666-3.169-2.6263.922-1.334-3.131-0.001
161A284ASN00.0880.0426.5580.0550.0550.0000.0000.0000.000
162A285ASP-1-0.800-0.9087.973-0.932-0.9320.0000.0000.0000.000
163A286LYS10.8850.9438.9700.5150.5150.0000.0000.0000.000
164A287GLY0-0.031-0.0204.890-0.115-0.1150.0000.0000.0000.000
165A288LYS10.8700.9523.511-1.529-1.0970.003-0.192-0.243-0.001
166A289CYS0-0.078-0.0235.2510.1150.1150.0000.0000.0000.000
167A290VAL00.003-0.0086.203-0.006-0.0060.0000.0000.0000.000
168A291GLY00.0440.0029.2660.0170.0170.0000.0000.0000.000
169A292ILE0-0.053-0.0119.6950.0930.0930.0000.0000.0000.000
170A293ALA00.0230.01011.402-0.066-0.0660.0000.0000.0000.000
171A294PHE0-0.014-0.02113.1480.0340.0340.0000.0000.0000.000
172A295GLN00.0330.02216.800-0.008-0.0080.0000.0000.0000.000
173A296SER0-0.012-0.01619.563-0.004-0.0040.0000.0000.0000.000
174A297LEU0-0.0010.01022.9290.0020.0020.0000.0000.0000.000
175A298LYS10.9610.98125.461-0.022-0.0220.0000.0000.0000.000
176A299HIS0-0.058-0.02825.5510.0010.0010.0000.0000.0000.000
177A300GLU-1-0.910-0.93625.6560.0580.0580.0000.0000.0000.000
178A301ASP-1-0.918-0.96922.8510.0650.0650.0000.0000.0000.000
179A302ALA00.005-0.00224.295-0.002-0.0020.0000.0000.0000.000
180A303GLU-1-0.954-0.98725.4650.0130.0130.0000.0000.0000.000
181A304ASN0-0.124-0.07222.1250.0000.0000.0000.0000.0000.000
182A305ILE0-0.0090.00721.875-0.011-0.0110.0000.0000.0000.000
183A306GLY00.0470.03018.1190.0140.0140.0000.0000.0000.000
184A307TYR0-0.044-0.01518.202-0.020-0.0200.0000.0000.0000.000
185A308VAL00.0180.00312.6820.0170.0170.0000.0000.0000.000
186A309ILE0-0.0150.00515.001-0.018-0.0180.0000.0000.0000.000
187A310PRO00.0280.02614.2180.0090.0090.0000.0000.0000.000
188A311THR00.0670.00011.7610.0270.0270.0000.0000.0000.000
189A312PRO00.0120.01614.5040.0160.0160.0000.0000.0000.000
190A313VAL00.0560.03718.0160.0080.0080.0000.0000.0000.000
191A314ILE0-0.033-0.00912.3350.0140.0140.0000.0000.0000.000
192A315VAL0-0.025-0.02115.8280.0050.0050.0000.0000.0000.000
193A316HIS00.010-0.00517.7900.0040.0040.0000.0000.0000.000
194A317PHE0-0.0240.00017.6300.0050.0050.0000.0000.0000.000
195A318ILE0-0.018-0.01614.8160.0040.0040.0000.0000.0000.000
196A319GLN0-0.008-0.00819.3700.0000.0000.0000.0000.0000.000
197A320ASP-1-0.895-0.95122.233-0.019-0.0190.0000.0000.0000.000
198A321TYR0-0.076-0.01820.6880.0040.0040.0000.0000.0000.000
199A322GLU-1-0.927-0.97019.612-0.037-0.0370.0000.0000.0000.000
200A323LYS10.8420.93423.7180.0290.0290.0000.0000.0000.000