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

tag_button

FMODB ID: 49MVN

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2094067.804267
FMO2-HF: Nuclear repulsion 2018544.164987
FMO2-HF: Total energy -75523.63928
FMO2-MP2: Total energy -75744.958564


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.
-11.194-4.8972.892-3.115-6.0710.003
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 : 0.032 / 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].
3A126ASP-1-0.847-0.9243.541-2.0450.025-0.002-0.882-1.1850.002
4A127ALA00.0220.0393.2670.1940.7290.037-0.164-0.4080.000
5A128VAL0-0.0190.0034.8620.4790.618-0.001-0.026-0.1110.000
6A129VAL0-0.0050.0067.188-0.096-0.0960.0000.0000.0000.000
7A130LYS10.8590.94010.724-0.095-0.0950.0000.0000.0000.000
8A131VAL0-0.021-0.01914.228-0.018-0.0180.0000.0000.0000.000
9A132PHE0-0.036-0.02316.796-0.003-0.0030.0000.0000.0000.000
10A133CYS00.0060.00720.444-0.006-0.0060.0000.0000.0000.000
11A134VAL0-0.029-0.01423.3380.0000.0000.0000.0000.0000.000
12A135HIS00.0630.03625.802-0.002-0.0020.0000.0000.0000.000
13A136THR0-0.017-0.02927.695-0.003-0.0030.0000.0000.0000.000
14A137GLU-1-0.771-0.82230.9380.0400.0400.0000.0000.0000.000
15A138PRO00.0950.04530.939-0.002-0.0020.0000.0000.0000.000
16A139ASN00.0070.00533.650-0.003-0.0030.0000.0000.0000.000
17A140PHE0-0.020-0.02036.7800.0010.0010.0000.0000.0000.000
18A141SER00.0050.00838.048-0.001-0.0010.0000.0000.0000.000
19A142LEU00.0400.00839.654-0.001-0.0010.0000.0000.0000.000
20A143PRO0-0.007-0.00343.3180.0000.0000.0000.0000.0000.000
21A144TRP00.0330.01745.2720.0000.0000.0000.0000.0000.000
22A145GLN0-0.044-0.01141.8800.0000.0000.0000.0000.0000.000
23A146ARG10.9780.98039.241-0.027-0.0270.0000.0000.0000.000
24A147LYS10.8730.94636.056-0.028-0.0280.0000.0000.0000.000
25A148ARG10.8270.89133.547-0.038-0.0380.0000.0000.0000.000
26A149GLN00.018-0.00431.7520.0000.0000.0000.0000.0000.000
27A150TYR0-0.065-0.04727.639-0.001-0.0010.0000.0000.0000.000
28A151SER00.0030.00124.7330.0000.0000.0000.0000.0000.000
29A152SER0-0.006-0.00223.5580.0020.0020.0000.0000.0000.000
30A153GLY00.001-0.00720.1690.0000.0000.0000.0000.0000.000
31A154SER00.0030.02316.526-0.008-0.0080.0000.0000.0000.000
32A155SER00.003-0.00211.6990.0040.0040.0000.0000.0000.000
33A156GLY00.0600.04311.612-0.029-0.0290.0000.0000.0000.000
34A157PHE0-0.025-0.0156.5640.0940.0940.0000.0000.0000.000
35A158ILE00.0090.0196.896-0.044-0.0440.0000.0000.0000.000
36A159ILE00.0120.0036.6670.2620.2620.0000.0000.0000.000
37A160GLY00.0280.0048.944-0.119-0.1190.0000.0000.0000.000
38A161GLY00.006-0.00611.1670.0120.0120.0000.0000.0000.000
39A162ARG10.7940.89213.1440.0140.0140.0000.0000.0000.000
40A163ARG10.8690.92512.569-0.057-0.0570.0000.0000.0000.000
41A164VAL0-0.022-0.01610.7730.0260.0260.0000.0000.0000.000
42A165LEU00.0140.03210.781-0.047-0.0470.0000.0000.0000.000
43A166THR0-0.003-0.03212.0780.0360.0360.0000.0000.0000.000
44A167ASN0-0.035-0.01614.491-0.024-0.0240.0000.0000.0000.000
45A168ALA0-0.0010.00617.488-0.002-0.0020.0000.0000.0000.000
46A169HIS10.8900.91119.667-0.089-0.0890.0000.0000.0000.000
47A170SER0-0.071-0.04519.240-0.009-0.0090.0000.0000.0000.000
48A171VAL0-0.047-0.03019.521-0.004-0.0040.0000.0000.0000.000
49A172GLU-1-0.890-0.92522.5170.0480.0480.0000.0000.0000.000
50A173HIS0-0.045-0.02325.785-0.003-0.0030.0000.0000.0000.000
51A174HIS00.0070.00427.4680.0030.0030.0000.0000.0000.000
52A175THR0-0.036-0.01426.755-0.003-0.0030.0000.0000.0000.000
53A176GLN00.0300.02225.1710.0030.0030.0000.0000.0000.000
54A177VAL00.0580.01719.2250.0010.0010.0000.0000.0000.000
55A178LYS10.8760.93520.114-0.051-0.0510.0000.0000.0000.000
56A179LEU00.0100.01413.7620.0110.0110.0000.0000.0000.000
57A180LYS10.8660.94514.863-0.139-0.1390.0000.0000.0000.000
58A181LYS10.9120.95510.9130.0760.0760.0000.0000.0000.000
59A182ARG10.8710.9266.452-0.258-0.2580.0000.0000.0000.000
60A183GLY0-0.037-0.01111.2170.0340.0340.0000.0000.0000.000
61A184SER00.0370.02013.4850.0060.0060.0000.0000.0000.000
62A185ASP-1-0.894-0.95016.4370.0820.0820.0000.0000.0000.000
63A186THR0-0.022-0.00618.083-0.002-0.0020.0000.0000.0000.000
64A187LYS10.8600.93217.795-0.069-0.0690.0000.0000.0000.000
65A188TYR00.0440.02115.926-0.006-0.0060.0000.0000.0000.000
66A189LEU0-0.064-0.03019.1280.0080.0080.0000.0000.0000.000
67A190ALA00.0110.00617.914-0.004-0.0040.0000.0000.0000.000
68A191THR0-0.052-0.02719.534-0.006-0.0060.0000.0000.0000.000
69A192VAL00.007-0.01619.9640.0080.0080.0000.0000.0000.000
70A193LEU0-0.051-0.00918.329-0.008-0.0080.0000.0000.0000.000
71A194ALA00.0210.00721.091-0.008-0.0080.0000.0000.0000.000
72A195ILE0-0.009-0.00721.0080.0130.0130.0000.0000.0000.000
73A196GLY0-0.0100.00621.656-0.007-0.0070.0000.0000.0000.000
74A197THR0-0.028-0.04023.0550.0000.0000.0000.0000.0000.000
75A198GLU-1-0.886-0.92724.9620.0250.0250.0000.0000.0000.000
76A199CYS0-0.051-0.02320.5990.0020.0020.0000.0000.0000.000
77A200ASP-1-0.713-0.83220.1300.0860.0860.0000.0000.0000.000
78A201ILE0-0.009-0.00815.7380.0190.0190.0000.0000.0000.000
79A202ALA00.0330.00917.217-0.019-0.0190.0000.0000.0000.000
80A203LEU0-0.034-0.00415.1470.0290.0290.0000.0000.0000.000
81A204LEU0-0.022-0.02115.540-0.021-0.0210.0000.0000.0000.000
82A205THR00.043-0.00315.6710.0040.0040.0000.0000.0000.000
83A206VAL00.0330.02215.6850.0020.0020.0000.0000.0000.000
84A207THR0-0.007-0.00517.874-0.006-0.0060.0000.0000.0000.000
85A208ASP-1-0.855-0.93018.7830.0010.0010.0000.0000.0000.000
86A209ASP-1-0.773-0.88117.695-0.015-0.0150.0000.0000.0000.000
87A210GLU-1-0.878-0.93316.585-0.013-0.0130.0000.0000.0000.000
88A211PHE0-0.082-0.05512.209-0.012-0.0120.0000.0000.0000.000
89A212TRP0-0.054-0.03311.170-0.020-0.0200.0000.0000.0000.000
90A213GLU-1-0.943-0.95311.682-0.089-0.0890.0000.0000.0000.000
91A214GLY0-0.046-0.01611.5610.0020.0020.0000.0000.0000.000
92A215VAL0-0.018-0.0166.385-0.048-0.0480.0000.0000.0000.000
93A216SER0-0.034-0.0084.9160.1770.1770.0000.0000.0000.000
94A217PRO0-0.029-0.0074.010-0.922-0.6700.000-0.055-0.1970.000
95A218VAL0-0.031-0.0182.794-1.563-0.2950.402-0.496-1.1730.004
96A219GLU-1-0.904-0.9514.413-0.996-0.9230.000-0.025-0.0480.000
97A220PHE0-0.019-0.0196.346-0.055-0.0550.0000.0000.0000.000
98A221GLY0-0.005-0.0088.843-0.136-0.1360.0000.0000.0000.000
99A222ASP-1-0.928-0.95710.427-0.251-0.2510.0000.0000.0000.000
100A223LEU0-0.031-0.01613.063-0.010-0.0100.0000.0000.0000.000
101A224PRO0-0.0070.01413.603-0.015-0.0150.0000.0000.0000.000
102A225ALA0-0.016-0.01615.4740.0330.0330.0000.0000.0000.000
103A226LEU0-0.001-0.02418.238-0.006-0.0060.0000.0000.0000.000
104A227GLN0-0.058-0.04120.104-0.001-0.0010.0000.0000.0000.000
105A228ASP-1-0.823-0.87814.722-0.210-0.2100.0000.0000.0000.000
106A229ALA0-0.030-0.01514.0200.0220.0220.0000.0000.0000.000
107A230VAL0-0.027-0.03110.908-0.073-0.0730.0000.0000.0000.000
108A231THR0-0.051-0.0256.9040.1040.1040.0000.0000.0000.000
109A232VAL00.0190.0128.196-0.108-0.1080.0000.0000.0000.000
110A233VAL0-0.026-0.0044.672-0.0170.046-0.001-0.007-0.0550.000
111A234GLY00.0340.0047.9000.0610.0610.0000.0000.0000.000
112A235TYR0-0.070-0.04510.1220.0160.0160.0000.0000.0000.000
113A236PRO00.0730.04713.656-0.017-0.0170.0000.0000.0000.000
114A237ILE00.005-0.02116.7380.0010.0010.0000.0000.0000.000
115A238GLY0-0.014-0.00419.838-0.003-0.0030.0000.0000.0000.000
116A239GLY00.0070.01819.154-0.005-0.0050.0000.0000.0000.000
117A240ASP-1-0.839-0.95316.7490.1160.1160.0000.0000.0000.000
118A241THR0-0.038-0.01414.4520.0050.0050.0000.0000.0000.000
119A242ILE0-0.012-0.0197.866-0.014-0.0140.0000.0000.0000.000
120A243SER0-0.032-0.01411.2050.0130.0130.0000.0000.0000.000
121A244VAL0-0.026-0.0277.5550.0290.0290.0000.0000.0000.000
122A245THR0-0.0220.0029.9210.0020.0020.0000.0000.0000.000
123A246SER00.009-0.00111.421-0.055-0.0550.0000.0000.0000.000
124A247GLY00.0400.01613.2360.0310.0310.0000.0000.0000.000
125A248VAL0-0.0050.01114.698-0.046-0.0460.0000.0000.0000.000
126A249VAL0-0.0130.00115.6320.0240.0240.0000.0000.0000.000
127A250SER00.0220.00318.0700.0020.0020.0000.0000.0000.000
128A251ARG10.7750.85821.1290.0090.0090.0000.0000.0000.000
129A252MET0-0.0020.00020.288-0.006-0.0060.0000.0000.0000.000
130A253GLU-1-0.874-0.90222.3660.0040.0040.0000.0000.0000.000
131A254ILE0-0.004-0.01723.249-0.001-0.0010.0000.0000.0000.000
132A255LEU00.0220.02625.4450.0020.0020.0000.0000.0000.000
133A256SER00.015-0.01127.335-0.005-0.0050.0000.0000.0000.000
134A257TYR0-0.035-0.03125.8800.0030.0030.0000.0000.0000.000
135A258VAL0-0.029-0.02532.100-0.001-0.0010.0000.0000.0000.000
136A259HIS00.017-0.00331.127-0.001-0.0010.0000.0000.0000.000
137A260GLY0-0.0040.01133.750-0.001-0.0010.0000.0000.0000.000
138A261SER0-0.050-0.01128.814-0.003-0.0030.0000.0000.0000.000
139A262THR0-0.011-0.02026.5100.0010.0010.0000.0000.0000.000
140A263GLU-1-0.828-0.88122.237-0.012-0.0120.0000.0000.0000.000
141A264LEU0-0.0070.00217.4340.0030.0030.0000.0000.0000.000
142A265LEU00.0050.00120.8980.0070.0070.0000.0000.0000.000
143A266GLY00.028-0.00419.6570.0120.0120.0000.0000.0000.000
144A267LEU0-0.0090.00415.054-0.013-0.0130.0000.0000.0000.000
145A268GLN00.0400.02618.7010.0170.0170.0000.0000.0000.000
146A269ILE0-0.011-0.01114.404-0.016-0.0160.0000.0000.0000.000
147A270ASP-1-0.900-0.93618.319-0.029-0.0290.0000.0000.0000.000
148A271ALA00.0450.01516.4620.0030.0030.0000.0000.0000.000
149A272ALA00.0140.01718.5480.0020.0020.0000.0000.0000.000
150A273ILE0-0.044-0.01714.8280.0080.0080.0000.0000.0000.000
151A274ASN00.0370.00916.870-0.005-0.0050.0000.0000.0000.000
152A275SER00.0730.02117.3520.0120.0120.0000.0000.0000.000
153A276GLY0-0.063-0.02517.5590.0030.0030.0000.0000.0000.000
154A277ASN0-0.021-0.00512.5820.0170.0170.0000.0000.0000.000
155A278SER00.0230.01613.4660.0180.0180.0000.0000.0000.000
156A279GLY0-0.017-0.00913.642-0.007-0.0070.0000.0000.0000.000
157A280GLY00.0140.0099.8930.0610.0610.0000.0000.0000.000
158A281PRO0-0.0260.0035.324-0.071-0.0710.0000.0000.0000.000
159A282ALA00.0350.0127.765-0.172-0.1720.0000.0000.0000.000
160A283PHE0-0.028-0.0302.704-3.608-2.2132.453-1.264-2.585-0.002
161A284ASN00.0990.0436.693-0.024-0.0240.0000.0000.0000.000
162A285ASP-1-0.812-0.9118.029-0.814-0.8140.0000.0000.0000.000
163A286LYS10.8450.9258.9920.3630.3630.0000.0000.0000.000
164A287GLY0-0.020-0.0094.913-0.139-0.1390.0000.0000.0000.000
165A288LYS10.8390.9283.477-0.977-0.5240.005-0.195-0.263-0.001
166A289CYS0-0.082-0.0275.160-0.099-0.050-0.001-0.001-0.0460.000
167A290VAL00.010-0.0076.288-0.067-0.0670.0000.0000.0000.000
168A291GLY00.0450.0089.397-0.026-0.0260.0000.0000.0000.000
169A292ILE0-0.060-0.0149.8560.1030.1030.0000.0000.0000.000
170A293ALA00.0230.01211.692-0.065-0.0650.0000.0000.0000.000
171A294PHE0-0.001-0.01713.3440.0250.0250.0000.0000.0000.000
172A295GLN00.0180.01717.023-0.007-0.0070.0000.0000.0000.000
173A296SER0-0.028-0.02019.766-0.001-0.0010.0000.0000.0000.000
174A297LEU00.0150.00923.1310.0010.0010.0000.0000.0000.000
175A298LYS10.9500.97325.695-0.024-0.0240.0000.0000.0000.000
176A299HIS0-0.070-0.02625.9080.0020.0020.0000.0000.0000.000
177A300GLU-1-0.876-0.91725.4240.0500.0500.0000.0000.0000.000
178A301ASP-1-0.895-0.95922.7460.0490.0490.0000.0000.0000.000
179A302ALA0-0.002-0.00124.305-0.002-0.0020.0000.0000.0000.000
180A303GLU-1-0.941-0.98725.4880.0120.0120.0000.0000.0000.000
181A304ASN0-0.116-0.06522.129-0.001-0.0010.0000.0000.0000.000
182A305ILE0-0.0020.01421.950-0.008-0.0080.0000.0000.0000.000
183A306GLY00.0380.02518.3150.0100.0100.0000.0000.0000.000
184A307TYR0-0.028-0.00818.391-0.015-0.0150.0000.0000.0000.000
185A308VAL00.006-0.00312.7670.0140.0140.0000.0000.0000.000
186A309ILE0-0.0100.00915.180-0.017-0.0170.0000.0000.0000.000
187A310PRO00.0210.02614.3640.0240.0240.0000.0000.0000.000
188A311THR00.0820.00511.7810.0150.0150.0000.0000.0000.000
189A312PRO00.0010.01414.5930.0120.0120.0000.0000.0000.000
190A313VAL00.0440.02818.0880.0030.0030.0000.0000.0000.000
191A314ILE0-0.023-0.00612.2810.0100.0100.0000.0000.0000.000
192A315VAL0-0.024-0.02015.7220.0020.0020.0000.0000.0000.000
193A316HIS0-0.008-0.01917.7430.0000.0000.0000.0000.0000.000
194A317PHE0-0.019-0.00117.422-0.001-0.0010.0000.0000.0000.000
195A318ILE0-0.020-0.01314.7440.0010.0010.0000.0000.0000.000
196A319GLN0-0.002-0.00519.334-0.010-0.0100.0000.0000.0000.000
197A320ASP-1-0.869-0.93022.1670.0140.0140.0000.0000.0000.000
198A321TYR0-0.069-0.02120.4520.0000.0000.0000.0000.0000.000
199A322GLU-1-0.881-0.92419.6110.0270.0270.0000.0000.0000.000
200A323LYS10.8140.91723.755-0.017-0.0170.0000.0000.0000.000