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: 987M2

Calculation Name: 5I32-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I32

Chain ID: A

ChEMBL ID:

UniProt ID: Q41951

Base Structure: X-ray

Registration Date: 2023-09-22

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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2536362.337317
FMO2-HF: Nuclear repulsion 2454443.709823
FMO2-HF: Total energy -81918.627494
FMO2-MP2: Total energy -82161.465609


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-3.6770.2236.092-5.112-4.879-0.033
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.008
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].
3A3GLY00.0290.0123.846-0.2180.500-0.002-0.295-0.4210.001
4A4VAL0-0.016-0.0136.2840.5120.5120.0000.0000.0000.000
5A5ALA00.0390.0319.6470.1280.1280.0000.0000.0000.000
6A6PHE00.025-0.00112.1220.0710.0710.0000.0000.0000.000
7A7GLY00.0630.02615.6560.0280.0280.0000.0000.0000.000
8A8SER0-0.020-0.01717.6460.0210.0210.0000.0000.0000.000
9A9PHE00.0500.00921.2720.0000.0000.0000.0000.0000.000
10A10ASP-1-0.891-0.93724.478-0.128-0.1280.0000.0000.0000.000
11A11ASP-1-0.827-0.91019.529-0.231-0.2310.0000.0000.0000.000
12A12SER0-0.034-0.00720.6720.0060.0060.0000.0000.0000.000
13A13PHE00.0090.01623.0340.0040.0040.0000.0000.0000.000
14A14SER00.0080.01823.7510.0200.0200.0000.0000.0000.000
15A15LEU00.008-0.02026.559-0.001-0.0010.0000.0000.0000.000
16A16ALA0-0.0080.01823.6850.0080.0080.0000.0000.0000.000
17A17SER00.0510.00622.4740.0020.0020.0000.0000.0000.000
18A18LEU00.0000.00324.061-0.002-0.0020.0000.0000.0000.000
19A19ARG10.8810.93527.1420.0640.0640.0000.0000.0000.000
20A20ALA00.0290.02922.5040.0040.0040.0000.0000.0000.000
21A21TYR0-0.021-0.04722.290-0.006-0.0060.0000.0000.0000.000
22A22LEU00.0050.00826.1560.0030.0030.0000.0000.0000.000
23A23ALA00.0280.01325.7640.0050.0050.0000.0000.0000.000
24A24GLU-1-0.703-0.80522.304-0.144-0.1440.0000.0000.0000.000
25A25PHE0-0.0330.00925.8130.0030.0030.0000.0000.0000.000
26A26ILE0-0.008-0.00829.1970.0050.0050.0000.0000.0000.000
27A27SER0-0.009-0.02126.7290.0050.0050.0000.0000.0000.000
28A28THR0-0.024-0.04226.5280.0010.0010.0000.0000.0000.000
29A29LEU0-0.040-0.00128.5310.0030.0030.0000.0000.0000.000
30A30LEU0-0.006-0.01231.8250.0040.0040.0000.0000.0000.000
31A31PHE0-0.014-0.00927.1030.0030.0030.0000.0000.0000.000
32A32VAL0-0.007-0.00629.8150.0030.0030.0000.0000.0000.000
33A33PHE0-0.0080.00132.2700.0040.0040.0000.0000.0000.000
34A34ALA00.0430.01134.1900.0030.0030.0000.0000.0000.000
35A35GLY00.0380.01533.0700.0030.0030.0000.0000.0000.000
36A36VAL0-0.001-0.00533.7510.0030.0030.0000.0000.0000.000
37A37GLY00.0550.02236.0980.0030.0030.0000.0000.0000.000
38A38SER0-0.064-0.04436.5850.0040.0040.0000.0000.0000.000
39A39ALA00.0140.00937.4320.0030.0030.0000.0000.0000.000
40A40ILE00.0100.00739.4320.0020.0020.0000.0000.0000.000
41A41ALA0-0.023-0.01042.0110.0030.0030.0000.0000.0000.000
42A42TYR0-0.018-0.02441.9780.0030.0030.0000.0000.0000.000
43A43ALA00.0330.03843.6150.0020.0020.0000.0000.0000.000
44A44LYS10.9390.96145.4920.0310.0310.0000.0000.0000.000
45A45LEU0-0.082-0.04545.5990.0020.0020.0000.0000.0000.000
46A46THR0-0.047-0.03246.6460.0010.0010.0000.0000.0000.000
47A47SER0-0.080-0.02949.3560.0010.0010.0000.0000.0000.000
48A48ASP-1-0.938-0.98246.674-0.039-0.0390.0000.0000.0000.000
49A49ALA0-0.0030.02147.368-0.001-0.0010.0000.0000.0000.000
50A50ALA00.0190.00244.244-0.002-0.0020.0000.0000.0000.000
51A51LEU0-0.0250.00437.6660.0020.0020.0000.0000.0000.000
52A52ASP-1-0.790-0.89142.148-0.027-0.0270.0000.0000.0000.000
53A53THR0-0.002-0.01439.607-0.001-0.0010.0000.0000.0000.000
54A54PRO00.002-0.00540.2290.0000.0000.0000.0000.0000.000
55A55GLY00.0610.02641.0530.0000.0000.0000.0000.0000.000
56A56LEU0-0.043-0.01334.503-0.002-0.0020.0000.0000.0000.000
57A57VAL0-0.009-0.01036.152-0.002-0.0020.0000.0000.0000.000
58A58ALA0-0.0090.00036.6280.0000.0000.0000.0000.0000.000
59A59ILE00.0160.00934.516-0.001-0.0010.0000.0000.0000.000
60A60ALA00.0050.01732.432-0.004-0.0040.0000.0000.0000.000
61A61VAL0-0.007-0.00632.082-0.001-0.0010.0000.0000.0000.000
62A62CYS0-0.070-0.01333.4130.0000.0000.0000.0000.0000.000
63A63HIS00.0120.00729.955-0.008-0.0080.0000.0000.0000.000
64A64GLY00.0210.02028.606-0.004-0.0040.0000.0000.0000.000
65A65PHE0-0.020-0.02828.9670.0010.0010.0000.0000.0000.000
66A66ALA00.0190.01430.8890.0000.0000.0000.0000.0000.000
67A67LEU0-0.013-0.00123.704-0.003-0.0030.0000.0000.0000.000
68A68PHE00.0150.00926.296-0.002-0.0020.0000.0000.0000.000
69A69VAL0-0.011-0.00226.9920.0010.0010.0000.0000.0000.000
70A70ALA00.0050.00927.456-0.001-0.0010.0000.0000.0000.000
71A71VAL00.0160.01821.629-0.005-0.0050.0000.0000.0000.000
72A72ALA0-0.017-0.01224.0070.0000.0000.0000.0000.0000.000
73A73ILE0-0.060-0.03325.9440.0030.0030.0000.0000.0000.000
74A74GLY00.0550.03424.534-0.001-0.0010.0000.0000.0000.000
75A75ALA0-0.0030.00421.372-0.008-0.0080.0000.0000.0000.000
76A76ASN0-0.046-0.02821.134-0.002-0.0020.0000.0000.0000.000
77A77ILE0-0.052-0.02623.4540.0040.0040.0000.0000.0000.000
78A78SER0-0.037-0.04621.459-0.001-0.0010.0000.0000.0000.000
79A79GLY0-0.0030.02518.398-0.029-0.0290.0000.0000.0000.000
80A80GLY0-0.045-0.01719.3660.0050.0050.0000.0000.0000.000
81A81HIS00.0230.01016.323-0.011-0.0110.0000.0000.0000.000
82A82VAL0-0.025-0.01620.2220.0030.0030.0000.0000.0000.000
83A83ASN00.015-0.01220.722-0.004-0.0040.0000.0000.0000.000
84A84PRO00.0540.03419.896-0.020-0.0200.0000.0000.0000.000
85A85ALA00.0280.01418.015-0.038-0.0380.0000.0000.0000.000
86A86VAL0-0.0150.00416.137-0.037-0.0370.0000.0000.0000.000
87A87THR00.015-0.00514.956-0.032-0.0320.0000.0000.0000.000
88A88PHE0-0.041-0.01214.716-0.065-0.0650.0000.0000.0000.000
89A89GLY00.0510.02611.993-0.091-0.0910.0000.0000.0000.000
90A90LEU0-0.0080.00210.263-0.122-0.1220.0000.0000.0000.000
91A91ALA00.0010.00910.129-0.133-0.1330.0000.0000.0000.000
92A92VAL0-0.060-0.0388.485-0.176-0.1760.0000.0000.0000.000
93A93GLY00.0190.0265.710-0.309-0.3090.0000.0000.0000.000
94A94GLY0-0.024-0.0036.539-0.074-0.0740.0000.0000.0000.000
95A95GLN0-0.074-0.0476.8230.4610.4610.0000.0000.0000.000
96A96ILE0-0.038-0.01610.4520.1410.1410.0000.0000.0000.000
97A97THR0-0.006-0.00612.798-0.102-0.1020.0000.0000.0000.000
98A98VAL00.0290.00914.1660.0340.0340.0000.0000.0000.000
99A99ILE0-0.042-0.00816.3530.0440.0440.0000.0000.0000.000
100A100THR00.0120.01218.0660.0150.0150.0000.0000.0000.000
101A101GLY00.0360.01317.5830.0280.0280.0000.0000.0000.000
102A102VAL00.0020.00318.4840.0260.0260.0000.0000.0000.000
103A103PHE00.010-0.00321.5250.0260.0260.0000.0000.0000.000
104A104TYR0-0.017-0.03319.6150.0210.0210.0000.0000.0000.000
105A105TRP0-0.040-0.01118.7120.0210.0210.0000.0000.0000.000
106A106ILE0-0.011-0.00123.2280.0180.0180.0000.0000.0000.000
107A107ALA00.0050.00525.6120.0140.0140.0000.0000.0000.000
108A108GLN0-0.009-0.03320.7860.0060.0060.0000.0000.0000.000
109A109LEU0-0.006-0.00526.0140.0120.0120.0000.0000.0000.000
110A110LEU0-0.0060.01228.5940.0110.0110.0000.0000.0000.000
111A111GLY00.0220.01230.1200.0090.0090.0000.0000.0000.000
112A112SER0-0.018-0.04729.5520.0110.0110.0000.0000.0000.000
113A113THR00.016-0.01631.5770.0060.0060.0000.0000.0000.000
114A114ALA0-0.010-0.00334.3360.0060.0060.0000.0000.0000.000
115A115ALA0-0.016-0.00234.2380.0060.0060.0000.0000.0000.000
116A116CYS0-0.0180.00634.5810.0050.0050.0000.0000.0000.000
117A117PHE00.0240.01137.5210.0040.0040.0000.0000.0000.000
118A118LEU0-0.026-0.01038.1500.0040.0040.0000.0000.0000.000
119A119LEU0-0.0130.01037.4830.0040.0040.0000.0000.0000.000
120A120LYS10.8830.96541.3170.0540.0540.0000.0000.0000.000
121A121TYR0-0.027-0.00743.5720.0030.0030.0000.0000.0000.000
122A122VAL0-0.011-0.01543.3610.0020.0020.0000.0000.0000.000
123A123THR0-0.070-0.05343.3040.0020.0020.0000.0000.0000.000
124A124GLY0-0.0120.00146.4010.0010.0010.0000.0000.0000.000
125A125GLY0-0.0020.00047.6260.0010.0010.0000.0000.0000.000
126A126LEU0-0.022-0.00845.781-0.001-0.0010.0000.0000.0000.000
127A127ALA00.0270.01643.711-0.003-0.0030.0000.0000.0000.000
128A128VAL00.0310.00937.8760.0010.0010.0000.0000.0000.000
129A129PRO0-0.022-0.00537.670-0.002-0.0020.0000.0000.0000.000
130A130THR00.002-0.00235.654-0.002-0.0020.0000.0000.0000.000
131A131HIS0-0.061-0.02130.316-0.001-0.0010.0000.0000.0000.000
132A132SER0-0.009-0.00233.395-0.003-0.0030.0000.0000.0000.000
133A133VAL0-0.023-0.01331.5290.0000.0000.0000.0000.0000.000
134A134ALA00.0080.01634.0910.0030.0030.0000.0000.0000.000
135A135ALA00.008-0.01136.899-0.001-0.0010.0000.0000.0000.000
136A136GLY0-0.010-0.00139.3680.0040.0040.0000.0000.0000.000
137A137LEU0-0.064-0.01032.4520.0010.0010.0000.0000.0000.000
138A138GLY00.0500.02534.247-0.002-0.0020.0000.0000.0000.000
139A139SER0-0.013-0.03431.366-0.002-0.0020.0000.0000.0000.000
140A140ILE0-0.0160.00627.580-0.009-0.0090.0000.0000.0000.000
141A141GLU-1-0.779-0.89827.623-0.089-0.0890.0000.0000.0000.000
142A142GLY00.0180.02028.4180.0000.0000.0000.0000.0000.000
143A143VAL0-0.009-0.01623.796-0.005-0.0050.0000.0000.0000.000
144A144VAL0-0.009-0.01123.734-0.011-0.0110.0000.0000.0000.000
145A145MET00.0090.01423.775-0.001-0.0010.0000.0000.0000.000
146A146GLU-1-0.710-0.85324.052-0.113-0.1130.0000.0000.0000.000
147A147ILE0-0.0370.00818.671-0.010-0.0100.0000.0000.0000.000
148A148ILE00.0050.00719.498-0.009-0.0090.0000.0000.0000.000
149A149ILE0-0.0160.00320.4320.0040.0040.0000.0000.0000.000
150A150THR0-0.008-0.02518.0840.0050.0050.0000.0000.0000.000
151A151PHE0-0.0270.00413.011-0.009-0.0090.0000.0000.0000.000
152A152ALA00.0110.00516.2640.0060.0060.0000.0000.0000.000
153A153LEU0-0.0050.01618.3180.0150.0150.0000.0000.0000.000
154A154VAL00.0140.00112.9800.0110.0110.0000.0000.0000.000
155A155TYR00.0300.01612.4290.0020.0020.0000.0000.0000.000
156A156THR0-0.033-0.02014.1890.0450.0450.0000.0000.0000.000
157A157VAL00.0000.00814.8080.0250.0250.0000.0000.0000.000
158A158TYR0-0.024-0.0387.488-0.022-0.0220.0000.0000.0000.000
159A159ALA0-0.0080.00012.1790.0490.0490.0000.0000.0000.000
160A160THR0-0.087-0.05013.4660.0290.0290.0000.0000.0000.000
161A161ALA00.018-0.00315.1890.0140.0140.0000.0000.0000.000
162A162ALA0-0.0210.00610.5610.0060.0060.0000.0000.0000.000
163A163ASP-1-0.729-0.8409.7560.4810.4810.0000.0000.0000.000
164A164PRO0-0.007-0.0098.860-0.025-0.0250.0000.0000.0000.000
165A165LYS10.7710.8649.174-0.633-0.6330.0000.0000.0000.000
166A166LYS10.8700.94713.545-0.078-0.0780.0000.0000.0000.000
167A167GLY00.0360.01315.491-0.018-0.0180.0000.0000.0000.000
168A168SER00.005-0.00818.703-0.015-0.0150.0000.0000.0000.000
169A169LEU00.0240.01316.818-0.020-0.0200.0000.0000.0000.000
170A170GLY00.0390.01618.945-0.020-0.0200.0000.0000.0000.000
171A171THR0-0.072-0.03519.519-0.012-0.0120.0000.0000.0000.000
172A172ILE0-0.013-0.00722.305-0.009-0.0090.0000.0000.0000.000
173A173ALA00.0290.02918.966-0.009-0.0090.0000.0000.0000.000
174A174PRO00.0200.00220.840-0.011-0.0110.0000.0000.0000.000
175A175LEU00.0000.01023.327-0.007-0.0070.0000.0000.0000.000
176A176ALA0-0.0030.00321.251-0.003-0.0030.0000.0000.0000.000
177A177ILE00.016-0.00218.413-0.008-0.0080.0000.0000.0000.000
178A178GLY00.0130.01021.929-0.010-0.0100.0000.0000.0000.000
179A179LEU0-0.005-0.02125.698-0.003-0.0030.0000.0000.0000.000
180A180ILE0-0.0260.00621.0390.0000.0000.0000.0000.0000.000
181A181VAL00.0340.00623.639-0.005-0.0050.0000.0000.0000.000
182A182GLY00.0220.01525.7270.0000.0000.0000.0000.0000.000
183A183ALA0-0.010-0.02026.7870.0010.0010.0000.0000.0000.000
184A184ASN00.028-0.01322.6590.0070.0070.0000.0000.0000.000
185A185ILE0-0.0110.00327.137-0.002-0.0020.0000.0000.0000.000
186A186LEU0-0.031-0.01930.1750.0010.0010.0000.0000.0000.000
187A187ALA0-0.0180.00928.7010.0020.0020.0000.0000.0000.000
188A188ALA00.0400.00328.168-0.001-0.0010.0000.0000.0000.000
189A189GLY0-0.0070.00830.300-0.004-0.0040.0000.0000.0000.000
190A190PRO0-0.019-0.02433.135-0.002-0.0020.0000.0000.0000.000
191A191PHE0-0.038-0.00931.7890.0010.0010.0000.0000.0000.000
192A192SER0-0.003-0.03128.5570.0000.0000.0000.0000.0000.000
193A193GLY00.0590.04031.273-0.005-0.0050.0000.0000.0000.000
194A194GLY0-0.023-0.01228.1360.0020.0020.0000.0000.0000.000
195A195SER0-0.035-0.02426.8640.0010.0010.0000.0000.0000.000
196A196MET0-0.059-0.00822.3260.0040.0040.0000.0000.0000.000
197A197ASN00.000-0.00522.078-0.023-0.0230.0000.0000.0000.000
198A198PRO00.0720.04222.0700.0110.0110.0000.0000.0000.000
199A199ALA00.0360.01225.0660.0100.0100.0000.0000.0000.000
200A200ARG10.8580.93826.8390.0910.0910.0000.0000.0000.000
201A201SER00.0280.01728.3430.0070.0070.0000.0000.0000.000
202A202PHE0-0.009-0.00429.1010.0050.0050.0000.0000.0000.000
203A203GLY00.0170.01530.9460.0040.0040.0000.0000.0000.000
204A204PRO00.004-0.02532.6430.0040.0040.0000.0000.0000.000
205A205ALA00.0150.02633.6010.0040.0040.0000.0000.0000.000
206A206VAL0-0.043-0.02734.1260.0040.0040.0000.0000.0000.000
207A207ALA0-0.038-0.02136.7950.0040.0040.0000.0000.0000.000
208A208ALA0-0.052-0.01938.7940.0050.0050.0000.0000.0000.000
209A209GLY0-0.0210.00039.5690.0030.0030.0000.0000.0000.000
210A210ASP-1-0.865-0.92538.708-0.075-0.0750.0000.0000.0000.000
211A211PHE00.024-0.00832.258-0.005-0.0050.0000.0000.0000.000
212A212SER0-0.037-0.00834.681-0.007-0.0070.0000.0000.0000.000
213A213GLY00.0100.00533.3160.0010.0010.0000.0000.0000.000
214A214HIS00.0450.02129.421-0.012-0.0120.0000.0000.0000.000
215A215TRP00.0440.00727.645-0.010-0.0100.0000.0000.0000.000
216A216VAL00.0110.01626.678-0.015-0.0150.0000.0000.0000.000
217A217TYR0-0.059-0.05325.641-0.011-0.0110.0000.0000.0000.000
218A218TRP0-0.039-0.02122.876-0.013-0.0130.0000.0000.0000.000
219A219VAL00.001-0.01421.994-0.019-0.0190.0000.0000.0000.000
220A220GLY00.0330.02021.180-0.017-0.0170.0000.0000.0000.000
221A221PRO00.0210.00220.307-0.017-0.0170.0000.0000.0000.000
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