FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: V5491

Calculation Name: 5IF3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IF3

Chain ID: A

ChEMBL ID:

UniProt ID: A4JKB1

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2045691.15652
FMO2-HF: Nuclear repulsion 1968549.071749
FMO2-HF: Total energy -77142.084771
FMO2-MP2: Total energy -77368.511782


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:6:CYS)


Summations of interaction energy for fragment #1(A:6:CYS)
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.
-2.167-0.694-0.005-0.673-0.7950.003
Interaction energy analysis for fragmet #1(A:6:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.029
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].
3A8PRO00.0640.0373.795-1.4090.064-0.005-0.673-0.7950.003
4A9ARG10.9100.9456.0040.3810.3810.0000.0000.0000.000
5A10VAL00.0040.0157.8160.2680.2680.0000.0000.0000.000
6A11ARG10.8170.8736.470-0.650-0.6500.0000.0000.0000.000
7A12ALA00.0080.00212.3950.0750.0750.0000.0000.0000.000
8A13ILE00.0060.01015.765-0.018-0.0180.0000.0000.0000.000
9A14VAL00.0020.00518.3410.0080.0080.0000.0000.0000.000
10A15THR00.0490.03421.019-0.006-0.0060.0000.0000.0000.000
11A16GLY00.003-0.00724.033-0.002-0.0020.0000.0000.0000.000
12A17HIS0-0.010-0.00420.6600.0170.0170.0000.0000.0000.000
13A18THR0-0.036-0.00923.470-0.014-0.0140.0000.0000.0000.000
14A19ARG10.9740.97925.3350.1160.1160.0000.0000.0000.000
15A20GLY00.0150.01328.0460.0030.0030.0000.0000.0000.000
16A21LEU00.0650.03227.179-0.011-0.0110.0000.0000.0000.000
17A22GLY00.0560.02524.819-0.013-0.0130.0000.0000.0000.000
18A23ALA0-0.026-0.00323.237-0.021-0.0210.0000.0000.0000.000
19A24SER00.0320.01322.950-0.020-0.0200.0000.0000.0000.000
20A25LEU0-0.036-0.01721.904-0.020-0.0200.0000.0000.0000.000
21A26ALA00.0080.00118.939-0.032-0.0320.0000.0000.0000.000
22A27GLU-1-0.854-0.92918.089-0.323-0.3230.0000.0000.0000.000
23A28GLN0-0.005-0.00718.463-0.031-0.0310.0000.0000.0000.000
24A29LEU0-0.033-0.01916.103-0.029-0.0290.0000.0000.0000.000
25A30LEU00.0230.00912.720-0.080-0.0800.0000.0000.0000.000
26A31GLN0-0.029-0.00713.684-0.105-0.1050.0000.0000.0000.000
27A32GLN0-0.084-0.03314.9450.0010.0010.0000.0000.0000.000
28A33ASP-1-0.862-0.9087.959-1.964-1.9640.0000.0000.0000.000
29A34ILE0-0.052-0.01210.207-0.105-0.1050.0000.0000.0000.000
30A35ALA00.0200.0099.0440.0190.0190.0000.0000.0000.000
31A36VAL0-0.012-0.01411.1440.1560.1560.0000.0000.0000.000
32A37LEU0-0.0130.00814.272-0.011-0.0110.0000.0000.0000.000
33A38GLY00.0250.00215.9540.0190.0190.0000.0000.0000.000
34A39VAL0-0.008-0.00419.1760.0160.0160.0000.0000.0000.000
35A40SER0-0.005-0.03221.9820.0070.0070.0000.0000.0000.000
36A41ARG10.9430.99024.9520.0690.0690.0000.0000.0000.000
37A42SER00.0120.01026.4320.0060.0060.0000.0000.0000.000
38A43ARG10.9240.95519.1620.1830.1830.0000.0000.0000.000
39A44HIS0-0.034-0.03421.1870.0100.0100.0000.0000.0000.000
40A45PRO0-0.029-0.01422.723-0.011-0.0110.0000.0000.0000.000
41A46SER00.019-0.00222.548-0.002-0.0020.0000.0000.0000.000
42A47LEU00.0170.01717.698-0.028-0.0280.0000.0000.0000.000
43A48ALA00.0510.02016.516-0.062-0.0620.0000.0000.0000.000
44A49ALA0-0.024-0.00616.112-0.062-0.0620.0000.0000.0000.000
45A50THR0-0.049-0.01216.934-0.013-0.0130.0000.0000.0000.000
46A51ALA0-0.041-0.02213.701-0.062-0.0620.0000.0000.0000.000
47A52GLY00.0440.02011.840-0.194-0.1940.0000.0000.0000.000
48A53ASP-1-0.899-0.9628.384-0.931-0.9310.0000.0000.0000.000
49A54ARG10.7270.8527.7561.4761.4760.0000.0000.0000.000
50A55LEU0-0.030-0.0069.9660.1480.1480.0000.0000.0000.000
51A56VAL00.0200.01311.5230.0250.0250.0000.0000.0000.000
52A57GLU-1-0.775-0.87614.154-0.228-0.2280.0000.0000.0000.000
53A58THR0-0.023-0.01717.9210.0280.0280.0000.0000.0000.000
54A59GLU-1-0.951-0.96920.177-0.099-0.0990.0000.0000.0000.000
55A60LEU00.026-0.00523.7930.0150.0150.0000.0000.0000.000
56A61ASP-1-0.827-0.90025.930-0.065-0.0650.0000.0000.0000.000
57A62LEU00.012-0.01125.3630.0080.0080.0000.0000.0000.000
58A63SER0-0.091-0.06729.3250.0050.0050.0000.0000.0000.000
59A64ASP-1-0.826-0.90231.915-0.016-0.0160.0000.0000.0000.000
60A65THR00.036-0.00731.5090.0020.0020.0000.0000.0000.000
61A66ALA00.0240.02431.7280.0060.0060.0000.0000.0000.000
62A67ALA00.0170.01029.3200.0060.0060.0000.0000.0000.000
63A68VAL0-0.033-0.01626.7330.0030.0030.0000.0000.0000.000
64A69ALA0-0.001-0.00226.8570.0080.0080.0000.0000.0000.000
65A70ALA00.0120.01027.6860.0100.0100.0000.0000.0000.000
66A71TRP0-0.001-0.01419.1130.0110.0110.0000.0000.0000.000
67A72LEU0-0.079-0.04722.7670.0120.0120.0000.0000.0000.000
68A73ALA0-0.035-0.00123.6990.0160.0160.0000.0000.0000.000
69A74GLY00.0010.01322.7480.0120.0120.0000.0000.0000.000
70A75GLY0-0.024-0.03018.9130.0080.0080.0000.0000.0000.000
71A76ALA0-0.0010.00916.6640.0380.0380.0000.0000.0000.000
72A77LEU00.0510.02215.7500.0150.0150.0000.0000.0000.000
73A78ARG11.0000.98615.731-0.190-0.1900.0000.0000.0000.000
74A79SER00.0050.00311.7070.0510.0510.0000.0000.0000.000
75A80PHE0-0.0220.00411.2790.1480.1480.0000.0000.0000.000
76A81VAL00.0000.00111.1870.0080.0080.0000.0000.0000.000
77A82ASP-1-0.898-0.93310.8470.9020.9020.0000.0000.0000.000
78A83GLY00.0640.0488.8350.2460.2460.0000.0000.0000.000
79A84ALA0-0.0290.0028.794-0.007-0.0070.0000.0000.0000.000
80A85SER0-0.033-0.01510.1810.0150.0150.0000.0000.0000.000
81A86LEU0-0.057-0.02512.0600.0080.0080.0000.0000.0000.000
82A87VAL00.0280.01513.395-0.049-0.0490.0000.0000.0000.000
83A88LEU0-0.017-0.00915.5960.0230.0230.0000.0000.0000.000
84A89LEU00.0140.01618.331-0.014-0.0140.0000.0000.0000.000
85A90PHE00.0300.00719.1090.0060.0060.0000.0000.0000.000
86A91ASN0-0.010-0.02323.241-0.006-0.0060.0000.0000.0000.000
87A92ASN0-0.014-0.03525.5770.0050.0050.0000.0000.0000.000
88A93ALA0-0.061-0.01927.2170.0020.0020.0000.0000.0000.000
89A94GLY00.0190.00029.0240.0080.0080.0000.0000.0000.000
90A95VAL0-0.077-0.03532.788-0.006-0.0060.0000.0000.0000.000
91A96VAL00.0320.00336.1000.0040.0040.0000.0000.0000.000
92A97ASP-1-0.938-0.93539.414-0.054-0.0540.0000.0000.0000.000
93A98PRO0-0.042-0.02440.7520.0000.0000.0000.0000.0000.000
94A99ILE00.0330.00342.8880.0020.0020.0000.0000.0000.000
95A100GLY00.005-0.00145.9240.0010.0010.0000.0000.0000.000
96A101PRO0-0.025-0.02149.2510.0010.0010.0000.0000.0000.000
97A102LEU00.0750.02050.030-0.001-0.0010.0000.0000.0000.000
98A103ALA0-0.025-0.01052.1240.0000.0000.0000.0000.0000.000
99A104ALA0-0.027-0.01251.0680.0000.0000.0000.0000.0000.000
100A105GLN0-0.069-0.02847.3980.0000.0000.0000.0000.0000.000
101A106ASP-1-0.788-0.89546.200-0.028-0.0280.0000.0000.0000.000
102A107PRO00.029-0.00546.053-0.001-0.0010.0000.0000.0000.000
103A108ALA00.0080.00743.6500.0010.0010.0000.0000.0000.000
104A109LEU0-0.006-0.00841.497-0.002-0.0020.0000.0000.0000.000
105A110VAL0-0.0040.00241.334-0.002-0.0020.0000.0000.0000.000
106A111ALA0-0.0020.00441.1540.0000.0000.0000.0000.0000.000
107A112ARG10.8910.95033.1280.0530.0530.0000.0000.0000.000
108A113ALA00.0400.02036.577-0.002-0.0020.0000.0000.0000.000
109A114VAL00.0070.00136.822-0.001-0.0010.0000.0000.0000.000
110A115ALA0-0.0080.00234.9100.0010.0010.0000.0000.0000.000
111A116LEU0-0.017-0.01530.3690.0000.0000.0000.0000.0000.000
112A117ASN0-0.033-0.03231.877-0.007-0.0070.0000.0000.0000.000
113A118VAL0-0.009-0.00233.456-0.001-0.0010.0000.0000.0000.000
114A119ALA00.0030.00732.9630.0030.0030.0000.0000.0000.000
115A120ALA00.0450.03128.5980.0050.0050.0000.0000.0000.000
116A121PRO00.0080.00427.9240.0040.0040.0000.0000.0000.000
117A122LEU0-0.0060.01428.1000.0050.0050.0000.0000.0000.000
118A123MET0-0.045-0.01328.5390.0060.0060.0000.0000.0000.000
119A124LEU00.002-0.00323.0280.0100.0100.0000.0000.0000.000
120A125SER0-0.045-0.04423.8880.0050.0050.0000.0000.0000.000
121A126ALA0-0.0040.00824.7550.0090.0090.0000.0000.0000.000
122A127ALA00.0310.00923.3850.0130.0130.0000.0000.0000.000
123A128LEU0-0.008-0.00917.8000.0200.0200.0000.0000.0000.000
124A129VAL0-0.011-0.01320.1660.0250.0250.0000.0000.0000.000
125A130GLN0-0.050-0.02521.8400.0100.0100.0000.0000.0000.000
126A131ALA0-0.047-0.00618.2810.0210.0210.0000.0000.0000.000
127A132ALA00.0000.00716.5820.0500.0500.0000.0000.0000.000
128A133ALA00.0300.02416.317-0.028-0.0280.0000.0000.0000.000
129A134ALA0-0.0120.00016.563-0.002-0.0020.0000.0000.0000.000
130A135PRO0-0.015-0.02414.3090.0400.0400.0000.0000.0000.000
131A136THR0-0.021-0.01413.239-0.026-0.0260.0000.0000.0000.000
132A137GLU-1-0.736-0.83915.569-0.020-0.0200.0000.0000.0000.000
133A138CYS0-0.029-0.01117.037-0.010-0.0100.0000.0000.0000.000
134A139ARG10.8370.89519.5700.0600.0600.0000.0000.0000.000
135A140VAL00.0320.02121.307-0.014-0.0140.0000.0000.0000.000
136A141LEU00.0050.00323.9940.0030.0030.0000.0000.0000.000
137A142HIS0-0.012-0.01025.803-0.014-0.0140.0000.0000.0000.000
138A143VAL00.0150.02227.311-0.002-0.0020.0000.0000.0000.000
139A144SER00.000-0.01829.9190.0060.0060.0000.0000.0000.000
140A145SER00.032-0.01233.619-0.006-0.0060.0000.0000.0000.000
141A146GLY00.0550.03436.6540.0040.0040.0000.0000.0000.000
142A147ALA00.000-0.01439.8400.0040.0040.0000.0000.0000.000
143A148ALA0-0.0080.00437.8140.0030.0030.0000.0000.0000.000
144A149ARG10.7470.84034.9040.0500.0500.0000.0000.0000.000
145A150ASN0-0.035-0.00242.3340.0040.0040.0000.0000.0000.000
146A151ALA00.0370.01544.480-0.002-0.0020.0000.0000.0000.000
147A152TYR00.0280.00243.347-0.001-0.0010.0000.0000.0000.000
148A153ALA00.0480.01947.7520.0010.0010.0000.0000.0000.000
149A154GLY00.0000.00448.895-0.002-0.0020.0000.0000.0000.000
150A155TRP00.0470.02340.084-0.002-0.0020.0000.0000.0000.000
151A156SER00.0440.02744.327-0.001-0.0010.0000.0000.0000.000
152A157VAL00.0590.03741.3260.0010.0010.0000.0000.0000.000
153A158TYR00.0350.01235.7070.0000.0000.0000.0000.0000.000
154A159CYS0-0.018-0.00739.815-0.001-0.0010.0000.0000.0000.000
155A160ALA00.0050.01441.2590.0010.0010.0000.0000.0000.000
156A161THR0-0.054-0.03237.0000.0000.0000.0000.0000.0000.000
157A162LYS10.9160.94732.4020.0640.0640.0000.0000.0000.000
158A163ALA00.0210.01536.9270.0000.0000.0000.0000.0000.000
159A164ALA0-0.020-0.00437.1780.0030.0030.0000.0000.0000.000
160A165LEU0-0.0060.00131.5630.0030.0030.0000.0000.0000.000
161A166ASP-1-0.769-0.83733.785-0.040-0.0400.0000.0000.0000.000
162A167HIS00.0290.01135.6940.0000.0000.0000.0000.0000.000
163A168HIS00.0620.04729.606-0.002-0.0020.0000.0000.0000.000
164A169ALA00.0140.00531.6280.0040.0040.0000.0000.0000.000
165A170ARG10.8720.93132.5930.0250.0250.0000.0000.0000.000
166A171ALA00.0110.00935.6080.0030.0030.0000.0000.0000.000
167A172VAL00.0390.02128.8630.0030.0030.0000.0000.0000.000
168A173ALA0-0.052-0.02631.1670.0050.0050.0000.0000.0000.000
169A174LEU0-0.065-0.03132.2070.0020.0020.0000.0000.0000.000
170A175ASP-1-0.922-0.93931.5770.0300.0300.0000.0000.0000.000
171A176ALA0-0.032-0.01731.2910.0000.0000.0000.0000.0000.000
172A177ASN0-0.035-0.02026.3900.0100.0100.0000.0000.0000.000
173A178ARG10.8370.90918.678-0.153-0.1530.0000.0000.0000.000
174A179ALA00.012-0.01020.8280.0000.0000.0000.0000.0000.000
175A180LEU0-0.0080.00921.551-0.001-0.0010.0000.0000.0000.000
176A181ARG10.8500.92521.9710.0060.0060.0000.0000.0000.000
177A182ILE00.0290.01724.724-0.005-0.0050.0000.0000.0000.000
178A183CYS0-0.029-0.01227.3090.0010.0010.0000.0000.0000.000
179A184SER00.0100.00328.773-0.007-0.0070.0000.0000.0000.000
180A185VAL00.028-0.00128.7320.0030.0030.0000.0000.0000.000
181A186ALA0-0.027-0.00131.567-0.003-0.0030.0000.0000.0000.000
182A187PRO0-0.0020.00030.634-0.001-0.0010.0000.0000.0000.000
183A188GLY00.0080.00832.408-0.005-0.0050.0000.0000.0000.000
184A189VAL0-0.0090.00131.9700.0000.0000.0000.0000.0000.000
185A190VAL00.0020.00134.5880.0030.0030.0000.0000.0000.000
186A222SER0-0.0140.00157.5060.0000.0000.0000.0000.0000.000
187A223THR0-0.033-0.05057.9190.0010.0010.0000.0000.0000.000
188A224PRO00.0480.00357.069-0.001-0.0010.0000.0000.0000.000
189A225ASP-1-0.863-0.92659.0730.0040.0040.0000.0000.0000.000
190A226GLU-1-0.914-0.94661.9110.0040.0040.0000.0000.0000.000
191A227ALA00.0150.00557.708-0.001-0.0010.0000.0000.0000.000
192A228ALA00.0210.00859.843-0.001-0.0010.0000.0000.0000.000
193A229ARG10.9260.97360.981-0.003-0.0030.0000.0000.0000.000
194A230HIS00.0410.02261.246-0.001-0.0010.0000.0000.0000.000
195A231LEU00.0180.00956.429-0.001-0.0010.0000.0000.0000.000
196A232ILE00.0050.01060.515-0.001-0.0010.0000.0000.0000.000
197A233ARG10.8930.93863.3470.0020.0020.0000.0000.0000.000
198A234TYR00.0090.00058.0620.0000.0000.0000.0000.0000.000
199A235ALA00.0100.00560.790-0.001-0.0010.0000.0000.0000.000
200A236LEU0-0.046-0.02662.292-0.001-0.0010.0000.0000.0000.000
201A237SER0-0.083-0.02864.4280.0000.0000.0000.0000.0000.000
202A238ASP-1-0.862-0.94465.764-0.009-0.0090.0000.0000.0000.000
203A239ALA0-0.053-0.02464.517-0.001-0.0010.0000.0000.0000.000
204A240PHE0-0.042-0.00957.762-0.001-0.0010.0000.0000.0000.000
205A241GLY0-0.003-0.00658.578-0.001-0.0010.0000.0000.0000.000
206A242ALA0-0.051-0.01559.059-0.001-0.0010.0000.0000.0000.000
207A243GLU-1-0.906-0.95656.407-0.017-0.0170.0000.0000.0000.000
208A244PRO0-0.058-0.01852.1450.0010.0010.0000.0000.0000.000
209A245THR0-0.045-0.02749.6710.0000.0000.0000.0000.0000.000
210A246ALA00.012-0.00253.0470.0000.0000.0000.0000.0000.000
211A247ASP-1-0.774-0.85853.378-0.002-0.0020.0000.0000.0000.000
212A248VAL00.028-0.00155.4120.0000.0000.0000.0000.0000.000
213A249ARG10.8000.86851.6270.0000.0000.0000.0000.0000.000
214A250ASN0-0.021-0.00955.8460.0010.0010.0000.0000.0000.000
215A251LEU0-0.0450.00059.810-0.001-0.0010.0000.0000.0000.000
216A252PRO0-0.0130.00162.4950.0010.0010.0000.0000.0000.000