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: YZ242

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2044495.154077
FMO2-HF: Nuclear repulsion 1967353.482764
FMO2-HF: Total energy -77141.671314
FMO2-MP2: Total energy -77368.111632


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.
-1.839-0.526-0.004-0.563-0.7460.003
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 : -0.034 / q_NPA : -0.033
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].
3A8PRO00.0660.0373.795-1.2530.060-0.004-0.563-0.7460.003
4A9ARG10.9140.9485.8640.3310.3310.0000.0000.0000.000
5A10VAL00.0160.0217.8200.2750.2750.0000.0000.0000.000
6A11ARG10.8240.8766.337-0.810-0.8100.0000.0000.0000.000
7A12ALA00.0100.00312.4100.0720.0720.0000.0000.0000.000
8A13ILE00.0080.01015.765-0.011-0.0110.0000.0000.0000.000
9A14VAL0-0.0010.00218.3410.0010.0010.0000.0000.0000.000
10A15THR00.0480.03121.019-0.004-0.0040.0000.0000.0000.000
11A16GLY00.004-0.01324.022-0.007-0.0070.0000.0000.0000.000
12A17HIS0-0.016-0.00620.5090.0120.0120.0000.0000.0000.000
13A18THR0-0.040-0.01223.459-0.019-0.0190.0000.0000.0000.000
14A19ARG10.9890.98425.3240.0990.0990.0000.0000.0000.000
15A20GLY00.0160.01328.0360.0040.0040.0000.0000.0000.000
16A21LEU00.0640.03227.133-0.013-0.0130.0000.0000.0000.000
17A22GLY00.0500.02324.819-0.015-0.0150.0000.0000.0000.000
18A23ALA0-0.029-0.00523.237-0.020-0.0200.0000.0000.0000.000
19A24SER00.0410.01822.966-0.022-0.0220.0000.0000.0000.000
20A25LEU0-0.040-0.02021.881-0.025-0.0250.0000.0000.0000.000
21A26ALA00.0070.00218.939-0.035-0.0350.0000.0000.0000.000
22A27GLU-1-0.864-0.94918.040-0.346-0.3460.0000.0000.0000.000
23A28GLN00.000-0.00518.317-0.038-0.0380.0000.0000.0000.000
24A29LEU0-0.038-0.02016.071-0.037-0.0370.0000.0000.0000.000
25A30LEU00.0210.01112.812-0.092-0.0920.0000.0000.0000.000
26A31GLN0-0.0260.00413.476-0.141-0.1410.0000.0000.0000.000
27A32GLN0-0.082-0.03214.793-0.015-0.0150.0000.0000.0000.000
28A33ASP-1-0.897-0.9518.095-2.129-2.1290.0000.0000.0000.000
29A34ILE0-0.059-0.01110.071-0.085-0.0850.0000.0000.0000.000
30A35ALA00.0110.0059.0500.0150.0150.0000.0000.0000.000
31A36VAL0-0.009-0.01111.1440.1590.1590.0000.0000.0000.000
32A37LEU0-0.0070.01014.261-0.001-0.0010.0000.0000.0000.000
33A38GLY00.0230.00015.9430.0100.0100.0000.0000.0000.000
34A39VAL0-0.002-0.00119.1660.0220.0220.0000.0000.0000.000
35A40SER0-0.020-0.04321.972-0.002-0.0020.0000.0000.0000.000
36A41ARG10.9721.00324.9420.0460.0460.0000.0000.0000.000
37A42SER00.0220.01826.4230.0070.0070.0000.0000.0000.000
38A43ARG10.9350.96419.2920.1230.1230.0000.0000.0000.000
39A44HIS0-0.024-0.01121.2140.0080.0080.0000.0000.0000.000
40A45PRO0-0.030-0.01422.715-0.009-0.0090.0000.0000.0000.000
41A46SER00.018-0.00222.533-0.002-0.0020.0000.0000.0000.000
42A47LEU00.0230.02017.648-0.032-0.0320.0000.0000.0000.000
43A48ALA00.0510.02416.508-0.069-0.0690.0000.0000.0000.000
44A49ALA0-0.025-0.00816.080-0.062-0.0620.0000.0000.0000.000
45A50THR0-0.045-0.00916.843-0.026-0.0260.0000.0000.0000.000
46A51ALA0-0.039-0.02113.620-0.083-0.0830.0000.0000.0000.000
47A52GLY00.0400.01611.841-0.210-0.2100.0000.0000.0000.000
48A53ASP-1-0.884-0.9548.402-0.728-0.7280.0000.0000.0000.000
49A54ARG10.7460.8707.9741.5751.5750.0000.0000.0000.000
50A55LEU0-0.037-0.0119.9560.1400.1400.0000.0000.0000.000
51A56VAL00.0220.01611.5800.0390.0390.0000.0000.0000.000
52A57GLU-1-0.784-0.88114.145-0.212-0.2120.0000.0000.0000.000
53A58THR0-0.023-0.02317.9110.0400.0400.0000.0000.0000.000
54A59GLU-1-0.961-0.97520.168-0.050-0.0500.0000.0000.0000.000
55A60LEU00.020-0.00723.7840.0170.0170.0000.0000.0000.000
56A61ASP-1-0.874-0.92525.921-0.034-0.0340.0000.0000.0000.000
57A62LEU0-0.001-0.01925.4830.0080.0080.0000.0000.0000.000
58A63SER0-0.106-0.06829.3140.0030.0030.0000.0000.0000.000
59A64ASP-1-0.816-0.90031.8640.0200.0200.0000.0000.0000.000
60A65THR00.024-0.01331.4990.0050.0050.0000.0000.0000.000
61A66ALA00.0300.02731.7190.0090.0090.0000.0000.0000.000
62A67ALA00.0180.01429.2930.0100.0100.0000.0000.0000.000
63A68VAL0-0.033-0.01726.7570.0080.0080.0000.0000.0000.000
64A69ALA00.003-0.00226.8480.0120.0120.0000.0000.0000.000
65A70ALA00.0110.00927.6860.0140.0140.0000.0000.0000.000
66A71TRP0-0.006-0.01419.1340.0160.0160.0000.0000.0000.000
67A72LEU0-0.078-0.04822.9060.0190.0190.0000.0000.0000.000
68A73ALA0-0.036-0.00123.6990.0200.0200.0000.0000.0000.000
69A74GLY0-0.0030.01222.7400.0160.0160.0000.0000.0000.000
70A75GLY0-0.024-0.02818.9130.0080.0080.0000.0000.0000.000
71A76ALA0-0.0020.00716.6520.0530.0530.0000.0000.0000.000
72A77LEU00.0450.02215.7410.0240.0240.0000.0000.0000.000
73A78ARG11.0070.99115.731-0.327-0.3270.0000.0000.0000.000
74A79SER0-0.028-0.01212.4890.1170.1170.0000.0000.0000.000
75A80PHE00.0150.02011.2790.1580.1580.0000.0000.0000.000
76A81VAL0-0.005-0.00711.1870.0060.0060.0000.0000.0000.000
77A82ASP-1-0.916-0.94110.6181.1961.1960.0000.0000.0000.000
78A83GLY00.0620.0458.8780.2680.2680.0000.0000.0000.000
79A84ALA0-0.0290.0058.825-0.014-0.0140.0000.0000.0000.000
80A85SER0-0.029-0.01210.2090.0130.0130.0000.0000.0000.000
81A86LEU0-0.040-0.01712.074-0.003-0.0030.0000.0000.0000.000
82A87VAL00.0250.01313.409-0.049-0.0490.0000.0000.0000.000
83A88LEU0-0.028-0.01815.6160.0190.0190.0000.0000.0000.000
84A89LEU00.0180.02218.350-0.010-0.0100.0000.0000.0000.000
85A90PHE00.0210.00319.2300.0010.0010.0000.0000.0000.000
86A91ASN0-0.008-0.01923.2410.0000.0000.0000.0000.0000.000
87A92ASN0-0.004-0.02625.6720.0010.0010.0000.0000.0000.000
88A93ALA0-0.070-0.02427.2100.0000.0000.0000.0000.0000.000
89A94GLY00.0340.00429.0240.0090.0090.0000.0000.0000.000
90A95VAL0-0.084-0.04132.788-0.007-0.0070.0000.0000.0000.000
91A96VAL00.0430.00536.0880.0040.0040.0000.0000.0000.000
92A97ASP-1-0.951-0.94039.414-0.044-0.0440.0000.0000.0000.000
93A98PRO0-0.043-0.02440.7410.0010.0010.0000.0000.0000.000
94A99ILE00.0270.00042.7770.0010.0010.0000.0000.0000.000
95A100GLY00.0090.00145.9130.0010.0010.0000.0000.0000.000
96A101PRO0-0.018-0.02349.2510.0010.0010.0000.0000.0000.000
97A102LEU00.0700.01950.0730.0000.0000.0000.0000.0000.000
98A103ALA0-0.025-0.01052.1130.0010.0010.0000.0000.0000.000
99A104ALA0-0.026-0.01050.9840.0000.0000.0000.0000.0000.000
100A105GLN0-0.068-0.02547.5400.0010.0010.0000.0000.0000.000
101A106ASP-1-0.811-0.90846.281-0.013-0.0130.0000.0000.0000.000
102A107PRO00.0320.00046.043-0.001-0.0010.0000.0000.0000.000
103A108ALA00.0240.01743.5860.0010.0010.0000.0000.0000.000
104A109LEU0-0.004-0.01241.4630.0000.0000.0000.0000.0000.000
105A110VAL00.0010.00741.323-0.002-0.0020.0000.0000.0000.000
106A111ALA0-0.0010.00541.0790.0000.0000.0000.0000.0000.000
107A112ARG10.9540.98433.9480.0340.0340.0000.0000.0000.000
108A113ALA00.0260.01336.566-0.001-0.0010.0000.0000.0000.000
109A114VAL00.0050.00036.811-0.001-0.0010.0000.0000.0000.000
110A115ALA00.0000.00534.8220.0020.0020.0000.0000.0000.000
111A116LEU0-0.020-0.01330.3720.0020.0020.0000.0000.0000.000
112A117ASN0-0.028-0.02931.866-0.005-0.0050.0000.0000.0000.000
113A118VAL0-0.010-0.00233.456-0.002-0.0020.0000.0000.0000.000
114A119ALA00.0020.00732.9630.0040.0040.0000.0000.0000.000
115A120ALA00.0390.02828.5800.0070.0070.0000.0000.0000.000
116A121PRO00.0060.00227.9270.0070.0070.0000.0000.0000.000
117A122LEU0-0.0150.00228.1300.0070.0070.0000.0000.0000.000
118A123MET0-0.041-0.01028.5900.0070.0070.0000.0000.0000.000
119A124LEU00.004-0.00423.0950.0140.0140.0000.0000.0000.000
120A125SER0-0.039-0.03623.9230.0070.0070.0000.0000.0000.000
121A126ALA00.0040.01324.7890.0110.0110.0000.0000.0000.000
122A127ALA00.0210.00523.3060.0170.0170.0000.0000.0000.000
123A128LEU0-0.002-0.01117.8300.0270.0270.0000.0000.0000.000
124A129VAL0-0.009-0.01120.2030.0300.0300.0000.0000.0000.000
125A130GLN0-0.052-0.02721.8780.0070.0070.0000.0000.0000.000
126A131ALA0-0.046-0.00518.2140.0260.0260.0000.0000.0000.000
127A132ALA0-0.0060.00316.6230.0640.0640.0000.0000.0000.000
128A133ALA00.0250.01616.429-0.037-0.0370.0000.0000.0000.000
129A134ALA0-0.017-0.00416.598-0.005-0.0050.0000.0000.0000.000
130A135PRO0-0.013-0.02614.4020.0500.0500.0000.0000.0000.000
131A136THR0-0.029-0.01913.267-0.030-0.0300.0000.0000.0000.000
132A137GLU-1-0.938-0.96815.5950.0370.0370.0000.0000.0000.000
133A138CYS0-0.0070.00017.057-0.008-0.0080.0000.0000.0000.000
134A139ARG10.9300.95519.5920.0550.0550.0000.0000.0000.000
135A140VAL00.0350.02321.324-0.012-0.0120.0000.0000.0000.000
136A141LEU00.0000.00024.012-0.001-0.0010.0000.0000.0000.000
137A142HIS0-0.014-0.01225.816-0.012-0.0120.0000.0000.0000.000
138A143VAL00.0140.02427.334-0.005-0.0050.0000.0000.0000.000
139A144SER00.006-0.00629.9190.0070.0070.0000.0000.0000.000
140A145SER00.027-0.02333.619-0.008-0.0080.0000.0000.0000.000
141A146GLY00.0530.03436.6540.0040.0040.0000.0000.0000.000
142A147ALA0-0.008-0.01839.8410.0040.0040.0000.0000.0000.000
143A148ALA0-0.022-0.00537.8360.0030.0030.0000.0000.0000.000
144A149ARG10.7540.85934.8790.0470.0470.0000.0000.0000.000
145A150ASN0-0.0250.00142.3450.0040.0040.0000.0000.0000.000
146A151ALA00.0340.01644.480-0.001-0.0010.0000.0000.0000.000
147A152TYR00.0230.00043.395-0.002-0.0020.0000.0000.0000.000
148A153ALA00.0520.02047.7520.0010.0010.0000.0000.0000.000
149A154GLY0-0.0040.00248.895-0.002-0.0020.0000.0000.0000.000
150A155TRP00.0480.02640.167-0.001-0.0010.0000.0000.0000.000
151A156SER00.0450.02244.327-0.001-0.0010.0000.0000.0000.000
152A157VAL00.0610.03841.2910.0020.0020.0000.0000.0000.000
153A158TYR00.0240.01436.0800.0000.0000.0000.0000.0000.000
154A159CYS0-0.011-0.00339.815-0.001-0.0010.0000.0000.0000.000
155A160ALA00.0110.02041.2590.0010.0010.0000.0000.0000.000
156A161THR0-0.054-0.03437.0240.0000.0000.0000.0000.0000.000
157A162LYS10.9150.94732.6110.0530.0530.0000.0000.0000.000
158A163ALA00.0270.01636.9450.0000.0000.0000.0000.0000.000
159A164ALA0-0.020-0.00437.1120.0030.0030.0000.0000.0000.000
160A165LEU0-0.0060.00131.6340.0040.0040.0000.0000.0000.000
161A166ASP-1-0.753-0.84833.805-0.032-0.0320.0000.0000.0000.000
162A167HIS00.0240.00635.7120.0000.0000.0000.0000.0000.000
163A168HIS00.0580.04829.657-0.002-0.0020.0000.0000.0000.000
164A169ALA00.0130.00531.6650.0050.0050.0000.0000.0000.000
165A170ARG10.8740.92832.6120.0160.0160.0000.0000.0000.000
166A171ALA00.0170.01135.6260.0020.0020.0000.0000.0000.000
167A172VAL00.0490.02928.8960.0030.0030.0000.0000.0000.000
168A173ALA0-0.069-0.03431.1850.0060.0060.0000.0000.0000.000
169A174LEU0-0.070-0.03532.2250.0010.0010.0000.0000.0000.000
170A175ASP-1-0.913-0.93231.5010.0530.0530.0000.0000.0000.000
171A176ALA0-0.040-0.01931.314-0.001-0.0010.0000.0000.0000.000
172A177ASN0-0.017-0.01426.4290.0140.0140.0000.0000.0000.000
173A178ARG10.8610.93718.741-0.215-0.2150.0000.0000.0000.000
174A179ALA00.019-0.00420.813-0.002-0.0020.0000.0000.0000.000
175A180LEU0-0.0120.00821.5720.0020.0020.0000.0000.0000.000
176A181ARG10.9190.96922.9600.0040.0040.0000.0000.0000.000
177A182ILE00.0340.01824.741-0.003-0.0030.0000.0000.0000.000
178A183CYS0-0.032-0.01127.325-0.002-0.0020.0000.0000.0000.000
179A184SER00.0100.00628.786-0.006-0.0060.0000.0000.0000.000
180A185VAL00.026-0.00428.7070.0020.0020.0000.0000.0000.000
181A186ALA0-0.033-0.00231.574-0.002-0.0020.0000.0000.0000.000
182A187PRO0-0.002-0.00130.653-0.003-0.0030.0000.0000.0000.000
183A188GLY00.0090.00932.408-0.007-0.0070.0000.0000.0000.000
184A189VAL0-0.0030.00432.025-0.001-0.0010.0000.0000.0000.000
185A190VAL0-0.004-0.00134.6160.0040.0040.0000.0000.0000.000
186A222SER0-0.001-0.01457.5880.0000.0000.0000.0000.0000.000
187A223THR0-0.0080.01057.9520.0010.0010.0000.0000.0000.000
188A224PRO00.0490.00357.090-0.001-0.0010.0000.0000.0000.000
189A225ASP-1-0.851-0.91659.1080.0140.0140.0000.0000.0000.000
190A226GLU-1-0.972-0.99561.9680.0130.0130.0000.0000.0000.000
191A227ALA00.0080.00157.754-0.001-0.0010.0000.0000.0000.000
192A228ALA00.0280.01159.875-0.001-0.0010.0000.0000.0000.000
193A229ARG10.9460.97561.014-0.011-0.0110.0000.0000.0000.000
194A230HIS00.0220.00461.229-0.002-0.0020.0000.0000.0000.000
195A231LEU00.0120.00656.423-0.001-0.0010.0000.0000.0000.000
196A232ILE00.0060.01060.545-0.001-0.0010.0000.0000.0000.000
197A233ARG10.9070.95663.378-0.006-0.0060.0000.0000.0000.000
198A234TYR00.006-0.00158.270-0.001-0.0010.0000.0000.0000.000
199A235ALA00.0050.00760.840-0.001-0.0010.0000.0000.0000.000
200A236LEU0-0.044-0.02562.319-0.001-0.0010.0000.0000.0000.000
201A237SER0-0.091-0.03464.461-0.001-0.0010.0000.0000.0000.000
202A238ASP-1-0.846-0.93565.789-0.004-0.0040.0000.0000.0000.000
203A239ALA0-0.064-0.02964.470-0.001-0.0010.0000.0000.0000.000
204A240PHE0-0.032-0.01057.621-0.001-0.0010.0000.0000.0000.000
205A241GLY0-0.007-0.00958.600-0.001-0.0010.0000.0000.0000.000
206A242ALA0-0.047-0.01359.079-0.001-0.0010.0000.0000.0000.000
207A243GLU-1-0.903-0.95356.380-0.013-0.0130.0000.0000.0000.000
208A244PRO0-0.059-0.02152.1590.0010.0010.0000.0000.0000.000
209A245THR0-0.075-0.04149.7390.0010.0010.0000.0000.0000.000
210A246ALA00.0430.01353.0680.0000.0000.0000.0000.0000.000
211A247ASP-1-0.773-0.85853.3910.0080.0080.0000.0000.0000.000
212A248VAL00.0350.00155.436-0.001-0.0010.0000.0000.0000.000
213A249ARG10.7900.86451.822-0.009-0.0090.0000.0000.0000.000
214A250ASN0-0.021-0.00455.7350.0010.0010.0000.0000.0000.000
215A251LEU0-0.042-0.00359.831-0.001-0.0010.0000.0000.0000.000
216A252PRO0-0.021-0.00162.5180.0010.0010.0000.0000.0000.000