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: 2J4KR

Calculation Name: 4YB9-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YB9

Chain ID: D

ChEMBL ID:

UniProt ID: P58353

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 437
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7758830.980523
FMO2-HF: Nuclear repulsion 7591452.448325
FMO2-HF: Total energy -167378.532198
FMO2-MP2: Total energy -167866.318948


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(D:19:LEU)


Summations of interaction energy for fragment #1(D:19:LEU)
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.
-4.664-0.4291.853-2.186-3.9010
Interaction energy analysis for fragmet #1(D:19:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.003
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].
3D21THR00.0180.0003.528-2.993-0.927-0.001-0.939-1.1260.003
4D22LEU0-0.017-0.0072.389-2.368-0.9211.851-1.031-2.267-0.003
5D23ILE0-0.014-0.0053.931-0.0540.6180.004-0.215-0.4600.000
6D24ALA0-0.012-0.0015.6480.2780.2780.0000.0000.0000.000
7D25ALA0-0.0110.0157.2630.1460.1460.0000.0000.0000.000
8D26PHE0-0.004-0.0077.3280.0970.0970.0000.0000.0000.000
9D27GLY00.0470.01810.9450.0110.0110.0000.0000.0000.000
10D28SER00.014-0.00512.3020.0320.0320.0000.0000.0000.000
11D29SER0-0.007-0.00515.0280.0070.0070.0000.0000.0000.000
12D30PHE00.0280.02514.4430.0070.0070.0000.0000.0000.000
13D31GLN00.0230.02216.3420.0160.0160.0000.0000.0000.000
14D32TYR0-0.0040.00218.9520.0070.0070.0000.0000.0000.000
15D33GLY00.0370.00419.6630.0050.0050.0000.0000.0000.000
16D34TYR0-0.063-0.03919.8870.0040.0040.0000.0000.0000.000
17D35ASN0-0.013-0.03321.7440.0080.0080.0000.0000.0000.000
18D36VAL0-0.0470.00124.2700.0020.0020.0000.0000.0000.000
19D37ALA00.0270.00924.8930.0010.0010.0000.0000.0000.000
20D38ALA0-0.0130.00625.2940.0040.0040.0000.0000.0000.000
21D39ILE0-0.050-0.02327.0320.0050.0050.0000.0000.0000.000
22D40ASN00.001-0.00129.644-0.001-0.0010.0000.0000.0000.000
23D41SER00.0110.02529.4490.0000.0000.0000.0000.0000.000
24D42PRO00.0240.01630.1540.0010.0010.0000.0000.0000.000
25D43SER0-0.039-0.02933.1530.0010.0010.0000.0000.0000.000
26D44GLU-1-0.960-0.97635.7290.0080.0080.0000.0000.0000.000
27D45PHE00.0870.04534.8530.0000.0000.0000.0000.0000.000
28D46MET0-0.074-0.01833.8080.0010.0010.0000.0000.0000.000
29D47LYS10.9190.95437.683-0.003-0.0030.0000.0000.0000.000
30D48ASP-1-0.814-0.90440.8390.0140.0140.0000.0000.0000.000
31D49PHE0-0.035-0.01039.4810.0000.0000.0000.0000.0000.000
32D50TYR0-0.062-0.05537.4740.0010.0010.0000.0000.0000.000
33D51ALA00.0210.01142.8960.0000.0000.0000.0000.0000.000
34D52TYR00.0540.01442.3060.0000.0000.0000.0000.0000.000
35D53THR0-0.008-0.00843.2720.0010.0010.0000.0000.0000.000
36D54TYR0-0.086-0.04446.0200.0000.0000.0000.0000.0000.000
37D55TYR0-0.011-0.00248.338-0.001-0.0010.0000.0000.0000.000
38D56ASP-1-0.836-0.91848.0550.0210.0210.0000.0000.0000.000
39D57ARG10.7310.87044.923-0.022-0.0220.0000.0000.0000.000
40D58VAL0-0.031-0.00751.1330.0000.0000.0000.0000.0000.000
41D59GLY00.0150.02653.2330.0000.0000.0000.0000.0000.000
42D60GLU-1-0.962-0.98054.7450.0070.0070.0000.0000.0000.000
43D61TYR00.014-0.00951.7040.0000.0000.0000.0000.0000.000
44D62MET0-0.050-0.00345.460-0.001-0.0010.0000.0000.0000.000
45D63ASN00.016-0.00350.861-0.001-0.0010.0000.0000.0000.000
46D64GLU-1-0.805-0.91149.6180.0040.0040.0000.0000.0000.000
47D65PHE0-0.014-0.00548.2090.0000.0000.0000.0000.0000.000
48D66TYR00.013-0.00747.273-0.001-0.0010.0000.0000.0000.000
49D67LEU00.0730.03843.6270.0000.0000.0000.0000.0000.000
50D68THR0-0.0090.00243.3670.0000.0000.0000.0000.0000.000
51D69LEU0-0.075-0.02942.822-0.001-0.0010.0000.0000.0000.000
52D70LEU0-0.007-0.00541.700-0.001-0.0010.0000.0000.0000.000
53D71TRP00.0280.00434.6120.0010.0010.0000.0000.0000.000
54D72SER00.030-0.00337.916-0.001-0.0010.0000.0000.0000.000
55D73VAL0-0.0160.02137.983-0.002-0.0020.0000.0000.0000.000
56D74THR0-0.0020.01434.5110.0000.0000.0000.0000.0000.000
57D75VAL00.0190.02332.7750.0000.0000.0000.0000.0000.000
58D76SER0-0.040-0.04632.845-0.003-0.0030.0000.0000.0000.000
59D77MET00.0320.00334.386-0.003-0.0030.0000.0000.0000.000
60D78PHE0-0.0200.01424.626-0.001-0.0010.0000.0000.0000.000
61D79PRO0-0.022-0.00329.850-0.002-0.0020.0000.0000.0000.000
62D80PHE00.0100.00430.885-0.003-0.0030.0000.0000.0000.000
63D81GLY00.0390.00331.171-0.001-0.0010.0000.0000.0000.000
64D82GLY00.0080.01428.2170.0000.0000.0000.0000.0000.000
65D83PHE00.025-0.00328.987-0.004-0.0040.0000.0000.0000.000
66D84LEU0-0.0080.00331.777-0.001-0.0010.0000.0000.0000.000
67D85GLY00.0310.00228.3570.0000.0000.0000.0000.0000.000
68D86SER0-0.087-0.03027.427-0.003-0.0030.0000.0000.0000.000
69D87LEU0-0.033-0.01928.447-0.004-0.0040.0000.0000.0000.000
70D88MET0-0.034-0.01228.7580.0010.0010.0000.0000.0000.000
71D89VAL00.0390.01324.1250.0020.0020.0000.0000.0000.000
72D90GLY0-0.012-0.00126.617-0.003-0.0030.0000.0000.0000.000
73D91PRO00.0180.00128.913-0.001-0.0010.0000.0000.0000.000
74D92LEU00.0630.04925.6680.0030.0030.0000.0000.0000.000
75D93VAL00.0270.02522.7170.0020.0020.0000.0000.0000.000
76D94ASN0-0.109-0.06024.872-0.006-0.0060.0000.0000.0000.000
77D95ASN0-0.053-0.03727.2650.0040.0040.0000.0000.0000.000
78D96LEU00.0310.02924.0210.0020.0020.0000.0000.0000.000
79D97GLY00.0390.03722.2350.0030.0030.0000.0000.0000.000
80D98ARG10.7820.85818.1750.0770.0770.0000.0000.0000.000
81D99LYS10.9140.94913.823-0.042-0.0420.0000.0000.0000.000
82D100GLY00.0360.02517.2100.0170.0170.0000.0000.0000.000
83D101THR0-0.010-0.02720.4290.0120.0120.0000.0000.0000.000
84D102LEU0-0.020-0.00915.0290.0040.0040.0000.0000.0000.000
85D103LEU00.0150.01415.6160.0140.0140.0000.0000.0000.000
86D104PHE0-0.0170.00118.9610.0090.0090.0000.0000.0000.000
87D105ASN00.031-0.01219.9460.0010.0010.0000.0000.0000.000
88D106ASN00.002-0.01516.2180.0090.0090.0000.0000.0000.000
89D107ILE00.0020.00020.1290.0090.0090.0000.0000.0000.000
90D108PHE0-0.052-0.01722.6470.0000.0000.0000.0000.0000.000
91D109SER00.026-0.01421.695-0.008-0.0080.0000.0000.0000.000
92D110ILE0-0.045-0.01620.5900.0020.0020.0000.0000.0000.000
93D111VAL00.0090.01024.4360.0000.0000.0000.0000.0000.000
94D112PRO00.0200.01226.2740.0000.0000.0000.0000.0000.000
95D113ALA0-0.0010.00724.377-0.001-0.0010.0000.0000.0000.000
96D114LEU00.0150.00126.4340.0010.0010.0000.0000.0000.000
97D115LEU0-0.036-0.01128.568-0.002-0.0020.0000.0000.0000.000
98D116MET0-0.015-0.00927.408-0.005-0.0050.0000.0000.0000.000
99D117GLY0-0.0030.00929.534-0.001-0.0010.0000.0000.0000.000
100D118PHE00.015-0.00130.0190.0020.0020.0000.0000.0000.000
101D119SER0-0.018-0.02433.417-0.004-0.0040.0000.0000.0000.000
102D120GLU-1-0.966-0.96834.4730.0510.0510.0000.0000.0000.000
103D121LEU0-0.043-0.01136.328-0.002-0.0020.0000.0000.0000.000
104D122ALA0-0.029-0.00538.943-0.002-0.0020.0000.0000.0000.000
105D123LYS10.9450.95139.680-0.021-0.0210.0000.0000.0000.000
106D124SER00.0800.05538.1300.0010.0010.0000.0000.0000.000
107D125PHE0-0.036-0.04438.367-0.001-0.0010.0000.0000.0000.000
108D126GLU-1-0.933-0.95637.4520.0230.0230.0000.0000.0000.000
109D127MET0-0.012-0.01534.998-0.001-0.0010.0000.0000.0000.000
110D128ILE00.0740.05533.5790.0020.0020.0000.0000.0000.000
111D129ILE00.0000.00533.812-0.002-0.0020.0000.0000.0000.000
112D130VAL0-0.007-0.01335.086-0.003-0.0030.0000.0000.0000.000
113D131ALA00.0270.02230.8830.0000.0000.0000.0000.0000.000
114D132ARG10.8620.91928.3890.0000.0000.0000.0000.0000.000
115D133VAL0-0.0130.00130.376-0.004-0.0040.0000.0000.0000.000
116D134LEU0-0.010-0.01329.681-0.004-0.0040.0000.0000.0000.000
117D135VAL00.0210.01524.819-0.001-0.0010.0000.0000.0000.000
118D136GLY00.0100.00425.704-0.005-0.0050.0000.0000.0000.000
119D137ILE0-0.054-0.01827.021-0.007-0.0070.0000.0000.0000.000
120D138CYS0-0.0130.00122.646-0.006-0.0060.0000.0000.0000.000
121D139ALA00.0500.04722.288-0.009-0.0090.0000.0000.0000.000
122D140GLY0-0.0010.00722.936-0.013-0.0130.0000.0000.0000.000
123D141LEU0-0.0200.01523.102-0.006-0.0060.0000.0000.0000.000
124D142SER0-0.009-0.03518.777-0.011-0.0110.0000.0000.0000.000
125D143SER0-0.021-0.02719.562-0.020-0.0200.0000.0000.0000.000
126D144ASN0-0.059-0.01521.122-0.006-0.0060.0000.0000.0000.000
127D145VAL00.0430.00218.623-0.013-0.0130.0000.0000.0000.000
128D146VAL00.0340.02714.251-0.011-0.0110.0000.0000.0000.000
129D147PRO00.0320.01415.725-0.030-0.0300.0000.0000.0000.000
130D148MET0-0.038-0.00317.300-0.003-0.0030.0000.0000.0000.000
131D149TYR0-0.073-0.07011.966-0.002-0.0020.0000.0000.0000.000
132D150LEU00.008-0.01010.132-0.014-0.0140.0000.0000.0000.000
133D151GLY00.0120.02014.208-0.023-0.0230.0000.0000.0000.000
134D152GLU-1-0.827-0.88417.185-0.094-0.0940.0000.0000.0000.000
135D153LEU0-0.058-0.02411.8290.0090.0090.0000.0000.0000.000
136D154ALA0-0.0260.01713.370-0.016-0.0160.0000.0000.0000.000
137D155PRO00.0130.00213.1810.0360.0360.0000.0000.0000.000
138D156LYS10.8220.89916.1820.1130.1130.0000.0000.0000.000
139D157ASN0-0.011-0.01218.7740.0010.0010.0000.0000.0000.000
140D158TRP00.0080.0128.9690.0000.0000.0000.0000.0000.000
141D159ARG10.9740.97215.2450.1710.1710.0000.0000.0000.000
142D160GLY00.0270.00515.689-0.020-0.0200.0000.0000.0000.000
143D161ALA00.0260.02913.0490.0100.0100.0000.0000.0000.000
144D162LEU0-0.024-0.02013.508-0.023-0.0230.0000.0000.0000.000
145D163GLY00.0100.00714.7700.0190.0190.0000.0000.0000.000
146D164VAL00.0450.01517.1690.0160.0160.0000.0000.0000.000
147D165VAL00.0040.01910.7500.0020.0020.0000.0000.0000.000
148D166PRO00.003-0.00113.580-0.009-0.0090.0000.0000.0000.000
149D167GLN00.0410.01214.7000.0280.0280.0000.0000.0000.000
150D168LEU00.0470.02312.5670.0180.0180.0000.0000.0000.000
151D169PHE00.005-0.0058.9120.0150.0150.0000.0000.0000.000
152D170ILE0-0.0310.00014.7060.0350.0350.0000.0000.0000.000
153D171THR0-0.025-0.02217.5530.0160.0160.0000.0000.0000.000
154D172ILE00.0130.00612.9150.0140.0140.0000.0000.0000.000
155D173GLY00.0170.00317.0350.0230.0230.0000.0000.0000.000
156D174ILE0-0.028-0.00418.7250.0160.0160.0000.0000.0000.000
157D175LEU00.0060.00818.2360.0090.0090.0000.0000.0000.000
158D176VAL0-0.015-0.01716.7080.0120.0120.0000.0000.0000.000
159D177ALA00.0310.00820.0510.0130.0130.0000.0000.0000.000
160D178GLN00.0150.00823.2820.0000.0000.0000.0000.0000.000
161D179ILE0-0.029-0.01119.5910.0040.0040.0000.0000.0000.000
162D180PHE0-0.032-0.02819.4460.0110.0110.0000.0000.0000.000
163D181GLY00.0100.00824.4090.0050.0050.0000.0000.0000.000
164D182LEU0-0.016-0.00827.055-0.004-0.0040.0000.0000.0000.000
165D183ARG10.8230.87428.782-0.007-0.0070.0000.0000.0000.000
166D184SER0-0.017-0.00530.2150.0020.0020.0000.0000.0000.000
167D185LEU0-0.063-0.03224.7520.0040.0040.0000.0000.0000.000
168D186LEU0-0.010-0.00725.2720.0050.0050.0000.0000.0000.000
169D187ALA0-0.060-0.01029.178-0.001-0.0010.0000.0000.0000.000
170D188ASN00.0610.02331.6180.0010.0010.0000.0000.0000.000
171D189GLU-1-0.887-0.95135.0960.0270.0270.0000.0000.0000.000
172D190GLU-1-0.933-0.97334.9750.0400.0400.0000.0000.0000.000
173D191GLY00.0110.01332.1040.0050.0050.0000.0000.0000.000
174D192TRP00.0170.00130.5490.0040.0040.0000.0000.0000.000
175D193PRO00.0420.02030.3440.0000.0000.0000.0000.0000.000
176D194ILE0-0.0150.00026.4540.0050.0050.0000.0000.0000.000
177D195LEU0-0.0020.01525.3350.0060.0060.0000.0000.0000.000
178D196LEU0-0.001-0.00525.644-0.002-0.0020.0000.0000.0000.000
179D197GLY00.0180.00926.073-0.001-0.0010.0000.0000.0000.000
180D198LEU0-0.0140.00021.0800.0130.0130.0000.0000.0000.000
181D199THR00.002-0.00520.9970.0040.0040.0000.0000.0000.000
182D200GLY0-0.006-0.00820.585-0.005-0.0050.0000.0000.0000.000
183D201ILE00.0010.00817.2340.0180.0180.0000.0000.0000.000
184D202PRO00.009-0.00715.1280.0360.0360.0000.0000.0000.000
185D203ALA00.0130.01314.9320.0050.0050.0000.0000.0000.000
186D204VAL00.003-0.00916.7650.0080.0080.0000.0000.0000.000
187D205LEU0-0.0300.00210.4800.0420.0420.0000.0000.0000.000
188D206GLN0-0.001-0.00311.8800.0860.0860.0000.0000.0000.000
189D207LEU0-0.028-0.02512.971-0.003-0.0030.0000.0000.0000.000
190D208LEU0-0.0240.00812.7340.0060.0060.0000.0000.0000.000
191D209PHE00.002-0.0237.7930.1090.1090.0000.0000.0000.000
192D210LEU00.0150.0239.626-0.045-0.0450.0000.0000.0000.000
193D211PRO00.0330.02011.240-0.053-0.0530.0000.0000.0000.000
194D212PHE00.0200.0267.328-0.047-0.0470.0000.0000.0000.000
195D213PHE0-0.016-0.0144.700-0.111-0.061-0.001-0.001-0.0480.000
196D214PRO0-0.006-0.00310.0220.0230.0230.0000.0000.0000.000
197D215GLU-1-0.900-0.93513.126-0.004-0.0040.0000.0000.0000.000
198D216SER0-0.020-0.03616.040-0.022-0.0220.0000.0000.0000.000
199D217PRO00.0600.01517.0930.0160.0160.0000.0000.0000.000
200D218ARG10.8240.90420.1970.0860.0860.0000.0000.0000.000
201D219TYR0-0.046-0.03821.7600.0070.0070.0000.0000.0000.000
202D220LEU00.010-0.00720.2690.0080.0080.0000.0000.0000.000
203D221LEU00.0340.03824.0580.0070.0070.0000.0000.0000.000
204D222ILE0-0.063-0.01426.3030.0060.0060.0000.0000.0000.000
205D223GLN0-0.064-0.04126.8810.0030.0030.0000.0000.0000.000
206D224LYS10.8660.92325.7520.0050.0050.0000.0000.0000.000
207D225LYS10.8290.93728.1270.0270.0270.0000.0000.0000.000
208D226ASP-1-0.802-0.89326.152-0.002-0.0020.0000.0000.0000.000
209D227GLU-1-0.830-0.91525.831-0.038-0.0380.0000.0000.0000.000
210D228ALA0-0.011-0.01225.207-0.005-0.0050.0000.0000.0000.000
211D229ALA00.0110.00822.4280.0000.0000.0000.0000.0000.000
212D230ALA00.0060.01420.804-0.005-0.0050.0000.0000.0000.000
213D231LYS10.8760.92820.4900.0330.0330.0000.0000.0000.000
214D232SER0-0.051-0.02919.492-0.009-0.0090.0000.0000.0000.000
215D233ALA0-0.027-0.01716.043-0.002-0.0020.0000.0000.0000.000
216D234LEU00.0060.01015.449-0.027-0.0270.0000.0000.0000.000
217D235ARG10.9500.96816.5330.0510.0510.0000.0000.0000.000
218D236ARG10.8780.95110.277-0.021-0.0210.0000.0000.0000.000
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