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: 721KK

Calculation Name: 2YT4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YT4

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WYQ5

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2299134.134862
FMO2-HF: Nuclear repulsion 2217098.089376
FMO2-HF: Total energy -82036.045486
FMO2-MP2: Total energy -82272.764501


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:489:GLY)


Summations of interaction energy for fragment #1(A:489: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.
-1.2560.4822.128-2.01-1.856-0.001
Interaction energy analysis for fragmet #1(A:489:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.019
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].
3A491HIS0-0.032-0.0333.798-1.338-0.543-0.011-0.487-0.2970.000
4A492MET00.0000.0215.6910.3550.3550.0000.0000.0000.000
5A493SER00.0270.0058.980-0.124-0.1240.0000.0000.0000.000
6A494VAL0-0.0030.01512.2030.0420.0420.0000.0000.0000.000
7A495GLN00.0550.04014.351-0.046-0.0460.0000.0000.0000.000
8A496ASP-1-0.885-0.94518.0800.0250.0250.0000.0000.0000.000
9A497ALA0-0.038-0.07321.351-0.009-0.0090.0000.0000.0000.000
10A498PRO00.0020.02222.4940.0080.0080.0000.0000.0000.000
11A499THR00.1010.03824.380-0.002-0.0020.0000.0000.0000.000
12A500LYS10.8730.93423.8300.0080.0080.0000.0000.0000.000
13A501LYS10.9170.97721.0010.0210.0210.0000.0000.0000.000
14A502GLU-1-0.873-0.94416.813-0.032-0.0320.0000.0000.0000.000
15A503PHE0-0.080-0.03615.018-0.029-0.0290.0000.0000.0000.000
16A504VAL00.0710.03310.3270.0200.0200.0000.0000.0000.000
17A505ILE0-0.053-0.0248.657-0.033-0.0330.0000.0000.0000.000
18A506ASN00.0800.0386.554-0.382-0.3820.0000.0000.0000.000
19A507PRO0-0.007-0.0042.875-0.2390.1210.054-0.091-0.3240.000
20A508ASN00.0380.0092.1440.6961.1402.084-1.334-1.194-0.001
21A509GLY00.0450.0254.1200.1260.2220.003-0.063-0.0350.000
22A510LYS10.7780.8776.8550.7180.7180.0000.0000.0000.000
23A511SER00.0000.0017.6210.0050.0050.0000.0000.0000.000
24A512GLU-1-0.763-0.8708.9700.3530.3530.0000.0000.0000.000
25A513VAL0-0.017-0.01210.759-0.009-0.0090.0000.0000.0000.000
26A514CYS0-0.026-0.00911.719-0.002-0.0020.0000.0000.0000.000
27A515ILE00.0380.0356.383-0.006-0.0060.0000.0000.0000.000
28A516LEU00.0130.00910.6970.0080.0080.0000.0000.0000.000
29A517HIS0-0.019-0.01113.6200.0100.0100.0000.0000.0000.000
30A518GLU-1-0.810-0.89311.789-0.327-0.3270.0000.0000.0000.000
31A519TYR0-0.006-0.01012.9830.0080.0080.0000.0000.0000.000
32A520MET00.0230.03114.7370.0070.0070.0000.0000.0000.000
33A521GLN00.0330.02518.068-0.007-0.0070.0000.0000.0000.000
34A522ARG10.8070.89112.8010.2270.2270.0000.0000.0000.000
35A523VAL0-0.048-0.02016.2490.0000.0000.0000.0000.0000.000
36A524LEU0-0.036-0.00719.0710.0050.0050.0000.0000.0000.000
37A525LYS10.8960.96721.1860.0430.0430.0000.0000.0000.000
38A526VAL00.0240.00721.9120.0030.0030.0000.0000.0000.000
39A527ARG10.9480.97021.5840.0200.0200.0000.0000.0000.000
40A528PRO0-0.009-0.01318.5780.0060.0060.0000.0000.0000.000
41A529VAL0-0.0300.00821.517-0.009-0.0090.0000.0000.0000.000
42A530TYR0-0.006-0.02117.1600.0110.0110.0000.0000.0000.000
43A531ASN00.0010.00523.590-0.004-0.0040.0000.0000.0000.000
44A532PHE0-0.020-0.03922.7580.0040.0040.0000.0000.0000.000
45A533PHE00.0260.02224.952-0.003-0.0030.0000.0000.0000.000
46A534GLU-1-0.948-0.97328.1020.0410.0410.0000.0000.0000.000
47A535CYS0-0.025-0.01127.2760.0050.0050.0000.0000.0000.000
48A536GLU-1-0.891-0.93730.1410.0480.0480.0000.0000.0000.000
49A537ASN00.013-0.01427.613-0.004-0.0040.0000.0000.0000.000
50A538PRO00.018-0.00329.3450.0010.0010.0000.0000.0000.000
51A539SER0-0.0090.01025.691-0.002-0.0020.0000.0000.0000.000
52A540GLU-1-1.035-1.03221.9690.1310.1310.0000.0000.0000.000
53A541PRO00.0350.04425.6110.0020.0020.0000.0000.0000.000
54A542PHE0-0.034-0.01423.928-0.004-0.0040.0000.0000.0000.000
55A543GLY00.0920.04724.0780.0110.0110.0000.0000.0000.000
56A544ALA0-0.094-0.05821.117-0.012-0.0120.0000.0000.0000.000
57A545SER00.0410.02422.2660.0150.0150.0000.0000.0000.000
58A546VAL00.0150.01518.685-0.014-0.0140.0000.0000.0000.000
59A547THR0-0.004-0.00922.0890.0050.0050.0000.0000.0000.000
60A548ILE0-0.010-0.03521.512-0.007-0.0070.0000.0000.0000.000
61A549ASP-1-0.929-0.97225.3300.0260.0260.0000.0000.0000.000
62A550GLY00.0020.00529.0110.0010.0010.0000.0000.0000.000
63A551VAL0-0.0130.01526.7830.0030.0030.0000.0000.0000.000
64A552THR0-0.023-0.01424.404-0.003-0.0030.0000.0000.0000.000
65A553TYR0-0.046-0.03120.6320.0030.0030.0000.0000.0000.000
66A554GLY00.0490.03818.9810.0080.0080.0000.0000.0000.000
67A555SER0-0.021-0.03120.053-0.024-0.0240.0000.0000.0000.000
68A556GLY0-0.024-0.02919.6280.0210.0210.0000.0000.0000.000
69A557THR00.0210.00820.354-0.017-0.0170.0000.0000.0000.000
70A558ALA0-0.003-0.02819.4850.0190.0190.0000.0000.0000.000
71A559SER00.1120.07421.356-0.008-0.0080.0000.0000.0000.000
72A560SER00.0190.00720.243-0.012-0.0120.0000.0000.0000.000
73A561LYS11.0191.01721.247-0.012-0.0120.0000.0000.0000.000
74A562LYS10.9430.96515.8720.0190.0190.0000.0000.0000.000
75A563LEU00.007-0.00316.2060.0010.0010.0000.0000.0000.000
76A564ALA00.0310.02916.9490.0210.0210.0000.0000.0000.000
77A565LYS10.9340.97717.863-0.002-0.0020.0000.0000.0000.000
78A566ASN0-0.013-0.02112.829-0.022-0.0220.0000.0000.0000.000
79A567LYS10.9330.99014.104-0.134-0.1340.0000.0000.0000.000
80A568ALA00.0480.03315.8920.0210.0210.0000.0000.0000.000
81A569ALA0-0.016-0.00614.1480.0050.0050.0000.0000.0000.000
82A570ARG10.8810.9107.544-0.780-0.7800.0000.0000.0000.000
83A571ALA00.0410.03112.8760.0330.0330.0000.0000.0000.000
84A572THR00.029-0.00116.051-0.006-0.0060.0000.0000.0000.000
85A573LEU0-0.046-0.02710.646-0.022-0.0220.0000.0000.0000.000
86A574GLU-1-0.944-0.96912.7800.4390.4390.0000.0000.0000.000
87A575ILE0-0.032-0.00414.402-0.010-0.0100.0000.0000.0000.000
88A576LEU0-0.038-0.02616.301-0.025-0.0250.0000.0000.0000.000
89A577ILE0-0.064-0.03311.634-0.031-0.0310.0000.0000.0000.000
90A578PRO0-0.028-0.02713.9310.0550.0550.0000.0000.0000.000
91A579ASP-1-0.769-0.86412.5700.4140.4140.0000.0000.0000.000
92A580PHE0-0.0180.0557.9800.2050.2050.0000.0000.0000.000
93A581VAL0-0.014-0.0499.3750.1440.1440.0000.0000.0000.000
94A582LYS10.8300.9144.507-2.413-2.274-0.001-0.030-0.1080.000
95A583GLN00.043-0.0125.2370.7280.632-0.001-0.0050.1020.000
96A592SER0-0.001-0.01320.0680.0040.0040.0000.0000.0000.000
97A593GLU-1-0.916-0.97820.6250.1640.1640.0000.0000.0000.000
98A594GLU-1-0.793-0.88022.4660.1140.1140.0000.0000.0000.000
99A595LEU0-0.077-0.04524.065-0.010-0.0100.0000.0000.0000.000
100A596GLU-1-0.971-0.99119.5940.2020.2020.0000.0000.0000.000
101A597TYR0-0.0010.01222.618-0.006-0.0060.0000.0000.0000.000
102A598PHE0-0.039-0.04025.236-0.014-0.0140.0000.0000.0000.000
103A599ASN00.1020.03219.326-0.017-0.0170.0000.0000.0000.000
104A600HIS0-0.094-0.05520.676-0.001-0.0010.0000.0000.0000.000
105A601ILE0-0.0530.00024.884-0.011-0.0110.0000.0000.0000.000
106A602SER0-0.018-0.01127.4570.0060.0060.0000.0000.0000.000
107A603ILE00.0740.03226.8920.0020.0020.0000.0000.0000.000
108A604GLU-1-0.908-0.95730.2180.0310.0310.0000.0000.0000.000
109A605ASP-1-0.813-0.86131.9940.0410.0410.0000.0000.0000.000
110A606SER00.014-0.01833.9720.0020.0020.0000.0000.0000.000
111A607ARG10.8580.90532.211-0.046-0.0460.0000.0000.0000.000
112A608VAL0-0.0040.00631.4890.0020.0020.0000.0000.0000.000
113A609TYR00.0320.01133.8930.0020.0020.0000.0000.0000.000
114A610GLU-1-0.912-0.94836.4230.0480.0480.0000.0000.0000.000
115A611LEU00.0180.01331.5190.0020.0020.0000.0000.0000.000
116A612THR0-0.001-0.00531.3610.0020.0020.0000.0000.0000.000
117A613SER0-0.035-0.00733.5160.0010.0010.0000.0000.0000.000
118A614LYS10.9270.97035.841-0.057-0.0570.0000.0000.0000.000
119A615ALA0-0.042-0.03231.1240.0010.0010.0000.0000.0000.000
120A616GLY00.0320.02932.8250.0050.0050.0000.0000.0000.000
121A617LEU0-0.065-0.04228.8010.0040.0040.0000.0000.0000.000
122A618LEU00.013-0.00430.985-0.007-0.0070.0000.0000.0000.000
123A619SER0-0.040-0.01733.1460.0000.0000.0000.0000.0000.000
124A620PRO00.0420.00633.8850.0010.0010.0000.0000.0000.000
125A621TYR0-0.021-0.02934.9610.0000.0000.0000.0000.0000.000
126A622GLN00.0190.02735.1960.0030.0030.0000.0000.0000.000
127A623ILE00.0440.02329.2080.0010.0010.0000.0000.0000.000
128A624LEU00.0030.00132.1170.0010.0010.0000.0000.0000.000
129A625HIS0-0.009-0.00934.3520.0010.0010.0000.0000.0000.000
130A626GLU-1-0.853-0.90930.7360.0810.0810.0000.0000.0000.000
131A627CYS0-0.064-0.02130.117-0.001-0.0010.0000.0000.0000.000
132A628LEU0-0.010-0.02331.552-0.002-0.0020.0000.0000.0000.000
133A629LYS10.8610.92633.797-0.070-0.0700.0000.0000.0000.000
134A630ARG10.8250.91824.884-0.111-0.1110.0000.0000.0000.000
135A631ASN0-0.003-0.02129.1100.0000.0000.0000.0000.0000.000
136A632HIS00.0420.02432.355-0.003-0.0030.0000.0000.0000.000
137A633GLY00.0020.01134.624-0.002-0.0020.0000.0000.0000.000
138A634MET0-0.0010.00032.2590.0000.0000.0000.0000.0000.000
139A635GLY0-0.036-0.01636.879-0.001-0.0010.0000.0000.0000.000
140A636ASP-1-0.885-0.93040.5890.0290.0290.0000.0000.0000.000
141A637THR0-0.007-0.02739.029-0.001-0.0010.0000.0000.0000.000
142A638SER0-0.059-0.01342.2040.0010.0010.0000.0000.0000.000
143A639ILE00.009-0.01043.2860.0000.0000.0000.0000.0000.000
144A640LYS10.9750.99846.084-0.019-0.0190.0000.0000.0000.000
145A641PHE0-0.041-0.03849.0750.0000.0000.0000.0000.0000.000
146A642GLU-1-0.893-0.95250.9940.0170.0170.0000.0000.0000.000
147A643VAL0-0.058-0.03853.7220.0000.0000.0000.0000.0000.000
148A644VAL00.1240.06456.002-0.001-0.0010.0000.0000.0000.000
149A645PRO00.0180.01158.6410.0010.0010.0000.0000.0000.000
150A646GLY00.021-0.00555.3070.0000.0000.0000.0000.0000.000
151A647LYS10.9250.96854.731-0.016-0.0160.0000.0000.0000.000
152A648ASN0-0.027-0.01856.0920.0000.0000.0000.0000.0000.000
153A649GLN00.0070.00755.583-0.001-0.0010.0000.0000.0000.000
154A650LYS10.9170.97646.886-0.018-0.0180.0000.0000.0000.000
155A651SER00.0460.01851.562-0.001-0.0010.0000.0000.0000.000
156A652GLU-1-0.878-0.94049.4190.0170.0170.0000.0000.0000.000
157A653TYR0-0.032-0.01342.5920.0010.0010.0000.0000.0000.000
158A654VAL00.013-0.01546.121-0.001-0.0010.0000.0000.0000.000
159A655MET0-0.043-0.00839.2880.0010.0010.0000.0000.0000.000
160A656ALA00.0160.01142.811-0.001-0.0010.0000.0000.0000.000
161A657CYS00.024-0.00237.9880.0030.0030.0000.0000.0000.000
162A658GLY00.0940.07138.9810.0000.0000.0000.0000.0000.000
163A659LYS10.8870.94834.403-0.022-0.0220.0000.0000.0000.000
164A660HIS0-0.018-0.00534.913-0.001-0.0010.0000.0000.0000.000
165A661THR00.0260.01439.9860.0020.0020.0000.0000.0000.000
166A662VAL00.0070.00139.150-0.001-0.0010.0000.0000.0000.000
167A663ARG10.9800.98942.523-0.016-0.0160.0000.0000.0000.000
168A664GLY0-0.050-0.02744.1640.0000.0000.0000.0000.0000.000
169A665TRP00.0590.04545.4040.0000.0000.0000.0000.0000.000
170A666CYS0-0.116-0.05045.8320.0020.0020.0000.0000.0000.000
171A667LYS11.0060.99347.170-0.023-0.0230.0000.0000.0000.000
172A668ASN00.0810.03747.3190.0000.0000.0000.0000.0000.000
173A669LYS11.0651.02947.449-0.027-0.0270.0000.0000.0000.000
174A670ARG10.9020.95943.381-0.039-0.0390.0000.0000.0000.000
175A671VAL00.0140.00042.1040.0020.0020.0000.0000.0000.000
176A672GLY00.0260.01042.3730.0010.0010.0000.0000.0000.000
177A673LYS10.9690.99942.026-0.038-0.0380.0000.0000.0000.000
178A674GLN00.0510.06238.4040.0030.0030.0000.0000.0000.000
179A675LEU00.0360.02537.9450.0010.0010.0000.0000.0000.000
180A676ALA0-0.011-0.00338.2550.0000.0000.0000.0000.0000.000
181A677SER00.007-0.04336.7610.0000.0000.0000.0000.0000.000
182A678GLN0-0.059-0.03633.699-0.001-0.0010.0000.0000.0000.000
183A679LYS10.9480.98733.893-0.025-0.0250.0000.0000.0000.000
184A680ILE00.0150.01634.799-0.001-0.0010.0000.0000.0000.000
185A681LEU00.0330.01130.8040.0000.0000.0000.0000.0000.000
186A682GLN0-0.0230.00928.1920.0030.0030.0000.0000.0000.000
187A683LEU0-0.047-0.04630.762-0.002-0.0020.0000.0000.0000.000
188A684LEU0-0.0030.00231.239-0.001-0.0010.0000.0000.0000.000
189A685HIS10.7730.87026.223-0.062-0.0620.0000.0000.0000.000
190A686PRO00.0050.00127.3850.0030.0030.0000.0000.0000.000
191A687HIS00.0170.01823.930-0.005-0.0050.0000.0000.0000.000
192A688VAL00.0120.01722.6790.0050.0050.0000.0000.0000.000
193A689LYS10.9610.99923.656-0.056-0.0560.0000.0000.0000.000
194A690ASN0-0.074-0.04820.8970.0030.0030.0000.0000.0000.000
195A691TRP00.0730.03024.7660.0000.0000.0000.0000.0000.000
196A692GLY00.0650.03822.7250.0030.0030.0000.0000.0000.000
197A693SER0-0.005-0.01421.0750.0190.0190.0000.0000.0000.000
198A694LEU0-0.004-0.01422.0920.0030.0030.0000.0000.0000.000
199A695LEU0-0.0170.00824.3390.0010.0010.0000.0000.0000.000
200A696ARG10.8690.96718.278-0.203-0.2030.0000.0000.0000.000
201A697MET0-0.0220.02121.8670.0040.0040.0000.0000.0000.000
202A698TYR00.021-0.00823.821-0.006-0.0060.0000.0000.0000.000
203A699GLY00.0270.01325.666-0.008-0.0080.0000.0000.0000.000
204A700ARG10.9400.97617.363-0.279-0.2790.0000.0000.0000.000
205A701GLU-1-0.917-0.94721.3440.1430.1430.0000.0000.0000.000