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: QNY4Y

Calculation Name: 5DZ9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DZ9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8E589

Base Structure: X-ray

Registration Date: 2023-09-26

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 334
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4610929.913535
FMO2-HF: Nuclear repulsion 4483451.804889
FMO2-HF: Total energy -127478.108646
FMO2-MP2: Total energy -127859.55739


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:-5:VAL)


Summations of interaction energy for fragment #1(A:-5:VAL)
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.
-9.371-1.4696.33-4.069-10.161-0.019
Interaction energy analysis for fragmet #1(A:-5:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.024
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].
3A-3PHE0-0.0100.0023.014-1.5040.5190.026-0.878-1.1710.001
4A-2GLN00.0240.0062.430-2.548-0.5161.491-1.298-2.225-0.005
5A-1GLY00.0280.0133.4160.6250.5080.0250.356-0.2650.000
6A0PRO00.0120.0165.5590.1020.1020.0000.0000.0000.000
7A554PRO00.0100.0277.9840.0620.0620.0000.0000.0000.000
8A555THR0-0.066-0.03911.0840.0390.0390.0000.0000.0000.000
9A556LYS10.8060.89414.3690.2860.2860.0000.0000.0000.000
10A557LYS10.9520.98418.1310.2810.2810.0000.0000.0000.000
11A558VAL00.0310.01321.2430.0010.0010.0000.0000.0000.000
12A559LEU0-0.057-0.02223.873-0.004-0.0040.0000.0000.0000.000
13A560ASP-1-0.726-0.84927.334-0.117-0.1170.0000.0000.0000.000
14A561GLU-1-0.896-0.95230.538-0.112-0.1120.0000.0000.0000.000
15A562ASN0-0.104-0.05032.6480.0070.0070.0000.0000.0000.000
16A563GLY00.0050.00728.326-0.001-0.0010.0000.0000.0000.000
17A564GLN0-0.035-0.01627.061-0.018-0.0180.0000.0000.0000.000
18A565SER0-0.045-0.03024.502-0.003-0.0030.0000.0000.0000.000
19A566ILE0-0.011-0.00626.5190.0090.0090.0000.0000.0000.000
20A567ASN00.0320.00622.6710.0110.0110.0000.0000.0000.000
21A568GLY00.0000.01126.2460.0040.0040.0000.0000.0000.000
22A569LYS10.8600.93728.5230.1470.1470.0000.0000.0000.000
23A570SER00.0510.03431.644-0.004-0.0040.0000.0000.0000.000
24A571VAL0-0.003-0.01532.2870.0000.0000.0000.0000.0000.000
25A572LEU00.0090.01735.3850.0030.0030.0000.0000.0000.000
26A573PRO00.019-0.00437.230-0.004-0.0040.0000.0000.0000.000
27A574ASN0-0.028-0.00338.094-0.005-0.0050.0000.0000.0000.000
28A575ALA00.0130.02034.5310.0000.0000.0000.0000.0000.000
29A576THR0-0.007-0.00231.2040.0040.0040.0000.0000.0000.000
30A577LEU0-0.0260.00328.235-0.002-0.0020.0000.0000.0000.000
31A578ASP-1-0.777-0.88527.844-0.146-0.1460.0000.0000.0000.000
32A579TYR00.004-0.02022.680-0.010-0.0100.0000.0000.0000.000
33A580VAL00.0170.01519.8020.0040.0040.0000.0000.0000.000
34A581ALA0-0.004-0.00817.311-0.012-0.0120.0000.0000.0000.000
35A582LYS10.7870.88412.3190.5280.5280.0000.0000.0000.000
36A583GLN00.0800.06510.9500.0130.0130.0000.0000.0000.000
37A584ASN0-0.062-0.0238.0600.1690.1690.0000.0000.0000.000
38A585PHE00.0480.0066.578-0.105-0.1050.0000.0000.0000.000
39A586SER0-0.040-0.0246.233-0.055-0.0550.0000.0000.0000.000
40A587GLN00.0180.0092.568-0.6010.5410.586-0.330-1.3970.000
41A588TYR0-0.091-0.0792.485-3.001-1.3364.096-1.549-4.211-0.013
42A589LYS10.8900.9404.1900.5000.5450.000-0.013-0.0320.000
43A590GLY0-0.0110.0067.3240.1200.1200.0000.0000.0000.000
44A591ILE0-0.0120.0043.203-0.2510.1450.051-0.089-0.3570.000
45A592LYS10.8690.9186.855-0.637-0.6370.0000.0000.0000.000
46A593ALA00.0420.0387.1200.0740.0740.0000.0000.0000.000
47A594SER00.0590.0268.762-0.086-0.0860.0000.0000.0000.000
48A595ALA00.0500.00812.169-0.061-0.0610.0000.0000.0000.000
49A596GLU-1-0.838-0.90613.4440.0920.0920.0000.0000.0000.000
50A597ALA00.0360.0199.217-0.043-0.0430.0000.0000.0000.000
51A598ILE0-0.036-0.02811.010-0.090-0.0900.0000.0000.0000.000
52A599ALA0-0.034-0.01612.337-0.043-0.0430.0000.0000.0000.000
53A600LYS10.8130.91512.311-0.052-0.0520.0000.0000.0000.000
54A601GLY0-0.0140.00713.819-0.029-0.0290.0000.0000.0000.000
55A602PHE0-0.027-0.0278.774-0.046-0.0460.0000.0000.0000.000
56A603ALA0-0.017-0.00612.3990.0590.0590.0000.0000.0000.000
57A604PHE00.0010.00012.666-0.082-0.0820.0000.0000.0000.000
58A605VAL00.0210.00314.9120.0490.0490.0000.0000.0000.000
59A606ASP-1-0.779-0.87417.061-0.271-0.2710.0000.0000.0000.000
60A607GLN00.029-0.00519.9050.0180.0180.0000.0000.0000.000
61A608PRO00.0220.01721.956-0.008-0.0080.0000.0000.0000.000
62A609ASN0-0.003-0.01025.102-0.005-0.0050.0000.0000.0000.000
63A610GLU-1-0.811-0.91427.695-0.128-0.1280.0000.0000.0000.000
64A611ALA0-0.0040.00130.8940.0060.0060.0000.0000.0000.000
65A612LEU0-0.048-0.00527.1710.0040.0040.0000.0000.0000.000
66A613ALA00.005-0.00231.0460.0020.0020.0000.0000.0000.000
67A614GLU-1-0.847-0.91830.885-0.118-0.1180.0000.0000.0000.000
68A615LEU0-0.070-0.03224.502-0.005-0.0050.0000.0000.0000.000
69A616THR00.0030.00229.0860.0060.0060.0000.0000.0000.000
70A617VAL00.001-0.00424.179-0.010-0.0100.0000.0000.0000.000
71A618LYS10.8150.88526.4100.1610.1610.0000.0000.0000.000
72A619SER0-0.005-0.01124.5500.0030.0030.0000.0000.0000.000
73A620ILE0-0.0010.00419.139-0.012-0.0120.0000.0000.0000.000
74A621LYS10.9030.95719.8470.1610.1610.0000.0000.0000.000
75A622ALA00.0400.03916.251-0.034-0.0340.0000.0000.0000.000
76A623SER0-0.024-0.01913.9780.0290.0290.0000.0000.0000.000
77A624ASN0-0.026-0.03216.723-0.006-0.0060.0000.0000.0000.000
78A625GLY00.0260.01718.7120.0190.0190.0000.0000.0000.000
79A626ASP-1-0.819-0.86719.981-0.116-0.1160.0000.0000.0000.000
80A627ASP-1-0.811-0.88921.247-0.154-0.1540.0000.0000.0000.000
81A628VAL00.004-0.01117.4670.0030.0030.0000.0000.0000.000
82A629SER0-0.061-0.05220.676-0.002-0.0020.0000.0000.0000.000
83A630SER0-0.011-0.01322.9230.0020.0020.0000.0000.0000.000
84A631LEU0-0.042-0.01419.5290.0080.0080.0000.0000.0000.000
85A632LEU0-0.020-0.00416.959-0.009-0.0090.0000.0000.0000.000
86A633GLU-1-0.901-0.95420.923-0.094-0.0940.0000.0000.0000.000
87A634MET0-0.044-0.01021.982-0.013-0.0130.0000.0000.0000.000
88A635ARG10.9060.94421.5310.1570.1570.0000.0000.0000.000
89A636HIS0-0.003-0.01424.213-0.013-0.0130.0000.0000.0000.000
90A637VAL0-0.021-0.00124.4960.0110.0110.0000.0000.0000.000
91A638LEU00.0650.01927.177-0.007-0.0070.0000.0000.0000.000
92A639SER00.012-0.01627.234-0.004-0.0040.0000.0000.0000.000
93A640LYS10.9030.94323.1860.1310.1310.0000.0000.0000.000
94A641ASP-1-0.839-0.88524.903-0.112-0.1120.0000.0000.0000.000
95A642THR0-0.033-0.02127.4870.0090.0090.0000.0000.0000.000
96A643LEU0-0.0040.01521.7120.0020.0020.0000.0000.0000.000
97A644ASP-1-0.761-0.86924.068-0.094-0.0940.0000.0000.0000.000
98A645GLN00.045-0.00424.091-0.010-0.0100.0000.0000.0000.000
99A646LYS10.8580.92719.7250.0980.0980.0000.0000.0000.000
100A647LEU0-0.024-0.01919.338-0.014-0.0140.0000.0000.0000.000
101A648GLN0-0.024-0.00719.615-0.019-0.0190.0000.0000.0000.000
102A649SER0-0.056-0.03719.743-0.008-0.0080.0000.0000.0000.000
103A650LEU0-0.017-0.00113.821-0.011-0.0110.0000.0000.0000.000
104A651ILE0-0.012-0.02215.134-0.039-0.0390.0000.0000.0000.000
105A652LYS10.8580.92415.9250.0840.0840.0000.0000.0000.000
106A653GLU-1-0.797-0.88315.479-0.119-0.1190.0000.0000.0000.000
107A654ALA0-0.0360.00211.755-0.015-0.0150.0000.0000.0000.000
108A655GLY00.0030.00312.138-0.080-0.0800.0000.0000.0000.000
109A656ILE0-0.080-0.03612.253-0.007-0.0070.0000.0000.0000.000
110A657SER00.003-0.01415.9850.0380.0380.0000.0000.0000.000
111A658PRO0-0.048-0.01819.0690.0030.0030.0000.0000.0000.000
112A659VAL0-0.020-0.01021.5220.0140.0140.0000.0000.0000.000
113A660GLY00.006-0.00224.9430.0150.0150.0000.0000.0000.000
114A661GLU-1-0.854-0.91226.209-0.127-0.1270.0000.0000.0000.000
115A662PHE0-0.083-0.03320.882-0.013-0.0130.0000.0000.0000.000
116A663TYR00.0770.02922.7010.0100.0100.0000.0000.0000.000
117A664MET0-0.034-0.02018.103-0.029-0.0290.0000.0000.0000.000
118A665TRP00.0230.01118.1720.0190.0190.0000.0000.0000.000
119A666THR00.0190.00817.053-0.026-0.0260.0000.0000.0000.000
120A667ALA00.001-0.00115.5270.0220.0220.0000.0000.0000.000
121A668LYS10.8420.91617.5820.1270.1270.0000.0000.0000.000
122A669ASP-1-0.808-0.89019.550-0.038-0.0380.0000.0000.0000.000
123A670PRO00.008-0.00214.889-0.012-0.0120.0000.0000.0000.000
124A671GLN00.0490.02114.789-0.023-0.0230.0000.0000.0000.000
125A672ALA00.0140.00516.1000.0060.0060.0000.0000.0000.000
126A673PHE00.0250.01012.697-0.004-0.0040.0000.0000.0000.000
127A674TYR00.0410.0048.481-0.008-0.0080.0000.0000.0000.000
128A675LYS10.8600.92412.361-0.064-0.0640.0000.0000.0000.000
129A676ALA0-0.0210.00014.9320.0070.0070.0000.0000.0000.000
130A677TYR0-0.026-0.05013.208-0.001-0.0010.0000.0000.0000.000
131A678VAL00.0060.0227.381-0.018-0.0180.0000.0000.0000.000
132A679GLN00.0150.0118.241-0.087-0.0870.0000.0000.0000.000
133A680LYS10.8630.9389.7200.1420.1420.0000.0000.0000.000
134A681GLY0-0.0130.0068.2670.0160.0160.0000.0000.0000.000
135A682LEU0-0.090-0.0419.138-0.004-0.0040.0000.0000.0000.000
136A683ASP-1-0.724-0.8349.901-0.655-0.6550.0000.0000.0000.000
137A684ILE00.0070.01511.9330.0710.0710.0000.0000.0000.000
138A685THR0-0.028-0.02214.636-0.049-0.0490.0000.0000.0000.000
139A686TYR0-0.005-0.02015.2580.0430.0430.0000.0000.0000.000
140A687ASN0-0.023-0.01219.729-0.010-0.0100.0000.0000.0000.000
141A688LEU00.011-0.00120.7050.0110.0110.0000.0000.0000.000
142A689SER00.025-0.00124.7370.0010.0010.0000.0000.0000.000
143A690PHE00.0170.03624.3610.0030.0030.0000.0000.0000.000
144A691LYS10.8750.93929.6890.1040.1040.0000.0000.0000.000
145A692VAL00.0330.01232.447-0.006-0.0060.0000.0000.0000.000
146A693LYS10.8000.90931.9400.1210.1210.0000.0000.0000.000
147A694LYS10.9600.98436.1710.0720.0720.0000.0000.0000.000
148A695GLU-1-0.844-0.94538.026-0.084-0.0840.0000.0000.0000.000
149A696PHE0-0.0350.00133.3160.0010.0010.0000.0000.0000.000
150A697THR0-0.002-0.01237.679-0.002-0.0020.0000.0000.0000.000
151A698LYS10.9630.99438.3230.0810.0810.0000.0000.0000.000
152A699GLY00.0290.02735.2240.0010.0010.0000.0000.0000.000
153A700GLN0-0.048-0.03529.481-0.009-0.0090.0000.0000.0000.000
154A701ILE00.0560.03928.214-0.001-0.0010.0000.0000.0000.000
155A702LYS10.8730.92725.2750.1650.1650.0000.0000.0000.000
156A703ASN0-0.004-0.00221.521-0.014-0.0140.0000.0000.0000.000
157A704GLY00.0380.03019.250-0.010-0.0100.0000.0000.0000.000
158A705VAL0-0.0270.00114.6460.0160.0160.0000.0000.0000.000
159A706ALA00.0240.00813.018-0.032-0.0320.0000.0000.0000.000
160A707GLN0-0.039-0.0487.8670.1060.1060.0000.0000.0000.000
161A708ILE0-0.0070.0109.918-0.053-0.0530.0000.0000.0000.000
162A709ASP-1-0.742-0.8406.281-1.039-1.0390.0000.0000.0000.000
163A710PHE0-0.043-0.0265.420-0.040-0.0400.0000.0000.0000.000
164A711GLY00.0230.0129.4630.0870.0870.0000.0000.0000.000
165A712ASN0-0.034-0.0126.1330.1180.1180.0000.0000.0000.000
166A713GLY00.0310.0168.133-0.040-0.0400.0000.0000.0000.000
167A714TYR0-0.052-0.0233.426-1.021-0.3050.055-0.268-0.503-0.002
168A715THR00.0410.0039.3360.0670.0670.0000.0000.0000.000
169A716GLY00.0090.01411.648-0.083-0.0830.0000.0000.0000.000
170A717ASN0-0.076-0.04513.3720.0100.0100.0000.0000.0000.000
171A718ILE00.012-0.00516.5300.0080.0080.0000.0000.0000.000
172A719VAL0-0.073-0.02820.0730.0000.0000.0000.0000.0000.000
173A720VAL0-0.007-0.02122.9420.0060.0060.0000.0000.0000.000
174A721ASN0-0.015-0.01826.595-0.007-0.0070.0000.0000.0000.000
175A722ASP-1-0.856-0.92230.035-0.127-0.1270.0000.0000.0000.000
176A723LEU0-0.0140.00733.3690.0030.0030.0000.0000.0000.000
177A724THR0-0.039-0.03735.6670.0030.0030.0000.0000.0000.000
178A725THR00.009-0.03239.1630.0010.0010.0000.0000.0000.000
179A726PRO0-0.053-0.02242.0550.0010.0010.0000.0000.0000.000
180A727GLU-1-0.888-0.93145.126-0.059-0.0590.0000.0000.0000.000
181A728VAL0-0.022-0.02048.2400.0000.0000.0000.0000.0000.000
182A729HIS10.8050.86251.4440.0520.0520.0000.0000.0000.000
183A730LYS10.7540.89555.3510.0400.0400.0000.0000.0000.000
184A731ASP-1-0.785-0.86359.071-0.037-0.0370.0000.0000.0000.000
185A732VAL0-0.039-0.01962.2610.0000.0000.0000.0000.0000.000
186A733LEU00.0190.02263.5450.0000.0000.0000.0000.0000.000
187A734ASP-1-0.799-0.89667.717-0.029-0.0290.0000.0000.0000.000
188A735LYS10.8020.88669.1710.0300.0300.0000.0000.0000.000
189A736GLU-1-0.775-0.86763.208-0.037-0.0370.0000.0000.0000.000
190A737ASP-1-0.963-0.97863.300-0.036-0.0360.0000.0000.0000.000
191A738GLY0-0.0260.00165.6940.0010.0010.0000.0000.0000.000
192A739LYS10.7560.85766.6710.0290.0290.0000.0000.0000.000
193A740SER00.003-0.02764.9620.0000.0000.0000.0000.0000.000
194A741ILE0-0.039-0.01866.8740.0010.0010.0000.0000.0000.000
195A742ASN00.0510.02563.7630.0010.0010.0000.0000.0000.000
196A743ASN0-0.056-0.03866.2870.0000.0000.0000.0000.0000.000
197A744ASP-1-0.803-0.87970.069-0.028-0.0280.0000.0000.0000.000
198A745THR0-0.073-0.04973.0540.0000.0000.0000.0000.0000.000
199A746VAL00.0110.01173.1640.0000.0000.0000.0000.0000.000
200A747LYS10.8360.91276.5140.0240.0240.0000.0000.0000.000
201A748LEU00.0150.00079.0520.0000.0000.0000.0000.0000.000
202A749GLY0-0.018-0.01279.8250.0010.0010.0000.0000.0000.000
203A750ASP-1-0.830-0.89476.687-0.025-0.0250.0000.0000.0000.000
204A751GLU-1-0.876-0.93273.745-0.027-0.0270.0000.0000.0000.000
205A752VAL00.0000.00770.1660.0000.0000.0000.0000.0000.000
206A753THR0-0.021-0.02665.4070.0000.0000.0000.0000.0000.000
207A754TYR0-0.014-0.01963.5490.0000.0000.0000.0000.0000.000
208A755LYS10.7900.89657.5380.0430.0430.0000.0000.0000.000
209A756LEU0-0.036-0.02457.303-0.001-0.0010.0000.0000.0000.000
210A757GLU-1-0.871-0.92954.352-0.048-0.0480.0000.0000.0000.000
211A758GLY00.0510.01152.263-0.001-0.0010.0000.0000.0000.000
212A759TRP00.0180.02741.092-0.001-0.0010.0000.0000.0000.000
213A760VAL0-0.016-0.00245.4710.0010.0010.0000.0000.0000.000
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