Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: Z6J9N

Calculation Name: 4Y5J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y5J

Chain ID: A

ChEMBL ID:

UniProt ID: Q9VEZ3

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2651357.717224
FMO2-HF: Nuclear repulsion 2564044.970679
FMO2-HF: Total energy -87312.746545
FMO2-MP2: Total energy -87568.499256


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:592:ILE)


Summations of interaction energy for fragment #1(A:592:ILE)
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.
-10.45-4.375.822-3.536-8.364-0.013
Interaction energy analysis for fragmet #1(A:592:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.028
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].
3A594PRO00.0480.0313.809-1.0700.422-0.008-0.698-0.7860.002
4A595ALA00.0330.0026.4550.5500.5500.0000.0000.0000.000
5A596GLU-1-0.873-0.9478.326-0.223-0.2230.0000.0000.0000.000
6A597ILE00.0270.0197.6490.1340.1340.0000.0000.0000.000
7A598LEU0-0.041-0.0164.3130.0170.128-0.001-0.009-0.1010.000
8A599ASN00.0060.0128.9190.1350.1350.0000.0000.0000.000
9A600GLY00.0540.02312.4500.0000.0000.0000.0000.0000.000
10A601LEU0-0.005-0.0208.5840.0000.0000.0000.0000.0000.000
11A602VAL0-0.097-0.05812.9350.0420.0420.0000.0000.0000.000
12A603ASP-1-0.790-0.86015.6470.0750.0750.0000.0000.0000.000
13A604SER00.0250.01918.2790.0090.0090.0000.0000.0000.000
14A605ASN0-0.009-0.01621.458-0.003-0.0030.0000.0000.0000.000
15A606TRP00.0500.00620.2740.0030.0030.0000.0000.0000.000
16A607LYS10.9420.97520.185-0.022-0.0220.0000.0000.0000.000
17A608ASN0-0.001-0.00617.860-0.030-0.0300.0000.0000.0000.000
18A609ARG10.7500.85515.670-0.208-0.2080.0000.0000.0000.000
19A610LEU0-0.038-0.01515.4220.0170.0170.0000.0000.0000.000
20A611ALA00.0240.01816.235-0.007-0.0070.0000.0000.0000.000
21A612ALA0-0.0040.00311.967-0.040-0.0400.0000.0000.0000.000
22A613VAL0-0.030-0.02011.3740.0030.0030.0000.0000.0000.000
23A614GLU-1-0.892-0.96312.560-0.037-0.0370.0000.0000.0000.000
24A615GLN0-0.056-0.02810.5340.0400.0400.0000.0000.0000.000
25A616LEU0-0.012-0.0125.788-0.043-0.0430.0000.0000.0000.000
26A617LEU0-0.036-0.0319.268-0.049-0.0490.0000.0000.0000.000
27A618GLY00.0160.02111.795-0.010-0.0100.0000.0000.0000.000
28A619GLU-1-0.858-0.9326.661-0.991-0.9910.0000.0000.0000.000
29A620ILE0-0.028-0.0196.441-0.115-0.1150.0000.0000.0000.000
30A621SER0-0.014-0.0058.4250.0500.0500.0000.0000.0000.000
31A622GLY0-0.0230.0038.4580.0750.0750.0000.0000.0000.000
32A623PHE0-0.0160.0022.826-2.195-0.4060.552-0.748-1.593-0.009
33A624ASP-1-0.823-0.9265.373-0.082-0.0820.0000.0000.0000.000
34A625ALA00.0260.0036.9680.1620.1620.0000.0000.0000.000
35A626LYS10.8560.9239.3930.2340.2340.0000.0000.0000.000
36A627GLN00.0340.0372.038-3.042-1.6272.284-1.424-2.274-0.006
37A628ALA00.012-0.0067.0860.1260.1260.0000.0000.0000.000
38A629GLY00.000-0.0056.9250.1500.1500.0000.0000.0000.000
39A630ILE00.0050.0142.5710.228-0.0641.949-0.281-1.375-0.001
40A631SER00.0700.0324.8070.1500.217-0.001-0.002-0.0640.000
41A632GLN00.0090.0007.5650.0750.0750.0000.0000.0000.000
42A633ILE0-0.019-0.0062.734-1.015-0.1490.700-0.228-1.3380.001
43A634LEU00.0440.0322.790-0.4000.2170.348-0.144-0.8210.000
44A635ILE00.0520.0254.895-0.085-0.070-0.001-0.002-0.0120.000
45A636ARG10.8710.9387.768-0.988-0.9880.0000.0000.0000.000
46A637THR0-0.051-0.0245.3670.1800.1800.0000.0000.0000.000
47A638ILE0-0.017-0.0047.978-0.175-0.1750.0000.0000.0000.000
48A639SER0-0.062-0.04610.945-0.097-0.0970.0000.0000.0000.000
49A640GLY0-0.020-0.00611.861-0.066-0.0660.0000.0000.0000.000
50A641ARG10.8330.9258.593-1.197-1.1970.0000.0000.0000.000
51A642LYS10.9470.96813.863-0.489-0.4890.0000.0000.0000.000
52A643PRO00.0450.02017.1640.0140.0140.0000.0000.0000.000
53A644GLY0-0.0150.01615.041-0.009-0.0090.0000.0000.0000.000
54A645LEU00.0870.02515.142-0.028-0.0280.0000.0000.0000.000
55A646LYS10.8470.91317.820-0.318-0.3180.0000.0000.0000.000
56A647GLU-1-0.786-0.86118.1530.2270.2270.0000.0000.0000.000
57A648MET00.0190.01921.013-0.020-0.0200.0000.0000.0000.000
58A649ASN0-0.0120.00221.969-0.019-0.0190.0000.0000.0000.000
59A650PHE00.0770.02022.0160.0100.0100.0000.0000.0000.000
60A651GLN00.0230.02021.3820.0030.0030.0000.0000.0000.000
61A652VAL00.0230.00117.069-0.002-0.0020.0000.0000.0000.000
62A653LEU0-0.017-0.00817.4630.0220.0220.0000.0000.0000.000
63A654LYS10.8780.93618.158-0.035-0.0350.0000.0000.0000.000
64A655PHE00.0390.00516.0270.0020.0020.0000.0000.0000.000
65A656LYS10.8290.90113.583-0.334-0.3340.0000.0000.0000.000
66A657LEU0-0.021-0.01113.6820.0310.0310.0000.0000.0000.000
67A658ASP-1-0.740-0.84615.3750.0530.0530.0000.0000.0000.000
68A659ILE0-0.0020.0299.008-0.009-0.0090.0000.0000.0000.000
69A660ILE0-0.011-0.01011.1180.0060.0060.0000.0000.0000.000
70A661ARG10.7770.87412.304-0.037-0.0370.0000.0000.0000.000
71A662SER00.017-0.01212.007-0.019-0.0190.0000.0000.0000.000
72A663VAL0-0.051-0.0167.512-0.031-0.0310.0000.0000.0000.000
73A664ALA0-0.031-0.02610.136-0.009-0.0090.0000.0000.0000.000
74A665GLU-1-0.847-0.92013.1520.0090.0090.0000.0000.0000.000
75A666ASN0-0.062-0.02611.034-0.055-0.0550.0000.0000.0000.000
76A667TYR0-0.065-0.0357.124-0.038-0.0380.0000.0000.0000.000
77A668PRO0-0.005-0.00810.5870.0410.0410.0000.0000.0000.000
78A669LEU00.0080.02011.4690.0740.0740.0000.0000.0000.000
79A670THR00.0090.01313.222-0.015-0.0150.0000.0000.0000.000
80A671THR00.0840.02815.3120.0250.0250.0000.0000.0000.000
81A672THR00.0130.00415.4720.0030.0030.0000.0000.0000.000
82A673THR0-0.016-0.01110.6940.0690.0690.0000.0000.0000.000
83A674VAL00.0150.02813.8240.0140.0140.0000.0000.0000.000
84A675ASP-1-0.772-0.87516.4990.2150.2150.0000.0000.0000.000
85A676LEU0-0.079-0.02312.5540.0010.0010.0000.0000.0000.000
86A677VAL00.011-0.00313.7880.0140.0140.0000.0000.0000.000
87A678ILE0-0.0020.01016.926-0.026-0.0260.0000.0000.0000.000
88A679ASN00.0120.00319.662-0.012-0.0120.0000.0000.0000.000
89A680GLU-1-0.729-0.85119.0150.2820.2820.0000.0000.0000.000
90A681ILE0-0.030-0.00816.671-0.013-0.0130.0000.0000.0000.000
91A682ILE00.0220.01220.766-0.019-0.0190.0000.0000.0000.000
92A683GLU-1-0.904-0.94423.8020.1820.1820.0000.0000.0000.000
93A684LYS10.7480.85621.206-0.223-0.2230.0000.0000.0000.000
94A685LEU00.0070.01824.388-0.011-0.0110.0000.0000.0000.000
95A686ALA0-0.045-0.02426.531-0.011-0.0110.0000.0000.0000.000
96A687ASP-1-0.833-0.89325.5060.0980.0980.0000.0000.0000.000
97A688ALA00.013-0.00627.848-0.003-0.0030.0000.0000.0000.000
98A689LYS10.8440.93226.585-0.063-0.0630.0000.0000.0000.000
99A690ASN0-0.042-0.04522.647-0.007-0.0070.0000.0000.0000.000
100A691GLY00.0340.03623.6270.0060.0060.0000.0000.0000.000
101A692ALA00.000-0.00525.2430.0030.0030.0000.0000.0000.000
102A693ALA00.0390.02020.213-0.001-0.0010.0000.0000.0000.000
103A694ALA00.0060.00420.4160.0090.0090.0000.0000.0000.000
104A695ALA00.016-0.00421.4480.0070.0070.0000.0000.0000.000
105A696ASP-1-0.791-0.89021.1620.0550.0550.0000.0000.0000.000
106A697VAL0-0.051-0.01216.3840.0000.0000.0000.0000.0000.000
107A698LEU0-0.0100.00418.5490.0090.0090.0000.0000.0000.000
108A699SER00.0180.01221.1020.0020.0020.0000.0000.0000.000
109A700ALA00.0370.03016.775-0.006-0.0060.0000.0000.0000.000
110A701PHE00.011-0.01814.1890.0070.0070.0000.0000.0000.000
111A702ALA0-0.038-0.00818.3240.0020.0020.0000.0000.0000.000
112A703GLU-1-0.822-0.89619.8910.0300.0300.0000.0000.0000.000
113A704ALA00.0000.01415.577-0.007-0.0070.0000.0000.0000.000
114A705THR0-0.072-0.04417.4980.0110.0110.0000.0000.0000.000
115A706LYS10.9110.93119.769-0.096-0.0960.0000.0000.0000.000
116A707LEU00.0430.03423.5660.0110.0110.0000.0000.0000.000
117A708GLU-1-0.816-0.91325.8150.0830.0830.0000.0000.0000.000
118A709TYR0-0.077-0.04820.9030.0000.0000.0000.0000.0000.000
119A710VAL0-0.0050.00121.1430.0090.0090.0000.0000.0000.000
120A711VAL00.0400.01423.8000.0020.0020.0000.0000.0000.000
121A712GLY00.0300.02427.527-0.001-0.0010.0000.0000.0000.000
122A713LYS10.8170.89222.316-0.193-0.1930.0000.0000.0000.000
123A714VAL0-0.007-0.01324.5510.0030.0030.0000.0000.0000.000
124A715LEU0-0.020-0.00526.850-0.002-0.0020.0000.0000.0000.000
125A716SER0-0.033-0.02728.798-0.004-0.0040.0000.0000.0000.000
126A717PHE00.0360.01525.831-0.001-0.0010.0000.0000.0000.000
127A718ALA0-0.006-0.00728.778-0.002-0.0020.0000.0000.0000.000
128A719PHE0-0.029-0.02230.987-0.006-0.0060.0000.0000.0000.000
129A720GLU-1-0.865-0.91228.9300.1350.1350.0000.0000.0000.000
130A721GLN00.0020.02229.457-0.003-0.0030.0000.0000.0000.000
131A722LYS10.8430.89232.012-0.103-0.1030.0000.0000.0000.000
132A723SER00.0010.01632.669-0.008-0.0080.0000.0000.0000.000
133A724PRO00.0350.00034.0830.0020.0020.0000.0000.0000.000
134A725LYS10.8630.92832.622-0.065-0.0650.0000.0000.0000.000
135A726VAL00.0270.01528.730-0.001-0.0010.0000.0000.0000.000
136A727GLN0-0.010-0.00530.915-0.004-0.0040.0000.0000.0000.000
137A728SER0-0.010-0.02433.454-0.001-0.0010.0000.0000.0000.000
138A729GLU-1-0.788-0.85429.8490.0610.0610.0000.0000.0000.000
139A730ALA00.0200.02329.0010.0010.0010.0000.0000.0000.000
140A731PHE00.007-0.00630.041-0.002-0.0020.0000.0000.0000.000
141A732ASN0-0.033-0.04132.220-0.006-0.0060.0000.0000.0000.000
142A733TRP00.019-0.00424.158-0.001-0.0010.0000.0000.0000.000
143A734VAL00.0260.01529.036-0.003-0.0030.0000.0000.0000.000
144A735ASN00.0340.02030.276-0.006-0.0060.0000.0000.0000.000
145A736ARG10.7950.86825.154-0.058-0.0580.0000.0000.0000.000
146A737SER0-0.008-0.01427.229-0.004-0.0040.0000.0000.0000.000
147A738ILE00.004-0.00629.074-0.003-0.0030.0000.0000.0000.000
148A739ILE0-0.0250.00432.292-0.004-0.0040.0000.0000.0000.000
149A740GLU-1-0.827-0.89926.5520.0400.0400.0000.0000.0000.000
150A741PHE00.0220.00523.403-0.004-0.0040.0000.0000.0000.000
151A742GLY00.0190.02329.357-0.002-0.0020.0000.0000.0000.000
152A743PHE00.009-0.00831.8910.0050.0050.0000.0000.0000.000
153A744GLN0-0.091-0.03929.2060.0010.0010.0000.0000.0000.000
154A745LEU0-0.010-0.02429.6090.0070.0070.0000.0000.0000.000
155A746GLN00.0040.00232.562-0.008-0.0080.0000.0000.0000.000
156A747PRO00.0040.00434.9820.0020.0020.0000.0000.0000.000
157A748LYS10.8730.92538.133-0.051-0.0510.0000.0000.0000.000
158A749THR00.0890.04134.162-0.002-0.0020.0000.0000.0000.000
159A750LEU00.0640.04233.1360.0020.0020.0000.0000.0000.000
160A751ILE0-0.011-0.00736.1710.0000.0000.0000.0000.0000.000
161A752GLU-1-0.915-0.96138.9730.0570.0570.0000.0000.0000.000
162A753ASP-1-0.841-0.90933.9950.0820.0820.0000.0000.0000.000
163A754VAL0-0.011-0.01836.8000.0000.0000.0000.0000.0000.000
164A755ARG10.8220.90138.581-0.047-0.0470.0000.0000.0000.000
165A756LYS10.8370.91736.346-0.078-0.0780.0000.0000.0000.000
166A757GLY00.0170.00638.8260.0010.0010.0000.0000.0000.000
167A758VAL0-0.020-0.01839.584-0.002-0.0020.0000.0000.0000.000
168A759GLN0-0.073-0.07242.9100.0000.0000.0000.0000.0000.000
169A760SER00.0160.03740.3140.0000.0000.0000.0000.0000.000
170A761THR00.0280.00642.983-0.003-0.0030.0000.0000.0000.000
171A762ASN00.0210.00940.561-0.003-0.0030.0000.0000.0000.000
172A763PRO00.0390.01742.5210.0000.0000.0000.0000.0000.000
173A764THR00.0220.00838.102-0.002-0.0020.0000.0000.0000.000
174A765VAL0-0.026-0.00136.9920.0000.0000.0000.0000.0000.000
175A766ARG10.8730.95138.970-0.045-0.0450.0000.0000.0000.000
176A767ALA0-0.019-0.00941.247-0.001-0.0010.0000.0000.0000.000
177A768SER00.0060.00036.0780.0000.0000.0000.0000.0000.000
178A769ALA00.0240.01237.9280.0000.0000.0000.0000.0000.000
179A770ILE0-0.021-0.01338.938-0.001-0.0010.0000.0000.0000.000
180A771GLN0-0.012-0.01039.186-0.001-0.0010.0000.0000.0000.000
181A772MET0-0.0220.01834.2400.0000.0000.0000.0000.0000.000
182A773VAL0-0.001-0.00838.001-0.001-0.0010.0000.0000.0000.000
183A774GLY00.0290.02041.150-0.002-0.0020.0000.0000.0000.000
184A775THR0-0.005-0.01035.924-0.003-0.0030.0000.0000.0000.000
185A776MET0-0.018-0.01637.4150.0000.0000.0000.0000.0000.000
186A777SER0-0.051-0.03939.464-0.002-0.0020.0000.0000.0000.000
187A778MET00.0250.02038.878-0.002-0.0020.0000.0000.0000.000
188A779TYR0-0.023-0.02635.943-0.001-0.0010.0000.0000.0000.000
189A780MET0-0.066-0.01639.3460.0010.0010.0000.0000.0000.000
190A781GLY00.0330.03342.866-0.001-0.0010.0000.0000.0000.000
191A782LYS10.9230.93846.304-0.019-0.0190.0000.0000.0000.000
192A783ALA00.0340.01947.6200.0000.0000.0000.0000.0000.000
193A784LEU00.0070.00842.2000.0010.0010.0000.0000.0000.000
194A785MET00.0080.01146.0730.0020.0020.0000.0000.0000.000
195A786MET00.0430.02348.7140.0000.0000.0000.0000.0000.000
196A787PHE0-0.041-0.00545.2580.0010.0010.0000.0000.0000.000
197A788PHE00.022-0.01142.6020.0030.0030.0000.0000.0000.000
198A789ASP-1-0.819-0.89348.7610.0270.0270.0000.0000.0000.000
199A790SER0-0.0090.00751.325-0.001-0.0010.0000.0000.0000.000
200A791GLU-1-0.832-0.88547.3940.0440.0440.0000.0000.0000.000
201A792LYS10.9690.97551.243-0.041-0.0410.0000.0000.0000.000
202A793PRO00.0510.01852.9740.0000.0000.0000.0000.0000.000
203A794ALA00.0220.01653.6750.0000.0000.0000.0000.0000.000
204A795LEU0-0.0060.00746.4650.0000.0000.0000.0000.0000.000
205A796LYS10.8510.90949.521-0.028-0.0280.0000.0000.0000.000
206A797SER00.0310.01251.143-0.001-0.0010.0000.0000.0000.000
207A798GLN0-0.042-0.02546.5560.0000.0000.0000.0000.0000.000
208A799ILE00.006-0.00245.8580.0000.0000.0000.0000.0000.000
209A800GLN0-0.020-0.02747.7230.0000.0000.0000.0000.0000.000
210A801VAL0-0.001-0.00349.225-0.001-0.0010.0000.0000.0000.000
211A802GLU-1-0.825-0.90443.5150.0290.0290.0000.0000.0000.000
212A803PHE0-0.0100.00745.5470.0000.0000.0000.0000.0000.000
213A804ASP-1-0.842-0.93447.2270.0210.0210.0000.0000.0000.000
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