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: 8583Y

Calculation Name: 5AR1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5AR1

Chain ID: A

ChEMBL ID:

UniProt ID: P32458

Base Structure: X-ray

Registration Date: 2023-06-21

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2785048.313039
FMO2-HF: Nuclear repulsion 2695762.534979
FMO2-HF: Total energy -89285.77806
FMO2-MP2: Total energy -89547.25481


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:21:ILE)


Summations of interaction energy for fragment #1(A:21: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.
-15.583-7.277.083-5.218-10.178-0.041
Interaction energy analysis for fragmet #1(A:21:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.030
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].
3A23PHE00.0100.0042.867-3.111-0.5310.302-1.331-1.552-0.005
4A24THR00.0060.0205.0740.2030.256-0.001-0.004-0.0480.000
5A25VAL0-0.0190.0048.683-0.040-0.0400.0000.0000.0000.000
6A26MET00.0110.00611.3390.0780.0780.0000.0000.0000.000
7A27ILE0-0.0040.01315.111-0.020-0.0200.0000.0000.0000.000
8A28VAL00.0260.00618.3620.0300.0300.0000.0000.0000.000
9A29GLY00.0340.02721.577-0.015-0.0150.0000.0000.0000.000
10A30GLN0-0.0230.00225.0650.0140.0140.0000.0000.0000.000
11A31SER00.0370.00728.395-0.006-0.0060.0000.0000.0000.000
12A32GLY0-0.017-0.00129.807-0.001-0.0010.0000.0000.0000.000
13A33SER0-0.046-0.03129.1910.0050.0050.0000.0000.0000.000
14A34GLY00.0290.01629.2040.0020.0020.0000.0000.0000.000
15A35ARG10.9040.94223.6090.0590.0590.0000.0000.0000.000
16A36SER0-0.023-0.01823.931-0.010-0.0100.0000.0000.0000.000
17A37THR0-0.007-0.01324.6650.0000.0000.0000.0000.0000.000
18A38PHE00.0340.03118.679-0.006-0.0060.0000.0000.0000.000
19A39ILE00.0630.03017.918-0.023-0.0230.0000.0000.0000.000
20A40ASN0-0.063-0.03119.118-0.016-0.0160.0000.0000.0000.000
21A41THR0-0.063-0.01821.1440.0070.0070.0000.0000.0000.000
22A42LEU0-0.0070.00814.488-0.022-0.0220.0000.0000.0000.000
23A68LEU0-0.042-0.02819.032-0.003-0.0030.0000.0000.0000.000
24A69ARG10.7140.85718.174-0.013-0.0130.0000.0000.0000.000
25A70GLU-1-0.817-0.91414.2870.0860.0860.0000.0000.0000.000
26A71GLU-1-0.865-0.92914.881-0.004-0.0040.0000.0000.0000.000
27A72THR0-0.0030.00310.083-0.074-0.0740.0000.0000.0000.000
28A73VAL0-0.070-0.02510.4720.0310.0310.0000.0000.0000.000
29A74GLU-1-0.820-0.9159.5610.0720.0720.0000.0000.0000.000
30A75LEU0-0.106-0.06010.8530.0580.0580.0000.0000.0000.000
31A76GLU-1-0.870-0.9256.0080.0620.0620.0000.0000.0000.000
32A77ASP-1-0.851-0.9166.561-0.949-0.9490.0000.0000.0000.000
33A78ASP-1-0.803-0.8915.257-1.696-1.6960.0000.0000.0000.000
34A79GLU-1-0.957-0.9867.371-0.449-0.4490.0000.0000.0000.000
35A80GLY0-0.074-0.0499.5760.1490.1490.0000.0000.0000.000
36A81VAL0-0.051-0.0233.7180.0010.2900.004-0.042-0.2520.000
37A82LYS10.7720.8844.4550.2280.430-0.001-0.067-0.1330.000
38A83ILE0-0.014-0.0162.243-8.865-5.9604.750-2.808-4.848-0.034
39A84GLN0-0.024-0.0183.4341.1301.5820.003-0.031-0.4230.000
40A85LEU00.0100.0045.561-0.221-0.2210.0000.0000.0000.000
41A86ASN0-0.002-0.0147.9750.4520.4520.0000.0000.0000.000
42A87ILE00.0190.0139.900-0.007-0.0070.0000.0000.0000.000
43A88ILE0-0.0140.00112.9030.0870.0870.0000.0000.0000.000
44A89ASP-1-0.808-0.90115.650-0.120-0.1200.0000.0000.0000.000
45A90THR0-0.001-0.01419.2170.0290.0290.0000.0000.0000.000
46A91PRO0-0.028-0.03222.127-0.006-0.0060.0000.0000.0000.000
47A92GLY00.0410.03225.996-0.004-0.0040.0000.0000.0000.000
48A93PHE0-0.006-0.00525.7460.0060.0060.0000.0000.0000.000
49A94GLY0-0.044-0.02430.2560.0020.0020.0000.0000.0000.000
50A95ASP-1-0.911-0.93732.037-0.052-0.0520.0000.0000.0000.000
51A96SER00.067-0.00432.519-0.006-0.0060.0000.0000.0000.000
52A97LEU00.0080.02433.8130.0010.0010.0000.0000.0000.000
53A98ASP-1-0.903-0.95535.408-0.026-0.0260.0000.0000.0000.000
54A99ASN0-0.0290.00132.1460.0080.0080.0000.0000.0000.000
55A100SER00.0300.01231.814-0.001-0.0010.0000.0000.0000.000
56A101PRO00.0270.00330.581-0.002-0.0020.0000.0000.0000.000
57A102SER0-0.075-0.03328.0250.0020.0020.0000.0000.0000.000
58A103PHE0-0.012-0.01626.059-0.003-0.0030.0000.0000.0000.000
59A104GLU-1-0.915-0.95425.481-0.004-0.0040.0000.0000.0000.000
60A105ILE00.0230.00025.0400.0040.0040.0000.0000.0000.000
61A106ILE0-0.018-0.00120.3120.0070.0070.0000.0000.0000.000
62A107SER0-0.006-0.00520.9840.0010.0010.0000.0000.0000.000
63A108ASP-1-0.842-0.91622.1140.0240.0240.0000.0000.0000.000
64A109TYR0-0.047-0.01214.4710.0250.0250.0000.0000.0000.000
65A110ILE0-0.003-0.01516.9670.0140.0140.0000.0000.0000.000
66A111ARG10.8930.94518.0480.0060.0060.0000.0000.0000.000
67A112HIS0-0.0030.00218.662-0.006-0.0060.0000.0000.0000.000
68A113GLN0-0.056-0.04414.2500.0450.0450.0000.0000.0000.000
69A114TYR0-0.069-0.04713.9970.0230.0230.0000.0000.0000.000
70A115ASP-1-0.836-0.90317.3700.0890.0890.0000.0000.0000.000
71A116GLU-1-0.883-0.93716.5810.2500.2500.0000.0000.0000.000
72A117ILE0-0.0130.00513.1440.0360.0360.0000.0000.0000.000
73A118LEU00.0550.04116.1920.0110.0110.0000.0000.0000.000
74A119LEU0-0.052-0.01419.266-0.001-0.0010.0000.0000.0000.000
75A120GLU-1-0.901-0.94415.0770.4400.4400.0000.0000.0000.000
76A121GLU-1-0.860-0.92414.8920.2120.2120.0000.0000.0000.000
77A122SER0-0.037-0.01618.867-0.025-0.0250.0000.0000.0000.000
78A123ARG10.6570.82618.542-0.306-0.3060.0000.0000.0000.000
79A133GLY00.0250.00510.2440.0210.0210.0000.0000.0000.000
80A134ARG10.8820.92810.376-0.227-0.2270.0000.0000.0000.000
81A135VAL0-0.011-0.01510.185-0.048-0.0480.0000.0000.0000.000
82A136HIS00.0510.0386.402-0.015-0.0150.0000.0000.0000.000
83A137CYS0-0.028-0.01110.180-0.005-0.0050.0000.0000.0000.000
84A138CYS00.0080.00912.8060.0240.0240.0000.0000.0000.000
85A139LEU00.0170.01314.5870.0080.0080.0000.0000.0000.000
86A140TYR0-0.033-0.05118.0230.0240.0240.0000.0000.0000.000
87A141LEU0-0.004-0.01721.6430.0020.0020.0000.0000.0000.000
88A142ILE00.0420.02724.1240.0170.0170.0000.0000.0000.000
89A143ASN0-0.069-0.01827.3740.0020.0020.0000.0000.0000.000
90A144PRO00.0540.03830.2170.0040.0040.0000.0000.0000.000
91A145THR00.001-0.02232.4300.0050.0050.0000.0000.0000.000
92A146GLY0-0.078-0.02835.5000.0050.0050.0000.0000.0000.000
93A147HIS0-0.062-0.04535.991-0.001-0.0010.0000.0000.0000.000
94A148GLY00.0220.03033.9200.0030.0030.0000.0000.0000.000
95A149LEU0-0.021-0.01028.204-0.005-0.0050.0000.0000.0000.000
96A150LYS10.8190.89232.1360.0730.0730.0000.0000.0000.000
97A151GLU-1-0.889-0.95032.394-0.052-0.0520.0000.0000.0000.000
98A152ILE0-0.033-0.02330.2090.0010.0010.0000.0000.0000.000
99A153ASP-1-0.757-0.84928.397-0.088-0.0880.0000.0000.0000.000
100A154VAL00.0070.00327.902-0.006-0.0060.0000.0000.0000.000
101A155GLU-1-0.806-0.91228.880-0.050-0.0500.0000.0000.0000.000
102A156PHE00.0180.01822.2100.0020.0020.0000.0000.0000.000
103A157ILE0-0.010-0.01723.716-0.002-0.0020.0000.0000.0000.000
104A158ARG10.8020.90024.2300.0560.0560.0000.0000.0000.000
105A159GLN0-0.065-0.03226.1650.0070.0070.0000.0000.0000.000
106A160LEU0-0.007-0.00821.1850.0040.0040.0000.0000.0000.000
107A161GLY00.0460.03220.508-0.007-0.0070.0000.0000.0000.000
108A162SER0-0.062-0.03220.747-0.009-0.0090.0000.0000.0000.000
109A163LEU00.0040.00819.1360.0070.0070.0000.0000.0000.000
110A164VAL00.0170.00714.462-0.001-0.0010.0000.0000.0000.000
111A165ASN00.0520.01912.3290.0450.0450.0000.0000.0000.000
112A166ILE0-0.0180.00215.829-0.033-0.0330.0000.0000.0000.000
113A167ILE00.0300.01615.674-0.001-0.0010.0000.0000.0000.000
114A168PRO0-0.0050.01019.2250.0040.0040.0000.0000.0000.000
115A169VAL00.017-0.00419.705-0.014-0.0140.0000.0000.0000.000
116A170ILE0-0.024-0.01122.9760.0200.0200.0000.0000.0000.000
117A171SER00.003-0.01226.031-0.001-0.0010.0000.0000.0000.000
118A172LYS10.9020.93126.8400.0900.0900.0000.0000.0000.000
119A173SER00.0430.02126.9510.0050.0050.0000.0000.0000.000
120A174ASP-1-0.904-0.95029.511-0.119-0.1190.0000.0000.0000.000
121A175SER0-0.105-0.06631.3670.0090.0090.0000.0000.0000.000
122A176LEU0-0.028-0.00132.8460.0070.0070.0000.0000.0000.000
123A177THR0-0.049-0.06035.068-0.004-0.0040.0000.0000.0000.000
124A178ARG10.8900.92332.6900.1250.1250.0000.0000.0000.000
125A179ASP-1-0.869-0.92535.114-0.098-0.0980.0000.0000.0000.000
126A180GLU-1-0.791-0.85736.422-0.083-0.0830.0000.0000.0000.000
127A181LEU00.0260.02730.061-0.002-0.0020.0000.0000.0000.000
128A182LYS10.8050.89832.3780.1000.1000.0000.0000.0000.000
129A183LEU0-0.056-0.02234.230-0.001-0.0010.0000.0000.0000.000
130A184ASN00.024-0.01231.7570.0020.0020.0000.0000.0000.000
131A185LYS10.8420.92126.4200.1820.1820.0000.0000.0000.000
132A186LYS10.9370.97130.5900.0910.0910.0000.0000.0000.000
133A187LEU00.000-0.00433.2630.0010.0010.0000.0000.0000.000
134A188ILE00.0160.00927.7140.0020.0020.0000.0000.0000.000
135A189MET00.0100.00926.291-0.003-0.0030.0000.0000.0000.000
136A190GLU-1-0.970-0.97430.097-0.072-0.0720.0000.0000.0000.000
137A191ASP-1-0.795-0.91432.068-0.075-0.0750.0000.0000.0000.000
138A192ILE0-0.012-0.01625.8260.0030.0030.0000.0000.0000.000
139A193ASP-1-0.887-0.92829.495-0.107-0.1070.0000.0000.0000.000
140A194ARG10.8310.92131.5640.0670.0670.0000.0000.0000.000
141A195TRP0-0.068-0.04331.7860.0120.0120.0000.0000.0000.000
142A196ASN0-0.081-0.04530.1700.0050.0050.0000.0000.0000.000
143A197LEU0-0.0190.00726.6810.0040.0040.0000.0000.0000.000
144A198PRO0-0.0040.00922.695-0.009-0.0090.0000.0000.0000.000
145A199ILE0-0.001-0.00221.008-0.006-0.0060.0000.0000.0000.000
146A200TYR00.0370.01313.2330.0170.0170.0000.0000.0000.000
147A201ASN0-0.030-0.01918.726-0.033-0.0330.0000.0000.0000.000
148A202PHE00.0220.00415.1790.0160.0160.0000.0000.0000.000
149A203PRO0-0.0100.00716.4690.0140.0140.0000.0000.0000.000
150A204PHE00.0170.00316.335-0.037-0.0370.0000.0000.0000.000
151A205ASP-1-0.889-0.93815.149-0.215-0.2150.0000.0000.0000.000
152A206GLU-1-0.979-1.00018.166-0.162-0.1620.0000.0000.0000.000
153A207ASP-1-0.950-0.97120.902-0.130-0.1300.0000.0000.0000.000
154A208GLU-1-0.954-0.96015.239-0.219-0.2190.0000.0000.0000.000
155A209ILE0-0.039-0.01114.107-0.013-0.0130.0000.0000.0000.000
156A210SER0-0.055-0.04717.9900.0130.0130.0000.0000.0000.000
157A211ASP-1-0.912-0.97621.592-0.174-0.1740.0000.0000.0000.000
158A212GLU-1-0.891-0.90421.001-0.306-0.3060.0000.0000.0000.000
159A213ASP-1-0.839-0.93817.230-0.377-0.3770.0000.0000.0000.000
160A214TYR0-0.024-0.00619.533-0.007-0.0070.0000.0000.0000.000
161A215GLU-1-0.907-0.96021.996-0.171-0.1710.0000.0000.0000.000
162A216THR0-0.055-0.04318.6030.0000.0000.0000.0000.0000.000
163A217ASN0-0.012-0.01118.748-0.023-0.0230.0000.0000.0000.000
164A218MET0-0.045-0.00920.2910.0140.0140.0000.0000.0000.000
165A219TYR0-0.065-0.04622.8980.0070.0070.0000.0000.0000.000
166A220LEU00.0240.00116.9930.0070.0070.0000.0000.0000.000
167A221ARG10.8370.90420.4960.2290.2290.0000.0000.0000.000
168A222THR0-0.073-0.04222.9300.0190.0190.0000.0000.0000.000
169A223LEU0-0.041-0.01622.0470.0120.0120.0000.0000.0000.000
170A224LEU0-0.0040.03620.7500.0040.0040.0000.0000.0000.000
171A225PRO00.014-0.02223.8890.0150.0150.0000.0000.0000.000
172A226PHE00.0040.01017.6100.0080.0080.0000.0000.0000.000
173A227ALA0-0.0090.01123.0510.0080.0080.0000.0000.0000.000
174A228ILE0-0.038-0.01218.173-0.005-0.0050.0000.0000.0000.000
175A229ILE00.004-0.00422.8250.0090.0090.0000.0000.0000.000
176A230GLY00.0200.02424.6420.0000.0000.0000.0000.0000.000
177A231SER0-0.046-0.02220.7540.0010.0010.0000.0000.0000.000
178A232ASN0-0.067-0.04217.406-0.065-0.0650.0000.0000.0000.000
179A233GLU-1-0.896-0.96820.251-0.212-0.2120.0000.0000.0000.000
180A234VAL00.0470.03620.0530.0190.0190.0000.0000.0000.000
181A235TYR0-0.047-0.03822.9320.0130.0130.0000.0000.0000.000
182A236GLU-1-0.786-0.86526.730-0.166-0.1660.0000.0000.0000.000
183A237MET0-0.073-0.04628.9410.0080.0080.0000.0000.0000.000
184A238GLY0-0.033-0.00632.4290.0110.0110.0000.0000.0000.000
185A261ILE00.0300.01728.5890.0040.0040.0000.0000.0000.000
186A262SER0-0.061-0.04727.4380.0030.0030.0000.0000.0000.000
187A263ASP-1-0.829-0.89328.777-0.142-0.1420.0000.0000.0000.000
188A264PHE00.000-0.00225.9720.0040.0040.0000.0000.0000.000
189A265VAL00.0140.01121.5370.0010.0010.0000.0000.0000.000
190A266ILE00.0230.01817.881-0.014-0.0140.0000.0000.0000.000
191A267LEU00.0110.00515.5680.0090.0090.0000.0000.0000.000
192A268ARG10.8590.91915.5530.3490.3490.0000.0000.0000.000
193A269ASN00.008-0.00210.288-0.022-0.0220.0000.0000.0000.000
194A270ALA00.0720.0329.680-0.105-0.1050.0000.0000.0000.000
195A271LEU0-0.0110.01410.145-0.056-0.0560.0000.0000.0000.000
196A272LEU00.0220.02110.856-0.006-0.0060.0000.0000.0000.000
197A273ILE00.0140.0045.490-0.057-0.0570.0000.0000.0000.000
198A274SER0-0.052-0.0297.016-0.133-0.1330.0000.0000.0000.000
199A275HIS00.0810.0298.7680.0180.0180.0000.0000.0000.000
200A276LEU0-0.053-0.0226.2550.0940.0940.0000.0000.0000.000
201A277HIS00.007-0.0042.338-1.325-0.2221.655-0.744-2.014-0.004
202A278ASP-1-0.857-0.9195.952-0.398-0.3980.0000.0000.0000.000
203A279LEU0-0.068-0.0389.3950.1260.1260.0000.0000.0000.000
204A280LYS10.7960.8772.604-0.2330.4960.371-0.191-0.9080.002
205A281ASN0-0.0150.0097.5840.1920.1920.0000.0000.0000.000
206A282TYR00.0920.0529.4220.1060.1060.0000.0000.0000.000
207A283THR0-0.058-0.03810.4490.0610.0610.0000.0000.0000.000
208A284HIS0-0.023-0.01010.3850.0790.0790.0000.0000.0000.000
209A285GLU-1-0.856-0.94512.402-0.187-0.1870.0000.0000.0000.000
210A286ILE0-0.035-0.01014.5900.0120.0120.0000.0000.0000.000
211A287LEU0-0.055-0.01715.5180.0180.0180.0000.0000.0000.000
212A288TYR0-0.042-0.03114.6610.0100.0100.0000.0000.0000.000
213A289GLU-1-0.825-0.89316.5580.0570.0570.0000.0000.0000.000
214A290ARG10.8620.94018.6500.0870.0870.0000.0000.0000.000
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