FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

tag_button

FMODB ID: JQ539

Calculation Name: 4PRS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PRS

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WZ62

Base Structure: X-ray

Registration Date: 2023-09-23

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2531294.032177
FMO2-HF: Nuclear repulsion 2444854.657544
FMO2-HF: Total energy -86439.374634
FMO2-MP2: Total energy -86698.026371


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-8.748-1.01910.233-7.024-10.939-0.068
Interaction energy analysis for fragmet #1(A:1:ALA)
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 : 0.007
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].
3A3ASP-1-0.911-0.9463.778-0.8611.275-0.006-1.006-1.1230.005
4A4GLU-1-0.910-0.9712.8597.9518.1963.442-1.092-2.595-0.016
5A5ILE0-0.041-0.0123.042-0.6200.0620.123-0.245-0.5600.000
6A6LYS10.9120.9506.0450.0980.0980.0000.0000.0000.000
7A7SER0-0.053-0.0267.855-0.034-0.0340.0000.0000.0000.000
8A8ARG10.6960.8395.400-0.364-0.3640.0000.0000.0000.000
9A9GLY00.0400.01910.090-0.024-0.0240.0000.0000.0000.000
10A10TYR0-0.030-0.02510.233-0.018-0.0180.0000.0000.0000.000
11A11LEU00.0180.0176.3300.0170.0170.0000.0000.0000.000
12A12LEU0-0.039-0.0127.694-0.024-0.0240.0000.0000.0000.000
13A13VAL00.0330.0058.6710.0280.0280.0000.0000.0000.000
14A14GLY0-0.014-0.00311.149-0.005-0.0050.0000.0000.0000.000
15A15LEU0-0.035-0.04413.460-0.011-0.0110.0000.0000.0000.000
16A16SER00.011-0.00816.7820.0060.0060.0000.0000.0000.000
17A17ALA0-0.043-0.02020.450-0.004-0.0040.0000.0000.0000.000
18A18ASP-1-0.912-0.95322.599-0.009-0.0090.0000.0000.0000.000
19A19PHE00.0050.00922.803-0.002-0.0020.0000.0000.0000.000
20A20PRO00.0040.02724.874-0.002-0.0020.0000.0000.0000.000
21A21PRO0-0.007-0.01526.555-0.001-0.0010.0000.0000.0000.000
22A22PHE0-0.031-0.02021.628-0.001-0.0010.0000.0000.0000.000
23A23GLH0-0.035-0.06019.5950.0000.0000.0000.0000.0000.000
24A24PHE0-0.018-0.00522.1890.0000.0000.0000.0000.0000.000
25A25VAL00.0400.02524.6080.0010.0010.0000.0000.0000.000
26A26ASP-1-0.855-0.94326.5460.0010.0010.0000.0000.0000.000
27A27GLU-1-0.929-0.97328.9960.0000.0000.0000.0000.0000.000
28A28ASN0-0.104-0.04429.3560.0010.0010.0000.0000.0000.000
29A29GLY0-0.020-0.00428.4730.0020.0020.0000.0000.0000.000
30A30ASN0-0.051-0.02524.5170.0050.0050.0000.0000.0000.000
31A31ILE00.0190.02419.942-0.003-0.0030.0000.0000.0000.000
32A32VAL0-0.033-0.02421.6680.0010.0010.0000.0000.0000.000
33A33GLY00.0630.01322.8790.0000.0000.0000.0000.0000.000
34A34PHE0-0.013-0.00220.937-0.001-0.0010.0000.0000.0000.000
35A35ASP-1-0.673-0.80617.517-0.043-0.0430.0000.0000.0000.000
36A36VAL0-0.035-0.01116.9560.0000.0000.0000.0000.0000.000
37A37ASP-1-0.920-0.96017.477-0.016-0.0160.0000.0000.0000.000
38A38LEU0-0.019-0.00215.813-0.004-0.0040.0000.0000.0000.000
39A39ALA00.011-0.00213.102-0.007-0.0070.0000.0000.0000.000
40A40LYS10.8950.95513.3260.0040.0040.0000.0000.0000.000
41A41GLU-1-0.878-0.92315.480-0.048-0.0480.0000.0000.0000.000
42A42ILE00.009-0.0099.468-0.008-0.0080.0000.0000.0000.000
43A43ALA00.0100.00410.909-0.016-0.0160.0000.0000.0000.000
44A44ARG10.9000.93711.9420.0240.0240.0000.0000.0000.000
45A45ARG10.8280.92812.9960.0820.0820.0000.0000.0000.000
46A46LEU0-0.024-0.0077.178-0.011-0.0110.0000.0000.0000.000
47A47GLY0-0.072-0.02410.9180.0220.0220.0000.0000.0000.000
48A48VAL0-0.056-0.0169.2260.0230.0230.0000.0000.0000.000
49A49GLU-1-0.944-0.96812.5290.0460.0460.0000.0000.0000.000
50A50LEU00.0130.00212.1450.0010.0010.0000.0000.0000.000
51A51LYS10.9020.94612.341-0.061-0.0610.0000.0000.0000.000
52A52ILE00.0310.01912.8700.0080.0080.0000.0000.0000.000
53A53VAL0-0.055-0.03513.0420.0040.0040.0000.0000.0000.000
54A54ASP-1-0.824-0.91815.6860.0050.0050.0000.0000.0000.000
55A55MET0-0.085-0.02014.4870.0030.0030.0000.0000.0000.000
56A56THR00.0790.03219.838-0.003-0.0030.0000.0000.0000.000
57A57PHE00.0640.01919.972-0.001-0.0010.0000.0000.0000.000
58A58ASP-1-0.899-0.95219.528-0.027-0.0270.0000.0000.0000.000
59A59GLY0-0.062-0.02119.087-0.003-0.0030.0000.0000.0000.000
60A60LEU0-0.020-0.00915.1780.0040.0040.0000.0000.0000.000
61A61ILE00.023-0.00114.0370.0040.0040.0000.0000.0000.000
62A62PRO00.0080.00113.730-0.005-0.0050.0000.0000.0000.000
63A63SER00.0450.01713.5770.0070.0070.0000.0000.0000.000
64A64LEU00.0200.0237.7570.0150.0150.0000.0000.0000.000
65A65LEU0-0.015-0.0139.347-0.003-0.0030.0000.0000.0000.000
66A66THR0-0.089-0.03811.100-0.005-0.0050.0000.0000.0000.000
67A67LYS10.9040.9457.2990.1860.1860.0000.0000.0000.000
68A68LYS10.9130.9689.198-0.037-0.0370.0000.0000.0000.000
69A69ILE0-0.0220.0079.2610.0040.0040.0000.0000.0000.000
70A70ASP-1-0.725-0.8494.3200.3540.449-0.001-0.010-0.0840.000
71A71VAL0-0.016-0.0055.6990.0270.0270.0000.0000.0000.000
72A72ILE0-0.0200.0078.227-0.003-0.0030.0000.0000.0000.000
73A73ILE0-0.007-0.01611.552-0.020-0.0200.0000.0000.0000.000
74A74SER00.0140.00014.4240.0100.0100.0000.0000.0000.000
75A75GLY00.0650.04517.7830.0000.0000.0000.0000.0000.000
76A76MET0-0.040-0.00116.345-0.003-0.0030.0000.0000.0000.000
77A77THR0-0.055-0.04318.943-0.009-0.0090.0000.0000.0000.000
78A78ILE00.0120.01717.640-0.003-0.0030.0000.0000.0000.000
79A79THR00.0110.00319.9150.0060.0060.0000.0000.0000.000
80A80GLU-1-0.811-0.91920.304-0.113-0.1130.0000.0000.0000.000
81A81GLU-1-0.909-0.94620.984-0.083-0.0830.0000.0000.0000.000
82A82ARG10.9300.94517.3610.0550.0550.0000.0000.0000.000
83A83LYS10.9010.95616.4190.1110.1110.0000.0000.0000.000
84A84LYS10.8820.95316.4310.0730.0730.0000.0000.0000.000
85A85VAL0-0.036-0.01414.476-0.009-0.0090.0000.0000.0000.000
86A86VAL0-0.039-0.01911.634-0.019-0.0190.0000.0000.0000.000
87A87ALA0-0.0070.0049.7180.0040.0040.0000.0000.0000.000
88A88PHE0-0.014-0.02511.3650.0250.0250.0000.0000.0000.000
89A89SER0-0.002-0.00412.110-0.018-0.0180.0000.0000.0000.000
90A90ASP-1-0.922-0.96213.139-0.155-0.1550.0000.0000.0000.000
91A91PRO0-0.029-0.01216.5690.0060.0060.0000.0000.0000.000
92A92TYR0-0.112-0.08416.7490.0000.0000.0000.0000.0000.000
93A93PHE0-0.033-0.02119.4760.0080.0080.0000.0000.0000.000
94A94ASP-1-0.842-0.90222.711-0.066-0.0660.0000.0000.0000.000
95A95ALA0-0.025-0.01325.7940.0050.0050.0000.0000.0000.000
96A96GLY00.0940.02627.456-0.002-0.0020.0000.0000.0000.000
97A97GLN0-0.033-0.00631.0270.0030.0030.0000.0000.0000.000
98A98VAL0-0.036-0.00634.574-0.002-0.0020.0000.0000.0000.000
99A99ILE00.0400.02537.0830.0020.0020.0000.0000.0000.000
100A100VAL0-0.027-0.01739.897-0.001-0.0010.0000.0000.0000.000
101A101VAL00.0310.00442.3640.0010.0010.0000.0000.0000.000
102A102ARG10.9990.99345.7610.0150.0150.0000.0000.0000.000
103A103LYS10.9040.95143.9940.0210.0210.0000.0000.0000.000
104A104ASP-1-0.904-0.95648.168-0.017-0.0170.0000.0000.0000.000
105A105SER0-0.082-0.02850.8180.0010.0010.0000.0000.0000.000
106A106ASP-1-0.806-0.90251.337-0.017-0.0170.0000.0000.0000.000
107A107PHE0-0.103-0.05348.573-0.001-0.0010.0000.0000.0000.000
108A108ARG10.8520.90445.5470.0200.0200.0000.0000.0000.000
109A109PRO00.0260.04044.912-0.001-0.0010.0000.0000.0000.000
110A110LYS10.9110.95242.3670.0250.0250.0000.0000.0000.000
111A111THR00.0190.00241.116-0.001-0.0010.0000.0000.0000.000
112A112TYR00.0640.00738.0220.0010.0010.0000.0000.0000.000
113A113GLU-1-0.837-0.92443.873-0.018-0.0180.0000.0000.0000.000
114A114ASP-1-0.872-0.91246.196-0.021-0.0210.0000.0000.0000.000
115A115LEU0-0.085-0.05543.8860.0010.0010.0000.0000.0000.000
116A116VAL00.0390.03048.3100.0010.0010.0000.0000.0000.000
117A117GLY0-0.070-0.03550.8080.0000.0000.0000.0000.0000.000
118A118LYS10.8590.94950.3190.0160.0160.0000.0000.0000.000
119A119THR0-0.024-0.01950.9370.0000.0000.0000.0000.0000.000
120A120VAL0-0.0100.00344.5890.0000.0000.0000.0000.0000.000
121A121ALA00.0030.00746.0500.0010.0010.0000.0000.0000.000
122A122VAL0-0.0020.00341.436-0.001-0.0010.0000.0000.0000.000
123A123GLN00.027-0.00137.4200.0000.0000.0000.0000.0000.000
124A124ILE00.002-0.01340.113-0.001-0.0010.0000.0000.0000.000
125A125GLY0-0.007-0.00538.9510.0000.0000.0000.0000.0000.000
126A126THR0-0.059-0.02635.734-0.001-0.0010.0000.0000.0000.000
127A127THR00.0700.00732.5550.0010.0010.0000.0000.0000.000
128A128GLY00.0400.02835.5820.0000.0000.0000.0000.0000.000
129A129ASP-1-0.785-0.87938.428-0.014-0.0140.0000.0000.0000.000
130A130ILE00.0120.01536.3160.0000.0000.0000.0000.0000.000
131A131GLU-1-0.836-0.91136.645-0.024-0.0240.0000.0000.0000.000
132A132VAL0-0.020-0.03040.0490.0000.0000.0000.0000.0000.000
133A133SER0-0.041-0.02843.0910.0010.0010.0000.0000.0000.000
134A134LYS10.8120.91438.0860.0230.0230.0000.0000.0000.000
135A135TYR0-0.059-0.02442.5820.0000.0000.0000.0000.0000.000
136A136ASP-1-0.861-0.93847.464-0.013-0.0130.0000.0000.0000.000
137A137GLY0-0.059-0.02550.9070.0010.0010.0000.0000.0000.000
138A138ILE0-0.031-0.00146.2700.0000.0000.0000.0000.0000.000
139A139LYS10.9681.00250.2740.0120.0120.0000.0000.0000.000
140A140VAL00.0040.00445.7440.0000.0000.0000.0000.0000.000
141A141VAL0-0.067-0.03248.1700.0010.0010.0000.0000.0000.000
142A142ARG10.8680.90544.8120.0120.0120.0000.0000.0000.000
143A143PHE00.0020.00144.2130.0010.0010.0000.0000.0000.000
144A144ASP-1-0.827-0.91642.450-0.010-0.0100.0000.0000.0000.000
145A145LYS10.9270.97139.4230.0090.0090.0000.0000.0000.000
146A146PHE00.0700.02335.6850.0000.0000.0000.0000.0000.000
147A147THR00.004-0.00140.559-0.001-0.0010.0000.0000.0000.000
148A148ASP-1-0.861-0.93742.362-0.011-0.0110.0000.0000.0000.000
149A149ALA00.0040.01542.8960.0000.0000.0000.0000.0000.000
150A150PHE00.019-0.00839.0320.0000.0000.0000.0000.0000.000
151A151LEU0-0.048-0.02244.7310.0000.0000.0000.0000.0000.000
152A152GLU-1-0.927-0.96447.898-0.011-0.0110.0000.0000.0000.000
153A153LEU0-0.0020.00945.2640.0000.0000.0000.0000.0000.000
154A154LYS10.7860.89145.8360.0160.0160.0000.0000.0000.000
155A155ARG10.8570.93449.9330.0110.0110.0000.0000.0000.000
156A156GLY0-0.0130.00552.2520.0000.0000.0000.0000.0000.000
157A157ARG10.8710.94152.8120.0100.0100.0000.0000.0000.000
158A158ALA00.0050.00348.9160.0000.0000.0000.0000.0000.000
159A159ASP-1-0.882-0.94850.388-0.015-0.0150.0000.0000.0000.000
160A160ALA0-0.028-0.02945.137-0.001-0.0010.0000.0000.0000.000
161A161VAL0-0.0180.00440.8720.0010.0010.0000.0000.0000.000
162A162VAL0-0.0190.00738.712-0.001-0.0010.0000.0000.0000.000
163A163LEU0-0.0220.00035.8010.0010.0010.0000.0000.0000.000
164A164ASP-1-0.802-0.90531.508-0.029-0.0290.0000.0000.0000.000
165A165SER00.0580.02130.7960.0010.0010.0000.0000.0000.000
166A166ALA00.0250.02028.5850.0000.0000.0000.0000.0000.000
167A167THR0-0.010-0.02330.6830.0010.0010.0000.0000.0000.000
168A168ALA0-0.008-0.01833.3880.0010.0010.0000.0000.0000.000
169A169ARG10.9100.95631.7120.0380.0380.0000.0000.0000.000
170A170ALA00.0220.02732.5760.0010.0010.0000.0000.0000.000
171A171PHE00.010-0.00634.5460.0020.0020.0000.0000.0000.000
172A172VAL0-0.004-0.00138.1400.0010.0010.0000.0000.0000.000
173A173ALA0-0.028-0.00536.2230.0010.0010.0000.0000.0000.000
174A174LYN0-0.0170.02338.3750.0000.0000.0000.0000.0000.000
175A175ASN0-0.099-0.07840.6840.0020.0020.0000.0000.0000.000
176A176PRO00.0520.02343.546-0.001-0.0010.0000.0000.0000.000
177A177ASP-1-0.796-0.90844.714-0.017-0.0170.0000.0000.0000.000
178A178LEU0-0.0180.00243.3890.0000.0000.0000.0000.0000.000
179A179VAL0-0.040-0.02842.319-0.001-0.0010.0000.0000.0000.000
180A180ILE00.0100.01036.2780.0010.0010.0000.0000.0000.000
181A181SER0-0.058-0.03940.4520.0000.0000.0000.0000.0000.000
182A182SER0-0.033-0.02037.9970.0000.0000.0000.0000.0000.000
183A183GLY00.0060.00236.489-0.001-0.0010.0000.0000.0000.000
184A184VAL0-0.034-0.00130.7250.0020.0020.0000.0000.0000.000
185A185LEU0-0.010-0.00633.769-0.001-0.0010.0000.0000.0000.000
186A186SER00.007-0.01532.1920.0000.0000.0000.0000.0000.000
187A187SER0-0.056-0.02029.290-0.001-0.0010.0000.0000.0000.000
188A188GLU-1-0.838-0.89325.046-0.046-0.0460.0000.0000.0000.000
189A189GLN0-0.056-0.03922.122-0.003-0.0030.0000.0000.0000.000
190A190TYR00.0140.00819.426-0.003-0.0030.0000.0000.0000.000
191A191GLY00.0290.00616.481-0.008-0.0080.0000.0000.0000.000
192A192ILE0-0.038-0.01610.5730.0140.0140.0000.0000.0000.000
193A193ALA00.0030.01711.568-0.030-0.0300.0000.0000.0000.000
194A194VAL00.0450.0026.1140.0700.0700.0000.0000.0000.000
195A195ARG10.7740.8853.567-0.251-0.0860.000-0.039-0.1260.000
196A196LYS10.9010.9466.7830.0980.0980.0000.0000.0000.000
197A197GLU-1-0.891-0.9585.444-0.503-0.5030.0000.0000.0000.000
198A198ASP-1-0.838-0.8992.660-4.170-2.8101.582-1.115-1.828-0.014
199A199THR0-0.006-0.0274.2070.1970.281-0.001-0.008-0.0750.000
200A200ASP-1-0.753-0.8622.209-10.954-8.9144.404-3.041-3.403-0.046
201A201LEU00.004-0.0082.425-0.2890.5510.690-0.446-1.0850.003
202A202LEU0-0.0140.0074.2960.2280.3100.000-0.022-0.0600.000
203A203GLU-1-0.872-0.9497.481-0.237-0.2370.0000.0000.0000.000
204A204PHE0-0.045-0.0177.1480.1310.1310.0000.0000.0000.000
205A205ILE00.0300.0007.6260.1060.1060.0000.0000.0000.000
206A206ASN00.0470.02310.2000.0790.0790.0000.0000.0000.000
207A207SER0-0.080-0.04612.0930.0520.0520.0000.0000.0000.000
208A208VAL00.0120.01912.0990.0320.0320.0000.0000.0000.000
209A209LEU0-0.013-0.00614.4040.0250.0250.0000.0000.0000.000
210A210ARG10.9090.95614.1530.2070.2070.0000.0000.0000.000
211A211GLU-1-0.907-0.94617.163-0.071-0.0710.0000.0000.0000.000
212A212LEU0-0.030-0.02017.5930.0120.0120.0000.0000.0000.000
213A213LYS10.9080.95520.4590.0900.0900.0000.0000.0000.000
214A214LYS10.8380.94522.2630.0750.0750.0000.0000.0000.000
215A215SER0-0.012-0.01624.3830.0060.0060.0000.0000.0000.000
216A216PRO00.021-0.02327.897-0.001-0.0010.0000.0000.0000.000
217A217TYR00.0020.00530.4120.0020.0020.0000.0000.0000.000
218A218ASP-1-0.769-0.88327.134-0.053-0.0530.0000.0000.0000.000
219A219VAL00.000-0.00126.970-0.001-0.0010.0000.0000.0000.000
220A220LEU0-0.051-0.01629.4000.0020.0020.0000.0000.0000.000
221A221ILE00.003-0.01031.1350.0020.0020.0000.0000.0000.000
222A222GLU-1-0.802-0.88525.701-0.060-0.0600.0000.0000.0000.000
223A223LYS10.8610.96330.3810.0250.0250.0000.0000.0000.000
224A224TRP0-0.055-0.03833.1110.0030.0030.0000.0000.0000.000
225A225PHE0-0.062-0.01833.4130.0020.0020.0000.0000.0000.000
226A226SER0-0.035-0.02530.447-0.003-0.0030.0000.0000.0000.000