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: 3J1QL

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 OptHSide
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 -2532896.234573
FMO2-HF: Nuclear repulsion 2446455.388951
FMO2-HF: Total energy -86440.845623
FMO2-MP2: Total energy -86699.370868


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.
-20.385-11.44412.21-9.33-11.821-0.097
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 : 0.011 / q_NPA : 0.009
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-1-0.903-0.9483.303-2.730-0.525-0.005-1.032-1.1680.005
4A4GLU-1-0.888-0.9432.235-8.555-6.0653.905-2.912-3.483-0.042
5A5ILE0-0.049-0.0223.1010.6761.4190.088-0.278-0.5540.000
6A6LYS10.9270.9616.0702.0842.0840.0000.0000.0000.000
7A7SER0-0.063-0.0397.8640.4400.4400.0000.0000.0000.000
8A8ARG10.6900.8195.7010.3240.3240.0000.0000.0000.000
9A9GLY00.0380.02110.1110.1490.1490.0000.0000.0000.000
10A10TYR0-0.013-0.01910.4340.1140.1140.0000.0000.0000.000
11A11LEU00.0060.0166.390-0.075-0.0750.0000.0000.0000.000
12A12LEU0-0.039-0.0177.8030.0240.0240.0000.0000.0000.000
13A13VAL00.0280.0078.7100.1340.1340.0000.0000.0000.000
14A14GLY0-0.009-0.00111.188-0.038-0.0380.0000.0000.0000.000
15A15LEU0-0.034-0.04313.4450.0040.0040.0000.0000.0000.000
16A16SER00.002-0.02816.7650.0030.0030.0000.0000.0000.000
17A17ALA0-0.040-0.02220.424-0.007-0.0070.0000.0000.0000.000
18A18ASP-1-0.896-0.93222.6050.0940.0940.0000.0000.0000.000
19A19PHE00.0070.00922.825-0.002-0.0020.0000.0000.0000.000
20A20PRO00.0080.03424.870-0.003-0.0030.0000.0000.0000.000
21A21PRO0-0.011-0.01926.6950.0030.0030.0000.0000.0000.000
22A22PHE0-0.025-0.01621.594-0.010-0.0100.0000.0000.0000.000
23A23GLH0-0.031-0.04919.504-0.004-0.0040.0000.0000.0000.000
24A24PHE0-0.026-0.00622.2120.0060.0060.0000.0000.0000.000
25A25VAL00.0340.02024.660-0.007-0.0070.0000.0000.0000.000
26A26ASP-1-0.836-0.91926.598-0.007-0.0070.0000.0000.0000.000
27A27GLU-1-0.927-0.96329.0670.0020.0020.0000.0000.0000.000
28A28ASN0-0.132-0.07229.519-0.003-0.0030.0000.0000.0000.000
29A29GLY0-0.015-0.00128.557-0.003-0.0030.0000.0000.0000.000
30A30ASN0-0.055-0.03124.612-0.002-0.0020.0000.0000.0000.000
31A31ILE00.0190.02319.9440.0050.0050.0000.0000.0000.000
32A32VAL0-0.033-0.03121.757-0.013-0.0130.0000.0000.0000.000
33A33GLY00.0750.02122.9470.0130.0130.0000.0000.0000.000
34A34PHE0-0.029-0.01121.362-0.010-0.0100.0000.0000.0000.000
35A35ASP-1-0.686-0.81817.5690.0910.0910.0000.0000.0000.000
36A36VAL0-0.0210.00117.007-0.004-0.0040.0000.0000.0000.000
37A37ASP-1-0.851-0.91917.571-0.063-0.0630.0000.0000.0000.000
38A38LEU0-0.0120.00315.983-0.026-0.0260.0000.0000.0000.000
39A39ALA00.006-0.00113.186-0.025-0.0250.0000.0000.0000.000
40A40LYS10.8270.90713.4480.0020.0020.0000.0000.0000.000
41A41GLU-1-0.807-0.89115.633-0.234-0.2340.0000.0000.0000.000
42A42ILE0-0.006-0.0139.593-0.054-0.0540.0000.0000.0000.000
43A43ALA00.0060.00311.087-0.098-0.0980.0000.0000.0000.000
44A44ARG10.8730.92212.1140.0820.0820.0000.0000.0000.000
45A45ARG10.7400.85613.2150.2320.2320.0000.0000.0000.000
46A46LEU0-0.031-0.0097.266-0.090-0.0900.0000.0000.0000.000
47A47GLY0-0.065-0.02111.119-0.139-0.1390.0000.0000.0000.000
48A48VAL0-0.056-0.0159.398-0.009-0.0090.0000.0000.0000.000
49A49GLU-1-0.941-0.96712.746-0.145-0.1450.0000.0000.0000.000
50A50LEU00.012-0.00112.327-0.032-0.0320.0000.0000.0000.000
51A51LYS10.9000.94912.4730.0200.0200.0000.0000.0000.000
52A52ILE00.0390.02012.9610.0340.0340.0000.0000.0000.000
53A53VAL0-0.062-0.04013.172-0.016-0.0160.0000.0000.0000.000
54A54ASP-1-0.809-0.91015.7190.1250.1250.0000.0000.0000.000
55A55MET0-0.081-0.02214.4690.0240.0240.0000.0000.0000.000
56A56THR00.0760.03219.8060.0000.0000.0000.0000.0000.000
57A57PHE00.0610.02019.9060.0310.0310.0000.0000.0000.000
58A58ASP-1-0.903-0.95419.4270.2020.2020.0000.0000.0000.000
59A59GLY0-0.060-0.01918.9850.0190.0190.0000.0000.0000.000
60A60LEU0-0.028-0.01015.1280.0450.0450.0000.0000.0000.000
61A61ILE00.0270.00013.9210.0650.0650.0000.0000.0000.000
62A62PRO00.0180.00513.7550.0790.0790.0000.0000.0000.000
63A63SER00.0530.03313.5810.0630.0630.0000.0000.0000.000
64A64LEU00.0080.0147.5630.0620.0620.0000.0000.0000.000
65A65LEU0-0.018-0.0139.3700.1960.1960.0000.0000.0000.000
66A66THR0-0.071-0.03711.0700.0530.0530.0000.0000.0000.000
67A67LYS10.8280.9045.736-2.378-2.3780.0000.0000.0000.000
68A68LYS10.8610.9359.152-0.522-0.5220.0000.0000.0000.000
69A69ILE0-0.0070.0209.231-0.112-0.1120.0000.0000.0000.000
70A70ASP-1-0.729-0.8344.3280.6020.683-0.001-0.008-0.0720.000
71A71VAL0-0.002-0.0055.6200.2670.2670.0000.0000.0000.000
72A72ILE0-0.0290.0058.180-0.104-0.1040.0000.0000.0000.000
73A73ILE0-0.010-0.01511.597-0.003-0.0030.0000.0000.0000.000
74A74SER00.018-0.00214.404-0.022-0.0220.0000.0000.0000.000
75A75GLY00.0560.04217.7470.0040.0040.0000.0000.0000.000
76A76MET0-0.050-0.00816.4350.0200.0200.0000.0000.0000.000
77A77THR0-0.064-0.06518.8490.0060.0060.0000.0000.0000.000
78A78ILE00.0090.01717.6620.0280.0280.0000.0000.0000.000
79A79THR00.024-0.00119.948-0.012-0.0120.0000.0000.0000.000
80A80GLU-1-0.784-0.88320.2920.2270.2270.0000.0000.0000.000
81A81GLU-1-0.844-0.90420.9430.2470.2470.0000.0000.0000.000
82A82ARG10.9310.95417.396-0.196-0.1960.0000.0000.0000.000
83A83LYS10.8970.94116.394-0.167-0.1670.0000.0000.0000.000
84A84LYS10.8280.91216.370-0.198-0.1980.0000.0000.0000.000
85A85VAL0-0.049-0.02314.4960.0270.0270.0000.0000.0000.000
86A86VAL0-0.044-0.01811.6740.1010.1010.0000.0000.0000.000
87A87ALA00.0020.0089.696-0.085-0.0850.0000.0000.0000.000
88A88PHE0-0.004-0.02211.3630.0310.0310.0000.0000.0000.000
89A89SER00.006-0.00312.0560.0010.0010.0000.0000.0000.000
90A90ASP-1-0.916-0.95513.1000.0690.0690.0000.0000.0000.000
91A91PRO0-0.024-0.00516.5350.0030.0030.0000.0000.0000.000
92A92TYR0-0.111-0.08716.909-0.021-0.0210.0000.0000.0000.000
93A93PHE0-0.009-0.00619.475-0.016-0.0160.0000.0000.0000.000
94A94ASP-1-0.840-0.89322.7080.0730.0730.0000.0000.0000.000
95A95ALA0-0.020-0.01025.752-0.009-0.0090.0000.0000.0000.000
96A96GLY00.0840.02227.3980.0040.0040.0000.0000.0000.000
97A97GLN0-0.034-0.00330.961-0.009-0.0090.0000.0000.0000.000
98A98VAL0-0.035-0.01234.4900.0020.0020.0000.0000.0000.000
99A99ILE00.0290.02237.068-0.001-0.0010.0000.0000.0000.000
100A100VAL0-0.024-0.01739.860-0.001-0.0010.0000.0000.0000.000
101A101VAL00.0420.01242.3600.0000.0000.0000.0000.0000.000
102A102ARG10.9270.94045.761-0.010-0.0100.0000.0000.0000.000
103A103LYS10.8630.92644.376-0.005-0.0050.0000.0000.0000.000
104A104ASP-1-0.859-0.92048.1690.0070.0070.0000.0000.0000.000
105A105SER0-0.0420.00150.7840.0000.0000.0000.0000.0000.000
106A106ASP-1-0.800-0.89651.3260.0130.0130.0000.0000.0000.000
107A107PHE0-0.087-0.04248.7630.0020.0020.0000.0000.0000.000
108A108ARG10.8360.88645.677-0.016-0.0160.0000.0000.0000.000
109A109PRO00.0290.03744.9180.0010.0010.0000.0000.0000.000
110A110LYS10.8500.90942.337-0.029-0.0290.0000.0000.0000.000
111A111THR0-0.013-0.01941.0780.0030.0030.0000.0000.0000.000
112A112TYR00.0630.00337.224-0.004-0.0040.0000.0000.0000.000
113A113GLU-1-0.765-0.87043.7880.0400.0400.0000.0000.0000.000
114A114ASP-1-0.840-0.89245.6310.0310.0310.0000.0000.0000.000
115A115LEU0-0.053-0.04043.890-0.003-0.0030.0000.0000.0000.000
116A116VAL00.0410.03448.237-0.001-0.0010.0000.0000.0000.000
117A117GLY0-0.054-0.03150.727-0.001-0.0010.0000.0000.0000.000
118A118LYS10.7960.91450.214-0.026-0.0260.0000.0000.0000.000
119A119THR0-0.046-0.01750.8210.0010.0010.0000.0000.0000.000
120A120VAL0-0.0050.00444.600-0.001-0.0010.0000.0000.0000.000
121A121ALA00.0030.00346.0490.0000.0000.0000.0000.0000.000
122A122VAL0-0.0010.00341.4340.0010.0010.0000.0000.0000.000
123A123GLN00.022-0.00937.514-0.001-0.0010.0000.0000.0000.000
124A124ILE0-0.005-0.02140.0920.0030.0030.0000.0000.0000.000
125A125GLY0-0.0080.00238.9290.0000.0000.0000.0000.0000.000
126A126THR0-0.053-0.02435.7180.0040.0040.0000.0000.0000.000
127A127THR00.0660.00932.9230.0000.0000.0000.0000.0000.000
128A128GLY00.0500.03335.5300.0010.0010.0000.0000.0000.000
129A129ASP-1-0.780-0.87638.3790.0310.0310.0000.0000.0000.000
130A130ILE00.0140.02036.1190.0000.0000.0000.0000.0000.000
131A131GLU-1-0.836-0.90936.9550.0590.0590.0000.0000.0000.000
132A132VAL0-0.008-0.02239.973-0.001-0.0010.0000.0000.0000.000
133A133SER0-0.037-0.02343.019-0.003-0.0030.0000.0000.0000.000
134A134LYS10.7800.89437.832-0.058-0.0580.0000.0000.0000.000
135A135TYR0-0.099-0.06242.5820.0010.0010.0000.0000.0000.000
136A136ASP-1-0.878-0.94547.3770.0320.0320.0000.0000.0000.000
137A137GLY0-0.045-0.02350.824-0.002-0.0020.0000.0000.0000.000
138A138ILE0-0.039-0.00446.075-0.001-0.0010.0000.0000.0000.000
139A139LYS10.9480.98250.205-0.018-0.0180.0000.0000.0000.000
140A140VAL00.0060.00345.725-0.001-0.0010.0000.0000.0000.000
141A141VAL0-0.068-0.03148.137-0.001-0.0010.0000.0000.0000.000
142A142ARG10.8600.89744.819-0.029-0.0290.0000.0000.0000.000
143A143PHE00.0200.00744.360-0.002-0.0020.0000.0000.0000.000
144A144ASP-1-0.773-0.86542.2300.0140.0140.0000.0000.0000.000
145A145LYS10.8630.92340.313-0.009-0.0090.0000.0000.0000.000
146A146PHE00.0630.02335.8700.0000.0000.0000.0000.0000.000
147A147THR00.0070.00240.5690.0000.0000.0000.0000.0000.000
148A148ASP-1-0.863-0.94042.3860.0060.0060.0000.0000.0000.000
149A149ALA0-0.0010.01142.9080.0000.0000.0000.0000.0000.000
150A150PHE00.013-0.01038.9910.0000.0000.0000.0000.0000.000
151A151LEU0-0.043-0.01344.734-0.001-0.0010.0000.0000.0000.000
152A152GLU-1-0.823-0.91047.8900.0100.0100.0000.0000.0000.000
153A153LEU0-0.0100.00645.2150.0000.0000.0000.0000.0000.000
154A154LYS10.7680.86045.670-0.003-0.0030.0000.0000.0000.000
155A155ARG10.8160.90149.936-0.008-0.0080.0000.0000.0000.000
156A156GLY0-0.0100.00752.2440.0000.0000.0000.0000.0000.000
157A157ARG10.8400.93052.816-0.008-0.0080.0000.0000.0000.000
158A158ALA0-0.024-0.01748.9730.0010.0010.0000.0000.0000.000
159A159ASP-1-0.858-0.92450.2940.0170.0170.0000.0000.0000.000
160A160ALA0-0.029-0.03045.1710.0000.0000.0000.0000.0000.000
161A161VAL0-0.0210.00440.9180.0000.0000.0000.0000.0000.000
162A162VAL0-0.0180.00238.6240.0010.0010.0000.0000.0000.000
163A163LEU0-0.0050.00135.845-0.001-0.0010.0000.0000.0000.000
164A164ASP-1-0.778-0.89031.3200.0350.0350.0000.0000.0000.000
165A165SER00.0520.02830.555-0.007-0.0070.0000.0000.0000.000
166A166ALA00.0290.02328.587-0.005-0.0050.0000.0000.0000.000
167A167THR0-0.019-0.03430.675-0.007-0.0070.0000.0000.0000.000
168A168ALA0-0.017-0.01933.392-0.004-0.0040.0000.0000.0000.000
169A169ARG10.8970.94131.810-0.032-0.0320.0000.0000.0000.000
170A170ALA00.0270.03132.662-0.004-0.0040.0000.0000.0000.000
171A171PHE00.006-0.01234.573-0.003-0.0030.0000.0000.0000.000
172A172VAL00.001-0.00438.156-0.002-0.0020.0000.0000.0000.000
173A173ALA0-0.022-0.00536.302-0.001-0.0010.0000.0000.0000.000
174A174LYN0-0.0230.01738.400-0.002-0.0020.0000.0000.0000.000
175A175ASN0-0.087-0.05240.719-0.001-0.0010.0000.0000.0000.000
176A176PRO00.0630.02743.5730.0020.0020.0000.0000.0000.000
177A177ASP-1-0.791-0.88744.7350.0040.0040.0000.0000.0000.000
178A178LEU0-0.0050.01143.5350.0020.0020.0000.0000.0000.000
179A179VAL0-0.039-0.03142.318-0.002-0.0020.0000.0000.0000.000
180A180ILE00.0250.02136.2540.0010.0010.0000.0000.0000.000
181A181SER0-0.024-0.01040.444-0.001-0.0010.0000.0000.0000.000
182A182SER0-0.012-0.00238.0230.0000.0000.0000.0000.0000.000
183A183GLY00.0130.00836.459-0.002-0.0020.0000.0000.0000.000
184A184VAL0-0.029-0.00730.692-0.002-0.0020.0000.0000.0000.000
185A185LEU00.0080.00533.7300.0040.0040.0000.0000.0000.000
186A186SER0-0.004-0.02032.1970.0000.0000.0000.0000.0000.000
187A187SER0-0.046-0.01229.1220.0010.0010.0000.0000.0000.000
188A188GLU-1-0.842-0.88124.9300.1280.1280.0000.0000.0000.000
189A189GLN0-0.052-0.04422.050-0.001-0.0010.0000.0000.0000.000
190A190TYR00.0180.01019.4480.0160.0160.0000.0000.0000.000
191A191GLY00.0330.00616.441-0.018-0.0180.0000.0000.0000.000
192A192ILE0-0.033-0.01110.5030.0110.0110.0000.0000.0000.000
193A193ALA0-0.0030.01011.4500.0230.0230.0000.0000.0000.000
194A194VAL00.0520.0066.0930.0120.0120.0000.0000.0000.000
195A195ARG10.7480.8553.519-3.097-2.8750.003-0.067-0.1570.001
196A196LYS10.8560.9206.720-0.408-0.4080.0000.0000.0000.000
197A197GLU-1-0.812-0.9065.4481.6101.6100.0000.0000.0000.000
198A198ASP-1-0.833-0.8872.7173.9305.0031.395-0.864-1.604-0.007
199A199THR0-0.007-0.0294.094-1.019-0.943-0.0010.002-0.0780.000
200A200ASP-1-0.738-0.8532.055-11.162-9.9916.196-3.744-3.622-0.056
201A201LEU00.009-0.0032.486-1.133-0.3350.630-0.404-1.0240.002
202A202LEU0-0.0130.0054.309-0.094-0.0120.000-0.023-0.0590.000
203A203GLU-1-0.790-0.8817.442-0.095-0.0950.0000.0000.0000.000
204A204PHE0-0.0130.0077.154-0.042-0.0420.0000.0000.0000.000
205A205ILE00.025-0.0017.6020.0350.0350.0000.0000.0000.000
206A206ASN00.006-0.01010.2310.0200.0200.0000.0000.0000.000
207A207SER0-0.051-0.03912.1150.0080.0080.0000.0000.0000.000
208A208VAL00.0040.01012.2320.0090.0090.0000.0000.0000.000
209A209LEU0-0.029-0.01614.4430.0180.0180.0000.0000.0000.000
210A210ARG10.8160.90114.1420.0860.0860.0000.0000.0000.000
211A211GLU-1-0.839-0.89217.621-0.222-0.2220.0000.0000.0000.000
212A212LEU0-0.040-0.02217.3760.0090.0090.0000.0000.0000.000
213A213LYS10.8870.94719.911-0.007-0.0070.0000.0000.0000.000
214A214LYS10.7990.91622.6520.1130.1130.0000.0000.0000.000
215A215SER0-0.024-0.05024.427-0.004-0.0040.0000.0000.0000.000
216A216PRO00.025-0.02327.949-0.003-0.0030.0000.0000.0000.000
217A217TYR00.0050.01030.4720.0000.0000.0000.0000.0000.000
218A218ASP-1-0.761-0.85427.434-0.045-0.0450.0000.0000.0000.000
219A219VAL0-0.0030.00327.118-0.002-0.0020.0000.0000.0000.000
220A220LEU0-0.054-0.01729.450-0.001-0.0010.0000.0000.0000.000
221A221ILE00.005-0.01131.2550.0020.0020.0000.0000.0000.000
222A222GLU-1-0.777-0.86625.579-0.094-0.0940.0000.0000.0000.000
223A223LYS10.8700.96130.4150.0630.0630.0000.0000.0000.000
224A224TRP0-0.061-0.04433.1540.0000.0000.0000.0000.0000.000
225A225PHE0-0.053-0.01433.4950.0050.0050.0000.0000.0000.000
226A226SER0-0.031-0.01330.4280.0020.0020.0000.0000.0000.000