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

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FMODB ID: LNKJ9

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2534600.772182
FMO2-HF: Nuclear repulsion 2448159.01813
FMO2-HF: Total energy -86441.754052
FMO2-MP2: Total energy -86699.933384


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.
-20.478-10.99713.332-10.342-12.469-0.111
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 : 0.009 / q_NPA : 0.014
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-1-0.812-0.9023.376-2.634-0.508-0.004-1.067-1.0550.004
4A4GLU-1-0.869-0.9262.115-10.344-8.0095.910-4.033-4.213-0.056
5A5ILE0-0.041-0.0203.1770.7641.5860.071-0.335-0.5580.001
6A6LYS10.8450.9136.0692.6312.6310.0000.0000.0000.000
7A7SER0-0.079-0.0517.8870.4980.4980.0000.0000.0000.000
8A8ARG10.6980.8195.7560.6380.6380.0000.0000.0000.000
9A9GLY00.0260.02510.0490.1820.1820.0000.0000.0000.000
10A10TYR0-0.008-0.01510.7830.1010.1010.0000.0000.0000.000
11A11LEU00.0320.0296.562-0.085-0.0850.0000.0000.0000.000
12A12LEU0-0.046-0.0197.9960.0730.0730.0000.0000.0000.000
13A13VAL00.0160.0038.9550.1240.1240.0000.0000.0000.000
14A14GLY0-0.0020.00011.426-0.026-0.0260.0000.0000.0000.000
15A15LEU0-0.034-0.04313.6140.0080.0080.0000.0000.0000.000
16A16SER00.026-0.01317.0210.0050.0050.0000.0000.0000.000
17A17ALA0-0.034-0.01820.698-0.005-0.0050.0000.0000.0000.000
18A18ASP-1-0.866-0.92122.9310.0710.0710.0000.0000.0000.000
19A19PHE00.0000.01722.933-0.001-0.0010.0000.0000.0000.000
20A20PRO00.0110.02424.901-0.004-0.0040.0000.0000.0000.000
21A21PRO0-0.025-0.02426.7350.0040.0040.0000.0000.0000.000
22A22PHE0-0.020-0.01021.731-0.010-0.0100.0000.0000.0000.000
23A23GLH0-0.049-0.06119.612-0.006-0.0060.0000.0000.0000.000
24A24PHE0-0.035-0.00922.5380.0070.0070.0000.0000.0000.000
25A25VAL00.0300.01424.841-0.008-0.0080.0000.0000.0000.000
26A26ASP-1-0.780-0.88326.797-0.031-0.0310.0000.0000.0000.000
27A27GLU-1-0.940-0.96829.141-0.014-0.0140.0000.0000.0000.000
28A28ASN0-0.137-0.08230.156-0.001-0.0010.0000.0000.0000.000
29A29GLY0-0.0120.00228.975-0.004-0.0040.0000.0000.0000.000
30A30ASN0-0.100-0.05324.632-0.007-0.0070.0000.0000.0000.000
31A31ILE00.0080.00820.0490.0070.0070.0000.0000.0000.000
32A32VAL0-0.027-0.02222.211-0.016-0.0160.0000.0000.0000.000
33A33GLY00.0720.02423.1340.0130.0130.0000.0000.0000.000
34A34PHE0-0.033-0.01521.766-0.011-0.0110.0000.0000.0000.000
35A35ASP-1-0.701-0.82217.7270.0590.0590.0000.0000.0000.000
36A36VAL00.0080.00917.170-0.012-0.0120.0000.0000.0000.000
37A37ASP-1-0.853-0.92317.868-0.104-0.1040.0000.0000.0000.000
38A38LEU00.0030.01116.427-0.026-0.0260.0000.0000.0000.000
39A39ALA0-0.001-0.00713.579-0.030-0.0300.0000.0000.0000.000
40A40LYS10.8150.89613.7350.0350.0350.0000.0000.0000.000
41A41GLU-1-0.795-0.87015.776-0.277-0.2770.0000.0000.0000.000
42A42ILE00.003-0.0059.758-0.053-0.0530.0000.0000.0000.000
43A43ALA0-0.0040.00411.235-0.112-0.1120.0000.0000.0000.000
44A44ARG10.8870.92012.2560.1170.1170.0000.0000.0000.000
45A45ARG10.7280.83213.2400.2540.2540.0000.0000.0000.000
46A46LEU0-0.018-0.0067.099-0.081-0.0810.0000.0000.0000.000
47A47GLY0-0.052-0.00710.691-0.161-0.1610.0000.0000.0000.000
48A48VAL0-0.071-0.0269.520-0.007-0.0070.0000.0000.0000.000
49A49GLU-1-0.919-0.96012.843-0.204-0.2040.0000.0000.0000.000
50A50LEU0-0.012-0.01812.590-0.038-0.0380.0000.0000.0000.000
51A51LYS10.8700.94312.4670.0970.0970.0000.0000.0000.000
52A52ILE00.0470.01813.1330.0370.0370.0000.0000.0000.000
53A53VAL0-0.063-0.03613.382-0.017-0.0170.0000.0000.0000.000
54A54ASP-1-0.798-0.90515.9050.0870.0870.0000.0000.0000.000
55A55MET0-0.088-0.02714.5810.0240.0240.0000.0000.0000.000
56A56THR00.0720.03419.8760.0030.0030.0000.0000.0000.000
57A57PHE00.0510.01619.9480.0270.0270.0000.0000.0000.000
58A58ASP-1-0.908-0.95619.2250.1840.1840.0000.0000.0000.000
59A59GLY0-0.038-0.01618.9020.0230.0230.0000.0000.0000.000
60A60LEU0-0.020-0.00315.1630.0390.0390.0000.0000.0000.000
61A61ILE00.0450.01513.7840.0590.0590.0000.0000.0000.000
62A62PRO00.0150.00213.7150.0780.0780.0000.0000.0000.000
63A63SER00.0440.04413.4960.0610.0610.0000.0000.0000.000
64A64LEU00.0000.0177.7400.0520.0520.0000.0000.0000.000
65A65LEU00.0030.0029.2260.2130.2130.0000.0000.0000.000
66A66THR0-0.078-0.05310.7510.0910.0910.0000.0000.0000.000
67A67LYS10.7860.8914.832-2.975-2.9750.0000.0000.0000.000
68A68LYS10.8170.8979.171-0.525-0.5250.0000.0000.0000.000
69A69ILE00.0030.0259.490-0.113-0.1130.0000.0000.0000.000
70A70ASP-1-0.737-0.8464.4860.2890.349-0.001-0.005-0.0540.000
71A71VAL0-0.013-0.0095.9020.2890.2890.0000.0000.0000.000
72A72ILE0-0.0230.0028.444-0.098-0.0980.0000.0000.0000.000
73A73ILE0-0.023-0.02111.6510.0020.0020.0000.0000.0000.000
74A74SER00.0200.00114.669-0.026-0.0260.0000.0000.0000.000
75A75GLY00.0520.03917.9010.0080.0080.0000.0000.0000.000
76A76MET0-0.044-0.00716.5090.0210.0210.0000.0000.0000.000
77A77THR0-0.026-0.04518.7890.0120.0120.0000.0000.0000.000
78A78ILE00.0280.03217.7570.0290.0290.0000.0000.0000.000
79A79THR00.021-0.00119.936-0.012-0.0120.0000.0000.0000.000
80A80GLU-1-0.806-0.88720.4590.2380.2380.0000.0000.0000.000
81A81GLU-1-0.858-0.89822.0080.2360.2360.0000.0000.0000.000
82A82ARG10.9170.94917.628-0.177-0.1770.0000.0000.0000.000
83A83LYS10.8940.93016.542-0.185-0.1850.0000.0000.0000.000
84A84LYS10.8080.89416.821-0.202-0.2020.0000.0000.0000.000
85A85VAL0-0.041-0.00414.8440.0360.0360.0000.0000.0000.000
86A86VAL0-0.026-0.01312.0790.0880.0880.0000.0000.0000.000
87A87ALA0-0.015-0.0089.978-0.071-0.0710.0000.0000.0000.000
88A88PHE0-0.002-0.02711.9880.0120.0120.0000.0000.0000.000
89A89SER00.004-0.00512.4900.0080.0080.0000.0000.0000.000
90A90ASP-1-0.831-0.91113.4050.0730.0730.0000.0000.0000.000
91A91PRO0-0.0270.00616.572-0.004-0.0040.0000.0000.0000.000
92A92TYR0-0.078-0.05817.120-0.020-0.0200.0000.0000.0000.000
93A93PHE00.0000.00019.631-0.017-0.0170.0000.0000.0000.000
94A94ASP-1-0.851-0.90522.9880.0690.0690.0000.0000.0000.000
95A95ALA00.0120.00825.991-0.009-0.0090.0000.0000.0000.000
96A96GLY00.0760.03227.5380.0050.0050.0000.0000.0000.000
97A97GLN0-0.067-0.04231.003-0.009-0.0090.0000.0000.0000.000
98A98VAL0-0.040-0.01734.6250.0020.0020.0000.0000.0000.000
99A99ILE00.0190.01537.257-0.002-0.0020.0000.0000.0000.000
100A100VAL0-0.023-0.01040.081-0.001-0.0010.0000.0000.0000.000
101A101VAL00.0300.00442.6530.0000.0000.0000.0000.0000.000
102A102ARG10.9060.93145.947-0.008-0.0080.0000.0000.0000.000
103A103LYS10.8480.91844.602-0.003-0.0030.0000.0000.0000.000
104A104ASP-1-0.825-0.88448.4470.0060.0060.0000.0000.0000.000
105A105SER0-0.021-0.02551.2730.0000.0000.0000.0000.0000.000
106A106ASP-1-0.852-0.91851.2130.0130.0130.0000.0000.0000.000
107A107PHE0-0.047-0.01349.1350.0020.0020.0000.0000.0000.000
108A108ARG10.8390.88545.589-0.016-0.0160.0000.0000.0000.000
109A109PRO00.0260.03045.1760.0020.0020.0000.0000.0000.000
110A110LYS10.8560.91242.278-0.029-0.0290.0000.0000.0000.000
111A111THR0-0.015-0.02641.0890.0030.0030.0000.0000.0000.000
112A112TYR00.0760.01137.480-0.004-0.0040.0000.0000.0000.000
113A113GLU-1-0.788-0.87444.1120.0380.0380.0000.0000.0000.000
114A114ASP-1-0.828-0.88545.6880.0300.0300.0000.0000.0000.000
115A115LEU0-0.032-0.01944.066-0.003-0.0030.0000.0000.0000.000
116A116VAL00.0330.03048.299-0.002-0.0020.0000.0000.0000.000
117A117GLY0-0.039-0.02050.856-0.001-0.0010.0000.0000.0000.000
118A118LYS10.7710.89150.382-0.024-0.0240.0000.0000.0000.000
119A119THR0-0.075-0.01550.8410.0000.0000.0000.0000.0000.000
120A120VAL0-0.012-0.00644.6450.0000.0000.0000.0000.0000.000
121A121ALA0-0.0050.01146.4680.0000.0000.0000.0000.0000.000
122A122VAL00.001-0.00441.7910.0010.0010.0000.0000.0000.000
123A123GLN00.011-0.01038.003-0.001-0.0010.0000.0000.0000.000
124A124ILE00.018-0.00340.4430.0030.0030.0000.0000.0000.000
125A125GLY0-0.021-0.00539.531-0.001-0.0010.0000.0000.0000.000
126A126THR0-0.029-0.01836.0650.0030.0030.0000.0000.0000.000
127A127THR00.0380.00533.0220.0000.0000.0000.0000.0000.000
128A128GLY00.0470.02535.7100.0010.0010.0000.0000.0000.000
129A129ASP-1-0.779-0.87438.5170.0250.0250.0000.0000.0000.000
130A130ILE00.0140.02336.3030.0010.0010.0000.0000.0000.000
131A131GLU-1-0.856-0.91136.9760.0550.0550.0000.0000.0000.000
132A132VAL0-0.001-0.01339.9610.0000.0000.0000.0000.0000.000
133A133SER0-0.052-0.05443.070-0.002-0.0020.0000.0000.0000.000
134A134LYS10.7450.87537.809-0.053-0.0530.0000.0000.0000.000
135A135TYR0-0.062-0.04942.9300.0010.0010.0000.0000.0000.000
136A136ASP-1-0.892-0.94647.8170.0290.0290.0000.0000.0000.000
137A137GLY0-0.037-0.01351.141-0.002-0.0020.0000.0000.0000.000
138A138ILE00.0000.00546.428-0.001-0.0010.0000.0000.0000.000
139A139LYS10.9330.97050.476-0.014-0.0140.0000.0000.0000.000
140A140VAL00.007-0.00445.704-0.001-0.0010.0000.0000.0000.000
141A141VAL0-0.063-0.02648.358-0.001-0.0010.0000.0000.0000.000
142A142ARG10.8810.91544.819-0.023-0.0230.0000.0000.0000.000
143A143PHE00.008-0.00144.774-0.001-0.0010.0000.0000.0000.000
144A144ASP-1-0.775-0.87442.5040.0040.0040.0000.0000.0000.000
145A145LYS10.8470.92040.5560.0000.0000.0000.0000.0000.000
146A146PHE00.0560.02136.1350.0010.0010.0000.0000.0000.000
147A147THR0-0.007-0.00540.8020.0010.0010.0000.0000.0000.000
148A148ASP-1-0.845-0.92642.8850.0010.0010.0000.0000.0000.000
149A149ALA00.0000.01043.3490.0000.0000.0000.0000.0000.000
150A150PHE00.014-0.00739.3160.0010.0010.0000.0000.0000.000
151A151LEU0-0.021-0.00945.1310.0000.0000.0000.0000.0000.000
152A152GLU-1-0.760-0.86148.2870.0060.0060.0000.0000.0000.000
153A153LEU0-0.0320.00445.5530.0000.0000.0000.0000.0000.000
154A154LYS10.7810.86945.9870.0000.0000.0000.0000.0000.000
155A155ARG10.8040.88950.352-0.003-0.0030.0000.0000.0000.000
156A156GLY0-0.0080.00552.7540.0000.0000.0000.0000.0000.000
157A157ARG10.8050.89453.179-0.005-0.0050.0000.0000.0000.000
158A158ALA0-0.030-0.02549.2550.0010.0010.0000.0000.0000.000
159A159ASP-1-0.824-0.90450.7360.0140.0140.0000.0000.0000.000
160A160ALA0-0.026-0.02545.5950.0000.0000.0000.0000.0000.000
161A161VAL0-0.0180.00441.420-0.001-0.0010.0000.0000.0000.000
162A162VAL0-0.0110.00139.0460.0010.0010.0000.0000.0000.000
163A163LEU0-0.0090.00336.103-0.002-0.0020.0000.0000.0000.000
164A164ASP-1-0.726-0.85031.6420.0260.0260.0000.0000.0000.000
165A165SER00.0110.00530.307-0.006-0.0060.0000.0000.0000.000
166A166ALA00.0110.01328.971-0.004-0.0040.0000.0000.0000.000
167A167THR0-0.014-0.04631.058-0.007-0.0070.0000.0000.0000.000
168A168ALA0-0.008-0.00233.907-0.004-0.0040.0000.0000.0000.000
169A169ARG10.8870.94631.842-0.029-0.0290.0000.0000.0000.000
170A170ALA00.0160.01533.059-0.003-0.0030.0000.0000.0000.000
171A171PHE00.0270.00734.979-0.003-0.0030.0000.0000.0000.000
172A172VAL0-0.005-0.01238.474-0.002-0.0020.0000.0000.0000.000
173A173ALA0-0.031-0.00636.531-0.001-0.0010.0000.0000.0000.000
174A174LYN0-0.0110.02538.568-0.002-0.0020.0000.0000.0000.000
175A175ASN0-0.098-0.06440.765-0.001-0.0010.0000.0000.0000.000
176A176PRO00.0690.02743.6800.0020.0020.0000.0000.0000.000
177A177ASP-1-0.785-0.86844.9920.0010.0010.0000.0000.0000.000
178A178LEU00.0010.00943.5060.0020.0020.0000.0000.0000.000
179A179VAL0-0.040-0.02942.342-0.001-0.0010.0000.0000.0000.000
180A180ILE00.0300.02436.2960.0010.0010.0000.0000.0000.000
181A181SER0-0.040-0.02340.560-0.001-0.0010.0000.0000.0000.000
182A182SER0-0.018-0.00438.1740.0000.0000.0000.0000.0000.000
183A183GLY00.0150.01136.583-0.001-0.0010.0000.0000.0000.000
184A184VAL0-0.032-0.00530.748-0.003-0.0030.0000.0000.0000.000
185A185LEU00.0100.01533.8800.0050.0050.0000.0000.0000.000
186A186SER00.000-0.01932.303-0.001-0.0010.0000.0000.0000.000
187A187SER0-0.047-0.01029.6370.0000.0000.0000.0000.0000.000
188A188GLU-1-0.812-0.87425.2110.1180.1180.0000.0000.0000.000
189A189GLN0-0.047-0.03722.1980.0020.0020.0000.0000.0000.000
190A190TYR0-0.038-0.02319.8050.0170.0170.0000.0000.0000.000
191A191GLY00.033-0.00216.752-0.017-0.0170.0000.0000.0000.000
192A192ILE0-0.0080.00210.8530.0130.0130.0000.0000.0000.000
193A193ALA0-0.0030.00511.9220.0320.0320.0000.0000.0000.000
194A194VAL00.0360.0006.5580.0010.0010.0000.0000.0000.000
195A195ARG10.7420.8333.508-2.712-2.5180.002-0.064-0.1310.000
196A196LYS10.8160.8967.227-0.523-0.5230.0000.0000.0000.000
197A197GLU-1-0.771-0.8725.2941.6981.6980.0000.0000.0000.000
198A198ASP-1-0.749-0.8462.7164.1035.0551.745-0.956-1.741-0.007
199A199THR0-0.024-0.0413.656-1.089-1.0870.0000.092-0.0930.000
200A200ASP-1-0.755-0.8742.135-9.781-7.6955.189-3.591-3.684-0.055
201A201LEU00.007-0.0042.572-1.269-0.4360.420-0.363-0.8900.002
202A202LEU0-0.0200.0034.370-0.150-0.0790.000-0.020-0.0500.000
203A203GLU-1-0.742-0.8387.585-0.073-0.0730.0000.0000.0000.000
204A204PHE0-0.0200.0127.278-0.072-0.0720.0000.0000.0000.000
205A205ILE00.020-0.0017.7290.0210.0210.0000.0000.0000.000
206A206ASN00.014-0.00710.2680.0090.0090.0000.0000.0000.000
207A207SER0-0.038-0.03012.1430.0030.0030.0000.0000.0000.000
208A208VAL0-0.0020.00412.4210.0110.0110.0000.0000.0000.000
209A209LEU0-0.034-0.02014.3730.0200.0200.0000.0000.0000.000
210A210ARG10.7220.82814.2180.0210.0210.0000.0000.0000.000
211A211GLU-1-0.859-0.89317.638-0.223-0.2230.0000.0000.0000.000
212A212LEU0-0.017-0.01817.3990.0100.0100.0000.0000.0000.000
213A213LYS10.8400.92619.639-0.005-0.0050.0000.0000.0000.000
214A214LYS10.7930.89922.7200.1020.1020.0000.0000.0000.000
215A215SER0-0.023-0.04324.589-0.004-0.0040.0000.0000.0000.000
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