FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 3983L

Calculation Name: 5XCK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XCK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BI08

Base Structure: X-ray

Registration Date: 2023-06-26

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973558.215179
FMO2-HF: Nuclear repulsion 1902673.165119
FMO2-HF: Total energy -70885.050059
FMO2-MP2: Total energy -71091.19151


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-21.336-11.58111.667-9.374-12.05-0.046
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.000
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].
3A3VAL00.008-0.0043.8020.1721.657-0.017-0.644-0.8230.003
4A4LEU0-0.0110.0046.1090.1300.1300.0000.0000.0000.000
5A5VAL00.0060.0049.779-0.016-0.0160.0000.0000.0000.000
6A6ILE00.014-0.01312.3570.0770.0770.0000.0000.0000.000
7A7GLY00.0500.01015.677-0.028-0.0280.0000.0000.0000.000
8A8ASP-1-0.831-0.89318.984-0.176-0.1760.0000.0000.0000.000
9A9PHE0-0.026-0.00817.8520.0160.0160.0000.0000.0000.000
10A10HIS0-0.001-0.00823.5960.0090.0090.0000.0000.0000.000
11A11VAL00.0090.00627.169-0.010-0.0100.0000.0000.0000.000
12A12PRO00.0250.00830.2090.0090.0090.0000.0000.0000.000
13A13HIS0-0.032-0.02233.1950.0020.0020.0000.0000.0000.000
14A14ARG10.9310.98032.7700.0640.0640.0000.0000.0000.000
15A15SER0-0.023-0.00431.785-0.001-0.0010.0000.0000.0000.000
16A16ALA00.0220.00828.1560.0000.0000.0000.0000.0000.000
17A17ALA00.0050.01027.0060.0000.0000.0000.0000.0000.000
18A18ILE00.0190.00620.419-0.007-0.0070.0000.0000.0000.000
19A19PRO0-0.0020.00722.2750.0150.0150.0000.0000.0000.000
20A20GLN00.0700.02522.1880.0020.0020.0000.0000.0000.000
21A21VAL00.0260.01121.1300.0150.0150.0000.0000.0000.000
22A22PHE0-0.026-0.01918.1200.0160.0160.0000.0000.0000.000
23A23LEU00.0360.02017.1440.0200.0200.0000.0000.0000.000
24A24ASP-1-0.882-0.92917.8210.1630.1630.0000.0000.0000.000
25A25ARG10.8460.9249.662-0.207-0.2070.0000.0000.0000.000
26A26LEU0-0.016-0.01712.9630.0700.0700.0000.0000.0000.000
27A27ASN0-0.012-0.01512.8020.0970.0970.0000.0000.0000.000
28A28THR0-0.0220.00113.9460.0840.0840.0000.0000.0000.000
29A29GLY0-0.037-0.01610.3750.0680.0680.0000.0000.0000.000
30A30ARG10.9260.9663.351-9.569-7.6120.046-1.072-0.9310.011
31A31ILE00.0360.0216.9490.4620.4620.0000.0000.0000.000
32A32GLN0-0.102-0.0472.311-1.710-1.1444.259-1.911-2.915-0.010
33A33THR00.009-0.0204.994-0.957-0.851-0.001-0.005-0.1000.000
34A34VAL00.0130.0146.706-0.112-0.1120.0000.0000.0000.000
35A35LEU0-0.016-0.0099.206-0.018-0.0180.0000.0000.0000.000
36A36CYS0-0.046-0.01012.0340.0280.0280.0000.0000.0000.000
37A37THR00.0610.00215.613-0.003-0.0030.0000.0000.0000.000
38A38GLY00.0600.02618.5300.0120.0120.0000.0000.0000.000
39A39ASN0-0.073-0.05921.1340.0120.0120.0000.0000.0000.000
40A40LEU00.0310.02719.6300.0070.0070.0000.0000.0000.000
41A41CYS0-0.0080.00623.7080.0020.0020.0000.0000.0000.000
42A42GLY00.0020.00026.3660.0120.0120.0000.0000.0000.000
43A43LYS10.8470.90324.674-0.034-0.0340.0000.0000.0000.000
44A44GLU-1-0.869-0.94523.9900.0200.0200.0000.0000.0000.000
45A45THR0-0.023-0.01020.4430.0060.0060.0000.0000.0000.000
46A46TYR00.0430.02818.2550.0050.0050.0000.0000.0000.000
47A47ASP-1-0.799-0.89219.1860.0540.0540.0000.0000.0000.000
48A48ILE0-0.028-0.00718.1320.0280.0280.0000.0000.0000.000
49A49LEU0-0.013-0.01914.7500.0280.0280.0000.0000.0000.000
50A50ARG10.8830.94014.1530.0120.0120.0000.0000.0000.000
51A51THR0-0.035-0.00515.5090.0350.0350.0000.0000.0000.000
52A52LEU0-0.0430.00212.1540.0500.0500.0000.0000.0000.000
53A53ALA0-0.003-0.0039.1630.1640.1640.0000.0000.0000.000
54A54ARG10.8560.9407.118-0.395-0.3950.0000.0000.0000.000
55A55GLU-1-0.839-0.8937.484-0.663-0.6630.0000.0000.0000.000
56A56VAL0-0.011-0.0119.967-0.045-0.0450.0000.0000.0000.000
57A57HIS0-0.035-0.02210.1990.0440.0440.0000.0000.0000.000
58A58VAL0-0.023-0.02013.990-0.014-0.0140.0000.0000.0000.000
59A59VAL0-0.0320.02917.3110.0010.0010.0000.0000.0000.000
60A60LYS10.8680.94019.7490.1460.1460.0000.0000.0000.000
61A61GLY00.0690.01423.505-0.013-0.0130.0000.0000.0000.000
62A62ALA0-0.054-0.02924.8450.0110.0110.0000.0000.0000.000
63A63PHE0-0.032-0.03527.7830.0110.0110.0000.0000.0000.000
64A64ASP-1-0.779-0.85723.835-0.125-0.1250.0000.0000.0000.000
65A65GLU-1-0.905-0.96127.364-0.084-0.0840.0000.0000.0000.000
66A66MET0-0.080-0.02523.2690.0050.0050.0000.0000.0000.000
67A67GLN00.007-0.00426.933-0.010-0.0100.0000.0000.0000.000
68A68GLY0-0.009-0.01425.3090.0050.0050.0000.0000.0000.000
69A69LEU0-0.038-0.00620.543-0.007-0.0070.0000.0000.0000.000
70A70ASN0-0.011-0.01920.0380.0240.0240.0000.0000.0000.000
71A71GLU-1-0.827-0.90821.591-0.184-0.1840.0000.0000.0000.000
72A72THR0-0.085-0.06319.920-0.014-0.0140.0000.0000.0000.000
73A73GLU-1-0.827-0.87715.834-0.280-0.2800.0000.0000.0000.000
74A74VAL0-0.022-0.02614.988-0.040-0.0400.0000.0000.0000.000
75A75ILE0-0.010-0.0018.9060.0180.0180.0000.0000.0000.000
76A76LYS10.8710.94710.2980.9520.9520.0000.0000.0000.000
77A77ILE00.0170.0034.110-0.267-0.1190.000-0.024-0.1240.000
78A78GLY00.0420.0356.374-0.084-0.0840.0000.0000.0000.000
79A79ASN0-0.034-0.0386.9420.4110.4110.0000.0000.0000.000
80A80PHE00.001-0.0037.5100.2620.2620.0000.0000.0000.000
81A81LYS10.7720.8939.9860.3410.3410.0000.0000.0000.000
82A82ILE00.020-0.0018.2180.0270.0270.0000.0000.0000.000
83A83GLY00.0310.03212.6580.0480.0480.0000.0000.0000.000
84A84LEU0-0.039-0.00613.139-0.023-0.0230.0000.0000.0000.000
85A85MET00.020-0.00916.4530.0450.0450.0000.0000.0000.000
86A86ALA00.0800.04619.849-0.014-0.0140.0000.0000.0000.000
87A87GLY00.0360.01122.256-0.013-0.0130.0000.0000.0000.000
88A88HIS0-0.026-0.00524.0710.0050.0050.0000.0000.0000.000
89A89GLN00.012-0.01924.4290.0040.0040.0000.0000.0000.000
90A90VAL0-0.0280.00024.3450.0070.0070.0000.0000.0000.000
91A91ILE0-0.061-0.01927.7220.0090.0090.0000.0000.0000.000
92A92PRO0-0.015-0.03831.058-0.004-0.0040.0000.0000.0000.000
93A93TRP00.020-0.00228.7580.0090.0090.0000.0000.0000.000
94A94GLY00.0070.01525.6190.0050.0050.0000.0000.0000.000
95A95ASP-1-0.830-0.91726.670-0.180-0.1800.0000.0000.0000.000
96A96ARG10.9530.97525.5940.1710.1710.0000.0000.0000.000
97A97GLU-1-0.887-0.94525.833-0.218-0.2180.0000.0000.0000.000
98A98ALA0-0.011-0.00227.812-0.008-0.0080.0000.0000.0000.000
99A99LEU0-0.018-0.01821.869-0.011-0.0110.0000.0000.0000.000
100A100ALA00.0320.01323.179-0.028-0.0280.0000.0000.0000.000
101A101ILE0-0.040-0.01824.283-0.008-0.0080.0000.0000.0000.000
102A102TYR00.012-0.00622.960-0.002-0.0020.0000.0000.0000.000
103A103GLN0-0.032-0.02218.9780.0200.0200.0000.0000.0000.000
104A104ARG10.9120.95920.9480.2080.2080.0000.0000.0000.000
105A105GLN0-0.060-0.02623.560-0.001-0.0010.0000.0000.0000.000
106A106LEU0-0.0040.00219.2860.0020.0020.0000.0000.0000.000
107A107ASP-1-0.914-0.93819.753-0.422-0.4220.0000.0000.0000.000
108A108VAL0-0.032-0.01415.367-0.042-0.0420.0000.0000.0000.000
109A109ASP-1-0.810-0.90413.075-0.659-0.6590.0000.0000.0000.000
110A110ILE0-0.014-0.0089.6100.0100.0100.0000.0000.0000.000
111A111LEU0-0.0070.00213.8790.0010.0010.0000.0000.0000.000
112A112ILE0-0.033-0.01411.4840.0080.0080.0000.0000.0000.000
113A113THR0-0.032-0.02916.1420.0490.0490.0000.0000.0000.000
114A114GLY0-0.025-0.03019.434-0.016-0.0160.0000.0000.0000.000
115A115HIS00.0890.05721.2620.0150.0150.0000.0000.0000.000
116A116THR00.002-0.01424.5370.0120.0120.0000.0000.0000.000
117A117HIS0-0.051-0.02924.3020.0090.0090.0000.0000.0000.000
118A118LYS10.9060.95124.0110.1430.1430.0000.0000.0000.000
119A119LEU0-0.0440.00116.915-0.012-0.0120.0000.0000.0000.000
120A120GLU-1-0.846-0.90319.177-0.237-0.2370.0000.0000.0000.000
121A121THR00.009-0.02315.182-0.079-0.0790.0000.0000.0000.000
122A122LYS10.7730.85417.6740.3160.3160.0000.0000.0000.000
123A123GLU-1-0.885-0.93117.789-0.365-0.3650.0000.0000.0000.000
124A124VAL0-0.046-0.02819.2120.0490.0490.0000.0000.0000.000
125A125GLY00.0250.02821.087-0.019-0.0190.0000.0000.0000.000
126A126GLY0-0.040-0.02518.9270.0000.0000.0000.0000.0000.000
127A127LYS10.8280.91917.0130.4300.4300.0000.0000.0000.000
128A128TYR00.0170.00113.6700.0250.0250.0000.0000.0000.000
129A129PHE0-0.035-0.02415.837-0.038-0.0380.0000.0000.0000.000
130A130LEU0-0.009-0.00511.6470.0050.0050.0000.0000.0000.000
131A131ASN00.0600.02116.0660.0210.0210.0000.0000.0000.000
132A132PRO00.0430.02015.3820.0120.0120.0000.0000.0000.000
133A133GLY00.0350.02017.1940.0390.0390.0000.0000.0000.000
134A134SER00.0170.01720.2810.0000.0000.0000.0000.0000.000
135A135ALA00.0250.01219.0300.0140.0140.0000.0000.0000.000
136A136THR0-0.053-0.06921.0450.0190.0190.0000.0000.0000.000
137A137GLY0-0.013-0.00224.4110.0110.0110.0000.0000.0000.000
138A138ALA00.0000.01226.1680.0090.0090.0000.0000.0000.000
139A139TYR00.010-0.00928.155-0.007-0.0070.0000.0000.0000.000
140A140SER00.0790.02229.102-0.004-0.0040.0000.0000.0000.000
141A141PRO0-0.041-0.02131.2220.0040.0040.0000.0000.0000.000
142A142LEU0-0.0140.00529.2670.0020.0020.0000.0000.0000.000
143A143VAL0-0.044-0.02027.662-0.002-0.0020.0000.0000.0000.000
144A144ASP-1-0.919-0.94831.115-0.064-0.0640.0000.0000.0000.000
145A145ASN0-0.005-0.00930.3180.0100.0100.0000.0000.0000.000
146A146PRO0-0.081-0.02927.313-0.006-0.0060.0000.0000.0000.000
147A147VAL0-0.019-0.00724.2180.0100.0100.0000.0000.0000.000
148A148PRO0-0.035-0.01523.358-0.014-0.0140.0000.0000.0000.000
149A149SER0-0.040-0.04519.7030.0140.0140.0000.0000.0000.000
150A150PHE0-0.0280.00013.2150.0130.0130.0000.0000.0000.000
151A151MET00.0020.01212.312-0.022-0.0220.0000.0000.0000.000
152A152LEU0-0.045-0.0128.7550.0270.0270.0000.0000.0000.000
153A153LEU00.012-0.0026.4230.1520.1520.0000.0000.0000.000
154A154GLU-1-0.878-0.9243.435-0.666-0.1290.014-0.121-0.4300.000
155A155ILE0-0.024-0.0122.9110.0731.4500.136-0.447-1.066-0.002
156A156ASN00.004-0.0092.183-9.357-5.8447.201-5.227-5.488-0.047
157A157ASP-1-0.865-0.9283.3820.5330.5990.0290.077-0.173-0.001
158A158SER0-0.051-0.0326.498-0.266-0.2660.0000.0000.0000.000
159A159GLU-1-0.963-0.9817.1670.4250.4250.0000.0000.0000.000
160A160LEU0-0.015-0.0016.841-0.564-0.5640.0000.0000.0000.000
161A161THR00.0360.0126.9420.3220.3220.0000.0000.0000.000
162A162ILE0-0.025-0.0167.769-0.387-0.3870.0000.0000.0000.000
163A163TYR0-0.064-0.0467.1970.2120.2120.0000.0000.0000.000
164A164GLU-1-0.800-0.88511.812-0.345-0.3450.0000.0000.0000.000
165A165TYR0-0.020-0.00911.6810.1140.1140.0000.0000.0000.000
166A166THR00.0330.00816.971-0.012-0.0120.0000.0000.0000.000
167A167LEU0-0.021-0.00320.7150.0190.0190.0000.0000.0000.000
168A168VAL00.007-0.01423.752-0.006-0.0060.0000.0000.0000.000
169A169ASP-1-0.894-0.93726.752-0.016-0.0160.0000.0000.0000.000
170A170GLY0-0.0110.00428.3870.0060.0060.0000.0000.0000.000
171A171SER0-0.052-0.02626.0550.0100.0100.0000.0000.0000.000
172A172VAL0-0.003-0.01219.319-0.011-0.0110.0000.0000.0000.000
173A173LYS10.9330.96421.0560.1240.1240.0000.0000.0000.000
174A174CYS0-0.085-0.04714.959-0.011-0.0110.0000.0000.0000.000
175A175GLU-1-0.935-0.95216.731-0.127-0.1270.0000.0000.0000.000
176A176ARG10.9300.95812.7670.0220.0220.0000.0000.0000.000
177A177VAL00.0200.01412.9590.0380.0380.0000.0000.0000.000
178A178ASP-1-0.866-0.91511.108-0.351-0.3510.0000.0000.0000.000
179A179PHE00.016-0.00211.5910.0660.0660.0000.0000.0000.000
180A180ASN00.0450.01911.385-0.072-0.0720.0000.0000.0000.000
181A181LYS10.8730.95210.9610.2960.2960.0000.0000.0000.000