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: JL769

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973737.215749
FMO2-HF: Nuclear repulsion 1902853.226464
FMO2-HF: Total energy -70883.989285
FMO2-MP2: Total energy -71090.155416


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.
-16.542-18.31228.84-12.689-14.382-0.062
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 : 0.007 / q_NPA : -0.008
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].
3A3VAL00.002-0.0073.8020.2921.752-0.016-0.654-0.7900.003
4A4LEU0-0.0080.0016.1330.0900.0900.0000.0000.0000.000
5A5VAL00.0020.0059.803-0.024-0.0240.0000.0000.0000.000
6A6ILE00.019-0.01512.3800.0740.0740.0000.0000.0000.000
7A7GLY00.0600.01515.699-0.031-0.0310.0000.0000.0000.000
8A8ASP-1-0.869-0.92419.006-0.172-0.1720.0000.0000.0000.000
9A9PHE00.0110.01718.0280.0170.0170.0000.0000.0000.000
10A10HIS00.018-0.00123.6180.0080.0080.0000.0000.0000.000
11A11VAL00.0020.00627.190-0.012-0.0120.0000.0000.0000.000
12A12PRO00.0250.01030.2300.0090.0090.0000.0000.0000.000
13A13HIS0-0.026-0.02033.2140.0030.0030.0000.0000.0000.000
14A14ARG10.9220.97432.6880.0540.0540.0000.0000.0000.000
15A15SER0-0.037-0.00831.7810.0000.0000.0000.0000.0000.000
16A16ALA00.0410.01828.091-0.001-0.0010.0000.0000.0000.000
17A17ALA0-0.0070.00427.0230.0000.0000.0000.0000.0000.000
18A18ILE00.0110.00220.462-0.008-0.0080.0000.0000.0000.000
19A19PRO00.0020.00822.2630.0160.0160.0000.0000.0000.000
20A20GLN00.0500.01622.2180.0190.0190.0000.0000.0000.000
21A21VAL00.0410.01821.1320.0190.0190.0000.0000.0000.000
22A22PHE0-0.019-0.01618.1050.0230.0230.0000.0000.0000.000
23A23LEU00.0270.01117.1680.0280.0280.0000.0000.0000.000
24A24ASP-1-0.882-0.93517.8120.2310.2310.0000.0000.0000.000
25A25ARG10.8410.9299.669-0.377-0.3770.0000.0000.0000.000
26A26LEU0-0.028-0.02912.9650.0940.0940.0000.0000.0000.000
27A27ASN00.0190.01512.7740.1060.1060.0000.0000.0000.000
28A28THR0-0.040-0.01213.8860.1060.1060.0000.0000.0000.000
29A29GLY0-0.027-0.01310.3810.0800.0800.0000.0000.0000.000
30A30ARG10.9580.9933.603-10.038-8.0960.032-1.036-0.9370.008
31A31ILE00.0330.0086.9450.5110.5110.0000.0000.0000.000
32A32GLN0-0.084-0.0351.8843.695-6.93420.781-5.208-4.945-0.022
33A33THR00.002-0.0115.000-0.966-0.860-0.001-0.004-0.1010.000
34A34VAL00.0120.0146.716-0.105-0.1050.0000.0000.0000.000
35A35LEU0-0.017-0.0119.403-0.028-0.0280.0000.0000.0000.000
36A36CYS0-0.029-0.00812.0500.0190.0190.0000.0000.0000.000
37A37THR00.0470.00215.631-0.004-0.0040.0000.0000.0000.000
38A38GLY00.0610.03218.5480.0090.0090.0000.0000.0000.000
39A39ASN0-0.052-0.03421.1510.0090.0090.0000.0000.0000.000
40A40LEU00.0010.00819.6550.0080.0080.0000.0000.0000.000
41A41CYS0-0.0120.00823.725-0.002-0.0020.0000.0000.0000.000
42A42GLY00.0190.01326.3840.0120.0120.0000.0000.0000.000
43A43LYS10.9010.94324.688-0.052-0.0520.0000.0000.0000.000
44A44GLU-1-0.885-0.94824.0030.0470.0470.0000.0000.0000.000
45A45THR0-0.005-0.00220.4870.0110.0110.0000.0000.0000.000
46A46TYR00.0220.01918.0090.0090.0090.0000.0000.0000.000
47A47ASP-1-0.834-0.93019.1980.0880.0880.0000.0000.0000.000
48A48ILE0-0.036-0.01118.1470.0320.0320.0000.0000.0000.000
49A49LEU0-0.013-0.02215.1090.0340.0340.0000.0000.0000.000
50A50ARG10.8630.93213.913-0.029-0.0290.0000.0000.0000.000
51A51THR0-0.035-0.00815.5150.0370.0370.0000.0000.0000.000
52A52LEU0-0.0340.00912.0960.0550.0550.0000.0000.0000.000
53A53ALA0-0.008-0.0079.0690.1870.1870.0000.0000.0000.000
54A54ARG10.8840.9557.627-0.458-0.4580.0000.0000.0000.000
55A55GLU-1-0.866-0.9178.245-0.529-0.5290.0000.0000.0000.000
56A56VAL0-0.012-0.0139.974-0.032-0.0320.0000.0000.0000.000
57A57HIS0-0.044-0.03110.5920.0150.0150.0000.0000.0000.000
58A58VAL0-0.023-0.01913.998-0.011-0.0110.0000.0000.0000.000
59A59VAL0-0.0120.03617.322-0.001-0.0010.0000.0000.0000.000
60A60LYS10.9350.96819.7600.1460.1460.0000.0000.0000.000
61A61GLY00.0630.02123.517-0.014-0.0140.0000.0000.0000.000
62A62ALA0-0.048-0.02924.8610.0110.0110.0000.0000.0000.000
63A63PHE0-0.040-0.03627.7890.0100.0100.0000.0000.0000.000
64A64ASP-1-0.787-0.87823.766-0.106-0.1060.0000.0000.0000.000
65A65GLU-1-0.931-0.97127.379-0.075-0.0750.0000.0000.0000.000
66A66MET0-0.075-0.02723.5400.0050.0050.0000.0000.0000.000
67A67GLN00.008-0.00626.942-0.012-0.0120.0000.0000.0000.000
68A68GLY0-0.023-0.02125.3120.0060.0060.0000.0000.0000.000
69A69LEU0-0.038-0.00620.360-0.007-0.0070.0000.0000.0000.000
70A70ASN00.0110.01020.1890.0250.0250.0000.0000.0000.000
71A71GLU-1-0.908-0.95921.600-0.177-0.1770.0000.0000.0000.000
72A72THR0-0.060-0.04419.911-0.018-0.0180.0000.0000.0000.000
73A73GLU-1-0.869-0.92316.049-0.266-0.2660.0000.0000.0000.000
74A74VAL0-0.017-0.02214.924-0.041-0.0410.0000.0000.0000.000
75A75ILE00.0050.0068.5730.0240.0240.0000.0000.0000.000
76A76LYS10.8610.93810.2921.0241.0240.0000.0000.0000.000
77A77ILE00.0160.0024.168-0.237-0.0930.000-0.025-0.1190.000
78A78GLY00.0410.0346.389-0.130-0.1300.0000.0000.0000.000
79A79ASN0-0.045-0.0276.9650.4020.4020.0000.0000.0000.000
80A80PHE00.0200.0057.4740.2810.2810.0000.0000.0000.000
81A81LYS10.7890.90910.0160.4150.4150.0000.0000.0000.000
82A82ILE00.0310.0078.2240.0250.0250.0000.0000.0000.000
83A83GLY00.0240.02812.6900.0540.0540.0000.0000.0000.000
84A84LEU0-0.034-0.00113.377-0.024-0.0240.0000.0000.0000.000
85A85MET00.004-0.01416.4650.0460.0460.0000.0000.0000.000
86A86ALA00.0690.04319.866-0.013-0.0130.0000.0000.0000.000
87A87GLY00.0320.00522.273-0.013-0.0130.0000.0000.0000.000
88A88HIS0-0.0080.00724.0880.0040.0040.0000.0000.0000.000
89A89GLN00.0670.02724.1590.0060.0060.0000.0000.0000.000
90A90VAL0-0.0260.01824.3550.0050.0050.0000.0000.0000.000
91A91ILE0-0.065-0.02927.7440.0100.0100.0000.0000.0000.000
92A92PRO0-0.006-0.03031.077-0.005-0.0050.0000.0000.0000.000
93A93TRP00.017-0.01028.7650.0090.0090.0000.0000.0000.000
94A94GLY0-0.0030.01225.6290.0050.0050.0000.0000.0000.000
95A95ASP-1-0.831-0.89926.675-0.191-0.1910.0000.0000.0000.000
96A96ARG10.9600.96425.6060.1840.1840.0000.0000.0000.000
97A97GLU-1-0.884-0.93925.839-0.239-0.2390.0000.0000.0000.000
98A98ALA0-0.024-0.01427.824-0.008-0.0080.0000.0000.0000.000
99A99LEU0-0.025-0.02322.118-0.012-0.0120.0000.0000.0000.000
100A100ALA00.0370.01323.195-0.030-0.0300.0000.0000.0000.000
101A101ILE0-0.040-0.02124.294-0.010-0.0100.0000.0000.0000.000
102A102TYR00.027-0.00322.9660.0010.0010.0000.0000.0000.000
103A103GLN0-0.0110.00619.0640.0170.0170.0000.0000.0000.000
104A104ARG10.9200.95620.9710.2250.2250.0000.0000.0000.000
105A105GLN0-0.047-0.02523.586-0.007-0.0070.0000.0000.0000.000
106A106LEU0-0.0110.00118.7980.0020.0020.0000.0000.0000.000
107A107ASP-1-0.949-0.95419.787-0.448-0.4480.0000.0000.0000.000
108A108VAL0-0.071-0.03715.400-0.047-0.0470.0000.0000.0000.000
109A109ASP-1-0.833-0.92713.108-0.781-0.7810.0000.0000.0000.000
110A110ILE0-0.020-0.0119.7030.0110.0110.0000.0000.0000.000
111A111LEU0-0.0080.00013.8930.0070.0070.0000.0000.0000.000
112A112ILE0-0.034-0.01711.5620.0070.0070.0000.0000.0000.000
113A113THR0-0.039-0.03116.1610.0520.0520.0000.0000.0000.000
114A114GLY0-0.027-0.02719.448-0.016-0.0160.0000.0000.0000.000
115A115HIS00.0860.05321.2820.0160.0160.0000.0000.0000.000
116A116THR0-0.002-0.02624.6180.0140.0140.0000.0000.0000.000
117A117HIS0-0.048-0.02124.3400.0090.0090.0000.0000.0000.000
118A118LYS10.9220.95524.0270.1420.1420.0000.0000.0000.000
119A119LEU0-0.0340.00516.814-0.011-0.0110.0000.0000.0000.000
120A120GLU-1-0.982-0.99819.183-0.241-0.2410.0000.0000.0000.000
121A121THR0-0.002-0.01815.104-0.081-0.0810.0000.0000.0000.000
122A122LYS10.9250.96117.6590.3360.3360.0000.0000.0000.000
123A123GLU-1-0.890-0.93317.774-0.414-0.4140.0000.0000.0000.000
124A124VAL0-0.046-0.02819.1970.0560.0560.0000.0000.0000.000
125A125GLY00.0370.03021.082-0.021-0.0210.0000.0000.0000.000
126A126GLY0-0.049-0.03018.914-0.001-0.0010.0000.0000.0000.000
127A127LYS10.8670.94317.0260.4370.4370.0000.0000.0000.000
128A128TYR00.0250.01113.6060.0370.0370.0000.0000.0000.000
129A129PHE0-0.043-0.02015.842-0.033-0.0330.0000.0000.0000.000
130A130LEU0-0.001-0.00411.5870.0030.0030.0000.0000.0000.000
131A131ASN00.0700.02916.0680.0260.0260.0000.0000.0000.000
132A132PRO00.0480.02115.3590.0130.0130.0000.0000.0000.000
133A133GLY00.0320.01417.1980.0430.0430.0000.0000.0000.000
134A134SER0-0.003-0.00720.2810.0020.0020.0000.0000.0000.000
135A135ALA00.0260.01519.0460.0160.0160.0000.0000.0000.000
136A136THR0-0.061-0.08121.0450.0220.0220.0000.0000.0000.000
137A137GLY0-0.018-0.00424.4090.0100.0100.0000.0000.0000.000
138A138ALA00.0120.02226.1950.0070.0070.0000.0000.0000.000
139A139TYR00.016-0.01028.179-0.008-0.0080.0000.0000.0000.000
140A140SER00.0640.01228.979-0.004-0.0040.0000.0000.0000.000
141A141PRO0-0.044-0.02131.2450.0040.0040.0000.0000.0000.000
142A142LEU0-0.0090.01029.0900.0010.0010.0000.0000.0000.000
143A143VAL0-0.043-0.02127.686-0.002-0.0020.0000.0000.0000.000
144A144ASP-1-0.920-0.95031.115-0.056-0.0560.0000.0000.0000.000
145A145ASN0-0.005-0.00330.2320.0120.0120.0000.0000.0000.000
146A146PRO0-0.081-0.02927.354-0.006-0.0060.0000.0000.0000.000
147A147VAL0-0.033-0.01523.9240.0110.0110.0000.0000.0000.000
148A148PRO0-0.024-0.01123.228-0.014-0.0140.0000.0000.0000.000
149A149SER0-0.048-0.03919.4530.0150.0150.0000.0000.0000.000
150A150PHE0-0.0130.00713.0020.0180.0180.0000.0000.0000.000
151A151MET0-0.0090.00812.307-0.028-0.0280.0000.0000.0000.000
152A152LEU0-0.057-0.0138.4970.0470.0470.0000.0000.0000.000
153A153LEU00.007-0.0036.5230.1390.1390.0000.0000.0000.000
154A154GLU-1-0.918-0.9653.288-0.2560.7630.043-0.306-0.757-0.001
155A155ILE0-0.023-0.0082.8840.0901.4270.125-0.426-1.036-0.001
156A156ASN00.0390.0112.158-9.967-7.0557.814-5.238-5.488-0.048
157A157ASP-1-0.849-0.9093.1890.5540.4930.0620.208-0.209-0.001
158A158SER0-0.060-0.0586.552-0.191-0.1910.0000.0000.0000.000
159A159GLU-1-0.979-0.9957.2100.1310.1310.0000.0000.0000.000
160A160LEU0-0.033-0.0056.492-0.725-0.7250.0000.0000.0000.000
161A161THR00.0410.0306.9300.3640.3640.0000.0000.0000.000
162A162ILE0-0.019-0.0147.768-0.391-0.3910.0000.0000.0000.000
163A163TYR0-0.020-0.0076.8250.2470.2470.0000.0000.0000.000
164A164GLU-1-0.802-0.90511.687-0.339-0.3390.0000.0000.0000.000
165A165TYR0-0.029-0.00711.5270.1220.1220.0000.0000.0000.000
166A166THR00.0310.01316.782-0.016-0.0160.0000.0000.0000.000
167A167LEU0-0.004-0.00120.5280.0220.0220.0000.0000.0000.000
168A168VAL00.019-0.01223.540-0.010-0.0100.0000.0000.0000.000
169A169ASP-1-0.890-0.91926.5580.0020.0020.0000.0000.0000.000
170A170GLY0-0.0120.00628.1470.0070.0070.0000.0000.0000.000
171A171SER0-0.049-0.04025.8230.0120.0120.0000.0000.0000.000
172A172VAL0-0.018-0.02019.130-0.012-0.0120.0000.0000.0000.000
173A173LYS10.9080.95320.8960.1000.1000.0000.0000.0000.000
174A174CYS0-0.079-0.03514.708-0.003-0.0030.0000.0000.0000.000
175A175GLU-1-0.915-0.94216.620-0.137-0.1370.0000.0000.0000.000
176A176ARG10.8950.92612.846-0.021-0.0210.0000.0000.0000.000
177A177VAL00.0250.02112.9340.0370.0370.0000.0000.0000.000
178A178ASP-1-0.869-0.93311.346-0.445-0.4450.0000.0000.0000.000
179A179PHE0-0.006-0.01611.7190.0890.0890.0000.0000.0000.000
180A180ASN00.0410.00711.272-0.164-0.1640.0000.0000.0000.000
181A181LYS10.8870.95910.6960.5830.5830.0000.0000.0000.000