Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: VQMQ1

Calculation Name: 2CKZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CKZ

Chain ID: B

ChEMBL ID:

UniProt ID: P35718

Base Structure: X-ray

Registration Date: 2023-09-24

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1793098.019779
FMO2-HF: Nuclear repulsion 1720395.572511
FMO2-HF: Total energy -72702.447268
FMO2-MP2: Total energy -72913.46241


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(B:1:MET)


Summations of interaction energy for fragment #1(B: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.
-22.275-10.8211.659-8.671-14.445-0.057
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : 0.015
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].
3B3ILE0-0.0060.0063.8580.9762.473-0.017-0.761-0.7190.002
4B4LEU0-0.026-0.0126.4510.0850.0850.0000.0000.0000.000
5B5SER00.0180.01210.252-0.144-0.1440.0000.0000.0000.000
6B6LYS10.9240.96512.2250.1240.1240.0000.0000.0000.000
7B7ILE0-0.0080.00014.968-0.060-0.0600.0000.0000.0000.000
8B8ALA00.006-0.00218.3750.0390.0390.0000.0000.0000.000
9B9ASP-1-0.797-0.87422.116-0.032-0.0320.0000.0000.0000.000
10B10LEU0-0.026-0.00124.1820.0130.0130.0000.0000.0000.000
11B11VAL00.0020.00324.9110.0040.0040.0000.0000.0000.000
12B12ARG10.8680.91327.458-0.056-0.0560.0000.0000.0000.000
13B13ILE00.000-0.00129.4550.0110.0110.0000.0000.0000.000
14B14PRO0-0.005-0.01231.318-0.006-0.0060.0000.0000.0000.000
15B15PRO00.0790.04534.4250.0060.0060.0000.0000.0000.000
16B16ASP-1-0.906-0.96335.2090.0830.0830.0000.0000.0000.000
17B17GLN0-0.063-0.04929.1060.0200.0200.0000.0000.0000.000
18B18PHE0-0.016-0.00233.8670.0050.0050.0000.0000.0000.000
19B19HIS0-0.034-0.00635.9490.0030.0030.0000.0000.0000.000
20B20ARG10.9030.96430.235-0.136-0.1360.0000.0000.0000.000
21B21ASP-1-0.794-0.88529.1850.1600.1600.0000.0000.0000.000
22B22THR00.0460.02129.8200.0060.0060.0000.0000.0000.000
23B23ILE00.0650.03725.263-0.004-0.0040.0000.0000.0000.000
24B24SER0-0.051-0.03125.3360.0140.0140.0000.0000.0000.000
25B25ALA00.0250.00725.3440.0090.0090.0000.0000.0000.000
26B26ILE0-0.009-0.00523.915-0.003-0.0030.0000.0000.0000.000
27B27THR00.006-0.01220.2040.0000.0000.0000.0000.0000.000
28B28HIS0-0.0330.00221.1900.0300.0300.0000.0000.0000.000
29B29GLN0-0.034-0.03122.4500.0100.0100.0000.0000.0000.000
30B30LEU00.0170.01419.878-0.012-0.0120.0000.0000.0000.000
31B31ASN00.0330.01416.8100.0190.0190.0000.0000.0000.000
32B32ASN0-0.009-0.00218.9020.0090.0090.0000.0000.0000.000
33B33LYS10.7800.87420.830-0.003-0.0030.0000.0000.0000.000
34B34PHE0-0.008-0.03115.852-0.025-0.0250.0000.0000.0000.000
35B35ALA0-0.0050.00414.568-0.007-0.0070.0000.0000.0000.000
36B36ASN0-0.041-0.02212.0080.0340.0340.0000.0000.0000.000
37B37LYS10.8890.96913.350-0.145-0.1450.0000.0000.0000.000
38B38ILE00.0030.00012.604-0.035-0.0350.0000.0000.0000.000
39B39ILE00.0000.00713.2600.0570.0570.0000.0000.0000.000
40B40PRO00.045-0.00114.492-0.104-0.1040.0000.0000.0000.000
41B41ASN0-0.041-0.02715.538-0.017-0.0170.0000.0000.0000.000
42B42VAL0-0.0170.01811.398-0.056-0.0560.0000.0000.0000.000
43B43GLY00.0870.0309.525-0.313-0.3130.0000.0000.0000.000
44B44LEU0-0.0250.0078.0130.1900.1900.0000.0000.0000.000
45B45CYS0-0.053-0.0168.471-0.006-0.0060.0000.0000.0000.000
46B46ILE00.0100.0086.2990.0960.0960.0000.0000.0000.000
47B47THR0-0.001-0.02810.6650.0200.0200.0000.0000.0000.000
48B48ILE0-0.036-0.01213.031-0.032-0.0320.0000.0000.0000.000
49B49TYR0-0.056-0.02012.7090.0370.0370.0000.0000.0000.000
50B50ASP-1-0.799-0.90515.3500.2800.2800.0000.0000.0000.000
51B51LEU00.017-0.00418.770-0.040-0.0400.0000.0000.0000.000
52B52LEU0-0.060-0.03218.2210.0020.0020.0000.0000.0000.000
53B53THR00.000-0.00222.535-0.011-0.0110.0000.0000.0000.000
54B54VAL0-0.0010.00025.6120.0020.0020.0000.0000.0000.000
55B55GLU-1-0.888-0.91828.4200.0020.0020.0000.0000.0000.000
56B56GLU-1-0.915-0.96531.6670.0460.0460.0000.0000.0000.000
57B57GLY0-0.015-0.01234.326-0.004-0.0040.0000.0000.0000.000
58B58GLN00.0080.00935.154-0.002-0.0020.0000.0000.0000.000
59B59LEU00.0340.00936.5750.0010.0010.0000.0000.0000.000
60B60LYS10.8770.95534.902-0.019-0.0190.0000.0000.0000.000
61B61PRO00.006-0.00440.3680.0030.0030.0000.0000.0000.000
62B62GLY00.0110.01042.3700.0000.0000.0000.0000.0000.000
63B63ASP-1-0.795-0.85236.7540.0430.0430.0000.0000.0000.000
64B64GLY00.0250.01439.511-0.001-0.0010.0000.0000.0000.000
65B65SER0-0.033-0.02434.6390.0030.0030.0000.0000.0000.000
66B66SER00.0180.00933.531-0.004-0.0040.0000.0000.0000.000
67B67TYR0-0.079-0.07232.1520.0040.0040.0000.0000.0000.000
68B68ILE00.009-0.00429.615-0.002-0.0020.0000.0000.0000.000
69B69ASN0-0.025-0.00628.280-0.001-0.0010.0000.0000.0000.000
70B70VAL00.001-0.00923.3780.0120.0120.0000.0000.0000.000
71B71THR0-0.022-0.01420.821-0.028-0.0280.0000.0000.0000.000
72B72PHE0-0.016-0.01717.1270.0270.0270.0000.0000.0000.000
73B73ARG10.8840.93714.085-0.308-0.3080.0000.0000.0000.000
74B74ALA00.0250.01113.2010.0640.0640.0000.0000.0000.000
75B75VAL00.0210.0147.859-0.088-0.0880.0000.0000.0000.000
76B76VAL0-0.016-0.0168.0410.0810.0810.0000.0000.0000.000
77B77PHE00.0150.0052.491-2.515-1.4551.596-0.550-2.1060.001
78B78LYS10.7670.8574.2722.4732.819-0.001-0.102-0.2430.000
79B79PRO00.0060.0282.088-2.874-1.3383.134-2.394-2.2770.001
80B80PHE0-0.040-0.0142.9752.8972.4690.1050.847-0.524-0.001
81B81LEU0-0.015-0.0155.7470.0620.0620.0000.0000.0000.000
82B82GLY00.0240.0119.1770.2370.2370.0000.0000.0000.000
83B83GLU-1-0.850-0.9332.601-21.637-15.0454.074-5.092-5.574-0.060
84B84ILE00.004-0.0136.6720.3730.3730.0000.0000.0000.000
85B85VAL0-0.0090.0162.281-0.768-0.8792.519-0.394-2.015-0.001
86B86THR0-0.026-0.0313.2600.9361.1860.008-0.037-0.2210.000
87B87GLY0-0.0020.0014.2390.1420.278-0.001-0.031-0.1040.000
88B88TRP0-0.032-0.0076.911-0.070-0.0700.0000.0000.0000.000
89B89ILE00.0120.01910.710-0.001-0.0010.0000.0000.0000.000
90B90SER0-0.010-0.00713.5940.0250.0250.0000.0000.0000.000
91B91LYS10.9260.95015.2030.0640.0640.0000.0000.0000.000
92B92CYS0-0.0110.04217.560-0.051-0.0510.0000.0000.0000.000
93B93THR0-0.106-0.07319.7520.0360.0360.0000.0000.0000.000
94B94ALA00.0820.03922.216-0.020-0.0200.0000.0000.0000.000
95B95GLU-1-0.865-0.91521.739-0.177-0.1770.0000.0000.0000.000
96B96GLY0-0.008-0.02518.741-0.043-0.0430.0000.0000.0000.000
97B97ILE00.0080.02114.5300.0500.0500.0000.0000.0000.000
98B98LYS10.8170.90813.915-0.020-0.0200.0000.0000.0000.000
99B99VAL00.0210.0128.5010.0510.0510.0000.0000.0000.000
100B100SER0-0.0120.0029.8510.0710.0710.0000.0000.0000.000
101B101LEU0-0.006-0.0133.650-0.653-0.0760.242-0.157-0.6620.001
102B102LEU0-0.011-0.0127.4290.3140.3140.0000.0000.0000.000
103B103GLY00.0360.02810.8110.0740.0740.0000.0000.0000.000
104B104ILE0-0.052-0.0125.283-0.044-0.0440.0000.0000.0000.000
105B105PHE00.000-0.0227.330-0.357-0.3570.0000.0000.0000.000
106B106ASP-1-0.834-0.9339.0830.6070.6070.0000.0000.0000.000
107B107ASP-1-0.918-0.93411.609-0.219-0.2190.0000.0000.0000.000
108B108ILE00.014-0.0026.316-0.185-0.1850.0000.0000.0000.000
109B109PHE0-0.052-0.02210.6060.1290.1290.0000.0000.0000.000
110B110ILE00.0320.02410.854-0.141-0.1410.0000.0000.0000.000
111B111PRO00.0010.00314.4560.0740.0740.0000.0000.0000.000
112B112GLN00.0400.01418.195-0.046-0.0460.0000.0000.0000.000
113B113ASN0-0.028-0.02319.0960.0050.0050.0000.0000.0000.000
114B114MET0-0.058-0.01515.189-0.030-0.0300.0000.0000.0000.000
115B115LEU00.0260.01016.330-0.059-0.0590.0000.0000.0000.000
116B116PHE00.0570.02917.376-0.010-0.0100.0000.0000.0000.000
117B117GLU-1-0.939-0.96520.715-0.244-0.2440.0000.0000.0000.000
118B118GLY00.0120.00724.3000.0130.0130.0000.0000.0000.000
119B119CYS0-0.086-0.01121.7410.0160.0160.0000.0000.0000.000
120B120TYR0-0.011-0.00523.936-0.008-0.0080.0000.0000.0000.000
121B121TYR00.003-0.01022.9720.0040.0040.0000.0000.0000.000
122B122THR00.0150.00025.6430.0000.0000.0000.0000.0000.000
123B123PRO0-0.029-0.02427.2540.0070.0070.0000.0000.0000.000
124B124GLU-1-0.979-0.99528.908-0.049-0.0490.0000.0000.0000.000
125B125GLU-1-0.811-0.88526.913-0.060-0.0600.0000.0000.0000.000
126B126SER0-0.080-0.03423.5220.0100.0100.0000.0000.0000.000
127B127ALA00.0380.02722.093-0.002-0.0020.0000.0000.0000.000
128B128TRP0-0.074-0.04220.049-0.018-0.0180.0000.0000.0000.000
129B129ILE0-0.0140.00622.0000.0060.0060.0000.0000.0000.000
130B130TRP00.057-0.00219.685-0.025-0.0250.0000.0000.0000.000
131B131PRO0-0.043-0.00623.2470.0140.0140.0000.0000.0000.000
132B132MET0-0.036-0.02724.599-0.024-0.0240.0000.0000.0000.000
133B133ASP-1-0.887-0.94127.428-0.134-0.1340.0000.0000.0000.000
134B134GLU-1-0.917-0.96631.055-0.092-0.0920.0000.0000.0000.000
135B135GLU-1-0.918-0.93231.806-0.080-0.0800.0000.0000.0000.000
136B136THR0-0.045-0.00827.1720.0090.0090.0000.0000.0000.000
137B137LYS10.8210.88626.5370.0740.0740.0000.0000.0000.000
138B138LEU00.0160.00821.1120.0170.0170.0000.0000.0000.000
139B139TYR0-0.038-0.04522.049-0.024-0.0240.0000.0000.0000.000
140B140PHE0-0.031-0.03015.884-0.008-0.0080.0000.0000.0000.000
141B141ASP-1-0.815-0.91018.327-0.018-0.0180.0000.0000.0000.000
142B142VAL0-0.021-0.03917.165-0.002-0.0020.0000.0000.0000.000
143B143ASN0-0.082-0.05115.3700.0420.0420.0000.0000.0000.000
144B144GLU-1-0.801-0.87015.0070.0990.0990.0000.0000.0000.000
145B145LYS10.9070.95310.617-0.296-0.2960.0000.0000.0000.000
146B146ILE00.0160.0039.687-0.047-0.0470.0000.0000.0000.000
147B147ARG10.7890.8848.0070.4570.4570.0000.0000.0000.000
148B148PHE00.0290.0005.9410.0690.0690.0000.0000.0000.000
149B149ARG10.8570.9007.5210.7990.7990.0000.0000.0000.000
150B150ILE00.0000.0045.1530.3100.3100.0000.0000.0000.000
151B151GLU-1-0.765-0.8338.786-1.151-1.1510.0000.0000.0000.000
152B152ARG10.8970.93112.0180.8030.8030.0000.0000.0000.000
153B153GLU-1-0.749-0.8339.037-1.854-1.8540.0000.0000.0000.000
154B154VAL0-0.045-0.01811.9380.1370.1370.0000.0000.0000.000
155B155PHE00.0010.00611.5330.0010.0010.0000.0000.0000.000
156B156VAL0-0.036-0.01816.3430.0290.0290.0000.0000.0000.000
157B157ASP-1-0.904-0.94919.352-0.228-0.2280.0000.0000.0000.000
158B158VAL0-0.052-0.01820.8810.0270.0270.0000.0000.0000.000
159B190LYS10.9700.99720.5680.1530.1530.0000.0000.0000.000
160B191PRO0-0.011-0.01220.3890.0160.0160.0000.0000.0000.000
161B192PRO00.0200.01015.5440.0270.0270.0000.0000.0000.000
162B193ALA00.0330.00316.875-0.038-0.0380.0000.0000.0000.000
163B194TYR0-0.051-0.0518.056-0.094-0.0940.0000.0000.0000.000
164B195ALA00.0060.00511.9140.1180.1180.0000.0000.0000.000
165B196LEU0-0.0170.0006.342-0.119-0.1190.0000.0000.0000.000
166B197LEU0-0.015-0.01210.5830.2030.2030.0000.0000.0000.000
167B198GLY00.0260.00510.236-0.255-0.2550.0000.0000.0000.000
168B199SER0-0.065-0.05311.1300.1900.1900.0000.0000.0000.000
169B200CYS0-0.049-0.02912.023-0.074-0.0740.0000.0000.0000.000
170B201GLN0-0.016-0.00114.6670.0330.0330.0000.0000.0000.000
171B202THR0-0.053-0.03315.407-0.006-0.0060.0000.0000.0000.000
172B203ASP-1-0.846-0.92616.157-0.384-0.3840.0000.0000.0000.000
173B204GLY0-0.019-0.00814.635-0.064-0.0640.0000.0000.0000.000
174B205MET0-0.104-0.04310.898-0.126-0.1260.0000.0000.0000.000
175B206GLY00.0540.01612.6650.0790.0790.0000.0000.0000.000
176B207LEU0-0.011-0.00112.799-0.037-0.0370.0000.0000.0000.000
177B208VAL0-0.052-0.02310.202-0.010-0.0100.0000.0000.0000.000
178B209SER0-0.049-0.05013.446-0.006-0.0060.0000.0000.0000.000
179B210TRP0-0.011-0.00716.779-0.007-0.0070.0000.0000.0000.000
180B211TRP0-0.017-0.00215.0390.0010.0010.0000.0000.0000.000
181B212GLU-1-0.871-0.90812.405-0.080-0.0800.0000.0000.0000.000