Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 2N3ZR

Calculation Name: 3CKF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CKF

Chain ID: A

ChEMBL ID:

UniProt ID: Q45040

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2230253.227565
FMO2-HF: Nuclear repulsion 2149390.137071
FMO2-HF: Total energy -80863.090495
FMO2-MP2: Total energy -81102.664639


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:28:ASN)


Summations of interaction energy for fragment #1(A:28:ASN)
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.
2.2716.2140.008-1.869-2.082-0.001
Interaction energy analysis for fragmet #1(A:28:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.019
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].
3A30VAL0-0.025-0.0063.7003.1996.069-0.008-1.454-1.407-0.001
4A31SER00.0110.0126.515-0.641-0.6410.0000.0000.0000.000
5A32VAL0-0.037-0.0168.900-0.082-0.0820.0000.0000.0000.000
6A33ASP-1-0.841-0.90812.3830.9850.9850.0000.0000.0000.000
7A34LEU0-0.005-0.00115.512-0.111-0.1110.0000.0000.0000.000
8A35PRO00.0410.01618.3190.0380.0380.0000.0000.0000.000
9A36GLY0-0.008-0.01421.651-0.002-0.0020.0000.0000.0000.000
10A37SER0-0.073-0.02819.814-0.011-0.0110.0000.0000.0000.000
11A38MET0-0.0060.01917.9800.0460.0460.0000.0000.0000.000
12A39LYS10.8310.88712.474-1.106-1.1060.0000.0000.0000.000
13A40VAL0-0.0180.00711.975-0.079-0.0790.0000.0000.0000.000
14A41LEU0-0.015-0.0036.2190.3460.3460.0000.0000.0000.000
15A42VAL00.0370.0148.366-0.416-0.4160.0000.0000.0000.000
16A43SER0-0.017-0.0114.6450.3160.349-0.001-0.0340.0020.000
17A44LYS10.9380.9573.1781.2902.1840.018-0.370-0.5420.000
18A45SER0-0.020-0.0164.5700.8130.959-0.001-0.011-0.1350.000
19A46SER00.0290.0396.411-0.395-0.3950.0000.0000.0000.000
20A47ASN0-0.007-0.0268.838-0.152-0.1520.0000.0000.0000.000
21A48ALA00.001-0.00710.4130.1410.1410.0000.0000.0000.000
22A49ASP-1-0.894-0.92913.660-0.736-0.7360.0000.0000.0000.000
23A50GLY0-0.035-0.01613.5060.1040.1040.0000.0000.0000.000
24A51LYS10.8160.89513.0770.5950.5950.0000.0000.0000.000
25A52TYR0-0.010-0.0038.375-0.267-0.2670.0000.0000.0000.000
26A53ASP-1-0.880-0.9357.222-1.752-1.7520.0000.0000.0000.000
27A54LEU0-0.045-0.0388.706-0.013-0.0130.0000.0000.0000.000
28A55ILE00.0310.0098.703-0.027-0.0270.0000.0000.0000.000
29A56ALA00.0270.01111.2490.2270.2270.0000.0000.0000.000
30A57THR00.0110.02013.629-0.043-0.0430.0000.0000.0000.000
31A58VAL0-0.007-0.01315.9260.0470.0470.0000.0000.0000.000
32A59ASP-1-0.871-0.93519.4680.2000.2000.0000.0000.0000.000
33A60ALA0-0.041-0.03019.559-0.027-0.0270.0000.0000.0000.000
34A61LEU0-0.0140.01019.625-0.006-0.0060.0000.0000.0000.000
35A62GLU-1-0.945-0.97512.3910.3600.3600.0000.0000.0000.000
36A63LEU0-0.055-0.02415.491-0.073-0.0730.0000.0000.0000.000
37A64SER00.0340.00212.7970.0030.0030.0000.0000.0000.000
38A65GLY00.0210.00912.9780.0590.0590.0000.0000.0000.000
39A66THR0-0.0180.00312.045-0.102-0.1020.0000.0000.0000.000
40A67SER0-0.038-0.02813.3730.1300.1300.0000.0000.0000.000
41A68ASP-1-0.855-0.91714.087-0.526-0.5260.0000.0000.0000.000
42A69LYS10.8210.92515.5070.2420.2420.0000.0000.0000.000
43A70ASN00.0240.00411.1230.0040.0040.0000.0000.0000.000
44A71ASN0-0.011-0.00111.763-0.001-0.0010.0000.0000.0000.000
45A72GLY00.0590.02913.1280.1410.1410.0000.0000.0000.000
46A73SER0-0.017-0.01814.0170.0140.0140.0000.0000.0000.000
47A74GLY00.0330.02515.996-0.099-0.0990.0000.0000.0000.000
48A75VAL0-0.028-0.01617.6990.0680.0680.0000.0000.0000.000
49A76LEU0-0.0210.00213.694-0.054-0.0540.0000.0000.0000.000
50A77GLU-1-0.853-0.93917.352-0.110-0.1100.0000.0000.0000.000
51A78GLY00.0720.03018.081-0.012-0.0120.0000.0000.0000.000
52A79VAL0-0.056-0.02620.348-0.003-0.0030.0000.0000.0000.000
53A80LYS10.9610.99523.058-0.076-0.0760.0000.0000.0000.000
54A81ALA00.0400.01125.163-0.017-0.0170.0000.0000.0000.000
55A82ASP-1-0.872-0.91326.9120.0480.0480.0000.0000.0000.000
56A83ALA00.001-0.00828.073-0.009-0.0090.0000.0000.0000.000
57A84SER0-0.074-0.05728.186-0.014-0.0140.0000.0000.0000.000
58A85LYS10.8950.95925.4970.0860.0860.0000.0000.0000.000
59A86VAL0-0.005-0.00822.3920.0140.0140.0000.0000.0000.000
60A87LYS10.8680.94221.8030.1040.1040.0000.0000.0000.000
61A88LEU00.0070.00517.4790.0280.0280.0000.0000.0000.000
62A89THR0-0.007-0.00519.947-0.050-0.0500.0000.0000.0000.000
63A90ILE0-0.022-0.00316.4970.0420.0420.0000.0000.0000.000
64A91SER00.014-0.01420.375-0.036-0.0360.0000.0000.0000.000
65A92ASP-1-0.778-0.90920.696-0.136-0.1360.0000.0000.0000.000
66A93ASP-1-0.862-0.91320.4440.0360.0360.0000.0000.0000.000
67A94LEU0-0.057-0.03017.0600.0370.0370.0000.0000.0000.000
68A95GLY0-0.0070.01121.0220.0430.0430.0000.0000.0000.000
69A96GLN0-0.042-0.04523.8760.0020.0020.0000.0000.0000.000
70A97THR00.0270.02120.5690.0000.0000.0000.0000.0000.000
71A98THR0-0.038-0.02223.5190.0060.0060.0000.0000.0000.000
72A99LEU00.0170.01921.901-0.010-0.0100.0000.0000.0000.000
73A100GLU-1-0.881-0.94024.835-0.011-0.0110.0000.0000.0000.000
74A101VAL00.0020.00325.958-0.002-0.0020.0000.0000.0000.000
75A102PHE00.013-0.00226.951-0.001-0.0010.0000.0000.0000.000
76A103LYS10.9570.96730.1060.0110.0110.0000.0000.0000.000
77A104SER00.0570.02930.159-0.008-0.0080.0000.0000.0000.000
78A105ASP-1-0.812-0.87630.259-0.051-0.0510.0000.0000.0000.000
79A106GLY0-0.094-0.04729.583-0.013-0.0130.0000.0000.0000.000
80A107SER0-0.040-0.03730.2750.0000.0000.0000.0000.0000.000
81A108THR0-0.012-0.01533.4670.0060.0060.0000.0000.0000.000
82A109LEU0-0.0050.01530.4030.0040.0040.0000.0000.0000.000
83A110VAL0-0.034-0.02332.1520.0020.0020.0000.0000.0000.000
84A111SER0-0.034-0.03929.9510.0100.0100.0000.0000.0000.000
85A112LYS10.8870.94129.258-0.018-0.0180.0000.0000.0000.000
86A113LYS10.8440.93424.738-0.204-0.2040.0000.0000.0000.000
87A114VAL00.0330.01527.0740.0000.0000.0000.0000.0000.000
88A115THR0-0.029-0.01724.305-0.001-0.0010.0000.0000.0000.000
89A116ARG10.8400.90326.042-0.136-0.1360.0000.0000.0000.000
90A117ALA00.1100.05725.0940.0250.0250.0000.0000.0000.000
91A118ASP-1-0.784-0.83125.4830.1920.1920.0000.0000.0000.000
92A119GLY0-0.017-0.02425.4960.0220.0220.0000.0000.0000.000
93A120THR0-0.134-0.08026.3810.0000.0000.0000.0000.0000.000
94A121ARG10.8510.89627.392-0.207-0.2070.0000.0000.0000.000
95A122LEU0-0.0080.01330.063-0.004-0.0040.0000.0000.0000.000
96A123GLU-1-0.836-0.90430.3440.1630.1630.0000.0000.0000.000
97A124TYR00.010-0.01032.652-0.004-0.0040.0000.0000.0000.000
98A125THR00.016-0.00933.494-0.001-0.0010.0000.0000.0000.000
99A126GLY0-0.010-0.01035.745-0.003-0.0030.0000.0000.0000.000
100A127ILE0-0.025-0.00433.938-0.002-0.0020.0000.0000.0000.000
101A128LYS10.9010.95938.047-0.034-0.0340.0000.0000.0000.000
102A129SER00.0260.00539.979-0.001-0.0010.0000.0000.0000.000
103A130ASP-1-0.843-0.89441.4210.0080.0080.0000.0000.0000.000
104A131GLY0-0.008-0.00338.9510.0000.0000.0000.0000.0000.000
105A132SER0-0.065-0.04839.7930.0060.0060.0000.0000.0000.000
106A133GLY00.0320.00039.360-0.001-0.0010.0000.0000.0000.000
107A134LYS10.8770.94939.140-0.053-0.0530.0000.0000.0000.000
108A135ALA00.0210.00737.2360.0010.0010.0000.0000.0000.000
109A136LYS10.8510.91934.778-0.115-0.1150.0000.0000.0000.000
110A137GLU-1-0.734-0.84034.6600.1070.1070.0000.0000.0000.000
111A138VAL0-0.019-0.01531.3650.0010.0010.0000.0000.0000.000
112A139LEU00.004-0.00332.1150.0090.0090.0000.0000.0000.000
113A140LYS10.8960.93428.163-0.227-0.2270.0000.0000.0000.000
114A141GLY00.0540.03633.349-0.007-0.0070.0000.0000.0000.000
115A142TYR0-0.066-0.03336.095-0.011-0.0110.0000.0000.0000.000
116A143VAL00.0020.00335.4680.0070.0070.0000.0000.0000.000
117A144LEU0-0.042-0.00537.796-0.007-0.0070.0000.0000.0000.000
118A145GLU-1-0.765-0.87538.9340.1080.1080.0000.0000.0000.000
119A146GLY00.011-0.00441.144-0.004-0.0040.0000.0000.0000.000
120A147THR0-0.049-0.01441.9590.0010.0010.0000.0000.0000.000
121A148LEU0-0.0170.00136.8770.0020.0020.0000.0000.0000.000
122A149THR0-0.024-0.01640.892-0.004-0.0040.0000.0000.0000.000
123A150ALA00.0330.00940.5250.0010.0010.0000.0000.0000.000
124A151GLU-1-0.965-0.97240.7210.0150.0150.0000.0000.0000.000
125A152LYS10.8970.94740.851-0.032-0.0320.0000.0000.0000.000
126A153THR00.0040.02338.0320.0020.0020.0000.0000.0000.000
127A154THR0-0.010-0.01440.734-0.001-0.0010.0000.0000.0000.000
128A155LEU0-0.052-0.01738.1870.0010.0010.0000.0000.0000.000
129A156VAL00.011-0.00442.634-0.003-0.0030.0000.0000.0000.000
130A157VAL00.0040.01344.5170.0050.0050.0000.0000.0000.000
131A158LYS10.9090.94647.063-0.056-0.0560.0000.0000.0000.000
132A159GLU-1-0.850-0.92850.6890.0770.0770.0000.0000.0000.000
133A160GLY00.0020.01952.943-0.002-0.0020.0000.0000.0000.000
134A161THR0-0.057-0.05656.3200.0000.0000.0000.0000.0000.000
135A162VAL00.0090.02152.657-0.003-0.0030.0000.0000.0000.000
136A163THR0-0.047-0.02350.4400.0030.0030.0000.0000.0000.000
137A164LEU00.0090.01445.783-0.003-0.0030.0000.0000.0000.000
138A165SER00.020-0.00746.4600.0040.0040.0000.0000.0000.000
139A166LYS10.8670.92836.902-0.099-0.0990.0000.0000.0000.000
140A167ASN0-0.027-0.01542.6050.0000.0000.0000.0000.0000.000
141A168ILE00.007-0.00136.4220.0030.0030.0000.0000.0000.000
142A169SER00.0660.03838.748-0.003-0.0030.0000.0000.0000.000
143A170LYS11.0180.99535.1090.0180.0180.0000.0000.0000.000
144A171SER0-0.033-0.01934.1550.0010.0010.0000.0000.0000.000
145A172GLY0-0.002-0.00234.1410.0040.0040.0000.0000.0000.000
146A173GLU-1-0.979-0.97835.3280.0350.0350.0000.0000.0000.000
147A174VAL00.006-0.00237.5620.0000.0000.0000.0000.0000.000
148A175SER00.0040.00340.250-0.003-0.0030.0000.0000.0000.000
149A176VAL0-0.028-0.01743.6280.0030.0030.0000.0000.0000.000
150A177GLU-1-0.860-0.91446.1110.0350.0350.0000.0000.0000.000
151A178LEU0-0.003-0.01149.3760.0040.0040.0000.0000.0000.000
152A179ASN0-0.026-0.00252.058-0.005-0.0050.0000.0000.0000.000
153A180ASP-1-0.656-0.81455.0950.0490.0490.0000.0000.0000.000
154A181THR0-0.003-0.00357.730-0.002-0.0020.0000.0000.0000.000
155A182ASP-1-0.850-0.89460.5360.0400.0400.0000.0000.0000.000
156A183SER0-0.030-0.00962.565-0.001-0.0010.0000.0000.0000.000
157A184SER00.0390.01665.274-0.002-0.0020.0000.0000.0000.000
158A185ALA00.0240.01065.1190.0010.0010.0000.0000.0000.000
159A186ALA0-0.022-0.00765.3110.0010.0010.0000.0000.0000.000
160A187THR0-0.044-0.06562.5850.0010.0010.0000.0000.0000.000
161A188LYS10.8170.91960.823-0.034-0.0340.0000.0000.0000.000
162A189LYS10.8330.91755.766-0.052-0.0520.0000.0000.0000.000
163A190THR0-0.036-0.02057.007-0.002-0.0020.0000.0000.0000.000
164A191ALA00.018-0.01052.3400.0030.0030.0000.0000.0000.000
165A192ALA0-0.0080.01653.167-0.003-0.0030.0000.0000.0000.000
166A193TRP00.0390.02842.9510.0040.0040.0000.0000.0000.000
167A194ASN00.0020.00648.247-0.006-0.0060.0000.0000.0000.000
168A195SER00.0460.00544.9680.0040.0040.0000.0000.0000.000
169A196GLY00.0160.01743.9160.0010.0010.0000.0000.0000.000
170A197THR0-0.027-0.03143.8620.0010.0010.0000.0000.0000.000
171A198SER00.0070.01641.3700.0050.0050.0000.0000.0000.000
172A199THR0-0.045-0.02043.4060.0070.0070.0000.0000.0000.000
173A200LEU0-0.025-0.00446.245-0.005-0.0050.0000.0000.0000.000
174A201THR0-0.011-0.02948.6660.0020.0020.0000.0000.0000.000
175A202ILE0-0.030-0.01950.862-0.003-0.0030.0000.0000.0000.000
176A203THR0-0.021-0.01354.1400.0000.0000.0000.0000.0000.000
177A204VAL00.001-0.00857.9060.0000.0000.0000.0000.0000.000
178A205ASN0-0.0030.00760.638-0.001-0.0010.0000.0000.0000.000
179A206SER0-0.031-0.01663.286-0.001-0.0010.0000.0000.0000.000
180A207LYS10.9000.95861.410-0.042-0.0420.0000.0000.0000.000
181A208LYS10.9400.98954.199-0.045-0.0450.0000.0000.0000.000
182A209THR0-0.009-0.01856.0240.0020.0020.0000.0000.0000.000
183A210LYS10.8880.93350.958-0.064-0.0640.0000.0000.0000.000
184A211ASP-1-0.752-0.82348.4320.0550.0550.0000.0000.0000.000
185A212LEU0-0.031-0.02045.9060.0050.0050.0000.0000.0000.000
186A213VAL00.0050.00641.720-0.004-0.0040.0000.0000.0000.000
187A214PHE0-0.013-0.01640.4080.0070.0070.0000.0000.0000.000
188A215THR00.0420.00736.771-0.004-0.0040.0000.0000.0000.000
189A216SER00.0600.02033.993-0.001-0.0010.0000.0000.0000.000
190A217SER0-0.045-0.02232.1600.0030.0030.0000.0000.0000.000
191A218ASN0-0.082-0.05132.3350.0010.0010.0000.0000.0000.000
192A219THR0-0.024-0.00934.5670.0040.0040.0000.0000.0000.000
193A220ILE0-0.004-0.00637.012-0.010-0.0100.0000.0000.0000.000
194A221THR00.0090.01440.5590.0040.0040.0000.0000.0000.000
195A222VAL00.006-0.00642.933-0.007-0.0070.0000.0000.0000.000
196A223GLN00.001-0.00446.6720.0050.0050.0000.0000.0000.000
197A224GLN00.0140.00749.216-0.006-0.0060.0000.0000.0000.000
198A225TYR0-0.054-0.05552.356-0.002-0.0020.0000.0000.0000.000
199A226ASP-1-0.689-0.83955.7570.0490.0490.0000.0000.0000.000
200A227SER00.0210.00758.868-0.001-0.0010.0000.0000.0000.000
201A228ASN0-0.111-0.06961.940-0.003-0.0030.0000.0000.0000.000
202A229GLY00.0130.02159.032-0.002-0.0020.0000.0000.0000.000
203A230THR0-0.112-0.06459.192-0.001-0.0010.0000.0000.0000.000
204A231SER0-0.031-0.01956.688-0.001-0.0010.0000.0000.0000.000
205A232LEU0-0.0300.00649.9780.0010.0010.0000.0000.0000.000
206A233GLU-1-0.913-0.96153.6080.0630.0630.0000.0000.0000.000
207A234GLY0-0.0040.00651.7620.0030.0030.0000.0000.0000.000
208A235SER0-0.004-0.01546.375-0.001-0.0010.0000.0000.0000.000
209A236ALA0-0.021-0.00544.2800.0010.0010.0000.0000.0000.000
210A237VAL0-0.015-0.00243.8840.0060.0060.0000.0000.0000.000
211A238GLU-1-0.882-0.92736.5090.1490.1490.0000.0000.0000.000
212A239ILE0-0.050-0.02441.2320.0010.0010.0000.0000.0000.000
213A240THR0-0.014-0.02238.6460.0080.0080.0000.0000.0000.000
214A241LYS10.8380.87239.105-0.114-0.1140.0000.0000.0000.000
215A242LEU00.0530.02541.403-0.007-0.0070.0000.0000.0000.000
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