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: 76V8K

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2229818.926748
FMO2-HF: Nuclear repulsion 2148956.814447
FMO2-HF: Total energy -80862.112301
FMO2-MP2: Total energy -81101.625326


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.
2.9396.8490.01-1.854-2.066-0.002
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 : -0.012 / q_NPA : -0.018
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].
3A30VAL0-0.0190.0073.7243.0405.883-0.008-1.440-1.395-0.002
4A31SER0-0.007-0.0016.538-0.504-0.5040.0000.0000.0000.000
5A32VAL0-0.030-0.0138.853-0.100-0.1000.0000.0000.0000.000
6A33ASP-1-0.905-0.95212.3590.8840.8840.0000.0000.0000.000
7A34LEU0-0.033-0.02215.467-0.122-0.1220.0000.0000.0000.000
8A35PRO00.0400.01818.2650.0430.0430.0000.0000.0000.000
9A36GLY0-0.006-0.01621.5730.0030.0030.0000.0000.0000.000
10A37SER0-0.089-0.03419.7410.0150.0150.0000.0000.0000.000
11A38MET0-0.0090.01417.8760.0540.0540.0000.0000.0000.000
12A39LYS10.9510.96612.261-1.304-1.3040.0000.0000.0000.000
13A40VAL0-0.0220.00711.941-0.061-0.0610.0000.0000.0000.000
14A41LEU0-0.018-0.0076.1900.3230.3230.0000.0000.0000.000
15A42VAL00.0310.0168.348-0.381-0.3810.0000.0000.0000.000
16A43SER00.0230.0164.6340.3080.331-0.001-0.0330.0110.000
17A44LYS10.9280.9513.1232.0312.9310.020-0.371-0.5500.000
18A45SER0-0.018-0.0144.5700.8891.033-0.001-0.010-0.1320.000
19A46SER00.0210.0246.398-0.369-0.3690.0000.0000.0000.000
20A47ASN00.0430.0178.860-0.111-0.1110.0000.0000.0000.000
21A48ALA00.003-0.01510.4470.1320.1320.0000.0000.0000.000
22A49ASP-1-0.942-0.95913.697-0.703-0.7030.0000.0000.0000.000
23A50GLY0-0.041-0.02013.5180.1040.1040.0000.0000.0000.000
24A51LYS10.8840.94613.0910.6870.6870.0000.0000.0000.000
25A52TYR0-0.010-0.0038.286-0.287-0.2870.0000.0000.0000.000
26A53ASP-1-0.878-0.9357.193-1.611-1.6110.0000.0000.0000.000
27A54LEU0-0.047-0.0408.691-0.039-0.0390.0000.0000.0000.000
28A55ILE00.0310.0098.905-0.003-0.0030.0000.0000.0000.000
29A56ALA00.0280.00811.2210.2270.2270.0000.0000.0000.000
30A57THR0-0.0060.01713.549-0.072-0.0720.0000.0000.0000.000
31A58VAL0-0.013-0.01215.8500.0450.0450.0000.0000.0000.000
32A59ASP-1-0.956-0.97819.3930.2170.2170.0000.0000.0000.000
33A60ALA0-0.057-0.03719.513-0.025-0.0250.0000.0000.0000.000
34A61LEU0-0.0230.00119.546-0.002-0.0020.0000.0000.0000.000
35A62GLU-1-0.947-0.97112.3500.4030.4030.0000.0000.0000.000
36A63LEU0-0.058-0.03115.398-0.080-0.0800.0000.0000.0000.000
37A64SER00.0430.00412.7760.0080.0080.0000.0000.0000.000
38A65GLY00.0260.01212.9610.0570.0570.0000.0000.0000.000
39A66THR0-0.038-0.00812.157-0.112-0.1120.0000.0000.0000.000
40A67SER0-0.034-0.02113.3530.1320.1320.0000.0000.0000.000
41A68ASP-1-0.914-0.95714.088-0.587-0.5870.0000.0000.0000.000
42A69LYS10.9020.96715.4870.2890.2890.0000.0000.0000.000
43A70ASN00.009-0.00511.0300.0300.0300.0000.0000.0000.000
44A71ASN0-0.007-0.00711.723-0.033-0.0330.0000.0000.0000.000
45A72GLY00.0500.02513.1100.1450.1450.0000.0000.0000.000
46A73SER0-0.023-0.01314.0170.0340.0340.0000.0000.0000.000
47A74GLY00.0390.02415.980-0.104-0.1040.0000.0000.0000.000
48A75VAL0-0.020-0.01417.6900.0740.0740.0000.0000.0000.000
49A76LEU0-0.027-0.00313.690-0.054-0.0540.0000.0000.0000.000
50A77GLU-1-0.944-0.98717.335-0.135-0.1350.0000.0000.0000.000
51A78GLY00.0690.02718.065-0.007-0.0070.0000.0000.0000.000
52A79VAL0-0.056-0.02320.332-0.007-0.0070.0000.0000.0000.000
53A80LYS10.9690.99222.973-0.092-0.0920.0000.0000.0000.000
54A81ALA00.0450.01225.079-0.018-0.0180.0000.0000.0000.000
55A82ASP-1-0.892-0.92826.8320.0570.0570.0000.0000.0000.000
56A83ALA0-0.001-0.01228.054-0.011-0.0110.0000.0000.0000.000
57A84SER0-0.070-0.04028.163-0.017-0.0170.0000.0000.0000.000
58A85LYS10.9360.97725.4820.0930.0930.0000.0000.0000.000
59A86VAL0-0.003-0.00722.1330.0130.0130.0000.0000.0000.000
60A87LYS10.9791.00021.7730.1010.1010.0000.0000.0000.000
61A88LEU0-0.0040.00317.4620.0300.0300.0000.0000.0000.000
62A89THR0-0.007-0.00719.929-0.052-0.0520.0000.0000.0000.000
63A90ILE0-0.028-0.00416.5410.0450.0450.0000.0000.0000.000
64A91SER00.0360.00820.356-0.040-0.0400.0000.0000.0000.000
65A92ASP-1-0.835-0.94020.678-0.169-0.1690.0000.0000.0000.000
66A93ASP-1-0.883-0.94420.409-0.008-0.0080.0000.0000.0000.000
67A94LEU0-0.062-0.03317.0450.0360.0360.0000.0000.0000.000
68A95GLY0-0.0080.01521.0220.0460.0460.0000.0000.0000.000
69A96GLN0-0.044-0.04723.8710.0030.0030.0000.0000.0000.000
70A97THR0-0.0010.00920.535-0.016-0.0160.0000.0000.0000.000
71A98THR0-0.011-0.00723.4990.0090.0090.0000.0000.0000.000
72A99LEU00.0090.01621.848-0.009-0.0090.0000.0000.0000.000
73A100GLU-1-0.917-0.97024.754-0.013-0.0130.0000.0000.0000.000
74A101VAL00.0030.00625.9390.0000.0000.0000.0000.0000.000
75A102PHE00.0110.00126.868-0.002-0.0020.0000.0000.0000.000
76A103LYS10.9870.97530.0890.0000.0000.0000.0000.0000.000
77A104SER00.0440.02330.148-0.009-0.0090.0000.0000.0000.000
78A105ASP-1-0.847-0.91330.245-0.049-0.0490.0000.0000.0000.000
79A106GLY0-0.089-0.04629.575-0.013-0.0130.0000.0000.0000.000
80A107SER0-0.028-0.00930.261-0.001-0.0010.0000.0000.0000.000
81A108THR0-0.031-0.01733.4490.0050.0050.0000.0000.0000.000
82A109LEU0-0.0130.00230.3450.0050.0050.0000.0000.0000.000
83A110VAL0-0.038-0.02232.1330.0020.0020.0000.0000.0000.000
84A111SER0-0.036-0.04329.8200.0100.0100.0000.0000.0000.000
85A112LYS10.9440.98129.146-0.018-0.0180.0000.0000.0000.000
86A113LYS10.9580.99024.761-0.215-0.2150.0000.0000.0000.000
87A114VAL00.0190.00726.998-0.001-0.0010.0000.0000.0000.000
88A115THR0-0.042-0.02224.2100.0140.0140.0000.0000.0000.000
89A116ARG10.8380.88225.983-0.130-0.1300.0000.0000.0000.000
90A117ALA00.1070.05525.0600.0250.0250.0000.0000.0000.000
91A118ASP-1-0.770-0.83125.4460.1750.1750.0000.0000.0000.000
92A119GLY0-0.052-0.03425.4240.0230.0230.0000.0000.0000.000
93A120THR0-0.119-0.06126.3140.0020.0020.0000.0000.0000.000
94A121ARG10.8500.90427.396-0.212-0.2120.0000.0000.0000.000
95A122LEU00.0010.01429.977-0.002-0.0020.0000.0000.0000.000
96A123GLU-1-0.860-0.92130.5230.1630.1630.0000.0000.0000.000
97A124TYR00.000-0.02332.572-0.004-0.0040.0000.0000.0000.000
98A125THR00.020-0.00733.414-0.001-0.0010.0000.0000.0000.000
99A126GLY0-0.011-0.00935.664-0.004-0.0040.0000.0000.0000.000
100A127ILE0-0.019-0.00233.966-0.003-0.0030.0000.0000.0000.000
101A128LYS10.8960.95438.013-0.033-0.0330.0000.0000.0000.000
102A129SER00.0340.00839.960-0.001-0.0010.0000.0000.0000.000
103A130ASP-1-0.846-0.89141.4030.0060.0060.0000.0000.0000.000
104A131GLY0-0.014-0.00738.933-0.001-0.0010.0000.0000.0000.000
105A132SER0-0.057-0.04639.7740.0060.0060.0000.0000.0000.000
106A133GLY00.030-0.00239.279-0.001-0.0010.0000.0000.0000.000
107A134LYS10.8780.94839.020-0.055-0.0550.0000.0000.0000.000
108A135ALA00.0300.01437.1620.0010.0010.0000.0000.0000.000
109A136LYS10.9330.98035.233-0.122-0.1220.0000.0000.0000.000
110A137GLU-1-0.738-0.83134.5390.1010.1010.0000.0000.0000.000
111A138VAL0-0.037-0.02631.2240.0020.0020.0000.0000.0000.000
112A139LEU00.0120.00332.0240.0080.0080.0000.0000.0000.000
113A140LYS10.9600.96527.125-0.250-0.2500.0000.0000.0000.000
114A141GLY00.0600.04033.263-0.007-0.0070.0000.0000.0000.000
115A142TYR0-0.059-0.03036.002-0.008-0.0080.0000.0000.0000.000
116A143VAL0-0.0020.00135.3500.0060.0060.0000.0000.0000.000
117A144LEU0-0.043-0.00737.691-0.007-0.0070.0000.0000.0000.000
118A145GLU-1-0.827-0.92538.8320.1060.1060.0000.0000.0000.000
119A146GLY00.004-0.01141.079-0.005-0.0050.0000.0000.0000.000
120A147THR0-0.075-0.02541.885-0.001-0.0010.0000.0000.0000.000
121A148LEU00.0120.02037.0460.0020.0020.0000.0000.0000.000
122A149THR0-0.016-0.01340.814-0.004-0.0040.0000.0000.0000.000
123A150ALA00.0330.00640.5090.0010.0010.0000.0000.0000.000
124A151GLU-1-0.984-0.97140.7020.0050.0050.0000.0000.0000.000
125A152LYS10.9420.97140.840-0.026-0.0260.0000.0000.0000.000
126A153THR0-0.0080.02138.0500.0030.0030.0000.0000.0000.000
127A154THR00.0080.00140.661-0.002-0.0020.0000.0000.0000.000
128A155LEU0-0.052-0.01638.1220.0020.0020.0000.0000.0000.000
129A156VAL00.008-0.00542.548-0.004-0.0040.0000.0000.0000.000
130A157VAL0-0.0060.00744.5160.0050.0050.0000.0000.0000.000
131A158LYS10.8810.92346.972-0.055-0.0550.0000.0000.0000.000
132A159GLU-1-0.903-0.96750.5900.0730.0730.0000.0000.0000.000
133A160GLY00.0380.03352.849-0.003-0.0030.0000.0000.0000.000
134A161THR0-0.065-0.05956.2230.0000.0000.0000.0000.0000.000
135A162VAL00.0160.02752.389-0.003-0.0030.0000.0000.0000.000
136A163THR0-0.053-0.02350.3760.0030.0030.0000.0000.0000.000
137A164LEU00.0160.01645.747-0.003-0.0030.0000.0000.0000.000
138A165SER0-0.004-0.01546.3830.0030.0030.0000.0000.0000.000
139A166LYS10.8700.92437.038-0.092-0.0920.0000.0000.0000.000
140A167ASN0-0.030-0.01942.5350.0020.0020.0000.0000.0000.000
141A168ILE00.0060.00036.3740.0020.0020.0000.0000.0000.000
142A169SER00.0650.03838.653-0.002-0.0020.0000.0000.0000.000
143A170LYS11.0170.99434.7510.0300.0300.0000.0000.0000.000
144A171SER0-0.047-0.02834.1350.0010.0010.0000.0000.0000.000
145A172GLY00.0060.00334.1230.0020.0020.0000.0000.0000.000
146A173GLU-1-0.972-0.97635.3080.0230.0230.0000.0000.0000.000
147A174VAL00.0070.00137.5670.0000.0000.0000.0000.0000.000
148A175SER0-0.012-0.00240.209-0.004-0.0040.0000.0000.0000.000
149A176VAL0-0.012-0.01043.7020.0030.0030.0000.0000.0000.000
150A177GLU-1-0.853-0.92146.0600.0300.0300.0000.0000.0000.000
151A178LEU0-0.015-0.01749.3130.0040.0040.0000.0000.0000.000
152A179ASN0-0.040-0.01251.995-0.005-0.0050.0000.0000.0000.000
153A180ASP-1-0.656-0.81455.0190.0460.0460.0000.0000.0000.000
154A181THR0-0.022-0.02357.655-0.002-0.0020.0000.0000.0000.000
155A182ASP-1-0.874-0.90160.4590.0390.0390.0000.0000.0000.000
156A183SER0-0.043-0.03362.484-0.001-0.0010.0000.0000.0000.000
157A184SER00.0410.02765.198-0.002-0.0020.0000.0000.0000.000
158A185ALA00.0230.01265.0500.0010.0010.0000.0000.0000.000
159A186ALA0-0.029-0.01165.2500.0010.0010.0000.0000.0000.000
160A187THR0-0.062-0.08462.4010.0010.0010.0000.0000.0000.000
161A188LYS10.8830.96160.383-0.031-0.0310.0000.0000.0000.000
162A189LYS10.8440.92555.716-0.050-0.0500.0000.0000.0000.000
163A190THR0-0.045-0.02256.953-0.002-0.0020.0000.0000.0000.000
164A191ALA00.023-0.00852.2750.0020.0020.0000.0000.0000.000
165A192ALA0-0.0130.01353.130-0.003-0.0030.0000.0000.0000.000
166A193TRP00.0370.02543.0790.0040.0040.0000.0000.0000.000
167A194ASN0-0.0030.00947.988-0.006-0.0060.0000.0000.0000.000
168A195SER00.038-0.00144.8920.0040.0040.0000.0000.0000.000
169A196GLY00.0240.02143.9070.0000.0000.0000.0000.0000.000
170A197THR0-0.007-0.01843.8630.0000.0000.0000.0000.0000.000
171A198SER00.0040.01941.2250.0060.0060.0000.0000.0000.000
172A199THR0-0.047-0.02543.3840.0070.0070.0000.0000.0000.000
173A200LEU0-0.027-0.01046.217-0.005-0.0050.0000.0000.0000.000
174A201THR0-0.011-0.01948.6260.0030.0030.0000.0000.0000.000
175A202ILE0-0.016-0.01250.865-0.003-0.0030.0000.0000.0000.000
176A203THR0-0.025-0.01554.0920.0000.0000.0000.0000.0000.000
177A204VAL00.005-0.00557.8590.0000.0000.0000.0000.0000.000
178A205ASN0-0.0010.00760.584-0.002-0.0020.0000.0000.0000.000
179A206SER0-0.033-0.01763.257-0.001-0.0010.0000.0000.0000.000
180A207LYS10.8990.95661.345-0.039-0.0390.0000.0000.0000.000
181A208LYS10.9630.99755.337-0.035-0.0350.0000.0000.0000.000
182A209THR0-0.011-0.01955.9080.0020.0020.0000.0000.0000.000
183A210LYS10.8900.93851.073-0.061-0.0610.0000.0000.0000.000
184A211ASP-1-0.772-0.84248.2870.0480.0480.0000.0000.0000.000
185A212LEU0-0.045-0.03345.8630.0050.0050.0000.0000.0000.000
186A213VAL00.0230.01441.539-0.005-0.0050.0000.0000.0000.000
187A214PHE0-0.032-0.02440.3850.0070.0070.0000.0000.0000.000
188A215THR00.047-0.00436.702-0.005-0.0050.0000.0000.0000.000
189A216SER00.0310.00834.1950.0030.0030.0000.0000.0000.000
190A217SER0-0.020-0.00632.1240.0010.0010.0000.0000.0000.000
191A218ASN0-0.091-0.06132.0830.0010.0010.0000.0000.0000.000
192A219THR00.0130.03634.6000.0040.0040.0000.0000.0000.000
193A220ILE00.002-0.00336.957-0.010-0.0100.0000.0000.0000.000
194A221THR00.0190.01940.5980.0050.0050.0000.0000.0000.000
195A222VAL0-0.001-0.00842.886-0.007-0.0070.0000.0000.0000.000
196A223GLN0-0.004-0.00146.6240.0040.0040.0000.0000.0000.000
197A224GLN00.0100.00649.178-0.006-0.0060.0000.0000.0000.000
198A225TYR0-0.062-0.05152.437-0.001-0.0010.0000.0000.0000.000
199A226ASP-1-0.712-0.86455.7240.0450.0450.0000.0000.0000.000
200A227SER00.017-0.00558.837-0.001-0.0010.0000.0000.0000.000
201A228ASN0-0.106-0.05161.865-0.003-0.0030.0000.0000.0000.000
202A229GLY00.0090.02359.001-0.002-0.0020.0000.0000.0000.000
203A230THR0-0.072-0.04659.168-0.002-0.0020.0000.0000.0000.000
204A231SER0-0.055-0.02256.684-0.001-0.0010.0000.0000.0000.000
205A232LEU0-0.0190.01450.1120.0010.0010.0000.0000.0000.000
206A233GLU-1-0.899-0.95753.5800.0580.0580.0000.0000.0000.000
207A234GLY0-0.015-0.00751.7310.0030.0030.0000.0000.0000.000
208A235SER0-0.033-0.02946.3440.0010.0010.0000.0000.0000.000
209A236ALA0-0.008-0.00244.2470.0010.0010.0000.0000.0000.000
210A237VAL00.0070.00943.8390.0050.0050.0000.0000.0000.000
211A238GLU-1-0.959-0.98436.6840.1460.1460.0000.0000.0000.000
212A239ILE0-0.052-0.02341.1130.0020.0020.0000.0000.0000.000
213A240THR00.000-0.00638.6990.0080.0080.0000.0000.0000.000
214A241LYS10.8450.91539.015-0.110-0.1100.0000.0000.0000.000
215A242LEU00.0470.01441.310-0.007-0.0070.0000.0000.0000.000
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