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: JL349

Calculation Name: 3CDK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CDK

Chain ID: A

ChEMBL ID:

UniProt ID: P42315

Base Structure: X-ray

Registration Date: 2023-06-21

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2591026.827494
FMO2-HF: Nuclear repulsion 2505604.285808
FMO2-HF: Total energy -85422.541685
FMO2-MP2: Total energy -85673.989366


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:4:GLY)


Summations of interaction energy for fragment #1(A:4:GLY)
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.
-3.895-0.4060.245-1.919-1.815-0.003
Interaction energy analysis for fragmet #1(A:4:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.013
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].
3A6VAL0-0.021-0.0043.216-1.7190.5920.021-1.213-1.1190.002
4A7LEU0-0.0070.0034.548-0.820-0.768-0.001-0.013-0.0370.000
5A8SER0-0.025-0.0397.3940.2750.2750.0000.0000.0000.000
6A9SER0-0.041-0.0459.4370.0770.0770.0000.0000.0000.000
7A10SER00.0560.01612.507-0.055-0.0550.0000.0000.0000.000
8A11LYS10.9250.95814.708-0.038-0.0380.0000.0000.0000.000
9A12GLU-1-0.851-0.87410.320-0.177-0.1770.0000.0000.0000.000
10A13ALA00.0390.01512.076-0.034-0.0340.0000.0000.0000.000
11A14ALA00.005-0.00313.494-0.019-0.0190.0000.0000.0000.000
12A15LYS10.8810.94216.0600.1600.1600.0000.0000.0000.000
13A16LEU0-0.031-0.01712.236-0.025-0.0250.0000.0000.0000.000
14A17ILE0-0.039-0.00316.9180.0050.0050.0000.0000.0000.000
15A18HIS0-0.051-0.03219.2160.0140.0140.0000.0000.0000.000
16A19ASP-1-0.816-0.91123.330-0.063-0.0630.0000.0000.0000.000
17A20GLY0-0.0070.00127.084-0.002-0.0020.0000.0000.0000.000
18A21ASP-1-0.854-0.91522.211-0.139-0.1390.0000.0000.0000.000
19A22THR0-0.065-0.03125.2890.0170.0170.0000.0000.0000.000
20A23LEU0-0.005-0.00721.344-0.010-0.0100.0000.0000.0000.000
21A24ILE00.0040.00522.1260.0150.0150.0000.0000.0000.000
22A25ALA00.0120.00521.670-0.003-0.0030.0000.0000.0000.000
23A26GLY00.0030.01621.8170.0010.0010.0000.0000.0000.000
24A27GLY00.017-0.00123.1200.0040.0040.0000.0000.0000.000
25A28PHE0-0.089-0.04825.621-0.009-0.0090.0000.0000.0000.000
26A29GLY00.0330.02329.2640.0060.0060.0000.0000.0000.000
27A30LEU0-0.009-0.00628.803-0.001-0.0010.0000.0000.0000.000
28A31CYS0-0.086-0.03027.7150.0150.0150.0000.0000.0000.000
29A32GLY00.038-0.00123.370-0.005-0.0050.0000.0000.0000.000
30A33ILE00.0250.04022.958-0.006-0.0060.0000.0000.0000.000
31A34PRO0-0.0100.00919.0660.0190.0190.0000.0000.0000.000
32A35GLU-1-0.828-0.91120.4780.1030.1030.0000.0000.0000.000
33A36GLN00.014-0.00418.241-0.020-0.0200.0000.0000.0000.000
34A37LEU00.0070.01114.753-0.017-0.0170.0000.0000.0000.000
35A38ILE0-0.040-0.01418.542-0.023-0.0230.0000.0000.0000.000
36A39LEU0-0.004-0.00422.089-0.013-0.0130.0000.0000.0000.000
37A40SER0-0.015-0.01718.621-0.009-0.0090.0000.0000.0000.000
38A41ILE00.012-0.00119.383-0.018-0.0180.0000.0000.0000.000
39A42ARG10.8350.93822.039-0.008-0.0080.0000.0000.0000.000
40A43ASP-1-0.884-0.93922.602-0.002-0.0020.0000.0000.0000.000
41A44GLN0-0.105-0.05120.537-0.020-0.0200.0000.0000.0000.000
42A45GLY0-0.028-0.00223.764-0.007-0.0070.0000.0000.0000.000
43A46VAL0-0.0360.00123.1750.0030.0030.0000.0000.0000.000
44A47LYS10.8620.89726.3240.0700.0700.0000.0000.0000.000
45A48ASP-1-0.813-0.90028.742-0.060-0.0600.0000.0000.0000.000
46A49LEU00.0070.03025.266-0.001-0.0010.0000.0000.0000.000
47A50THR00.0260.00828.2690.0100.0100.0000.0000.0000.000
48A51VAL0-0.007-0.00426.831-0.004-0.0040.0000.0000.0000.000
49A52VAL0-0.010-0.01426.5400.0040.0040.0000.0000.0000.000
50A53SER00.004-0.01426.2200.0040.0040.0000.0000.0000.000
51A54ASN00.0230.02428.035-0.006-0.0060.0000.0000.0000.000
52A55ASN00.016-0.00930.1430.0040.0040.0000.0000.0000.000
53A56CYS00.0210.02730.349-0.002-0.0020.0000.0000.0000.000
54A57GLY0-0.0130.00230.3200.0000.0000.0000.0000.0000.000
55A58VAL0-0.003-0.01031.072-0.001-0.0010.0000.0000.0000.000
56A59ASP-1-0.844-0.94332.6490.0150.0150.0000.0000.0000.000
57A60ASP-1-0.841-0.88933.1220.0320.0320.0000.0000.0000.000
58A61TRP0-0.030-0.04125.3740.0000.0000.0000.0000.0000.000
59A62GLY00.0620.03426.331-0.002-0.0020.0000.0000.0000.000
60A63LEU00.0550.01425.742-0.004-0.0040.0000.0000.0000.000
61A64GLY00.0320.02128.011-0.007-0.0070.0000.0000.0000.000
62A65LEU0-0.0110.00126.859-0.004-0.0040.0000.0000.0000.000
63A66LEU00.0620.02724.876-0.003-0.0030.0000.0000.0000.000
64A67LEU00.0030.01829.202-0.004-0.0040.0000.0000.0000.000
65A68ALA0-0.032-0.01832.751-0.003-0.0030.0000.0000.0000.000
66A69ASN0-0.086-0.06028.7960.0040.0040.0000.0000.0000.000
67A70LYS10.8310.90332.3760.0140.0140.0000.0000.0000.000
68A71GLN00.0100.00825.8470.0060.0060.0000.0000.0000.000
69A72ILE0-0.043-0.01829.433-0.005-0.0050.0000.0000.0000.000
70A73LYS10.8720.94631.4220.0530.0530.0000.0000.0000.000
71A74LYS10.8890.93632.5500.0370.0370.0000.0000.0000.000
72A75MET0-0.0110.00631.715-0.001-0.0010.0000.0000.0000.000
73A76ILE0-0.025-0.01330.8860.0000.0000.0000.0000.0000.000
74A77ALA00.0140.00731.1140.0020.0020.0000.0000.0000.000
75A78SER0-0.048-0.03133.262-0.001-0.0010.0000.0000.0000.000
76A79TYR0-0.054-0.01935.0260.0000.0000.0000.0000.0000.000
77A80VAL00.0220.02335.3680.0020.0020.0000.0000.0000.000
78A81GLY00.0270.01036.1120.0020.0020.0000.0000.0000.000
79A82GLU-1-0.839-0.91738.2990.0220.0220.0000.0000.0000.000
80A83ASN00.0100.01635.081-0.002-0.0020.0000.0000.0000.000
81A84LYS10.9730.97338.822-0.009-0.0090.0000.0000.0000.000
82A85ILE0-0.050-0.02636.646-0.002-0.0020.0000.0000.0000.000
83A86PHE00.0440.00935.303-0.003-0.0030.0000.0000.0000.000
84A87GLU-1-0.850-0.93038.910-0.004-0.0040.0000.0000.0000.000
85A88ARG10.7410.84640.7430.0090.0090.0000.0000.0000.000
86A89GLN0-0.052-0.02735.920-0.002-0.0020.0000.0000.0000.000
87A90PHE00.0090.00740.637-0.002-0.0020.0000.0000.0000.000
88A91LEU0-0.009-0.01141.881-0.002-0.0020.0000.0000.0000.000
89A92SER0-0.063-0.02843.4030.0000.0000.0000.0000.0000.000
90A93GLY0-0.0150.00043.347-0.001-0.0010.0000.0000.0000.000
91A94GLU-1-0.797-0.85239.397-0.018-0.0180.0000.0000.0000.000
92A95LEU0-0.015-0.00335.022-0.002-0.0020.0000.0000.0000.000
93A96GLU-1-0.899-0.94936.606-0.032-0.0320.0000.0000.0000.000
94A97VAL0-0.007-0.02536.4820.0000.0000.0000.0000.0000.000
95A98GLU-1-0.815-0.88435.306-0.027-0.0270.0000.0000.0000.000
96A99LEU00.004-0.00135.8040.0010.0010.0000.0000.0000.000
97A100VAL0-0.008-0.00534.489-0.001-0.0010.0000.0000.0000.000
98A101PRO00.002-0.00536.0720.0030.0030.0000.0000.0000.000
99A102GLN00.0260.00533.0460.0020.0020.0000.0000.0000.000
100A103GLY00.0150.00832.8490.0000.0000.0000.0000.0000.000
101A104THR00.0070.00233.0960.0000.0000.0000.0000.0000.000
102A105LEU00.0230.01730.303-0.003-0.0030.0000.0000.0000.000
103A106ALA00.0050.00228.713-0.003-0.0030.0000.0000.0000.000
104A107GLU-1-0.824-0.89728.297-0.007-0.0070.0000.0000.0000.000
105A108ARG10.7650.87129.7020.0200.0200.0000.0000.0000.000
106A109ILE00.0190.01924.455-0.007-0.0070.0000.0000.0000.000
107A110ARG10.8670.91024.979-0.005-0.0050.0000.0000.0000.000
108A111ALA0-0.028-0.01525.619-0.006-0.0060.0000.0000.0000.000
109A112GLY00.0210.01026.429-0.005-0.0050.0000.0000.0000.000
110A113GLY00.0190.00422.389-0.011-0.0110.0000.0000.0000.000
111A114ALA0-0.094-0.03522.301-0.006-0.0060.0000.0000.0000.000
112A115GLY00.0020.01224.8720.0000.0000.0000.0000.0000.000
113A116ILE0-0.059-0.02526.4490.0030.0030.0000.0000.0000.000
114A117PRO00.0240.00829.8710.0010.0010.0000.0000.0000.000
115A118GLY00.015-0.00831.8500.0010.0010.0000.0000.0000.000
116A119PHE0-0.042-0.00132.6550.0010.0010.0000.0000.0000.000
117A120TYR00.0250.00635.9750.0000.0000.0000.0000.0000.000
118A121THR00.0190.01337.9720.0030.0030.0000.0000.0000.000
119A122ALA00.0220.00140.020-0.001-0.0010.0000.0000.0000.000
120A123THR0-0.056-0.02738.8220.0010.0010.0000.0000.0000.000
121A124GLY00.0720.01540.764-0.001-0.0010.0000.0000.0000.000
122A125VAL0-0.027-0.00343.426-0.001-0.0010.0000.0000.0000.000
123A126GLY00.0010.00946.4080.0010.0010.0000.0000.0000.000
124A127THR0-0.016-0.01345.1460.0010.0010.0000.0000.0000.000
125A128SER00.0490.02546.403-0.001-0.0010.0000.0000.0000.000
126A129ILE00.0250.01740.367-0.001-0.0010.0000.0000.0000.000
127A130ALA0-0.038-0.01642.155-0.002-0.0020.0000.0000.0000.000
128A131GLU-1-0.868-0.94544.356-0.014-0.0140.0000.0000.0000.000
129A132GLY0-0.038-0.01143.766-0.001-0.0010.0000.0000.0000.000
130A133LYS10.7880.89839.0140.0150.0150.0000.0000.0000.000
131A134GLU-1-0.744-0.84341.729-0.025-0.0250.0000.0000.0000.000
132A135HIS0-0.014-0.01443.8270.0020.0020.0000.0000.0000.000
133A136LYS10.8710.93944.5150.0120.0120.0000.0000.0000.000
134A137THR0-0.0030.00346.8610.0010.0010.0000.0000.0000.000
135A138PHE0-0.005-0.00542.481-0.001-0.0010.0000.0000.0000.000
136A139GLY00.0230.01047.4630.0010.0010.0000.0000.0000.000
137A140GLY00.0080.00949.5420.0010.0010.0000.0000.0000.000
138A141ARG10.9440.97244.577-0.002-0.0020.0000.0000.0000.000
139A142THR00.0190.00347.962-0.001-0.0010.0000.0000.0000.000
140A143TYR0-0.033-0.00942.5490.0020.0020.0000.0000.0000.000
141A144VAL00.0270.00641.516-0.001-0.0010.0000.0000.0000.000
142A145LEU0-0.036-0.00437.9420.0010.0010.0000.0000.0000.000
143A146GLU-1-0.775-0.88735.751-0.017-0.0170.0000.0000.0000.000
144A147ARG10.8450.87433.9580.0320.0320.0000.0000.0000.000
145A148GLY00.0030.00729.9390.0030.0030.0000.0000.0000.000
146A149ILE0-0.073-0.04026.942-0.002-0.0020.0000.0000.0000.000
147A150THR00.0190.00423.0290.0050.0050.0000.0000.0000.000
148A151GLY0-0.001-0.00122.7700.0050.0050.0000.0000.0000.000
149A152ASP-1-0.825-0.89821.537-0.141-0.1410.0000.0000.0000.000
150A153VAL00.0140.00117.073-0.030-0.0300.0000.0000.0000.000
151A154ALA0-0.029-0.00217.7660.0250.0250.0000.0000.0000.000
152A155ILE0-0.0070.00516.968-0.007-0.0070.0000.0000.0000.000
153A156VAL00.015-0.00315.9070.0110.0110.0000.0000.0000.000
154A157LYS10.7680.86817.002-0.157-0.1570.0000.0000.0000.000
155A158ALA0-0.014-0.01115.094-0.022-0.0220.0000.0000.0000.000
156A159TRP0-0.068-0.04717.2570.0060.0060.0000.0000.0000.000
157A160LYS10.8360.88814.160-0.397-0.3970.0000.0000.0000.000
158A161ALA00.0510.02510.010-0.097-0.0970.0000.0000.0000.000
159A162ASP-1-0.692-0.8348.0010.8140.8140.0000.0000.0000.000
160A163THR00.008-0.0023.288-0.775-0.4530.022-0.118-0.2270.000
161A164MET0-0.009-0.0123.041-1.214-0.4100.203-0.575-0.432-0.005
162A165GLY00.0060.0185.483-0.485-0.4850.0000.0000.0000.000
163A166ASN0-0.051-0.0398.142-0.233-0.2330.0000.0000.0000.000
164A167LEU0-0.0110.00211.0840.1070.1070.0000.0000.0000.000
165A168ILE00.0400.02513.901-0.048-0.0480.0000.0000.0000.000
166A169PHE00.0580.01817.2480.0160.0160.0000.0000.0000.000
167A170ARG10.9730.98120.285-0.186-0.1860.0000.0000.0000.000
168A171LYS10.9430.95723.537-0.118-0.1180.0000.0000.0000.000
169A172THR00.0610.01726.1450.0040.0040.0000.0000.0000.000
170A173ALA00.0390.02523.703-0.008-0.0080.0000.0000.0000.000
171A174ARG10.9290.98322.250-0.102-0.1020.0000.0000.0000.000
172A175ASN0-0.010-0.01723.330-0.011-0.0110.0000.0000.0000.000
173A176PHE00.0580.01924.906-0.002-0.0020.0000.0000.0000.000
174A177ASN00.0080.01319.539-0.018-0.0180.0000.0000.0000.000
175A178PRO0-0.025-0.00619.175-0.008-0.0080.0000.0000.0000.000
176A179ILE00.012-0.00619.903-0.012-0.0120.0000.0000.0000.000
177A180ALA00.0180.00420.954-0.015-0.0150.0000.0000.0000.000
178A181ALA0-0.013-0.00415.938-0.018-0.0180.0000.0000.0000.000
179A182MET0-0.050-0.01917.260-0.028-0.0280.0000.0000.0000.000
180A183ALA00.0230.02519.396-0.017-0.0170.0000.0000.0000.000
181A184GLY00.0050.00818.5080.0010.0010.0000.0000.0000.000
182A185LYS10.7960.90417.6200.1580.1580.0000.0000.0000.000
183A186ILE0-0.028-0.02213.794-0.058-0.0580.0000.0000.0000.000
184A187THR00.0180.01313.9880.0430.0430.0000.0000.0000.000
185A188ILE0-0.035-0.02012.279-0.073-0.0730.0000.0000.0000.000
186A189ALA0-0.008-0.00611.7620.0290.0290.0000.0000.0000.000
187A190GLU-1-0.759-0.87612.4070.2270.2270.0000.0000.0000.000
188A191ALA0-0.026-0.01212.732-0.017-0.0170.0000.0000.0000.000
189A192GLU-1-0.870-0.92014.7220.2320.2320.0000.0000.0000.000
190A193GLU-1-0.837-0.89714.3780.4550.4550.0000.0000.0000.000
191A194ILE0-0.004-0.0137.700-0.005-0.0050.0000.0000.0000.000
192A195VAL00.0060.01710.6200.0080.0080.0000.0000.0000.000
193A196GLU-1-0.906-0.9657.8511.3121.3120.0000.0000.0000.000
194A197ALA0-0.067-0.0456.754-0.252-0.2520.0000.0000.0000.000
195A198GLY00.0210.0058.615-0.086-0.0860.0000.0000.0000.000
196A199GLU-1-0.931-0.95912.2090.3660.3660.0000.0000.0000.000
197A200LEU0-0.124-0.05311.707-0.048-0.0480.0000.0000.0000.000
198A201ASP-1-0.816-0.91614.5850.1810.1810.0000.0000.0000.000
199A202PRO00.039-0.00216.054-0.008-0.0080.0000.0000.0000.000
200A203ASP-1-0.919-0.94917.3860.1070.1070.0000.0000.0000.000
201A204HIS0-0.130-0.06118.735-0.006-0.0060.0000.0000.0000.000
202A205ILE0-0.074-0.01613.4910.0030.0030.0000.0000.0000.000
203A206HIS0-0.080-0.04317.081-0.034-0.0340.0000.0000.0000.000
204A207THR0-0.001-0.00314.921-0.030-0.0300.0000.0000.0000.000
205A208PRO00.0310.02713.5590.0400.0400.0000.0000.0000.000
206A209GLY00.0550.0119.609-0.029-0.0290.0000.0000.0000.000
207A210ILE0-0.058-0.02510.073-0.133-0.1330.0000.0000.0000.000
208A211TYR0-0.028-0.01212.318-0.043-0.0430.0000.0000.0000.000
209A212VAL00.0290.01010.0120.0270.0270.0000.0000.0000.000
210A213GLN00.0220.0179.218-0.031-0.0310.0000.0000.0000.000
211A214HIS00.0140.0097.912-0.493-0.4930.0000.0000.0000.000
212A215VAL00.0110.0077.4230.1630.1630.0000.0000.0000.000
213A216VAL0-0.0040.0028.4090.0430.0430.0000.0000.0000.000
214A217LEU00.0210.01210.7400.0070.0070.0000.0000.0000.000
215A218GLY00.010-0.00512.868-0.090-0.0900.0000.0000.0000.000
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