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

tag_button

FMODB ID: 852GY

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2588077.823268
FMO2-HF: Nuclear repulsion 2502658.413733
FMO2-HF: Total energy -85419.409535
FMO2-MP2: Total energy -85671.163295


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.
-2.5390.3710.721-1.689-1.94-0.004
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 : -0.008 / 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].
3A6VAL0-0.037-0.0143.105-0.1031.5020.051-0.644-1.0110.001
4A7LEU00.0330.0254.9090.0220.069-0.001-0.010-0.0350.000
5A8SER00.013-0.0017.7030.3120.3120.0000.0000.0000.000
6A9SER0-0.043-0.0239.957-0.015-0.0150.0000.0000.0000.000
7A10SER00.0950.02912.972-0.068-0.0680.0000.0000.0000.000
8A11LYS10.9981.00015.275-0.103-0.1030.0000.0000.0000.000
9A12GLU-1-0.956-0.99210.174-0.190-0.1900.0000.0000.0000.000
10A13ALA00.0260.01212.468-0.053-0.0530.0000.0000.0000.000
11A14ALA0-0.0110.00213.659-0.034-0.0340.0000.0000.0000.000
12A15LYS10.9360.97315.5840.1540.1540.0000.0000.0000.000
13A16LEU0-0.071-0.02312.022-0.022-0.0220.0000.0000.0000.000
14A17ILE0-0.039-0.01216.733-0.007-0.0070.0000.0000.0000.000
15A18HIS0-0.037-0.02119.6620.0250.0250.0000.0000.0000.000
16A19ASP-1-0.873-0.95423.174-0.098-0.0980.0000.0000.0000.000
17A20GLY0-0.045-0.01326.966-0.006-0.0060.0000.0000.0000.000
18A21ASP-1-0.864-0.91622.231-0.203-0.2030.0000.0000.0000.000
19A22THR0-0.082-0.04125.0430.0220.0220.0000.0000.0000.000
20A23LEU00.009-0.00620.725-0.017-0.0170.0000.0000.0000.000
21A24ILE0-0.018-0.00221.9690.0190.0190.0000.0000.0000.000
22A25ALA0-0.0020.01221.213-0.012-0.0120.0000.0000.0000.000
23A26GLY0-0.005-0.00821.1370.0070.0070.0000.0000.0000.000
24A27GLY0-0.009-0.01222.3800.0050.0050.0000.0000.0000.000
25A28PHE0-0.067-0.03824.761-0.008-0.0080.0000.0000.0000.000
26A29GLY00.0510.02528.3200.0090.0090.0000.0000.0000.000
27A30LEU00.013-0.00228.028-0.002-0.0020.0000.0000.0000.000
28A31CYS0-0.066-0.01626.5100.0140.0140.0000.0000.0000.000
29A32GLY00.027-0.00822.338-0.007-0.0070.0000.0000.0000.000
30A33ILE00.0090.04122.272-0.015-0.0150.0000.0000.0000.000
31A34PRO00.0060.00918.3670.0220.0220.0000.0000.0000.000
32A35GLU-1-0.908-0.96420.0830.0860.0860.0000.0000.0000.000
33A36GLN00.000-0.00118.0050.0010.0010.0000.0000.0000.000
34A37LEU00.003-0.01814.842-0.013-0.0130.0000.0000.0000.000
35A38ILE0-0.034-0.00918.796-0.019-0.0190.0000.0000.0000.000
36A39LEU0-0.0110.00722.376-0.009-0.0090.0000.0000.0000.000
37A40SER0-0.003-0.00419.000-0.002-0.0020.0000.0000.0000.000
38A41ILE00.0240.00920.071-0.011-0.0110.0000.0000.0000.000
39A42ARG10.8130.89822.3900.0040.0040.0000.0000.0000.000
40A43ASP-1-0.944-0.97223.2360.0060.0060.0000.0000.0000.000
41A44GLN0-0.119-0.06420.082-0.016-0.0160.0000.0000.0000.000
42A45GLY0-0.0150.00423.749-0.006-0.0060.0000.0000.0000.000
43A46VAL0-0.0360.01023.5870.0010.0010.0000.0000.0000.000
44A47LYS10.9510.95926.1720.0870.0870.0000.0000.0000.000
45A48ASP-1-0.934-0.98328.770-0.086-0.0860.0000.0000.0000.000
46A49LEU00.0220.02925.340-0.005-0.0050.0000.0000.0000.000
47A50THR00.0180.02028.3580.0150.0150.0000.0000.0000.000
48A51VAL0-0.038-0.03026.594-0.009-0.0090.0000.0000.0000.000
49A52VAL00.0100.00326.3220.0090.0090.0000.0000.0000.000
50A53SER0-0.002-0.02525.663-0.002-0.0020.0000.0000.0000.000
51A54ASN00.0310.02527.579-0.001-0.0010.0000.0000.0000.000
52A55ASN00.0530.01129.5210.0040.0040.0000.0000.0000.000
53A56CYS00.0270.02029.725-0.007-0.0070.0000.0000.0000.000
54A57GLY0-0.054-0.01029.8090.0020.0020.0000.0000.0000.000
55A58VAL00.0060.00430.3900.0010.0010.0000.0000.0000.000
56A59ASP-1-0.921-0.99132.5250.0040.0040.0000.0000.0000.000
57A60ASP-1-0.902-0.93133.1700.0220.0220.0000.0000.0000.000
58A61TRP0-0.007-0.02925.230-0.003-0.0030.0000.0000.0000.000
59A62GLY00.0570.03126.054-0.005-0.0050.0000.0000.0000.000
60A63LEU00.0580.01025.321-0.002-0.0020.0000.0000.0000.000
61A64GLY00.0190.02528.042-0.006-0.0060.0000.0000.0000.000
62A65LEU00.022-0.00327.149-0.002-0.0020.0000.0000.0000.000
63A66LEU00.0270.03025.273-0.001-0.0010.0000.0000.0000.000
64A67LEU00.0140.01429.443-0.002-0.0020.0000.0000.0000.000
65A68ALA0-0.033-0.02532.918-0.001-0.0010.0000.0000.0000.000
66A69ASN0-0.095-0.04729.1710.0060.0060.0000.0000.0000.000
67A70LYS10.9200.95932.7680.0230.0230.0000.0000.0000.000
68A71GLN00.0250.03126.1430.0070.0070.0000.0000.0000.000
69A72ILE0-0.037-0.01329.701-0.008-0.0080.0000.0000.0000.000
70A73LYS11.0161.02731.7410.0830.0830.0000.0000.0000.000
71A74LYS10.9440.96832.5510.0740.0740.0000.0000.0000.000
72A75MET0-0.0070.01331.186-0.006-0.0060.0000.0000.0000.000
73A76ILE0-0.059-0.01830.9200.0020.0020.0000.0000.0000.000
74A77ALA00.0390.01430.863-0.002-0.0020.0000.0000.0000.000
75A78SER0-0.085-0.03432.9140.0020.0020.0000.0000.0000.000
76A79TYR0-0.042-0.02734.5430.0020.0020.0000.0000.0000.000
77A80VAL00.0330.02234.735-0.001-0.0010.0000.0000.0000.000
78A81GLY0-0.0280.00236.0670.0020.0020.0000.0000.0000.000
79A82GLU-1-0.930-0.97738.1990.0040.0040.0000.0000.0000.000
80A83ASN00.0800.05935.0720.0000.0000.0000.0000.0000.000
81A84LYS11.0030.98538.7280.0010.0010.0000.0000.0000.000
82A85ILE0-0.037-0.02436.605-0.001-0.0010.0000.0000.0000.000
83A86PHE00.012-0.00234.796-0.003-0.0030.0000.0000.0000.000
84A87GLU-1-0.912-0.97338.738-0.019-0.0190.0000.0000.0000.000
85A88ARG10.9070.96140.2230.0200.0200.0000.0000.0000.000
86A89GLN0-0.054-0.00836.207-0.004-0.0040.0000.0000.0000.000
87A90PHE00.0380.02240.520-0.002-0.0020.0000.0000.0000.000
88A91LEU0-0.051-0.02641.659-0.002-0.0020.0000.0000.0000.000
89A92SER0-0.063-0.03943.1030.0010.0010.0000.0000.0000.000
90A93GLY0-0.080-0.02743.648-0.001-0.0010.0000.0000.0000.000
91A94GLU-1-0.936-0.97339.641-0.034-0.0340.0000.0000.0000.000
92A95LEU0-0.0140.00634.714-0.003-0.0030.0000.0000.0000.000
93A96GLU-1-0.890-0.95236.732-0.053-0.0530.0000.0000.0000.000
94A97VAL0-0.034-0.02836.412-0.003-0.0030.0000.0000.0000.000
95A98GLU-1-0.915-0.96735.222-0.062-0.0620.0000.0000.0000.000
96A99LEU0-0.005-0.01335.695-0.001-0.0010.0000.0000.0000.000
97A100VAL0-0.0100.00033.903-0.001-0.0010.0000.0000.0000.000
98A101PRO00.0140.00535.8690.0030.0030.0000.0000.0000.000
99A102GLN00.0860.02732.591-0.001-0.0010.0000.0000.0000.000
100A103GLY0-0.0040.00432.574-0.003-0.0030.0000.0000.0000.000
101A104THR0-0.006-0.00533.064-0.003-0.0030.0000.0000.0000.000
102A105LEU00.0040.00329.604-0.005-0.0050.0000.0000.0000.000
103A106ALA00.004-0.00828.351-0.007-0.0070.0000.0000.0000.000
104A107GLU-1-0.893-0.94828.258-0.062-0.0620.0000.0000.0000.000
105A108ARG10.8760.92929.9170.0630.0630.0000.0000.0000.000
106A109ILE00.0050.02123.972-0.009-0.0090.0000.0000.0000.000
107A110ARG10.9530.97524.9080.0570.0570.0000.0000.0000.000
108A111ALA0-0.039-0.01225.682-0.010-0.0100.0000.0000.0000.000
109A112GLY00.0010.00326.473-0.005-0.0050.0000.0000.0000.000
110A113GLY00.0420.01722.568-0.014-0.0140.0000.0000.0000.000
111A114ALA0-0.099-0.03922.683-0.011-0.0110.0000.0000.0000.000
112A115GLY0-0.0020.01225.1050.0040.0040.0000.0000.0000.000
113A116ILE0-0.073-0.02926.8230.0090.0090.0000.0000.0000.000
114A117PRO00.0330.00730.1980.0010.0010.0000.0000.0000.000
115A118GLY00.010-0.00932.0860.0020.0020.0000.0000.0000.000
116A119PHE0-0.0130.00332.6020.0010.0010.0000.0000.0000.000
117A120TYR00.0320.01636.2240.0020.0020.0000.0000.0000.000
118A121THR00.0310.00837.8710.0030.0030.0000.0000.0000.000
119A122ALA00.0220.00639.9920.0000.0000.0000.0000.0000.000
120A123THR0-0.049-0.02538.9270.0030.0030.0000.0000.0000.000
121A124GLY00.0370.01341.482-0.003-0.0030.0000.0000.0000.000
122A125VAL00.0020.00243.3840.0000.0000.0000.0000.0000.000
123A126GLY0-0.017-0.01146.2160.0020.0020.0000.0000.0000.000
124A127THR0-0.0050.03244.3790.0020.0020.0000.0000.0000.000
125A128SER00.0700.01145.720-0.001-0.0010.0000.0000.0000.000
126A129ILE0-0.030-0.01540.754-0.002-0.0020.0000.0000.0000.000
127A130ALA0-0.026-0.01842.363-0.003-0.0030.0000.0000.0000.000
128A131GLU-1-0.915-0.95744.734-0.033-0.0330.0000.0000.0000.000
129A132GLY0-0.017-0.00743.898-0.002-0.0020.0000.0000.0000.000
130A133LYS10.8070.90738.6260.0450.0450.0000.0000.0000.000
131A134GLU-1-0.759-0.86241.617-0.054-0.0540.0000.0000.0000.000
132A135HIS0-0.020-0.00843.8870.0020.0020.0000.0000.0000.000
133A136LYS10.9150.96444.3670.0390.0390.0000.0000.0000.000
134A137THR0-0.005-0.00646.7530.0010.0010.0000.0000.0000.000
135A138PHE0-0.023-0.01443.033-0.001-0.0010.0000.0000.0000.000
136A139GLY00.0200.00847.5900.0010.0010.0000.0000.0000.000
137A140GLY00.000-0.00649.9730.0010.0010.0000.0000.0000.000
138A141ARG10.9650.98544.4370.0220.0220.0000.0000.0000.000
139A142THR00.007-0.00147.562-0.002-0.0020.0000.0000.0000.000
140A143TYR0-0.034-0.01142.5330.0020.0020.0000.0000.0000.000
141A144VAL00.0530.02940.8960.0000.0000.0000.0000.0000.000
142A145LEU0-0.077-0.03137.781-0.001-0.0010.0000.0000.0000.000
143A146GLU-1-0.801-0.89535.418-0.051-0.0510.0000.0000.0000.000
144A147ARG10.8460.88833.8110.0650.0650.0000.0000.0000.000
145A148GLY0-0.0100.00429.9100.0020.0020.0000.0000.0000.000
146A149ILE0-0.075-0.04126.7620.0000.0000.0000.0000.0000.000
147A150THR00.020-0.00624.114-0.005-0.0050.0000.0000.0000.000
148A151GLY00.017-0.00123.0370.0150.0150.0000.0000.0000.000
149A152ASP-1-0.854-0.90821.567-0.215-0.2150.0000.0000.0000.000
150A153VAL00.0180.00617.396-0.039-0.0390.0000.0000.0000.000
151A154ALA0-0.0120.00017.7010.0400.0400.0000.0000.0000.000
152A155ILE0-0.036-0.01516.830-0.025-0.0250.0000.0000.0000.000
153A156VAL00.012-0.01415.3210.0280.0280.0000.0000.0000.000
154A157LYS10.8630.95516.040-0.111-0.1110.0000.0000.0000.000
155A158ALA0-0.009-0.03014.233-0.013-0.0130.0000.0000.0000.000
156A159TRP0-0.095-0.05816.3500.0230.0230.0000.0000.0000.000
157A160LYS10.8900.94013.593-0.307-0.3070.0000.0000.0000.000
158A161ALA00.0720.0329.309-0.098-0.0980.0000.0000.0000.000
159A162ASP-1-0.733-0.8468.0530.4970.4970.0000.0000.0000.000
160A163THR0-0.006-0.0032.446-0.991-0.6270.522-0.377-0.5090.000
161A164MET0-0.004-0.0083.159-2.030-1.1360.149-0.658-0.385-0.005
162A165GLY0-0.008-0.0155.642-0.320-0.3200.0000.0000.0000.000
163A166ASN00.0050.0057.998-0.117-0.1170.0000.0000.0000.000
164A167LEU0-0.0080.00710.8980.1000.1000.0000.0000.0000.000
165A168ILE00.0650.03613.510-0.021-0.0210.0000.0000.0000.000
166A169PHE00.000-0.00816.6430.0190.0190.0000.0000.0000.000
167A170ARG10.9880.97819.499-0.127-0.1270.0000.0000.0000.000
168A171LYS10.9140.95122.526-0.095-0.0950.0000.0000.0000.000
169A172THR00.0590.01625.626-0.002-0.0020.0000.0000.0000.000
170A173ALA00.0170.01522.876-0.008-0.0080.0000.0000.0000.000
171A174ARG10.9580.99521.929-0.035-0.0350.0000.0000.0000.000
172A175ASN0-0.002-0.00722.836-0.020-0.0200.0000.0000.0000.000
173A176PHE00.0940.02024.413-0.001-0.0010.0000.0000.0000.000
174A177ASN0-0.015-0.00319.003-0.028-0.0280.0000.0000.0000.000
175A178PRO0-0.014-0.01318.758-0.019-0.0190.0000.0000.0000.000
176A179ILE0-0.018-0.01219.739-0.018-0.0180.0000.0000.0000.000
177A180ALA00.0370.01820.694-0.014-0.0140.0000.0000.0000.000
178A181ALA0-0.039-0.02815.761-0.022-0.0220.0000.0000.0000.000
179A182MET0-0.063-0.01617.069-0.034-0.0340.0000.0000.0000.000
180A183ALA00.0240.02019.220-0.016-0.0160.0000.0000.0000.000
181A184GLY0-0.024-0.00218.5690.0110.0110.0000.0000.0000.000
182A185LYS10.9400.97917.5810.2900.2900.0000.0000.0000.000
183A186ILE0-0.027-0.01113.381-0.079-0.0790.0000.0000.0000.000
184A187THR00.0010.00813.5600.0700.0700.0000.0000.0000.000
185A188ILE00.0120.00312.096-0.118-0.1180.0000.0000.0000.000
186A189ALA0-0.015-0.00510.9920.0770.0770.0000.0000.0000.000
187A190GLU-1-0.772-0.88011.6860.1190.1190.0000.0000.0000.000
188A191ALA0-0.011-0.01311.902-0.027-0.0270.0000.0000.0000.000
189A192GLU-1-0.833-0.89813.9030.2040.2040.0000.0000.0000.000
190A193GLU-1-0.870-0.93913.8940.4730.4730.0000.0000.0000.000
191A194ILE0-0.014-0.0067.207-0.057-0.0570.0000.0000.0000.000
192A195VAL0-0.0020.0039.9720.0820.0820.0000.0000.0000.000
193A196GLU-1-0.904-0.9637.4651.3261.3260.0000.0000.0000.000
194A197ALA0-0.057-0.0436.682-0.239-0.2390.0000.0000.0000.000
195A198GLY00.0180.0028.472-0.031-0.0310.0000.0000.0000.000
196A199GLU-1-0.884-0.94011.7800.3640.3640.0000.0000.0000.000
197A200LEU0-0.148-0.06711.631-0.061-0.0610.0000.0000.0000.000
198A201ASP-1-0.798-0.89514.5350.1190.1190.0000.0000.0000.000
199A202PRO0-0.004-0.02216.048-0.012-0.0120.0000.0000.0000.000
200A203ASP-1-0.920-0.95517.2080.0300.0300.0000.0000.0000.000
201A204HIS0-0.163-0.06918.2470.0090.0090.0000.0000.0000.000
202A205ILE0-0.063-0.02212.987-0.012-0.0120.0000.0000.0000.000
203A206HIS0-0.004-0.00816.876-0.017-0.0170.0000.0000.0000.000
204A207THR0-0.068-0.03514.391-0.030-0.0300.0000.0000.0000.000
205A208PRO00.0630.03514.0190.0100.0100.0000.0000.0000.000
206A209GLY00.0760.03010.182-0.029-0.0290.0000.0000.0000.000
207A210ILE0-0.065-0.02410.705-0.138-0.1380.0000.0000.0000.000
208A211TYR0-0.004-0.00712.666-0.042-0.0420.0000.0000.0000.000
209A212VAL00.0180.0259.1480.0110.0110.0000.0000.0000.000
210A213GLN00.004-0.0109.226-0.069-0.0690.0000.0000.0000.000
211A214HIS00.0250.0187.604-0.640-0.6400.0000.0000.0000.000
212A215VAL00.0040.0036.6660.2010.2010.0000.0000.0000.000
213A216VAL0-0.0060.0008.4150.1460.1460.0000.0000.0000.000
214A217LEU00.0230.01110.8040.0060.0060.0000.0000.0000.000
215A218GLY00.0130.00112.739-0.071-0.0710.0000.0000.0000.000
216A219ALA00.0020.01616.3820.0380.0380.0000.0000.0000.000
217A220SER0-0.009-0.01919.723-0.021-0.0210.0000.0000.0000.000
218A221GLN0-0.049-0.03921.384-0.024-0.0240.0000.0000.0000.000
219A222GLU-1-0.896-0.94424.0870.1020.1020.0000.0000.0000.000
220A223LYS10.7920.88921.847-0.148-0.1480.0000.0000.0000.000
221A224ARG10.9590.99026.447-0.039-0.0390.0000.0000.0000.000
222A225ILE0-0.061-0.03129.433-0.002-0.0020.0000.0000.0000.000
223A226GLU-1-0.938-0.96131.9320.0180.0180.0000.0000.0000.000
224A227LYS11.0150.99134.020-0.018-0.0180.0000.0000.0000.000
225A228ARG10.9530.97932.532-0.062-0.0620.0000.0000.0000.000
226A229THR0-0.0080.00237.145-0.001-0.0010.0000.0000.0000.000
227A230VAL0-0.022-0.01938.3540.0030.0030.0000.0000.0000.000
228A231GLN00.0230.01740.899-0.005-0.0050.0000.0000.0000.000
229A232GLN00.0080.00842.8640.0010.0010.0000.0000.0000.000