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: N91ZQ

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2588901.625104
FMO2-HF: Nuclear repulsion 2503480.045619
FMO2-HF: Total energy -85421.579484
FMO2-MP2: Total energy -85673.153694


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.
-2.4360.5980.67-1.742-1.964-0.005
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 : -0.012 / q_NPA : -0.017
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].
3A6VAL0-0.037-0.0163.111-0.3141.3530.051-0.691-1.0280.001
4A7LEU00.0170.0165.0640.1840.231-0.001-0.009-0.0360.000
5A8SER0-0.007-0.0047.8580.2650.2650.0000.0000.0000.000
6A9SER0-0.073-0.05310.101-0.042-0.0420.0000.0000.0000.000
7A10SER00.0720.01513.125-0.054-0.0540.0000.0000.0000.000
8A11LYS10.9991.00215.432-0.133-0.1330.0000.0000.0000.000
9A12GLU-1-0.881-0.92611.1460.1090.1090.0000.0000.0000.000
10A13ALA00.0440.01612.516-0.056-0.0560.0000.0000.0000.000
11A14ALA0-0.0040.00213.801-0.040-0.0400.0000.0000.0000.000
12A15LYS10.9330.96815.7620.0750.0750.0000.0000.0000.000
13A16LEU0-0.063-0.02512.113-0.023-0.0230.0000.0000.0000.000
14A17ILE0-0.035-0.00716.847-0.010-0.0100.0000.0000.0000.000
15A18HIS0-0.047-0.02919.3980.0240.0240.0000.0000.0000.000
16A19ASP-1-0.810-0.91323.285-0.069-0.0690.0000.0000.0000.000
17A20GLY0-0.047-0.01227.078-0.006-0.0060.0000.0000.0000.000
18A21ASP-1-0.851-0.90222.173-0.170-0.1700.0000.0000.0000.000
19A22THR0-0.057-0.02325.0230.0190.0190.0000.0000.0000.000
20A23LEU0-0.006-0.00920.721-0.015-0.0150.0000.0000.0000.000
21A24ILE0-0.012-0.00422.0170.0160.0160.0000.0000.0000.000
22A25ALA00.0010.01221.216-0.009-0.0090.0000.0000.0000.000
23A26GLY0-0.0100.00321.1370.0040.0040.0000.0000.0000.000
24A27GLY00.003-0.00122.3820.0050.0050.0000.0000.0000.000
25A28PHE0-0.082-0.04324.763-0.009-0.0090.0000.0000.0000.000
26A29GLY00.0530.02728.3230.0080.0080.0000.0000.0000.000
27A30LEU0-0.007-0.01628.029-0.001-0.0010.0000.0000.0000.000
28A31CYS0-0.059-0.01326.4840.0140.0140.0000.0000.0000.000
29A32GLY00.0510.00922.342-0.008-0.0080.0000.0000.0000.000
30A33ILE00.0180.03222.274-0.014-0.0140.0000.0000.0000.000
31A34PRO00.0060.00918.4350.0190.0190.0000.0000.0000.000
32A35GLU-1-0.880-0.94220.0860.0960.0960.0000.0000.0000.000
33A36GLN00.0260.01318.066-0.006-0.0060.0000.0000.0000.000
34A37LEU00.0380.00814.632-0.008-0.0080.0000.0000.0000.000
35A38ILE0-0.033-0.01018.800-0.018-0.0180.0000.0000.0000.000
36A39LEU0-0.0120.01122.403-0.009-0.0090.0000.0000.0000.000
37A40SER00.003-0.00119.1410.0020.0020.0000.0000.0000.000
38A41ILE00.0070.00319.952-0.011-0.0110.0000.0000.0000.000
39A42ARG10.8550.92122.539-0.016-0.0160.0000.0000.0000.000
40A43ASP-1-0.969-0.98423.3290.0330.0330.0000.0000.0000.000
41A44GLN0-0.132-0.07020.595-0.010-0.0100.0000.0000.0000.000
42A45GLY0-0.0100.00823.888-0.007-0.0070.0000.0000.0000.000
43A46VAL0-0.0420.00423.792-0.001-0.0010.0000.0000.0000.000
44A47LYS10.8530.90126.3030.0720.0720.0000.0000.0000.000
45A48ASP-1-0.825-0.91128.891-0.067-0.0670.0000.0000.0000.000
46A49LEU00.0430.03725.166-0.005-0.0050.0000.0000.0000.000
47A50THR00.0280.02728.3740.0110.0110.0000.0000.0000.000
48A51VAL0-0.029-0.02926.666-0.008-0.0080.0000.0000.0000.000
49A52VAL00.0020.00126.4860.0070.0070.0000.0000.0000.000
50A53SER0-0.005-0.02325.659-0.001-0.0010.0000.0000.0000.000
51A54ASN00.0240.02827.582-0.002-0.0020.0000.0000.0000.000
52A55ASN00.029-0.00229.5260.0040.0040.0000.0000.0000.000
53A56CYS00.0230.01429.728-0.005-0.0050.0000.0000.0000.000
54A57GLY0-0.043-0.00629.8130.0020.0020.0000.0000.0000.000
55A58VAL0-0.002-0.00130.3930.0000.0000.0000.0000.0000.000
56A59ASP-1-0.861-0.95732.5290.0110.0110.0000.0000.0000.000
57A60ASP-1-0.861-0.89733.3670.0360.0360.0000.0000.0000.000
58A61TRP00.024-0.00325.280-0.001-0.0010.0000.0000.0000.000
59A62GLY00.0660.03226.057-0.005-0.0050.0000.0000.0000.000
60A63LEU00.0710.01625.265-0.001-0.0010.0000.0000.0000.000
61A64GLY00.0160.01928.046-0.006-0.0060.0000.0000.0000.000
62A65LEU0-0.007-0.00427.090-0.002-0.0020.0000.0000.0000.000
63A66LEU00.0500.02525.153-0.001-0.0010.0000.0000.0000.000
64A67LEU0-0.0040.01329.454-0.003-0.0030.0000.0000.0000.000
65A68ALA0-0.024-0.01932.921-0.002-0.0020.0000.0000.0000.000
66A69ASN0-0.095-0.04629.2610.0050.0050.0000.0000.0000.000
67A70LYS10.9170.96032.9170.0120.0120.0000.0000.0000.000
68A71GLN00.0150.01326.4980.0060.0060.0000.0000.0000.000
69A72ILE0-0.046-0.01929.586-0.007-0.0070.0000.0000.0000.000
70A73LYS10.9030.95631.7410.0640.0640.0000.0000.0000.000
71A74LYS10.8970.94432.5510.0580.0580.0000.0000.0000.000
72A75MET0-0.0260.00831.066-0.003-0.0030.0000.0000.0000.000
73A76ILE0-0.051-0.02530.8840.0010.0010.0000.0000.0000.000
74A77ALA00.0370.01330.865-0.001-0.0010.0000.0000.0000.000
75A78SER0-0.055-0.02332.9160.0010.0010.0000.0000.0000.000
76A79TYR0-0.040-0.02134.5520.0010.0010.0000.0000.0000.000
77A80VAL00.0200.02134.7380.0000.0000.0000.0000.0000.000
78A81GLY00.0000.00236.0710.0020.0020.0000.0000.0000.000
79A82GLU-1-0.886-0.94538.2030.0110.0110.0000.0000.0000.000
80A83ASN00.0690.03834.8360.0010.0010.0000.0000.0000.000
81A84LYS10.9930.99738.731-0.007-0.0070.0000.0000.0000.000
82A85ILE0-0.040-0.02637.198-0.001-0.0010.0000.0000.0000.000
83A86PHE00.0270.00334.844-0.003-0.0030.0000.0000.0000.000
84A87GLU-1-0.893-0.96238.742-0.012-0.0120.0000.0000.0000.000
85A88ARG10.7490.85840.7780.0120.0120.0000.0000.0000.000
86A89GLN0-0.050-0.02036.179-0.003-0.0030.0000.0000.0000.000
87A90PHE00.0270.01840.453-0.002-0.0020.0000.0000.0000.000
88A91LEU0-0.025-0.01341.659-0.002-0.0020.0000.0000.0000.000
89A92SER0-0.051-0.02543.1550.0010.0010.0000.0000.0000.000
90A93GLY0-0.053-0.01443.650-0.001-0.0010.0000.0000.0000.000
91A94GLU-1-0.841-0.90539.144-0.021-0.0210.0000.0000.0000.000
92A95LEU0-0.0200.00034.971-0.002-0.0020.0000.0000.0000.000
93A96GLU-1-0.872-0.94236.614-0.043-0.0430.0000.0000.0000.000
94A97VAL0-0.032-0.02836.412-0.002-0.0020.0000.0000.0000.000
95A98GLU-1-0.823-0.90735.341-0.052-0.0520.0000.0000.0000.000
96A99LEU00.003-0.01035.697-0.001-0.0010.0000.0000.0000.000
97A100VAL0-0.011-0.00634.140-0.001-0.0010.0000.0000.0000.000
98A101PRO00.0080.00235.8710.0030.0030.0000.0000.0000.000
99A102GLN00.0640.01732.491-0.001-0.0010.0000.0000.0000.000
100A103GLY0-0.0070.00232.575-0.002-0.0020.0000.0000.0000.000
101A104THR00.002-0.00233.066-0.002-0.0020.0000.0000.0000.000
102A105LEU0-0.0060.00029.732-0.005-0.0050.0000.0000.0000.000
103A106ALA00.011-0.00628.352-0.006-0.0060.0000.0000.0000.000
104A107GLU-1-0.827-0.89828.259-0.059-0.0590.0000.0000.0000.000
105A108ARG10.8080.90829.9180.0500.0500.0000.0000.0000.000
106A109ILE00.0000.01624.069-0.008-0.0080.0000.0000.0000.000
107A110ARG10.8940.92524.9100.0490.0490.0000.0000.0000.000
108A111ALA0-0.029-0.00925.682-0.010-0.0100.0000.0000.0000.000
109A112GLY00.0090.00926.474-0.005-0.0050.0000.0000.0000.000
110A113GLY00.0300.01022.569-0.013-0.0130.0000.0000.0000.000
111A114ALA0-0.108-0.04022.682-0.011-0.0110.0000.0000.0000.000
112A115GLY0-0.0090.00925.1050.0020.0020.0000.0000.0000.000
113A116ILE0-0.058-0.02726.8210.0080.0080.0000.0000.0000.000
114A117PRO00.0330.01230.1970.0010.0010.0000.0000.0000.000
115A118GLY00.011-0.00732.0840.0030.0030.0000.0000.0000.000
116A119PHE0-0.0230.00332.4180.0010.0010.0000.0000.0000.000
117A120TYR00.0320.01336.2240.0010.0010.0000.0000.0000.000
118A121THR00.0270.00737.8920.0020.0020.0000.0000.0000.000
119A122ALA00.0200.00339.9930.0000.0000.0000.0000.0000.000
120A123THR0-0.038-0.01738.7880.0030.0030.0000.0000.0000.000
121A124GLY00.0320.01141.483-0.002-0.0020.0000.0000.0000.000
122A125VAL0-0.005-0.00643.3860.0000.0000.0000.0000.0000.000
123A126GLY0-0.010-0.00446.2170.0020.0020.0000.0000.0000.000
124A127THR00.0030.01444.5850.0020.0020.0000.0000.0000.000
125A128SER00.0730.02845.972-0.001-0.0010.0000.0000.0000.000
126A129ILE0-0.013-0.00340.410-0.002-0.0020.0000.0000.0000.000
127A130ALA0-0.022-0.01242.365-0.003-0.0030.0000.0000.0000.000
128A131GLU-1-0.884-0.93944.735-0.028-0.0280.0000.0000.0000.000
129A132GLY0-0.028-0.01143.899-0.002-0.0020.0000.0000.0000.000
130A133LYS10.7740.89038.8710.0360.0360.0000.0000.0000.000
131A134GLU-1-0.762-0.84941.635-0.047-0.0470.0000.0000.0000.000
132A135HIS0-0.024-0.00943.8870.0020.0020.0000.0000.0000.000
133A136LYS10.9060.96044.3140.0350.0350.0000.0000.0000.000
134A137THR0-0.018-0.01146.7530.0010.0010.0000.0000.0000.000
135A138PHE0-0.019-0.01142.819-0.001-0.0010.0000.0000.0000.000
136A139GLY00.0250.01147.5900.0010.0010.0000.0000.0000.000
137A140GLY0-0.003-0.00749.9730.0010.0010.0000.0000.0000.000
138A141ARG10.9630.98544.5290.0190.0190.0000.0000.0000.000
139A142THR00.017-0.00247.653-0.001-0.0010.0000.0000.0000.000
140A143TYR0-0.036-0.00442.2800.0020.0020.0000.0000.0000.000
141A144VAL00.0510.02441.044-0.001-0.0010.0000.0000.0000.000
142A145LEU0-0.066-0.02938.048-0.001-0.0010.0000.0000.0000.000
143A146GLU-1-0.771-0.88635.447-0.043-0.0430.0000.0000.0000.000
144A147ARG10.8510.87533.8900.0570.0570.0000.0000.0000.000
145A148GLY0-0.002-0.00129.9100.0020.0020.0000.0000.0000.000
146A149ILE0-0.085-0.04326.9010.0000.0000.0000.0000.0000.000
147A150THR00.033-0.00223.3620.0000.0000.0000.0000.0000.000
148A151GLY00.0150.00523.0350.0130.0130.0000.0000.0000.000
149A152ASP-1-0.832-0.89121.553-0.193-0.1930.0000.0000.0000.000
150A153VAL00.0150.00216.964-0.034-0.0340.0000.0000.0000.000
151A154ALA0-0.0060.01017.7530.0350.0350.0000.0000.0000.000
152A155ILE0-0.031-0.01916.811-0.018-0.0180.0000.0000.0000.000
153A156VAL0-0.001-0.01515.2440.0200.0200.0000.0000.0000.000
154A157LYS10.7980.90416.043-0.125-0.1250.0000.0000.0000.000
155A158ALA0-0.021-0.02614.192-0.017-0.0170.0000.0000.0000.000
156A159TRP0-0.044-0.03916.3520.0210.0210.0000.0000.0000.000
157A160LYS10.8300.89213.477-0.292-0.2920.0000.0000.0000.000
158A161ALA00.0670.0289.388-0.088-0.0880.0000.0000.0000.000
159A162ASP-1-0.723-0.8327.9320.4190.4190.0000.0000.0000.000
160A163THR0-0.005-0.0052.473-0.882-0.4800.470-0.369-0.504-0.001
161A164MET0-0.001-0.0113.159-2.005-1.0870.150-0.673-0.396-0.005
162A165GLY0-0.009-0.0045.640-0.288-0.2880.0000.0000.0000.000
163A166ASN0-0.020-0.0187.998-0.094-0.0940.0000.0000.0000.000
164A167LEU00.0040.01110.8980.0940.0940.0000.0000.0000.000
165A168ILE00.0410.03313.511-0.023-0.0230.0000.0000.0000.000
166A169PHE00.0490.00316.6440.0210.0210.0000.0000.0000.000
167A170ARG10.9890.98419.501-0.126-0.1260.0000.0000.0000.000
168A171LYS10.9120.94822.528-0.083-0.0830.0000.0000.0000.000
169A172THR00.0470.01325.628-0.002-0.0020.0000.0000.0000.000
170A173ALA00.0180.01322.897-0.008-0.0080.0000.0000.0000.000
171A174ARG10.9510.99321.828-0.030-0.0300.0000.0000.0000.000
172A175ASN00.011-0.00422.838-0.016-0.0160.0000.0000.0000.000
173A176PHE00.0820.02224.414-0.002-0.0020.0000.0000.0000.000
174A177ASN00.0040.01118.994-0.022-0.0220.0000.0000.0000.000
175A178PRO0-0.032-0.01818.751-0.018-0.0180.0000.0000.0000.000
176A179ILE00.0120.00019.739-0.017-0.0170.0000.0000.0000.000
177A180ALA00.0300.01020.714-0.014-0.0140.0000.0000.0000.000
178A181ALA0-0.041-0.02715.742-0.020-0.0200.0000.0000.0000.000
179A182MET0-0.060-0.02217.070-0.033-0.0330.0000.0000.0000.000
180A183ALA00.0280.02519.221-0.016-0.0160.0000.0000.0000.000
181A184GLY0-0.025-0.00318.5690.0110.0110.0000.0000.0000.000
182A185LYS10.8410.91017.5810.2060.2060.0000.0000.0000.000
183A186ILE0-0.032-0.01213.458-0.070-0.0700.0000.0000.0000.000
184A187THR00.0300.01713.7050.0710.0710.0000.0000.0000.000
185A188ILE0-0.009-0.00811.970-0.104-0.1040.0000.0000.0000.000
186A189ALA0-0.0070.00010.9830.0630.0630.0000.0000.0000.000
187A190GLU-1-0.759-0.88111.6900.1690.1690.0000.0000.0000.000
188A191ALA00.003-0.00311.865-0.032-0.0320.0000.0000.0000.000
189A192GLU-1-0.874-0.91413.9070.2070.2070.0000.0000.0000.000
190A193GLU-1-0.837-0.90713.8970.3950.3950.0000.0000.0000.000
191A194ILE00.003-0.0027.143-0.040-0.0400.0000.0000.0000.000
192A195VAL0-0.0060.0019.9870.0730.0730.0000.0000.0000.000
193A196GLU-1-0.901-0.9607.4621.1711.1710.0000.0000.0000.000
194A197ALA0-0.065-0.0486.644-0.203-0.2030.0000.0000.0000.000
195A198GLY00.0190.0048.470-0.032-0.0320.0000.0000.0000.000
196A199GLU-1-0.911-0.94811.7770.3250.3250.0000.0000.0000.000
197A200LEU0-0.123-0.05611.663-0.049-0.0490.0000.0000.0000.000
198A201ASP-1-0.803-0.90314.5340.0910.0910.0000.0000.0000.000
199A202PRO00.013-0.02015.918-0.010-0.0100.0000.0000.0000.000
200A203ASP-1-0.926-0.95517.2060.0190.0190.0000.0000.0000.000
201A204HIS0-0.160-0.06718.3630.0070.0070.0000.0000.0000.000
202A205ILE0-0.063-0.02213.275-0.011-0.0110.0000.0000.0000.000
203A206HIS0-0.056-0.02516.876-0.019-0.0190.0000.0000.0000.000
204A207THR0-0.0150.00014.382-0.011-0.0110.0000.0000.0000.000
205A208PRO00.0260.01914.0190.0090.0090.0000.0000.0000.000
206A209GLY00.0770.02510.181-0.023-0.0230.0000.0000.0000.000
207A210ILE0-0.072-0.03210.705-0.122-0.1220.0000.0000.0000.000
208A211TYR0-0.011-0.00812.666-0.036-0.0360.0000.0000.0000.000
209A212VAL00.0250.0299.4320.0180.0180.0000.0000.0000.000
210A213GLN0-0.001-0.0159.228-0.086-0.0860.0000.0000.0000.000
211A214HIS00.0000.0107.610-0.556-0.5560.0000.0000.0000.000
212A215VAL0-0.003-0.0066.7250.1490.1490.0000.0000.0000.000
213A216VAL00.0010.0018.4190.1830.1830.0000.0000.0000.000
214A217LEU00.0270.01710.808-0.016-0.0160.0000.0000.0000.000
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