Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 72JQK

Calculation Name: 1KZF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KZF

Chain ID: A

ChEMBL ID:

UniProt ID: P54656

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2265297.709011
FMO2-HF: Nuclear repulsion 2186081.077321
FMO2-HF: Total energy -79216.63169
FMO2-MP2: Total energy -79444.555105


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-29.366-18.3878.763-8.075-11.667-0.057
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.009
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].
3A3GLU-1-0.768-0.8602.515-20.063-14.4433.274-4.055-4.839-0.039
4A4LEU0-0.043-0.0314.9300.9841.033-0.001-0.005-0.0420.000
5A5PHE00.0270.0188.0780.3380.3380.0000.0000.0000.000
6A6ASP-1-0.770-0.88510.593-0.882-0.8820.0000.0000.0000.000
7A7VAL00.0020.01513.979-0.023-0.0230.0000.0000.0000.000
8A8SER0-0.008-0.04816.4570.0360.0360.0000.0000.0000.000
9A9TYR00.0360.03120.299-0.038-0.0380.0000.0000.0000.000
10A10GLU-1-0.778-0.87322.977-0.517-0.5170.0000.0000.0000.000
11A11GLU-1-0.807-0.87516.996-0.878-0.8780.0000.0000.0000.000
12A12LEU0-0.0130.00417.649-0.025-0.0250.0000.0000.0000.000
13A13GLN0-0.0180.00120.3220.0030.0030.0000.0000.0000.000
14A14THR0-0.096-0.06522.6720.0360.0360.0000.0000.0000.000
15A15THR0-0.107-0.05218.651-0.062-0.0620.0000.0000.0000.000
16A28PHE0-0.008-0.02915.699-0.001-0.0010.0000.0000.0000.000
17A29SER0-0.007-0.00812.7600.0080.0080.0000.0000.0000.000
18A30ASP-1-0.824-0.89811.946-1.227-1.2270.0000.0000.0000.000
19A31ARG10.8380.88912.9660.7020.7020.0000.0000.0000.000
20A32LEU0-0.0120.00415.8150.0200.0200.0000.0000.0000.000
21A33GLY00.0560.02112.5060.0150.0150.0000.0000.0000.000
22A34TRP0-0.0030.00313.546-0.149-0.1490.0000.0000.0000.000
23A35GLU-1-0.806-0.87714.930-0.705-0.7050.0000.0000.0000.000
24A36VAL0-0.046-0.01414.1100.0550.0550.0000.0000.0000.000
25A37ILE0-0.005-0.00810.9570.0090.0090.0000.0000.0000.000
26A38CYS0-0.018-0.00815.2280.0810.0810.0000.0000.0000.000
27A39SER0-0.103-0.06118.0640.0860.0860.0000.0000.0000.000
28A40GLN0-0.031-0.02913.780-0.115-0.1150.0000.0000.0000.000
29A41GLY00.0350.02217.891-0.043-0.0430.0000.0000.0000.000
30A42MET0-0.079-0.02119.4460.1060.1060.0000.0000.0000.000
31A43GLU-1-0.910-0.94422.531-0.460-0.4600.0000.0000.0000.000
32A44SER00.0170.00225.6570.0170.0170.0000.0000.0000.000
33A45ASP-1-0.799-0.86327.258-0.417-0.4170.0000.0000.0000.000
34A46GLU-1-0.920-0.97130.056-0.328-0.3280.0000.0000.0000.000
35A47PHE0-0.058-0.02628.6780.0190.0190.0000.0000.0000.000
36A48ASP-1-0.779-0.83725.160-0.577-0.5770.0000.0000.0000.000
37A49GLY00.0240.00527.3390.0170.0170.0000.0000.0000.000
38A50PRO0-0.037-0.03626.800-0.024-0.0240.0000.0000.0000.000
39A51GLY0-0.042-0.00826.0440.0290.0290.0000.0000.0000.000
40A52THR0-0.073-0.02823.568-0.004-0.0040.0000.0000.0000.000
41A53ARG10.7970.88416.6420.7680.7680.0000.0000.0000.000
42A54TYR0-0.036-0.06317.8480.0490.0490.0000.0000.0000.000
43A55ILE0-0.0200.00613.160-0.095-0.0950.0000.0000.0000.000
44A56LEU0-0.013-0.01712.1000.1010.1010.0000.0000.0000.000
45A57GLY00.0240.0039.215-0.184-0.1840.0000.0000.0000.000
46A58ILE0-0.030-0.0257.0480.4560.4560.0000.0000.0000.000
47A59CYS0-0.033-0.0142.698-0.962-0.3530.143-0.317-0.4360.001
48A60GLU-1-0.896-0.9563.535-4.433-3.6950.013-0.284-0.467-0.002
49A61GLY0-0.0110.0026.2830.9240.9240.0000.0000.0000.000
50A62GLN0-0.008-0.0048.8020.7020.7020.0000.0000.0000.000
51A63LEU00.0380.0339.502-0.565-0.5650.0000.0000.0000.000
52A64VAL0-0.026-0.0208.5120.3310.3310.0000.0000.0000.000
53A65CYS0-0.079-0.03011.4280.2430.2430.0000.0000.0000.000
54A66SER00.0830.04213.384-0.194-0.1940.0000.0000.0000.000
55A67VAL0-0.049-0.03015.7860.1280.1280.0000.0000.0000.000
56A68ARG10.8080.89118.5570.4390.4390.0000.0000.0000.000
57A69PHE00.006-0.01618.6160.0490.0490.0000.0000.0000.000
58A70THR00.0570.01422.943-0.021-0.0210.0000.0000.0000.000
59A71SER0-0.0020.02226.5390.0110.0110.0000.0000.0000.000
60A72LEU0-0.009-0.01428.6020.0060.0060.0000.0000.0000.000
61A73ASP-1-0.862-0.90431.697-0.271-0.2710.0000.0000.0000.000
62A74ARG10.8300.90030.4110.3030.3030.0000.0000.0000.000
63A75PRO0-0.011-0.01233.0580.0010.0010.0000.0000.0000.000
64A76ASN00.0570.03630.278-0.017-0.0170.0000.0000.0000.000
65A77MET00.019-0.00129.0630.0120.0120.0000.0000.0000.000
66A78ILE0-0.033-0.01730.6280.0200.0200.0000.0000.0000.000
67A79THR0-0.005-0.02434.0040.0120.0120.0000.0000.0000.000
68A80HIS00.0190.03835.4500.0090.0090.0000.0000.0000.000
69A81THR00.0210.01633.4660.0070.0070.0000.0000.0000.000
70A82PHE0-0.004-0.01831.8490.0100.0100.0000.0000.0000.000
71A83GLN00.0140.01637.0850.0190.0190.0000.0000.0000.000
72A84HIS00.0330.00139.1710.0070.0070.0000.0000.0000.000
73A85CYS0-0.071-0.02238.5140.0090.0090.0000.0000.0000.000
74A86PHE0-0.007-0.02535.6130.0050.0050.0000.0000.0000.000
75A87SER00.0520.03939.618-0.001-0.0010.0000.0000.0000.000
76A88ASP-1-0.867-0.90242.020-0.142-0.1420.0000.0000.0000.000
77A89VAL0-0.063-0.03237.2280.0060.0060.0000.0000.0000.000
78A90THR0-0.015-0.01239.347-0.007-0.0070.0000.0000.0000.000
79A91LEU00.0020.00734.2200.0010.0010.0000.0000.0000.000
80A92PRO0-0.025-0.01733.7670.0080.0080.0000.0000.0000.000
81A93ALA0-0.0010.00034.962-0.011-0.0110.0000.0000.0000.000
82A94TYR0-0.049-0.02527.315-0.007-0.0070.0000.0000.0000.000
83A95GLY00.018-0.00129.2420.0130.0130.0000.0000.0000.000
84A96THR0-0.037-0.02224.304-0.022-0.0220.0000.0000.0000.000
85A97GLU-1-0.762-0.85527.119-0.386-0.3860.0000.0000.0000.000
86A98SER00.0220.02222.388-0.028-0.0280.0000.0000.0000.000
87A99SER0-0.036-0.04023.6520.0320.0320.0000.0000.0000.000
88A100ARG10.8080.85222.7460.4640.4640.0000.0000.0000.000
89A101PHE00.0060.01017.711-0.063-0.0630.0000.0000.0000.000
90A102PHE0-0.0190.00116.5590.0910.0910.0000.0000.0000.000
91A103VAL00.024-0.00614.258-0.101-0.1010.0000.0000.0000.000
92A104ASP-1-0.788-0.86114.158-0.753-0.7530.0000.0000.0000.000
93A105LYS10.9560.95214.0060.3130.3130.0000.0000.0000.000
94A106ALA0-0.0410.00214.7400.0460.0460.0000.0000.0000.000
95A107ARG10.8800.91711.3671.3261.3260.0000.0000.0000.000
96A108ALA00.0070.0049.938-0.139-0.1390.0000.0000.0000.000
97A109ARG10.8460.9089.8530.3190.3190.0000.0000.0000.000
98A110ALA0-0.053-0.02711.1890.1460.1460.0000.0000.0000.000
99A111LEU0-0.022-0.0026.1710.2100.2100.0000.0000.0000.000
100A112LEU0-0.007-0.0055.312-0.261-0.2610.0000.0000.0000.000
101A113GLY00.0270.0367.1550.5400.5400.0000.0000.0000.000
102A114GLU-1-0.861-0.95110.514-0.361-0.3610.0000.0000.0000.000
103A115HIS0-0.077-0.04413.4170.0710.0710.0000.0000.0000.000
104A116TYR00.0510.0515.896-0.289-0.2890.0000.0000.0000.000
105A117PRO0-0.0020.01110.323-0.163-0.1630.0000.0000.0000.000
106A118ILE00.021-0.0139.0870.0120.0120.0000.0000.0000.000
107A119SER0-0.001-0.00211.629-0.076-0.0760.0000.0000.0000.000
108A120GLN0-0.063-0.04614.467-0.045-0.0450.0000.0000.0000.000
109A121VAL00.0150.0128.9820.0460.0460.0000.0000.0000.000
110A122LEU00.0080.01012.287-0.062-0.0620.0000.0000.0000.000
111A123PHE00.001-0.01514.4130.0310.0310.0000.0000.0000.000
112A124LEU00.0110.01011.8800.0360.0360.0000.0000.0000.000
113A125ALA00.0040.00512.3820.0240.0240.0000.0000.0000.000
114A126MET0-0.043-0.01214.2410.0270.0270.0000.0000.0000.000
115A127VAL00.0040.01317.8590.0350.0350.0000.0000.0000.000
116A128ASN0-0.041-0.04513.7020.0900.0900.0000.0000.0000.000
117A129TRP00.0060.00315.7400.0810.0810.0000.0000.0000.000
118A130ALA00.0160.00917.1550.0370.0370.0000.0000.0000.000
119A131GLN0-0.025-0.01719.3690.0280.0280.0000.0000.0000.000
120A132ASN0-0.055-0.02816.7380.0370.0370.0000.0000.0000.000
121A133ASN0-0.075-0.03318.1020.0150.0150.0000.0000.0000.000
122A134ALA0-0.0010.01621.6930.0210.0210.0000.0000.0000.000
123A135TYR00.0150.01423.3350.0200.0200.0000.0000.0000.000
124A136GLY00.0310.00924.482-0.006-0.0060.0000.0000.0000.000
125A137ASN0-0.092-0.05726.2180.0130.0130.0000.0000.0000.000
126A138ILE00.0310.03521.674-0.013-0.0130.0000.0000.0000.000
127A139TYR00.0360.01126.1600.0270.0270.0000.0000.0000.000
128A140THR0-0.025-0.02626.200-0.029-0.0290.0000.0000.0000.000
129A141ILE00.0170.02128.3330.0330.0330.0000.0000.0000.000
130A142VAL0-0.0160.00526.436-0.026-0.0260.0000.0000.0000.000
131A143SER00.0940.03228.6810.0250.0250.0000.0000.0000.000
132A144ARG10.9280.95629.7060.1440.1440.0000.0000.0000.000
133A145ALA0-0.033-0.02427.7380.0110.0110.0000.0000.0000.000
134A146MET00.0680.03521.5760.0160.0160.0000.0000.0000.000
135A147LEU00.0440.03625.7150.0000.0000.0000.0000.0000.000
136A148LYS10.9130.96427.6360.1680.1680.0000.0000.0000.000
137A149ILE0-0.017-0.00521.1020.0240.0240.0000.0000.0000.000
138A150LEU00.0800.03622.4140.0130.0130.0000.0000.0000.000
139A151THR0-0.030-0.00324.3450.0190.0190.0000.0000.0000.000
140A152ARG10.8780.92424.3640.1280.1280.0000.0000.0000.000
141A153SER0-0.037-0.01320.4970.0230.0230.0000.0000.0000.000
142A154GLY00.0120.01121.4870.0180.0180.0000.0000.0000.000
143A155TRP00.0130.01121.2810.0050.0050.0000.0000.0000.000
144A156GLN0-0.028-0.00323.9560.0060.0060.0000.0000.0000.000
145A157ILE0-0.043-0.02425.326-0.006-0.0060.0000.0000.0000.000
146A158LYS10.9510.98027.9700.1580.1580.0000.0000.0000.000
147A159VAL0-0.012-0.01531.636-0.017-0.0170.0000.0000.0000.000
148A160ILE0-0.067-0.02533.5120.0150.0150.0000.0000.0000.000
149A161LYS10.8350.87935.8670.1610.1610.0000.0000.0000.000
150A162GLU-1-0.797-0.84536.257-0.152-0.1520.0000.0000.0000.000
151A163ALA00.000-0.00237.5430.0080.0080.0000.0000.0000.000
152A164PHE0-0.003-0.01538.265-0.005-0.0050.0000.0000.0000.000
153A165LEU00.0240.02635.2540.0010.0010.0000.0000.0000.000
154A166THR00.015-0.00739.0360.0040.0040.0000.0000.0000.000
155A167GLU-1-0.866-0.93741.322-0.121-0.1210.0000.0000.0000.000
156A168LYS10.7740.88236.1290.1840.1840.0000.0000.0000.000
157A169GLU-1-0.869-0.91435.737-0.199-0.1990.0000.0000.0000.000
158A170ARG10.8450.91836.7580.1310.1310.0000.0000.0000.000
159A171ILE0-0.027-0.02633.355-0.013-0.0130.0000.0000.0000.000
160A172TYR0-0.064-0.07231.8210.0190.0190.0000.0000.0000.000
161A173LEU00.0630.05431.859-0.020-0.0200.0000.0000.0000.000
162A174LEU0-0.043-0.02627.8730.0210.0210.0000.0000.0000.000
163A175THR00.0180.00829.343-0.007-0.0070.0000.0000.0000.000
164A176LEU0-0.016-0.01823.5270.0220.0220.0000.0000.0000.000
165A177PRO0-0.0170.00525.750-0.021-0.0210.0000.0000.0000.000
166A178ALA00.0460.01122.471-0.019-0.0190.0000.0000.0000.000
167A179GLY00.0300.01923.6740.0030.0030.0000.0000.0000.000
168A180GLN00.001-0.02320.585-0.045-0.0450.0000.0000.0000.000
169A181ASP-1-0.913-0.95922.343-0.015-0.0150.0000.0000.0000.000
170A182ASP-1-0.805-0.91122.513-0.135-0.1350.0000.0000.0000.000
171A183LYS10.8650.95416.4230.2060.2060.0000.0000.0000.000
172A184GLN0-0.017-0.00718.0720.0330.0330.0000.0000.0000.000
173A185GLN0-0.031-0.01119.4710.0270.0270.0000.0000.0000.000
174A186LEU0-0.003-0.01416.9380.0310.0310.0000.0000.0000.000
175A187GLY00.0540.02614.514-0.008-0.0080.0000.0000.0000.000
176A188GLY00.0160.00314.7470.0920.0920.0000.0000.0000.000
177A189ASP-1-0.804-0.85416.9670.0240.0240.0000.0000.0000.000
178A190VAL00.0260.00710.7120.0360.0360.0000.0000.0000.000
179A191VAL00.0080.00612.2290.1110.1110.0000.0000.0000.000
180A192SER0-0.078-0.05213.3570.1030.1030.0000.0000.0000.000
181A193ARG10.7950.87113.9340.0290.0290.0000.0000.0000.000
182A194THR0-0.037-0.0358.9260.0490.0490.0000.0000.0000.000
183A195GLY0-0.0060.01210.3480.2370.2370.0000.0000.0000.000
184A196CYS0-0.065-0.0027.8310.1560.1560.0000.0000.0000.000
185A197PRO00.0550.0108.008-0.305-0.3050.0000.0000.0000.000
186A198PRO00.0240.00210.812-0.087-0.0870.0000.0000.0000.000
187A199VAL00.0270.01711.109-0.125-0.1250.0000.0000.0000.000
188A200ALA0-0.0010.0177.364-0.170-0.1700.0000.0000.0000.000
189A201VAL00.0280.0239.219-0.305-0.3050.0000.0000.0000.000
190A202THR0-0.083-0.06011.699-0.158-0.1580.0000.0000.0000.000
191A203THR0-0.025-0.0229.9220.0480.0480.0000.0000.0000.000
192A204TRP00.0090.00011.872-0.096-0.0960.0000.0000.0000.000
193A205PRO00.0160.0088.1630.1130.1130.0000.0000.0000.000
194A206LEU0-0.062-0.0068.2550.3850.3850.0000.0000.0000.000
195A207THR00.014-0.0082.666-0.643-0.2442.059-0.609-1.8490.001
196A208LEU0-0.041-0.0204.1411.7692.1670.000-0.069-0.3280.000
197A209PRO00.014-0.0092.709-3.131-0.8811.112-1.479-1.884-0.015
198A210VAL00.0050.0172.267-3.449-2.5332.163-1.257-1.822-0.003