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: MVM4Z

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2263184.776063
FMO2-HF: Nuclear repulsion 2183968.440353
FMO2-HF: Total energy -79216.33571
FMO2-MP2: Total energy -79444.342833


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.
-29.691-18.669.198-8.18-12.047-0.059
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 : -0.032 / q_NPA : -0.014
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-1-0.767-0.8702.529-20.776-14.1552.114-4.006-4.729-0.036
4A4LEU0-0.057-0.0295.0090.9450.991-0.001-0.004-0.0400.000
5A5PHE00.0310.0178.2430.2910.2910.0000.0000.0000.000
6A6ASP-1-0.757-0.88410.960-0.866-0.8660.0000.0000.0000.000
7A7VAL0-0.0210.00413.813-0.038-0.0380.0000.0000.0000.000
8A8SER0-0.047-0.07116.3200.0570.0570.0000.0000.0000.000
9A9TYR00.0600.04020.053-0.039-0.0390.0000.0000.0000.000
10A10GLU-1-0.783-0.87722.699-0.531-0.5310.0000.0000.0000.000
11A11GLU-1-0.799-0.88517.094-0.879-0.8790.0000.0000.0000.000
12A12LEU0-0.0220.00717.517-0.040-0.0400.0000.0000.0000.000
13A13GLN0-0.0310.00320.3270.0110.0110.0000.0000.0000.000
14A14THR0-0.123-0.08622.7580.0340.0340.0000.0000.0000.000
15A15THR0-0.101-0.05118.764-0.066-0.0660.0000.0000.0000.000
16A28PHE0-0.027-0.03715.4930.0110.0110.0000.0000.0000.000
17A29SER0-0.004-0.00812.2930.0310.0310.0000.0000.0000.000
18A30ASP-1-0.830-0.90012.200-1.352-1.3520.0000.0000.0000.000
19A31ARG10.8680.91313.3730.7200.7200.0000.0000.0000.000
20A32LEU0-0.002-0.00215.966-0.004-0.0040.0000.0000.0000.000
21A33GLY00.0620.02712.7560.0070.0070.0000.0000.0000.000
22A34TRP00.0190.00613.646-0.143-0.1430.0000.0000.0000.000
23A35GLU-1-0.829-0.89115.310-0.701-0.7010.0000.0000.0000.000
24A36VAL0-0.039-0.01514.3630.0730.0730.0000.0000.0000.000
25A37ILE0-0.012-0.00411.1200.0090.0090.0000.0000.0000.000
26A38CYS0-0.012-0.00715.3810.0760.0760.0000.0000.0000.000
27A39SER0-0.099-0.04918.3280.0900.0900.0000.0000.0000.000
28A40GLN0-0.043-0.03513.901-0.098-0.0980.0000.0000.0000.000
29A41GLY00.0100.01318.169-0.021-0.0210.0000.0000.0000.000
30A42MET0-0.081-0.02319.6050.1020.1020.0000.0000.0000.000
31A43GLU-1-0.916-0.94922.608-0.453-0.4530.0000.0000.0000.000
32A44SER00.021-0.00125.8100.0130.0130.0000.0000.0000.000
33A45ASP-1-0.779-0.84927.236-0.403-0.4030.0000.0000.0000.000
34A46GLU-1-0.930-0.97730.049-0.319-0.3190.0000.0000.0000.000
35A47PHE0-0.075-0.03528.7100.0160.0160.0000.0000.0000.000
36A48ASP-1-0.785-0.84624.972-0.562-0.5620.0000.0000.0000.000
37A49GLY00.0380.00327.0350.0160.0160.0000.0000.0000.000
38A50PRO0-0.039-0.02726.701-0.022-0.0220.0000.0000.0000.000
39A51GLY0-0.0300.00125.9290.0330.0330.0000.0000.0000.000
40A52THR0-0.086-0.03523.285-0.002-0.0020.0000.0000.0000.000
41A53ARG10.8270.91616.9190.7420.7420.0000.0000.0000.000
42A54TYR0-0.040-0.06217.5670.0440.0440.0000.0000.0000.000
43A55ILE0-0.0080.01612.903-0.078-0.0780.0000.0000.0000.000
44A56LEU0-0.004-0.00911.9040.1090.1090.0000.0000.0000.000
45A57GLY00.0410.0119.245-0.171-0.1710.0000.0000.0000.000
46A58ILE0-0.046-0.0367.3140.4020.4020.0000.0000.0000.000
47A59CYS0-0.033-0.0182.816-1.027-0.4240.085-0.302-0.3850.000
48A60GLU-1-0.897-0.9503.683-3.662-3.0120.007-0.211-0.446-0.001
49A61GLY0-0.010-0.0026.3700.9200.9200.0000.0000.0000.000
50A62GLN00.001-0.0028.6610.7110.7110.0000.0000.0000.000
51A63LEU00.0490.0389.520-0.523-0.5230.0000.0000.0000.000
52A64VAL0-0.027-0.0148.7810.3430.3430.0000.0000.0000.000
53A65CYS0-0.074-0.02711.5750.2200.2200.0000.0000.0000.000
54A66SER00.0880.03813.576-0.188-0.1880.0000.0000.0000.000
55A67VAL0-0.052-0.02415.8640.1310.1310.0000.0000.0000.000
56A68ARG10.8180.89818.4010.4140.4140.0000.0000.0000.000
57A69PHE00.017-0.00718.4560.0610.0610.0000.0000.0000.000
58A70THR00.0600.02722.999-0.025-0.0250.0000.0000.0000.000
59A71SER0-0.010-0.00226.5300.0080.0080.0000.0000.0000.000
60A72LEU0-0.003-0.00628.8160.0070.0070.0000.0000.0000.000
61A73ASP-1-0.871-0.91631.741-0.263-0.2630.0000.0000.0000.000
62A74ARG10.8320.90830.6810.2930.2930.0000.0000.0000.000
63A75PRO0-0.004-0.01133.0330.0020.0020.0000.0000.0000.000
64A76ASN00.0560.03330.478-0.016-0.0160.0000.0000.0000.000
65A77MET00.0160.00029.3150.0120.0120.0000.0000.0000.000
66A78ILE0-0.028-0.01030.8510.0200.0200.0000.0000.0000.000
67A79THR00.005-0.02034.2050.0130.0130.0000.0000.0000.000
68A80HIS00.0100.02435.4970.0090.0090.0000.0000.0000.000
69A81THR00.0260.02033.8460.0070.0070.0000.0000.0000.000
70A82PHE0-0.026-0.02732.0750.0110.0110.0000.0000.0000.000
71A83GLN00.0110.02037.2520.0180.0180.0000.0000.0000.000
72A84HIS00.025-0.00839.6140.0060.0060.0000.0000.0000.000
73A85CYS0-0.084-0.02938.5690.0090.0090.0000.0000.0000.000
74A86PHE00.005-0.02135.5220.0070.0070.0000.0000.0000.000
75A87SER00.0570.04539.6740.0000.0000.0000.0000.0000.000
76A88ASP-1-0.890-0.91842.113-0.131-0.1310.0000.0000.0000.000
77A89VAL0-0.055-0.02737.2310.0060.0060.0000.0000.0000.000
78A90THR0-0.019-0.00339.962-0.004-0.0040.0000.0000.0000.000
79A91LEU0-0.010-0.00434.2660.0000.0000.0000.0000.0000.000
80A92PRO0-0.019-0.01433.4970.0080.0080.0000.0000.0000.000
81A93ALA00.0040.00335.363-0.009-0.0090.0000.0000.0000.000
82A94TYR0-0.043-0.02527.493-0.011-0.0110.0000.0000.0000.000
83A95GLY00.027-0.00129.4180.0120.0120.0000.0000.0000.000
84A96THR0-0.0100.01024.278-0.023-0.0230.0000.0000.0000.000
85A97GLU-1-0.769-0.88427.056-0.347-0.3470.0000.0000.0000.000
86A98SER00.0060.01122.410-0.025-0.0250.0000.0000.0000.000
87A99SER0-0.026-0.03323.5230.0310.0310.0000.0000.0000.000
88A100ARG10.8190.86622.6980.4530.4530.0000.0000.0000.000
89A101PHE0-0.0140.00217.545-0.063-0.0630.0000.0000.0000.000
90A102PHE0-0.0020.00116.2510.0830.0830.0000.0000.0000.000
91A103VAL00.0230.00414.254-0.096-0.0960.0000.0000.0000.000
92A104ASP-1-0.817-0.88214.432-0.678-0.6780.0000.0000.0000.000
93A105LYS10.9600.95414.2570.2780.2780.0000.0000.0000.000
94A106ALA0-0.035-0.00414.9600.0330.0330.0000.0000.0000.000
95A107ARG10.8740.91811.3131.2671.2670.0000.0000.0000.000
96A108ALA00.0120.00310.193-0.128-0.1280.0000.0000.0000.000
97A109ARG10.8470.93910.1050.2850.2850.0000.0000.0000.000
98A110ALA0-0.067-0.02911.4590.1260.1260.0000.0000.0000.000
99A111LEU0-0.014-0.0046.4730.2220.2220.0000.0000.0000.000
100A112LEU0-0.023-0.0215.361-0.029-0.0290.0000.0000.0000.000
101A113GLY00.0290.0327.6210.4190.4190.0000.0000.0000.000
102A114GLU-1-0.856-0.95410.809-0.299-0.2990.0000.0000.0000.000
103A115HIS0-0.065-0.03913.3000.0700.0700.0000.0000.0000.000
104A116TYR00.0910.0676.402-0.244-0.2440.0000.0000.0000.000
105A117PRO0-0.028-0.00210.711-0.154-0.1540.0000.0000.0000.000
106A118ILE00.042-0.0079.1490.0030.0030.0000.0000.0000.000
107A119SER0-0.005-0.00511.700-0.081-0.0810.0000.0000.0000.000
108A120GLN0-0.052-0.04214.495-0.061-0.0610.0000.0000.0000.000
109A121VAL00.0110.0168.9430.0440.0440.0000.0000.0000.000
110A122LEU00.0150.01012.318-0.063-0.0630.0000.0000.0000.000
111A123PHE0-0.005-0.01614.0990.0260.0260.0000.0000.0000.000
112A124LEU00.0180.01311.7110.0270.0270.0000.0000.0000.000
113A125ALA00.0050.00012.1080.0220.0220.0000.0000.0000.000
114A126MET0-0.047-0.00813.9090.0170.0170.0000.0000.0000.000
115A127VAL00.0060.01917.5900.0310.0310.0000.0000.0000.000
116A128ASN0-0.043-0.04313.1790.0850.0850.0000.0000.0000.000
117A129TRP0-0.010-0.00215.9780.0640.0640.0000.0000.0000.000
118A130ALA00.0220.00917.3460.0350.0350.0000.0000.0000.000
119A131GLN0-0.026-0.01819.8130.0290.0290.0000.0000.0000.000
120A132ASN0-0.078-0.02817.3130.0520.0520.0000.0000.0000.000
121A133ASN0-0.062-0.04718.6230.0010.0010.0000.0000.0000.000
122A134ALA0-0.0150.01722.1680.0180.0180.0000.0000.0000.000
123A135TYR00.0210.01923.5050.0140.0140.0000.0000.0000.000
124A136GLY00.0160.00624.8460.0000.0000.0000.0000.0000.000
125A137ASN0-0.065-0.04826.0040.0110.0110.0000.0000.0000.000
126A138ILE00.0120.02121.471-0.014-0.0140.0000.0000.0000.000
127A139TYR00.0330.01526.0440.0290.0290.0000.0000.0000.000
128A140THR0-0.022-0.01925.716-0.031-0.0310.0000.0000.0000.000
129A141ILE00.0380.03128.2060.0310.0310.0000.0000.0000.000
130A142VAL0-0.025-0.00326.124-0.023-0.0230.0000.0000.0000.000
131A143SER00.1010.03428.1030.0260.0260.0000.0000.0000.000
132A144ARG10.9640.97529.4260.1300.1300.0000.0000.0000.000
133A145ALA0-0.041-0.02927.5200.0100.0100.0000.0000.0000.000
134A146MET00.0700.03521.4900.0150.0150.0000.0000.0000.000
135A147LEU00.0400.03925.6400.0030.0030.0000.0000.0000.000
136A148LYS10.9180.96327.7130.1440.1440.0000.0000.0000.000
137A149ILE0-0.027-0.01221.2590.0230.0230.0000.0000.0000.000
138A150LEU00.0650.03122.3030.0170.0170.0000.0000.0000.000
139A151THR0-0.0230.00124.3370.0210.0210.0000.0000.0000.000
140A152ARG10.8770.92824.5700.0970.0970.0000.0000.0000.000
141A153SER0-0.041-0.02120.6190.0210.0210.0000.0000.0000.000
142A154GLY00.0130.01621.7720.0200.0200.0000.0000.0000.000
143A155TRP00.0200.00320.7890.0020.0020.0000.0000.0000.000
144A156GLN0-0.040-0.01423.7590.0020.0020.0000.0000.0000.000
145A157ILE0-0.027-0.01325.466-0.007-0.0070.0000.0000.0000.000
146A158LYS10.9600.98427.9880.1410.1410.0000.0000.0000.000
147A159VAL0-0.010-0.01631.566-0.016-0.0160.0000.0000.0000.000
148A160ILE0-0.072-0.03133.2500.0140.0140.0000.0000.0000.000
149A161LYS10.8620.89535.5940.1480.1480.0000.0000.0000.000
150A162GLU-1-0.809-0.84436.094-0.135-0.1350.0000.0000.0000.000
151A163ALA00.003-0.00437.1870.0070.0070.0000.0000.0000.000
152A164PHE00.007-0.01538.111-0.004-0.0040.0000.0000.0000.000
153A165LEU00.0070.02134.9990.0000.0000.0000.0000.0000.000
154A166THR00.011-0.02138.7530.0050.0050.0000.0000.0000.000
155A167GLU-1-0.875-0.93341.171-0.108-0.1080.0000.0000.0000.000
156A168LYS10.8040.89536.2420.1680.1680.0000.0000.0000.000
157A169GLU-1-0.906-0.92935.701-0.184-0.1840.0000.0000.0000.000
158A170ARG10.8550.92636.2660.1210.1210.0000.0000.0000.000
159A171ILE0-0.024-0.01632.948-0.012-0.0120.0000.0000.0000.000
160A172TYR0-0.059-0.07031.8080.0190.0190.0000.0000.0000.000
161A173LEU00.0600.05331.743-0.019-0.0190.0000.0000.0000.000
162A174LEU0-0.043-0.02927.7650.0210.0210.0000.0000.0000.000
163A175THR00.0280.02029.051-0.009-0.0090.0000.0000.0000.000
164A176LEU0-0.045-0.03723.0650.0200.0200.0000.0000.0000.000
165A177PRO0-0.0240.00825.239-0.020-0.0200.0000.0000.0000.000
166A178ALA00.0400.01122.099-0.012-0.0120.0000.0000.0000.000
167A179GLY00.0360.02223.290-0.002-0.0020.0000.0000.0000.000
168A180GLN00.003-0.02420.556-0.036-0.0360.0000.0000.0000.000
169A181ASP-1-0.911-0.96422.3500.0130.0130.0000.0000.0000.000
170A182ASP-1-0.810-0.90722.413-0.100-0.1000.0000.0000.0000.000
171A183LYS10.8800.95216.0230.1300.1300.0000.0000.0000.000
172A184GLN0-0.041-0.02217.8470.0320.0320.0000.0000.0000.000
173A185GLN0-0.024-0.00119.3130.0330.0330.0000.0000.0000.000
174A186LEU0-0.015-0.01916.8710.0260.0260.0000.0000.0000.000
175A187GLY00.0570.02514.5360.0110.0110.0000.0000.0000.000
176A188GLY00.001-0.00514.8490.0970.0970.0000.0000.0000.000
177A189ASP-1-0.800-0.87017.1200.0910.0910.0000.0000.0000.000
178A190VAL00.0380.01010.8300.0330.0330.0000.0000.0000.000
179A191VAL00.0080.01112.5540.1170.1170.0000.0000.0000.000
180A192SER0-0.073-0.03113.6120.1020.1020.0000.0000.0000.000
181A193ARG10.8090.89014.139-0.045-0.0450.0000.0000.0000.000
182A194THR0-0.048-0.0429.0890.0550.0550.0000.0000.0000.000
183A195GLY0-0.031-0.00310.4970.2400.2400.0000.0000.0000.000
184A196CYS0-0.0500.0037.9170.1340.1340.0000.0000.0000.000
185A197PRO00.0460.0068.054-0.296-0.2960.0000.0000.0000.000
186A198PRO00.0480.00710.747-0.092-0.0920.0000.0000.0000.000
187A199VAL00.0170.00911.281-0.124-0.1240.0000.0000.0000.000
188A200ALA00.0100.0167.353-0.134-0.1340.0000.0000.0000.000
189A201VAL00.0160.0169.272-0.299-0.2990.0000.0000.0000.000
190A202THR0-0.087-0.05611.535-0.165-0.1650.0000.0000.0000.000
191A203THR0-0.020-0.00610.0770.0440.0440.0000.0000.0000.000
192A204TRP00.0180.01112.040-0.112-0.1120.0000.0000.0000.000
193A205PRO00.0310.0038.4610.1210.1210.0000.0000.0000.000
194A206LEU0-0.063-0.0118.2370.3410.3410.0000.0000.0000.000
195A207THR00.006-0.0072.961-0.748-0.2401.352-0.450-1.4100.000
196A208LEU0-0.048-0.0313.7541.5672.0550.003-0.109-0.3820.000
197A209PRO00.0060.0022.439-2.717-1.2453.078-1.783-2.766-0.019
198A210VAL00.0060.0132.197-3.781-3.1382.560-1.315-1.889-0.003