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: 94YZ2

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2264673.711507
FMO2-HF: Nuclear repulsion 2185458.229828
FMO2-HF: Total energy -79215.481679
FMO2-MP2: Total energy -79443.599601


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.
-19.456-12.18813.899-9.245-11.922-0.051
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 : -0.024 / 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-1-0.823-0.9282.282-11.527-6.5882.742-3.521-4.160-0.031
4A4LEU0-0.073-0.0395.0860.3740.412-0.001-0.003-0.0340.000
5A5PHE00.0420.0228.1920.4130.4130.0000.0000.0000.000
6A6ASP-1-0.764-0.88011.148-0.418-0.4180.0000.0000.0000.000
7A7VAL00.0050.01914.0890.0130.0130.0000.0000.0000.000
8A8SER0-0.008-0.02316.6770.0140.0140.0000.0000.0000.000
9A9TYR00.0700.04220.359-0.027-0.0270.0000.0000.0000.000
10A10GLU-1-0.817-0.93122.825-0.277-0.2770.0000.0000.0000.000
11A11GLU-1-0.848-0.90618.250-0.391-0.3910.0000.0000.0000.000
12A12LEU0-0.0310.01217.273-0.034-0.0340.0000.0000.0000.000
13A13GLN0-0.0440.00120.467-0.022-0.0220.0000.0000.0000.000
14A14THR0-0.146-0.09523.5200.0180.0180.0000.0000.0000.000
15A15THR0-0.073-0.04719.320-0.025-0.0250.0000.0000.0000.000
16A28PHE0-0.014-0.02315.4680.0100.0100.0000.0000.0000.000
17A29SER00.012-0.00712.6220.0230.0230.0000.0000.0000.000
18A30ASP-1-0.851-0.91012.999-0.971-0.9710.0000.0000.0000.000
19A31ARG10.8620.91814.0800.5260.5260.0000.0000.0000.000
20A32LEU0-0.001-0.00315.410-0.004-0.0040.0000.0000.0000.000
21A33GLY00.0550.02212.753-0.011-0.0110.0000.0000.0000.000
22A34TRP00.0350.01313.009-0.104-0.1040.0000.0000.0000.000
23A35GLU-1-0.839-0.90715.111-0.541-0.5410.0000.0000.0000.000
24A36VAL0-0.031-0.00514.4030.0520.0520.0000.0000.0000.000
25A37ILE00.006-0.00210.8760.0050.0050.0000.0000.0000.000
26A38CYS0-0.032-0.01715.0050.0680.0680.0000.0000.0000.000
27A39SER0-0.094-0.03718.3850.0660.0660.0000.0000.0000.000
28A40GLN0-0.050-0.03514.033-0.098-0.0980.0000.0000.0000.000
29A41GLY00.0110.01518.331-0.021-0.0210.0000.0000.0000.000
30A42MET0-0.097-0.04419.3130.0580.0580.0000.0000.0000.000
31A43GLU-1-0.901-0.94122.333-0.352-0.3520.0000.0000.0000.000
32A44SER00.0190.02225.5160.0100.0100.0000.0000.0000.000
33A45ASP-1-0.777-0.85327.002-0.275-0.2750.0000.0000.0000.000
34A46GLU-1-0.938-0.98829.860-0.217-0.2170.0000.0000.0000.000
35A47PHE0-0.108-0.05628.6520.0160.0160.0000.0000.0000.000
36A48ASP-1-0.792-0.85024.750-0.373-0.3730.0000.0000.0000.000
37A49GLY00.0310.00226.9760.0080.0080.0000.0000.0000.000
38A50PRO0-0.029-0.02226.743-0.009-0.0090.0000.0000.0000.000
39A51GLY0-0.036-0.00326.3110.0180.0180.0000.0000.0000.000
40A52THR0-0.054-0.01423.0430.0030.0030.0000.0000.0000.000
41A53ARG10.8350.90117.7240.3130.3130.0000.0000.0000.000
42A54TYR0-0.028-0.05117.3760.0140.0140.0000.0000.0000.000
43A55ILE0-0.0110.01512.986-0.016-0.0160.0000.0000.0000.000
44A56LEU0-0.013-0.01211.7540.0140.0140.0000.0000.0000.000
45A57GLY00.0380.0109.182-0.034-0.0340.0000.0000.0000.000
46A58ILE0-0.036-0.0336.8640.2240.2240.0000.0000.0000.000
47A59CYS0-0.018-0.0012.916-0.900-0.4480.065-0.193-0.3240.001
48A60GLU-1-0.907-0.9594.107-2.954-2.5530.000-0.073-0.3280.000
49A61GLY0-0.013-0.0036.2200.9150.9150.0000.0000.0000.000
50A62GLN00.0140.0038.6180.7000.7000.0000.0000.0000.000
51A63LEU00.0440.0339.636-0.479-0.4790.0000.0000.0000.000
52A64VAL0-0.033-0.0138.7500.2720.2720.0000.0000.0000.000
53A65CYS0-0.078-0.03611.6890.2030.2030.0000.0000.0000.000
54A66SER00.0370.01913.409-0.099-0.0990.0000.0000.0000.000
55A67VAL00.0060.00015.7560.0800.0800.0000.0000.0000.000
56A68ARG10.7890.88618.3910.2920.2920.0000.0000.0000.000
57A69PHE00.006-0.01518.4230.0380.0380.0000.0000.0000.000
58A70THR00.0540.02523.071-0.017-0.0170.0000.0000.0000.000
59A71SER00.0210.01526.5960.0070.0070.0000.0000.0000.000
60A72LEU0-0.002-0.01428.943-0.002-0.0020.0000.0000.0000.000
61A73ASP-1-0.934-0.95831.878-0.122-0.1220.0000.0000.0000.000
62A74ARG10.8960.95131.0730.1480.1480.0000.0000.0000.000
63A75PRO0-0.016-0.01833.0900.0000.0000.0000.0000.0000.000
64A76ASN00.0620.03830.565-0.011-0.0110.0000.0000.0000.000
65A77MET00.0180.00429.2950.0030.0030.0000.0000.0000.000
66A78ILE0-0.0240.00230.9270.0110.0110.0000.0000.0000.000
67A79THR0-0.012-0.02934.2480.0080.0080.0000.0000.0000.000
68A80HIS00.0060.01435.3880.0060.0060.0000.0000.0000.000
69A81THR00.0270.01533.8610.0050.0050.0000.0000.0000.000
70A82PHE0-0.036-0.03132.3880.0040.0040.0000.0000.0000.000
71A83GLN00.0290.03837.2280.0110.0110.0000.0000.0000.000
72A84HIS00.013-0.01539.6620.0060.0060.0000.0000.0000.000
73A85CYS0-0.085-0.03138.4010.0040.0040.0000.0000.0000.000
74A86PHE00.012-0.02035.1870.0050.0050.0000.0000.0000.000
75A87SER00.0270.03339.5330.0030.0030.0000.0000.0000.000
76A88ASP-1-0.878-0.92342.089-0.075-0.0750.0000.0000.0000.000
77A89VAL0-0.048-0.02437.0360.0060.0060.0000.0000.0000.000
78A90THR0-0.018-0.00439.878-0.002-0.0020.0000.0000.0000.000
79A91LEU0-0.019-0.00934.1210.0010.0010.0000.0000.0000.000
80A92PRO0-0.032-0.02033.6160.0050.0050.0000.0000.0000.000
81A93ALA00.0130.00835.497-0.006-0.0060.0000.0000.0000.000
82A94TYR0-0.018-0.00127.848-0.008-0.0080.0000.0000.0000.000
83A95GLY00.006-0.01429.5300.0080.0080.0000.0000.0000.000
84A96THR0-0.0100.01024.460-0.013-0.0130.0000.0000.0000.000
85A97GLU-1-0.799-0.92227.166-0.199-0.1990.0000.0000.0000.000
86A98SER0-0.0130.00322.406-0.015-0.0150.0000.0000.0000.000
87A99SER00.000-0.00823.5110.0130.0130.0000.0000.0000.000
88A100ARG10.8580.88222.6610.3400.3400.0000.0000.0000.000
89A101PHE0-0.0040.01017.366-0.052-0.0520.0000.0000.0000.000
90A102PHE00.0000.00015.9590.0430.0430.0000.0000.0000.000
91A103VAL00.014-0.00214.328-0.074-0.0740.0000.0000.0000.000
92A104ASP-1-0.832-0.89014.452-0.682-0.6820.0000.0000.0000.000
93A105LYS10.9530.95314.3180.2900.2900.0000.0000.0000.000
94A106ALA0-0.040-0.00714.9780.0080.0080.0000.0000.0000.000
95A107ARG10.8950.92511.4771.1711.1710.0000.0000.0000.000
96A108ALA00.0130.00410.235-0.165-0.1650.0000.0000.0000.000
97A109ARG10.9180.98110.0990.3810.3810.0000.0000.0000.000
98A110ALA0-0.059-0.02411.4190.0740.0740.0000.0000.0000.000
99A111LEU0-0.015-0.0066.4910.1850.1850.0000.0000.0000.000
100A112LEU0-0.025-0.0225.392-0.185-0.1850.0000.0000.0000.000
101A113GLY00.0300.0317.5680.3960.3960.0000.0000.0000.000
102A114GLU-1-0.937-1.00110.723-0.353-0.3530.0000.0000.0000.000
103A115HIS0-0.043-0.03013.3800.0510.0510.0000.0000.0000.000
104A116TYR00.0790.0666.9270.0700.0700.0000.0000.0000.000
105A117PRO0-0.029-0.00210.703-0.111-0.1110.0000.0000.0000.000
106A118ILE00.047-0.0049.2350.0410.0410.0000.0000.0000.000
107A119SER0-0.031-0.01411.726-0.006-0.0060.0000.0000.0000.000
108A120GLN00.0320.00114.661-0.031-0.0310.0000.0000.0000.000
109A121VAL00.0120.0178.9840.0570.0570.0000.0000.0000.000
110A122LEU00.0190.01312.2890.0010.0010.0000.0000.0000.000
111A123PHE0-0.009-0.01713.9520.0410.0410.0000.0000.0000.000
112A124LEU00.0160.01311.6470.0330.0330.0000.0000.0000.000
113A125ALA0-0.002-0.00111.9290.0510.0510.0000.0000.0000.000
114A126MET0-0.046-0.01213.7490.0300.0300.0000.0000.0000.000
115A127VAL00.0170.02417.4310.0290.0290.0000.0000.0000.000
116A128ASN0-0.034-0.03913.1850.0190.0190.0000.0000.0000.000
117A129TRP00.0020.01316.1760.0430.0430.0000.0000.0000.000
118A130ALA00.0230.00617.4080.0200.0200.0000.0000.0000.000
119A131GLN0-0.046-0.02419.6320.0180.0180.0000.0000.0000.000
120A132ASN0-0.072-0.02618.0930.0570.0570.0000.0000.0000.000
121A133ASN0-0.054-0.03919.2790.0000.0000.0000.0000.0000.000
122A134ALA0-0.0160.01822.859-0.004-0.0040.0000.0000.0000.000
123A135TYR00.0200.01223.619-0.007-0.0070.0000.0000.0000.000
124A136GLY00.0170.00424.6880.0050.0050.0000.0000.0000.000
125A137ASN0-0.056-0.04225.8900.0000.0000.0000.0000.0000.000
126A138ILE00.0000.01221.376-0.007-0.0070.0000.0000.0000.000
127A139TYR00.0430.02125.8660.0120.0120.0000.0000.0000.000
128A140THR0-0.013-0.00725.648-0.023-0.0230.0000.0000.0000.000
129A141ILE00.0540.03828.0160.0210.0210.0000.0000.0000.000
130A142VAL0-0.027-0.00126.301-0.021-0.0210.0000.0000.0000.000
131A143SER00.1050.03628.0310.0200.0200.0000.0000.0000.000
132A144ARG10.9860.98329.4420.1030.1030.0000.0000.0000.000
133A145ALA0-0.046-0.03127.5030.0080.0080.0000.0000.0000.000
134A146MET00.0680.03421.9390.0060.0060.0000.0000.0000.000
135A147LEU00.0400.03825.6490.0050.0050.0000.0000.0000.000
136A148LYS10.9000.94627.7160.1270.1270.0000.0000.0000.000
137A149ILE0-0.013-0.00421.3130.0160.0160.0000.0000.0000.000
138A150LEU00.0550.02522.3020.0130.0130.0000.0000.0000.000
139A151THR0-0.0170.01024.3310.0210.0210.0000.0000.0000.000
140A152ARG10.8760.93024.3410.0970.0970.0000.0000.0000.000
141A153SER0-0.046-0.02620.7390.0170.0170.0000.0000.0000.000
142A154GLY00.0210.02221.7480.0190.0190.0000.0000.0000.000
143A155TRP0-0.008-0.01320.6670.0050.0050.0000.0000.0000.000
144A156GLN0-0.021-0.00323.722-0.008-0.0080.0000.0000.0000.000
145A157ILE0-0.030-0.01025.455-0.002-0.0020.0000.0000.0000.000
146A158LYS10.9740.99027.9030.0600.0600.0000.0000.0000.000
147A159VAL0-0.025-0.02231.469-0.011-0.0110.0000.0000.0000.000
148A160ILE0-0.069-0.02933.1140.0100.0100.0000.0000.0000.000
149A161LYS10.8880.92035.4490.0910.0910.0000.0000.0000.000
150A162GLU-1-0.860-0.90235.992-0.095-0.0950.0000.0000.0000.000
151A163ALA00.0070.00037.1940.0060.0060.0000.0000.0000.000
152A164PHE0-0.001-0.01838.122-0.005-0.0050.0000.0000.0000.000
153A165LEU00.0050.02135.0400.0010.0010.0000.0000.0000.000
154A166THR00.018-0.02238.7750.0030.0030.0000.0000.0000.000
155A167GLU-1-0.880-0.94341.202-0.081-0.0810.0000.0000.0000.000
156A168LYS10.8290.91536.0810.1430.1430.0000.0000.0000.000
157A169GLU-1-0.944-0.94134.926-0.158-0.1580.0000.0000.0000.000
158A170ARG10.9190.96836.2520.0990.0990.0000.0000.0000.000
159A171ILE0-0.025-0.01633.220-0.011-0.0110.0000.0000.0000.000
160A172TYR0-0.081-0.06431.8350.0120.0120.0000.0000.0000.000
161A173LEU00.0630.05631.677-0.014-0.0140.0000.0000.0000.000
162A174LEU0-0.044-0.03527.4980.0140.0140.0000.0000.0000.000
163A175THR00.0080.01428.895-0.003-0.0030.0000.0000.0000.000
164A176LEU0-0.032-0.03022.8610.0070.0070.0000.0000.0000.000
165A177PRO0-0.0140.01325.064-0.007-0.0070.0000.0000.0000.000
166A178ALA00.0290.00322.002-0.008-0.0080.0000.0000.0000.000
167A179GLY00.0360.02423.1850.0100.0100.0000.0000.0000.000
168A180GLN00.0540.01220.419-0.020-0.0200.0000.0000.0000.000
169A181ASP-1-0.898-0.95922.3390.0990.0990.0000.0000.0000.000
170A182ASP-1-0.835-0.91922.4670.0070.0070.0000.0000.0000.000
171A183LYS10.8800.95116.152-0.196-0.1960.0000.0000.0000.000
172A184GLN0-0.077-0.04817.8470.0300.0300.0000.0000.0000.000
173A185GLN0-0.039-0.00519.3690.0300.0300.0000.0000.0000.000
174A186LEU0-0.018-0.01916.7850.0080.0080.0000.0000.0000.000
175A187GLY00.0470.01914.5700.0010.0010.0000.0000.0000.000
176A188GLY00.000-0.00814.9370.0710.0710.0000.0000.0000.000
177A189ASP-1-0.906-0.96217.2180.0770.0770.0000.0000.0000.000
178A190VAL00.0340.00610.8180.0000.0000.0000.0000.0000.000
179A191VAL00.007-0.00112.5830.0680.0680.0000.0000.0000.000
180A192SER0-0.078-0.02713.7120.0580.0580.0000.0000.0000.000
181A193ARG10.8930.96014.091-0.019-0.0190.0000.0000.0000.000
182A194THR0-0.043-0.0309.0750.0340.0340.0000.0000.0000.000
183A195GLY0-0.025-0.00110.4790.1630.1630.0000.0000.0000.000
184A196CYS0-0.0470.0058.2060.1070.1070.0000.0000.0000.000
185A197PRO00.028-0.0028.278-0.243-0.2430.0000.0000.0000.000
186A198PRO00.0580.01510.920-0.013-0.0130.0000.0000.0000.000
187A199VAL00.0310.01311.247-0.099-0.0990.0000.0000.0000.000
188A200ALA00.0050.0107.473-0.043-0.0430.0000.0000.0000.000
189A201VAL00.0160.0169.282-0.169-0.1690.0000.0000.0000.000
190A202THR0-0.108-0.05811.562-0.166-0.1660.0000.0000.0000.000
191A203THR0-0.013-0.01410.320-0.022-0.0220.0000.0000.0000.000
192A204TRP00.0070.00212.031-0.100-0.1000.0000.0000.0000.000
193A205PRO00.0360.0089.6070.0320.0320.0000.0000.0000.000
194A206LEU0-0.044-0.0028.0000.2740.2740.0000.0000.0000.000
195A207THR00.0420.0313.029-0.921-0.9802.410-0.697-1.6540.002
196A208LEU0-0.041-0.0303.6320.9291.4300.005-0.120-0.3860.000
197A209PRO0-0.0030.0002.537-3.623-1.6242.659-1.887-2.772-0.020
198A210VAL00.0250.0341.932-2.451-3.4546.019-2.751-2.264-0.003