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: 52Q1Z

Calculation Name: 5F17-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F17

Chain ID: A

ChEMBL ID:

UniProt ID: P19811

Base Structure: X-ray

Registration Date: 2023-06-26

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2491798.671612
FMO2-HF: Nuclear repulsion 2406262.369519
FMO2-HF: Total energy -85536.302093
FMO2-MP2: Total energy -85782.462693


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:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-1.4632.7943.204-2.813-4.6480.004
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.002
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].
3A3LYS10.9440.9972.176-4.491-0.2141.290-2.646-2.9210.003
4A4ILE00.0070.0173.923-0.639-0.5640.000-0.003-0.0720.000
5A5SER00.0550.0136.9560.5720.5720.0000.0000.0000.000
6A6CYS0-0.0140.0188.614-0.198-0.1980.0000.0000.0000.000
7A7LEU00.0400.01010.9830.0900.0900.0000.0000.0000.000
8A8PRO00.0570.02110.905-0.002-0.0020.0000.0000.0000.000
9A9ARG10.9090.95313.262-0.030-0.0300.0000.0000.0000.000
10A10VAL0-0.052-0.02715.723-0.008-0.0080.0000.0000.0000.000
11A11ALA00.006-0.00114.473-0.009-0.0090.0000.0000.0000.000
12A12GLN00.0410.02115.935-0.056-0.0560.0000.0000.0000.000
13A13ASN0-0.094-0.04718.295-0.007-0.0070.0000.0000.0000.000
14A14LEU0-0.021-0.00919.401-0.023-0.0230.0000.0000.0000.000
15A15GLY0-0.060-0.01220.696-0.007-0.0070.0000.0000.0000.000
16A16TYR0-0.068-0.03016.4560.0360.0360.0000.0000.0000.000
17A17HIS00.035-0.00416.1420.0280.0280.0000.0000.0000.000
18A18TYR00.0080.00114.3810.0320.0320.0000.0000.0000.000
19A19SER0-0.003-0.0279.8010.0840.0840.0000.0000.0000.000
20A20PRO0-0.0170.01110.2740.2130.2130.0000.0000.0000.000
21A21ASP-1-0.831-0.9256.5732.1282.1280.0000.0000.0000.000
22A22LEU0-0.026-0.0095.1052.0062.078-0.001-0.001-0.0700.000
23A23PRO0-0.013-0.0023.591-0.684-0.3240.006-0.080-0.2860.000
24A24GLY0-0.012-0.0046.172-0.609-0.6090.0000.0000.0000.000
25A25PHE0-0.040-0.0149.089-0.372-0.3720.0000.0000.0000.000
26A26CYS0-0.0090.01010.9610.1240.1240.0000.0000.0000.000
27A27PRO00.0220.01910.6820.0200.0200.0000.0000.0000.000
28A28ILE0-0.003-0.01512.096-0.223-0.2230.0000.0000.0000.000
29A29PRO0-0.0010.00713.2090.1630.1630.0000.0000.0000.000
30A30LYS11.0340.99410.817-1.541-1.5410.0000.0000.0000.000
31A31GLU-1-0.903-0.94815.0770.6630.6630.0000.0000.0000.000
32A32LEU0-0.027-0.02318.008-0.067-0.0670.0000.0000.0000.000
33A33ALA0-0.037-0.01615.195-0.043-0.0430.0000.0000.0000.000
34A34GLU-1-0.911-0.95317.2870.4860.4860.0000.0000.0000.000
35A35HIS0-0.059-0.03220.161-0.059-0.0590.0000.0000.0000.000
36A36TRP0-0.045-0.01618.472-0.056-0.0560.0000.0000.0000.000
37A37PRO00.0180.01619.0070.0420.0420.0000.0000.0000.000
38A38VAL0-0.057-0.01914.2300.0450.0450.0000.0000.0000.000
39A39VAL00.0390.00411.745-0.111-0.1110.0000.0000.0000.000
40A40SER0-0.0160.01310.0850.1670.1670.0000.0000.0000.000
41A41ASN0-0.071-0.0676.597-0.017-0.0170.0000.0000.0000.000
42A42ASP-1-0.968-0.9709.9710.8100.8100.0000.0000.0000.000
43A43ARG10.9010.95412.520-0.324-0.3240.0000.0000.0000.000
44A44TYR00.0270.00012.4390.0230.0230.0000.0000.0000.000
45A45PRO0-0.017-0.00518.228-0.042-0.0420.0000.0000.0000.000
46A46ASN00.0350.00320.690-0.067-0.0670.0000.0000.0000.000
47A47CYS0-0.0230.01816.1310.0540.0540.0000.0000.0000.000
48A48LEU00.0260.03515.605-0.074-0.0740.0000.0000.0000.000
49A49GLN00.029-0.00913.6230.1040.1040.0000.0000.0000.000
50A50ILE0-0.022-0.01010.600-0.114-0.1140.0000.0000.0000.000
51A51THR00.0030.00610.9540.0540.0540.0000.0000.0000.000
52A52LEU00.0280.00210.453-0.042-0.0420.0000.0000.0000.000
53A53GLN0-0.017-0.01413.363-0.038-0.0380.0000.0000.0000.000
54A54GLN0-0.040-0.01716.8660.0290.0290.0000.0000.0000.000
55A55VAL0-0.0330.00116.8520.0010.0010.0000.0000.0000.000
56A56CYS0-0.053-0.00919.8550.0000.0000.0000.0000.0000.000
57A57GLU-1-0.855-0.95323.1750.0080.0080.0000.0000.0000.000
58A58LEU0-0.037-0.02124.986-0.007-0.0070.0000.0000.0000.000
59A59SER0-0.038-0.00219.8550.0130.0130.0000.0000.0000.000
60A60LYS10.9300.96420.657-0.050-0.0500.0000.0000.0000.000
61A61PRO00.0110.02719.6200.0030.0030.0000.0000.0000.000
62A62CYS00.008-0.00817.4020.0290.0290.0000.0000.0000.000
63A63SER0-0.0240.00117.911-0.034-0.0340.0000.0000.0000.000
64A64ALA00.0130.00216.8420.0210.0210.0000.0000.0000.000
65A65GLY00.0760.04115.629-0.067-0.0670.0000.0000.0000.000
66A66TYR0-0.062-0.03310.0600.1370.1370.0000.0000.0000.000
67A67MET0-0.009-0.0107.2400.0230.0230.0000.0000.0000.000
68A68VAL00.0120.0134.6540.2040.293-0.001-0.009-0.0790.000
69A69GLY0-0.015-0.0062.235-2.195-1.8771.851-1.365-0.8040.003
70A70GLN00.0310.0012.9642.5361.6020.0591.291-0.416-0.002
71A71SER0-0.033-0.0055.4880.2680.2680.0000.0000.0000.000
72A72VAL00.0220.0107.531-0.018-0.0180.0000.0000.0000.000
73A73PHE0-0.042-0.0267.906-0.156-0.1560.0000.0000.0000.000
74A74VAL00.0120.00312.8850.1070.1070.0000.0000.0000.000
75A75GLN0-0.029-0.00516.519-0.022-0.0220.0000.0000.0000.000
76A76THR00.0140.00117.974-0.010-0.0100.0000.0000.0000.000
77A77PRO00.0180.00620.3720.0150.0150.0000.0000.0000.000
78A78GLY0-0.0120.00223.639-0.008-0.0080.0000.0000.0000.000
79A79VAL0-0.027-0.00819.1460.0090.0090.0000.0000.0000.000
80A80THR0-0.057-0.02417.6340.0060.0060.0000.0000.0000.000
81A81SER0-0.035-0.02314.255-0.054-0.0540.0000.0000.0000.000
82A82TYR00.014-0.01912.748-0.030-0.0300.0000.0000.0000.000
83A83TRP00.0150.00414.8120.0150.0150.0000.0000.0000.000
84A84LEU0-0.038-0.00814.9990.0460.0460.0000.0000.0000.000
85A85THR00.0210.00217.097-0.048-0.0480.0000.0000.0000.000
86A86GLU-1-0.825-0.90318.3340.2820.2820.0000.0000.0000.000
87A87TRP0-0.017-0.02217.938-0.056-0.0560.0000.0000.0000.000
88A88VAL00.007-0.01021.6750.0260.0260.0000.0000.0000.000
89A89ASP-1-0.864-0.92824.6350.2060.2060.0000.0000.0000.000
90A90GLY0-0.066-0.03023.293-0.017-0.0170.0000.0000.0000.000
91A91LYS10.9180.94424.361-0.155-0.1550.0000.0000.0000.000
92A92ALA0-0.0150.01623.5400.0150.0150.0000.0000.0000.000
93A93ARG10.8920.94724.090-0.217-0.2170.0000.0000.0000.000
94A94ALA00.0190.00624.4530.0030.0030.0000.0000.0000.000
95A95LEU00.0110.00420.4900.0100.0100.0000.0000.0000.000
96A96PRO0-0.0170.00324.701-0.019-0.0190.0000.0000.0000.000
97A97ASP-1-0.889-0.96025.3990.0280.0280.0000.0000.0000.000
98A98SER0-0.020-0.03823.4490.0160.0160.0000.0000.0000.000
99A99LEU0-0.075-0.01424.432-0.014-0.0140.0000.0000.0000.000
100A100PHE00.008-0.00119.1920.0200.0200.0000.0000.0000.000
101A101SER0-0.018-0.02319.130-0.024-0.0240.0000.0000.0000.000
102A102SER0-0.043-0.01918.514-0.024-0.0240.0000.0000.0000.000
103A103GLY00.0520.01716.207-0.055-0.0550.0000.0000.0000.000
104A104ARG10.7220.82617.0860.1280.1280.0000.0000.0000.000
105A105PHE00.0130.00819.603-0.009-0.0090.0000.0000.0000.000
106A106GLU-1-0.803-0.91914.403-0.029-0.0290.0000.0000.0000.000
107A107THR0-0.079-0.01415.678-0.056-0.0560.0000.0000.0000.000
108A108ASN0-0.044-0.02516.620-0.006-0.0060.0000.0000.0000.000
109A109SER0-0.0080.01619.8880.0150.0150.0000.0000.0000.000
110A110ARG10.9000.92621.4910.1220.1220.0000.0000.0000.000
111A111ALA00.0010.01624.3180.0170.0170.0000.0000.0000.000
112A112PHE00.012-0.00625.060-0.002-0.0020.0000.0000.0000.000
113A113LEU0-0.046-0.01021.855-0.016-0.0160.0000.0000.0000.000
114A114ASP-1-0.763-0.88324.743-0.197-0.1970.0000.0000.0000.000
115A115GLU-1-0.863-0.95327.593-0.135-0.1350.0000.0000.0000.000
116A116ALA0-0.076-0.02430.2740.0150.0150.0000.0000.0000.000
117A117GLU-1-0.751-0.87427.103-0.132-0.1320.0000.0000.0000.000
118A118GLU-1-0.925-0.95230.633-0.123-0.1230.0000.0000.0000.000
119A119LYS10.9630.96932.7610.1180.1180.0000.0000.0000.000
120A120PHE0-0.042-0.00732.8820.0110.0110.0000.0000.0000.000
121A121ALA00.025-0.00832.9410.0110.0110.0000.0000.0000.000
122A122ALA00.003-0.00134.9350.0070.0070.0000.0000.0000.000
123A123ALA0-0.0260.00037.9340.0060.0060.0000.0000.0000.000
124A124HIS10.8170.91336.9090.0660.0660.0000.0000.0000.000
125A125PRO00.0850.04337.7320.0010.0010.0000.0000.0000.000
126A126HIS10.8340.87739.1420.0370.0370.0000.0000.0000.000
127A127ALA0-0.0170.00036.5100.0040.0040.0000.0000.0000.000
128A128CYS0-0.0460.00233.6150.0000.0000.0000.0000.0000.000
129A129LEU00.0320.04034.057-0.004-0.0040.0000.0000.0000.000
130A130GLY00.0150.02436.280-0.003-0.0030.0000.0000.0000.000
131A131GLU-1-0.864-0.91337.776-0.039-0.0390.0000.0000.0000.000
132A132ILE00.006-0.01141.2210.0040.0040.0000.0000.0000.000
133A133ASN0-0.020-0.00443.5180.0010.0010.0000.0000.0000.000
134A134LYS10.9350.93846.0880.0190.0190.0000.0000.0000.000
135A135SER00.0210.02647.311-0.002-0.0020.0000.0000.0000.000
136A136THR00.0250.01643.1130.0010.0010.0000.0000.0000.000
137A137VAL0-0.032-0.02137.903-0.003-0.0030.0000.0000.0000.000
138A138GLY00.0260.01939.9750.0050.0050.0000.0000.0000.000
139A139GLY00.0580.02537.317-0.005-0.0050.0000.0000.0000.000
140A140SER0-0.041-0.02634.041-0.008-0.0080.0000.0000.0000.000
141A141HIS0-0.011-0.00932.1940.0050.0050.0000.0000.0000.000
142A142PHE00.0390.04328.0430.0060.0060.0000.0000.0000.000
143A143ILE00.0170.01023.2060.0020.0020.0000.0000.0000.000
144A144PHE0-0.019-0.00427.236-0.002-0.0020.0000.0000.0000.000
145A145SER0-0.070-0.03629.1780.0030.0030.0000.0000.0000.000
146A146GLN0-0.0010.00531.934-0.005-0.0050.0000.0000.0000.000
147A147TYR0-0.059-0.02833.887-0.003-0.0030.0000.0000.0000.000
148A148LEU00.0230.00829.4010.0110.0110.0000.0000.0000.000
149A149PRO00.0090.01529.581-0.006-0.0060.0000.0000.0000.000
150A150PRO00.0380.00428.524-0.007-0.0070.0000.0000.0000.000
151A151LEU0-0.022-0.01024.827-0.015-0.0150.0000.0000.0000.000
152A152LEU0-0.014-0.00624.3540.0120.0120.0000.0000.0000.000
153A153PRO00.0060.01722.470-0.010-0.0100.0000.0000.0000.000
154A154ALA00.001-0.00718.239-0.012-0.0120.0000.0000.0000.000
155A155ASP-1-0.912-0.95420.0600.1440.1440.0000.0000.0000.000
156A156ALA0-0.032-0.01221.936-0.020-0.0200.0000.0000.0000.000
157A157VAL0-0.025-0.02923.140-0.024-0.0240.0000.0000.0000.000
158A158ALA00.0420.02225.1380.0140.0140.0000.0000.0000.000
159A159LEU0-0.028-0.01127.052-0.012-0.0120.0000.0000.0000.000
160A160VAL00.0240.02028.2980.0040.0040.0000.0000.0000.000
161A161GLY0-0.040-0.01331.3170.0000.0000.0000.0000.0000.000
162A162ALA00.0360.01333.875-0.006-0.0060.0000.0000.0000.000
163A163SER0-0.058-0.04335.9140.0040.0040.0000.0000.0000.000
164A164LEU00.0310.03037.871-0.006-0.0060.0000.0000.0000.000
165A165ALA00.0360.00739.9460.0040.0040.0000.0000.0000.000
166A166GLY0-0.0050.00141.607-0.002-0.0020.0000.0000.0000.000
167A167LYS10.8950.95044.5120.0370.0370.0000.0000.0000.000
168A168ALA00.0140.00843.2340.0030.0030.0000.0000.0000.000
169A169ALA0-0.009-0.01540.456-0.003-0.0030.0000.0000.0000.000
170A170ALA0-0.008-0.00138.5630.0020.0020.0000.0000.0000.000
171A171ALA00.0180.01937.312-0.002-0.0020.0000.0000.0000.000
172A172ALA0-0.011-0.00334.2650.0010.0010.0000.0000.0000.000
173A173CYS0-0.030-0.00233.925-0.001-0.0010.0000.0000.0000.000
174A174SER0-0.017-0.02431.045-0.002-0.0020.0000.0000.0000.000
175A175VAL0-0.001-0.00727.402-0.008-0.0080.0000.0000.0000.000
176A176VAL0-0.0050.00725.3620.0100.0100.0000.0000.0000.000
177A177ASP-1-0.702-0.87120.983-0.106-0.1060.0000.0000.0000.000
178A178VAL00.0250.01123.308-0.020-0.0200.0000.0000.0000.000
179A179TYR0-0.014-0.01823.9900.0040.0040.0000.0000.0000.000
180A180ALA00.0570.00925.5560.0140.0140.0000.0000.0000.000
181A181PRO0-0.008-0.01028.5470.0140.0140.0000.0000.0000.000
182A182SER0-0.034-0.01826.7150.0030.0030.0000.0000.0000.000
183A183PHE0-0.025-0.02728.8610.0140.0140.0000.0000.0000.000
184A184GLU-1-0.862-0.94632.082-0.049-0.0490.0000.0000.0000.000
185A185PRO0-0.013-0.00132.4060.0040.0040.0000.0000.0000.000
186A186TYR0-0.011-0.00830.9930.0100.0100.0000.0000.0000.000
187A187LEU0-0.054-0.03635.7230.0050.0050.0000.0000.0000.000
188A188HIS0-0.039-0.00838.9290.0020.0020.0000.0000.0000.000
189A189PRO0-0.0380.00141.4000.0020.0020.0000.0000.0000.000
190A190GLU-1-0.873-0.94243.331-0.006-0.0060.0000.0000.0000.000
191A191THR0-0.048-0.04045.963-0.001-0.0010.0000.0000.0000.000
192A192LEU0-0.024-0.01246.012-0.001-0.0010.0000.0000.0000.000
193A193SER00.0120.00044.715-0.002-0.0020.0000.0000.0000.000
194A194ARG10.9871.00740.473-0.009-0.0090.0000.0000.0000.000
195A195VAL00.0130.01638.518-0.001-0.0010.0000.0000.0000.000
196A196TYR0-0.004-0.01835.5170.0040.0040.0000.0000.0000.000
197A197LYS10.8520.92232.252-0.060-0.0600.0000.0000.0000.000
198A198ILE00.0500.03129.5800.0000.0000.0000.0000.0000.000
199A199MET0-0.030-0.00125.5470.0080.0080.0000.0000.0000.000
200A200ILE00.0190.03223.347-0.015-0.0150.0000.0000.0000.000
201A201ASP-1-0.739-0.85719.7100.0450.0450.0000.0000.0000.000
202A202PHE00.030-0.00919.3920.0290.0290.0000.0000.0000.000
203A203LYS10.9300.97223.405-0.106-0.1060.0000.0000.0000.000
204A204PRO0-0.030-0.02225.443-0.021-0.0210.0000.0000.0000.000
205A205CYS00.0090.00327.983-0.002-0.0020.0000.0000.0000.000
206A206ARG10.8520.93030.870-0.041-0.0410.0000.0000.0000.000
207A207LEU00.0060.00833.000-0.003-0.0030.0000.0000.0000.000
208A208MET0-0.0270.00635.0860.0030.0030.0000.0000.0000.000
209A209VAL00.0320.00137.614-0.005-0.0050.0000.0000.0000.000
210A210TRP00.0000.01139.9460.0030.0030.0000.0000.0000.000
211A211ARG10.9430.96042.7660.0130.0130.0000.0000.0000.000
212A212ASN0-0.045-0.02843.1140.0030.0030.0000.0000.0000.000
213A213ALA00.0290.04143.127-0.001-0.0010.0000.0000.0000.000
214A214THR0-0.057-0.05039.011-0.003-0.0030.0000.0000.0000.000
215A215PHE00.0080.00532.6970.0040.0040.0000.0000.0000.000
216A216TYR00.0430.02734.726-0.004-0.0040.0000.0000.0000.000
217A217VAL00.0460.01430.3070.0030.0030.0000.0000.0000.000
218A218GLN00.0130.00932.9180.0010.0010.0000.0000.0000.000
219A219GLU-1-0.790-0.88526.9220.0830.0830.0000.0000.0000.000