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: YZM82

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2492181.291902
FMO2-HF: Nuclear repulsion 2406644.158052
FMO2-HF: Total energy -85537.13385
FMO2-MP2: Total energy -85783.332058


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.
-2.3442.8782.911-3.277-4.8560.004
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 : 0.012 / q_NPA : 0.003
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].
3A3LYS10.8390.9162.382-4.3480.3490.995-2.786-2.9060.004
4A4ILE00.0180.0174.033-0.693-0.5540.002-0.054-0.0870.000
5A5SER00.0410.0176.7570.6310.6310.0000.0000.0000.000
6A6CYS0-0.0100.0128.501-0.214-0.2140.0000.0000.0000.000
7A7LEU00.0350.01310.9420.1100.1100.0000.0000.0000.000
8A8PRO00.0420.01510.814-0.019-0.0190.0000.0000.0000.000
9A9ARG10.8990.92613.285-0.024-0.0240.0000.0000.0000.000
10A10VAL0-0.044-0.02215.665-0.007-0.0070.0000.0000.0000.000
11A11ALA00.0340.00814.360-0.013-0.0130.0000.0000.0000.000
12A12GLN0-0.0030.00116.034-0.029-0.0290.0000.0000.0000.000
13A13ASN0-0.086-0.04718.318-0.001-0.0010.0000.0000.0000.000
14A14LEU0-0.039-0.01419.644-0.025-0.0250.0000.0000.0000.000
15A15GLY0-0.038-0.00420.682-0.010-0.0100.0000.0000.0000.000
16A16TYR0-0.080-0.06216.5080.0390.0390.0000.0000.0000.000
17A17HIS00.0410.00116.1360.0460.0460.0000.0000.0000.000
18A18TYR00.0100.00814.3490.0530.0530.0000.0000.0000.000
19A19SER00.014-0.0139.8360.0700.0700.0000.0000.0000.000
20A20PRO0-0.0180.00810.3440.2680.2680.0000.0000.0000.000
21A21ASP-1-0.795-0.8636.8031.8881.8880.0000.0000.0000.000
22A22LEU0-0.013-0.0045.2001.8821.8820.0000.0000.0000.000
23A23PRO0-0.005-0.0013.733-0.916-0.4120.011-0.155-0.3600.001
24A24GLY0-0.015-0.0025.988-0.759-0.7590.0000.0000.0000.000
25A25PHE0-0.028-0.0089.196-0.452-0.4520.0000.0000.0000.000
26A26CYS0-0.0060.01210.8360.1770.1770.0000.0000.0000.000
27A27PRO00.0170.01310.568-0.012-0.0120.0000.0000.0000.000
28A28ILE0-0.003-0.01212.120-0.245-0.2450.0000.0000.0000.000
29A29PRO00.0040.00413.3780.1570.1570.0000.0000.0000.000
30A30LYS11.0250.99911.063-1.554-1.5540.0000.0000.0000.000
31A31GLU-1-0.905-0.95415.2650.7230.7230.0000.0000.0000.000
32A32LEU0-0.024-0.02318.241-0.069-0.0690.0000.0000.0000.000
33A33ALA0-0.035-0.01315.340-0.042-0.0420.0000.0000.0000.000
34A34GLU-1-0.904-0.95317.3490.4400.4400.0000.0000.0000.000
35A35HIS0-0.068-0.03320.080-0.064-0.0640.0000.0000.0000.000
36A36TRP0-0.043-0.02118.318-0.056-0.0560.0000.0000.0000.000
37A37PRO00.0250.01918.9750.0390.0390.0000.0000.0000.000
38A38VAL0-0.060-0.01814.2160.0570.0570.0000.0000.0000.000
39A39VAL00.0280.00111.726-0.124-0.1240.0000.0000.0000.000
40A40SER0-0.018-0.02110.0960.1990.1990.0000.0000.0000.000
41A41ASN0-0.039-0.0346.610-0.082-0.0820.0000.0000.0000.000
42A42ASP-1-0.949-0.95910.0340.6350.6350.0000.0000.0000.000
43A43ARG10.8500.93112.538-0.252-0.2520.0000.0000.0000.000
44A44TYR00.0470.00612.5340.0360.0360.0000.0000.0000.000
45A45PRO00.0070.00918.207-0.041-0.0410.0000.0000.0000.000
46A46ASN0-0.009-0.01720.687-0.058-0.0580.0000.0000.0000.000
47A47CYS0-0.0490.01316.0510.0510.0510.0000.0000.0000.000
48A48LEU00.0340.03615.759-0.076-0.0760.0000.0000.0000.000
49A49GLN0-0.005-0.01913.6170.0600.0600.0000.0000.0000.000
50A50ILE0-0.015-0.00710.639-0.106-0.1060.0000.0000.0000.000
51A51THR00.0110.00511.0800.0250.0250.0000.0000.0000.000
52A52LEU00.015-0.00210.786-0.033-0.0330.0000.0000.0000.000
53A53GLN0-0.016-0.01313.522-0.035-0.0350.0000.0000.0000.000
54A54GLN0-0.037-0.01717.0250.0240.0240.0000.0000.0000.000
55A55VAL0-0.0190.00416.872-0.007-0.0070.0000.0000.0000.000
56A56CYS0-0.053-0.02319.9810.0070.0070.0000.0000.0000.000
57A57GLU-1-0.856-0.94523.295-0.029-0.0290.0000.0000.0000.000
58A58LEU0-0.055-0.02925.266-0.006-0.0060.0000.0000.0000.000
59A59SER0-0.033-0.01020.1130.0110.0110.0000.0000.0000.000
60A60LYS10.8590.90820.610-0.021-0.0210.0000.0000.0000.000
61A61PRO00.0030.02319.450-0.002-0.0020.0000.0000.0000.000
62A62CYS00.014-0.00117.2260.0380.0380.0000.0000.0000.000
63A63SER0-0.037-0.00917.747-0.038-0.0380.0000.0000.0000.000
64A64ALA00.0060.00116.7090.0290.0290.0000.0000.0000.000
65A65GLY00.0810.04715.529-0.078-0.0780.0000.0000.0000.000
66A66TYR0-0.057-0.0309.8780.0550.0550.0000.0000.0000.000
67A67MET0-0.007-0.0077.1900.0190.0190.0000.0000.0000.000
68A68VAL00.0140.0134.7800.2020.299-0.001-0.011-0.0840.000
69A69GLY0-0.007-0.0042.279-3.021-2.3731.827-1.528-0.9470.001
70A70GLN00.0260.0002.9803.2282.3650.0771.257-0.472-0.002
71A71SER0-0.034-0.0025.3360.4310.4310.0000.0000.0000.000
72A72VAL00.0220.0047.407-0.029-0.0290.0000.0000.0000.000
73A73PHE0-0.050-0.0267.764-0.159-0.1590.0000.0000.0000.000
74A74VAL00.0200.00712.7870.1160.1160.0000.0000.0000.000
75A75GLN0-0.0180.00116.398-0.036-0.0360.0000.0000.0000.000
76A76THR0-0.005-0.00717.846-0.010-0.0100.0000.0000.0000.000
77A77PRO00.0230.00620.2170.0130.0130.0000.0000.0000.000
78A78GLY0-0.0150.00223.483-0.009-0.0090.0000.0000.0000.000
79A79VAL0-0.030-0.01118.9930.0080.0080.0000.0000.0000.000
80A80THR0-0.047-0.01317.4440.0090.0090.0000.0000.0000.000
81A81SER0-0.034-0.03014.132-0.056-0.0560.0000.0000.0000.000
82A82TYR00.010-0.02012.546-0.044-0.0440.0000.0000.0000.000
83A83TRP00.009-0.00114.6210.0260.0260.0000.0000.0000.000
84A84LEU0-0.036-0.00714.9740.0390.0390.0000.0000.0000.000
85A85THR00.0430.02017.199-0.043-0.0430.0000.0000.0000.000
86A86GLU-1-0.761-0.82518.4100.2740.2740.0000.0000.0000.000
87A87TRP0-0.029-0.03317.944-0.057-0.0570.0000.0000.0000.000
88A88VAL00.023-0.00721.7160.0290.0290.0000.0000.0000.000
89A89ASP-1-0.833-0.90524.6550.2090.2090.0000.0000.0000.000
90A90GLY0-0.065-0.03323.305-0.019-0.0190.0000.0000.0000.000
91A91LYS10.9190.94524.375-0.140-0.1400.0000.0000.0000.000
92A92ALA0-0.0070.02023.6240.0160.0160.0000.0000.0000.000
93A93ARG10.8460.89724.165-0.214-0.2140.0000.0000.0000.000
94A94ALA00.0120.00424.5420.0010.0010.0000.0000.0000.000
95A95LEU00.0240.00920.3990.0130.0130.0000.0000.0000.000
96A96PRO0-0.0060.00524.618-0.021-0.0210.0000.0000.0000.000
97A97ASP-1-0.834-0.91425.290-0.001-0.0010.0000.0000.0000.000
98A98SER0-0.020-0.03023.3940.0220.0220.0000.0000.0000.000
99A99LEU0-0.063-0.01024.320-0.017-0.0170.0000.0000.0000.000
100A100PHE00.0240.00419.4280.0210.0210.0000.0000.0000.000
101A101SER0-0.024-0.03219.049-0.026-0.0260.0000.0000.0000.000
102A102SER0-0.039-0.02318.436-0.029-0.0290.0000.0000.0000.000
103A103GLY00.0570.01716.160-0.064-0.0640.0000.0000.0000.000
104A104ARG10.7130.81717.0400.1500.1500.0000.0000.0000.000
105A105PHE0-0.028-0.01619.649-0.003-0.0030.0000.0000.0000.000
106A106GLU-1-0.768-0.88614.321-0.034-0.0340.0000.0000.0000.000
107A107THR0-0.068-0.01115.441-0.057-0.0570.0000.0000.0000.000
108A108ASN0-0.058-0.02816.475-0.006-0.0060.0000.0000.0000.000
109A109SER00.0080.02219.7400.0180.0180.0000.0000.0000.000
110A110ARG10.8910.91921.3880.1200.1200.0000.0000.0000.000
111A111ALA0-0.0010.01524.2360.0190.0190.0000.0000.0000.000
112A112PHE00.010-0.01124.969-0.003-0.0030.0000.0000.0000.000
113A113LEU0-0.043-0.01521.634-0.017-0.0170.0000.0000.0000.000
114A114ASP-1-0.754-0.86324.681-0.225-0.2250.0000.0000.0000.000
115A115GLU-1-0.751-0.86627.561-0.139-0.1390.0000.0000.0000.000
116A116ALA0-0.021-0.00430.1700.0160.0160.0000.0000.0000.000
117A117GLU-1-0.734-0.85626.879-0.156-0.1560.0000.0000.0000.000
118A118GLU-1-0.921-0.94530.525-0.144-0.1440.0000.0000.0000.000
119A119LYS10.8080.87232.6820.1510.1510.0000.0000.0000.000
120A120PHE0-0.024-0.00232.7700.0120.0120.0000.0000.0000.000
121A121ALA00.0160.00132.8300.0120.0120.0000.0000.0000.000
122A122ALA00.001-0.00534.8550.0090.0090.0000.0000.0000.000
123A123ALA0-0.0190.00537.8370.0070.0070.0000.0000.0000.000
124A124HIS10.7690.88736.5310.0800.0800.0000.0000.0000.000
125A125PRO00.0840.04037.6660.0010.0010.0000.0000.0000.000
126A126HIS10.8300.87439.0970.0410.0410.0000.0000.0000.000
127A127ALA0-0.0160.00236.3670.0050.0050.0000.0000.0000.000
128A128CYS0-0.066-0.00933.1930.0010.0010.0000.0000.0000.000
129A129LEU00.0390.04134.020-0.004-0.0040.0000.0000.0000.000
130A130GLY00.0100.02436.123-0.002-0.0020.0000.0000.0000.000
131A131GLU-1-0.868-0.91537.739-0.042-0.0420.0000.0000.0000.000
132A132ILE00.000-0.01140.9460.0040.0040.0000.0000.0000.000
133A133ASN0-0.0050.00543.4280.0020.0020.0000.0000.0000.000
134A134LYS10.9220.93046.0900.0190.0190.0000.0000.0000.000
135A135SER00.0390.03747.195-0.002-0.0020.0000.0000.0000.000
136A136THR00.0170.01543.1810.0020.0020.0000.0000.0000.000
137A137VAL0-0.036-0.02537.797-0.003-0.0030.0000.0000.0000.000
138A138GLY00.0320.02039.9750.0050.0050.0000.0000.0000.000
139A139GLY00.0560.02437.305-0.005-0.0050.0000.0000.0000.000
140A140SER0-0.047-0.02934.090-0.009-0.0090.0000.0000.0000.000
141A141HIS0-0.018-0.01832.1860.0050.0050.0000.0000.0000.000
142A142PHE00.0380.04128.0450.0070.0070.0000.0000.0000.000
143A143ILE00.0210.01223.0840.0040.0040.0000.0000.0000.000
144A144PHE0-0.016-0.00527.204-0.001-0.0010.0000.0000.0000.000
145A145SER0-0.074-0.03829.0340.0040.0040.0000.0000.0000.000
146A146GLN0-0.0010.00431.778-0.005-0.0050.0000.0000.0000.000
147A147TYR0-0.054-0.02533.729-0.001-0.0010.0000.0000.0000.000
148A148LEU00.0350.01329.3390.0120.0120.0000.0000.0000.000
149A149PRO00.0060.01429.408-0.006-0.0060.0000.0000.0000.000
150A150PRO00.0400.00828.272-0.008-0.0080.0000.0000.0000.000
151A151LEU0-0.027-0.01024.605-0.015-0.0150.0000.0000.0000.000
152A152LEU0-0.0050.00024.1380.0130.0130.0000.0000.0000.000
153A153PRO00.0090.01122.540-0.007-0.0070.0000.0000.0000.000
154A154ALA00.005-0.00418.246-0.014-0.0140.0000.0000.0000.000
155A155ASP-1-0.850-0.91420.1160.1760.1760.0000.0000.0000.000
156A156ALA0-0.052-0.01721.948-0.026-0.0260.0000.0000.0000.000
157A157VAL0-0.035-0.03623.136-0.029-0.0290.0000.0000.0000.000
158A158ALA00.0210.01225.1730.0180.0180.0000.0000.0000.000
159A159LEU0-0.025-0.01327.087-0.013-0.0130.0000.0000.0000.000
160A160VAL00.0270.01828.3620.0070.0070.0000.0000.0000.000
161A161GLY0-0.033-0.00631.377-0.001-0.0010.0000.0000.0000.000
162A162ALA00.0320.01233.781-0.006-0.0060.0000.0000.0000.000
163A163SER0-0.062-0.04835.8260.0050.0050.0000.0000.0000.000
164A164LEU00.0190.02537.683-0.006-0.0060.0000.0000.0000.000
165A165ALA00.0430.01039.7230.0040.0040.0000.0000.0000.000
166A166GLY0-0.005-0.00141.429-0.003-0.0030.0000.0000.0000.000
167A167LYS10.8910.95044.3300.0340.0340.0000.0000.0000.000
168A168ALA00.0200.01043.0100.0030.0030.0000.0000.0000.000
169A169ALA0-0.002-0.00840.311-0.002-0.0020.0000.0000.0000.000
170A170ALA0-0.008-0.00238.6370.0020.0020.0000.0000.0000.000
171A171ALA00.0160.01937.380-0.001-0.0010.0000.0000.0000.000
172A172ALA0-0.011-0.00534.3190.0010.0010.0000.0000.0000.000
173A173CYS0-0.030-0.00434.169-0.002-0.0020.0000.0000.0000.000
174A174SER0-0.009-0.02431.047-0.001-0.0010.0000.0000.0000.000
175A175VAL0-0.005-0.00327.481-0.010-0.0100.0000.0000.0000.000
176A176VAL00.0030.01125.4430.0120.0120.0000.0000.0000.000
177A177ASP-1-0.712-0.87020.807-0.132-0.1320.0000.0000.0000.000
178A178VAL00.0040.00223.249-0.024-0.0240.0000.0000.0000.000
179A179TYR0-0.013-0.03123.8440.0060.0060.0000.0000.0000.000
180A180ALA00.0550.03125.4600.0150.0150.0000.0000.0000.000
181A181PRO00.009-0.00328.3940.0150.0150.0000.0000.0000.000
182A182SER0-0.045-0.03526.6300.0010.0010.0000.0000.0000.000
183A183PHE0-0.023-0.02628.4860.0150.0150.0000.0000.0000.000
184A184GLU-1-0.790-0.90831.980-0.061-0.0610.0000.0000.0000.000
185A185PRO0-0.012-0.00132.3010.0050.0050.0000.0000.0000.000
186A186TYR0-0.007-0.00431.1720.0070.0070.0000.0000.0000.000
187A187LEU0-0.051-0.02835.5580.0070.0070.0000.0000.0000.000
188A188HIS0-0.063-0.03238.8260.0030.0030.0000.0000.0000.000
189A189PRO0-0.0170.01641.3440.0010.0010.0000.0000.0000.000
190A190GLU-1-0.853-0.93343.224-0.013-0.0130.0000.0000.0000.000
191A191THR0-0.055-0.03945.817-0.001-0.0010.0000.0000.0000.000
192A192LEU0-0.021-0.00645.921-0.002-0.0020.0000.0000.0000.000
193A193SER00.0160.00144.647-0.002-0.0020.0000.0000.0000.000
194A194ARG10.9360.98540.622-0.004-0.0040.0000.0000.0000.000
195A195VAL00.0300.01638.589-0.001-0.0010.0000.0000.0000.000
196A196TYR0-0.005-0.02535.5350.0040.0040.0000.0000.0000.000
197A197LYS10.8510.92432.475-0.058-0.0580.0000.0000.0000.000
198A198ILE00.0430.02529.394-0.001-0.0010.0000.0000.0000.000
199A199MET0-0.0250.00625.9220.0110.0110.0000.0000.0000.000
200A200ILE00.0200.02723.451-0.017-0.0170.0000.0000.0000.000
201A201ASP-1-0.743-0.85319.6560.0390.0390.0000.0000.0000.000
202A202PHE00.030-0.01018.9850.0310.0310.0000.0000.0000.000
203A203LYS10.8700.93523.353-0.103-0.1030.0000.0000.0000.000
204A204PRO0-0.023-0.01625.421-0.023-0.0230.0000.0000.0000.000
205A205CYS00.0130.00727.9820.0000.0000.0000.0000.0000.000
206A206ARG10.8290.91130.840-0.043-0.0430.0000.0000.0000.000
207A207LEU00.0120.00532.800-0.002-0.0020.0000.0000.0000.000
208A208MET0-0.0190.01335.0330.0020.0020.0000.0000.0000.000
209A209VAL00.0270.00037.468-0.005-0.0050.0000.0000.0000.000
210A210TRP0-0.0010.00939.8800.0030.0030.0000.0000.0000.000
211A211ARG10.9000.93742.6940.0190.0190.0000.0000.0000.000
212A212ASN0-0.033-0.02443.0240.0040.0040.0000.0000.0000.000
213A213ALA00.0280.03743.017-0.001-0.0010.0000.0000.0000.000
214A214THR0-0.047-0.04339.060-0.004-0.0040.0000.0000.0000.000
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