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: JQ3Q9

Calculation Name: 5YDP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5YDP

Chain ID: A

ChEMBL ID:

UniProt ID: G3EIL4

Base Structure: X-ray

Registration Date: 2023-09-20

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1926717.963536
FMO2-HF: Nuclear repulsion 1854953.289965
FMO2-HF: Total energy -71764.673571
FMO2-MP2: Total energy -71976.135789


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:26:GLY)


Summations of interaction energy for fragment #1(A:26:GLY)
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.
0.271.478-0.017-0.699-0.4930.001
Interaction energy analysis for fragmet #1(A:26:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.005
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].
3A28ARG10.8420.9073.8631.2142.422-0.017-0.699-0.4930.001
4A29TRP00.0550.0265.470-0.399-0.3990.0000.0000.0000.000
5A30SER00.0270.0238.826-0.047-0.0470.0000.0000.0000.000
6A31PRO00.0420.00010.592-0.114-0.1140.0000.0000.0000.000
7A32ARG10.8660.93612.703-0.282-0.2820.0000.0000.0000.000
8A33LEU0-0.0030.0096.676-0.048-0.0480.0000.0000.0000.000
9A34THR00.0710.02410.877-0.093-0.0930.0000.0000.0000.000
10A35VAL0-0.011-0.00312.900-0.042-0.0420.0000.0000.0000.000
11A36PHE00.0270.00112.379-0.008-0.0080.0000.0000.0000.000
12A37ASP-1-0.814-0.88711.006-0.301-0.3010.0000.0000.0000.000
13A38ALA00.0030.00414.399-0.006-0.0060.0000.0000.0000.000
14A39MET0-0.068-0.03717.6350.0100.0100.0000.0000.0000.000
15A40HIS0-0.030-0.01617.0140.0050.0050.0000.0000.0000.000
16A41GLN00.0430.02218.3580.0060.0060.0000.0000.0000.000
17A42LEU0-0.074-0.03520.1120.0090.0090.0000.0000.0000.000
18A43LEU00.012-0.00321.9570.0080.0080.0000.0000.0000.000
19A44GLU-1-0.883-0.92419.790-0.143-0.1430.0000.0000.0000.000
20A45SER0-0.042-0.01624.1390.0020.0020.0000.0000.0000.000
21A46ARG10.8150.90326.1750.0570.0570.0000.0000.0000.000
22A47ASP-1-0.743-0.86427.485-0.010-0.0100.0000.0000.0000.000
23A48TRP00.0750.03125.1180.0020.0020.0000.0000.0000.000
24A49SER0-0.027-0.01928.3130.0040.0040.0000.0000.0000.000
25A50ALA0-0.057-0.01330.7710.0020.0020.0000.0000.0000.000
26A51VAL00.0460.03525.033-0.004-0.0040.0000.0000.0000.000
27A52THR0-0.032-0.01728.3480.0090.0090.0000.0000.0000.000
28A53MET00.0370.02524.581-0.005-0.0050.0000.0000.0000.000
29A54SER0-0.011-0.02625.3900.0040.0040.0000.0000.0000.000
30A55ASP-1-0.819-0.89526.291-0.008-0.0080.0000.0000.0000.000
31A56VAL00.0690.03220.373-0.008-0.0080.0000.0000.0000.000
32A57ALA0-0.031-0.00921.2430.0000.0000.0000.0000.0000.000
33A58LYS10.8130.89922.2570.0080.0080.0000.0000.0000.000
34A59ALA00.0060.00720.749-0.006-0.0060.0000.0000.0000.000
35A60ALA00.0180.00917.413-0.019-0.0190.0000.0000.0000.000
36A61GLY00.0030.02217.6510.0060.0060.0000.0000.0000.000
37A62LEU0-0.014-0.00116.8420.0210.0210.0000.0000.0000.000
38A63SER00.0140.00820.927-0.008-0.0080.0000.0000.0000.000
39A64ARG11.0120.97723.585-0.025-0.0250.0000.0000.0000.000
40A65GLN00.0190.01625.7010.0000.0000.0000.0000.0000.000
41A66THR00.0350.01519.5040.0130.0130.0000.0000.0000.000
42A67LEU00.0130.03419.9350.0160.0160.0000.0000.0000.000
43A68TYR00.006-0.01522.4860.0050.0050.0000.0000.0000.000
44A69SER0-0.015-0.00923.4540.0020.0020.0000.0000.0000.000
45A70THR0-0.037-0.02518.8410.0150.0150.0000.0000.0000.000
46A71PHE0-0.0100.00316.8170.0160.0160.0000.0000.0000.000
47A72GLY00.0380.04422.404-0.009-0.0090.0000.0000.0000.000
48A73ASN0-0.031-0.04125.950-0.014-0.0140.0000.0000.0000.000
49A74ARG10.9200.94025.658-0.015-0.0150.0000.0000.0000.000
50A75GLN00.0180.01825.7490.0020.0020.0000.0000.0000.000
51A76GLY00.0490.03324.1180.0020.0020.0000.0000.0000.000
52A77LEU0-0.016-0.02420.2030.0110.0110.0000.0000.0000.000
53A78ALA00.0320.01320.8320.0010.0010.0000.0000.0000.000
54A79GLN00.0060.00421.9140.0080.0080.0000.0000.0000.000
55A80ALA0-0.021-0.01017.7830.0080.0080.0000.0000.0000.000
56A81TYR0-0.041-0.04417.2050.0130.0130.0000.0000.0000.000
57A82ALA00.0170.00317.792-0.006-0.0060.0000.0000.0000.000
58A83LEU0-0.002-0.00416.810-0.001-0.0010.0000.0000.0000.000
59A84GLN0-0.019-0.00611.001-0.033-0.0330.0000.0000.0000.000
60A85LEU0-0.0290.00214.948-0.016-0.0160.0000.0000.0000.000
61A86SER0-0.043-0.03017.618-0.006-0.0060.0000.0000.0000.000
62A87GLU-1-0.838-0.92010.8850.3180.3180.0000.0000.0000.000
63A88LYS10.8400.90413.3100.1220.1220.0000.0000.0000.000
64A89PHE0-0.005-0.01614.443-0.018-0.0180.0000.0000.0000.000
65A90ALA00.0350.02617.136-0.009-0.0090.0000.0000.0000.000
66A91GLY00.0160.01113.9650.0030.0030.0000.0000.0000.000
67A92GLU-1-0.792-0.87014.736-0.108-0.1080.0000.0000.0000.000
68A93ILE0-0.0080.01016.841-0.006-0.0060.0000.0000.0000.000
69A94ARG10.8470.90312.124-0.052-0.0520.0000.0000.0000.000
70A95ASP-1-0.856-0.90413.164-0.082-0.0820.0000.0000.0000.000
71A96SER0-0.021-0.04516.116-0.011-0.0110.0000.0000.0000.000
72A97ILE00.0140.00119.770-0.002-0.0020.0000.0000.0000.000
73A98ILE0-0.061-0.02014.9060.0010.0010.0000.0000.0000.000
74A99ARG10.7710.87415.6560.0930.0930.0000.0000.0000.000
75A100HIS0-0.046-0.02619.431-0.004-0.0040.0000.0000.0000.000
76A101PRO00.0220.01121.9910.0090.0090.0000.0000.0000.000
77A102GLY00.013-0.00424.563-0.004-0.0040.0000.0000.0000.000
78A103GLN0-0.015-0.00126.8960.0060.0060.0000.0000.0000.000
79A104ILE00.000-0.01027.433-0.002-0.0020.0000.0000.0000.000
80A105GLU-1-0.844-0.92127.799-0.010-0.0100.0000.0000.0000.000
81A106LEU0-0.0170.00225.809-0.001-0.0010.0000.0000.0000.000
82A107ALA00.001-0.00223.673-0.005-0.0050.0000.0000.0000.000
83A108LEU0-0.019-0.00123.7080.0000.0000.0000.0000.0000.000
84A109SER00.0350.02625.619-0.003-0.0030.0000.0000.0000.000
85A110GLU-1-0.766-0.83421.265-0.082-0.0820.0000.0000.0000.000
86A111GLY00.0430.01821.068-0.006-0.0060.0000.0000.0000.000
87A112ILE0-0.022-0.01021.8150.0000.0000.0000.0000.0000.000
88A113ASN00.0310.00624.500-0.001-0.0010.0000.0000.0000.000
89A114GLY0-0.046-0.01620.640-0.008-0.0080.0000.0000.0000.000
90A115PHE0-0.017-0.01320.411-0.007-0.0070.0000.0000.0000.000
91A116LEU00.0390.02821.380-0.003-0.0030.0000.0000.0000.000
92A117ARG10.9540.97819.2330.1270.1270.0000.0000.0000.000
93A118SER0-0.101-0.08717.800-0.016-0.0160.0000.0000.0000.000
94A119SER00.011-0.00520.4780.0020.0020.0000.0000.0000.000
95A120SER0-0.044-0.00422.8320.0020.0020.0000.0000.0000.000
96A121ARG10.8870.93119.2370.1330.1330.0000.0000.0000.000
97A122ASP-1-0.715-0.84120.161-0.042-0.0420.0000.0000.0000.000
98A123PRO0-0.0160.00020.6390.0120.0120.0000.0000.0000.000
99A124LEU0-0.042-0.00422.2610.0080.0080.0000.0000.0000.000
100A125ILE00.032-0.00222.5220.0070.0070.0000.0000.0000.000
101A126ARG10.9630.99025.4790.0530.0530.0000.0000.0000.000
102A127ALA00.0240.00927.0450.0030.0030.0000.0000.0000.000
103A128LEU0-0.0410.02227.1410.0050.0050.0000.0000.0000.000
104A129VAL00.0300.01529.5760.0040.0040.0000.0000.0000.000
105A130THR0-0.0120.00531.5190.0000.0000.0000.0000.0000.000
106A131GLY00.0220.00532.162-0.004-0.0040.0000.0000.0000.000
107A132ASH0-0.094-0.10332.0170.0020.0020.0000.0000.0000.000
108A133ILE00.0270.01036.2190.0000.0000.0000.0000.0000.000
109A134LYS10.8760.93832.8730.0080.0080.0000.0000.0000.000
110A135PRO0-0.0040.02331.7630.0020.0020.0000.0000.0000.000
111A136ASP-1-0.835-0.91632.2220.0210.0210.0000.0000.0000.000
112A137LEU0-0.047-0.04629.4220.0040.0040.0000.0000.0000.000
113A138LEU0-0.017-0.01426.3200.0050.0050.0000.0000.0000.000
114A139ARG10.8620.92929.060-0.009-0.0090.0000.0000.0000.000
115A140LEU00.0190.02030.0040.0020.0020.0000.0000.0000.000
116A141ILE0-0.030-0.03024.1910.0050.0050.0000.0000.0000.000
117A142THR00.0040.00526.2550.0030.0030.0000.0000.0000.000
118A143THR0-0.063-0.02628.262-0.005-0.0050.0000.0000.0000.000
119A144GLU-1-0.899-0.93730.9200.0510.0510.0000.0000.0000.000
120A145ALA0-0.032-0.02325.6540.0070.0070.0000.0000.0000.000
121A146GLY00.0410.02626.0180.0010.0010.0000.0000.0000.000
122A147PRO00.011-0.00822.3330.0030.0030.0000.0000.0000.000
123A148LEU00.0180.02621.4100.0130.0130.0000.0000.0000.000
124A149ILE00.0240.02721.7310.0010.0010.0000.0000.0000.000
125A150GLU-1-0.841-0.87621.7470.1270.1270.0000.0000.0000.000
126A151ARG10.7810.85613.945-0.275-0.2750.0000.0000.0000.000
127A152ALA00.0310.00917.8060.0090.0090.0000.0000.0000.000
128A153THR0-0.006-0.03619.637-0.006-0.0060.0000.0000.0000.000
129A154GLU-1-0.870-0.91116.9860.2480.2480.0000.0000.0000.000
130A155VAL0-0.032-0.00714.1070.0150.0150.0000.0000.0000.000
131A156LEU00.002-0.01416.584-0.012-0.0120.0000.0000.0000.000
132A157MET0-0.0190.00319.904-0.009-0.0090.0000.0000.0000.000
133A158PRO00.0490.02816.501-0.016-0.0160.0000.0000.0000.000
134A159ALA0-0.015-0.00118.444-0.016-0.0160.0000.0000.0000.000
135A160LEU0-0.0210.00619.546-0.016-0.0160.0000.0000.0000.000
136A161SER0-0.042-0.01822.387-0.005-0.0050.0000.0000.0000.000
137A162GLU-1-0.915-0.96618.3460.1630.1630.0000.0000.0000.000
138A163SER0-0.046-0.02819.932-0.008-0.0080.0000.0000.0000.000
139A164TRP0-0.020-0.03620.8400.0050.0050.0000.0000.0000.000
140A165MET0-0.0230.00623.799-0.004-0.0040.0000.0000.0000.000
141A166ARG10.8700.93922.037-0.059-0.0590.0000.0000.0000.000
142A167ILE00.0300.03326.3850.0000.0000.0000.0000.0000.000
143A168GLU-1-0.758-0.85626.9420.0780.0780.0000.0000.0000.000
144A169ALA00.0510.02225.9530.0000.0000.0000.0000.0000.000
145A170SER0-0.070-0.06126.9940.0020.0020.0000.0000.0000.000
146A171GLN00.000-0.01329.6930.0000.0000.0000.0000.0000.000
147A172ALA00.0250.02124.681-0.004-0.0040.0000.0000.0000.000
148A173ARG10.8500.88423.758-0.115-0.1150.0000.0000.0000.000
149A174LEU0-0.0240.00126.354-0.001-0.0010.0000.0000.0000.000
150A175ALA00.0500.02327.787-0.002-0.0020.0000.0000.0000.000
151A176ALA00.0130.01523.128-0.004-0.0040.0000.0000.0000.000
152A177SER0-0.032-0.01924.868-0.003-0.0030.0000.0000.0000.000
153A178ILE0-0.033-0.02026.622-0.003-0.0030.0000.0000.0000.000
154A179ILE00.0400.01323.964-0.004-0.0040.0000.0000.0000.000
155A180ALA0-0.0050.00223.502-0.005-0.0050.0000.0000.0000.000
156A181ARG10.9250.96124.768-0.059-0.0590.0000.0000.0000.000
157A182ILE00.0220.01528.248-0.004-0.0040.0000.0000.0000.000
158A183GLY00.0350.01625.115-0.005-0.0050.0000.0000.0000.000
159A184ILE00.004-0.01624.273-0.004-0.0040.0000.0000.0000.000
160A185SER0-0.0100.00626.867-0.003-0.0030.0000.0000.0000.000
161A186PHE00.0060.00228.523-0.003-0.0030.0000.0000.0000.000
162A187ILE0-0.055-0.01423.422-0.005-0.0050.0000.0000.0000.000
163A188SER0-0.090-0.06027.742-0.003-0.0030.0000.0000.0000.000
164A189LEU0-0.018-0.00930.748-0.001-0.0010.0000.0000.0000.000
165A190PRO0-0.0200.00130.5930.0000.0000.0000.0000.0000.000
166A191PRO0-0.035-0.01131.0270.0010.0010.0000.0000.0000.000
167A192GLU-1-0.947-0.97733.980-0.013-0.0130.0000.0000.0000.000
168A193ASP-1-0.859-0.91435.607-0.020-0.0200.0000.0000.0000.000
169A194PRO0-0.039-0.02531.8290.0010.0010.0000.0000.0000.000
170A195ASP-1-0.879-0.95231.026-0.041-0.0410.0000.0000.0000.000
171A196GLN0-0.080-0.05332.2160.0010.0010.0000.0000.0000.000
172A197LEU00.0160.03030.5870.0030.0030.0000.0000.0000.000
173A198ALA00.0150.00028.6280.0040.0040.0000.0000.0000.000
174A199SER00.0100.00930.3890.0020.0020.0000.0000.0000.000
175A200GLY00.0560.03332.8550.0020.0020.0000.0000.0000.000
176A201LEU0-0.042-0.02828.5580.0040.0040.0000.0000.0000.000
177A202THR0-0.040-0.04329.6580.0040.0040.0000.0000.0000.000
178A203GLU-1-0.957-0.97231.088-0.005-0.0050.0000.0000.0000.000
179A204VAL0-0.031-0.01434.1110.0030.0030.0000.0000.0000.000
180A205ILE0-0.036-0.02128.6500.0040.0040.0000.0000.0000.000
181A206ALA00.0230.01131.2410.0030.0030.0000.0000.0000.000
182A207PRO00.0620.02932.2140.0020.0020.0000.0000.0000.000
183A208TYR0-0.091-0.04530.2210.0020.0020.0000.0000.0000.000
184A209LEU00.009-0.00527.3080.0030.0030.0000.0000.0000.000
185A210GLN0-0.016-0.02630.9970.0030.0030.0000.0000.0000.000
186A211LYS10.9020.97133.692-0.022-0.0220.0000.0000.0000.000
187A212VAL0-0.026-0.02231.1070.0020.0020.0000.0000.0000.000
188A213VAL00.0010.02728.3250.0030.0030.0000.0000.0000.000
189A214GLN0-0.138-0.06830.250-0.008-0.0080.0000.0000.0000.000