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: G6K11

Calculation Name: 3SK9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SK9

Chain ID: A

ChEMBL ID:

UniProt ID: Q53VY2

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2995930.896196
FMO2-HF: Nuclear repulsion 2905353.663571
FMO2-HF: Total energy -90577.232625
FMO2-MP2: Total energy -90847.17316


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:4:SER)


Summations of interaction energy for fragment #1(A:4: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.
-13.417-7.8323.627-3.729-5.4820.028
Interaction energy analysis for fragmet #1(A:4:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.008
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].
3A6ALA00.0260.0202.926-3.580-0.9980.315-1.298-1.5990.008
4A7ALA0-0.009-0.0082.218-8.345-6.6502.958-1.949-2.7040.019
5A8LEU00.0100.0103.998-1.538-0.9930.013-0.190-0.3680.001
6A9ALA0-0.023-0.0166.078-0.135-0.1350.0000.0000.0000.000
7A10LEU0-0.041-0.0296.205-0.323-0.3230.0000.0000.0000.000
8A11TRP0-0.0260.0078.114-0.175-0.1750.0000.0000.0000.000
9A12ALA00.0400.0319.784-0.059-0.0590.0000.0000.0000.000
10A13LYS10.8110.91412.3970.2830.2830.0000.0000.0000.000
11A14SER0-0.004-0.00115.7530.0310.0310.0000.0000.0000.000
12A15GLY00.0190.01319.002-0.010-0.0100.0000.0000.0000.000
13A16ASN00.0530.01720.494-0.023-0.0230.0000.0000.0000.000
14A17PRO00.0070.00017.7920.0060.0060.0000.0000.0000.000
15A18PHE00.004-0.00916.921-0.034-0.0340.0000.0000.0000.000
16A19HIS00.0080.02318.259-0.010-0.0100.0000.0000.0000.000
17A20PRO00.0040.00112.9610.0130.0130.0000.0000.0000.000
18A21LEU00.002-0.00613.9830.0170.0170.0000.0000.0000.000
19A22LEU00.0410.00711.6220.0130.0130.0000.0000.0000.000
20A23ALA00.003-0.00414.6450.0000.0000.0000.0000.0000.000
21A24HIS0-0.0010.01617.308-0.008-0.0080.0000.0000.0000.000
22A25MET0-0.022-0.00215.8720.0190.0190.0000.0000.0000.000
23A26LEU0-0.033-0.02316.020-0.003-0.0030.0000.0000.0000.000
24A27ASP-1-0.724-0.84919.8170.0380.0380.0000.0000.0000.000
25A28THR00.0220.01222.408-0.010-0.0100.0000.0000.0000.000
26A29ALA00.0110.00222.209-0.004-0.0040.0000.0000.0000.000
27A30ALA0-0.032-0.01823.930-0.006-0.0060.0000.0000.0000.000
28A31VAL00.0240.00625.658-0.008-0.0080.0000.0000.0000.000
29A32ALA00.0070.01227.179-0.005-0.0050.0000.0000.0000.000
30A33LEU0-0.013-0.01027.038-0.005-0.0050.0000.0000.0000.000
31A34ALA0-0.049-0.02729.356-0.006-0.0060.0000.0000.0000.000
32A35VAL00.0440.01031.670-0.005-0.0050.0000.0000.0000.000
33A36LEU00.0160.01330.618-0.003-0.0030.0000.0000.0000.000
34A37ARG10.8890.93929.804-0.078-0.0780.0000.0000.0000.000
35A38MET0-0.036-0.00635.442-0.005-0.0050.0000.0000.0000.000
36A39GLU-1-0.827-0.89436.8150.0550.0550.0000.0000.0000.000
37A40PRO0-0.019-0.02539.224-0.001-0.0010.0000.0000.0000.000
38A41PRO00.0400.01141.4150.0030.0030.0000.0000.0000.000
39A42ARG10.9370.95942.353-0.043-0.0430.0000.0000.0000.000
40A43THR00.0250.01538.1400.0010.0010.0000.0000.0000.000
41A44ARG10.8770.94836.933-0.055-0.0550.0000.0000.0000.000
42A45ALA00.0340.01538.1480.0050.0050.0000.0000.0000.000
43A46LEU0-0.021-0.00839.8870.0030.0030.0000.0000.0000.000
44A47TYR0-0.006-0.01332.4340.0080.0080.0000.0000.0000.000
45A48ALA0-0.021-0.01235.5450.0070.0070.0000.0000.0000.000
46A49GLU-1-0.893-0.94237.0690.0780.0780.0000.0000.0000.000
47A50ASP-1-0.798-0.87735.5160.0960.0960.0000.0000.0000.000
48A51TRP0-0.025-0.02931.9060.0100.0100.0000.0000.0000.000
49A52GLY00.0500.03833.8570.0070.0070.0000.0000.0000.000
50A53LEU0-0.057-0.02630.1050.0030.0030.0000.0000.0000.000
51A54PRO00.0310.00733.822-0.007-0.0070.0000.0000.0000.000
52A55GLU-1-0.828-0.93034.2960.0770.0770.0000.0000.0000.000
53A56GLU-1-0.950-0.97131.4670.0910.0910.0000.0000.0000.000
54A57GLY00.0100.00129.9220.0060.0060.0000.0000.0000.000
55A58ALA0-0.002-0.00629.6570.0110.0110.0000.0000.0000.000
56A59LEU0-0.006-0.01030.6770.0050.0050.0000.0000.0000.000
57A60ALA00.0210.02226.3180.0040.0040.0000.0000.0000.000
58A61TRP00.023-0.00224.6930.0230.0230.0000.0000.0000.000
59A62ALA00.0160.01026.1490.0120.0120.0000.0000.0000.000
60A63ALA00.001-0.00626.0720.0020.0020.0000.0000.0000.000
61A64ALA00.003-0.00421.8140.0050.0050.0000.0000.0000.000
62A65LEU0-0.049-0.02222.0960.0210.0210.0000.0000.0000.000
63A66VAL00.0400.03323.7260.0070.0070.0000.0000.0000.000
64A67GLY00.0020.00521.539-0.008-0.0080.0000.0000.0000.000
65A68LEU0-0.105-0.05818.2160.0210.0210.0000.0000.0000.000
66A69HIS00.0390.03020.7340.0090.0090.0000.0000.0000.000
67A70ASP-1-0.744-0.86320.4020.1040.1040.0000.0000.0000.000
68A71LEU00.006-0.00715.1200.0070.0070.0000.0000.0000.000
69A72GLY0-0.047-0.03717.1550.0270.0270.0000.0000.0000.000
70A73LYS10.8700.92517.870-0.084-0.0840.0000.0000.0000.000
71A74ALA0-0.0080.01512.962-0.035-0.0350.0000.0000.0000.000
72A75SER00.002-0.02113.7840.0670.0670.0000.0000.0000.000
73A76PRO00.0280.01512.487-0.041-0.0410.0000.0000.0000.000
74A77VAL0-0.0280.00014.389-0.033-0.0330.0000.0000.0000.000
75A78PHE0-0.060-0.02017.115-0.014-0.0140.0000.0000.0000.000
76A79GLN0-0.029-0.00113.343-0.053-0.0530.0000.0000.0000.000
77A80ALA00.0170.01614.437-0.014-0.0140.0000.0000.0000.000
78A102TRP00.0290.00423.4330.0040.0040.0000.0000.0000.000
79A103VAL0-0.008-0.00724.0200.0020.0020.0000.0000.0000.000
80A104ALA00.0700.04624.726-0.002-0.0020.0000.0000.0000.000
81A105HIS00.046-0.00121.3000.0040.0040.0000.0000.0000.000
82A106GLY00.0920.04222.6290.0210.0210.0000.0000.0000.000
83A107VAL00.0000.00524.9980.0130.0130.0000.0000.0000.000
84A108PHE0-0.046-0.02719.2590.0140.0140.0000.0000.0000.000
85A109THR00.0000.00920.9900.0340.0340.0000.0000.0000.000
86A110GLU-1-0.794-0.88822.0240.1660.1660.0000.0000.0000.000
87A111LEU0-0.130-0.08522.0320.0130.0130.0000.0000.0000.000
88A112PHE0-0.029-0.02116.9780.0270.0270.0000.0000.0000.000
89A113LEU00.0950.04719.8720.0340.0340.0000.0000.0000.000
90A114ARG10.9170.97021.929-0.183-0.1830.0000.0000.0000.000
91A115ARG10.8420.92718.857-0.352-0.3520.0000.0000.0000.000
92A116LEU00.0320.00715.8370.0070.0070.0000.0000.0000.000
93A117LEU00.0240.01519.4540.0110.0110.0000.0000.0000.000
94A118LYS10.7990.91722.653-0.231-0.2310.0000.0000.0000.000
95A119GLU-1-0.846-0.90817.0480.5280.5280.0000.0000.0000.000
96A120LYS10.8350.91218.361-0.397-0.3970.0000.0000.0000.000
97A121GLY00.0360.02621.593-0.014-0.0140.0000.0000.0000.000
98A122LEU0-0.0170.00525.143-0.021-0.0210.0000.0000.0000.000
99A123PRO00.0300.01727.2430.0080.0080.0000.0000.0000.000
100A124GLU-1-0.888-0.96928.0790.2070.2070.0000.0000.0000.000
101A125ARG10.9120.94929.901-0.120-0.1200.0000.0000.0000.000
102A126ALA00.0880.06130.681-0.003-0.0030.0000.0000.0000.000
103A127ALA00.0170.01225.9670.0020.0020.0000.0000.0000.000
104A128ASN0-0.034-0.03927.5990.0150.0150.0000.0000.0000.000
105A129ASP-1-0.883-0.93429.2820.1250.1250.0000.0000.0000.000
106A130LEU00.0020.00127.715-0.004-0.0040.0000.0000.0000.000
107A131ALA0-0.055-0.02725.7620.0020.0020.0000.0000.0000.000
108A132ALA00.005-0.00626.841-0.002-0.0020.0000.0000.0000.000
109A133ALA0-0.028-0.00529.745-0.009-0.0090.0000.0000.0000.000
110A134LEU0-0.018-0.00924.690-0.006-0.0060.0000.0000.0000.000
111A135GLY0-0.0010.00526.0650.0060.0060.0000.0000.0000.000
112A136ALA0-0.067-0.03727.535-0.007-0.0070.0000.0000.0000.000
113A137HIS0-0.077-0.05129.075-0.012-0.0120.0000.0000.0000.000
114A138HIS00.0320.01132.1630.0010.0010.0000.0000.0000.000
115A139GLY00.0680.03432.288-0.004-0.0040.0000.0000.0000.000
116A140PHE0-0.054-0.00633.5090.0020.0020.0000.0000.0000.000
117A141PRO0-0.012-0.00731.6300.0030.0030.0000.0000.0000.000
118A142ALA00.0250.01228.929-0.008-0.0080.0000.0000.0000.000
119A143ASN00.0040.00930.8990.0060.0060.0000.0000.0000.000
120A144ALA0-0.018-0.03631.1100.0070.0070.0000.0000.0000.000
121A145GLU-1-0.838-0.91630.9070.0830.0830.0000.0000.0000.000
122A146GLU-1-0.821-0.90928.5530.0970.0970.0000.0000.0000.000
123A147LYS10.9500.96926.546-0.128-0.1280.0000.0000.0000.000
124A148SER0-0.037-0.00825.9390.0150.0150.0000.0000.0000.000
125A149ARG10.8770.92626.204-0.059-0.0590.0000.0000.0000.000
126A150ALA00.0430.03322.4860.0010.0010.0000.0000.0000.000
127A151ARG10.9360.94721.479-0.176-0.1760.0000.0000.0000.000
128A152ARG10.9190.94821.698-0.078-0.0780.0000.0000.0000.000
129A153HIS00.0430.03118.9720.0050.0050.0000.0000.0000.000
130A154LEU0-0.038-0.01116.8010.0140.0140.0000.0000.0000.000
131A155ARG10.8730.93916.967-0.125-0.1250.0000.0000.0000.000
132A156THR00.0280.01517.4220.0160.0160.0000.0000.0000.000
133A157GLU-1-0.831-0.87113.0710.3600.3600.0000.0000.0000.000
134A158ASP-1-0.834-0.9308.2090.7500.7500.0000.0000.0000.000
135A159PRO00.019-0.01310.170-0.004-0.0040.0000.0000.0000.000
136A160LEU00.0610.0452.679-0.814-0.0510.341-0.292-0.8110.000
137A161TRP00.0240.0067.365-0.014-0.0140.0000.0000.0000.000
138A162LYS10.8230.9129.687-0.534-0.5340.0000.0000.0000.000
139A163GLU-1-0.866-0.9427.4362.0592.0590.0000.0000.0000.000
140A164ALA00.0120.0077.3380.0340.0340.0000.0000.0000.000
141A165ARG10.7710.8698.599-0.517-0.5170.0000.0000.0000.000
142A166ARG10.8060.88511.635-0.736-0.7360.0000.0000.0000.000
143A167TRP00.0230.0087.3660.0290.0290.0000.0000.0000.000
144A168LEU0-0.009-0.01310.435-0.113-0.1130.0000.0000.0000.000
145A169LEU00.0190.01712.331-0.088-0.0880.0000.0000.0000.000
146A170GLU-1-0.866-0.93213.0250.4440.4440.0000.0000.0000.000
147A171GLU-1-0.857-0.90511.9610.4390.4390.0000.0000.0000.000
148A172VAL00.0140.00814.028-0.077-0.0770.0000.0000.0000.000
149A173PHE00.025-0.00617.341-0.039-0.0390.0000.0000.0000.000
150A174ARG10.8810.94112.329-0.590-0.5900.0000.0000.0000.000
151A175ARG10.7420.84813.371-0.272-0.2720.0000.0000.0000.000
152A176LEU0-0.017-0.01319.032-0.031-0.0310.0000.0000.0000.000
153A177GLY0-0.0240.01321.614-0.019-0.0190.0000.0000.0000.000
154A178ALA0-0.037-0.01622.710-0.014-0.0140.0000.0000.0000.000
155A179PRO0-0.0340.00123.7690.0190.0190.0000.0000.0000.000
156A180LEU0-0.015-0.01824.7620.0020.0020.0000.0000.0000.000
157A181PRO0-0.021-0.00627.033-0.010-0.0100.0000.0000.0000.000
158A182PRO00.0130.01830.4550.0090.0090.0000.0000.0000.000
159A183SER0-0.046-0.02630.8490.0010.0010.0000.0000.0000.000
160A184GLN0-0.119-0.07033.3400.0020.0020.0000.0000.0000.000
161A185GLY00.0500.03035.253-0.002-0.0020.0000.0000.0000.000
162A186ASN0-0.008-0.00833.253-0.010-0.0100.0000.0000.0000.000
163A187GLY0-0.084-0.05035.0090.0040.0040.0000.0000.0000.000
164A188GLU-1-0.765-0.88634.0590.1320.1320.0000.0000.0000.000
165A189ALA00.0710.02833.3590.0060.0060.0000.0000.0000.000
166A190ARG10.7630.88935.502-0.087-0.0870.0000.0000.0000.000
167A191PRO00.0890.02337.3940.0030.0030.0000.0000.0000.000
168A192GLU-1-0.888-0.96437.7270.0730.0730.0000.0000.0000.000
169A193ALA0-0.0280.01235.195-0.001-0.0010.0000.0000.0000.000
170A194VAL0-0.031-0.01332.3840.0050.0050.0000.0000.0000.000
171A195LEU0-0.007-0.00933.4320.0030.0030.0000.0000.0000.000
172A196ARG10.8060.88335.485-0.086-0.0860.0000.0000.0000.000
173A197VAL00.0150.01428.9030.0010.0010.0000.0000.0000.000
174A198MET0-0.057-0.00930.7870.0000.0000.0000.0000.0000.000
175A199ALA00.0170.01231.949-0.002-0.0020.0000.0000.0000.000
176A200LEU0-0.0070.00330.297-0.003-0.0030.0000.0000.0000.000
177A201ALA0-0.010-0.02427.348-0.002-0.0020.0000.0000.0000.000
178A202SER0-0.0150.00828.755-0.005-0.0050.0000.0000.0000.000
179A203PHE00.0170.00231.064-0.008-0.0080.0000.0000.0000.000
180A204ALA0-0.002-0.01427.802-0.006-0.0060.0000.0000.0000.000
181A205ASP-1-0.861-0.93624.9180.0820.0820.0000.0000.0000.000
182A206TRP0-0.015-0.00327.121-0.010-0.0100.0000.0000.0000.000
183A207VAL0-0.014-0.00829.758-0.008-0.0080.0000.0000.0000.000
184A208ALA0-0.021-0.01824.609-0.009-0.0090.0000.0000.0000.000
185A209SER0-0.046-0.02225.542-0.007-0.0070.0000.0000.0000.000
186A210ASP-1-0.851-0.89626.627-0.009-0.0090.0000.0000.0000.000
187A211PRO0-0.005-0.00426.296-0.001-0.0010.0000.0000.0000.000
188A212SER0-0.125-0.07827.747-0.006-0.0060.0000.0000.0000.000
189A213LEU0-0.050-0.02929.890-0.001-0.0010.0000.0000.0000.000
190A214PHE0-0.025-0.01124.5730.0030.0030.0000.0000.0000.000
191A215PRO00.0190.02525.145-0.003-0.0030.0000.0000.0000.000
192A216TYR00.013-0.00821.729-0.003-0.0030.0000.0000.0000.000
193A217GLY00.0250.01519.628-0.007-0.0070.0000.0000.0000.000
194A218ARG10.7470.87819.703-0.016-0.0160.0000.0000.0000.000
195A219ASP-1-0.798-0.90713.585-0.157-0.1570.0000.0000.0000.000
196A220PRO00.0340.01112.9670.0080.0080.0000.0000.0000.000
197A221ARG10.8630.9199.0110.4090.4090.0000.0000.0000.000
198A222ARG10.8820.96312.8660.0680.0680.0000.0000.0000.000
199A223GLY00.0520.01916.2830.0310.0310.0000.0000.0000.000
200A224ASP-1-0.942-0.98118.316-0.017-0.0170.0000.0000.0000.000
201A225TYR00.000-0.00218.007-0.002-0.0020.0000.0000.0000.000
202A226LEU00.0340.01220.096-0.002-0.0020.0000.0000.0000.000
203A227LYS10.9470.97221.943-0.043-0.0430.0000.0000.0000.000
204A228GLU-1-0.817-0.89223.422-0.010-0.0100.0000.0000.0000.000
205A229ALA00.0160.00422.545-0.003-0.0030.0000.0000.0000.000
206A230LEU00.000-0.01324.6580.0010.0010.0000.0000.0000.000
207A231ARG10.7780.88727.5240.0020.0020.0000.0000.0000.000
208A232LEU00.0020.00525.274-0.003-0.0030.0000.0000.0000.000
209A233ALA00.0290.01728.171-0.001-0.0010.0000.0000.0000.000
210A234GLN0-0.016-0.00429.8950.0030.0030.0000.0000.0000.000
211A235GLU-1-0.927-0.96532.401-0.005-0.0050.0000.0000.0000.000
212A236ALA00.0080.01431.486-0.002-0.0020.0000.0000.0000.000
213A237LEU0-0.011-0.01632.801-0.001-0.0010.0000.0000.0000.000
214A238ASN0-0.019-0.01535.4500.0010.0010.0000.0000.0000.000
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