FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: G5951

Calculation Name: 3S6K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3S6K

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-09-24

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 438
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7428346.4854
FMO2-HF: Nuclear repulsion 7260598.548122
FMO2-HF: Total energy -167747.937277
FMO2-MP2: Total energy -168243.790994


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:10:GLN)


Summations of interaction energy for fragment #1(A:10:GLN)
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.
-21.869-16.4881.799-2.989-4.190.012
Interaction energy analysis for fragmet #1(A:10:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.011
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].
3A12ARG10.9320.9583.297-5.309-3.1820.070-0.939-1.2580.006
4A13GLN0-0.041-0.0122.313-5.581-3.2661.726-1.679-2.3620.007
5A14THR0-0.011-0.0204.190-2.183-1.7570.002-0.149-0.2790.000
6A15ILE00.0670.0406.162-0.559-0.5590.0000.0000.0000.000
7A16VAL00.0430.0098.191-0.474-0.4740.0000.0000.0000.000
8A17ARG10.8690.9417.074-2.359-2.3590.0000.0000.0000.000
9A18LEU00.0090.0069.923-0.215-0.2150.0000.0000.0000.000
10A19LEU0-0.0010.00511.898-0.189-0.1890.0000.0000.0000.000
11A20SER0-0.031-0.04213.485-0.146-0.1460.0000.0000.0000.000
12A21SER0-0.0330.00515.249-0.102-0.1020.0000.0000.0000.000
13A22MET0-0.040-0.01717.469-0.053-0.0530.0000.0000.0000.000
14A23ALA00.0460.02519.631-0.007-0.0070.0000.0000.0000.000
15A24SER00.0180.00920.438-0.009-0.0090.0000.0000.0000.000
16A25ALA00.0030.01117.0310.0280.0280.0000.0000.0000.000
17A26LYS10.8440.93016.380-0.325-0.3250.0000.0000.0000.000
18A27GLU-1-0.763-0.87717.4320.4850.4850.0000.0000.0000.000
19A28ILE00.0120.01014.082-0.017-0.0170.0000.0000.0000.000
20A29SER0-0.045-0.04612.5740.0500.0500.0000.0000.0000.000
21A30GLN0-0.013-0.01012.6870.0600.0600.0000.0000.0000.000
22A31TYR00.014-0.00914.809-0.035-0.0350.0000.0000.0000.000
23A32LEU00.0050.0049.587-0.017-0.0170.0000.0000.0000.000
24A33LYS10.8220.8909.680-0.818-0.8180.0000.0000.0000.000
25A34ARG10.8010.91011.497-0.217-0.2170.0000.0000.0000.000
26A35PHE00.0610.04111.146-0.067-0.0670.0000.0000.0000.000
27A36SER0-0.074-0.0297.0910.0760.0760.0000.0000.0000.000
28A37GLN0-0.015-0.0098.4460.0510.0510.0000.0000.0000.000
29A38LEU00.0090.0079.6630.0160.0160.0000.0000.0000.000
30A39ASP-1-0.823-0.90312.803-0.685-0.6850.0000.0000.0000.000
31A40ALA0-0.0010.0069.750-0.177-0.1770.0000.0000.0000.000
32A41LYS10.8670.91111.0500.7260.7260.0000.0000.0000.000
33A42ARG10.8330.92114.0970.5260.5260.0000.0000.0000.000
34A43PHE00.0170.01311.5650.1190.1190.0000.0000.0000.000
35A44ALA0-0.015-0.01013.7060.0660.0660.0000.0000.0000.000
36A45VAL00.0460.03715.956-0.071-0.0710.0000.0000.0000.000
37A46VAL0-0.037-0.03217.8110.0590.0590.0000.0000.0000.000
38A47LYS10.8370.93320.1500.1060.1060.0000.0000.0000.000
39A48VAL00.003-0.00522.6040.0280.0280.0000.0000.0000.000
40A49GLY00.0340.00225.400-0.004-0.0040.0000.0000.0000.000
41A50GLY0-0.012-0.01728.8770.0040.0040.0000.0000.0000.000
42A51ALA0-0.021-0.01231.3150.0030.0030.0000.0000.0000.000
43A52VAL00.0010.00526.2320.0120.0120.0000.0000.0000.000
44A53LEU00.0050.00525.8060.0040.0040.0000.0000.0000.000
45A54ARG10.8170.90227.9410.0340.0340.0000.0000.0000.000
46A55ASP-1-0.904-0.94730.194-0.023-0.0230.0000.0000.0000.000
47A56ASP-1-0.874-0.94025.5770.0270.0270.0000.0000.0000.000
48A57LEU00.0280.01524.491-0.011-0.0110.0000.0000.0000.000
49A58GLU-1-0.869-0.92423.275-0.072-0.0720.0000.0000.0000.000
50A59ALA00.0340.02021.290-0.002-0.0020.0000.0000.0000.000
51A60LEU0-0.041-0.00220.057-0.006-0.0060.0000.0000.0000.000
52A61THR0-0.010-0.03219.285-0.030-0.0300.0000.0000.0000.000
53A62SER00.0430.03816.976-0.036-0.0360.0000.0000.0000.000
54A63SER0-0.090-0.06315.642-0.002-0.0020.0000.0000.0000.000
55A64LEU0-0.015-0.02014.521-0.039-0.0390.0000.0000.0000.000
56A65SER0-0.007-0.01213.710-0.135-0.1350.0000.0000.0000.000
57A66PHE00.0090.01710.950-0.138-0.1380.0000.0000.0000.000
58A67LEU0-0.038-0.0149.444-0.023-0.0230.0000.0000.0000.000
59A68GLN00.028-0.0148.505-0.228-0.2280.0000.0000.0000.000
60A69GLU-1-0.959-0.9648.520-0.603-0.6030.0000.0000.0000.000
61A70VAL0-0.043-0.0154.532-0.183-0.066-0.001-0.005-0.1100.000
62A71GLY0-0.030-0.0143.628-3.659-3.2630.002-0.217-0.181-0.001
63A72LEU0-0.071-0.0226.0050.3950.3950.0000.0000.0000.000
64A73THR00.009-0.0168.5440.3050.3050.0000.0000.0000.000
65A74PRO0-0.0340.00911.4400.0850.0850.0000.0000.0000.000
66A75ILE00.0400.01814.623-0.001-0.0010.0000.0000.0000.000
67A76VAL0-0.010-0.00417.6850.0690.0690.0000.0000.0000.000
68A77LEU00.0150.02020.476-0.005-0.0050.0000.0000.0000.000
69A78HIS0-0.015-0.01424.2100.0460.0460.0000.0000.0000.000
70A79GLY00.1010.03226.822-0.003-0.0030.0000.0000.0000.000
71A80ALA0-0.0390.00430.6300.0160.0160.0000.0000.0000.000
72A81GLY00.0120.00032.3530.0040.0040.0000.0000.0000.000
73A82PRO00.0330.00734.1960.0010.0010.0000.0000.0000.000
74A83GLN00.0610.02631.4720.0070.0070.0000.0000.0000.000
75A84LEU0-0.0010.01436.5230.0010.0010.0000.0000.0000.000
76A85ASP-1-0.740-0.81738.274-0.059-0.0590.0000.0000.0000.000
77A86ALA0-0.0070.01940.3620.0040.0040.0000.0000.0000.000
78A87GLU-1-0.926-0.97239.707-0.071-0.0710.0000.0000.0000.000
79A88LEU0-0.072-0.02941.985-0.001-0.0010.0000.0000.0000.000
80A89SER0-0.042-0.05743.9750.0030.0030.0000.0000.0000.000
81A90ALA0-0.0200.00945.4500.0030.0030.0000.0000.0000.000
82A91ALA0-0.0230.00047.1890.0010.0010.0000.0000.0000.000
83A92GLY00.0190.01048.3720.0020.0020.0000.0000.0000.000
84A93ILE0-0.027-0.03148.269-0.003-0.0030.0000.0000.0000.000
85A94GLH0-0.033-0.02442.530-0.002-0.0020.0000.0000.0000.000
86A95LYS10.9060.93847.2620.0350.0350.0000.0000.0000.000
87A96GLN0-0.014-0.02248.2210.0000.0000.0000.0000.0000.000
88A97THR0-0.0040.00145.022-0.003-0.0030.0000.0000.0000.000
89A98VAL0-0.0150.00447.3040.0030.0030.0000.0000.0000.000
90A99ASN00.0420.03846.1060.0050.0050.0000.0000.0000.000
91A100GLY00.0200.01343.8300.0000.0000.0000.0000.0000.000
92A101LEU0-0.028-0.02339.166-0.003-0.0030.0000.0000.0000.000
93A102ARG10.7840.84839.7340.0660.0660.0000.0000.0000.000
94A103VAL00.0190.01743.714-0.001-0.0010.0000.0000.0000.000
95A104THR0-0.030-0.01442.0190.0000.0000.0000.0000.0000.000
96A105SER00.0360.02445.160-0.001-0.0010.0000.0000.0000.000
97A106PRO00.0680.02245.894-0.003-0.0030.0000.0000.0000.000
98A107HIS00.0220.00245.596-0.008-0.0080.0000.0000.0000.000
99A108ALA00.0310.02644.8200.0000.0000.0000.0000.0000.000
100A109LEU00.0180.00041.249-0.002-0.0020.0000.0000.0000.000
101A110ALA0-0.051-0.02540.626-0.007-0.0070.0000.0000.0000.000
102A111ILE00.0140.01541.093-0.005-0.0050.0000.0000.0000.000
103A112VAL00.0540.02237.872-0.005-0.0050.0000.0000.0000.000
104A113ARG10.9771.00136.3210.1190.1190.0000.0000.0000.000
105A114LYS10.9170.95935.5210.1060.1060.0000.0000.0000.000
106A115VAL00.0580.03934.917-0.006-0.0060.0000.0000.0000.000
107A116PHE00.0080.01631.040-0.004-0.0040.0000.0000.0000.000
108A117GLN00.0200.01531.127-0.021-0.0210.0000.0000.0000.000
109A118ALA0-0.004-0.00230.846-0.011-0.0110.0000.0000.0000.000
110A119SER0-0.030-0.03730.074-0.005-0.0050.0000.0000.0000.000
111A120ASN00.0090.00525.5320.0040.0040.0000.0000.0000.000
112A121LEU00.0230.00726.073-0.017-0.0170.0000.0000.0000.000
113A122LYS10.8730.94926.4260.1390.1390.0000.0000.0000.000
114A123LEU00.0300.01922.0440.0060.0060.0000.0000.0000.000
115A124VAL0-0.020-0.01422.036-0.014-0.0140.0000.0000.0000.000
116A125GLU-1-0.867-0.95321.953-0.285-0.2850.0000.0000.0000.000
117A126ALA0-0.045-0.01723.4290.0070.0070.0000.0000.0000.000
118A127LEU0-0.014-0.00317.5090.0100.0100.0000.0000.0000.000
119A128GLN00.002-0.00218.556-0.063-0.0630.0000.0000.0000.000
120A129GLN0-0.068-0.04120.0420.0050.0050.0000.0000.0000.000
121A130ASN0-0.039-0.02016.7080.0570.0570.0000.0000.0000.000
122A131GLY00.0020.01316.5510.0290.0290.0000.0000.0000.000
123A132ALA0-0.050-0.01514.175-0.085-0.0850.0000.0000.0000.000
124A133ARG10.8740.93412.7811.1581.1580.0000.0000.0000.000
125A134ALA00.0120.02716.306-0.070-0.0700.0000.0000.0000.000
126A135THR00.019-0.01118.7570.0160.0160.0000.0000.0000.000
127A136SER00.000-0.00421.2400.0150.0150.0000.0000.0000.000
128A137ILE00.0050.01623.111-0.007-0.0070.0000.0000.0000.000
129A138THR0-0.031-0.01325.7170.0070.0070.0000.0000.0000.000
130A139GLY00.002-0.00329.0200.0240.0240.0000.0000.0000.000
131A140GLY00.0400.03029.431-0.022-0.0220.0000.0000.0000.000
132A141VAL0-0.037-0.01526.242-0.010-0.0100.0000.0000.0000.000
133A142PHE00.0290.00827.627-0.001-0.0010.0000.0000.0000.000
134A143GLU-1-0.817-0.89231.891-0.155-0.1550.0000.0000.0000.000
135A144ALA0-0.085-0.04835.0450.0110.0110.0000.0000.0000.000
136A145GLU-1-0.782-0.87737.214-0.116-0.1160.0000.0000.0000.000
137A146TYR0-0.029-0.03040.6790.0050.0050.0000.0000.0000.000
138A147LEU0-0.0050.01141.5870.0040.0040.0000.0000.0000.000
139A148ASN0-0.029-0.05344.5110.0030.0030.0000.0000.0000.000
140A149ARG10.8630.93247.5950.0610.0610.0000.0000.0000.000
141A150ASP-1-0.792-0.87949.332-0.059-0.0590.0000.0000.0000.000
142A151THR0-0.029-0.01349.5900.0000.0000.0000.0000.0000.000
143A152TYR00.0230.00945.6080.0040.0040.0000.0000.0000.000
144A153GLY0-0.0040.00046.310-0.003-0.0030.0000.0000.0000.000
145A154LEU0-0.026-0.01143.773-0.003-0.0030.0000.0000.0000.000
146A155VAL0-0.010-0.01040.465-0.003-0.0030.0000.0000.0000.000
147A156GLY00.013-0.01539.9330.0030.0030.0000.0000.0000.000
148A157GLU-1-0.861-0.92736.294-0.106-0.1060.0000.0000.0000.000
149A158VAL0-0.035-0.01532.293-0.004-0.0040.0000.0000.0000.000
150A159LYS10.7320.84034.0710.1320.1320.0000.0000.0000.000
151A160ALA00.0420.03232.9350.0010.0010.0000.0000.0000.000
152A161VAL0-0.033-0.00927.9610.0050.0050.0000.0000.0000.000
153A162ASN0-0.033-0.02028.222-0.015-0.0150.0000.0000.0000.000
154A163LEU00.0760.03320.984-0.026-0.0260.0000.0000.0000.000
155A164ALA00.0210.03022.979-0.043-0.0430.0000.0000.0000.000
156A165PRO0-0.044-0.03323.166-0.045-0.0450.0000.0000.0000.000
157A166ILE00.0060.00320.065-0.035-0.0350.0000.0000.0000.000
158A167GLU-1-0.819-0.92518.441-0.604-0.6040.0000.0000.0000.000
159A168ALA0-0.0080.02018.129-0.094-0.0940.0000.0000.0000.000
160A169SER0-0.0050.00518.301-0.049-0.0490.0000.0000.0000.000
161A170LEU00.002-0.00114.497-0.082-0.0820.0000.0000.0000.000
162A171GLN0-0.072-0.04213.413-0.199-0.1990.0000.0000.0000.000
163A172ALA0-0.0150.00814.074-0.120-0.1200.0000.0000.0000.000
164A173GLY0-0.0070.00411.690-0.106-0.1060.0000.0000.0000.000
165A174SER0-0.032-0.03312.400-0.029-0.0290.0000.0000.0000.000
166A175ILE0-0.009-0.00213.883-0.030-0.0300.0000.0000.0000.000
167A176PRO00.0010.01516.3450.0770.0770.0000.0000.0000.000
168A177VAL0-0.028-0.01819.8290.0250.0250.0000.0000.0000.000
169A178ILE00.0380.00822.0530.0200.0200.0000.0000.0000.000
170A179THR0-0.021-0.01825.0060.0170.0170.0000.0000.0000.000
171A180SER0-0.004-0.02428.6400.0000.0000.0000.0000.0000.000
172A181LEU0-0.071-0.04031.0210.0160.0160.0000.0000.0000.000
173A182GLY00.0430.01232.718-0.009-0.0090.0000.0000.0000.000
174A183GLU-1-0.941-0.97334.304-0.199-0.1990.0000.0000.0000.000
175A184THR00.001-0.00436.7630.0000.0000.0000.0000.0000.000
176A185PRO00.0290.00939.040-0.006-0.0060.0000.0000.0000.000
177A186SER0-0.044-0.01740.115-0.002-0.0020.0000.0000.0000.000
178A187GLY00.0270.01838.8790.0040.0040.0000.0000.0000.000
179A188GLN0-0.0370.00039.958-0.003-0.0030.0000.0000.0000.000
180A189ILE00.004-0.00136.897-0.001-0.0010.0000.0000.0000.000
181A190LEU0-0.045-0.01339.0540.0050.0050.0000.0000.0000.000
182A191ASN00.0070.00537.185-0.013-0.0130.0000.0000.0000.000
183A192VAL00.0500.03433.4060.0030.0030.0000.0000.0000.000
184A193ASN0-0.031-0.00535.0500.0000.0000.0000.0000.0000.000
185A194ALA00.0920.03230.740-0.007-0.0070.0000.0000.0000.000
186A195ASP-1-0.855-0.90730.155-0.084-0.0840.0000.0000.0000.000
187A196PHE00.0430.01430.835-0.003-0.0030.0000.0000.0000.000
188A197ALA00.0490.02530.326-0.007-0.0070.0000.0000.0000.000
189A198ALA0-0.021-0.01526.590-0.017-0.0170.0000.0000.0000.000
190A199ASN00.0210.00426.752-0.009-0.0090.0000.0000.0000.000
191A200GLU-1-0.821-0.89328.192-0.171-0.1710.0000.0000.0000.000
192A201LEU00.0050.00022.922-0.016-0.0160.0000.0000.0000.000
193A202VAL0-0.031-0.02723.083-0.031-0.0310.0000.0000.0000.000
194A203GLN0-0.032-0.01224.1590.0070.0070.0000.0000.0000.000
195A204GLU-1-0.812-0.92924.236-0.316-0.3160.0000.0000.0000.000
196A205LEU0-0.062-0.02318.638-0.032-0.0320.0000.0000.0000.000
197A206GLN0-0.040-0.03520.146-0.025-0.0250.0000.0000.0000.000
198A207PRO00.0010.01618.070-0.026-0.0260.0000.0000.0000.000
199A208TYR00.0130.00613.8880.0870.0870.0000.0000.0000.000
200A209LYS10.8080.90216.196-0.044-0.0440.0000.0000.0000.000
201A210ILE00.0310.01818.101-0.064-0.0640.0000.0000.0000.000
202A211ILE0-0.055-0.02618.3770.0440.0440.0000.0000.0000.000
203A212PHE00.0180.00121.453-0.031-0.0310.0000.0000.0000.000
204A213LEU00.0060.00121.1300.0260.0260.0000.0000.0000.000
205A214THR0-0.037-0.02924.372-0.015-0.0150.0000.0000.0000.000
206A215GLY00.0160.00227.7500.0130.0130.0000.0000.0000.000
207A216THR00.0060.00229.6440.0070.0070.0000.0000.0000.000
208A217GLY0-0.017-0.01727.6680.0110.0110.0000.0000.0000.000
209A218GLY00.0310.03028.4430.0140.0140.0000.0000.0000.000
210A219LEU0-0.048-0.01929.541-0.013-0.0130.0000.0000.0000.000
211A220LEU0-0.028-0.01132.6540.0110.0110.0000.0000.0000.000
212A221ASP-1-0.741-0.88135.4910.0840.0840.0000.0000.0000.000
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