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: VQ7Q1

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 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 438
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7429846.731477
FMO2-HF: Nuclear repulsion 7262111.349857
FMO2-HF: Total energy -167735.38162
FMO2-MP2: Total energy -168232.813013


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.
-12.89-8.2550.173-1.718-3.0910.002
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 : 0.043 / q_NPA : 0.020
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].
3A12ARG10.9730.9643.680-4.953-2.787-0.001-0.871-1.2940.006
4A13GLN00.000-0.0043.095-3.185-1.3480.167-0.620-1.385-0.003
5A14THR00.023-0.0274.534-0.259-0.074-0.001-0.025-0.1590.000
6A15ILE00.0110.0596.817-0.053-0.0530.0000.0000.0000.000
7A16VAL00.045-0.0108.190-0.155-0.1550.0000.0000.0000.000
8A17ARG10.8570.9507.976-0.389-0.3890.0000.0000.0000.000
9A18LEU00.009-0.00410.826-0.045-0.0450.0000.0000.0000.000
10A19LEU0-0.0350.02111.587-0.068-0.0680.0000.0000.0000.000
11A20SER0-0.024-0.03213.579-0.051-0.0510.0000.0000.0000.000
12A21SER0-0.0080.00715.376-0.036-0.0360.0000.0000.0000.000
13A22MET0-0.041-0.01317.947-0.006-0.0060.0000.0000.0000.000
14A23ALA00.0380.01019.804-0.008-0.0080.0000.0000.0000.000
15A24SER00.007-0.02120.866-0.008-0.0080.0000.0000.0000.000
16A25ALA00.0440.02116.2190.0120.0120.0000.0000.0000.000
17A26LYS10.9771.00616.383-0.098-0.0980.0000.0000.0000.000
18A27GLU-1-0.896-0.94117.7360.1740.1740.0000.0000.0000.000
19A28ILE00.0120.01314.517-0.010-0.0100.0000.0000.0000.000
20A29SER0-0.041-0.04512.3180.0210.0210.0000.0000.0000.000
21A30GLN00.0310.00912.2950.0360.0360.0000.0000.0000.000
22A31TYR00.0190.00714.399-0.012-0.0120.0000.0000.0000.000
23A32LEU0-0.026-0.0059.2370.0250.0250.0000.0000.0000.000
24A33LYS10.8720.9178.595-0.146-0.1460.0000.0000.0000.000
25A34ARG10.8880.97811.142-0.036-0.0360.0000.0000.0000.000
26A35PHE00.0700.03711.778-0.029-0.0290.0000.0000.0000.000
27A36SER0-0.133-0.0487.5820.1200.1200.0000.0000.0000.000
28A37GLN0-0.036-0.0128.540-0.043-0.0430.0000.0000.0000.000
29A38LEU00.033-0.0089.8040.0910.0910.0000.0000.0000.000
30A39ASP-1-0.801-0.88612.592-0.489-0.4890.0000.0000.0000.000
31A40ALA00.0070.0249.843-0.082-0.0820.0000.0000.0000.000
32A41LYS10.9290.93211.0640.5030.5030.0000.0000.0000.000
33A42ARG10.7890.90514.2790.3750.3750.0000.0000.0000.000
34A43PHE00.0460.03111.4030.0290.0290.0000.0000.0000.000
35A44ALA0-0.065-0.03213.5200.0750.0750.0000.0000.0000.000
36A45VAL00.0610.00215.922-0.021-0.0210.0000.0000.0000.000
37A46VAL0-0.0170.00217.4020.0270.0270.0000.0000.0000.000
38A47LYS10.9460.99220.2640.1030.1030.0000.0000.0000.000
39A48VAL0-0.0040.02922.9250.0200.0200.0000.0000.0000.000
40A49GLY00.0690.00925.478-0.001-0.0010.0000.0000.0000.000
41A50GLY0-0.004-0.01628.9330.0040.0040.0000.0000.0000.000
42A51ALA0-0.010-0.01131.3310.0030.0030.0000.0000.0000.000
43A52VAL00.0010.00126.1370.0070.0070.0000.0000.0000.000
44A53LEU0-0.047-0.00425.9940.0030.0030.0000.0000.0000.000
45A54ARG10.8720.93128.3650.0180.0180.0000.0000.0000.000
46A55ASP-1-0.925-0.95631.111-0.001-0.0010.0000.0000.0000.000
47A56ASP-1-0.904-0.95326.4400.0370.0370.0000.0000.0000.000
48A57LEU00.0230.00524.427-0.009-0.0090.0000.0000.0000.000
49A58GLU-1-0.875-0.93623.3150.0070.0070.0000.0000.0000.000
50A59ALA00.0310.01621.7630.0040.0040.0000.0000.0000.000
51A60LEU0-0.0200.01520.743-0.001-0.0010.0000.0000.0000.000
52A61THR0-0.031-0.03219.353-0.024-0.0240.0000.0000.0000.000
53A62SER00.0390.04517.653-0.014-0.0140.0000.0000.0000.000
54A63SER0-0.059-0.04916.2270.0170.0170.0000.0000.0000.000
55A64LEU0-0.049-0.03314.899-0.028-0.0280.0000.0000.0000.000
56A65SER0-0.005-0.03213.694-0.087-0.0870.0000.0000.0000.000
57A66PHE00.0290.00910.531-0.097-0.0970.0000.0000.0000.000
58A67LEU0-0.0330.0009.668-0.020-0.0200.0000.0000.0000.000
59A68GLN00.0360.0048.416-0.269-0.2690.0000.0000.0000.000
60A69GLU-1-0.965-0.9508.431-0.185-0.1850.0000.0000.0000.000
61A70VAL0-0.097-0.0454.8900.2210.2210.0000.0000.0000.000
62A71GLY0-0.042-0.0343.491-3.763-3.3160.008-0.202-0.253-0.001
63A72LEU0-0.056-0.0215.7680.4320.4320.0000.0000.0000.000
64A73THR00.0770.0178.9690.1460.1460.0000.0000.0000.000
65A74PRO0-0.034-0.00311.6320.0860.0860.0000.0000.0000.000
66A75ILE00.007-0.01715.011-0.019-0.0190.0000.0000.0000.000
67A76VAL0-0.039-0.01717.5940.0390.0390.0000.0000.0000.000
68A77LEU00.0250.01420.298-0.006-0.0060.0000.0000.0000.000
69A78HIS0-0.033-0.02424.0380.0290.0290.0000.0000.0000.000
70A79GLY00.0840.01726.513-0.004-0.0040.0000.0000.0000.000
71A80ALA0-0.063-0.03930.3150.0080.0080.0000.0000.0000.000
72A81GLY00.0460.02732.100-0.001-0.0010.0000.0000.0000.000
73A82PRO00.0280.03034.1290.0020.0020.0000.0000.0000.000
74A83GLN00.0390.00331.7420.0000.0000.0000.0000.0000.000
75A84LEU00.0040.03036.5250.0010.0010.0000.0000.0000.000
76A85ASP-1-0.793-0.88538.179-0.037-0.0370.0000.0000.0000.000
77A86ALA0-0.027-0.00540.3800.0030.0030.0000.0000.0000.000
78A87GLU-1-0.958-0.98839.842-0.034-0.0340.0000.0000.0000.000
79A88LEU0-0.037-0.01741.667-0.001-0.0010.0000.0000.0000.000
80A89SER0-0.059-0.03943.7470.0010.0010.0000.0000.0000.000
81A90ALA00.0070.01945.7290.0020.0020.0000.0000.0000.000
82A91ALA0-0.0110.00347.3430.0010.0010.0000.0000.0000.000
83A92GLY0-0.0010.00748.2060.0020.0020.0000.0000.0000.000
84A93ILE0-0.044-0.03848.564-0.002-0.0020.0000.0000.0000.000
85A94GLH0-0.013-0.00442.708-0.003-0.0030.0000.0000.0000.000
86A95LYS10.9470.95147.5730.0240.0240.0000.0000.0000.000
87A96GLN0-0.031-0.01049.394-0.002-0.0020.0000.0000.0000.000
88A97THR0-0.014-0.01545.400-0.001-0.0010.0000.0000.0000.000
89A98VAL00.0070.01247.3540.0000.0000.0000.0000.0000.000
90A99ASN00.0580.04844.6030.0040.0040.0000.0000.0000.000
91A100GLY0-0.0010.00344.0400.0000.0000.0000.0000.0000.000
92A101LEU0-0.042-0.01939.609-0.001-0.0010.0000.0000.0000.000
93A102ARG10.8800.91439.5980.0460.0460.0000.0000.0000.000
94A103VAL00.0250.00943.9270.0000.0000.0000.0000.0000.000
95A104THR0-0.046-0.00641.916-0.001-0.0010.0000.0000.0000.000
96A105SER00.0800.03845.210-0.001-0.0010.0000.0000.0000.000
97A106PRO00.1160.03845.715-0.002-0.0020.0000.0000.0000.000
98A107HIS0-0.0420.00045.673-0.004-0.0040.0000.0000.0000.000
99A108ALA00.014-0.01644.8550.0010.0010.0000.0000.0000.000
100A109LEU00.0660.05440.627-0.001-0.0010.0000.0000.0000.000
101A110ALA0-0.037-0.02540.320-0.003-0.0030.0000.0000.0000.000
102A111ILE00.023-0.00141.000-0.002-0.0020.0000.0000.0000.000
103A112VAL00.0620.04637.496-0.001-0.0010.0000.0000.0000.000
104A113ARG10.9380.99035.9170.0760.0760.0000.0000.0000.000
105A114LYS10.8840.94635.3180.0650.0650.0000.0000.0000.000
106A115VAL00.0690.04935.373-0.002-0.0020.0000.0000.0000.000
107A116PHE00.026-0.00931.409-0.001-0.0010.0000.0000.0000.000
108A117GLN0-0.031-0.00731.097-0.010-0.0100.0000.0000.0000.000
109A118ALA00.003-0.00330.737-0.005-0.0050.0000.0000.0000.000
110A119SER0-0.050-0.02430.328-0.002-0.0020.0000.0000.0000.000
111A120ASN00.0750.02825.481-0.004-0.0040.0000.0000.0000.000
112A121LEU0-0.006-0.00326.046-0.014-0.0140.0000.0000.0000.000
113A122LYS10.9300.97126.2320.0450.0450.0000.0000.0000.000
114A123LEU00.0150.00022.0140.0060.0060.0000.0000.0000.000
115A124VAL00.005-0.00521.289-0.004-0.0040.0000.0000.0000.000
116A125GLU-1-0.884-0.94521.680-0.134-0.1340.0000.0000.0000.000
117A126ALA0-0.0240.00322.6240.0050.0050.0000.0000.0000.000
118A127LEU0-0.002-0.00816.7560.0070.0070.0000.0000.0000.000
119A128GLN0-0.001-0.00418.380-0.038-0.0380.0000.0000.0000.000
120A129GLN0-0.054-0.03319.6080.0100.0100.0000.0000.0000.000
121A130ASN0-0.056-0.01817.0520.0400.0400.0000.0000.0000.000
122A131GLY00.0230.01716.1220.0370.0370.0000.0000.0000.000
123A132ALA0-0.078-0.02414.254-0.043-0.0430.0000.0000.0000.000
124A133ARG10.9500.97010.5890.7330.7330.0000.0000.0000.000
125A134ALA0-0.0170.01915.917-0.055-0.0550.0000.0000.0000.000
126A135THR0-0.027-0.09518.1900.0050.0050.0000.0000.0000.000
127A136SER0-0.0740.02920.700-0.009-0.0090.0000.0000.0000.000
128A137ILE00.0720.03822.344-0.005-0.0050.0000.0000.0000.000
129A138THR0-0.018-0.00325.2740.0090.0090.0000.0000.0000.000
130A139GLY0-0.046-0.02328.5970.0150.0150.0000.0000.0000.000
131A140GLY00.0550.03229.132-0.015-0.0150.0000.0000.0000.000
132A141VAL0-0.034-0.01425.421-0.005-0.0050.0000.0000.0000.000
133A142PHE00.0050.00726.845-0.001-0.0010.0000.0000.0000.000
134A143GLU-1-0.840-0.89331.260-0.113-0.1130.0000.0000.0000.000
135A144ALA0-0.070-0.02234.3610.0080.0080.0000.0000.0000.000
136A145GLU-1-0.928-0.97636.574-0.076-0.0760.0000.0000.0000.000
137A146TYR0-0.015-0.00739.9310.0020.0020.0000.0000.0000.000
138A147LEU0-0.0070.01441.2050.0020.0020.0000.0000.0000.000
139A148ASN0-0.008-0.03444.1720.0030.0030.0000.0000.0000.000
140A149ARG10.9560.99847.0170.0440.0440.0000.0000.0000.000
141A150ASP-1-0.863-0.92849.083-0.042-0.0420.0000.0000.0000.000
142A151THR0-0.067-0.03849.6580.0010.0010.0000.0000.0000.000
143A152TYR0-0.014-0.02045.8930.0010.0010.0000.0000.0000.000
144A153GLY00.0220.01046.7690.0000.0000.0000.0000.0000.000
145A154LEU0-0.041-0.01442.791-0.002-0.0020.0000.0000.0000.000
146A155VAL0-0.039-0.02340.134-0.003-0.0030.0000.0000.0000.000
147A156GLY0-0.028-0.04339.5640.0020.0020.0000.0000.0000.000
148A157GLU-1-0.905-0.94835.997-0.084-0.0840.0000.0000.0000.000
149A158VAL0-0.008-0.01331.552-0.001-0.0010.0000.0000.0000.000
150A159LYS10.8390.94933.7290.0960.0960.0000.0000.0000.000
151A160ALA00.0110.01632.225-0.001-0.0010.0000.0000.0000.000
152A161VAL0-0.023-0.01527.2550.0030.0030.0000.0000.0000.000
153A162ASN00.0120.01927.770-0.013-0.0130.0000.0000.0000.000
154A163LEU00.1030.03021.024-0.020-0.0200.0000.0000.0000.000
155A164ALA00.0410.03022.417-0.034-0.0340.0000.0000.0000.000
156A165PRO0-0.055-0.03322.591-0.031-0.0310.0000.0000.0000.000
157A166ILE00.004-0.00819.487-0.015-0.0150.0000.0000.0000.000
158A167GLU-1-0.958-0.98018.178-0.412-0.4120.0000.0000.0000.000
159A168ALA00.0010.03017.887-0.060-0.0600.0000.0000.0000.000
160A169SER00.074-0.00317.773-0.073-0.0730.0000.0000.0000.000
161A170LEU0-0.0390.00413.345-0.066-0.0660.0000.0000.0000.000
162A171GLN0-0.069-0.03413.469-0.111-0.1110.0000.0000.0000.000
163A172ALA0-0.067-0.01813.896-0.072-0.0720.0000.0000.0000.000
164A173GLY0-0.040-0.01811.579-0.137-0.1370.0000.0000.0000.000
165A174SER0-0.042-0.05112.2800.0340.0340.0000.0000.0000.000
166A175ILE0-0.0020.00314.005-0.001-0.0010.0000.0000.0000.000
167A176PRO00.0300.02415.9680.0690.0690.0000.0000.0000.000
168A177VAL0-0.039-0.04319.3150.0310.0310.0000.0000.0000.000
169A178ILE00.0520.05221.7810.0240.0240.0000.0000.0000.000
170A179THR0-0.052-0.03724.6100.0140.0140.0000.0000.0000.000
171A180SER00.0130.01828.2440.0000.0000.0000.0000.0000.000
172A181LEU0-0.058-0.04931.1790.0110.0110.0000.0000.0000.000
173A182GLY00.0480.00432.517-0.008-0.0080.0000.0000.0000.000
174A183GLU-1-0.881-0.97133.637-0.137-0.1370.0000.0000.0000.000
175A184THR0-0.058-0.04336.606-0.001-0.0010.0000.0000.0000.000
176A185PRO00.0810.05937.865-0.004-0.0040.0000.0000.0000.000
177A186SER0-0.052-0.02139.243-0.003-0.0030.0000.0000.0000.000
178A187GLY00.0300.00238.4840.0040.0040.0000.0000.0000.000
179A188GLN0-0.0110.01439.493-0.003-0.0030.0000.0000.0000.000
180A189ILE00.0110.02236.543-0.002-0.0020.0000.0000.0000.000
181A190LEU0-0.004-0.02538.6730.0060.0060.0000.0000.0000.000
182A191ASN0-0.019-0.01837.128-0.009-0.0090.0000.0000.0000.000
183A192VAL00.0560.04933.2340.0020.0020.0000.0000.0000.000
184A193ASN0-0.052-0.03535.4830.0000.0000.0000.0000.0000.000
185A194ALA00.0770.02630.741-0.007-0.0070.0000.0000.0000.000
186A195ASP-1-0.974-0.98930.194-0.072-0.0720.0000.0000.0000.000
187A196PHE00.0400.00131.001-0.001-0.0010.0000.0000.0000.000
188A197ALA00.0660.04729.498-0.004-0.0040.0000.0000.0000.000
189A198ALA0-0.034-0.01826.022-0.009-0.0090.0000.0000.0000.000
190A199ASN0-0.022-0.00326.467-0.014-0.0140.0000.0000.0000.000
191A200GLU-1-0.846-0.93728.009-0.127-0.1270.0000.0000.0000.000
192A201LEU00.0040.01221.916-0.011-0.0110.0000.0000.0000.000
193A202VAL0-0.011-0.00622.154-0.020-0.0200.0000.0000.0000.000
194A203GLN00.0830.06923.511-0.001-0.0010.0000.0000.0000.000
195A204GLU-1-0.867-0.95723.581-0.229-0.2290.0000.0000.0000.000
196A205LEU0-0.072-0.02717.375-0.024-0.0240.0000.0000.0000.000
197A206GLN0-0.033-0.02819.783-0.030-0.0300.0000.0000.0000.000
198A207PRO00.0300.02217.819-0.012-0.0120.0000.0000.0000.000
199A208TYR00.0500.03514.6350.0330.0330.0000.0000.0000.000
200A209LYS10.7340.86415.8440.0290.0290.0000.0000.0000.000
201A210ILE00.022-0.02217.768-0.027-0.0270.0000.0000.0000.000
202A211ILE00.0270.04918.8020.0170.0170.0000.0000.0000.000
203A212PHE0-0.010-0.02721.622-0.016-0.0160.0000.0000.0000.000
204A213LEU00.0520.02921.2370.0130.0130.0000.0000.0000.000
205A214THR0-0.055-0.02925.147-0.007-0.0070.0000.0000.0000.000
206A215GLY0-0.004-0.00228.3890.0070.0070.0000.0000.0000.000
207A216THR00.0070.00030.4010.0060.0060.0000.0000.0000.000
208A217GLY0-0.001-0.01929.1840.0070.0070.0000.0000.0000.000
209A218GLY00.0200.02029.5650.0060.0060.0000.0000.0000.000
210A219LEU0-0.050-0.02930.282-0.004-0.0040.0000.0000.0000.000
211A220LEU0-0.017-0.00833.1280.0060.0060.0000.0000.0000.000
212A221ASP-1-0.687-0.85436.2090.0330.0330.0000.0000.0000.000
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