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: 1NZNZ

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 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 438
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7425849.121885
FMO2-HF: Nuclear repulsion 7258106.477678
FMO2-HF: Total energy -167742.644207
FMO2-MP2: Total energy -168239.21301


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.
-15.238-10.070.204-2.105-3.266-0.001
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 : 0.042 / q_NPA : 0.012
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].
3A12ARG10.9620.9753.818-5.947-3.7270.012-0.997-1.2350.006
4A13GLN0-0.029-0.0162.844-3.029-1.2510.175-0.634-1.319-0.003
5A14THR00.008-0.0264.452-0.2060.020-0.001-0.035-0.1900.000
6A15ILE00.0370.0456.820-0.206-0.2060.0000.0000.0000.000
7A16VAL00.0460.0018.102-0.261-0.2610.0000.0000.0000.000
8A17ARG10.8640.9537.848-0.583-0.5830.0000.0000.0000.000
9A18LEU00.001-0.00810.509-0.095-0.0950.0000.0000.0000.000
10A19LEU0-0.0320.00511.833-0.115-0.1150.0000.0000.0000.000
11A20SER00.008-0.02113.456-0.080-0.0800.0000.0000.0000.000
12A21SER0-0.043-0.00715.265-0.064-0.0640.0000.0000.0000.000
13A22MET0-0.030-0.00917.881-0.013-0.0130.0000.0000.0000.000
14A23ALA00.0430.01719.696-0.009-0.0090.0000.0000.0000.000
15A24SER00.0070.00920.587-0.011-0.0110.0000.0000.0000.000
16A25ALA00.0340.01716.1970.0200.0200.0000.0000.0000.000
17A26LYS10.9250.97516.236-0.164-0.1640.0000.0000.0000.000
18A27GLU-1-0.798-0.88517.5970.2580.2580.0000.0000.0000.000
19A28ILE00.0060.00914.233-0.011-0.0110.0000.0000.0000.000
20A29SER0-0.046-0.05012.2340.0320.0320.0000.0000.0000.000
21A30GLN00.0000.00112.1480.0380.0380.0000.0000.0000.000
22A31TYR0-0.025-0.02414.257-0.017-0.0170.0000.0000.0000.000
23A32LEU0-0.018-0.0039.3410.0420.0420.0000.0000.0000.000
24A33LYS10.8740.9258.894-0.133-0.1330.0000.0000.0000.000
25A34ARG10.8140.91611.016-0.128-0.1280.0000.0000.0000.000
26A35PHE00.0720.03711.502-0.035-0.0350.0000.0000.0000.000
27A36SER0-0.076-0.0087.3600.0600.0600.0000.0000.0000.000
28A37GLN0-0.056-0.0358.449-0.092-0.0920.0000.0000.0000.000
29A38LEU00.0440.0029.7440.0590.0590.0000.0000.0000.000
30A39ASP-1-0.833-0.89812.756-0.397-0.3970.0000.0000.0000.000
31A40ALA00.0020.0179.961-0.046-0.0460.0000.0000.0000.000
32A41LYS10.8970.92511.2020.4490.4490.0000.0000.0000.000
33A42ARG10.8160.91814.4340.2800.2800.0000.0000.0000.000
34A43PHE00.0390.02411.4560.0580.0580.0000.0000.0000.000
35A44ALA0-0.050-0.02713.6060.0590.0590.0000.0000.0000.000
36A45VAL00.0740.01015.921-0.033-0.0330.0000.0000.0000.000
37A46VAL0-0.0320.00517.4470.0210.0210.0000.0000.0000.000
38A47LYS10.8600.93319.9010.0440.0440.0000.0000.0000.000
39A48VAL0-0.0120.00222.3710.0200.0200.0000.0000.0000.000
40A49GLY00.0650.01625.134-0.003-0.0030.0000.0000.0000.000
41A50GLY0-0.013-0.01728.6040.0040.0040.0000.0000.0000.000
42A51ALA0-0.029-0.00331.0370.0010.0010.0000.0000.0000.000
43A52VAL00.004-0.00525.7250.0070.0070.0000.0000.0000.000
44A53LEU0-0.0350.00325.8750.0040.0040.0000.0000.0000.000
45A54ARG10.8640.92428.073-0.012-0.0120.0000.0000.0000.000
46A55ASP-1-0.918-0.94830.7140.0310.0310.0000.0000.0000.000
47A56ASP-1-0.897-0.94925.7540.0920.0920.0000.0000.0000.000
48A57LEU00.0320.01224.254-0.006-0.0060.0000.0000.0000.000
49A58GLU-1-0.869-0.93523.0210.0390.0390.0000.0000.0000.000
50A59ALA00.0360.02221.3570.0100.0100.0000.0000.0000.000
51A60LEU0-0.043-0.00420.3180.0090.0090.0000.0000.0000.000
52A61THR0-0.020-0.04019.087-0.019-0.0190.0000.0000.0000.000
53A62SER00.0290.02917.237-0.014-0.0140.0000.0000.0000.000
54A63SER0-0.071-0.04415.7620.0280.0280.0000.0000.0000.000
55A64LEU0-0.045-0.03014.469-0.010-0.0100.0000.0000.0000.000
56A65SER00.002-0.01413.427-0.093-0.0930.0000.0000.0000.000
57A66PHE00.0400.01510.418-0.082-0.0820.0000.0000.0000.000
58A67LEU0-0.045-0.0089.265-0.007-0.0070.0000.0000.0000.000
59A68GLN00.0320.0078.094-0.267-0.2670.0000.0000.0000.000
60A69GLU-1-0.945-0.9508.390-0.122-0.1220.0000.0000.0000.000
61A70VAL0-0.083-0.0444.5010.1300.254-0.001-0.006-0.1160.000
62A71GLY0-0.050-0.0333.251-4.908-4.0880.019-0.433-0.406-0.004
63A72LEU0-0.068-0.0265.6360.4580.4580.0000.0000.0000.000
64A73THR00.0670.0208.7820.1160.1160.0000.0000.0000.000
65A74PRO0-0.025-0.00211.4960.0720.0720.0000.0000.0000.000
66A75ILE00.012-0.01014.773-0.031-0.0310.0000.0000.0000.000
67A76VAL0-0.056-0.03317.5400.0360.0360.0000.0000.0000.000
68A77LEU00.0480.02720.103-0.010-0.0100.0000.0000.0000.000
69A78HIS0-0.014-0.01323.8430.0310.0310.0000.0000.0000.000
70A79GLY00.0470.00726.298-0.005-0.0050.0000.0000.0000.000
71A80ALA0-0.067-0.03930.0950.0080.0080.0000.0000.0000.000
72A81GLY00.0640.03331.876-0.003-0.0030.0000.0000.0000.000
73A82PRO00.0180.00833.8260.0010.0010.0000.0000.0000.000
74A83GLN00.0740.02631.5220.0010.0010.0000.0000.0000.000
75A84LEU0-0.0060.01836.1150.0000.0000.0000.0000.0000.000
76A85ASP-1-0.736-0.82037.987-0.016-0.0160.0000.0000.0000.000
77A86ALA0-0.024-0.00640.1480.0020.0020.0000.0000.0000.000
78A87GLU-1-0.955-0.98839.648-0.020-0.0200.0000.0000.0000.000
79A88LEU0-0.045-0.01441.560-0.002-0.0020.0000.0000.0000.000
80A89SER0-0.059-0.04143.5890.0000.0000.0000.0000.0000.000
81A90ALA0-0.0030.01545.5140.0010.0010.0000.0000.0000.000
82A91ALA0-0.0090.00347.2090.0010.0010.0000.0000.0000.000
83A92GLY00.0020.00748.0590.0010.0010.0000.0000.0000.000
84A93ILE0-0.044-0.04048.418-0.002-0.0020.0000.0000.0000.000
85A94GLH0-0.011-0.01442.491-0.003-0.0030.0000.0000.0000.000
86A95LYS10.9390.95147.3540.0080.0080.0000.0000.0000.000
87A96GLN0-0.015-0.00249.183-0.002-0.0020.0000.0000.0000.000
88A97THR0-0.019-0.01845.148-0.001-0.0010.0000.0000.0000.000
89A98VAL00.0040.00947.0750.0010.0010.0000.0000.0000.000
90A99ASN00.0600.04845.1480.0040.0040.0000.0000.0000.000
91A100GLY00.0070.00543.9030.0010.0010.0000.0000.0000.000
92A101LEU0-0.043-0.01639.2840.0000.0000.0000.0000.0000.000
93A102ARG10.8250.85639.3040.0210.0210.0000.0000.0000.000
94A103VAL0-0.0080.00543.6890.0000.0000.0000.0000.0000.000
95A104THR00.0050.01041.7760.0000.0000.0000.0000.0000.000
96A105SER00.0360.01845.073-0.002-0.0020.0000.0000.0000.000
97A106PRO00.1290.04945.648-0.001-0.0010.0000.0000.0000.000
98A107HIS0-0.0500.00045.656-0.004-0.0040.0000.0000.0000.000
99A108ALA00.012-0.02044.7410.0010.0010.0000.0000.0000.000
100A109LEU00.0920.05640.5340.0000.0000.0000.0000.0000.000
101A110ALA0-0.051-0.02840.279-0.002-0.0020.0000.0000.0000.000
102A111ILE00.0080.00140.995-0.003-0.0030.0000.0000.0000.000
103A112VAL00.0700.03737.1220.0000.0000.0000.0000.0000.000
104A113ARG10.9370.99235.8970.0630.0630.0000.0000.0000.000
105A114LYS10.9130.95535.3240.0510.0510.0000.0000.0000.000
106A115VAL00.0620.05034.963-0.002-0.0020.0000.0000.0000.000
107A116PHE00.0340.00031.1140.0000.0000.0000.0000.0000.000
108A117GLN0-0.017-0.00431.043-0.011-0.0110.0000.0000.0000.000
109A118ALA00.001-0.00730.737-0.004-0.0040.0000.0000.0000.000
110A119SER0-0.049-0.02530.185-0.001-0.0010.0000.0000.0000.000
111A120ASN00.0740.03425.2920.0010.0010.0000.0000.0000.000
112A121LEU0-0.0130.00026.025-0.010-0.0100.0000.0000.0000.000
113A122LYS10.9430.97026.2440.0270.0270.0000.0000.0000.000
114A123LEU0-0.001-0.00821.8950.0060.0060.0000.0000.0000.000
115A124VAL0-0.034-0.01621.774-0.004-0.0040.0000.0000.0000.000
116A125GLU-1-0.877-0.94621.744-0.134-0.1340.0000.0000.0000.000
117A126ALA0-0.045-0.01422.6600.0040.0040.0000.0000.0000.000
118A127LEU00.011-0.00217.1780.0120.0120.0000.0000.0000.000
119A128GLN0-0.011-0.00918.379-0.033-0.0330.0000.0000.0000.000
120A129GLN0-0.076-0.04119.7070.0090.0090.0000.0000.0000.000
121A130ASN0-0.051-0.02016.9720.0340.0340.0000.0000.0000.000
122A131GLY00.0270.01816.1450.0390.0390.0000.0000.0000.000
123A132ALA0-0.084-0.02814.265-0.048-0.0480.0000.0000.0000.000
124A133ARG10.9360.96511.6660.7520.7520.0000.0000.0000.000
125A134ALA0-0.0250.00716.083-0.053-0.0530.0000.0000.0000.000
126A135THR0-0.032-0.03818.4370.0020.0020.0000.0000.0000.000
127A136SER0-0.028-0.03020.8670.0020.0020.0000.0000.0000.000
128A137ILE00.0290.02122.184-0.008-0.0080.0000.0000.0000.000
129A138THR0-0.031-0.01225.3790.0010.0010.0000.0000.0000.000
130A139GLY0-0.010-0.00228.6890.0150.0150.0000.0000.0000.000
131A140GLY00.0640.04729.218-0.014-0.0140.0000.0000.0000.000
132A141VAL0-0.036-0.00625.612-0.004-0.0040.0000.0000.0000.000
133A142PHE00.0390.01027.0340.0000.0000.0000.0000.0000.000
134A143GLU-1-0.819-0.88131.360-0.094-0.0940.0000.0000.0000.000
135A144ALA0-0.080-0.02034.4720.0070.0070.0000.0000.0000.000
136A145GLU-1-0.877-0.93936.671-0.063-0.0630.0000.0000.0000.000
137A146TYR0-0.010-0.00740.0360.0030.0030.0000.0000.0000.000
138A147LEU0-0.0180.00641.2570.0020.0020.0000.0000.0000.000
139A148ASN0-0.003-0.01644.2620.0010.0010.0000.0000.0000.000
140A149ARG10.8780.94147.0950.0320.0320.0000.0000.0000.000
141A150ASP-1-0.818-0.89349.165-0.030-0.0300.0000.0000.0000.000
142A151THR0-0.045-0.03049.8090.0010.0010.0000.0000.0000.000
143A152TYR0-0.001-0.01645.8560.0020.0020.0000.0000.0000.000
144A153GLY00.0170.00946.6930.0000.0000.0000.0000.0000.000
145A154LEU0-0.032-0.01943.369-0.002-0.0020.0000.0000.0000.000
146A155VAL0-0.040-0.02040.159-0.002-0.0020.0000.0000.0000.000
147A156GLY0-0.017-0.03639.6360.0010.0010.0000.0000.0000.000
148A157GLU-1-0.891-0.94436.110-0.054-0.0540.0000.0000.0000.000
149A158VAL00.000-0.00832.037-0.003-0.0030.0000.0000.0000.000
150A159LYS10.7910.89633.8350.0780.0780.0000.0000.0000.000
151A160ALA00.0090.01532.457-0.001-0.0010.0000.0000.0000.000
152A161VAL0-0.032-0.02427.3740.0030.0030.0000.0000.0000.000
153A162ASN00.0030.01727.920-0.018-0.0180.0000.0000.0000.000
154A163LEU00.0820.03820.737-0.015-0.0150.0000.0000.0000.000
155A164ALA00.0570.04722.543-0.032-0.0320.0000.0000.0000.000
156A165PRO0-0.045-0.02822.715-0.031-0.0310.0000.0000.0000.000
157A166ILE0-0.026-0.02319.552-0.014-0.0140.0000.0000.0000.000
158A167GLU-1-0.879-0.95318.306-0.379-0.3790.0000.0000.0000.000
159A168ALA00.0180.03118.019-0.061-0.0610.0000.0000.0000.000
160A169SER00.1020.04417.881-0.058-0.0580.0000.0000.0000.000
161A170LEU0-0.0380.00413.727-0.066-0.0660.0000.0000.0000.000
162A171GLN0-0.079-0.04113.596-0.104-0.1040.0000.0000.0000.000
163A172ALA0-0.058-0.01414.016-0.083-0.0830.0000.0000.0000.000
164A173GLY0-0.029-0.02111.796-0.146-0.1460.0000.0000.0000.000
165A174SER0-0.008-0.02012.544-0.041-0.0410.0000.0000.0000.000
166A175ILE0-0.027-0.01113.8980.0110.0110.0000.0000.0000.000
167A176PRO00.0450.03416.2340.0590.0590.0000.0000.0000.000
168A177VAL0-0.062-0.04419.3590.0300.0300.0000.0000.0000.000
169A178ILE00.0680.04021.7470.0180.0180.0000.0000.0000.000
170A179THR0-0.035-0.01524.5670.0140.0140.0000.0000.0000.000
171A180SER0-0.024-0.01228.1630.0010.0010.0000.0000.0000.000
172A181LEU0-0.072-0.04831.0530.0090.0090.0000.0000.0000.000
173A182GLY00.0580.00232.593-0.006-0.0060.0000.0000.0000.000
174A183GLU-1-0.915-0.99534.150-0.120-0.1200.0000.0000.0000.000
175A184THR0-0.074-0.04336.709-0.001-0.0010.0000.0000.0000.000
176A185PRO00.0980.06337.974-0.003-0.0030.0000.0000.0000.000
177A186SER0-0.048-0.01139.358-0.004-0.0040.0000.0000.0000.000
178A187GLY00.036-0.00138.5870.0030.0030.0000.0000.0000.000
179A188GLN0-0.0270.00639.583-0.002-0.0020.0000.0000.0000.000
180A189ILE00.0240.02036.3680.0000.0000.0000.0000.0000.000
181A190LEU0-0.046-0.02238.7770.0050.0050.0000.0000.0000.000
182A191ASN0-0.012-0.02136.996-0.007-0.0070.0000.0000.0000.000
183A192VAL00.0640.05433.1430.0020.0020.0000.0000.0000.000
184A193ASN0-0.036-0.01635.0870.0020.0020.0000.0000.0000.000
185A194ALA00.0970.03230.552-0.005-0.0050.0000.0000.0000.000
186A195ASP-1-0.855-0.91330.117-0.025-0.0250.0000.0000.0000.000
187A196PHE00.012-0.00531.0580.0010.0010.0000.0000.0000.000
188A197ALA00.0550.04830.125-0.005-0.0050.0000.0000.0000.000
189A198ALA0-0.001-0.00626.099-0.009-0.0090.0000.0000.0000.000
190A199ASN0-0.003-0.01226.549-0.004-0.0040.0000.0000.0000.000
191A200GLU-1-0.829-0.92328.106-0.093-0.0930.0000.0000.0000.000
192A201LEU00.0370.02522.418-0.010-0.0100.0000.0000.0000.000
193A202VAL0-0.053-0.02022.877-0.017-0.0170.0000.0000.0000.000
194A203GLN00.0210.02723.6240.0010.0010.0000.0000.0000.000
195A204GLU-1-0.843-0.93923.886-0.194-0.1940.0000.0000.0000.000
196A205LEU0-0.075-0.04318.018-0.022-0.0220.0000.0000.0000.000
197A206GLN0-0.043-0.04819.919-0.016-0.0160.0000.0000.0000.000
198A207PRO0-0.0120.00617.924-0.006-0.0060.0000.0000.0000.000
199A208TYR00.0290.03214.1810.0430.0430.0000.0000.0000.000
200A209LYS10.7750.88215.868-0.116-0.1160.0000.0000.0000.000
201A210ILE00.016-0.00817.815-0.036-0.0360.0000.0000.0000.000
202A211ILE0-0.0020.01718.2810.0070.0070.0000.0000.0000.000
203A212PHE00.005-0.01021.230-0.021-0.0210.0000.0000.0000.000
204A213LEU00.0380.02621.2470.0120.0120.0000.0000.0000.000
205A214THR0-0.039-0.02724.672-0.014-0.0140.0000.0000.0000.000
206A215GLY0-0.006-0.00427.8760.0100.0100.0000.0000.0000.000
207A216THR00.0210.00529.9130.0050.0050.0000.0000.0000.000
208A217GLY0-0.016-0.02628.5770.0070.0070.0000.0000.0000.000
209A218GLY00.0320.04128.9280.0100.0100.0000.0000.0000.000
210A219LEU0-0.041-0.02329.670-0.009-0.0090.0000.0000.0000.000
211A220LEU0-0.022-0.01032.5060.0080.0080.0000.0000.0000.000
212A221ASP-1-0.723-0.87035.5800.0770.0770.0000.0000.0000.000
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