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: N9M4Q

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3011652.478676
FMO2-HF: Nuclear repulsion 2921074.097171
FMO2-HF: Total energy -90578.381504
FMO2-MP2: Total energy -90848.322919


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.
-13.035-6.6443.783-4.241-5.9320.025
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 : 0.077 / q_NPA : 0.041
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].
3A6ALA00.0260.0212.996-3.951-0.8530.328-1.628-1.7980.011
4A7ALA0-0.004-0.0062.310-7.129-5.0722.460-1.955-2.5610.014
5A8LEU00.0130.0063.990-0.988-0.4660.005-0.183-0.3440.000
6A9ALA0-0.020-0.0096.0590.1590.1590.0000.0000.0000.000
7A10LEU0-0.040-0.0246.322-0.154-0.1540.0000.0000.0000.000
8A11TRP0-0.0340.0067.803-0.101-0.1010.0000.0000.0000.000
9A12ALA00.0360.0299.4440.0070.0070.0000.0000.0000.000
10A13LYS10.8140.91512.0450.4460.4460.0000.0000.0000.000
11A14SER00.027-0.00415.557-0.006-0.0060.0000.0000.0000.000
12A15GLY00.0390.03419.0400.0100.0100.0000.0000.0000.000
13A16ASN00.019-0.00220.431-0.007-0.0070.0000.0000.0000.000
14A17PRO00.006-0.00417.773-0.008-0.0080.0000.0000.0000.000
15A18PHE00.001-0.00316.837-0.025-0.0250.0000.0000.0000.000
16A19HIS00.0380.02518.3200.0130.0130.0000.0000.0000.000
17A20PRO00.001-0.00312.997-0.014-0.0140.0000.0000.0000.000
18A21LEU0-0.034-0.01613.9230.0270.0270.0000.0000.0000.000
19A22LEU00.0440.00511.4780.0250.0250.0000.0000.0000.000
20A23ALA0-0.0090.00114.5760.0160.0160.0000.0000.0000.000
21A24HIS00.0110.00617.3340.0060.0060.0000.0000.0000.000
22A25MET0-0.0310.00416.0130.0070.0070.0000.0000.0000.000
23A26LEU0-0.017-0.01315.8380.0090.0090.0000.0000.0000.000
24A27ASP-1-0.712-0.81819.653-0.007-0.0070.0000.0000.0000.000
25A28THR0-0.003-0.01222.394-0.001-0.0010.0000.0000.0000.000
26A29ALA00.0250.00521.9370.0010.0010.0000.0000.0000.000
27A30ALA0-0.023-0.01223.7160.0020.0020.0000.0000.0000.000
28A31VAL00.013-0.00325.443-0.001-0.0010.0000.0000.0000.000
29A32ALA00.0180.01726.8670.0000.0000.0000.0000.0000.000
30A33LEU00.007-0.00726.3750.0000.0000.0000.0000.0000.000
31A34ALA0-0.023-0.00728.9390.0000.0000.0000.0000.0000.000
32A35VAL00.0330.00131.323-0.001-0.0010.0000.0000.0000.000
33A36LEU0-0.0130.00029.9280.0000.0000.0000.0000.0000.000
34A37ARG10.8300.89229.443-0.043-0.0430.0000.0000.0000.000
35A38MET0-0.0450.01534.985-0.001-0.0010.0000.0000.0000.000
36A39GLU-1-0.777-0.88136.9590.0060.0060.0000.0000.0000.000
37A40PRO0-0.026-0.01438.8320.0020.0020.0000.0000.0000.000
38A41PRO00.0350.00840.9480.0010.0010.0000.0000.0000.000
39A42ARG10.9370.96741.740-0.010-0.0100.0000.0000.0000.000
40A43THR00.0220.01138.0510.0010.0010.0000.0000.0000.000
41A44ARG10.8270.90436.245-0.021-0.0210.0000.0000.0000.000
42A45ALA00.0090.00337.6240.0030.0030.0000.0000.0000.000
43A46LEU0-0.021-0.00339.7150.0010.0010.0000.0000.0000.000
44A47TYR0-0.005-0.03332.2190.0020.0020.0000.0000.0000.000
45A48ALA0-0.029-0.02034.8610.0040.0040.0000.0000.0000.000
46A49GLU-1-0.862-0.91636.5520.0220.0220.0000.0000.0000.000
47A50ASP-1-0.801-0.86734.9700.0200.0200.0000.0000.0000.000
48A51TRP0-0.025-0.02031.6950.0010.0010.0000.0000.0000.000
49A52GLY00.0450.03633.1610.0050.0050.0000.0000.0000.000
50A53LEU0-0.032-0.01629.7040.0040.0040.0000.0000.0000.000
51A54PRO00.024-0.00233.541-0.004-0.0040.0000.0000.0000.000
52A55GLU-1-0.810-0.89633.7040.0320.0320.0000.0000.0000.000
53A56GLU-1-0.836-0.90230.7260.0490.0490.0000.0000.0000.000
54A57GLY00.0140.00729.3840.0040.0040.0000.0000.0000.000
55A58ALA00.0020.00129.1640.0040.0040.0000.0000.0000.000
56A59LEU0-0.018-0.01530.437-0.002-0.0020.0000.0000.0000.000
57A60ALA00.0310.01725.911-0.001-0.0010.0000.0000.0000.000
58A61TRP00.000-0.00924.2550.0070.0070.0000.0000.0000.000
59A62ALA00.0110.01025.9650.0000.0000.0000.0000.0000.000
60A63ALA00.0170.00325.860-0.005-0.0050.0000.0000.0000.000
61A64ALA0-0.011-0.00921.536-0.002-0.0020.0000.0000.0000.000
62A65LEU0-0.045-0.01921.8520.0010.0010.0000.0000.0000.000
63A66VAL00.0230.01723.580-0.008-0.0080.0000.0000.0000.000
64A67GLY00.0040.00721.247-0.010-0.0100.0000.0000.0000.000
65A68LEU0-0.090-0.05518.132-0.001-0.0010.0000.0000.0000.000
66A69HIS0-0.015-0.00220.649-0.017-0.0170.0000.0000.0000.000
67A70ASP-1-0.724-0.82120.105-0.097-0.0970.0000.0000.0000.000
68A71LEU00.002-0.00114.774-0.027-0.0270.0000.0000.0000.000
69A72GLY0-0.011-0.01116.857-0.031-0.0310.0000.0000.0000.000
70A73LYS10.8220.87717.4060.0730.0730.0000.0000.0000.000
71A74ALA00.0010.02012.707-0.053-0.0530.0000.0000.0000.000
72A75SER0-0.007-0.02813.438-0.031-0.0310.0000.0000.0000.000
73A76PRO00.005-0.00512.3010.0290.0290.0000.0000.0000.000
74A77VAL0-0.046-0.00714.5730.0250.0250.0000.0000.0000.000
75A78PHE0-0.028-0.00817.0730.0370.0370.0000.0000.0000.000
76A79GLN0-0.037-0.01113.345-0.011-0.0110.0000.0000.0000.000
77A80ALA00.0210.02014.483-0.027-0.0270.0000.0000.0000.000
78A102TRP00.0330.00822.848-0.003-0.0030.0000.0000.0000.000
79A103VAL0-0.020-0.02124.3440.0120.0120.0000.0000.0000.000
80A104ALA00.0650.04524.756-0.011-0.0110.0000.0000.0000.000
81A105HIS00.0500.01521.001-0.007-0.0070.0000.0000.0000.000
82A106GLY00.1040.05322.4090.0010.0010.0000.0000.0000.000
83A107VAL0-0.032-0.02124.8720.0110.0110.0000.0000.0000.000
84A108PHE0-0.033-0.01518.5420.0030.0030.0000.0000.0000.000
85A109THR00.000-0.00420.681-0.004-0.0040.0000.0000.0000.000
86A110GLU-1-0.725-0.83421.802-0.026-0.0260.0000.0000.0000.000
87A111LEU0-0.087-0.06421.5350.0100.0100.0000.0000.0000.000
88A112PHE0-0.026-0.00816.434-0.003-0.0030.0000.0000.0000.000
89A113LEU00.0700.04519.6100.0200.0200.0000.0000.0000.000
90A114ARG10.8600.92221.7990.0300.0300.0000.0000.0000.000
91A115ARG10.8660.93818.7620.0280.0280.0000.0000.0000.000
92A116LEU00.0390.00715.2440.0110.0110.0000.0000.0000.000
93A117LEU00.0140.01119.0910.0230.0230.0000.0000.0000.000
94A118LYS10.7500.88322.309-0.005-0.0050.0000.0000.0000.000
95A119GLU-1-0.834-0.88717.0850.0640.0640.0000.0000.0000.000
96A120LYS10.7960.87717.609-0.196-0.1960.0000.0000.0000.000
97A121GLY00.0390.02420.9850.0040.0040.0000.0000.0000.000
98A122LEU0-0.025-0.00124.554-0.008-0.0080.0000.0000.0000.000
99A123PRO00.0240.00626.901-0.004-0.0040.0000.0000.0000.000
100A124GLU-1-0.827-0.91227.9990.0090.0090.0000.0000.0000.000
101A125ARG10.9110.95529.506-0.017-0.0170.0000.0000.0000.000
102A126ALA00.1050.05930.245-0.003-0.0030.0000.0000.0000.000
103A127ALA00.0260.01225.603-0.001-0.0010.0000.0000.0000.000
104A128ASN0-0.064-0.04527.031-0.010-0.0100.0000.0000.0000.000
105A129ASP-1-0.879-0.94028.945-0.001-0.0010.0000.0000.0000.000
106A130LEU00.0120.00127.366-0.004-0.0040.0000.0000.0000.000
107A131ALA0-0.032-0.01225.288-0.003-0.0030.0000.0000.0000.000
108A132ALA0-0.026-0.01426.476-0.009-0.0090.0000.0000.0000.000
109A133ALA0-0.037-0.01129.538-0.004-0.0040.0000.0000.0000.000
110A134LEU0-0.0100.00224.123-0.002-0.0020.0000.0000.0000.000
111A135GLY00.0160.00725.493-0.007-0.0070.0000.0000.0000.000
112A136ALA0-0.088-0.05727.2730.0000.0000.0000.0000.0000.000
113A137HIS0-0.078-0.04828.7390.0010.0010.0000.0000.0000.000
114A138HIS00.0610.03431.5810.0070.0070.0000.0000.0000.000
115A139GLY00.0670.03531.9820.0030.0030.0000.0000.0000.000
116A140PHE0-0.030-0.00533.4260.0020.0020.0000.0000.0000.000
117A141PRO0-0.021-0.00830.951-0.004-0.0040.0000.0000.0000.000
118A142ALA00.0210.01328.770-0.002-0.0020.0000.0000.0000.000
119A143ASN00.011-0.02030.7990.0030.0030.0000.0000.0000.000
120A144ALA00.0260.00530.726-0.005-0.0050.0000.0000.0000.000
121A145GLU-1-0.710-0.81730.351-0.084-0.0840.0000.0000.0000.000
122A146GLU-1-0.804-0.87228.477-0.070-0.0700.0000.0000.0000.000
123A147LYS10.8450.89925.9870.0340.0340.0000.0000.0000.000
124A148SER0-0.0200.00825.431-0.012-0.0120.0000.0000.0000.000
125A149ARG10.8190.88025.8230.0790.0790.0000.0000.0000.000
126A150ALA00.0400.02922.002-0.014-0.0140.0000.0000.0000.000
127A151ARG10.9470.95621.1000.0500.0500.0000.0000.0000.000
128A152ARG10.7320.84221.7270.0870.0870.0000.0000.0000.000
129A153HIS00.0920.05118.800-0.020-0.0200.0000.0000.0000.000
130A154LEU0-0.016-0.00316.489-0.031-0.0310.0000.0000.0000.000
131A155ARG10.8850.94716.5450.1070.1070.0000.0000.0000.000
132A156THR00.0250.01316.9020.0160.0160.0000.0000.0000.000
133A157GLU-1-0.801-0.83013.108-0.396-0.3960.0000.0000.0000.000
134A158ASP-1-0.823-0.9187.569-1.238-1.2380.0000.0000.0000.000
135A159PRO00.004-0.0208.862-0.009-0.0090.0000.0000.0000.000
136A160LEU00.0470.0412.417-1.078-0.3640.990-0.475-1.2290.000
137A161TRP00.0310.0006.5330.1460.1460.0000.0000.0000.000
138A162LYS10.7860.8769.2930.5700.5700.0000.0000.0000.000
139A163GLU-1-0.896-0.9416.583-0.158-0.1580.0000.0000.0000.000
140A164ALA00.003-0.0037.0540.3050.3050.0000.0000.0000.000
141A165ARG10.7900.8528.3610.4790.4790.0000.0000.0000.000
142A166ARG10.7880.85011.3200.0080.0080.0000.0000.0000.000
143A167TRP00.0230.0037.0590.1550.1550.0000.0000.0000.000
144A168LEU0-0.021-0.01710.1130.0040.0040.0000.0000.0000.000
145A169LEU00.0170.02212.185-0.016-0.0160.0000.0000.0000.000
146A170GLU-1-0.821-0.90012.6940.2730.2730.0000.0000.0000.000
147A171GLU-1-0.793-0.86911.4490.4010.4010.0000.0000.0000.000
148A172VAL00.0110.00313.560-0.043-0.0430.0000.0000.0000.000
149A173PHE00.022-0.00816.909-0.019-0.0190.0000.0000.0000.000
150A174ARG10.8360.91811.492-0.505-0.5050.0000.0000.0000.000
151A175ARG10.7240.84513.100-0.219-0.2190.0000.0000.0000.000
152A176LEU0-0.014-0.01618.556-0.020-0.0200.0000.0000.0000.000
153A177GLY0-0.0230.00920.982-0.013-0.0130.0000.0000.0000.000
154A178ALA0-0.025-0.00422.102-0.010-0.0100.0000.0000.0000.000
155A179PRO0-0.038-0.00723.2400.0130.0130.0000.0000.0000.000
156A180LEU00.002-0.00424.362-0.003-0.0030.0000.0000.0000.000
157A181PRO00.005-0.00126.649-0.002-0.0020.0000.0000.0000.000
158A182PRO0-0.0240.00230.2800.0030.0030.0000.0000.0000.000
159A183SER0-0.056-0.02330.624-0.004-0.0040.0000.0000.0000.000
160A184GLN0-0.119-0.07332.8120.0030.0030.0000.0000.0000.000
161A185GLY00.0540.02734.782-0.002-0.0020.0000.0000.0000.000
162A186ASN0-0.022-0.00732.953-0.007-0.0070.0000.0000.0000.000
163A187GLY0-0.068-0.04434.973-0.002-0.0020.0000.0000.0000.000
164A188GLU-1-0.758-0.87933.7120.0400.0400.0000.0000.0000.000
165A189ALA00.0800.03233.0360.0030.0030.0000.0000.0000.000
166A190ARG10.7380.85735.196-0.022-0.0220.0000.0000.0000.000
167A191PRO00.0520.00237.0480.0000.0000.0000.0000.0000.000
168A192GLU-1-0.832-0.92037.1920.0050.0050.0000.0000.0000.000
169A193ALA00.0110.03234.570-0.001-0.0010.0000.0000.0000.000
170A194VAL0-0.037-0.02132.1600.0010.0010.0000.0000.0000.000
171A195LEU0-0.019-0.01832.984-0.002-0.0020.0000.0000.0000.000
172A196ARG10.7820.84634.797-0.016-0.0160.0000.0000.0000.000
173A197VAL00.0000.00428.388-0.001-0.0010.0000.0000.0000.000
174A198MET0-0.0520.00530.231-0.003-0.0030.0000.0000.0000.000
175A199ALA0-0.003-0.00331.680-0.004-0.0040.0000.0000.0000.000
176A200LEU00.0270.01630.063-0.002-0.0020.0000.0000.0000.000
177A201ALA0-0.012-0.01427.445-0.001-0.0010.0000.0000.0000.000
178A202SER0-0.053-0.03328.778-0.005-0.0050.0000.0000.0000.000
179A203PHE0-0.006-0.00331.093-0.004-0.0040.0000.0000.0000.000
180A204ALA00.008-0.01027.730-0.003-0.0030.0000.0000.0000.000
181A205ASP-1-0.792-0.88924.450-0.043-0.0430.0000.0000.0000.000
182A206TRP0-0.0010.01026.901-0.005-0.0050.0000.0000.0000.000
183A207VAL0-0.006-0.00829.702-0.003-0.0030.0000.0000.0000.000
184A208ALA0-0.013-0.00924.278-0.001-0.0010.0000.0000.0000.000
185A209SER0-0.030-0.02725.298-0.009-0.0090.0000.0000.0000.000
186A210ASP-1-0.832-0.87726.502-0.048-0.0480.0000.0000.0000.000
187A211PRO0-0.011-0.01026.6100.0040.0040.0000.0000.0000.000
188A212SER0-0.088-0.06928.0130.0030.0030.0000.0000.0000.000
189A213LEU0-0.045-0.00729.8590.0050.0050.0000.0000.0000.000
190A214PHE0-0.007-0.01124.6010.0070.0070.0000.0000.0000.000
191A215PRO00.0080.02125.105-0.007-0.0070.0000.0000.0000.000
192A216TYR00.0090.00121.707-0.003-0.0030.0000.0000.0000.000
193A217GLY00.0080.00619.7770.0030.0030.0000.0000.0000.000
194A218ARG10.7120.83319.6760.0230.0230.0000.0000.0000.000
195A219ASP-1-0.769-0.87013.613-0.052-0.0520.0000.0000.0000.000
196A220PRO00.0380.01513.0410.0160.0160.0000.0000.0000.000
197A221ARG10.8310.8849.6050.1810.1810.0000.0000.0000.000
198A222ARG10.8510.93312.6770.0230.0230.0000.0000.0000.000
199A223GLY00.0650.02416.0450.0110.0110.0000.0000.0000.000
200A224ASP-1-0.867-0.93617.9650.0230.0230.0000.0000.0000.000
201A225TYR0-0.0010.00218.032-0.003-0.0030.0000.0000.0000.000
202A226LEU00.0400.01620.004-0.008-0.0080.0000.0000.0000.000
203A227LYS10.9070.95421.688-0.069-0.0690.0000.0000.0000.000
204A228GLU-1-0.768-0.85123.418-0.008-0.0080.0000.0000.0000.000
205A229ALA00.0010.00822.393-0.005-0.0050.0000.0000.0000.000
206A230LEU00.015-0.00324.512-0.003-0.0030.0000.0000.0000.000
207A231ARG10.7370.83627.2910.0020.0020.0000.0000.0000.000
208A232LEU0-0.022-0.01025.356-0.003-0.0030.0000.0000.0000.000
209A233ALA00.0160.02127.909-0.003-0.0030.0000.0000.0000.000
210A234GLN0-0.010-0.03829.6760.0000.0000.0000.0000.0000.000
211A235GLU-1-0.877-0.91532.349-0.014-0.0140.0000.0000.0000.000
212A236ALA00.0260.01031.337-0.002-0.0020.0000.0000.0000.000
213A237LEU0-0.016-0.01532.249-0.002-0.0020.0000.0000.0000.000
214A238ASN0-0.018-0.00835.1980.0010.0010.0000.0000.0000.000
215A239ARG10.7950.88332.9640.0200.0200.0000.0000.0000.000
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