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: 85ZLY

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2997053.620377
FMO2-HF: Nuclear repulsion 2906475.507586
FMO2-HF: Total energy -90578.112791
FMO2-MP2: Total energy -90848.076899


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.
-13.68-6.5892.393-4.046-5.4370.026
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 : 0.074 / q_NPA : 0.039
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].
3A6ALA00.0210.0172.925-4.374-0.9490.285-1.818-1.8920.012
4A7ALA0-0.001-0.0062.426-7.205-4.8271.665-1.720-2.3220.015
5A8LEU00.0130.0104.107-0.994-0.5480.003-0.145-0.3040.000
6A9ALA0-0.022-0.0146.0660.1330.1330.0000.0000.0000.000
7A10LEU0-0.041-0.0286.371-0.168-0.1680.0000.0000.0000.000
8A11TRP0-0.0350.0048.007-0.100-0.1000.0000.0000.0000.000
9A12ALA00.0430.0359.631-0.008-0.0080.0000.0000.0000.000
10A13LYS10.8260.91912.2450.4470.4470.0000.0000.0000.000
11A14SER00.0250.01515.617-0.006-0.0060.0000.0000.0000.000
12A15GLY00.0200.01619.0500.0100.0100.0000.0000.0000.000
13A16ASN00.0480.01420.342-0.003-0.0030.0000.0000.0000.000
14A17PRO00.009-0.00417.668-0.005-0.0050.0000.0000.0000.000
15A18PHE0-0.003-0.00816.789-0.023-0.0230.0000.0000.0000.000
16A19HIS00.0200.02418.3940.0130.0130.0000.0000.0000.000
17A20PRO00.0010.00213.242-0.015-0.0150.0000.0000.0000.000
18A21LEU0-0.010-0.01214.2520.0250.0250.0000.0000.0000.000
19A22LEU00.0450.00911.7110.0240.0240.0000.0000.0000.000
20A23ALA00.001-0.00314.8350.0180.0180.0000.0000.0000.000
21A24HIS0-0.0100.00217.5650.0000.0000.0000.0000.0000.000
22A25MET0-0.0230.00216.1580.0070.0070.0000.0000.0000.000
23A26LEU0-0.024-0.01716.1560.0080.0080.0000.0000.0000.000
24A27ASP-1-0.721-0.82119.955-0.003-0.0030.0000.0000.0000.000
25A28THR00.0310.01022.574-0.002-0.0020.0000.0000.0000.000
26A29ALA00.002-0.00222.3320.0010.0010.0000.0000.0000.000
27A30ALA0-0.029-0.01424.0660.0020.0020.0000.0000.0000.000
28A31VAL00.0270.00825.779-0.001-0.0010.0000.0000.0000.000
29A32ALA00.0010.00527.280-0.001-0.0010.0000.0000.0000.000
30A33LEU0-0.004-0.00427.0650.0000.0000.0000.0000.0000.000
31A34ALA0-0.042-0.02329.444-0.001-0.0010.0000.0000.0000.000
32A35VAL00.0410.00831.778-0.001-0.0010.0000.0000.0000.000
33A36LEU00.0070.00830.8190.0000.0000.0000.0000.0000.000
34A37ARG10.8420.90530.050-0.044-0.0440.0000.0000.0000.000
35A38MET0-0.0280.00935.519-0.001-0.0010.0000.0000.0000.000
36A39GLU-1-0.783-0.86837.2190.0060.0060.0000.0000.0000.000
37A40PRO0-0.029-0.02339.3210.0020.0020.0000.0000.0000.000
38A41PRO00.0390.00641.4870.0010.0010.0000.0000.0000.000
39A42ARG10.9280.95842.401-0.010-0.0100.0000.0000.0000.000
40A43THR00.0320.01538.2850.0000.0000.0000.0000.0000.000
41A44ARG10.8430.91636.653-0.021-0.0210.0000.0000.0000.000
42A45ALA00.0090.00438.1810.0030.0030.0000.0000.0000.000
43A46LEU0-0.0050.00339.9900.0010.0010.0000.0000.0000.000
44A47TYR0-0.019-0.02932.4760.0030.0030.0000.0000.0000.000
45A48ALA0-0.025-0.01735.5630.0030.0030.0000.0000.0000.000
46A49GLU-1-0.860-0.90737.0740.0220.0220.0000.0000.0000.000
47A50ASP-1-0.813-0.87535.6070.0190.0190.0000.0000.0000.000
48A51TRP0-0.021-0.02431.9990.0020.0020.0000.0000.0000.000
49A52GLY00.0480.03933.8290.0040.0040.0000.0000.0000.000
50A53LEU0-0.055-0.02430.1830.0040.0040.0000.0000.0000.000
51A54PRO00.0320.00533.844-0.004-0.0040.0000.0000.0000.000
52A55GLU-1-0.801-0.90034.2760.0320.0320.0000.0000.0000.000
53A56GLU-1-0.900-0.94331.5600.0520.0520.0000.0000.0000.000
54A57GLY00.0180.00629.8980.0040.0040.0000.0000.0000.000
55A58ALA0-0.006-0.00329.6500.0040.0040.0000.0000.0000.000
56A59LEU00.005-0.00530.702-0.001-0.0010.0000.0000.0000.000
57A60ALA00.0190.01826.397-0.001-0.0010.0000.0000.0000.000
58A61TRP00.022-0.00324.8090.0080.0080.0000.0000.0000.000
59A62ALA00.0150.00826.1880.0000.0000.0000.0000.0000.000
60A63ALA0-0.002-0.00726.230-0.005-0.0050.0000.0000.0000.000
61A64ALA00.0050.00021.806-0.002-0.0020.0000.0000.0000.000
62A65LEU0-0.048-0.01722.175-0.001-0.0010.0000.0000.0000.000
63A66VAL00.0300.02623.826-0.008-0.0080.0000.0000.0000.000
64A67GLY00.0010.00721.655-0.011-0.0110.0000.0000.0000.000
65A68LEU0-0.106-0.06118.246-0.002-0.0020.0000.0000.0000.000
66A69HIS00.0410.03320.861-0.014-0.0140.0000.0000.0000.000
67A70ASP-1-0.741-0.84020.425-0.085-0.0850.0000.0000.0000.000
68A71LEU0-0.001-0.00415.205-0.025-0.0250.0000.0000.0000.000
69A72GLY0-0.040-0.03217.155-0.032-0.0320.0000.0000.0000.000
70A73LYS10.8540.89917.9170.0740.0740.0000.0000.0000.000
71A74ALA0-0.0100.01312.994-0.052-0.0520.0000.0000.0000.000
72A75SER00.007-0.01113.927-0.024-0.0240.0000.0000.0000.000
73A76PRO00.0150.00812.3880.0190.0190.0000.0000.0000.000
74A77VAL0-0.028-0.00114.5110.0240.0240.0000.0000.0000.000
75A78PHE0-0.046-0.01717.2400.0330.0330.0000.0000.0000.000
76A79GLN0-0.033-0.00213.410-0.009-0.0090.0000.0000.0000.000
77A80ALA00.0220.01914.490-0.030-0.0300.0000.0000.0000.000
78A102TRP00.019-0.00123.113-0.004-0.0040.0000.0000.0000.000
79A103VAL0-0.015-0.01724.2150.0120.0120.0000.0000.0000.000
80A104ALA00.0620.04424.859-0.011-0.0110.0000.0000.0000.000
81A105HIS00.035-0.01121.415-0.012-0.0120.0000.0000.0000.000
82A106GLY00.1000.04822.7640.0010.0010.0000.0000.0000.000
83A107VAL0-0.018-0.00925.0760.0090.0090.0000.0000.0000.000
84A108PHE0-0.032-0.01819.3160.0020.0020.0000.0000.0000.000
85A109THR00.0040.00520.987-0.004-0.0040.0000.0000.0000.000
86A110GLU-1-0.718-0.84022.024-0.030-0.0300.0000.0000.0000.000
87A111LEU0-0.099-0.07021.8240.0090.0090.0000.0000.0000.000
88A112PHE0-0.023-0.01916.811-0.001-0.0010.0000.0000.0000.000
89A113LEU00.0720.03919.7930.0200.0200.0000.0000.0000.000
90A114ARG10.8620.93921.9390.0350.0350.0000.0000.0000.000
91A115ARG10.8660.93418.6390.0510.0510.0000.0000.0000.000
92A116LEU00.0260.00815.5170.0090.0090.0000.0000.0000.000
93A117LEU00.0180.01119.4640.0230.0230.0000.0000.0000.000
94A118LYS10.7650.88622.6670.0000.0000.0000.0000.0000.000
95A119GLU-1-0.819-0.87217.2130.0640.0640.0000.0000.0000.000
96A120LYS10.8060.88418.033-0.191-0.1910.0000.0000.0000.000
97A121GLY00.0410.02721.6090.0050.0050.0000.0000.0000.000
98A122LEU0-0.0110.01225.157-0.007-0.0070.0000.0000.0000.000
99A123PRO00.0280.01027.254-0.004-0.0040.0000.0000.0000.000
100A124GLU-1-0.818-0.91528.2280.0060.0060.0000.0000.0000.000
101A125ARG10.9210.95029.909-0.015-0.0150.0000.0000.0000.000
102A126ALA00.0810.05830.737-0.004-0.0040.0000.0000.0000.000
103A127ALA00.0150.00826.012-0.002-0.0020.0000.0000.0000.000
104A128ASN0-0.059-0.04827.610-0.010-0.0100.0000.0000.0000.000
105A129ASP-1-0.888-0.93629.290-0.004-0.0040.0000.0000.0000.000
106A130LEU00.0130.00427.813-0.003-0.0030.0000.0000.0000.000
107A131ALA0-0.040-0.01925.682-0.004-0.0040.0000.0000.0000.000
108A132ALA0-0.030-0.02626.841-0.008-0.0080.0000.0000.0000.000
109A133ALA0-0.0150.00129.745-0.004-0.0040.0000.0000.0000.000
110A134LEU0-0.013-0.00524.615-0.001-0.0010.0000.0000.0000.000
111A135GLY0-0.0040.00626.174-0.007-0.0070.0000.0000.0000.000
112A136ALA0-0.061-0.03627.535-0.001-0.0010.0000.0000.0000.000
113A137HIS0-0.077-0.05429.1820.0010.0010.0000.0000.0000.000
114A138HIS00.0420.01732.1730.0060.0060.0000.0000.0000.000
115A139GLY00.0680.03232.2910.0030.0030.0000.0000.0000.000
116A140PHE0-0.0420.00233.5090.0030.0030.0000.0000.0000.000
117A141PRO0-0.025-0.01531.570-0.004-0.0040.0000.0000.0000.000
118A142ALA00.0190.01628.768-0.002-0.0020.0000.0000.0000.000
119A143ASN00.0300.00330.8040.0010.0010.0000.0000.0000.000
120A144ALA00.022-0.00630.932-0.005-0.0050.0000.0000.0000.000
121A145GLU-1-0.729-0.84330.662-0.088-0.0880.0000.0000.0000.000
122A146GLU-1-0.827-0.90228.584-0.074-0.0740.0000.0000.0000.000
123A147LYS10.8360.90526.3490.0380.0380.0000.0000.0000.000
124A148SER0-0.0290.00325.686-0.014-0.0140.0000.0000.0000.000
125A149ARG10.8350.89425.9810.0830.0830.0000.0000.0000.000
126A150ALA00.0500.03122.458-0.015-0.0150.0000.0000.0000.000
127A151ARG10.9440.95621.3330.0560.0560.0000.0000.0000.000
128A152ARG10.8010.88721.3530.0920.0920.0000.0000.0000.000
129A153HIS00.0620.03719.065-0.026-0.0260.0000.0000.0000.000
130A154LEU0-0.037-0.01116.557-0.029-0.0290.0000.0000.0000.000
131A155ARG10.8990.94816.5420.1070.1070.0000.0000.0000.000
132A156THR00.0210.01517.1020.0080.0080.0000.0000.0000.000
133A157GLU-1-0.808-0.83212.755-0.408-0.4080.0000.0000.0000.000
134A158ASP-1-0.825-0.9197.604-1.365-1.3650.0000.0000.0000.000
135A159PRO00.024-0.0179.240-0.005-0.0050.0000.0000.0000.000
136A160LEU00.0440.0382.638-1.006-0.1640.440-0.363-0.919-0.001
137A161TRP00.0210.0016.7060.1980.1980.0000.0000.0000.000
138A162LYS10.7690.8719.4920.5620.5620.0000.0000.0000.000
139A163GLU-1-0.870-0.9416.843-0.207-0.2070.0000.0000.0000.000
140A164ALA00.001-0.0037.2640.3070.3070.0000.0000.0000.000
141A165ARG10.7620.8438.5990.4700.4700.0000.0000.0000.000
142A166ARG10.7830.85211.6410.0230.0230.0000.0000.0000.000
143A167TRP00.006-0.0037.3140.1250.1250.0000.0000.0000.000
144A168LEU0-0.015-0.01310.4400.0050.0050.0000.0000.0000.000
145A169LEU00.0160.01412.418-0.019-0.0190.0000.0000.0000.000
146A170GLU-1-0.841-0.90413.0450.2670.2670.0000.0000.0000.000
147A171GLU-1-0.810-0.88811.9470.3950.3950.0000.0000.0000.000
148A172VAL00.0130.01014.043-0.036-0.0360.0000.0000.0000.000
149A173PHE00.030-0.00217.393-0.017-0.0170.0000.0000.0000.000
150A174ARG10.8540.92512.154-0.477-0.4770.0000.0000.0000.000
151A175ARG10.7280.84513.486-0.230-0.2300.0000.0000.0000.000
152A176LEU0-0.021-0.01319.068-0.018-0.0180.0000.0000.0000.000
153A177GLY0-0.0200.01521.596-0.012-0.0120.0000.0000.0000.000
154A178ALA0-0.036-0.01522.690-0.011-0.0110.0000.0000.0000.000
155A179PRO0-0.037-0.00423.7210.0130.0130.0000.0000.0000.000
156A180LEU0-0.015-0.01424.793-0.005-0.0050.0000.0000.0000.000
157A181PRO0-0.013-0.00326.977-0.001-0.0010.0000.0000.0000.000
158A182PRO00.0110.01530.4740.0030.0030.0000.0000.0000.000
159A183SER0-0.046-0.02731.033-0.003-0.0030.0000.0000.0000.000
160A184GLN0-0.129-0.07333.4960.0030.0030.0000.0000.0000.000
161A185GLY00.0500.02935.403-0.002-0.0020.0000.0000.0000.000
162A186ASN0-0.018-0.00933.272-0.007-0.0070.0000.0000.0000.000
163A187GLY0-0.078-0.04835.044-0.002-0.0020.0000.0000.0000.000
164A188GLU-1-0.751-0.87733.9970.0380.0380.0000.0000.0000.000
165A189ALA00.0690.02833.3650.0030.0030.0000.0000.0000.000
166A190ARG10.7290.84835.518-0.022-0.0220.0000.0000.0000.000
167A191PRO00.0840.01837.4440.0000.0000.0000.0000.0000.000
168A192GLU-1-0.850-0.94037.8050.0030.0030.0000.0000.0000.000
169A193ALA0-0.0050.02535.2420.0000.0000.0000.0000.0000.000
170A194VAL0-0.032-0.01832.4390.0010.0010.0000.0000.0000.000
171A195LEU0-0.011-0.01033.528-0.002-0.0020.0000.0000.0000.000
172A196ARG10.8010.86835.500-0.015-0.0150.0000.0000.0000.000
173A197VAL00.0070.00928.9800.0000.0000.0000.0000.0000.000
174A198MET0-0.057-0.00930.908-0.003-0.0030.0000.0000.0000.000
175A199ALA00.0150.00732.096-0.004-0.0040.0000.0000.0000.000
176A200LEU00.0020.01030.396-0.002-0.0020.0000.0000.0000.000
177A201ALA0-0.012-0.02027.646-0.001-0.0010.0000.0000.0000.000
178A202SER0-0.023-0.00328.926-0.005-0.0050.0000.0000.0000.000
179A203PHE00.0140.00131.256-0.004-0.0040.0000.0000.0000.000
180A204ALA00.001-0.01128.009-0.002-0.0020.0000.0000.0000.000
181A205ASP-1-0.842-0.92224.867-0.042-0.0420.0000.0000.0000.000
182A206TRP0-0.0110.01027.317-0.005-0.0050.0000.0000.0000.000
183A207VAL0-0.005-0.00630.115-0.003-0.0030.0000.0000.0000.000
184A208ALA0-0.013-0.01424.830-0.002-0.0020.0000.0000.0000.000
185A209SER0-0.041-0.03225.768-0.008-0.0080.0000.0000.0000.000
186A210ASP-1-0.849-0.88626.866-0.047-0.0470.0000.0000.0000.000
187A211PRO0-0.006-0.00526.5630.0040.0040.0000.0000.0000.000
188A212SER0-0.118-0.08328.0900.0030.0030.0000.0000.0000.000
189A213LEU0-0.053-0.03330.1150.0050.0050.0000.0000.0000.000
190A214PHE0-0.027-0.01024.9390.0070.0070.0000.0000.0000.000
191A215PRO00.0160.02125.477-0.007-0.0070.0000.0000.0000.000
192A216TYR00.014-0.00322.025-0.002-0.0020.0000.0000.0000.000
193A217GLY00.0340.02119.9810.0010.0010.0000.0000.0000.000
194A218ARG10.7310.85120.0000.0230.0230.0000.0000.0000.000
195A219ASP-1-0.777-0.87613.830-0.037-0.0370.0000.0000.0000.000
196A220PRO00.0350.01613.2460.0160.0160.0000.0000.0000.000
197A221ARG10.8380.8889.6210.1530.1530.0000.0000.0000.000
198A222ARG10.8420.92513.0340.0050.0050.0000.0000.0000.000
199A223GLY00.0660.02616.4200.0120.0120.0000.0000.0000.000
200A224ASP-1-0.908-0.95318.3850.0310.0310.0000.0000.0000.000
201A225TYR0-0.006-0.01318.233-0.005-0.0050.0000.0000.0000.000
202A226LEU00.0350.01720.267-0.009-0.0090.0000.0000.0000.000
203A227LYS10.9460.97022.089-0.076-0.0760.0000.0000.0000.000
204A228GLU-1-0.771-0.85423.640-0.003-0.0030.0000.0000.0000.000
205A229ALA00.0190.00822.780-0.006-0.0060.0000.0000.0000.000
206A230LEU00.000-0.01024.872-0.003-0.0030.0000.0000.0000.000
207A231ARG10.7450.84627.703-0.003-0.0030.0000.0000.0000.000
208A232LEU0-0.014-0.00225.609-0.003-0.0030.0000.0000.0000.000
209A233ALA00.0310.01728.379-0.004-0.0040.0000.0000.0000.000
210A234GLN0-0.032-0.02630.1250.0000.0000.0000.0000.0000.000
211A235GLU-1-0.875-0.93532.691-0.011-0.0110.0000.0000.0000.000
212A236ALA0-0.0050.01131.717-0.002-0.0020.0000.0000.0000.000
213A237LEU0-0.007-0.01432.883-0.002-0.0020.0000.0000.0000.000
214A238ASN0-0.021-0.01435.6580.0000.0000.0000.0000.0000.000
215A239ARG10.8820.94933.7530.0180.0180.0000.0000.0000.000
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