FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 981M2

Calculation Name: 4YWK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YWK

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U3I4

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2280803.165066
FMO2-HF: Nuclear repulsion 2201296.210524
FMO2-HF: Total energy -79506.954541
FMO2-MP2: Total energy -79741.949197


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:1:VAL)


Summations of interaction energy for fragment #1(A:1:VAL)
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.
-10.154-4.5353.955-3.38-6.19-0.005
Interaction energy analysis for fragmet #1(A:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.007
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].
3A3ARG10.9500.9513.587-0.4951.0140.003-0.777-0.7340.005
4A4GLU-1-0.993-1.0026.5910.3500.3500.0000.0000.0000.000
5A5GLU-1-0.775-0.8692.144-2.158-2.6653.541-0.833-2.200-0.004
6A6MET0-0.035-0.0193.184-1.518-0.2890.273-0.474-1.0270.003
7A7ILE0-0.040-0.0154.652-0.588-0.506-0.001-0.010-0.0710.000
8A8GLU-1-0.957-0.9657.653-0.155-0.1550.0000.0000.0000.000
9A9ARG10.7150.8173.1321.1971.9780.064-0.255-0.589-0.002
10A10PHE00.018-0.0077.592-0.126-0.1260.0000.0000.0000.000
11A11ALA0-0.018-0.0099.724-0.110-0.1100.0000.0000.0000.000
12A12ASN00.0030.00210.147-0.003-0.0030.0000.0000.0000.000
13A13PHE0-0.0100.00911.368-0.020-0.0200.0000.0000.0000.000
14A14LEU0-0.062-0.04013.010-0.036-0.0360.0000.0000.0000.000
15A15ARG10.7340.84515.293-0.111-0.1110.0000.0000.0000.000
16A16GLU-1-0.951-0.99014.967-0.054-0.0540.0000.0000.0000.000
17A17TYR0-0.0340.00215.804-0.016-0.0160.0000.0000.0000.000
18A18THR0-0.082-0.04517.5590.0040.0040.0000.0000.0000.000
19A19ASP-1-0.834-0.91720.8590.0330.0330.0000.0000.0000.000
20A20GLU-1-0.968-0.98623.0980.0080.0080.0000.0000.0000.000
21A21ASP-1-0.971-0.97825.7310.0130.0130.0000.0000.0000.000
22A22GLY0-0.065-0.03524.863-0.002-0.0020.0000.0000.0000.000
23A23ASN0-0.033-0.02525.518-0.001-0.0010.0000.0000.0000.000
24A24PRO00.0280.02421.7750.0050.0050.0000.0000.0000.000
25A25VAL00.002-0.01521.0820.0100.0100.0000.0000.0000.000
26A26TYR0-0.017-0.04317.8840.0170.0170.0000.0000.0000.000
27A27ARG11.0041.01520.127-0.054-0.0540.0000.0000.0000.000
28A28GLY00.0030.00522.0070.0000.0000.0000.0000.0000.000
29A29LYS10.8670.93421.093-0.131-0.1310.0000.0000.0000.000
30A30ILE00.0290.02318.4390.0050.0050.0000.0000.0000.000
31A31THR00.008-0.00522.440-0.007-0.0070.0000.0000.0000.000
32A32ASP-1-0.905-0.95125.8190.0790.0790.0000.0000.0000.000
33A33LEU0-0.075-0.04121.512-0.003-0.0030.0000.0000.0000.000
34A34LEU0-0.039-0.01725.869-0.003-0.0030.0000.0000.0000.000
35A35THR0-0.059-0.01528.710-0.007-0.0070.0000.0000.0000.000
36A36ILE00.008-0.00531.8890.0010.0010.0000.0000.0000.000
37A37THR0-0.054-0.03434.067-0.003-0.0030.0000.0000.0000.000
38A38PRO0-0.0230.02828.7120.0000.0000.0000.0000.0000.000
39A39LYS10.9200.94825.950-0.090-0.0900.0000.0000.0000.000
40A40ARG10.9700.97425.076-0.113-0.1130.0000.0000.0000.000
41A41SER0-0.004-0.01521.7250.0170.0170.0000.0000.0000.000
42A42VAL0-0.0040.00918.377-0.021-0.0210.0000.0000.0000.000
43A43ALA0-0.0050.00518.9010.0240.0240.0000.0000.0000.000
44A44ILE00.018-0.00214.088-0.022-0.0220.0000.0000.0000.000
45A45ASP-1-0.802-0.89517.3520.1190.1190.0000.0000.0000.000
46A46TRP00.010-0.03511.346-0.040-0.0400.0000.0000.0000.000
47A47MET0-0.0080.00714.289-0.012-0.0120.0000.0000.0000.000
48A48HIS0-0.0020.04116.181-0.014-0.0140.0000.0000.0000.000
49A49LEU00.0330.0289.472-0.038-0.0380.0000.0000.0000.000
50A50ASN0-0.006-0.01411.505-0.052-0.0520.0000.0000.0000.000
51A51SER0-0.127-0.07012.565-0.064-0.0640.0000.0000.0000.000
52A52PHE0-0.013-0.00511.177-0.030-0.0300.0000.0000.0000.000
53A53ASP-1-0.761-0.8796.565-0.483-0.4830.0000.0000.0000.000
54A54SER00.0270.0108.4920.0880.0880.0000.0000.0000.000
55A55GLU-1-0.921-0.9393.323-5.252-3.8310.051-0.653-0.819-0.005
56A56LEU00.0340.0244.3660.2100.4170.000-0.025-0.1820.000
57A57ALA00.006-0.0095.3890.2920.288-0.0010.0000.0050.000
58A58HIS0-0.024-0.0127.3510.0800.0800.0000.0000.0000.000
59A59GLU-1-0.839-0.9283.602-1.165-0.2640.025-0.353-0.573-0.002
60A60VAL0-0.033-0.0116.307-0.111-0.1110.0000.0000.0000.000
61A61ILE0-0.060-0.0269.333-0.144-0.1440.0000.0000.0000.000
62A62GLU-1-0.869-0.9508.1480.0190.0190.0000.0000.0000.000
63A63ASN0-0.100-0.0455.441-0.186-0.1860.0000.0000.0000.000
64A64PRO0-0.0010.0138.8200.1940.1940.0000.0000.0000.000
65A65GLU-1-0.870-0.92511.4590.2960.2960.0000.0000.0000.000
66A66GLU-1-0.899-0.9417.0720.3250.3250.0000.0000.0000.000
67A67GLY00.0470.0247.7520.1790.1790.0000.0000.0000.000
68A68ILE0-0.034-0.0348.685-0.056-0.0560.0000.0000.0000.000
69A69SER0-0.028-0.00611.637-0.055-0.0550.0000.0000.0000.000
70A70ALA00.0410.0227.914-0.092-0.0920.0000.0000.0000.000
71A71ALA00.0170.0119.877-0.126-0.1260.0000.0000.0000.000
72A72GLU-1-0.836-0.92911.6770.2070.2070.0000.0000.0000.000
73A73ASP-1-0.874-0.94112.1490.2920.2920.0000.0000.0000.000
74A74ALA00.0070.00711.046-0.072-0.0720.0000.0000.0000.000
75A75ILE0-0.026-0.01913.065-0.077-0.0770.0000.0000.0000.000
76A76GLN0-0.066-0.03816.495-0.056-0.0560.0000.0000.0000.000
77A77ILE00.0060.01713.888-0.033-0.0330.0000.0000.0000.000
78A78VAL00.0230.01715.678-0.033-0.0330.0000.0000.0000.000
79A79LEU0-0.045-0.02018.197-0.026-0.0260.0000.0000.0000.000
80A80ARG10.9580.98520.199-0.116-0.1160.0000.0000.0000.000
81A81GLU-1-0.945-0.97617.6480.0700.0700.0000.0000.0000.000
82A82ASP-1-0.831-0.89819.9220.0660.0660.0000.0000.0000.000
83A83PHE0-0.088-0.05922.024-0.010-0.0100.0000.0000.0000.000
84A84GLN0-0.041-0.00224.666-0.006-0.0060.0000.0000.0000.000
85A85ARG10.8220.91124.839-0.080-0.0800.0000.0000.0000.000
86A86GLU-1-0.909-0.97123.3770.0890.0890.0000.0000.0000.000
87A87ASP-1-0.910-0.94824.9630.0810.0810.0000.0000.0000.000
88A88VAL0-0.0020.00324.241-0.004-0.0040.0000.0000.0000.000
89A89GLY0-0.0130.00325.011-0.002-0.0020.0000.0000.0000.000
90A90LYS10.8490.90717.119-0.269-0.2690.0000.0000.0000.000
91A91ILE00.0010.01819.820-0.015-0.0150.0000.0000.0000.000
92A92HIS0-0.062-0.02418.9510.0420.0420.0000.0000.0000.000
93A93ALA00.0010.01014.936-0.021-0.0210.0000.0000.0000.000
94A94ARG10.7460.92216.866-0.165-0.1650.0000.0000.0000.000
95A95PHE00.0510.02211.889-0.015-0.0150.0000.0000.0000.000
96A96TYR00.0090.00216.996-0.020-0.0200.0000.0000.0000.000
97A97ASN0-0.031-0.02518.2430.0020.0020.0000.0000.0000.000
98A98LEU00.014-0.00415.3920.0040.0040.0000.0000.0000.000
99A99PRO0-0.0070.00015.346-0.019-0.0190.0000.0000.0000.000
100A100GLU-1-0.963-0.97018.4900.0310.0310.0000.0000.0000.000
101A101THR0-0.013-0.01020.6790.0190.0190.0000.0000.0000.000
102A102LEU0-0.0270.00621.528-0.009-0.0090.0000.0000.0000.000
103A103MET0-0.001-0.00725.1770.0020.0020.0000.0000.0000.000
104A104VAL00.0110.00427.7450.0020.0020.0000.0000.0000.000
105A105LYS10.7800.87628.921-0.029-0.0290.0000.0000.0000.000
106A106ASP-1-0.848-0.91526.4360.0350.0350.0000.0000.0000.000
107A107ILE0-0.090-0.02523.8000.0010.0010.0000.0000.0000.000
108A108GLY00.019-0.01123.977-0.005-0.0050.0000.0000.0000.000
109A109ALA0-0.112-0.07022.9360.0080.0080.0000.0000.0000.000
110A110GLU-1-0.883-0.95219.9680.0440.0440.0000.0000.0000.000
111A111HIS00.0930.05918.4200.0070.0070.0000.0000.0000.000
112A112ILE0-0.085-0.04318.1320.0160.0160.0000.0000.0000.000
113A113ASN0-0.045-0.03213.923-0.002-0.0020.0000.0000.0000.000
114A114LYS10.9440.99813.291-0.057-0.0570.0000.0000.0000.000
115A115LEU0-0.039-0.00113.727-0.015-0.0150.0000.0000.0000.000
116A116ILE0-0.026-0.01615.413-0.022-0.0220.0000.0000.0000.000
117A117GLN00.0570.01218.6750.0240.0240.0000.0000.0000.000
118A118VAL0-0.048-0.01521.391-0.014-0.0140.0000.0000.0000.000
119A119GLU-1-0.901-0.94824.9890.0560.0560.0000.0000.0000.000
120A120GLY0-0.027-0.03428.315-0.003-0.0030.0000.0000.0000.000
121A121ILE0-0.083-0.03731.504-0.001-0.0010.0000.0000.0000.000
122A122VAL00.0540.04432.7530.0000.0000.0000.0000.0000.000
123A123THR0-0.049-0.02935.091-0.003-0.0030.0000.0000.0000.000
124A124ARG10.8920.93236.525-0.048-0.0480.0000.0000.0000.000
125A125VAL00.0730.03734.6510.0030.0030.0000.0000.0000.000
126A126GLY0-0.049-0.01135.376-0.005-0.0050.0000.0000.0000.000
127A127GLU-1-0.911-0.95135.1650.0660.0660.0000.0000.0000.000
128A128ILE0-0.087-0.04234.737-0.005-0.0050.0000.0000.0000.000
129A129LYS10.9801.01433.861-0.049-0.0490.0000.0000.0000.000
130A130PRO0-0.037-0.02830.073-0.004-0.0040.0000.0000.0000.000
131A182PHE00.017-0.00226.2500.0030.0030.0000.0000.0000.000
132A183GLN00.0680.03030.341-0.009-0.0090.0000.0000.0000.000
133A184SER0-0.045-0.01630.3310.0050.0050.0000.0000.0000.000
134A185PHE00.1030.05129.695-0.004-0.0040.0000.0000.0000.000
135A186ARG10.7350.85831.549-0.049-0.0490.0000.0000.0000.000
136A187ILE00.0480.03227.979-0.004-0.0040.0000.0000.0000.000
137A188GLN0-0.033-0.03131.9260.0000.0000.0000.0000.0000.000
138A189ASP-1-0.715-0.86632.3830.0430.0430.0000.0000.0000.000
139A190ARG10.8820.94130.433-0.054-0.0540.0000.0000.0000.000
140A191PRO00.0180.01635.835-0.002-0.0020.0000.0000.0000.000
141A192GLU-1-0.759-0.86636.5800.0320.0320.0000.0000.0000.000
142A193THR0-0.054-0.03433.483-0.001-0.0010.0000.0000.0000.000
143A194LEU0-0.061-0.01436.468-0.001-0.0010.0000.0000.0000.000
144A195LYS10.8770.93337.076-0.021-0.0210.0000.0000.0000.000
145A196GLY00.0250.00341.3850.0010.0010.0000.0000.0000.000
146A197GLY0-0.007-0.00544.400-0.001-0.0010.0000.0000.0000.000
147A198GLU-1-0.849-0.90936.5590.0240.0240.0000.0000.0000.000
148A199MET00.000-0.00940.4970.0010.0010.0000.0000.0000.000
149A200PRO0-0.0060.01136.9970.0010.0010.0000.0000.0000.000
150A201ARG10.9300.96732.954-0.035-0.0350.0000.0000.0000.000
151A202PHE00.025-0.00932.8260.0010.0010.0000.0000.0000.000
152A203ILE0-0.0170.00026.064-0.002-0.0020.0000.0000.0000.000
153A204ASP-1-0.785-0.86430.3540.0590.0590.0000.0000.0000.000
154A205GLY00.0370.02027.1750.0050.0050.0000.0000.0000.000
155A206ILE0-0.048-0.03126.368-0.009-0.0090.0000.0000.0000.000
156A207LEU00.0560.02224.8370.0110.0110.0000.0000.0000.000
157A208LEU00.0570.05324.423-0.011-0.0110.0000.0000.0000.000
158A209ASP-1-0.836-0.99024.9270.1390.1390.0000.0000.0000.000
159A210ASP-1-0.827-0.92125.9060.1180.1180.0000.0000.0000.000
160A211ILE0-0.106-0.06826.228-0.005-0.0050.0000.0000.0000.000
161A212VAL0-0.050-0.01228.261-0.006-0.0060.0000.0000.0000.000
162A213ASP-1-0.883-0.93531.0760.0650.0650.0000.0000.0000.000
163A214VAL0-0.078-0.03928.8750.0000.0000.0000.0000.0000.000
164A215ALA0-0.009-0.00232.166-0.002-0.0020.0000.0000.0000.000
165A216LEU00.0340.01833.9880.0000.0000.0000.0000.0000.000
166A217PRO0-0.070-0.05237.0860.0000.0000.0000.0000.0000.000
167A218GLY0-0.030-0.01438.413-0.002-0.0020.0000.0000.0000.000
168A219ASP-1-0.815-0.88534.8090.0500.0500.0000.0000.0000.000
169A220ARG10.7450.82833.515-0.036-0.0360.0000.0000.0000.000
170A221VAL00.0020.00429.2720.0000.0000.0000.0000.0000.000
171A222ILE00.0260.01524.355-0.005-0.0050.0000.0000.0000.000
172A223VAL0-0.015-0.01024.4500.0040.0040.0000.0000.0000.000
173A224THR00.0600.01918.892-0.006-0.0060.0000.0000.0000.000
174A225GLY00.010-0.00619.498-0.002-0.0020.0000.0000.0000.000
175A226ILE00.0570.05615.429-0.004-0.0040.0000.0000.0000.000
176A227LEU0-0.050-0.02818.819-0.019-0.0190.0000.0000.0000.000
177A228ARG10.7870.87917.460-0.190-0.1900.0000.0000.0000.000
178A229VAL0-0.020-0.02123.100-0.010-0.0100.0000.0000.0000.000
179A230VAL00.0160.01826.5610.0020.0020.0000.0000.0000.000
180A231LEU0-0.036-0.01330.005-0.004-0.0040.0000.0000.0000.000
181A232GLU-1-0.886-0.94332.7770.0430.0430.0000.0000.0000.000
182A233LYS10.9790.96635.519-0.044-0.0440.0000.0000.0000.000
183A234ARG10.8030.85739.049-0.036-0.0360.0000.0000.0000.000
184A235GLU-1-0.827-0.87040.7420.0310.0310.0000.0000.0000.000
185A236LYS10.9050.96037.162-0.040-0.0400.0000.0000.0000.000
186A237THR00.012-0.00139.4150.0000.0000.0000.0000.0000.000
187A238PRO0-0.034-0.02337.1240.0010.0010.0000.0000.0000.000
188A239ILE00.0000.01932.908-0.002-0.0020.0000.0000.0000.000
189A240PHE00.0330.00428.5340.0010.0010.0000.0000.0000.000
190A241ARG10.8170.91529.497-0.057-0.0570.0000.0000.0000.000
191A242LYS10.9940.99123.907-0.066-0.0660.0000.0000.0000.000
192A243ILE0-0.020-0.00425.784-0.007-0.0070.0000.0000.0000.000
193A244LEU00.0170.01121.6010.0030.0030.0000.0000.0000.000
194A245GLU-1-0.867-0.92220.8310.1730.1730.0000.0000.0000.000
195A246VAL0-0.048-0.02721.2960.0140.0140.0000.0000.0000.000
196A247ASN00.0010.00317.1510.0080.0080.0000.0000.0000.000
197A248HIS00.0260.01620.2770.0150.0150.0000.0000.0000.000
198A249ILE0-0.013-0.00922.310-0.007-0.0070.0000.0000.0000.000
199A250GLU-1-0.896-0.93925.7720.0910.0910.0000.0000.0000.000