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: MNMYZ

Calculation Name: 4H8S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4H8S

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NEU8

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 382
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4457552.68112
FMO2-HF: Nuclear repulsion 4303213.675093
FMO2-HF: Total energy -154339.006028
FMO2-MP2: Total energy -154779.15952


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:TYR)


Summations of interaction energy for fragment #1(A:-4:TYR)
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.
-1.6170.4620.027-0.908-1.198-0.002
Interaction energy analysis for fragmet #1(A:-4:TYR)
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 : -0.037
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].
3A-2GLN00.0140.0013.113-1.6380.4410.027-0.908-1.198-0.002
4A-1SER0-0.019-0.0166.1830.2410.2410.0000.0000.0000.000
5A0ASN00.0310.0189.628-0.048-0.0480.0000.0000.0000.000
6A1ALA0-0.009-0.00112.4280.0580.0580.0000.0000.0000.000
7A2PRO0-0.044-0.03316.2090.0080.0080.0000.0000.0000.000
8A3ALA00.0150.01117.7510.0090.0090.0000.0000.0000.000
9A4VAL0-0.0180.00120.3420.0000.0000.0000.0000.0000.000
10A5ASP-1-0.897-0.93622.597-0.137-0.1370.0000.0000.0000.000
11A6LYS10.8860.94325.0390.0980.0980.0000.0000.0000.000
12A7LEU0-0.0010.00628.1690.0000.0000.0000.0000.0000.000
13A8LEU00.038-0.01328.1510.0000.0000.0000.0000.0000.000
14A9LEU0-0.0020.01431.7510.0010.0010.0000.0000.0000.000
15A10GLU-1-0.942-0.99233.108-0.072-0.0720.0000.0000.0000.000
16A11GLU-1-0.923-0.94531.405-0.060-0.0600.0000.0000.0000.000
17A12ALA0-0.0010.00535.6150.0010.0010.0000.0000.0000.000
18A13LEU0-0.041-0.02938.0750.0030.0030.0000.0000.0000.000
19A14GLN0-0.062-0.03537.1430.0030.0030.0000.0000.0000.000
20A15ASP-1-0.799-0.85737.514-0.030-0.0300.0000.0000.0000.000
21A16SER00.0230.02433.5440.0030.0030.0000.0000.0000.000
22A17PRO00.0540.00934.543-0.002-0.0020.0000.0000.0000.000
23A18GLN00.026-0.00529.5300.0010.0010.0000.0000.0000.000
24A19THR0-0.0120.00030.001-0.002-0.0020.0000.0000.0000.000
25A20ARG10.8130.86831.9300.0270.0270.0000.0000.0000.000
26A21SER0-0.058-0.02729.2910.0010.0010.0000.0000.0000.000
27A22LEU00.0400.02226.0320.0010.0010.0000.0000.0000.000
28A23LEU00.002-0.00329.014-0.003-0.0030.0000.0000.0000.000
29A24SER00.0070.00331.3030.0010.0010.0000.0000.0000.000
30A25VAL0-0.019-0.00225.6620.0010.0010.0000.0000.0000.000
31A26PHE0-0.022-0.01727.793-0.003-0.0030.0000.0000.0000.000
32A27GLU-1-0.860-0.90029.738-0.038-0.0380.0000.0000.0000.000
33A28GLU-1-0.904-0.94528.869-0.026-0.0260.0000.0000.0000.000
34A29ASP-1-0.882-0.94326.695-0.078-0.0780.0000.0000.0000.000
35A30ALA00.006-0.01028.7140.0000.0000.0000.0000.0000.000
36A31GLY00.0140.01331.9920.0010.0010.0000.0000.0000.000
37A32THR00.0310.01528.662-0.001-0.0010.0000.0000.0000.000
38A33LEU0-0.0100.01230.189-0.001-0.0010.0000.0000.0000.000
39A34THR0-0.059-0.04631.4800.0010.0010.0000.0000.0000.000
40A35ASP-1-0.886-0.93533.473-0.031-0.0310.0000.0000.0000.000
41A36TYR0-0.030-0.01830.6910.0000.0000.0000.0000.0000.000
42A37THR0-0.005-0.02633.2060.0010.0010.0000.0000.0000.000
43A38ASN00.0170.02835.2960.0010.0010.0000.0000.0000.000
44A39GLN0-0.035-0.00934.8190.0030.0030.0000.0000.0000.000
45A40LEU0-0.023-0.01032.8300.0010.0010.0000.0000.0000.000
46A41LEU00.0320.01336.2140.0010.0010.0000.0000.0000.000
47A42GLN00.0130.00239.3800.0010.0010.0000.0000.0000.000
48A43ALA0-0.022-0.01437.7150.0020.0020.0000.0000.0000.000
49A44MET0-0.019-0.01837.4290.0000.0000.0000.0000.0000.000
50A45GLN00.0360.01240.5450.0020.0020.0000.0000.0000.000
51A46ARG10.9540.99342.8250.0290.0290.0000.0000.0000.000
52A47VAL0-0.022-0.00240.7560.0010.0010.0000.0000.0000.000
53A48TYR00.0100.00643.8840.0010.0010.0000.0000.0000.000
54A49GLY00.0040.00546.2780.0010.0010.0000.0000.0000.000
55A50ALA0-0.014-0.02146.4550.0010.0010.0000.0000.0000.000
56A51GLN00.0000.01646.2460.0020.0020.0000.0000.0000.000
57A52ASN0-0.001-0.02049.1160.0020.0020.0000.0000.0000.000
58A53GLU-1-0.924-0.96151.581-0.020-0.0200.0000.0000.0000.000
59A54MET00.0530.03851.2790.0010.0010.0000.0000.0000.000
60A55CYS0-0.077-0.01153.3700.0000.0000.0000.0000.0000.000
61A56LEU00.0140.00655.3150.0010.0010.0000.0000.0000.000
62A57ALA00.0160.01355.8870.0010.0010.0000.0000.0000.000
63A58THR0-0.011-0.02355.9960.0010.0010.0000.0000.0000.000
64A59GLN0-0.0090.00058.6520.0000.0000.0000.0000.0000.000
65A60GLN0-0.067-0.03561.1270.0010.0010.0000.0000.0000.000
66A61LEU00.0080.00859.7730.0010.0010.0000.0000.0000.000
67A62SER00.026-0.01262.8240.0010.0010.0000.0000.0000.000
68A63LYS10.9550.97864.7260.0150.0150.0000.0000.0000.000
69A64GLN0-0.017-0.02066.1730.0010.0010.0000.0000.0000.000
70A65LEU0-0.0170.00663.7160.0000.0000.0000.0000.0000.000
71A66LEU0-0.010-0.01068.0040.0000.0000.0000.0000.0000.000
72A67ALA0-0.038-0.02070.6380.0000.0000.0000.0000.0000.000
73A68TYR0-0.045-0.04572.0770.0000.0000.0000.0000.0000.000
74A69GLU-1-0.801-0.89273.824-0.012-0.0120.0000.0000.0000.000
75A70LYS10.7560.87574.0500.0130.0130.0000.0000.0000.000
76A71GLN0-0.0180.01076.1290.0000.0000.0000.0000.0000.000
77A72ASN0-0.042-0.01379.0550.0000.0000.0000.0000.0000.000
78A73PHE00.0290.00576.5440.0000.0000.0000.0000.0000.000
79A74ALA0-0.012-0.00482.5800.0000.0000.0000.0000.0000.000
80A75LEU00.0190.00883.9160.0000.0000.0000.0000.0000.000
81A76GLY0-0.005-0.02085.1970.0000.0000.0000.0000.0000.000
82A77LYS10.7430.84277.8740.0100.0100.0000.0000.0000.000
83A78GLY00.1200.07979.9060.0000.0000.0000.0000.0000.000
84A79ASP-1-0.862-0.90376.636-0.010-0.0100.0000.0000.0000.000
85A80GLU-1-0.839-0.90777.307-0.010-0.0100.0000.0000.0000.000
86A81GLU-1-0.859-0.94373.943-0.011-0.0110.0000.0000.0000.000
87A82VAL00.0160.01772.062-0.001-0.0010.0000.0000.0000.000
88A83ILE00.0200.01671.982-0.001-0.0010.0000.0000.0000.000
89A84SER0-0.073-0.04172.4030.0000.0000.0000.0000.0000.000
90A85THR00.0060.00168.344-0.001-0.0010.0000.0000.0000.000
91A86LEU00.0020.00367.912-0.001-0.0010.0000.0000.0000.000
92A87HIS0-0.028-0.01167.899-0.001-0.0010.0000.0000.0000.000
93A88TYR0-0.014-0.00361.913-0.001-0.0010.0000.0000.0000.000
94A89PHE00.000-0.03262.096-0.001-0.0010.0000.0000.0000.000
95A90SER00.0070.01063.0330.0000.0000.0000.0000.0000.000
96A91LYS10.8060.88863.5670.0180.0180.0000.0000.0000.000
97A92VAL0-0.0090.00058.799-0.001-0.0010.0000.0000.0000.000
98A93VAL0-0.0030.00659.077-0.001-0.0010.0000.0000.0000.000
99A94ASP-1-0.820-0.89759.355-0.018-0.0180.0000.0000.0000.000
100A95GLU-1-0.817-0.89858.874-0.020-0.0200.0000.0000.0000.000
101A96LEU0-0.007-0.00852.929-0.001-0.0010.0000.0000.0000.000
102A97ASN0-0.022-0.00755.002-0.001-0.0010.0000.0000.0000.000
103A98LEU00.0240.02955.544-0.001-0.0010.0000.0000.0000.000
104A99LEU0-0.008-0.00851.817-0.001-0.0010.0000.0000.0000.000
105A100HIS00.019-0.00750.200-0.001-0.0010.0000.0000.0000.000
106A101THR0-0.055-0.04851.400-0.001-0.0010.0000.0000.0000.000
107A102GLU-1-0.904-0.95250.245-0.033-0.0330.0000.0000.0000.000
108A103LEU0-0.0110.00844.876-0.001-0.0010.0000.0000.0000.000
109A104ALA0-0.0040.00247.847-0.001-0.0010.0000.0000.0000.000
110A105LYS10.8360.89848.4030.0300.0300.0000.0000.0000.000
111A106GLN00.0490.01445.290-0.003-0.0030.0000.0000.0000.000
112A107LEU0-0.0090.00342.702-0.002-0.0020.0000.0000.0000.000
113A108ALA00.0150.00443.887-0.002-0.0020.0000.0000.0000.000
114A109ASP-1-0.854-0.90845.331-0.035-0.0350.0000.0000.0000.000
115A110THR0-0.079-0.05941.909-0.002-0.0020.0000.0000.0000.000
116A111MET0-0.0150.00138.844-0.002-0.0020.0000.0000.0000.000
117A112VAL00.005-0.00639.981-0.001-0.0010.0000.0000.0000.000
118A113LEU00.0000.01742.1580.0000.0000.0000.0000.0000.000
119A114PRO0-0.001-0.00538.2530.0000.0000.0000.0000.0000.000
120A115ILE00.0310.01735.214-0.002-0.0020.0000.0000.0000.000
121A116ILE00.0040.01638.9990.0000.0000.0000.0000.0000.000
122A117GLN00.0470.01942.0490.0010.0010.0000.0000.0000.000
123A118PHE00.0250.02532.9240.0000.0000.0000.0000.0000.000
124A119ARG10.8810.92138.4640.0370.0370.0000.0000.0000.000
125A120GLU-1-0.937-0.97839.901-0.032-0.0320.0000.0000.0000.000
126A121LYS10.8340.91442.0580.0410.0410.0000.0000.0000.000
127A122ASP-1-0.768-0.87437.522-0.054-0.0540.0000.0000.0000.000
128A123LEU0-0.004-0.01134.4690.0000.0000.0000.0000.0000.000
129A124THR0-0.024-0.00638.3590.0020.0020.0000.0000.0000.000
130A125GLU-1-0.942-0.95440.813-0.044-0.0440.0000.0000.0000.000
131A126VAL00.0300.01635.9300.0010.0010.0000.0000.0000.000
132A127SER00.0180.00839.1450.0020.0020.0000.0000.0000.000
133A128THR0-0.050-0.02641.1010.0030.0030.0000.0000.0000.000
134A129LEU0-0.031-0.03140.7380.0020.0020.0000.0000.0000.000
135A130LYS10.8860.95738.1080.0320.0320.0000.0000.0000.000
136A131ASP-1-0.863-0.93241.003-0.026-0.0260.0000.0000.0000.000
137A132LEU0-0.054-0.01544.2790.0020.0020.0000.0000.0000.000
138A133PHE00.003-0.01038.8770.0010.0010.0000.0000.0000.000
139A134GLY00.0380.01142.8630.0010.0010.0000.0000.0000.000
140A135LEU0-0.0180.00343.5670.0020.0020.0000.0000.0000.000
141A136ALA00.002-0.00846.3270.0010.0010.0000.0000.0000.000
142A137SER00.0110.01143.4430.0000.0000.0000.0000.0000.000
143A138ASN00.0180.01845.5720.0020.0020.0000.0000.0000.000
144A139GLU-1-0.877-0.92047.741-0.021-0.0210.0000.0000.0000.000
145A140HIS00.0230.00045.6000.0010.0010.0000.0000.0000.000
146A141ASP-1-0.874-0.93045.624-0.019-0.0190.0000.0000.0000.000
147A142LEU0-0.031-0.02748.5460.0010.0010.0000.0000.0000.000
148A143SER0-0.050-0.02251.6750.0010.0010.0000.0000.0000.000
149A144MET00.0310.00948.0220.0000.0000.0000.0000.0000.000
150A145ALA0-0.0130.01651.4020.0010.0010.0000.0000.0000.000
151A146LYS10.8210.87953.4120.0150.0150.0000.0000.0000.000
152A147TYR00.0200.00153.6100.0000.0000.0000.0000.0000.000
153A148SER0-0.034-0.02652.4300.0000.0000.0000.0000.0000.000
154A149ARG10.8950.95254.7900.0110.0110.0000.0000.0000.000
155A150LEU0-0.0330.00958.1190.0010.0010.0000.0000.0000.000
156A151PRO00.0060.01659.7040.0000.0000.0000.0000.0000.000
157A152LYS11.0090.99958.5780.0080.0080.0000.0000.0000.000
158A153LYS10.9180.96861.9130.0050.0050.0000.0000.0000.000
159A154LYS10.9480.96565.6880.0070.0070.0000.0000.0000.000
160A155GLU-1-0.780-0.88962.351-0.011-0.0110.0000.0000.0000.000
161A156ASN0-0.038-0.01965.4550.0000.0000.0000.0000.0000.000
162A157GLU-1-0.750-0.87264.224-0.013-0.0130.0000.0000.0000.000
163A158LYS10.8030.90065.2090.0120.0120.0000.0000.0000.000
164A159VAL00.0770.02563.4160.0000.0000.0000.0000.0000.000
165A160LYS10.8050.88460.0230.0120.0120.0000.0000.0000.000
166A161THR0-0.021-0.01960.208-0.001-0.0010.0000.0000.0000.000
167A162GLU-1-0.875-0.92460.703-0.013-0.0130.0000.0000.0000.000
168A163VAL00.0260.01257.130-0.001-0.0010.0000.0000.0000.000
169A164GLY00.0360.02456.130-0.001-0.0010.0000.0000.0000.000
170A165LYS10.9260.96155.5840.0190.0190.0000.0000.0000.000
171A166GLU-1-0.844-0.91456.427-0.016-0.0160.0000.0000.0000.000
172A167VAL0-0.0120.01050.997-0.001-0.0010.0000.0000.0000.000
173A168ALA0-0.019-0.00151.516-0.001-0.0010.0000.0000.0000.000
174A169ALA0-0.006-0.01051.441-0.002-0.0020.0000.0000.0000.000
175A170ALA00.0800.03850.8470.0000.0000.0000.0000.0000.000
176A171ARG10.9690.99146.7620.0230.0230.0000.0000.0000.000
177A172ARG10.8940.95446.8840.0290.0290.0000.0000.0000.000
178A173LYS10.8360.89847.5640.0220.0220.0000.0000.0000.000
179A174GLN00.0320.03042.0020.0000.0000.0000.0000.0000.000
180A175HIS00.0560.01841.177-0.001-0.0010.0000.0000.0000.000
181A176LEU0-0.044-0.01542.879-0.002-0.0020.0000.0000.0000.000
182A177SER00.016-0.01943.836-0.002-0.0020.0000.0000.0000.000
183A178SER0-0.007-0.00439.625-0.002-0.0020.0000.0000.0000.000
184A179LEU0-0.0050.00138.821-0.003-0.0030.0000.0000.0000.000
185A180GLN00.001-0.01039.178-0.002-0.0020.0000.0000.0000.000
186A181TYR0-0.041-0.04936.888-0.003-0.0030.0000.0000.0000.000
187A182TYR00.0320.00534.896-0.002-0.0020.0000.0000.0000.000
188A183CYS0-0.052-0.03034.820-0.005-0.0050.0000.0000.0000.000
189A184ALA00.0130.02435.747-0.004-0.0040.0000.0000.0000.000
190A185LEU00.0290.01532.423-0.003-0.0030.0000.0000.0000.000
191A186ASN00.0140.00430.814-0.006-0.0060.0000.0000.0000.000
192A187ALA00.0070.00531.022-0.006-0.0060.0000.0000.0000.000
193A188LEU0-0.007-0.00231.924-0.003-0.0030.0000.0000.0000.000
194A189GLN00.0060.01127.020-0.006-0.0060.0000.0000.0000.000
195A190TYR0-0.009-0.00227.747-0.004-0.0040.0000.0000.0000.000
196A191ARG10.8520.89830.1210.0620.0620.0000.0000.0000.000
197A192LYS10.8490.94026.5200.0910.0910.0000.0000.0000.000
198A193GLN0-0.004-0.00124.2440.0040.0040.0000.0000.0000.000
199A194MET00.0080.00028.7980.0020.0020.0000.0000.0000.000
200A195ALA00.0190.00931.9100.0030.0030.0000.0000.0000.000
201A196MET0-0.0010.00129.1550.0050.0050.0000.0000.0000.000
202A197MET0-0.062-0.03027.5810.0000.0000.0000.0000.0000.000
203A198GLU-1-0.946-0.97831.273-0.061-0.0610.0000.0000.0000.000
204A199PRO0-0.033-0.01334.0370.0030.0030.0000.0000.0000.000
205A200MET00.020-0.00333.2010.0040.0040.0000.0000.0000.000
206A201ILE0-0.0090.00732.3990.0020.0020.0000.0000.0000.000
207A202GLY00.0360.01935.9980.0020.0020.0000.0000.0000.000
208A203PHE00.005-0.00336.6390.0030.0030.0000.0000.0000.000
209A204ALA00.0000.00436.4270.0020.0020.0000.0000.0000.000
210A205HIS00.017-0.00337.8050.0020.0020.0000.0000.0000.000
211A206GLY00.0240.02140.9670.0020.0020.0000.0000.0000.000
212A207GLN00.014-0.01240.8670.0040.0040.0000.0000.0000.000
213A208ILE0-0.0080.01038.4550.0010.0010.0000.0000.0000.000
214A209ASN0-0.035-0.02542.8480.0030.0030.0000.0000.0000.000
215A210PHE0-0.0180.00745.8480.0020.0020.0000.0000.0000.000
216A211PHE00.0180.00344.2720.0020.0020.0000.0000.0000.000
217A212LYS10.7770.88245.7540.0320.0320.0000.0000.0000.000
218A213LYS10.8740.92447.5310.0310.0310.0000.0000.0000.000
219A214GLY00.0390.01749.8910.0010.0010.0000.0000.0000.000
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221A216GLU-1-0.879-0.91850.638-0.027-0.0270.0000.0000.0000.000
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