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: 98Y92

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 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 382
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4456422.728918
FMO2-HF: Nuclear repulsion 4302086.124092
FMO2-HF: Total energy -154336.604826
FMO2-MP2: Total energy -154776.860439


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.
-1.8760.227-0.003-0.98-1.12-0.001
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 : -0.022 / q_NPA : -0.029
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-2GLN00.0190.0023.676-1.7680.335-0.003-0.980-1.120-0.001
4A-1SER0-0.022-0.0166.0740.2580.2580.0000.0000.0000.000
5A0ASN00.0380.0169.523-0.108-0.1080.0000.0000.0000.000
6A1ALA0-0.020-0.00112.3220.0940.0940.0000.0000.0000.000
7A2PRO0-0.048-0.03416.102-0.003-0.0030.0000.0000.0000.000
8A3ALA00.0190.01017.6500.0050.0050.0000.0000.0000.000
9A4VAL0-0.0100.01120.3420.0040.0040.0000.0000.0000.000
10A5ASP-1-0.899-0.94122.375-0.243-0.2430.0000.0000.0000.000
11A6LYS10.9310.95325.0020.1670.1670.0000.0000.0000.000
12A7LEU0-0.0010.01028.007-0.005-0.0050.0000.0000.0000.000
13A8LEU00.027-0.01228.2020.0040.0040.0000.0000.0000.000
14A9LEU0-0.0190.00931.4910.0040.0040.0000.0000.0000.000
15A10GLU-1-0.963-0.99833.019-0.127-0.1270.0000.0000.0000.000
16A11GLU-1-0.973-0.98730.591-0.134-0.1340.0000.0000.0000.000
17A12ALA00.0040.00535.3450.0010.0010.0000.0000.0000.000
18A13LEU0-0.052-0.03537.7840.0050.0050.0000.0000.0000.000
19A14GLN0-0.074-0.04336.9090.0030.0030.0000.0000.0000.000
20A15ASP-1-0.821-0.89337.250-0.074-0.0740.0000.0000.0000.000
21A16SER00.0410.03932.9750.0030.0030.0000.0000.0000.000
22A17PRO00.0390.00833.817-0.003-0.0030.0000.0000.0000.000
23A18GLN00.021-0.01829.2620.0020.0020.0000.0000.0000.000
24A19THR00.0540.05829.665-0.011-0.0110.0000.0000.0000.000
25A20ARG10.8710.92231.5910.0710.0710.0000.0000.0000.000
26A21SER0-0.065-0.03929.1050.0000.0000.0000.0000.0000.000
27A22LEU00.0450.02525.8650.0010.0010.0000.0000.0000.000
28A23LEU0-0.014-0.01028.691-0.001-0.0010.0000.0000.0000.000
29A24SER00.0070.00431.2200.0050.0050.0000.0000.0000.000
30A25VAL0-0.0040.00725.7460.0040.0040.0000.0000.0000.000
31A26PHE0-0.027-0.02327.886-0.001-0.0010.0000.0000.0000.000
32A27GLU-1-0.894-0.94529.706-0.078-0.0780.0000.0000.0000.000
33A28GLU-1-0.929-0.96028.903-0.070-0.0700.0000.0000.0000.000
34A29ASP-1-0.976-0.97826.270-0.129-0.1290.0000.0000.0000.000
35A30ALA00.023-0.00528.6820.0040.0040.0000.0000.0000.000
36A31GLY0-0.0030.00631.9600.0050.0050.0000.0000.0000.000
37A32THR00.0310.02228.6510.0020.0020.0000.0000.0000.000
38A33LEU00.0010.01129.3820.0030.0030.0000.0000.0000.000
39A34THR0-0.070-0.06031.4480.0060.0060.0000.0000.0000.000
40A35ASP-1-0.880-0.93133.387-0.053-0.0530.0000.0000.0000.000
41A36TYR0-0.037-0.02030.2820.0030.0030.0000.0000.0000.000
42A37THR0-0.025-0.03333.1770.0040.0040.0000.0000.0000.000
43A38ASN00.0400.02935.2650.0030.0030.0000.0000.0000.000
44A39GLN0-0.0010.00634.7730.0030.0030.0000.0000.0000.000
45A40LEU0-0.028-0.01433.1210.0030.0030.0000.0000.0000.000
46A41LEU00.0210.00936.1840.0030.0030.0000.0000.0000.000
47A42GLN00.0140.00639.3490.0020.0020.0000.0000.0000.000
48A43ALA0-0.031-0.02037.7240.0030.0030.0000.0000.0000.000
49A44MET0-0.025-0.02137.5410.0020.0020.0000.0000.0000.000
50A45GLN00.0400.01340.5150.0020.0020.0000.0000.0000.000
51A46ARG10.9630.99842.8410.0280.0280.0000.0000.0000.000
52A47VAL0-0.029-0.00540.6510.0020.0020.0000.0000.0000.000
53A48TYR00.0110.00743.8560.0010.0010.0000.0000.0000.000
54A49GLY0-0.0010.00246.2480.0010.0010.0000.0000.0000.000
55A50ALA0-0.014-0.02146.4670.0010.0010.0000.0000.0000.000
56A51GLN0-0.0040.00946.7340.0020.0020.0000.0000.0000.000
57A52ASN0-0.016-0.02749.0880.0020.0020.0000.0000.0000.000
58A53GLU-1-0.901-0.95251.561-0.018-0.0180.0000.0000.0000.000
59A54MET00.0450.03551.2780.0020.0020.0000.0000.0000.000
60A55CYS0-0.077-0.02152.6820.0010.0010.0000.0000.0000.000
61A56LEU00.0190.00355.2860.0010.0010.0000.0000.0000.000
62A57ALA00.0160.01455.9410.0010.0010.0000.0000.0000.000
63A58THR0-0.005-0.00855.9210.0010.0010.0000.0000.0000.000
64A59GLN00.0090.00658.7140.0000.0000.0000.0000.0000.000
65A60GLN0-0.076-0.04161.1040.0010.0010.0000.0000.0000.000
66A61LEU00.0060.00860.0370.0010.0010.0000.0000.0000.000
67A62SER00.0160.00762.9510.0010.0010.0000.0000.0000.000
68A63LYS10.9780.99364.8560.0140.0140.0000.0000.0000.000
69A64GLN0-0.034-0.02966.3210.0010.0010.0000.0000.0000.000
70A65LEU0-0.0190.00563.8910.0010.0010.0000.0000.0000.000
71A66LEU00.000-0.00668.1690.0000.0000.0000.0000.0000.000
72A67ALA0-0.056-0.02470.8000.0000.0000.0000.0000.0000.000
73A68TYR00.0290.01472.2590.0000.0000.0000.0000.0000.000
74A69GLU-1-0.883-0.95273.986-0.009-0.0090.0000.0000.0000.000
75A70LYS10.8640.93874.6300.0100.0100.0000.0000.0000.000
76A71GLN0-0.0160.00576.1390.0000.0000.0000.0000.0000.000
77A72ASN0-0.039-0.00779.2060.0000.0000.0000.0000.0000.000
78A73PHE00.012-0.00777.0410.0000.0000.0000.0000.0000.000
79A74ALA0-0.007-0.00182.7440.0000.0000.0000.0000.0000.000
80A75LEU00.0230.00984.0960.0000.0000.0000.0000.0000.000
81A76GLY0-0.009-0.01985.3920.0000.0000.0000.0000.0000.000
82A77LYS10.7410.85578.2760.0060.0060.0000.0000.0000.000
83A78GLY00.1460.09279.5160.0000.0000.0000.0000.0000.000
84A79ASP-1-0.950-0.97576.950-0.006-0.0060.0000.0000.0000.000
85A80GLU-1-0.834-0.91377.503-0.005-0.0050.0000.0000.0000.000
86A81GLU-1-0.863-0.94674.511-0.005-0.0050.0000.0000.0000.000
87A82VAL00.0030.01272.2940.0000.0000.0000.0000.0000.000
88A83ILE00.0230.01672.178-0.001-0.0010.0000.0000.0000.000
89A84SER0-0.063-0.03472.5990.0000.0000.0000.0000.0000.000
90A85THR0-0.0070.00068.5170.0000.0000.0000.0000.0000.000
91A86LEU00.0130.00268.115-0.001-0.0010.0000.0000.0000.000
92A87HIS0-0.0160.00368.087-0.001-0.0010.0000.0000.0000.000
93A88TYR0-0.025-0.00562.680-0.001-0.0010.0000.0000.0000.000
94A89PHE00.018-0.02862.160-0.001-0.0010.0000.0000.0000.000
95A90SER0-0.0040.00863.222-0.001-0.0010.0000.0000.0000.000
96A91LYS10.9370.97563.6490.0120.0120.0000.0000.0000.000
97A92VAL00.0040.00958.895-0.001-0.0010.0000.0000.0000.000
98A93VAL00.0010.00559.137-0.001-0.0010.0000.0000.0000.000
99A94ASP-1-0.844-0.93759.413-0.015-0.0150.0000.0000.0000.000
100A95GLU-1-0.954-0.97958.600-0.018-0.0180.0000.0000.0000.000
101A96LEU0-0.016-0.02253.138-0.001-0.0010.0000.0000.0000.000
102A97ASN0-0.031-0.00954.978-0.002-0.0020.0000.0000.0000.000
103A98LEU00.0320.04355.482-0.002-0.0020.0000.0000.0000.000
104A99LEU0-0.006-0.01051.798-0.002-0.0020.0000.0000.0000.000
105A100HIS00.0110.00250.521-0.001-0.0010.0000.0000.0000.000
106A101THR0-0.017-0.04751.370-0.001-0.0010.0000.0000.0000.000
107A102GLU-1-1.028-1.02150.155-0.033-0.0330.0000.0000.0000.000
108A103LEU00.0040.01944.858-0.002-0.0020.0000.0000.0000.000
109A104ALA0-0.015-0.00547.810-0.002-0.0020.0000.0000.0000.000
110A105LYS10.9150.96748.3700.0320.0320.0000.0000.0000.000
111A106GLN00.0540.02344.767-0.004-0.0040.0000.0000.0000.000
112A107LEU00.005-0.00943.057-0.003-0.0030.0000.0000.0000.000
113A108ALA0-0.002-0.00643.854-0.003-0.0030.0000.0000.0000.000
114A109ASP-1-0.893-0.95645.297-0.041-0.0410.0000.0000.0000.000
115A110THR0-0.093-0.04941.894-0.003-0.0030.0000.0000.0000.000
116A111MET0-0.0180.00038.887-0.003-0.0030.0000.0000.0000.000
117A112VAL0-0.002-0.01139.947-0.002-0.0020.0000.0000.0000.000
118A113LEU0-0.0070.01342.124-0.002-0.0020.0000.0000.0000.000
119A114PRO00.0040.00138.185-0.001-0.0010.0000.0000.0000.000
120A115ILE00.0340.01435.205-0.004-0.0040.0000.0000.0000.000
121A116ILE00.0050.01738.964-0.001-0.0010.0000.0000.0000.000
122A117GLN00.008-0.00942.029-0.002-0.0020.0000.0000.0000.000
123A118PHE00.0000.01433.139-0.001-0.0010.0000.0000.0000.000
124A119ARG10.9000.94438.7220.0540.0540.0000.0000.0000.000
125A120GLU-1-0.939-0.99239.866-0.045-0.0450.0000.0000.0000.000
126A121LYS10.8650.93842.0240.0560.0560.0000.0000.0000.000
127A122ASP-1-0.791-0.89437.393-0.078-0.0780.0000.0000.0000.000
128A123LEU0-0.014-0.01934.517-0.002-0.0020.0000.0000.0000.000
129A124THR0-0.024-0.00938.3240.0000.0000.0000.0000.0000.000
130A125GLU-1-0.925-0.95240.690-0.071-0.0710.0000.0000.0000.000
131A126VAL00.0280.01435.9750.0000.0000.0000.0000.0000.000
132A127SER0-0.001-0.00139.1100.0010.0010.0000.0000.0000.000
133A128THR0-0.046-0.01341.0680.0030.0030.0000.0000.0000.000
134A129LEU0-0.034-0.03140.4170.0020.0020.0000.0000.0000.000
135A130LYS10.9390.99337.7410.0630.0630.0000.0000.0000.000
136A131ASP-1-0.886-0.94940.970-0.053-0.0530.0000.0000.0000.000
137A132LEU0-0.069-0.02844.2480.0020.0020.0000.0000.0000.000
138A133PHE00.002-0.01339.1910.0010.0010.0000.0000.0000.000
139A134GLY00.0210.00342.8590.0010.0010.0000.0000.0000.000
140A135LEU0-0.0180.00643.4870.0020.0020.0000.0000.0000.000
141A136ALA00.002-0.01146.1430.0020.0020.0000.0000.0000.000
142A137SER0-0.018-0.00443.1700.0000.0000.0000.0000.0000.000
143A138ASN00.0110.01445.2210.0020.0020.0000.0000.0000.000
144A139GLU-1-0.897-0.95347.414-0.043-0.0430.0000.0000.0000.000
145A140HIS00.004-0.00645.9070.0020.0020.0000.0000.0000.000
146A141ASP-1-0.881-0.93645.267-0.051-0.0510.0000.0000.0000.000
147A142LEU0-0.030-0.02648.1940.0020.0020.0000.0000.0000.000
148A143SER0-0.052-0.01951.3080.0020.0020.0000.0000.0000.000
149A144MET00.0260.00547.6600.0010.0010.0000.0000.0000.000
150A145ALA0-0.0120.01651.0680.0020.0020.0000.0000.0000.000
151A146LYS10.8500.90953.0660.0350.0350.0000.0000.0000.000
152A147TYR00.0160.00453.2360.0010.0010.0000.0000.0000.000
153A148SER0-0.038-0.03252.1040.0000.0000.0000.0000.0000.000
154A149ARG10.8970.95454.4640.0330.0330.0000.0000.0000.000
155A150LEU0-0.0350.00857.7850.0020.0020.0000.0000.0000.000
156A151PRO00.0100.02259.3890.0000.0000.0000.0000.0000.000
157A152LYS11.0030.99558.7340.0290.0290.0000.0000.0000.000
158A153LYS10.9230.97061.6160.0230.0230.0000.0000.0000.000
159A154LYS10.9350.95765.3920.0210.0210.0000.0000.0000.000
160A155GLU-1-0.799-0.91262.444-0.030-0.0300.0000.0000.0000.000
161A156ASN0-0.057-0.02765.1310.0010.0010.0000.0000.0000.000
162A157GLU-1-0.813-0.91964.271-0.031-0.0310.0000.0000.0000.000
163A158LYS10.8770.94864.9250.0280.0280.0000.0000.0000.000
164A159VAL00.1020.04263.012-0.001-0.0010.0000.0000.0000.000
165A160LYS10.9170.96658.9900.0330.0330.0000.0000.0000.000
166A161THR0-0.030-0.02259.912-0.002-0.0020.0000.0000.0000.000
167A162GLU-1-0.950-0.97560.411-0.031-0.0310.0000.0000.0000.000
168A163VAL00.0400.01856.748-0.001-0.0010.0000.0000.0000.000
169A164GLY00.0250.01755.831-0.002-0.0020.0000.0000.0000.000
170A165LYS10.9300.96355.2880.0400.0400.0000.0000.0000.000
171A166GLU-1-0.887-0.95456.126-0.036-0.0360.0000.0000.0000.000
172A167VAL0-0.0170.00950.701-0.001-0.0010.0000.0000.0000.000
173A168ALA0-0.018-0.00151.210-0.002-0.0020.0000.0000.0000.000
174A169ALA0-0.011-0.01351.145-0.003-0.0030.0000.0000.0000.000
175A170ALA00.0850.04250.5400.0000.0000.0000.0000.0000.000
176A171ARG11.0131.01346.3970.0550.0550.0000.0000.0000.000
177A172ARG10.8860.94646.5800.0560.0560.0000.0000.0000.000
178A173LYS10.8640.93647.2650.0450.0450.0000.0000.0000.000
179A174GLN00.0550.03841.6940.0020.0020.0000.0000.0000.000
180A175HIS00.0480.01841.060-0.003-0.0030.0000.0000.0000.000
181A176LEU0-0.040-0.01942.595-0.003-0.0030.0000.0000.0000.000
182A177SER00.005-0.01143.705-0.003-0.0030.0000.0000.0000.000
183A178SER00.001-0.00239.366-0.003-0.0030.0000.0000.0000.000
184A179LEU00.0090.00738.772-0.005-0.0050.0000.0000.0000.000
185A180GLN0-0.007-0.01639.150-0.003-0.0030.0000.0000.0000.000
186A181TYR0-0.005-0.00636.376-0.002-0.0020.0000.0000.0000.000
187A182TYR00.0260.00334.749-0.004-0.0040.0000.0000.0000.000
188A183CYS0-0.056-0.03134.784-0.006-0.0060.0000.0000.0000.000
189A184ALA00.0180.03035.708-0.004-0.0040.0000.0000.0000.000
190A185LEU00.0300.01532.351-0.003-0.0030.0000.0000.0000.000
191A186ASN00.0160.00130.779-0.011-0.0110.0000.0000.0000.000
192A187ALA00.0030.00430.983-0.008-0.0080.0000.0000.0000.000
193A188LEU0-0.003-0.00332.111-0.001-0.0010.0000.0000.0000.000
194A189GLN0-0.0160.00326.679-0.008-0.0080.0000.0000.0000.000
195A190TYR0-0.007-0.00727.796-0.008-0.0080.0000.0000.0000.000
196A191ARG10.9130.94830.0820.0870.0870.0000.0000.0000.000
197A192LYS10.9651.00225.6830.1500.1500.0000.0000.0000.000
198A193GLN0-0.020-0.01023.9620.0060.0060.0000.0000.0000.000
199A194MET00.0130.00428.7610.0060.0060.0000.0000.0000.000
200A195ALA00.0190.00531.8420.0060.0060.0000.0000.0000.000
201A196MET0-0.0050.00429.0660.0060.0060.0000.0000.0000.000
202A197MET0-0.060-0.03027.1770.0020.0020.0000.0000.0000.000
203A198GLU-1-0.948-0.97931.221-0.073-0.0730.0000.0000.0000.000
204A199PRO0-0.028-0.01133.9100.0050.0050.0000.0000.0000.000
205A200MET00.021-0.00833.0850.0060.0060.0000.0000.0000.000
206A201ILE0-0.0110.01232.7030.0040.0040.0000.0000.0000.000
207A202GLY00.0330.01635.9520.0040.0040.0000.0000.0000.000
208A203PHE00.0150.00237.1620.0040.0040.0000.0000.0000.000
209A204ALA0-0.0030.00036.4010.0040.0040.0000.0000.0000.000
210A205HIS00.006-0.00537.8910.0040.0040.0000.0000.0000.000
211A206GLY00.0230.02140.9260.0030.0030.0000.0000.0000.000
212A207GLN00.020-0.01140.8610.0040.0040.0000.0000.0000.000
213A208ILE0-0.0090.01338.5240.0020.0020.0000.0000.0000.000
214A209ASN0-0.029-0.02742.8180.0030.0030.0000.0000.0000.000
215A210PHE0-0.0250.00545.8280.0020.0020.0000.0000.0000.000
216A211PHE00.0190.00244.3810.0020.0020.0000.0000.0000.000
217A212LYS10.8320.92445.7840.0260.0260.0000.0000.0000.000
218A213LYS10.9520.96747.5060.0270.0270.0000.0000.0000.000
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