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

tag_button

FMODB ID: 52Z7Z

Calculation Name: 4P4H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P4H

Chain ID: A

ChEMBL ID:

UniProt ID: O95786

Base Structure: X-ray

Registration Date: 2023-06-21

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2214774.517058
FMO2-HF: Nuclear repulsion 2136402.806161
FMO2-HF: Total energy -78371.710897
FMO2-MP2: Total energy -78598.355134


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-7.182-7.64314.374-4.398-9.514-0.013
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : 0.000
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].
3A3THR00.023-0.0152.044-2.594-5.02211.706-3.273-6.005-0.007
4A4GLU-1-0.942-0.9991.888-2.212-1.1582.664-0.971-2.747-0.006
5A5GLN00.0770.0463.804-0.2650.5240.005-0.148-0.6460.000
6A6ARG10.9210.9855.322-1.004-0.880-0.001-0.006-0.1160.000
7A7ARG10.9560.9895.857-2.247-2.2470.0000.0000.0000.000
8A8SER0-0.0010.0137.057-0.076-0.0760.0000.0000.0000.000
9A9LEU0-0.015-0.0159.092-0.004-0.0040.0000.0000.0000.000
10A10GLN0-0.053-0.03910.9800.1550.1550.0000.0000.0000.000
11A11ALA0-0.050-0.00212.6260.0050.0050.0000.0000.0000.000
12A12PHE00.0160.00612.5270.0030.0030.0000.0000.0000.000
13A13GLN00.0460.02115.7860.0040.0040.0000.0000.0000.000
14A14ASP-1-0.945-0.97417.0870.0550.0550.0000.0000.0000.000
15A15TYR0-0.057-0.03018.146-0.003-0.0030.0000.0000.0000.000
16A16ILE00.0370.02614.805-0.006-0.0060.0000.0000.0000.000
17A17ARG10.9370.97219.350-0.056-0.0560.0000.0000.0000.000
18A18LYS10.8230.91422.2430.0410.0410.0000.0000.0000.000
19A19THR0-0.040-0.01021.779-0.004-0.0040.0000.0000.0000.000
20A20LEU0-0.012-0.00919.5200.0000.0000.0000.0000.0000.000
21A21ASP-1-0.798-0.85223.0570.0090.0090.0000.0000.0000.000
22A22PRO00.002-0.01122.415-0.010-0.0100.0000.0000.0000.000
23A23THR0-0.077-0.08223.754-0.006-0.0060.0000.0000.0000.000
24A24TYR0-0.042-0.02025.9250.0000.0000.0000.0000.0000.000
25A25ILE00.0380.02319.063-0.008-0.0080.0000.0000.0000.000
26A26LEU0-0.015-0.02721.681-0.009-0.0090.0000.0000.0000.000
27A27SER0-0.036-0.00223.3570.0050.0050.0000.0000.0000.000
28A28TYR00.0180.01121.3410.0020.0020.0000.0000.0000.000
29A29MET0-0.0280.00715.913-0.012-0.0120.0000.0000.0000.000
30A30ALA0-0.0060.00419.9650.0200.0200.0000.0000.0000.000
31A31PRO0-0.036-0.02918.1870.0180.0180.0000.0000.0000.000
32A32TRP00.0270.04013.251-0.011-0.0110.0000.0000.0000.000
33A33PHE0-0.011-0.01317.9860.0390.0390.0000.0000.0000.000
34A34ARG10.8960.96220.820-0.193-0.1930.0000.0000.0000.000
35A35GLU-1-0.866-0.94823.6710.0470.0470.0000.0000.0000.000
36A36GLU-1-0.970-0.98126.0090.1450.1450.0000.0000.0000.000
37A37GLU-1-0.832-0.94320.4260.2010.2010.0000.0000.0000.000
38A38VAL00.0310.02124.364-0.007-0.0070.0000.0000.0000.000
39A39GLN00.0470.02525.917-0.011-0.0110.0000.0000.0000.000
40A40TYR0-0.043-0.03226.2600.0000.0000.0000.0000.0000.000
41A41ILE0-0.027-0.01022.078-0.002-0.0020.0000.0000.0000.000
42A42GLN0-0.011-0.01726.386-0.007-0.0070.0000.0000.0000.000
43A43ALA0-0.041-0.01229.556-0.005-0.0050.0000.0000.0000.000
44A44GLU-1-0.884-0.96027.3860.0860.0860.0000.0000.0000.000
45A45LYS10.8450.95429.177-0.001-0.0010.0000.0000.0000.000
46A46ASN0-0.035-0.02130.685-0.006-0.0060.0000.0000.0000.000
47A47ASN0-0.048-0.01233.234-0.005-0.0050.0000.0000.0000.000
48A48LYS10.8910.93730.896-0.078-0.0780.0000.0000.0000.000
49A49GLY00.0250.03731.923-0.002-0.0020.0000.0000.0000.000
50A50PRO00.0360.00128.5580.0070.0070.0000.0000.0000.000
51A51MET00.0060.01125.9460.0040.0040.0000.0000.0000.000
52A52ALA0-0.0070.00725.5090.0060.0060.0000.0000.0000.000
53A53ALA00.0690.04225.7340.0120.0120.0000.0000.0000.000
54A54ALA00.0330.01722.0820.0060.0060.0000.0000.0000.000
55A55THR0-0.084-0.06021.2040.0070.0070.0000.0000.0000.000
56A56LEU0-0.032-0.00220.8320.0260.0260.0000.0000.0000.000
57A57PHE0-0.009-0.01017.4760.0250.0250.0000.0000.0000.000
58A58LEU00.0350.00215.9870.0070.0070.0000.0000.0000.000
59A59LYS10.8520.95116.029-0.221-0.2210.0000.0000.0000.000
60A60PHE00.051-0.00116.4930.0530.0530.0000.0000.0000.000
61A61LEU00.0110.03313.2360.0260.0260.0000.0000.0000.000
62A62LEU0-0.065-0.04211.1170.0610.0610.0000.0000.0000.000
63A63GLU-1-0.958-0.97912.0380.5370.5370.0000.0000.0000.000
64A64LEU0-0.0240.00413.3090.0490.0490.0000.0000.0000.000
65A65GLN0-0.028-0.01710.1920.1300.1300.0000.0000.0000.000
66A66GLU-1-0.980-0.97611.1390.2780.2780.0000.0000.0000.000
67A67GLU-1-0.904-0.9619.0800.7660.7660.0000.0000.0000.000
68A68GLY0-0.031-0.0298.442-0.087-0.0870.0000.0000.0000.000
69A69TRP00.0560.0247.339-0.295-0.2950.0000.0000.0000.000
70A70PHE0-0.023-0.0107.317-0.106-0.1060.0000.0000.0000.000
71A71ARG10.8600.9299.3650.7810.7810.0000.0000.0000.000
72A72GLY00.1040.03710.8140.0680.0680.0000.0000.0000.000
73A73PHE0-0.026-0.01312.6980.0680.0680.0000.0000.0000.000
74A74LEU0-0.020-0.01910.3050.0380.0380.0000.0000.0000.000
75A75ASP-1-0.840-0.93014.072-0.411-0.4110.0000.0000.0000.000
76A76ALA0-0.021-0.01216.2910.0430.0430.0000.0000.0000.000
77A77LEU0-0.038-0.03416.2460.0280.0280.0000.0000.0000.000
78A78ASP-1-0.921-0.95318.215-0.228-0.2280.0000.0000.0000.000
79A79HIS0-0.042-0.01719.9380.0370.0370.0000.0000.0000.000
80A80ALA0-0.042-0.02821.8580.0200.0200.0000.0000.0000.000
81A81GLY00.0040.01423.1840.0180.0180.0000.0000.0000.000
82A82TYR0-0.041-0.04121.0010.0140.0140.0000.0000.0000.000
83A83SER00.0580.02220.362-0.010-0.0100.0000.0000.0000.000
84A84GLY00.0450.01620.1840.0190.0190.0000.0000.0000.000
85A85LEU0-0.024-0.02717.6980.0020.0020.0000.0000.0000.000
86A86TYR0-0.051-0.00514.967-0.041-0.0410.0000.0000.0000.000
87A87GLU-1-0.915-0.95815.442-0.266-0.2660.0000.0000.0000.000
88A88ALA0-0.0290.01816.378-0.029-0.0290.0000.0000.0000.000
89A89ILE0-0.032-0.03111.251-0.016-0.0160.0000.0000.0000.000
90A90GLU-1-0.919-0.95611.092-0.736-0.7360.0000.0000.0000.000
91A91SER0-0.063-0.04711.319-0.075-0.0750.0000.0000.0000.000
92A92TRP0-0.039-0.0247.0240.1380.1380.0000.0000.0000.000
93A93ASP-1-0.895-0.92712.796-0.127-0.1270.0000.0000.0000.000
94A94PHE00.0750.00614.4870.0050.0050.0000.0000.0000.000
95A95LYS10.9040.94918.9300.1570.1570.0000.0000.0000.000
96A96LYS10.8360.89521.6620.1810.1810.0000.0000.0000.000
97A97ILE00.0620.02919.9640.0150.0150.0000.0000.0000.000
98A98GLU-1-0.885-0.94223.093-0.031-0.0310.0000.0000.0000.000
99A99LYS10.9170.96124.7950.0880.0880.0000.0000.0000.000
100A100LEU0-0.0040.00026.2870.0080.0080.0000.0000.0000.000
101A101GLU-1-0.835-0.90027.447-0.017-0.0170.0000.0000.0000.000
102A102GLU-1-0.957-0.97829.268-0.032-0.0320.0000.0000.0000.000
103A103TYR00.0420.01132.1760.0050.0050.0000.0000.0000.000
104A104ARG10.8580.92128.1440.0330.0330.0000.0000.0000.000
105A105LEU0-0.020-0.01932.2770.0070.0070.0000.0000.0000.000
106A106LEU0-0.040-0.00134.5400.0050.0050.0000.0000.0000.000
107A107LEU00.0610.01635.0280.0030.0030.0000.0000.0000.000
108A108LYS10.9160.95731.6620.0080.0080.0000.0000.0000.000
109A109ARG10.8750.93936.8540.0060.0060.0000.0000.0000.000
110A110LEU00.0220.01840.3720.0010.0010.0000.0000.0000.000
111A111GLN0-0.0070.00938.3050.0000.0000.0000.0000.0000.000
112A112PRO0-0.014-0.01641.5750.0000.0000.0000.0000.0000.000
113A113GLU-1-0.880-0.95245.173-0.010-0.0100.0000.0000.0000.000
114A114PHE0-0.008-0.00240.128-0.001-0.0010.0000.0000.0000.000
115A115LYS10.9000.95343.828-0.001-0.0010.0000.0000.0000.000
116A116THR0-0.048-0.03044.9790.0000.0000.0000.0000.0000.000
117A117ARG10.8830.95047.8500.0110.0110.0000.0000.0000.000
118A118ILE00.0130.03142.912-0.002-0.0020.0000.0000.0000.000
119A119ILE00.0340.01046.2360.0020.0020.0000.0000.0000.000
120A120PRO0-0.0240.00242.366-0.002-0.0020.0000.0000.0000.000
121A121THR00.017-0.03643.253-0.002-0.0020.0000.0000.0000.000
122A122ASP-1-0.949-0.94344.989-0.025-0.0250.0000.0000.0000.000
123A123ILE00.0560.02441.003-0.002-0.0020.0000.0000.0000.000
124A124ILE0-0.043-0.02438.150-0.003-0.0030.0000.0000.0000.000
125A125SER00.017-0.00438.467-0.003-0.0030.0000.0000.0000.000
126A126ASP-1-0.882-0.94038.842-0.047-0.0470.0000.0000.0000.000
127A127LEU0-0.009-0.00235.918-0.004-0.0040.0000.0000.0000.000
128A128SER0-0.032-0.01734.651-0.004-0.0040.0000.0000.0000.000
129A129GLU-1-0.907-0.95131.846-0.081-0.0810.0000.0000.0000.000
130A130CYS0-0.105-0.03030.238-0.009-0.0090.0000.0000.0000.000
131A131LEU0-0.0110.01629.717-0.001-0.0010.0000.0000.0000.000
132A132ILE00.0350.03925.686-0.005-0.0050.0000.0000.0000.000
133A133ASN00.0560.01429.4090.0110.0110.0000.0000.0000.000
134A134GLN00.0670.03230.5330.0010.0010.0000.0000.0000.000
135A135GLU-1-0.815-0.92829.674-0.039-0.0390.0000.0000.0000.000
136A136CYS0-0.041-0.02133.2110.0050.0050.0000.0000.0000.000
137A137GLU-1-0.926-0.96035.861-0.026-0.0260.0000.0000.0000.000
138A138GLU-1-0.876-0.94233.831-0.005-0.0050.0000.0000.0000.000
139A139ILE00.0020.00436.1690.0040.0040.0000.0000.0000.000
140A140LEU00.0320.01239.4430.0030.0030.0000.0000.0000.000
141A141GLN0-0.0040.00741.1510.0040.0040.0000.0000.0000.000
142A142ILE0-0.022-0.01540.2760.0030.0030.0000.0000.0000.000
143A143CYS0-0.062-0.03143.0940.0010.0010.0000.0000.0000.000
144A144SER0-0.059-0.01345.3910.0020.0020.0000.0000.0000.000
145A145THR0-0.031-0.01445.4470.0020.0020.0000.0000.0000.000
146A146LYS10.9310.95644.465-0.004-0.0040.0000.0000.0000.000
147A147GLY00.0280.03247.9300.0010.0010.0000.0000.0000.000
148A148MET00.006-0.01246.9670.0000.0000.0000.0000.0000.000
149A149MET00.0100.01745.7740.0000.0000.0000.0000.0000.000
150A150ALA00.0150.00244.5810.0000.0000.0000.0000.0000.000
151A151GLY00.0350.01842.2070.0000.0000.0000.0000.0000.000
152A152ALA00.007-0.00741.087-0.002-0.0020.0000.0000.0000.000
153A153GLU-1-0.901-0.97440.1770.0000.0000.0000.0000.0000.000
154A154LYS10.9040.97234.4930.0080.0080.0000.0000.0000.000
155A155LEU00.024-0.00336.413-0.002-0.0020.0000.0000.0000.000
156A156VAL00.0050.01236.038-0.004-0.0040.0000.0000.0000.000
157A157GLU-1-0.908-0.95632.745-0.005-0.0050.0000.0000.0000.000
158A158CYS0-0.027-0.02231.5790.0000.0000.0000.0000.0000.000
159A159LEU00.0520.02830.917-0.006-0.0060.0000.0000.0000.000
160A160LEU0-0.117-0.04831.089-0.003-0.0030.0000.0000.0000.000
161A161ARG10.8070.91127.1910.0250.0250.0000.0000.0000.000
162A162SER0-0.025-0.01826.420-0.012-0.0120.0000.0000.0000.000
163A163ASP-1-0.770-0.89822.621-0.127-0.1270.0000.0000.0000.000
164A164LYS10.8460.94524.7270.0980.0980.0000.0000.0000.000
165A165GLU-1-0.797-0.89825.659-0.128-0.1280.0000.0000.0000.000
166A166ASN00.005-0.01327.3760.0070.0070.0000.0000.0000.000
167A167TRP00.0800.04029.1750.0110.0110.0000.0000.0000.000
168A168PRO00.0140.01031.3580.0050.0050.0000.0000.0000.000
169A169LYS10.9460.96934.1550.0720.0720.0000.0000.0000.000
170A170THR00.036-0.01533.6190.0050.0050.0000.0000.0000.000
171A171LEU00.0100.01936.3220.0030.0030.0000.0000.0000.000
172A172LYS10.8890.95438.0380.0390.0390.0000.0000.0000.000
173A173LEU0-0.003-0.00138.3080.0020.0020.0000.0000.0000.000
174A174ALA00.0520.02940.1160.0020.0020.0000.0000.0000.000
175A175LEU0-0.038-0.02841.4110.0030.0030.0000.0000.0000.000
176A176GLU-1-0.924-0.96344.021-0.030-0.0300.0000.0000.0000.000
177A177LYS10.8030.92944.5020.0400.0400.0000.0000.0000.000
178A178GLU-1-0.878-0.93646.307-0.031-0.0310.0000.0000.0000.000
179A179ARG10.9290.94848.6510.0240.0240.0000.0000.0000.000
180A180ASN00.0990.05746.2200.0030.0030.0000.0000.0000.000
181A181LYS10.8540.92849.2590.0140.0140.0000.0000.0000.000
182A182PHE00.038-0.00341.6420.0020.0020.0000.0000.0000.000
183A183SER0-0.074-0.03845.105-0.001-0.0010.0000.0000.0000.000
184A184GLU-1-0.976-1.00245.032-0.027-0.0270.0000.0000.0000.000
185A185LEU0-0.0490.00744.5230.0020.0020.0000.0000.0000.000
186A186TRP0-0.047-0.02535.9450.0010.0010.0000.0000.0000.000
187A187ILE00.0160.00640.965-0.001-0.0010.0000.0000.0000.000
188A188VAL0-0.0110.00136.189-0.002-0.0020.0000.0000.0000.000