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: JLRM9

Calculation Name: 4HH8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HH8

Chain ID: A

ChEMBL ID:

UniProt ID: P18892

Base Structure: X-ray

Registration Date: 2023-06-26

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 OptAll
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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2193382.937367
FMO2-HF: Nuclear repulsion 2109479.584004
FMO2-HF: Total energy -83903.353364
FMO2-MP2: Total energy -84144.93358


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-12.263-3.7732.595-4.676-6.41-0.034
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.010
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].
3A3PHE0-0.040-0.0312.903-1.1142.2570.363-1.634-2.101-0.005
4A4ASP-1-0.827-0.8842.739-5.143-4.1590.538-0.655-0.867-0.008
5A5VAL0-0.028-0.0205.3500.3730.410-0.001-0.001-0.0350.000
6A6ILE0-0.070-0.0297.9060.0960.0960.0000.0000.0000.000
7A7GLY00.0780.03711.5270.0510.0510.0000.0000.0000.000
8A8PRO0-0.030-0.02314.6620.0010.0010.0000.0000.0000.000
9A9PRO0-0.055-0.02718.154-0.009-0.0090.0000.0000.0000.000
10A10GLU-1-0.959-0.97319.808-0.199-0.1990.0000.0000.0000.000
11A11PRO0-0.049-0.03922.107-0.012-0.0120.0000.0000.0000.000
12A12ILE00.0090.02121.4640.0080.0080.0000.0000.0000.000
13A13LEU0-0.018-0.00224.5520.0090.0090.0000.0000.0000.000
14A14ALA00.0160.00727.929-0.003-0.0030.0000.0000.0000.000
15A15VAL0-0.007-0.00929.8460.0050.0050.0000.0000.0000.000
16A16VAL0-0.007-0.01333.342-0.002-0.0020.0000.0000.0000.000
17A17GLY0-0.047-0.02034.7730.0050.0050.0000.0000.0000.000
18A18GLU-1-0.952-0.97133.181-0.103-0.1030.0000.0000.0000.000
19A19ASP-1-0.815-0.90529.429-0.134-0.1340.0000.0000.0000.000
20A20ALA0-0.057-0.02626.611-0.001-0.0010.0000.0000.0000.000
21A21GLU-1-0.884-0.95623.063-0.204-0.2040.0000.0000.0000.000
22A22LEU0-0.043-0.01819.342-0.007-0.0070.0000.0000.0000.000
23A23PRO00.014-0.00618.274-0.023-0.0230.0000.0000.0000.000
24A24CYS0-0.079-0.02212.7270.0090.0090.0000.0000.0000.000
25A25ARG10.9480.98112.5740.6040.6040.0000.0000.0000.000
26A26LEU00.0080.0176.758-0.104-0.1040.0000.0000.0000.000
27A27SER0-0.091-0.0427.9120.3500.3500.0000.0000.0000.000
28A28PRO00.036-0.0017.297-0.382-0.3820.0000.0000.0000.000
29A29ASN0-0.059-0.03510.149-0.090-0.0900.0000.0000.0000.000
30A30VAL0-0.025-0.0139.0850.1240.1240.0000.0000.0000.000
31A31SER0-0.014-0.01611.585-0.025-0.0250.0000.0000.0000.000
32A32ALA00.0840.03810.801-0.024-0.0240.0000.0000.0000.000
33A33LYS10.8800.94211.7590.2290.2290.0000.0000.0000.000
34A34GLY0-0.019-0.00813.8830.0130.0130.0000.0000.0000.000
35A35MET0-0.0160.0226.3970.0360.0360.0000.0000.0000.000
36A36GLU-1-0.815-0.89310.729-0.150-0.1500.0000.0000.0000.000
37A37LEU0-0.042-0.01610.720-0.095-0.0950.0000.0000.0000.000
38A38ARG10.7540.84912.7970.2640.2640.0000.0000.0000.000
39A39TRP00.0200.01514.025-0.070-0.0700.0000.0000.0000.000
40A40PHE0-0.056-0.03412.8930.0570.0570.0000.0000.0000.000
41A41ARG10.9030.94418.1030.1450.1450.0000.0000.0000.000
42A42GLU-1-0.855-0.90419.068-0.171-0.1710.0000.0000.0000.000
43A43LYS10.8940.94019.2630.0970.0970.0000.0000.0000.000
44A44VAL00.0410.03013.821-0.002-0.0020.0000.0000.0000.000
45A45SER00.0090.01216.686-0.001-0.0010.0000.0000.0000.000
46A46PRO0-0.062-0.04719.5650.0120.0120.0000.0000.0000.000
47A47ALA00.0000.01718.449-0.007-0.0070.0000.0000.0000.000
48A48VAL0-0.049-0.02619.8540.0180.0180.0000.0000.0000.000
49A49PHE00.0330.00916.8600.0100.0100.0000.0000.0000.000
50A50LEU0-0.067-0.03215.500-0.027-0.0270.0000.0000.0000.000
51A51SER0-0.0080.00316.5350.0290.0290.0000.0000.0000.000
52A52ARG10.8340.88714.9930.0690.0690.0000.0000.0000.000
53A53GLU-1-0.932-0.95715.103-0.060-0.0600.0000.0000.0000.000
54A54GLY0-0.034-0.01416.8980.0100.0100.0000.0000.0000.000
55A55GLN0-0.078-0.04218.7290.0090.0090.0000.0000.0000.000
56A56GLU-1-0.793-0.90419.774-0.151-0.1510.0000.0000.0000.000
57A57GLN0-0.043-0.03018.7960.0300.0300.0000.0000.0000.000
58A58GLU-1-0.846-0.92221.998-0.084-0.0840.0000.0000.0000.000
59A59GLY0-0.069-0.03525.0370.0030.0030.0000.0000.0000.000
60A60GLU-1-0.793-0.88018.011-0.094-0.0940.0000.0000.0000.000
61A61GLU-1-0.779-0.88021.579-0.156-0.1560.0000.0000.0000.000
62A62MET0-0.024-0.01722.3500.0220.0220.0000.0000.0000.000
63A63ALA0-0.022-0.01925.825-0.002-0.0020.0000.0000.0000.000
64A64GLU-1-0.903-0.93328.461-0.102-0.1020.0000.0000.0000.000
65A65TYR0-0.005-0.03725.227-0.007-0.0070.0000.0000.0000.000
66A66ARG10.8710.92126.1530.0810.0810.0000.0000.0000.000
67A67GLY0-0.0080.00427.8520.0040.0040.0000.0000.0000.000
68A68ARG10.7210.86228.7500.1250.1250.0000.0000.0000.000
69A69VAL0-0.026-0.00623.604-0.009-0.0090.0000.0000.0000.000
70A70SER00.0130.01523.8260.0140.0140.0000.0000.0000.000
71A71LEU0-0.016-0.00316.959-0.016-0.0160.0000.0000.0000.000
72A72VAL0-0.0130.01920.1140.0200.0200.0000.0000.0000.000
73A73GLU-1-0.900-0.98118.882-0.230-0.2300.0000.0000.0000.000
74A74ASP-1-0.895-0.94719.919-0.212-0.2120.0000.0000.0000.000
75A75HIS0-0.032-0.01718.951-0.001-0.0010.0000.0000.0000.000
76A76ILE00.0070.01214.863-0.034-0.0340.0000.0000.0000.000
77A77ALA0-0.060-0.04114.981-0.028-0.0280.0000.0000.0000.000
78A78GLU-1-0.926-0.94914.994-0.362-0.3620.0000.0000.0000.000
79A79GLY00.0240.01011.947-0.059-0.0590.0000.0000.0000.000
80A80SER0-0.052-0.03112.605-0.078-0.0780.0000.0000.0000.000
81A81VAL00.007-0.00314.0180.0450.0450.0000.0000.0000.000
82A82ALA00.0310.01116.868-0.027-0.0270.0000.0000.0000.000
83A83VAL00.0100.02218.1110.0130.0130.0000.0000.0000.000
84A84ARG10.8080.90020.5900.1420.1420.0000.0000.0000.000
85A85ILE0-0.023-0.02622.9700.0040.0040.0000.0000.0000.000
86A86GLN00.0190.01226.514-0.002-0.0020.0000.0000.0000.000
87A87GLU-1-0.905-0.94730.248-0.096-0.0960.0000.0000.0000.000
88A88VAL0-0.042-0.00528.9820.0020.0020.0000.0000.0000.000
89A89LYS10.8560.89330.0380.1230.1230.0000.0000.0000.000
90A90ALA00.0690.03631.646-0.008-0.0080.0000.0000.0000.000
91A91SER0-0.005-0.00330.937-0.006-0.0060.0000.0000.0000.000
92A92ASP-1-0.699-0.79427.532-0.137-0.1370.0000.0000.0000.000
93A93ASP-1-0.788-0.85726.597-0.165-0.1650.0000.0000.0000.000
94A94GLY00.0230.00525.1050.0080.0080.0000.0000.0000.000
95A95GLU-1-0.856-0.91718.705-0.308-0.3080.0000.0000.0000.000
96A96TYR0-0.037-0.04318.9750.0190.0190.0000.0000.0000.000
97A97ARG10.7680.86213.8320.3710.3710.0000.0000.0000.000
98A99PHE00.014-0.0078.692-0.136-0.1360.0000.0000.0000.000
99A100PHE00.0350.0097.2410.1200.1200.0000.0000.0000.000
100A101ARG10.8850.9356.317-0.108-0.1080.0000.0000.0000.000
101A102GLN0-0.029-0.0176.172-0.093-0.0930.0000.0000.0000.000
102A103ASP-1-0.872-0.9376.7390.3860.3860.0000.0000.0000.000
103A104GLU-1-0.970-0.9945.5361.3571.3570.0000.0000.0000.000
104A105ASN0-0.051-0.0182.604-0.6711.3281.189-1.376-1.812-0.012
105A106TYR00.000-0.0212.818-0.745-0.1700.144-0.221-0.499-0.001
106A107GLU-1-0.866-0.9112.913-5.204-3.6850.363-0.786-1.096-0.008
107A108GLU-1-0.908-0.9645.062-0.101-0.096-0.001-0.0030.0000.000
108A109ALA00.0120.0138.620-0.099-0.0990.0000.0000.0000.000
109A110ILE0-0.022-0.01511.3850.0770.0770.0000.0000.0000.000
110A111VAL00.024-0.00115.183-0.008-0.0080.0000.0000.0000.000
111A112HIS0-0.019-0.00318.3420.0410.0410.0000.0000.0000.000
112A113LEU00.0130.01921.716-0.001-0.0010.0000.0000.0000.000
113A114LYS10.7600.85524.4230.1720.1720.0000.0000.0000.000
114A115VAL00.0410.02327.8360.0020.0020.0000.0000.0000.000
115A116ALA0-0.007-0.01230.5820.0050.0050.0000.0000.0000.000
116A117ALA00.0180.01334.1170.0000.0000.0000.0000.0000.000
117A118LEU0-0.007-0.00837.7210.0020.0020.0000.0000.0000.000
118A119GLY00.0700.04940.8380.0010.0010.0000.0000.0000.000
119A120SER0-0.039-0.03543.8760.0000.0000.0000.0000.0000.000
120A121ASP-1-0.840-0.91447.604-0.061-0.0610.0000.0000.0000.000
121A122PRO0-0.043-0.00849.2350.0010.0010.0000.0000.0000.000
122A123HIS00.0140.00251.3710.0010.0010.0000.0000.0000.000
123A124ILE00.019-0.00154.581-0.001-0.0010.0000.0000.0000.000
124A125SER0-0.032-0.00757.2660.0020.0020.0000.0000.0000.000
125A126MET0-0.014-0.00360.0100.0000.0000.0000.0000.0000.000
126A127LYS10.8650.91960.1950.0360.0360.0000.0000.0000.000
127A128VAL00.0160.01665.0100.0000.0000.0000.0000.0000.000
128A129GLN0-0.013-0.00766.8900.0000.0000.0000.0000.0000.000
129A130GLU-1-0.922-0.96769.301-0.025-0.0250.0000.0000.0000.000
130A131SER0-0.055-0.03970.9150.0000.0000.0000.0000.0000.000
131A132GLY00.0060.01571.5830.0000.0000.0000.0000.0000.000
132A133GLU-1-0.781-0.84066.222-0.030-0.0300.0000.0000.0000.000
133A134ILE0-0.009-0.01164.0770.0000.0000.0000.0000.0000.000
134A135GLN0-0.028-0.01161.630-0.002-0.0020.0000.0000.0000.000
135A136LEU0-0.007-0.00158.6970.0000.0000.0000.0000.0000.000
136A137GLU-1-0.829-0.90355.933-0.040-0.0400.0000.0000.0000.000
137A138CYS0-0.0340.00051.7970.0000.0000.0000.0000.0000.000
138A139THR0-0.035-0.03151.5180.0000.0000.0000.0000.0000.000
139A140SER00.0040.01747.695-0.001-0.0010.0000.0000.0000.000
140A141VAL00.0350.00846.3320.0010.0010.0000.0000.0000.000
141A142GLY00.0740.05342.871-0.001-0.0010.0000.0000.0000.000
142A143TRP0-0.023-0.02540.764-0.005-0.0050.0000.0000.0000.000
143A144TYR00.0040.01032.0620.0040.0040.0000.0000.0000.000
144A145PRO00.0370.03233.778-0.003-0.0030.0000.0000.0000.000
145A146GLU-1-0.879-0.96536.173-0.084-0.0840.0000.0000.0000.000
146A147PRO0-0.0430.01039.321-0.002-0.0020.0000.0000.0000.000
147A148GLN00.0480.00941.4920.0010.0010.0000.0000.0000.000
148A149VAL0-0.017-0.01943.0420.0000.0000.0000.0000.0000.000
149A150GLN0-0.042-0.01046.8780.0000.0000.0000.0000.0000.000
150A151TRP00.000-0.01149.2430.0010.0010.0000.0000.0000.000
151A152GLN00.0450.01450.3840.0010.0010.0000.0000.0000.000
152A153THR0-0.010-0.01854.8360.0020.0020.0000.0000.0000.000
153A154HIS0-0.050-0.04657.5270.0000.0000.0000.0000.0000.000
154A155ARG10.8260.91159.1920.0370.0370.0000.0000.0000.000
155A156GLY00.0550.04454.855-0.001-0.0010.0000.0000.0000.000
156A157GLU-1-0.949-0.96754.072-0.042-0.0420.0000.0000.0000.000
157A158GLU-1-0.859-0.91448.856-0.058-0.0580.0000.0000.0000.000
158A159PHE0-0.083-0.04853.3280.0020.0020.0000.0000.0000.000
159A160PRO00.0260.01451.097-0.001-0.0010.0000.0000.0000.000
160A161SER0-0.014-0.04250.5670.0020.0020.0000.0000.0000.000
161A162MET0-0.057-0.02653.1730.0010.0010.0000.0000.0000.000
162A163SER0-0.018-0.01252.5990.0010.0010.0000.0000.0000.000
163A164GLU-1-0.772-0.84247.327-0.057-0.0570.0000.0000.0000.000
164A165SER0-0.077-0.04247.8720.0020.0020.0000.0000.0000.000
165A166ARG10.7840.87542.3020.0650.0650.0000.0000.0000.000
166A167ASN0-0.025-0.01144.3630.0020.0020.0000.0000.0000.000
167A168PRO0-0.0230.00740.2250.0000.0000.0000.0000.0000.000
168A169ASP-1-0.824-0.91841.620-0.066-0.0660.0000.0000.0000.000
169A170GLU-1-0.982-0.99941.340-0.057-0.0570.0000.0000.0000.000
170A171GLU-1-0.927-0.96438.691-0.069-0.0690.0000.0000.0000.000
171A172GLY0-0.038-0.01637.238-0.006-0.0060.0000.0000.0000.000
172A173LEU0-0.047-0.03037.386-0.004-0.0040.0000.0000.0000.000
173A174PHE0-0.021-0.00837.4470.0060.0060.0000.0000.0000.000
174A175THR0-0.030-0.00642.2690.0010.0010.0000.0000.0000.000
175A176VAL0-0.026-0.02145.3090.0000.0000.0000.0000.0000.000
176A177ARG10.8690.91947.1940.0450.0450.0000.0000.0000.000
177A178ALA00.0230.02149.987-0.001-0.0010.0000.0000.0000.000
178A179SER00.0080.00151.9050.0010.0010.0000.0000.0000.000
179A180VAL00.0100.01355.2620.0000.0000.0000.0000.0000.000
180A181ILE0-0.022-0.01857.5470.0010.0010.0000.0000.0000.000
181A182ILE0-0.0030.00760.0880.0000.0000.0000.0000.0000.000
182A183ARG10.7870.84261.8440.0330.0330.0000.0000.0000.000
183A184ASP-1-0.761-0.87265.467-0.031-0.0310.0000.0000.0000.000
184A185SER0-0.011-0.01167.3400.0000.0000.0000.0000.0000.000
185A186SER0-0.100-0.07066.9970.0000.0000.0000.0000.0000.000
186A187MET0-0.0490.01461.473-0.001-0.0010.0000.0000.0000.000
187A188LYS10.8840.92564.1430.0340.0340.0000.0000.0000.000
188A189ASN0-0.0320.00161.0560.0020.0020.0000.0000.0000.000
189A190VAL00.0240.01157.4980.0000.0000.0000.0000.0000.000
190A191SER0-0.019-0.00653.7960.0010.0010.0000.0000.0000.000
191A193ALA00.0680.03348.0530.0000.0000.0000.0000.0000.000
192A194ILE0-0.027-0.02744.5690.0000.0000.0000.0000.0000.000
193A195ARG10.8480.89839.5470.0840.0840.0000.0000.0000.000
194A196ASN0-0.005-0.00936.749-0.004-0.0040.0000.0000.0000.000
195A197LEU0-0.009-0.02536.823-0.003-0.0030.0000.0000.0000.000
196A198LEU0-0.0150.01230.240-0.003-0.0030.0000.0000.0000.000
197A199LEU00.0180.01033.412-0.006-0.0060.0000.0000.0000.000
198A200GLY0-0.0080.00435.7250.0010.0010.0000.0000.0000.000
199A201GLN0-0.053-0.01937.3300.0080.0080.0000.0000.0000.000
200A202GLU-1-0.844-0.92540.711-0.074-0.0740.0000.0000.0000.000
201A203LYS10.8000.89944.0090.0680.0680.0000.0000.0000.000
202A204GLU-1-0.878-0.92847.419-0.054-0.0540.0000.0000.0000.000
203A205VAL0-0.028-0.00450.8010.0010.0010.0000.0000.0000.000
204A206GLU-1-0.809-0.89954.433-0.042-0.0420.0000.0000.0000.000
205A207VAL0-0.030-0.01957.5500.0010.0010.0000.0000.0000.000
206A208SER0-0.029-0.04760.7420.0010.0010.0000.0000.0000.000
207A209ILE00.0000.00862.2140.0010.0010.0000.0000.0000.000
208A210PRO0-0.055-0.01566.1500.0010.0010.0000.0000.0000.000
209A211ALA00.0300.01169.7350.0000.0000.0000.0000.0000.000