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: 856JY

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2187350.097388
FMO2-HF: Nuclear repulsion 2103448.862213
FMO2-HF: Total energy -83901.235174
FMO2-MP2: Total energy -84142.718317


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.
-8.558-0.71.624-4.181-5.3-0.007
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 : 0.070 / q_NPA : 0.033
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].
3A3PHE0-0.064-0.0422.949-2.1542.4610.210-2.396-2.4290.001
4A4ASP-1-0.872-0.9283.240-5.433-4.8020.086-0.327-0.390-0.002
5A5VAL0-0.014-0.0065.7670.4500.4500.0000.0000.0000.000
6A6ILE0-0.056-0.0248.4230.0530.0530.0000.0000.0000.000
7A7GLY00.0580.02311.7390.0720.0720.0000.0000.0000.000
8A8PRO0-0.025-0.02314.840-0.029-0.0290.0000.0000.0000.000
9A9PRO0-0.049-0.02618.385-0.001-0.0010.0000.0000.0000.000
10A10GLU-1-0.943-0.97620.194-0.200-0.2000.0000.0000.0000.000
11A11PRO0-0.057-0.03322.130-0.004-0.0040.0000.0000.0000.000
12A12ILE00.0060.01621.806-0.004-0.0040.0000.0000.0000.000
13A13LEU0-0.026-0.00524.9920.0120.0120.0000.0000.0000.000
14A14ALA00.0200.00128.471-0.002-0.0020.0000.0000.0000.000
15A15VAL00.0050.00630.3430.0040.0040.0000.0000.0000.000
16A16VAL0-0.015-0.01833.7300.0010.0010.0000.0000.0000.000
17A17GLY0-0.038-0.02134.8670.0010.0010.0000.0000.0000.000
18A18GLU-1-0.945-0.96533.060-0.059-0.0590.0000.0000.0000.000
19A19ASP-1-0.846-0.93129.248-0.059-0.0590.0000.0000.0000.000
20A20ALA0-0.041-0.01726.589-0.007-0.0070.0000.0000.0000.000
21A21GLU-1-0.912-0.96423.178-0.131-0.1310.0000.0000.0000.000
22A22LEU0-0.031-0.01619.672-0.012-0.0120.0000.0000.0000.000
23A23PRO00.006-0.00218.321-0.003-0.0030.0000.0000.0000.000
24A24CYS0-0.078-0.02912.9170.0080.0080.0000.0000.0000.000
25A25ARG10.9460.98212.9300.6090.6090.0000.0000.0000.000
26A26LEU00.0150.0196.872-0.086-0.0860.0000.0000.0000.000
27A27SER0-0.066-0.0138.5120.2660.2660.0000.0000.0000.000
28A28PRO00.024-0.0017.707-0.419-0.4190.0000.0000.0000.000
29A29ASN00.0220.02110.342-0.077-0.0770.0000.0000.0000.000
30A30VAL0-0.043-0.0268.8280.1210.1210.0000.0000.0000.000
31A31SER0-0.009-0.01311.9660.0180.0180.0000.0000.0000.000
32A32ALA00.0950.03911.114-0.031-0.0310.0000.0000.0000.000
33A33LYS10.8730.93212.1140.2000.2000.0000.0000.0000.000
34A34GLY0-0.013-0.00614.0300.0030.0030.0000.0000.0000.000
35A35MET0-0.0120.0216.6970.0240.0240.0000.0000.0000.000
36A36GLU-1-0.903-0.96510.8140.3400.3400.0000.0000.0000.000
37A37LEU0-0.0200.00710.899-0.034-0.0340.0000.0000.0000.000
38A38ARG10.8710.92312.976-0.162-0.1620.0000.0000.0000.000
39A39TRP00.0400.02614.386-0.031-0.0310.0000.0000.0000.000
40A40PHE0-0.015-0.02113.4010.0380.0380.0000.0000.0000.000
41A41ARG10.9460.97318.6220.0060.0060.0000.0000.0000.000
42A42GLU-1-0.928-0.94819.6340.0120.0120.0000.0000.0000.000
43A43LYS10.9000.94319.924-0.092-0.0920.0000.0000.0000.000
44A44VAL00.0400.02814.547-0.013-0.0130.0000.0000.0000.000
45A45SER0-0.0070.01517.221-0.013-0.0130.0000.0000.0000.000
46A46PRO0-0.034-0.03119.9580.0070.0070.0000.0000.0000.000
47A47ALA0-0.0070.00518.478-0.005-0.0050.0000.0000.0000.000
48A48VAL0-0.036-0.01420.270-0.001-0.0010.0000.0000.0000.000
49A49PHE00.0410.01718.117-0.007-0.0070.0000.0000.0000.000
50A50LEU0-0.049-0.01815.7570.0100.0100.0000.0000.0000.000
51A51SER00.0260.03816.5100.0060.0060.0000.0000.0000.000
52A52ARG10.8560.88615.002-0.223-0.2230.0000.0000.0000.000
53A53GLU-1-0.933-0.95715.7630.2220.2220.0000.0000.0000.000
54A54GLY0-0.049-0.02717.041-0.014-0.0140.0000.0000.0000.000
55A55GLN0-0.061-0.03418.915-0.008-0.0080.0000.0000.0000.000
56A56GLU-1-0.833-0.91620.2660.0190.0190.0000.0000.0000.000
57A57GLN0-0.084-0.05119.7800.0190.0190.0000.0000.0000.000
58A58GLU-1-0.832-0.91922.3890.0350.0350.0000.0000.0000.000
59A59GLY0-0.096-0.04125.450-0.002-0.0020.0000.0000.0000.000
60A60GLU-1-0.908-0.93819.7820.2050.2050.0000.0000.0000.000
61A61GLU-1-0.786-0.89721.9040.0290.0290.0000.0000.0000.000
62A62MET0-0.069-0.04822.5450.0040.0040.0000.0000.0000.000
63A63ALA0-0.021-0.02026.027-0.008-0.0080.0000.0000.0000.000
64A64GLU-1-0.953-0.97628.4380.0090.0090.0000.0000.0000.000
65A65TYR0-0.008-0.02525.569-0.007-0.0070.0000.0000.0000.000
66A66ARG10.9510.96927.327-0.059-0.0590.0000.0000.0000.000
67A67GLY00.0100.01128.371-0.001-0.0010.0000.0000.0000.000
68A68ARG10.6960.85728.6910.0240.0240.0000.0000.0000.000
69A69VAL0-0.0160.00723.675-0.011-0.0110.0000.0000.0000.000
70A70SER00.0050.00123.9690.0060.0060.0000.0000.0000.000
71A71LEU0-0.0160.00717.251-0.011-0.0110.0000.0000.0000.000
72A72VAL00.0200.01420.8290.0070.0070.0000.0000.0000.000
73A73GLU-1-0.930-0.99719.442-0.108-0.1080.0000.0000.0000.000
74A74ASP-1-0.921-0.95620.394-0.145-0.1450.0000.0000.0000.000
75A75HIS0-0.021-0.01019.168-0.007-0.0070.0000.0000.0000.000
76A76ILE00.0730.04115.427-0.043-0.0430.0000.0000.0000.000
77A77ALA0-0.089-0.05515.232-0.030-0.0300.0000.0000.0000.000
78A78GLU-1-0.995-0.99215.518-0.356-0.3560.0000.0000.0000.000
79A79GLY00.0240.01012.501-0.069-0.0690.0000.0000.0000.000
80A80SER0-0.064-0.03412.942-0.048-0.0480.0000.0000.0000.000
81A81VAL00.0160.01214.3920.0390.0390.0000.0000.0000.000
82A82ALA00.0280.00417.095-0.028-0.0280.0000.0000.0000.000
83A83VAL00.0140.04018.5220.0200.0200.0000.0000.0000.000
84A84ARG10.9090.95920.8800.0590.0590.0000.0000.0000.000
85A85ILE0-0.042-0.02523.5360.0140.0140.0000.0000.0000.000
86A86GLN0-0.003-0.00826.628-0.009-0.0090.0000.0000.0000.000
87A87GLU-1-0.928-0.97130.284-0.026-0.0260.0000.0000.0000.000
88A88VAL0-0.050-0.00829.0510.0060.0060.0000.0000.0000.000
89A89LYS11.0070.99531.5860.0180.0180.0000.0000.0000.000
90A90ALA00.0700.02531.673-0.004-0.0040.0000.0000.0000.000
91A91SER00.003-0.00131.512-0.002-0.0020.0000.0000.0000.000
92A92ASP-1-0.792-0.86827.771-0.032-0.0320.0000.0000.0000.000
93A93ASP-1-0.858-0.90326.694-0.082-0.0820.0000.0000.0000.000
94A94GLY00.0220.00425.3800.0120.0120.0000.0000.0000.000
95A95GLU-1-0.994-0.99319.139-0.110-0.1100.0000.0000.0000.000
96A96TYR0-0.051-0.05219.0100.0280.0280.0000.0000.0000.000
97A97ARG10.9400.96713.6780.0750.0750.0000.0000.0000.000
98A99PHE00.006-0.0098.305-0.046-0.0460.0000.0000.0000.000
99A100PHE00.0420.0187.3900.0220.0220.0000.0000.0000.000
100A101ARG10.9190.9536.684-0.867-0.8670.0000.0000.0000.000
101A102GLN0-0.013-0.0066.302-0.269-0.2690.0000.0000.0000.000
102A103ASP-1-0.917-0.9646.8641.1131.1130.0000.0000.0000.000
103A104GLU-1-0.984-0.9956.4112.1172.1170.0000.0000.0000.000
104A105ASN0-0.049-0.0152.3481.0352.3641.217-0.995-1.551-0.003
105A106TYR0-0.023-0.0293.069-1.500-1.1730.041-0.062-0.3060.000
106A107GLU-1-0.870-0.9163.337-2.930-1.9770.071-0.401-0.622-0.003
107A108GLU-1-0.986-1.0165.3270.3030.306-0.0010.000-0.0020.000
108A109ALA00.0180.0208.891-0.127-0.1270.0000.0000.0000.000
109A110ILE0-0.019-0.01211.7690.0870.0870.0000.0000.0000.000
110A111VAL00.0180.00215.496-0.038-0.0380.0000.0000.0000.000
111A112HIS0-0.018-0.00318.4650.0420.0420.0000.0000.0000.000
112A113LEU00.0060.01521.957-0.011-0.0110.0000.0000.0000.000
113A114LYS10.9000.94824.7720.1080.1080.0000.0000.0000.000
114A115VAL00.0320.01428.138-0.003-0.0030.0000.0000.0000.000
115A116ALA0-0.029-0.01931.1080.0020.0020.0000.0000.0000.000
116A117ALA00.0190.01234.5660.0010.0010.0000.0000.0000.000
117A118LEU0-0.0010.00038.0340.0000.0000.0000.0000.0000.000
118A119GLY00.0840.04541.0720.0020.0020.0000.0000.0000.000
119A120SER0-0.005-0.00544.270-0.001-0.0010.0000.0000.0000.000
120A121ASP-1-0.891-0.95347.965-0.038-0.0380.0000.0000.0000.000
121A122PRO0-0.052-0.01249.2240.0020.0020.0000.0000.0000.000
122A123HIS00.0180.01751.6680.0000.0000.0000.0000.0000.000
123A124ILE00.0190.00255.1730.0000.0000.0000.0000.0000.000
124A125SER0-0.050-0.01457.5920.0010.0010.0000.0000.0000.000
125A126MET00.0080.00360.311-0.001-0.0010.0000.0000.0000.000
126A127LYS10.9330.95762.2780.0160.0160.0000.0000.0000.000
127A128VAL00.0040.01665.5630.0000.0000.0000.0000.0000.000
128A129GLN00.0220.00867.5210.0010.0010.0000.0000.0000.000
129A130GLU-1-0.982-1.01269.485-0.012-0.0120.0000.0000.0000.000
130A131SER0-0.039-0.00871.2160.0000.0000.0000.0000.0000.000
131A132GLY0-0.018-0.00671.8040.0000.0000.0000.0000.0000.000
132A133GLU-1-0.864-0.93266.760-0.019-0.0190.0000.0000.0000.000
133A134ILE0-0.013-0.00264.1180.0010.0010.0000.0000.0000.000
134A135GLN0-0.0180.00161.645-0.001-0.0010.0000.0000.0000.000
135A136LEU0-0.015-0.00958.6600.0000.0000.0000.0000.0000.000
136A137GLU-1-0.946-0.97955.402-0.019-0.0190.0000.0000.0000.000
137A138CYS0-0.053-0.01751.8700.0000.0000.0000.0000.0000.000
138A139THR0-0.001-0.00751.6580.0000.0000.0000.0000.0000.000
139A140SER00.003-0.00647.773-0.001-0.0010.0000.0000.0000.000
140A141VAL00.0170.01146.9330.0010.0010.0000.0000.0000.000
141A142GLY00.0680.03443.220-0.002-0.0020.0000.0000.0000.000
142A143TRP0-0.039-0.02741.043-0.005-0.0050.0000.0000.0000.000
143A144TYR00.0200.03032.6930.0030.0030.0000.0000.0000.000
144A145PRO00.0350.02934.270-0.004-0.0040.0000.0000.0000.000
145A146GLU-1-0.897-0.97136.544-0.039-0.0390.0000.0000.0000.000
146A147PRO0-0.0220.01939.209-0.004-0.0040.0000.0000.0000.000
147A148GLN0-0.002-0.01041.5790.0020.0020.0000.0000.0000.000
148A149VAL00.020-0.00143.5480.0000.0000.0000.0000.0000.000
149A150GLN0-0.0010.01647.3220.0000.0000.0000.0000.0000.000
150A151TRP00.003-0.00749.2880.0010.0010.0000.0000.0000.000
151A152GLN00.0720.03451.839-0.001-0.0010.0000.0000.0000.000
152A153THR0-0.022-0.00654.8710.0020.0020.0000.0000.0000.000
153A154HIS0-0.002-0.01657.4200.0000.0000.0000.0000.0000.000
154A155ARG10.9000.93258.9700.0310.0310.0000.0000.0000.000
155A156GLY00.0530.05555.164-0.001-0.0010.0000.0000.0000.000
156A157GLU-1-1.013-1.00454.067-0.040-0.0400.0000.0000.0000.000
157A158GLU-1-0.886-0.95648.765-0.045-0.0450.0000.0000.0000.000
158A159PHE0-0.097-0.04253.1800.0010.0010.0000.0000.0000.000
159A160PRO00.0250.00951.2660.0000.0000.0000.0000.0000.000
160A161SER00.002-0.01450.3640.0010.0010.0000.0000.0000.000
161A162MET0-0.060-0.03453.0980.0000.0000.0000.0000.0000.000
162A163SER0-0.073-0.04152.7020.0010.0010.0000.0000.0000.000
163A164GLU-1-0.751-0.87047.025-0.035-0.0350.0000.0000.0000.000
164A165SER0-0.022-0.00548.2630.0020.0020.0000.0000.0000.000
165A166ARG10.7640.86342.4950.0350.0350.0000.0000.0000.000
166A167ASN0-0.017-0.00844.8420.0030.0030.0000.0000.0000.000
167A168PRO0-0.0260.00540.529-0.001-0.0010.0000.0000.0000.000
168A169ASP-1-0.814-0.91541.977-0.019-0.0190.0000.0000.0000.000
169A170GLU-1-0.986-1.00341.981-0.002-0.0020.0000.0000.0000.000
170A171GLU-1-0.970-0.98238.785-0.017-0.0170.0000.0000.0000.000
171A172GLY0-0.050-0.02537.719-0.003-0.0030.0000.0000.0000.000
172A173LEU0-0.024-0.00838.057-0.005-0.0050.0000.0000.0000.000
173A174PHE0-0.017-0.00537.5500.0040.0040.0000.0000.0000.000
174A175THR0-0.039-0.00742.603-0.002-0.0020.0000.0000.0000.000
175A176VAL0-0.025-0.02145.6720.0010.0010.0000.0000.0000.000
176A177ARG10.9240.96247.5010.0180.0180.0000.0000.0000.000
177A178ALA00.0250.01450.3870.0000.0000.0000.0000.0000.000
178A179SER00.0290.02352.2760.0010.0010.0000.0000.0000.000
179A180VAL0-0.0040.01955.4270.0000.0000.0000.0000.0000.000
180A181ILE0-0.011-0.01657.6510.0010.0010.0000.0000.0000.000
181A182ILE00.001-0.00460.034-0.001-0.0010.0000.0000.0000.000
182A183ARG10.8840.93761.0070.0220.0220.0000.0000.0000.000
183A184ASP-1-0.793-0.91465.255-0.026-0.0260.0000.0000.0000.000
184A185SER0-0.066-0.02967.3850.0010.0010.0000.0000.0000.000
185A186SER0-0.060-0.03767.8790.0000.0000.0000.0000.0000.000
186A187MET0-0.0400.00761.309-0.001-0.0010.0000.0000.0000.000
187A188LYS10.9350.96964.6890.0270.0270.0000.0000.0000.000
188A189ASN00.0130.00161.0190.0020.0020.0000.0000.0000.000
189A190VAL0-0.014-0.01257.3930.0000.0000.0000.0000.0000.000
190A191SER00.0200.02554.1900.0010.0010.0000.0000.0000.000
191A193ALA00.0800.04148.1160.0000.0000.0000.0000.0000.000
192A194ILE0-0.026-0.01944.6770.0010.0010.0000.0000.0000.000
193A195ARG10.8820.91040.1130.0660.0660.0000.0000.0000.000
194A196ASN0-0.005-0.01937.015-0.003-0.0030.0000.0000.0000.000
195A197LEU0-0.024-0.04137.121-0.004-0.0040.0000.0000.0000.000
196A198LEU0-0.0050.01330.510-0.005-0.0050.0000.0000.0000.000
197A199LEU00.0070.00433.812-0.006-0.0060.0000.0000.0000.000
198A200GLY0-0.0290.00236.020-0.002-0.0020.0000.0000.0000.000
199A201GLN0-0.048-0.03038.4600.0040.0040.0000.0000.0000.000
200A202GLU-1-0.836-0.90441.259-0.055-0.0550.0000.0000.0000.000
201A203LYS10.8040.91844.5640.0430.0430.0000.0000.0000.000
202A204GLU-1-0.908-0.95747.878-0.043-0.0430.0000.0000.0000.000
203A205VAL0-0.042-0.00851.1750.0010.0010.0000.0000.0000.000
204A206GLU-1-0.887-0.94654.678-0.034-0.0340.0000.0000.0000.000
205A207VAL0-0.033-0.02557.8070.0010.0010.0000.0000.0000.000
206A208SER0-0.016-0.02160.9160.0000.0000.0000.0000.0000.000
207A209ILE00.0200.00462.5520.0010.0010.0000.0000.0000.000
208A210PRO0-0.057-0.02866.4670.0000.0000.0000.0000.0000.000
209A211ALA00.0030.01270.2170.0000.0000.0000.0000.0000.000