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: MVM6Z

Calculation Name: 5H0J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H0J

Chain ID: A

ChEMBL ID:

UniProt ID: C6Y1J8

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 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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3170814.920292
FMO2-HF: Nuclear repulsion 3075960.389369
FMO2-HF: Total energy -94854.530923
FMO2-MP2: Total energy -95129.544237


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.
-9.538-3.4018.912-4.571-10.478-0.03
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 : -0.041 / q_NPA : -0.035
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].
3A3THR0-0.019-0.0133.847-1.2910.266-0.017-0.675-0.8650.000
4A4PHE0-0.008-0.0224.127-1.192-1.1020.000-0.043-0.0470.000
5A5ALA00.0300.0025.999-0.154-0.1540.0000.0000.0000.000
6A6ASP-1-0.809-0.8842.146-3.639-3.7413.496-1.026-2.368-0.003
7A7LYS10.8520.9302.742-2.590-0.1021.972-1.434-3.026-0.015
8A8VAL0-0.0160.0013.3520.7040.6330.0360.259-0.2240.000
9A9ILE0-0.0030.0025.1160.3110.3110.0000.0000.0000.000
10A10GLN0-0.020-0.0192.336-4.780-2.8683.425-1.598-3.739-0.012
11A11PHE0-0.017-0.0264.2850.6560.9190.000-0.054-0.2090.000
12A12ASN00.0040.0006.9320.3900.3900.0000.0000.0000.000
13A13LYS10.8670.9184.8442.9652.9650.0000.0000.0000.000
14A14ASP-1-0.822-0.8956.207-0.452-0.4520.0000.0000.0000.000
15A15LEU0-0.092-0.0268.9280.1870.1870.0000.0000.0000.000
16A16SER00.0140.00212.0300.0250.0250.0000.0000.0000.000
17A17TYR0-0.063-0.05015.1740.0060.0060.0000.0000.0000.000
18A18THR00.0210.00617.0470.0050.0050.0000.0000.0000.000
19A19GLY00.0180.02019.8130.0200.0200.0000.0000.0000.000
20A20SER0-0.027-0.01222.8910.0090.0090.0000.0000.0000.000
21A21THR00.0150.00526.370-0.015-0.0150.0000.0000.0000.000
22A22LEU0-0.0120.00725.3670.0030.0030.0000.0000.0000.000
23A23PRO00.009-0.00729.2330.0070.0070.0000.0000.0000.000
24A24PRO00.0540.01732.283-0.007-0.0070.0000.0000.0000.000
25A25GLY00.0110.01533.809-0.001-0.0010.0000.0000.0000.000
26A26ILE0-0.076-0.03628.313-0.008-0.0080.0000.0000.0000.000
27A27ARG10.8830.93526.5640.1770.1770.0000.0000.0000.000
28A28ILE00.0110.00120.376-0.004-0.0040.0000.0000.0000.000
29A29MET0-0.0390.01421.555-0.003-0.0030.0000.0000.0000.000
30A30ASN00.029-0.01315.094-0.049-0.0490.0000.0000.0000.000
31A31PRO00.0830.03116.838-0.011-0.0110.0000.0000.0000.000
32A32PHE00.003-0.00112.362-0.007-0.0070.0000.0000.0000.000
33A33LYS10.7740.88511.2580.6570.6570.0000.0000.0000.000
34A34GLU-1-0.877-0.89616.356-0.245-0.2450.0000.0000.0000.000
35A35HIS0-0.037-0.02118.3870.0220.0220.0000.0000.0000.000
36A36GLU-1-0.824-0.91316.310-0.422-0.4220.0000.0000.0000.000
37A37GLN0-0.014-0.00815.692-0.054-0.0540.0000.0000.0000.000
38A38THR0-0.015-0.01415.287-0.030-0.0300.0000.0000.0000.000
39A39MET0-0.0100.0018.651-0.027-0.0270.0000.0000.0000.000
40A40HIS00.0850.04511.839-0.178-0.1780.0000.0000.0000.000
41A41ILE0-0.0120.00713.955-0.007-0.0070.0000.0000.0000.000
42A42VAL0-0.029-0.0159.582-0.013-0.0130.0000.0000.0000.000
43A43GLU-1-0.843-0.9207.644-1.933-1.9330.0000.0000.0000.000
44A44ALA00.0100.00410.7280.0090.0090.0000.0000.0000.000
45A45PHE00.012-0.00913.5060.0570.0570.0000.0000.0000.000
46A46TYR0-0.022-0.0179.1080.0660.0660.0000.0000.0000.000
47A47HIS00.0340.0066.6050.2340.2340.0000.0000.0000.000
48A48LYS10.8850.96911.0800.5080.5080.0000.0000.0000.000
49A49TYR0-0.010-0.02513.4880.0840.0840.0000.0000.0000.000
50A50TYR0-0.056-0.0669.4370.0550.0550.0000.0000.0000.000
51A51ASN0-0.0010.0168.915-0.235-0.2350.0000.0000.0000.000
52A52ASP-1-0.722-0.8639.539-0.371-0.3710.0000.0000.0000.000
53A53ASN0-0.010-0.0297.234-0.171-0.1710.0000.0000.0000.000
54A54GLN0-0.0350.00310.4300.0950.0950.0000.0000.0000.000
55A55SER0-0.016-0.00612.492-0.094-0.0940.0000.0000.0000.000
56A56ARG10.7800.88112.3060.6010.6010.0000.0000.0000.000
57A57TYR00.0200.01215.1660.0210.0210.0000.0000.0000.000
58A58LEU00.0120.00815.029-0.032-0.0320.0000.0000.0000.000
59A59ILE00.0070.00917.6310.0500.0500.0000.0000.0000.000
60A60LEU00.0020.00318.026-0.035-0.0350.0000.0000.0000.000
61A61GLY00.0380.01920.7920.0290.0290.0000.0000.0000.000
62A62ILE0-0.067-0.02922.7720.0110.0110.0000.0000.0000.000
63A63ASN00.002-0.02921.1160.0190.0190.0000.0000.0000.000
64A64PRO00.0130.02418.4120.0150.0150.0000.0000.0000.000
65A65GLY00.0090.01121.3690.0290.0290.0000.0000.0000.000
66A66ARG10.8300.85723.2130.2190.2190.0000.0000.0000.000
67A67PHE0-0.046-0.01425.056-0.001-0.0010.0000.0000.0000.000
68A68GLY00.014-0.00524.804-0.013-0.0130.0000.0000.0000.000
69A69SER0-0.001-0.02820.315-0.009-0.0090.0000.0000.0000.000
70A70GLY0-0.0180.00419.983-0.043-0.0430.0000.0000.0000.000
71A71LEU0-0.052-0.03720.723-0.010-0.0100.0000.0000.0000.000
72A72THR0-0.009-0.02118.979-0.012-0.0120.0000.0000.0000.000
73A73GLY00.0110.00415.539-0.059-0.0590.0000.0000.0000.000
74A74ILE0-0.0190.00514.530-0.068-0.0680.0000.0000.0000.000
75A75PRO0-0.005-0.01615.8010.0730.0730.0000.0000.0000.000
76A76PHE0-0.002-0.00718.8520.0110.0110.0000.0000.0000.000
77A77THR00.0350.07319.8170.0280.0280.0000.0000.0000.000
78A78ASP-1-0.740-0.82421.372-0.279-0.2790.0000.0000.0000.000
79A79PRO00.0260.00623.685-0.002-0.0020.0000.0000.0000.000
80A80LYS10.9410.98824.6530.1910.1910.0000.0000.0000.000
81A81ARG10.8300.87624.4410.2390.2390.0000.0000.0000.000
82A82LEU00.0160.01118.752-0.006-0.0060.0000.0000.0000.000
83A83ILE00.0050.01322.575-0.004-0.0040.0000.0000.0000.000
84A84THR0-0.094-0.10225.2680.0020.0020.0000.0000.0000.000
85A85GLU-1-0.838-0.87724.142-0.218-0.2180.0000.0000.0000.000
86A86CYS0-0.069-0.01820.003-0.019-0.0190.0000.0000.0000.000
87A87ASN0-0.037-0.00221.3710.0010.0010.0000.0000.0000.000
88A88ILE0-0.0130.00817.192-0.012-0.0120.0000.0000.0000.000
89A89PRO00.005-0.00920.8580.0140.0140.0000.0000.0000.000
90A90TYR0-0.019-0.02821.450-0.038-0.0380.0000.0000.0000.000
91A91SER00.0220.01223.0620.0360.0360.0000.0000.0000.000
92A92GLY00.0420.02624.672-0.012-0.0120.0000.0000.0000.000
93A93LYS10.9510.98127.3460.2240.2240.0000.0000.0000.000
94A94LEU00.0630.03927.788-0.017-0.0170.0000.0000.0000.000
95A95SER0-0.026-0.01827.0750.0090.0090.0000.0000.0000.000
96A96HIS00.0480.03327.916-0.019-0.0190.0000.0000.0000.000
97A97GLU-1-0.759-0.88524.546-0.289-0.2890.0000.0000.0000.000
98A98PRO0-0.027-0.02528.811-0.004-0.0040.0000.0000.0000.000
99A99SER0-0.001-0.01426.7650.0110.0110.0000.0000.0000.000
100A100SER00.0480.01224.420-0.002-0.0020.0000.0000.0000.000
101A101VAL0-0.051-0.02226.408-0.001-0.0010.0000.0000.0000.000
102A102PHE00.0080.00428.4740.0020.0020.0000.0000.0000.000
103A103ILE00.005-0.00122.9630.0060.0060.0000.0000.0000.000
104A104TYR00.0820.00720.574-0.006-0.0060.0000.0000.0000.000
105A105GLU-1-0.821-0.88126.617-0.153-0.1530.0000.0000.0000.000
106A106MET0-0.063-0.00824.5430.0090.0090.0000.0000.0000.000
107A107ILE00.0080.00421.7030.0050.0050.0000.0000.0000.000
108A108ASN0-0.037-0.03425.726-0.001-0.0010.0000.0000.0000.000
109A109ALA0-0.015-0.00128.1450.0080.0080.0000.0000.0000.000
110A110PHE0-0.064-0.03523.6330.0090.0090.0000.0000.0000.000
111A111GLY00.0070.01027.1770.0060.0060.0000.0000.0000.000
112A112GLY00.0110.01625.3170.0020.0020.0000.0000.0000.000
113A113ALA0-0.014-0.03020.754-0.009-0.0090.0000.0000.0000.000
114A114GLU-1-0.936-0.96618.845-0.319-0.3190.0000.0000.0000.000
115A115ALA00.0380.01819.210-0.018-0.0180.0000.0000.0000.000
116A116PHE00.0000.00220.215-0.005-0.0050.0000.0000.0000.000
117A117TYR0-0.004-0.02715.833-0.005-0.0050.0000.0000.0000.000
118A118LYS10.8400.94614.4250.3630.3630.0000.0000.0000.000
119A119GLN0-0.0060.00116.5330.0070.0070.0000.0000.0000.000
120A120PHE0-0.022-0.01317.6910.0090.0090.0000.0000.0000.000
121A121TYR00.0050.00811.702-0.077-0.0770.0000.0000.0000.000
122A122ILE0-0.0080.00515.3350.0560.0560.0000.0000.0000.000
123A123SER00.0370.01714.170-0.042-0.0420.0000.0000.0000.000
124A124SER0-0.035-0.04616.6020.0390.0390.0000.0000.0000.000
125A125PRO0-0.0050.01118.075-0.018-0.0180.0000.0000.0000.000
126A126CYS0-0.0170.02619.1950.0020.0020.0000.0000.0000.000
127A127PRO00.0410.03514.680-0.005-0.0050.0000.0000.0000.000
128A128LEU00.007-0.00516.331-0.034-0.0340.0000.0000.0000.000
129A129GLY00.0450.02519.0100.0230.0230.0000.0000.0000.000
130A130PHE00.017-0.00322.5460.0070.0070.0000.0000.0000.000
131A131THR0-0.0010.00825.8870.0060.0060.0000.0000.0000.000
132A132SER00.0260.00428.6610.0050.0050.0000.0000.0000.000
133A133ILE00.0030.00131.909-0.007-0.0070.0000.0000.0000.000
134A134ALA00.0020.01834.8010.0060.0060.0000.0000.0000.000
135A135ALA00.0440.00938.499-0.002-0.0020.0000.0000.0000.000
136A136ASN00.0060.00740.343-0.003-0.0030.0000.0000.0000.000
137A137GLY00.0610.03638.0930.0000.0000.0000.0000.0000.000
138A138LYS10.8830.93635.2960.1300.1300.0000.0000.0000.000
139A139GLU-1-0.793-0.89129.092-0.198-0.1980.0000.0000.0000.000
140A140LYS10.8890.95332.7020.1240.1240.0000.0000.0000.000
141A141ASN00.007-0.00227.229-0.021-0.0210.0000.0000.0000.000
142A142TYR0-0.008-0.00228.3710.0130.0130.0000.0000.0000.000
143A143ASN00.002-0.01027.185-0.024-0.0240.0000.0000.0000.000
144A144TYR00.025-0.01024.4220.0190.0190.0000.0000.0000.000
145A145TYR00.0050.00726.7020.0120.0120.0000.0000.0000.000
146A146ASP-1-0.809-0.90829.961-0.132-0.1320.0000.0000.0000.000
147A147SER00.0010.00532.0640.0090.0090.0000.0000.0000.000
148A148LYS10.9020.93632.2580.0830.0830.0000.0000.0000.000
149A149ALA00.0330.01732.6990.0010.0010.0000.0000.0000.000
150A150LEU0-0.0020.01027.2530.0010.0010.0000.0000.0000.000
151A151GLU-1-0.789-0.89428.000-0.104-0.1040.0000.0000.0000.000
152A152LYS10.9340.96027.7460.0600.0600.0000.0000.0000.000
153A153ALA0-0.030-0.00227.8770.0050.0050.0000.0000.0000.000
154A154VAL00.0260.00723.3370.0010.0010.0000.0000.0000.000
155A155TYR0-0.039-0.01723.092-0.016-0.0160.0000.0000.0000.000
156A156GLU-1-0.796-0.92422.452-0.074-0.0740.0000.0000.0000.000
157A157PHE00.0050.00616.348-0.007-0.0070.0000.0000.0000.000
158A158ILE0-0.031-0.01718.427-0.028-0.0280.0000.0000.0000.000
159A159ILE0-0.026-0.00219.111-0.022-0.0220.0000.0000.0000.000
160A160GLU-1-0.799-0.88916.161-0.035-0.0350.0000.0000.0000.000
161A161ASN0-0.027-0.00514.380-0.073-0.0730.0000.0000.0000.000
162A162ILE0-0.022-0.01214.348-0.049-0.0490.0000.0000.0000.000
163A163ARG10.8770.92114.409-0.041-0.0410.0000.0000.0000.000
164A164LYS10.9220.9799.1390.5740.5740.0000.0000.0000.000
165A165GLN00.0130.00310.313-0.166-0.1660.0000.0000.0000.000
166A166LEU00.0090.00211.739-0.064-0.0640.0000.0000.0000.000
167A167THR0-0.057-0.0398.552-0.037-0.0370.0000.0000.0000.000
168A168LEU0-0.0010.0166.842-0.114-0.1140.0000.0000.0000.000
169A169GLY00.0270.0228.348-0.120-0.1200.0000.0000.0000.000
170A170ILE0-0.028-0.00711.1870.0210.0210.0000.0000.0000.000
171A171THR00.0370.01914.4640.0520.0520.0000.0000.0000.000
172A172THR00.0090.00317.5140.0010.0010.0000.0000.0000.000
173A173ASP-1-0.795-0.85619.850-0.082-0.0820.0000.0000.0000.000
174A174THR00.008-0.01922.0590.0160.0160.0000.0000.0000.000
175A175CYS0-0.072-0.00920.223-0.023-0.0230.0000.0000.0000.000
176A176PHE00.0500.01621.9360.0220.0220.0000.0000.0000.000
177A177CYS0-0.0110.01623.054-0.020-0.0200.0000.0000.0000.000
178A178LEU00.0140.01623.8080.0170.0170.0000.0000.0000.000
179A179GLY00.002-0.02926.479-0.007-0.0070.0000.0000.0000.000
180A180THR00.0070.01329.3770.0020.0020.0000.0000.0000.000
181A181GLY00.0140.02532.4000.0100.0100.0000.0000.0000.000
182A182LYS10.8740.91331.5960.1210.1210.0000.0000.0000.000
183A183ASN0-0.010-0.00224.6830.0070.0070.0000.0000.0000.000
184A184GLU-1-0.731-0.87327.768-0.113-0.1130.0000.0000.0000.000
185A185LYS10.7840.88629.5400.1100.1100.0000.0000.0000.000
186A186PHE0-0.014-0.00324.1600.0110.0110.0000.0000.0000.000
187A187LEU00.0580.01122.4000.0040.0040.0000.0000.0000.000
188A188MET00.0010.01026.2790.0050.0050.0000.0000.0000.000
189A189LYS10.8860.96228.7450.1030.1030.0000.0000.0000.000
190A190VAL0-0.003-0.00122.7660.0090.0090.0000.0000.0000.000
191A191ASN00.006-0.01224.3410.0040.0040.0000.0000.0000.000
192A192ALA00.0000.00525.8790.0100.0100.0000.0000.0000.000
193A193GLN0-0.027-0.00426.7830.0120.0120.0000.0000.0000.000
194A194TYR0-0.009-0.02122.4370.0080.0080.0000.0000.0000.000
195A195LYS10.8540.93823.2010.0400.0400.0000.0000.0000.000
196A196PHE00.0200.01019.0470.0000.0000.0000.0000.0000.000
197A197PHE00.005-0.00518.337-0.017-0.0170.0000.0000.0000.000
198A198LYS10.8770.94822.8610.0800.0800.0000.0000.0000.000
199A199ARG10.8650.91925.4300.1070.1070.0000.0000.0000.000
200A200ILE0-0.007-0.01124.411-0.014-0.0140.0000.0000.0000.000
201A201VAL00.0080.00826.2090.0130.0130.0000.0000.0000.000
202A202ALA0-0.0060.00527.171-0.015-0.0150.0000.0000.0000.000
203A203LEU00.0030.00026.8160.0070.0070.0000.0000.0000.000
204A204GLU-1-0.782-0.88529.888-0.132-0.1320.0000.0000.0000.000
205A205HIS00.0400.03326.0030.0020.0020.0000.0000.0000.000
206A206PRO00.0830.04126.2620.0120.0120.0000.0000.0000.000
207A207ARG10.8810.94029.5920.1820.1820.0000.0000.0000.000
208A208PHE0-0.010-0.00831.4580.0090.0090.0000.0000.0000.000
209A209ILE00.0200.00831.0710.0100.0100.0000.0000.0000.000
210A210MET0-0.015-0.01132.2060.0100.0100.0000.0000.0000.000
211A211GLN0-0.0270.01934.965-0.003-0.0030.0000.0000.0000.000
212A212TYR00.0010.00236.7660.0030.0030.0000.0000.0000.000
213A213LYS10.8860.95537.0390.1080.1080.0000.0000.0000.000
214A214THR00.0250.00337.2940.0020.0020.0000.0000.0000.000
215A215ALA00.0230.00938.777-0.002-0.0020.0000.0000.0000.000
216A216SER0-0.018-0.00939.5840.0020.0020.0000.0000.0000.000
217A217LYS10.8230.88934.3110.1500.1500.0000.0000.0000.000
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