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: 2JR1R

Calculation Name: 3RON-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RON

Chain ID: A

ChEMBL ID:

UniProt ID: P0A382

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptHSide
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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2244566.150305
FMO2-HF: Nuclear repulsion 2167472.884765
FMO2-HF: Total energy -77093.265541
FMO2-MP2: Total energy -77318.688064


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:38:ASN)


Summations of interaction energy for fragment #1(A:38:ASN)
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.
-23.277-11.1735.471-7.45-10.120.003
Interaction energy analysis for fragmet #1(A:38:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.011
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].
3A40LEU00.0090.0222.202-13.032-7.5602.543-3.906-4.1090.029
4A41LEU00.0120.0023.5980.6170.9970.040-0.140-0.2790.000
5A42SER0-0.053-0.0294.591-0.694-0.579-0.001-0.004-0.1100.000
6A43ILE0-0.019-0.0106.908-0.479-0.4790.0000.0000.0000.000
7A44ASN0-0.018-0.0189.6000.0260.0260.0000.0000.0000.000
8A45GLU-1-0.814-0.90912.0950.1570.1570.0000.0000.0000.000
9A46ILE0-0.058-0.03511.776-0.023-0.0230.0000.0000.0000.000
10A47ASP-1-0.841-0.91316.342-0.042-0.0420.0000.0000.0000.000
11A48ASN0-0.042-0.02819.116-0.027-0.0270.0000.0000.0000.000
12A49PRO00.0910.02817.026-0.027-0.0270.0000.0000.0000.000
13A50ASN0-0.0240.01516.576-0.061-0.0610.0000.0000.0000.000
14A51TYR00.032-0.00615.320-0.012-0.0120.0000.0000.0000.000
15A52ILE00.0120.01511.195-0.040-0.0400.0000.0000.0000.000
16A53LEU0-0.023-0.00710.229-0.160-0.1600.0000.0000.0000.000
17A54GLN00.032-0.00410.108-0.190-0.1900.0000.0000.0000.000
18A55ALA00.0600.0309.514-0.105-0.1050.0000.0000.0000.000
19A56ILE0-0.007-0.0015.228-0.148-0.1480.0000.0000.0000.000
20A57MET0-0.040-0.0165.375-1.182-1.1820.0000.0000.0000.000
21A58LEU0-0.002-0.0116.850-0.202-0.2020.0000.0000.0000.000
22A59ALA00.0460.0193.2210.0560.4080.019-0.100-0.2700.000
23A60ASN0-0.057-0.0442.351-10.434-7.7871.481-1.777-2.350-0.022
24A61ALA00.0010.0223.6411.6531.6800.0030.063-0.0930.000
25A62PHE00.054-0.0075.8520.4830.4830.0000.0000.0000.000
26A63GLN00.0740.0532.5112.4235.2661.389-1.541-2.690-0.004
27A64ASN0-0.084-0.0464.4940.1420.216-0.001-0.015-0.0570.000
28A65ALA0-0.015-0.0147.656-0.206-0.2060.0000.0000.0000.000
29A66LEU0-0.0270.0035.009-0.321-0.224-0.001-0.002-0.0940.000
30A67VAL0-0.026-0.0159.317-0.263-0.2630.0000.0000.0000.000
31A68PRO00.0260.00912.4300.0750.0750.0000.0000.0000.000
32A69THR00.0250.02814.272-0.007-0.0070.0000.0000.0000.000
33A70SER00.006-0.00116.740-0.053-0.0530.0000.0000.0000.000
34A71THR00.0850.02619.9460.0070.0070.0000.0000.0000.000
35A72ASP-1-0.946-0.97721.2140.1710.1710.0000.0000.0000.000
36A73PHE0-0.076-0.03117.040-0.018-0.0180.0000.0000.0000.000
37A74GLY00.020-0.00119.246-0.009-0.0090.0000.0000.0000.000
38A75ASP-1-0.937-0.95914.8990.2480.2480.0000.0000.0000.000
39A76ALA00.0210.00312.788-0.016-0.0160.0000.0000.0000.000
40A77LEU00.0040.0267.6600.0090.0090.0000.0000.0000.000
41A78ARG10.8190.91110.345-0.621-0.6210.0000.0000.0000.000
42A79PHE00.0180.0178.523-0.099-0.0990.0000.0000.0000.000
43A80SER00.0230.01910.157-0.250-0.2500.0000.0000.0000.000
44A81MET00.015-0.00713.049-0.003-0.0030.0000.0000.0000.000
45A82PRO00.015-0.00115.269-0.049-0.0490.0000.0000.0000.000
46A83LYS10.9190.96711.924-0.512-0.5120.0000.0000.0000.000
47A84GLY00.0250.00211.661-0.038-0.0380.0000.0000.0000.000
48A85LEU0-0.024-0.02312.596-0.100-0.1000.0000.0000.0000.000
49A86GLU-1-0.937-0.96415.2500.2030.2030.0000.0000.0000.000
50A87ILE0-0.031-0.0199.166-0.059-0.0590.0000.0000.0000.000
51A88ALA00.0110.01212.676-0.112-0.1120.0000.0000.0000.000
52A89ASN0-0.042-0.01913.757-0.056-0.0560.0000.0000.0000.000
53A90THR0-0.089-0.04713.266-0.040-0.0400.0000.0000.0000.000
54A91ILE0-0.060-0.00910.083-0.068-0.0680.0000.0000.0000.000
55A92THR0-0.0080.02113.8560.0640.0640.0000.0000.0000.000
56A93PRO0-0.013-0.03214.694-0.063-0.0630.0000.0000.0000.000
57A94MET00.0320.01816.594-0.012-0.0120.0000.0000.0000.000
58A95GLY00.0210.01716.863-0.008-0.0080.0000.0000.0000.000
59A96ALA0-0.037-0.02117.7710.0140.0140.0000.0000.0000.000
60A97VAL00.0070.00615.9520.0080.0080.0000.0000.0000.000
61A98VAL0-0.049-0.02318.265-0.009-0.0090.0000.0000.0000.000
62A99SER0-0.037-0.02118.949-0.004-0.0040.0000.0000.0000.000
63A100TYR00.024-0.00418.1410.0230.0230.0000.0000.0000.000
64A101VAL0-0.031-0.01017.969-0.037-0.0370.0000.0000.0000.000
65A102ASP-1-0.802-0.90318.2690.4800.4800.0000.0000.0000.000
66A103GLN0-0.0200.00120.232-0.045-0.0450.0000.0000.0000.000
67A104ASN00.0310.01621.2640.0540.0540.0000.0000.0000.000
68A105VAL00.0000.00722.825-0.027-0.0270.0000.0000.0000.000
69A106THR0-0.017-0.00624.4400.0100.0100.0000.0000.0000.000
70A107GLN0-0.036-0.03527.060-0.002-0.0020.0000.0000.0000.000
71A108THR00.0260.00529.0370.0030.0030.0000.0000.0000.000
72A109ASN0-0.027-0.02131.8190.0010.0010.0000.0000.0000.000
73A110ASN00.0230.02530.479-0.007-0.0070.0000.0000.0000.000
74A111GLN00.0180.00729.7610.0050.0050.0000.0000.0000.000
75A112VAL00.0340.02623.5000.0120.0120.0000.0000.0000.000
76A113SER00.0360.01824.9830.0240.0240.0000.0000.0000.000
77A114VAL0-0.0130.00726.3350.0080.0080.0000.0000.0000.000
78A115MET0-0.0260.00921.9850.0130.0130.0000.0000.0000.000
79A116ILE00.0030.01220.9960.0220.0220.0000.0000.0000.000
80A117ASN0-0.021-0.03422.3740.0180.0180.0000.0000.0000.000
81A118LYS10.8880.94324.763-0.205-0.2050.0000.0000.0000.000
82A119VAL00.0290.00818.0520.0050.0050.0000.0000.0000.000
83A120LEU00.0080.00619.8050.0220.0220.0000.0000.0000.000
84A121GLU-1-0.860-0.90421.5400.1930.1930.0000.0000.0000.000
85A122VAL0-0.035-0.00820.080-0.011-0.0110.0000.0000.0000.000
86A123LEU00.0100.00015.6880.0030.0030.0000.0000.0000.000
87A124LYS10.8900.92319.264-0.212-0.2120.0000.0000.0000.000
88A125THR0-0.057-0.02322.037-0.035-0.0350.0000.0000.0000.000
89A126VAL0-0.0320.01416.960-0.023-0.0230.0000.0000.0000.000
90A127LEU00.016-0.00316.463-0.024-0.0240.0000.0000.0000.000
91A128GLY00.0220.01919.972-0.037-0.0370.0000.0000.0000.000
92A129VAL00.0130.00023.4040.0080.0080.0000.0000.0000.000
93A130ALA00.0350.01325.5960.0020.0020.0000.0000.0000.000
94A131LEU00.0020.02017.708-0.006-0.0060.0000.0000.0000.000
95A132SER00.0580.01021.1650.0200.0200.0000.0000.0000.000
96A133GLY0-0.038-0.00422.1920.0030.0030.0000.0000.0000.000
97A134SER0-0.066-0.05521.355-0.013-0.0130.0000.0000.0000.000
98A135VAL0-0.0020.00217.597-0.011-0.0110.0000.0000.0000.000
99A136ILE00.0130.02319.5630.0380.0380.0000.0000.0000.000
100A137ASP-1-0.858-0.90621.3600.1480.1480.0000.0000.0000.000
101A138GLN00.003-0.02516.6100.0290.0290.0000.0000.0000.000
102A139LEU0-0.030-0.01016.4280.0700.0700.0000.0000.0000.000
103A140THR0-0.028-0.04217.7650.0430.0430.0000.0000.0000.000
104A141ALA0-0.006-0.00217.8870.0150.0150.0000.0000.0000.000
105A142ALA0-0.0050.00313.4750.0180.0180.0000.0000.0000.000
106A143VAL00.0110.01015.0090.0690.0690.0000.0000.0000.000
107A144THR0-0.011-0.02517.156-0.022-0.0220.0000.0000.0000.000
108A145ASN0-0.025-0.00215.484-0.064-0.0640.0000.0000.0000.000
109A146THR00.0410.03814.6190.0720.0720.0000.0000.0000.000
110A147PHE0-0.036-0.02115.730-0.010-0.0100.0000.0000.0000.000
111A148THR0-0.036-0.01319.065-0.052-0.0520.0000.0000.0000.000
112A149ASN0-0.009-0.01718.5950.0040.0040.0000.0000.0000.000
113A150LEU00.0550.03716.224-0.011-0.0110.0000.0000.0000.000
114A151ASN00.0320.02617.175-0.025-0.0250.0000.0000.0000.000
115A152THR0-0.054-0.03816.546-0.031-0.0310.0000.0000.0000.000
116A153GLN00.0260.01113.3100.0650.0650.0000.0000.0000.000
117A154LYS10.8470.94512.707-0.029-0.0290.0000.0000.0000.000
118A155ASN00.016-0.00812.3700.0570.0570.0000.0000.0000.000
119A156GLU-1-0.907-0.9318.732-0.600-0.6000.0000.0000.0000.000
120A157ALA00.001-0.0024.207-0.0490.048-0.001-0.028-0.0680.000
121A158TRP00.0120.0066.2830.4350.4350.0000.0000.0000.000
122A159ILE0-0.065-0.0187.4260.2440.2440.0000.0000.0000.000
123A160PHE00.0240.0186.995-0.215-0.2150.0000.0000.0000.000
124A161TRP0-0.023-0.02412.3190.0640.0640.0000.0000.0000.000
125A162GLY00.000-0.00715.881-0.009-0.0090.0000.0000.0000.000
126A163LYS10.8290.91018.036-0.217-0.2170.0000.0000.0000.000
127A164GLU-1-0.824-0.90120.0300.1490.1490.0000.0000.0000.000
128A165THR0-0.011-0.00923.500-0.015-0.0150.0000.0000.0000.000
129A166ALA00.023-0.00227.2950.0020.0020.0000.0000.0000.000
130A167ASN0-0.023-0.02029.754-0.002-0.0020.0000.0000.0000.000
131A168GLN0-0.088-0.04324.798-0.003-0.0030.0000.0000.0000.000
132A169THR00.0360.01120.717-0.013-0.0130.0000.0000.0000.000
133A170ASN0-0.037-0.01820.1140.0080.0080.0000.0000.0000.000
134A171TYR0-0.016-0.02014.911-0.057-0.0570.0000.0000.0000.000
135A172THR00.009-0.02611.789-0.049-0.0490.0000.0000.0000.000
136A173TYR0-0.007-0.02011.0100.0170.0170.0000.0000.0000.000
137A174ASN00.0000.0026.910-0.290-0.2900.0000.0000.0000.000
138A175VAL00.0420.0287.3230.5150.5150.0000.0000.0000.000
139A176LEU0-0.017-0.0135.046-0.085-0.0850.0000.0000.0000.000
140A177PHE00.0090.0238.119-0.122-0.1220.0000.0000.0000.000
141A178ALA00.0150.0139.253-0.084-0.0840.0000.0000.0000.000
142A179ILE0-0.007-0.00611.251-0.025-0.0250.0000.0000.0000.000
143A180GLN00.0550.01815.033-0.050-0.0500.0000.0000.0000.000
144A181ASN00.0900.04817.573-0.008-0.0080.0000.0000.0000.000
145A182ALA00.0420.00521.031-0.002-0.0020.0000.0000.0000.000
146A183GLN0-0.066-0.02922.658-0.001-0.0010.0000.0000.0000.000
147A184THR0-0.075-0.02818.1760.0150.0150.0000.0000.0000.000
148A185GLY00.0030.01421.524-0.010-0.0100.0000.0000.0000.000
149A186GLY0-0.003-0.01222.146-0.014-0.0140.0000.0000.0000.000
150A187VAL0-0.041-0.02418.611-0.018-0.0180.0000.0000.0000.000
151A188MET0-0.0230.00612.526-0.022-0.0220.0000.0000.0000.000
152A189TYR00.010-0.01214.9840.0090.0090.0000.0000.0000.000
153A190CYS00.0020.0089.038-0.002-0.0020.0000.0000.0000.000
154A191VAL0-0.025-0.02111.477-0.023-0.0230.0000.0000.0000.000
155A192PRO00.0170.0178.3160.2050.2050.0000.0000.0000.000
156A193VAL0-0.025-0.0119.534-0.358-0.3580.0000.0000.0000.000
157A194GLY00.0010.01710.0580.3830.3830.0000.0000.0000.000
158A195PHE0-0.030-0.02511.853-0.250-0.2500.0000.0000.0000.000
159A196GLU-1-0.871-0.93714.1800.5380.5380.0000.0000.0000.000
160A197ILE0-0.034-0.00916.155-0.070-0.0700.0000.0000.0000.000
161A198LYS10.9771.00619.139-0.285-0.2850.0000.0000.0000.000
162A199VAL00.0380.01722.299-0.001-0.0010.0000.0000.0000.000
163A200SER0-0.030-0.02224.461-0.009-0.0090.0000.0000.0000.000
164A201ALA00.0160.01226.539-0.015-0.0150.0000.0000.0000.000
165A202VAL00.0020.03626.1100.0140.0140.0000.0000.0000.000
166A203LYS10.8970.94018.149-0.126-0.1260.0000.0000.0000.000
167A204GLU-1-0.886-0.96023.3720.1020.1020.0000.0000.0000.000
168A205GLN00.024-0.00224.9870.0020.0020.0000.0000.0000.000
169A206VAL00.0050.01320.9480.0060.0060.0000.0000.0000.000
170A207LEU0-0.108-0.05619.0390.0100.0100.0000.0000.0000.000
171A208PHE0-0.071-0.05321.951-0.008-0.0080.0000.0000.0000.000
172A209PHE00.0020.02823.433-0.006-0.0060.0000.0000.0000.000
173A210THR0-0.010-0.01923.9080.0090.0090.0000.0000.0000.000
174A211ILE00.028-0.01324.2360.0060.0060.0000.0000.0000.000
175A212GLN00.001-0.00526.5020.0050.0050.0000.0000.0000.000
176A213ASP-1-0.795-0.85927.7270.1190.1190.0000.0000.0000.000
177A214SER0-0.017-0.03429.3590.0060.0060.0000.0000.0000.000
178A215ALA00.0050.01327.055-0.004-0.0040.0000.0000.0000.000
179A216SER00.012-0.00228.8460.0020.0020.0000.0000.0000.000
180A217TYR00.0210.01221.765-0.003-0.0030.0000.0000.0000.000
181A218ASN0-0.096-0.06824.080-0.014-0.0140.0000.0000.0000.000
182A219VAL00.0480.03418.7130.0170.0170.0000.0000.0000.000
183A220ASN0-0.0060.00918.3630.0290.0290.0000.0000.0000.000
184A221ILE00.0220.00816.3900.0700.0700.0000.0000.0000.000
185A222GLN0-0.0170.00214.846-0.008-0.0080.0000.0000.0000.000
186A223SER00.003-0.01413.6490.1080.1080.0000.0000.0000.000
187A224LEU0-0.017-0.00212.618-0.107-0.1070.0000.0000.0000.000
188A225LYS10.8890.95614.069-0.133-0.1330.0000.0000.0000.000
189A226PHE00.0270.01012.340-0.040-0.0400.0000.0000.0000.000
190A227ALA00.0180.01214.470-0.010-0.0100.0000.0000.0000.000
191A228GLN00.0350.01213.429-0.056-0.0560.0000.0000.0000.000
192A229PRO00.0330.02816.5050.0040.0040.0000.0000.0000.000
193A230LEU0-0.0060.02117.069-0.042-0.0420.0000.0000.0000.000
194A231VAL0-0.036-0.02216.2240.0150.0150.0000.0000.0000.000
195A232SER0-0.007-0.00816.950-0.033-0.0330.0000.0000.0000.000
196A233SER0-0.007-0.01015.670-0.012-0.0120.0000.0000.0000.000
197A234SER00.013-0.00318.1070.0260.0260.0000.0000.0000.000
198A235GLN0-0.043-0.01212.591-0.010-0.0100.0000.0000.0000.000
199A236TYR0-0.019-0.02415.071-0.034-0.0340.0000.0000.0000.000
200A237PRO0-0.031-0.00210.3200.0300.0300.0000.0000.0000.000
201A238ILE00.0450.0249.6660.0580.0580.0000.0000.0000.000