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: 72NRK

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2243859.424564
FMO2-HF: Nuclear repulsion 2166767.91077
FMO2-HF: Total energy -77091.513794
FMO2-MP2: Total energy -77317.110877


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.
-22.164-10.2114.537-7.07-9.417-0.001
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 : -0.048 / q_NPA : -0.045
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].
3A40LEU00.0210.0202.457-12.807-6.8051.153-3.516-3.6390.026
4A41LEU00.0100.0053.5002.1632.6470.066-0.208-0.3420.000
5A42SER0-0.052-0.0264.298-1.071-0.930-0.001-0.015-0.1250.000
6A43ILE0-0.013-0.0106.572-0.854-0.8540.0000.0000.0000.000
7A44ASN0-0.029-0.0239.5090.0830.0830.0000.0000.0000.000
8A45GLU-1-0.831-0.92011.9330.3640.3640.0000.0000.0000.000
9A46ILE0-0.044-0.02712.496-0.046-0.0460.0000.0000.0000.000
10A47ASP-1-0.851-0.91816.6760.0120.0120.0000.0000.0000.000
11A48ASN0-0.071-0.04319.344-0.057-0.0570.0000.0000.0000.000
12A49PRO00.0970.02717.352-0.029-0.0290.0000.0000.0000.000
13A50ASN0-0.0230.01016.961-0.107-0.1070.0000.0000.0000.000
14A51TYR00.024-0.00315.423-0.049-0.0490.0000.0000.0000.000
15A52ILE00.0100.01011.644-0.021-0.0210.0000.0000.0000.000
16A53LEU0-0.007-0.00110.526-0.164-0.1640.0000.0000.0000.000
17A54GLN00.0420.00410.334-0.268-0.2680.0000.0000.0000.000
18A55ALA00.0640.0309.730-0.121-0.1210.0000.0000.0000.000
19A56ILE0-0.011-0.0025.6000.0310.0310.0000.0000.0000.000
20A57MET0-0.037-0.0205.445-1.484-1.4840.0000.0000.0000.000
21A58LEU0-0.005-0.0096.781-0.370-0.3700.0000.0000.0000.000
22A59ALA00.0450.0143.533-0.1690.2440.005-0.096-0.3210.000
23A60ASN0-0.069-0.0532.447-11.026-8.8111.840-1.803-2.252-0.020
24A61ALA00.0100.0253.4131.5711.5680.0040.128-0.1280.000
25A62PHE00.048-0.0095.9030.4160.4160.0000.0000.0000.000
26A63GLN00.0590.0442.3971.7904.3391.472-1.517-2.504-0.007
27A64ASN0-0.080-0.0454.4160.6440.723-0.001-0.016-0.0620.000
28A65ALA0-0.010-0.0247.611-0.062-0.0620.0000.0000.0000.000
29A66LEU0-0.0210.0045.534-0.052-0.0520.0000.0000.0000.000
30A67VAL0-0.052-0.0249.421-0.352-0.3520.0000.0000.0000.000
31A68PRO00.0260.01112.4340.1590.1590.0000.0000.0000.000
32A69THR00.0420.03114.287-0.044-0.0440.0000.0000.0000.000
33A70SER00.0010.00016.751-0.066-0.0660.0000.0000.0000.000
34A71THR00.0650.01719.9080.0240.0240.0000.0000.0000.000
35A72ASP-1-0.883-0.95021.2350.3470.3470.0000.0000.0000.000
36A73PHE0-0.117-0.05616.810-0.034-0.0340.0000.0000.0000.000
37A74GLY00.0250.00919.5010.0000.0000.0000.0000.0000.000
38A75ASP-1-0.937-0.95515.4460.7260.7260.0000.0000.0000.000
39A76ALA00.0230.00512.9810.0590.0590.0000.0000.0000.000
40A77LEU00.0010.0227.869-0.080-0.0800.0000.0000.0000.000
41A78ARG10.8480.93110.735-0.926-0.9260.0000.0000.0000.000
42A79PHE00.0340.0158.802-0.166-0.1660.0000.0000.0000.000
43A80SER00.0050.01210.375-0.261-0.2610.0000.0000.0000.000
44A81MET00.0180.00413.179-0.033-0.0330.0000.0000.0000.000
45A82PRO00.0340.01015.443-0.082-0.0820.0000.0000.0000.000
46A83LYS10.9280.97711.818-0.486-0.4860.0000.0000.0000.000
47A84GLY00.010-0.00811.722-0.092-0.0920.0000.0000.0000.000
48A85LEU0-0.031-0.02212.680-0.135-0.1350.0000.0000.0000.000
49A86GLU-1-0.931-0.96715.5120.1490.1490.0000.0000.0000.000
50A87ILE0-0.039-0.0179.144-0.102-0.1020.0000.0000.0000.000
51A88ALA00.0090.01412.607-0.168-0.1680.0000.0000.0000.000
52A89ASN0-0.033-0.01613.775-0.058-0.0580.0000.0000.0000.000
53A90THR0-0.112-0.06313.148-0.081-0.0810.0000.0000.0000.000
54A91ILE0-0.055-0.00510.152-0.115-0.1150.0000.0000.0000.000
55A92THR0-0.0130.02113.7670.1210.1210.0000.0000.0000.000
56A93PRO0-0.005-0.03114.589-0.111-0.1110.0000.0000.0000.000
57A94MET00.0220.00616.586-0.005-0.0050.0000.0000.0000.000
58A95GLY00.0300.02316.9590.0000.0000.0000.0000.0000.000
59A96ALA0-0.036-0.01817.9110.0110.0110.0000.0000.0000.000
60A97VAL00.0060.00716.1800.0250.0250.0000.0000.0000.000
61A98VAL0-0.045-0.02518.449-0.015-0.0150.0000.0000.0000.000
62A99SER0-0.045-0.02419.220-0.006-0.0060.0000.0000.0000.000
63A100TYR00.021-0.00718.3590.0320.0320.0000.0000.0000.000
64A101VAL0-0.046-0.01617.865-0.050-0.0500.0000.0000.0000.000
65A102ASP-1-0.828-0.92418.3330.6840.6840.0000.0000.0000.000
66A103GLN0-0.0080.00320.344-0.063-0.0630.0000.0000.0000.000
67A104ASN00.0290.02721.3870.0740.0740.0000.0000.0000.000
68A105VAL00.0090.01422.922-0.043-0.0430.0000.0000.0000.000
69A106THR0-0.041-0.01924.5880.0180.0180.0000.0000.0000.000
70A107GLN00.019-0.02027.204-0.009-0.0090.0000.0000.0000.000
71A108THR0-0.012-0.01029.1690.0060.0060.0000.0000.0000.000
72A109ASN0-0.033-0.02131.998-0.001-0.0010.0000.0000.0000.000
73A110ASN00.0380.04330.390-0.017-0.0170.0000.0000.0000.000
74A111GLN00.004-0.00329.9630.0130.0130.0000.0000.0000.000
75A112VAL00.0220.02023.6020.0180.0180.0000.0000.0000.000
76A113SER00.0190.01025.0140.0380.0380.0000.0000.0000.000
77A114VAL0-0.043-0.01326.3190.0080.0080.0000.0000.0000.000
78A115MET0-0.0170.01922.2290.0120.0120.0000.0000.0000.000
79A116ILE00.0010.00820.9280.0290.0290.0000.0000.0000.000
80A117ASN00.012-0.01322.3380.0360.0360.0000.0000.0000.000
81A118LYS10.9250.96824.718-0.366-0.3660.0000.0000.0000.000
82A119VAL00.0330.01218.1230.0020.0020.0000.0000.0000.000
83A120LEU00.0040.00219.7570.0290.0290.0000.0000.0000.000
84A121GLU-1-0.972-0.97421.4570.3340.3340.0000.0000.0000.000
85A122VAL0-0.021-0.00919.937-0.020-0.0200.0000.0000.0000.000
86A123LEU00.0130.00015.655-0.001-0.0010.0000.0000.0000.000
87A124LYS10.9790.98819.167-0.380-0.3800.0000.0000.0000.000
88A125THR0-0.040-0.00521.883-0.057-0.0570.0000.0000.0000.000
89A126VAL0-0.0400.00617.106-0.041-0.0410.0000.0000.0000.000
90A127LEU00.011-0.00516.384-0.038-0.0380.0000.0000.0000.000
91A128GLY00.0170.01619.988-0.059-0.0590.0000.0000.0000.000
92A129VAL00.013-0.00123.3320.0190.0190.0000.0000.0000.000
93A130ALA00.0310.00625.5150.0080.0080.0000.0000.0000.000
94A131LEU00.0120.02918.323-0.006-0.0060.0000.0000.0000.000
95A132SER00.0480.01020.9200.0430.0430.0000.0000.0000.000
96A133GLY0-0.042-0.00721.9370.0110.0110.0000.0000.0000.000
97A134SER0-0.076-0.06521.478-0.015-0.0150.0000.0000.0000.000
98A135VAL00.0140.01717.287-0.014-0.0140.0000.0000.0000.000
99A136ILE00.0020.00919.2840.0660.0660.0000.0000.0000.000
100A137ASP-1-0.856-0.91921.1290.3230.3230.0000.0000.0000.000
101A138GLN0-0.001-0.02716.2620.0500.0500.0000.0000.0000.000
102A139LEU0-0.037-0.00916.4860.1170.1170.0000.0000.0000.000
103A140THR0-0.022-0.02617.5510.0620.0620.0000.0000.0000.000
104A141ALA00.000-0.00717.6750.0230.0230.0000.0000.0000.000
105A142ALA0-0.0010.00513.3700.0370.0370.0000.0000.0000.000
106A143VAL00.0140.01614.9420.1030.1030.0000.0000.0000.000
107A144THR0-0.012-0.01317.093-0.036-0.0360.0000.0000.0000.000
108A145ASN0-0.031-0.00115.286-0.104-0.1040.0000.0000.0000.000
109A146THR00.0220.02014.5070.1310.1310.0000.0000.0000.000
110A147PHE0-0.023-0.01915.777-0.008-0.0080.0000.0000.0000.000
111A148THR0-0.041-0.02919.098-0.087-0.0870.0000.0000.0000.000
112A149ASN00.013-0.01518.2450.0290.0290.0000.0000.0000.000
113A150LEU00.0630.05216.2980.0150.0150.0000.0000.0000.000
114A151ASN00.0470.01417.0650.0210.0210.0000.0000.0000.000
115A152THR0-0.050-0.04116.251-0.040-0.0400.0000.0000.0000.000
116A153GLN00.0300.04613.0560.1630.1630.0000.0000.0000.000
117A154LYS10.8320.94812.594-0.274-0.2740.0000.0000.0000.000
118A155ASN00.004-0.01712.2390.0720.0720.0000.0000.0000.000
119A156GLU-1-0.909-0.9338.6080.1920.1920.0000.0000.0000.000
120A157ALA00.001-0.0014.2350.1070.180-0.001-0.027-0.0440.000
121A158TRP00.008-0.0066.0390.6850.6850.0000.0000.0000.000
122A159ILE0-0.072-0.0247.6350.0540.0540.0000.0000.0000.000
123A160PHE00.0180.0197.244-0.084-0.0840.0000.0000.0000.000
124A161TRP0-0.011-0.01712.595-0.061-0.0610.0000.0000.0000.000
125A162GLY00.002-0.00916.2900.0070.0070.0000.0000.0000.000
126A163LYS10.8460.91818.397-0.456-0.4560.0000.0000.0000.000
127A164GLU-1-0.946-0.96720.8730.4740.4740.0000.0000.0000.000
128A165THR0-0.015-0.01123.982-0.028-0.0280.0000.0000.0000.000
129A166ALA00.026-0.00227.7450.0070.0070.0000.0000.0000.000
130A167ASN0-0.026-0.02230.0250.0040.0040.0000.0000.0000.000
131A168GLN0-0.073-0.02624.991-0.029-0.0290.0000.0000.0000.000
132A169THR00.023-0.00620.932-0.005-0.0050.0000.0000.0000.000
133A170ASN0-0.037-0.03220.082-0.014-0.0140.0000.0000.0000.000
134A171TYR0-0.019-0.01815.209-0.060-0.0600.0000.0000.0000.000
135A172THR00.002-0.02711.842-0.079-0.0790.0000.0000.0000.000
136A173TYR0-0.007-0.03711.2220.0810.0810.0000.0000.0000.000
137A174ASN00.0090.0116.992-0.579-0.5790.0000.0000.0000.000
138A175VAL00.0470.0387.3990.7090.7090.0000.0000.0000.000
139A176LEU0-0.010-0.0095.410-0.173-0.1730.0000.0000.0000.000
140A177PHE00.0030.0217.913-0.036-0.0360.0000.0000.0000.000
141A178ALA00.0170.0109.635-0.144-0.1440.0000.0000.0000.000
142A179ILE0-0.014-0.00511.637-0.061-0.0610.0000.0000.0000.000
143A180GLN00.0760.02115.408-0.092-0.0920.0000.0000.0000.000
144A181ASN00.0830.04017.897-0.018-0.0180.0000.0000.0000.000
145A182ALA00.0600.01021.377-0.011-0.0110.0000.0000.0000.000
146A183GLN0-0.054-0.02222.932-0.015-0.0150.0000.0000.0000.000
147A184THR0-0.069-0.00918.7810.0220.0220.0000.0000.0000.000
148A185GLY0-0.0060.00721.846-0.021-0.0210.0000.0000.0000.000
149A186GLY00.002-0.01322.399-0.017-0.0170.0000.0000.0000.000
150A187VAL0-0.034-0.01818.746-0.038-0.0380.0000.0000.0000.000
151A188MET0-0.0290.00812.724-0.006-0.0060.0000.0000.0000.000
152A189TYR00.004-0.01615.299-0.009-0.0090.0000.0000.0000.000
153A190CYS0-0.0060.0079.2440.0740.0740.0000.0000.0000.000
154A191VAL0-0.027-0.02311.768-0.097-0.0970.0000.0000.0000.000
155A192PRO00.0180.0198.4670.3490.3490.0000.0000.0000.000
156A193VAL0-0.017-0.0099.515-0.515-0.5150.0000.0000.0000.000
157A194GLY00.0020.01610.1320.4940.4940.0000.0000.0000.000
158A195PHE0-0.025-0.02212.009-0.356-0.3560.0000.0000.0000.000
159A196GLU-1-0.925-0.97514.4190.8700.8700.0000.0000.0000.000
160A197ILE0-0.027-0.00716.203-0.119-0.1190.0000.0000.0000.000
161A198LYS10.9791.00519.375-0.500-0.5000.0000.0000.0000.000
162A199VAL00.0490.02522.409-0.013-0.0130.0000.0000.0000.000
163A200SER0-0.034-0.02924.687-0.009-0.0090.0000.0000.0000.000
164A201ALA00.0190.01326.790-0.029-0.0290.0000.0000.0000.000
165A202VAL00.0190.05426.2080.0300.0300.0000.0000.0000.000
166A203LYS11.0281.01617.906-0.519-0.5190.0000.0000.0000.000
167A204GLU-1-0.915-0.97023.2610.3270.3270.0000.0000.0000.000
168A205GLN00.0210.00124.848-0.002-0.0020.0000.0000.0000.000
169A206VAL00.0040.01221.1900.0090.0090.0000.0000.0000.000
170A207LEU0-0.110-0.05518.8580.0290.0290.0000.0000.0000.000
171A208PHE0-0.076-0.05521.8300.0000.0000.0000.0000.0000.000
172A209PHE00.0150.03823.437-0.023-0.0230.0000.0000.0000.000
173A210THR0-0.030-0.02023.9700.0210.0210.0000.0000.0000.000
174A211ILE00.044-0.01324.1540.0040.0040.0000.0000.0000.000
175A212GLN0-0.012-0.00926.509-0.002-0.0020.0000.0000.0000.000
176A213ASP-1-0.795-0.87827.7900.2960.2960.0000.0000.0000.000
177A214SER0-0.017-0.03429.4360.0020.0020.0000.0000.0000.000
178A215ALA0-0.0140.00427.264-0.002-0.0020.0000.0000.0000.000
179A216SER00.0100.00529.027-0.005-0.0050.0000.0000.0000.000
180A217TYR00.0210.00821.9210.0260.0260.0000.0000.0000.000
181A218ASN0-0.086-0.06824.276-0.030-0.0300.0000.0000.0000.000
182A219VAL00.0430.03518.8600.0310.0310.0000.0000.0000.000
183A220ASN0-0.0020.01418.7200.0230.0230.0000.0000.0000.000
184A221ILE00.017-0.00116.3530.1070.1070.0000.0000.0000.000
185A222GLN00.0000.00614.950-0.078-0.0780.0000.0000.0000.000
186A223SER00.0040.00013.6510.1590.1590.0000.0000.0000.000
187A224LEU00.0030.00612.617-0.165-0.1650.0000.0000.0000.000
188A225LYS10.8880.95414.377-0.225-0.2250.0000.0000.0000.000
189A226PHE00.0170.00912.580-0.081-0.0810.0000.0000.0000.000
190A227ALA00.0300.01814.7330.0220.0220.0000.0000.0000.000
191A228GLN00.0350.01913.337-0.061-0.0610.0000.0000.0000.000
192A229PRO00.0380.02616.6520.0220.0220.0000.0000.0000.000
193A230LEU0-0.0080.01817.265-0.064-0.0640.0000.0000.0000.000
194A231VAL0-0.033-0.02916.2450.0040.0040.0000.0000.0000.000
195A232SER0-0.034-0.01717.008-0.057-0.0570.0000.0000.0000.000
196A233SER00.020-0.00516.125-0.060-0.0600.0000.0000.0000.000
197A234SER00.006-0.00118.4180.0510.0510.0000.0000.0000.000
198A235GLN0-0.0330.00512.9340.0770.0770.0000.0000.0000.000
199A236TYR0-0.036-0.03315.429-0.046-0.0460.0000.0000.0000.000
200A237PRO0-0.034-0.00210.6290.0240.0240.0000.0000.0000.000
201A238ILE00.0440.0219.6720.1200.1200.0000.0000.0000.000