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: LN849

Calculation Name: 4OXP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OXP

Chain ID: A

ChEMBL ID:

UniProt ID: Q9A749

Base Structure: X-ray

Registration Date: 2023-09-24

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2325100.19473
FMO2-HF: Nuclear repulsion 2244740.04814
FMO2-HF: Total energy -80360.146589
FMO2-MP2: Total energy -80596.909672


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:36:LYS)


Summations of interaction energy for fragment #1(A:36:LYS)
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.
-90.652-93.2133.058-17.43-13.069-0.192
Interaction energy analysis for fragmet #1(A:36:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.835 / q_NPA : 0.891
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].
3A38LEU00.025-0.0042.539-14.678-10.2191.454-2.383-3.530-0.015
4A39ARG10.8530.9205.02928.35628.471-0.001-0.006-0.1080.000
5A40GLY00.0200.0237.968-1.670-1.6700.0000.0000.0000.000
6A41ASN00.0380.0223.1157.4577.8660.002-0.161-0.2500.000
7A42ILE0-0.058-0.0337.5894.2084.2080.0000.0000.0000.000
8A43TYR00.0440.0155.252-3.584-3.5840.0000.0000.0000.000
9A44LEU00.0140.02510.6562.4572.4570.0000.0000.0000.000
10A45ALA00.0220.00412.900-1.378-1.3780.0000.0000.0000.000
11A46LYS10.9470.97314.96018.53418.5340.0000.0000.0000.000
12A47VAL00.0070.00918.380-0.485-0.4850.0000.0000.0000.000
13A48THR0-0.005-0.00119.2510.8480.8480.0000.0000.0000.000
14A49ARG10.7960.87521.30214.01014.0100.0000.0000.0000.000
15A50VAL00.0010.00323.460-0.556-0.5560.0000.0000.0000.000
16A51GLU-1-0.803-0.89224.881-11.490-11.4900.0000.0000.0000.000
17A52PRO00.0170.00227.542-0.016-0.0160.0000.0000.0000.000
18A53SER00.0310.01029.8370.2070.2070.0000.0000.0000.000
19A54LEU0-0.027-0.01024.7390.0170.0170.0000.0000.0000.000
20A55GLN0-0.039-0.01227.262-0.294-0.2940.0000.0000.0000.000
21A56ALA00.0220.02623.185-0.313-0.3130.0000.0000.0000.000
22A57ALA00.0130.00822.0130.4840.4840.0000.0000.0000.000
23A58PHE0-0.030-0.00918.576-0.463-0.4630.0000.0000.0000.000
24A59ILE0-0.017-0.01615.0740.5660.5660.0000.0000.0000.000
25A60GLU-1-0.839-0.93013.991-22.168-22.1680.0000.0000.0000.000
26A61TYR0-0.073-0.0648.0700.5730.5730.0000.0000.0000.000
27A62GLY00.0480.0349.975-2.162-2.1620.0000.0000.0000.000
28A63GLY0-0.0030.0198.525-3.490-3.4900.0000.0000.0000.000
29A64ASN0-0.042-0.0286.9092.1672.1670.0000.0000.0000.000
30A65ARG10.8110.89410.82920.78420.7840.0000.0000.0000.000
31A66HIS0-0.023-0.00212.939-0.442-0.4420.0000.0000.0000.000
32A67GLY00.0370.02514.2380.2610.2610.0000.0000.0000.000
33A68PHE0-0.052-0.03514.9041.1671.1670.0000.0000.0000.000
34A69LEU00.0270.00417.656-0.705-0.7050.0000.0000.0000.000
35A70ALA00.0450.02519.7840.6850.6850.0000.0000.0000.000
36A71PHE00.0440.00723.292-0.342-0.3420.0000.0000.0000.000
37A72ASN00.024-0.00324.4710.1900.1900.0000.0000.0000.000
38A73GLU-1-0.827-0.89320.560-14.225-14.2250.0000.0000.0000.000
39A74ILE0-0.0100.01121.182-0.819-0.8190.0000.0000.0000.000
40A75HIS00.0140.01522.6840.6990.6990.0000.0000.0000.000
41A76PRO00.0450.00024.4420.0170.0170.0000.0000.0000.000
42A77ASP-1-0.827-0.92425.337-11.361-11.3610.0000.0000.0000.000
43A78TYR0-0.036-0.01219.1540.0300.0300.0000.0000.0000.000
44A79TYR0-0.0020.01425.5690.3030.3030.0000.0000.0000.000
45A80GLN0-0.010-0.01127.3900.5800.5800.0000.0000.0000.000
46A81ILE0-0.0170.00131.0980.2630.2630.0000.0000.0000.000
47A82PRO00.0290.00433.878-0.156-0.1560.0000.0000.0000.000
48A83VAL00.0470.02133.953-0.091-0.0910.0000.0000.0000.000
49A84ALA00.0650.02635.542-0.082-0.0820.0000.0000.0000.000
50A85ASP-1-0.791-0.85836.595-8.679-8.6790.0000.0000.0000.000
51A86ARG10.8620.91929.72410.57710.5770.0000.0000.0000.000
52A87GLU-1-0.805-0.89333.898-8.755-8.7550.0000.0000.0000.000
53A88ALA0-0.051-0.01236.037-0.009-0.0090.0000.0000.0000.000
54A89LEU0-0.041-0.01232.2650.0130.0130.0000.0000.0000.000
55A90MET0-0.075-0.01727.800-0.272-0.2720.0000.0000.0000.000
56A91ARG10.8630.92132.9588.4138.4130.0000.0000.0000.000
57A92ASP-1-0.820-0.88234.106-9.475-9.4750.0000.0000.0000.000
58A93ASP-1-0.858-0.91236.640-7.977-7.9770.0000.0000.0000.000
59A129ASP-1-0.833-0.91132.292-10.096-10.0960.0000.0000.0000.000
60A130VAL00.0660.01932.9330.0090.0090.0000.0000.0000.000
61A131GLU-1-0.783-0.84726.768-12.153-12.1530.0000.0000.0000.000
62A132GLU-1-0.729-0.83831.422-9.238-9.2380.0000.0000.0000.000
63A133GLU-1-0.810-0.86333.930-8.508-8.5080.0000.0000.0000.000
64A134LEU0-0.013-0.01127.896-0.098-0.0980.0000.0000.0000.000
65A135ALA0-0.028-0.00430.670-0.219-0.2190.0000.0000.0000.000
66A136ARG10.7800.84031.6678.5198.5190.0000.0000.0000.000
67A137ARG10.8570.91429.44910.44110.4410.0000.0000.0000.000
68A138LYS10.8010.89123.75713.25413.2540.0000.0000.0000.000
69A139ARG10.7980.85530.7679.2489.2480.0000.0000.0000.000
70A140ARG10.7360.85733.8669.0529.0520.0000.0000.0000.000
71A141LEU00.0120.00829.1910.1740.1740.0000.0000.0000.000
72A142MET0-0.025-0.01129.204-0.042-0.0420.0000.0000.0000.000
73A143ARG10.9310.97932.7108.4648.4640.0000.0000.0000.000
74A144LYS10.8190.90835.7748.9228.9220.0000.0000.0000.000
75A145TYR0-0.031-0.04532.8080.0900.0900.0000.0000.0000.000
76A146LYS10.8620.91932.6828.7208.7200.0000.0000.0000.000
77A147ILE00.0040.01325.1790.0590.0590.0000.0000.0000.000
78A148GLN00.0910.03229.779-0.405-0.4050.0000.0000.0000.000
79A149GLU-1-0.837-0.91231.388-8.766-8.7660.0000.0000.0000.000
80A150VAL0-0.038-0.00329.2840.1390.1390.0000.0000.0000.000
81A151ILE00.0230.03124.484-0.326-0.3260.0000.0000.0000.000
82A152ARG10.8480.91626.61910.32010.3200.0000.0000.0000.000
83A153ARG10.9580.96624.79410.99910.9990.0000.0000.0000.000
84A154ARG10.9250.95122.83712.24812.2480.0000.0000.0000.000
85A155GLN00.0370.04022.7770.0430.0430.0000.0000.0000.000
86A156ILE00.0270.01118.073-0.530-0.5300.0000.0000.0000.000
87A157MET0-0.070-0.03418.2331.0581.0580.0000.0000.0000.000
88A158LEU00.0700.04714.122-1.009-1.0090.0000.0000.0000.000
89A159VAL0-0.069-0.04312.9131.3401.3400.0000.0000.0000.000
90A160GLN00.0230.00611.6120.3000.3000.0000.0000.0000.000
91A161VAL0-0.0050.0048.4462.6312.6310.0000.0000.0000.000
92A162VAL00.0130.01111.398-0.260-0.2600.0000.0000.0000.000
93A163LYS10.7490.85512.22221.64221.6420.0000.0000.0000.000
94A164GLU-1-0.712-0.8597.024-34.323-34.3230.0000.0000.0000.000
95A165GLU-1-0.762-0.8627.760-23.665-23.6650.0000.0000.0000.000
96A166ARG10.9430.9568.23319.42719.4270.0000.0000.0000.000
97A167GLY00.0560.03810.1171.4431.4430.0000.0000.0000.000
98A168ASN00.0540.02312.017-1.150-1.1500.0000.0000.0000.000
99A169LYS10.9400.97113.77015.60815.6080.0000.0000.0000.000
100A170GLY00.0900.04612.585-1.040-1.0400.0000.0000.0000.000
101A171ALA00.0200.02810.1640.9550.9550.0000.0000.0000.000
102A172VAL0-0.068-0.03712.0811.7261.7260.0000.0000.0000.000
103A173LEU00.0100.01312.347-1.330-1.3300.0000.0000.0000.000
104A174THR0-0.003-0.01515.6991.5171.5170.0000.0000.0000.000
105A175THR00.015-0.00516.297-0.887-0.8870.0000.0000.0000.000
106A176TYR0-0.024-0.00918.6040.5250.5250.0000.0000.0000.000
107A177LEU0-0.0150.00214.807-0.222-0.2220.0000.0000.0000.000
108A178SER0-0.069-0.04215.6951.2001.2000.0000.0000.0000.000
109A179LEU00.0740.04013.948-1.358-1.3580.0000.0000.0000.000
110A180ALA00.008-0.00314.0741.8301.8300.0000.0000.0000.000
111A181GLY00.0900.06215.397-0.707-0.7070.0000.0000.0000.000
112A182ARG10.9080.93917.99914.24014.2400.0000.0000.0000.000
113A183TYR0-0.097-0.10719.7570.2960.2960.0000.0000.0000.000
114A184GLY0-0.008-0.00821.1900.7620.7620.0000.0000.0000.000
115A185VAL0-0.0150.00917.776-0.792-0.7920.0000.0000.0000.000
116A186LEU00.0280.02119.5071.0121.0120.0000.0000.0000.000
117A187MET0-0.011-0.01119.440-1.073-1.0730.0000.0000.0000.000
118A188PRO00.0380.00118.5230.8560.8560.0000.0000.0000.000
119A189ASN00.0170.01220.4830.7260.7260.0000.0000.0000.000
120A190THR0-0.029-0.02722.2570.2430.2430.0000.0000.0000.000
121A191ALA00.0250.02224.7540.0610.0610.0000.0000.0000.000
122A192ARG10.8350.89125.96212.44612.4460.0000.0000.0000.000
123A193GLY00.0380.04029.1140.2480.2480.0000.0000.0000.000
124A194GLY0-0.041-0.01228.249-0.024-0.0240.0000.0000.0000.000
125A195GLY0-0.030-0.02928.3350.5640.5640.0000.0000.0000.000
126A196ILE0-0.045-0.01628.023-0.295-0.2950.0000.0000.0000.000
127A197SER00.0370.02224.7400.1670.1670.0000.0000.0000.000
128A198ARG10.8310.86026.81211.40611.4060.0000.0000.0000.000
129A199LYS10.9600.98226.12911.80211.8020.0000.0000.0000.000
130A200ILE00.0040.02129.2630.1960.1960.0000.0000.0000.000
131A201THR0-0.022-0.02132.1090.2850.2850.0000.0000.0000.000
132A202ALA00.0550.03234.4720.2930.2930.0000.0000.0000.000
133A203VAL00.0550.01336.310-0.138-0.1380.0000.0000.0000.000
134A204THR00.0450.02038.674-0.002-0.0020.0000.0000.0000.000
135A205ASP-1-0.774-0.87733.457-9.158-9.1580.0000.0000.0000.000
136A206ARG10.9390.98534.1678.6508.6500.0000.0000.0000.000
137A207LYS10.9670.98835.2087.5817.5810.0000.0000.0000.000
138A208ARG10.8540.92232.0329.4919.4910.0000.0000.0000.000
139A209LEU0-0.012-0.01829.877-0.066-0.0660.0000.0000.0000.000
140A210LYS10.9190.97133.0459.4799.4790.0000.0000.0000.000
141A211SER00.0140.01834.649-0.032-0.0320.0000.0000.0000.000
142A212VAL0-0.028-0.01331.0900.0160.0160.0000.0000.0000.000
143A213VAL0-0.001-0.01929.242-0.157-0.1570.0000.0000.0000.000
144A214GLN00.0250.01431.669-0.221-0.2210.0000.0000.0000.000
145A215SER00.005-0.00134.700-0.035-0.0350.0000.0000.0000.000
146A216LEU0-0.065-0.03028.245-0.097-0.0970.0000.0000.0000.000
147A217ASP-1-0.890-0.92731.194-9.452-9.4520.0000.0000.0000.000
148A218VAL0-0.059-0.02127.365-0.193-0.1930.0000.0000.0000.000
149A219PRO00.0210.00927.3220.2550.2550.0000.0000.0000.000
150A220GLN00.0580.01627.877-0.454-0.4540.0000.0000.0000.000
151A221GLY00.0180.02027.8470.2490.2490.0000.0000.0000.000
152A222MET0-0.0470.00623.976-0.609-0.6090.0000.0000.0000.000
153A223GLY00.0550.02624.8340.6420.6420.0000.0000.0000.000
154A224LEU00.0240.01122.980-0.561-0.5610.0000.0000.0000.000
155A225ILE0-0.012-0.00123.1360.6860.6860.0000.0000.0000.000
156A226VAL00.0030.00623.409-0.567-0.5670.0000.0000.0000.000
157A227ARG10.8730.91817.95917.03517.0350.0000.0000.0000.000
158A228THR00.023-0.00723.9640.2580.2580.0000.0000.0000.000
159A229ALA00.0350.02922.8370.4700.4700.0000.0000.0000.000
160A230GLY00.0410.00924.7940.1660.1660.0000.0000.0000.000
161A231ALA0-0.042-0.02426.8780.4450.4450.0000.0000.0000.000
162A232LYS10.8520.91829.2539.6939.6930.0000.0000.0000.000
163A233ARG10.8640.95526.88211.51111.5110.0000.0000.0000.000
164A234THR00.0540.00630.0000.3810.3810.0000.0000.0000.000
165A235LYS10.9790.98630.9308.4248.4240.0000.0000.0000.000
166A236ALA00.0520.02531.629-0.020-0.0200.0000.0000.0000.000
167A237GLU-1-0.720-0.82226.314-12.192-12.1920.0000.0000.0000.000
168A238ILE00.0100.00326.148-0.497-0.4970.0000.0000.0000.000
169A239LYS10.8320.91526.2259.6209.6200.0000.0000.0000.000
170A240ARG10.8640.91325.30511.13611.1360.0000.0000.0000.000
171A241ASP-1-0.790-0.88521.305-15.707-15.7070.0000.0000.0000.000
172A242TYR00.021-0.00721.977-0.784-0.7840.0000.0000.0000.000
173A243GLU-1-0.750-0.84923.333-11.971-11.9710.0000.0000.0000.000
174A244TYR0-0.037-0.00614.5690.1950.1950.0000.0000.0000.000
175A245LEU00.015-0.00117.531-0.557-0.5570.0000.0000.0000.000
176A246LEU0-0.007-0.00619.489-0.420-0.4200.0000.0000.0000.000
177A247ARG10.8880.92720.71713.24913.2490.0000.0000.0000.000
178A248LEU0-0.0030.01813.135-0.129-0.1290.0000.0000.0000.000
179A249TRP00.0300.00416.389-1.133-1.1330.0000.0000.0000.000
180A250GLU-1-0.835-0.90618.387-14.084-14.0840.0000.0000.0000.000
181A251ASN00.0180.00816.0280.6750.6750.0000.0000.0000.000
182A252ILE0-0.0200.00112.972-0.578-0.5780.0000.0000.0000.000
183A253ARG10.8290.89415.43813.87813.8780.0000.0000.0000.000
184A254GLU-1-0.845-0.90118.642-14.880-14.8800.0000.0000.0000.000
185A255ASN0-0.001-0.01712.2661.1341.1340.0000.0000.0000.000
186A256THR0-0.118-0.06915.358-0.175-0.1750.0000.0000.0000.000
187A257LEU0-0.038-0.01316.7710.4020.4020.0000.0000.0000.000
188A258HIS0-0.059-0.01717.5610.7000.7000.0000.0000.0000.000
189A259SER0-0.026-0.01414.372-1.458-1.4580.0000.0000.0000.000
190A260ILE0-0.010-0.02215.7701.1931.1930.0000.0000.0000.000
191A261ALA0-0.044-0.03115.638-0.865-0.8650.0000.0000.0000.000
192A262PRO0-0.078-0.02412.284-0.035-0.0350.0000.0000.0000.000
193A263ALA00.0640.03110.594-0.583-0.5830.0000.0000.0000.000
194A264LEU0-0.019-0.0083.9381.0681.1980.000-0.019-0.1100.000
195A265ILE0-0.031-0.0128.0441.3221.3220.0000.0000.0000.000
196A266TYR0-0.018-0.0488.9442.3662.3660.0000.0000.0000.000
197A267GLU-1-0.757-0.8411.709-165.608-173.27931.603-14.861-9.071-0.177
198A268GLU-1-0.903-0.9356.068-23.747-23.7470.0000.0000.0000.000
199A269GLU-1-0.968-0.9856.348-36.253-36.2530.0000.0000.0000.000
200A270ASP-1-1.027-0.9958.279-26.323-26.3230.0000.0000.0000.000