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: 3JYRL

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2321501.804651
FMO2-HF: Nuclear repulsion 2241142.848915
FMO2-HF: Total energy -80358.955736
FMO2-MP2: Total energy -80595.877933


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.
-90.622-87.63725.827-16.091-12.722-0.184
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 : 0.838 / q_NPA : 0.894
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].
3A38LEU00.0450.0022.519-12.165-7.7361.078-2.131-3.376-0.005
4A39ARG10.8730.9335.01928.78028.894-0.001-0.005-0.1080.000
5A40GLY00.0200.0138.165-1.105-1.1050.0000.0000.0000.000
6A41ASN00.0460.0242.8358.3658.9710.011-0.280-0.338-0.001
7A42ILE0-0.077-0.0457.3064.8514.8510.0000.0000.0000.000
8A43TYR00.0370.0184.933-3.128-3.1280.0000.0000.0000.000
9A44LEU00.0040.01510.4722.2892.2890.0000.0000.0000.000
10A45ALA00.0270.00613.313-0.818-0.8180.0000.0000.0000.000
11A46LYS10.9620.98014.94818.83118.8310.0000.0000.0000.000
12A47VAL0-0.030-0.00318.389-0.407-0.4070.0000.0000.0000.000
13A48THR0-0.0020.00919.2250.8120.8120.0000.0000.0000.000
14A49ARG10.8090.87321.32213.95313.9530.0000.0000.0000.000
15A50VAL00.0010.00623.524-0.488-0.4880.0000.0000.0000.000
16A51GLU-1-0.822-0.90424.847-11.325-11.3250.0000.0000.0000.000
17A52PRO00.0110.00027.391-0.051-0.0510.0000.0000.0000.000
18A53SER00.0200.00829.7690.2390.2390.0000.0000.0000.000
19A54LEU0-0.011-0.00824.4630.0380.0380.0000.0000.0000.000
20A55GLN0-0.0230.00127.184-0.245-0.2450.0000.0000.0000.000
21A56ALA00.0130.01322.856-0.315-0.3150.0000.0000.0000.000
22A57ALA00.0250.02021.9720.4480.4480.0000.0000.0000.000
23A58PHE0-0.011-0.00318.337-0.510-0.5100.0000.0000.0000.000
24A59ILE00.001-0.00714.9740.5960.5960.0000.0000.0000.000
25A60GLU-1-0.860-0.94613.585-22.419-22.4190.0000.0000.0000.000
26A61TYR0-0.029-0.0307.9020.5550.5550.0000.0000.0000.000
27A62GLY00.0470.0259.573-2.345-2.3450.0000.0000.0000.000
28A63GLY0-0.0170.0178.071-2.685-2.6850.0000.0000.0000.000
29A64ASN0-0.055-0.0396.8772.5592.5590.0000.0000.0000.000
30A65ARG10.8600.94410.54520.74620.7460.0000.0000.0000.000
31A66HIS0-0.002-0.00212.596-0.490-0.4900.0000.0000.0000.000
32A67GLY00.0090.00214.044-0.120-0.1200.0000.0000.0000.000
33A68PHE0-0.066-0.04614.6051.1951.1950.0000.0000.0000.000
34A69LEU00.017-0.00417.616-0.607-0.6070.0000.0000.0000.000
35A70ALA00.0500.04019.6660.7200.7200.0000.0000.0000.000
36A71PHE00.0780.02222.963-0.376-0.3760.0000.0000.0000.000
37A72ASN00.009-0.00624.6070.1130.1130.0000.0000.0000.000
38A73GLU-1-0.862-0.92820.344-14.373-14.3730.0000.0000.0000.000
39A74ILE0-0.028-0.00221.151-0.774-0.7740.0000.0000.0000.000
40A75HIS00.0110.03122.4340.7480.7480.0000.0000.0000.000
41A76PRO00.1010.01724.249-0.006-0.0060.0000.0000.0000.000
42A77ASP-1-0.864-0.93424.907-11.621-11.6210.0000.0000.0000.000
43A78TYR0-0.023-0.01619.178-0.157-0.1570.0000.0000.0000.000
44A79TYR0-0.021-0.00525.3320.2280.2280.0000.0000.0000.000
45A80GLN0-0.045-0.02727.1740.5540.5540.0000.0000.0000.000
46A81ILE0-0.0070.00130.7770.2420.2420.0000.0000.0000.000
47A82PRO00.0580.02633.780-0.140-0.1400.0000.0000.0000.000
48A83VAL00.0760.02533.776-0.112-0.1120.0000.0000.0000.000
49A84ALA00.0170.00435.411-0.087-0.0870.0000.0000.0000.000
50A85ASP-1-0.862-0.90036.003-8.595-8.5950.0000.0000.0000.000
51A86ARG10.8490.90829.31810.75310.7530.0000.0000.0000.000
52A87GLU-1-0.795-0.88433.271-8.906-8.9060.0000.0000.0000.000
53A88ALA0-0.040-0.00535.6040.0190.0190.0000.0000.0000.000
54A89LEU0-0.024-0.01332.4770.0760.0760.0000.0000.0000.000
55A90MET0-0.057-0.01227.991-0.223-0.2230.0000.0000.0000.000
56A91ARG10.8480.90132.9968.4558.4550.0000.0000.0000.000
57A92ASP-1-0.778-0.87033.928-9.390-9.3900.0000.0000.0000.000
58A93ASP-1-0.888-0.90836.416-7.898-7.8980.0000.0000.0000.000
59A129ASP-1-0.829-0.91632.379-10.075-10.0750.0000.0000.0000.000
60A130VAL00.0280.01133.5320.0190.0190.0000.0000.0000.000
61A131GLU-1-0.767-0.84427.345-11.968-11.9680.0000.0000.0000.000
62A132GLU-1-0.738-0.86131.681-9.224-9.2240.0000.0000.0000.000
63A133GLU-1-0.806-0.86134.355-8.501-8.5010.0000.0000.0000.000
64A134LEU0-0.020-0.01527.948-0.106-0.1060.0000.0000.0000.000
65A135ALA0-0.050-0.01930.854-0.185-0.1850.0000.0000.0000.000
66A136ARG10.7990.84731.8218.4368.4360.0000.0000.0000.000
67A137ARG10.8380.91629.61110.32310.3230.0000.0000.0000.000
68A138LYS10.8340.91523.64213.21813.2180.0000.0000.0000.000
69A139ARG10.8270.88830.6949.2909.2900.0000.0000.0000.000
70A140ARG10.7610.86733.5689.0359.0350.0000.0000.0000.000
71A141LEU00.000-0.00229.5400.1870.1870.0000.0000.0000.000
72A142MET0-0.035-0.00529.018-0.085-0.0850.0000.0000.0000.000
73A143ARG10.9370.97732.6988.3648.3640.0000.0000.0000.000
74A144LYS10.8380.93435.7058.8558.8550.0000.0000.0000.000
75A145TYR0-0.039-0.04032.6770.1100.1100.0000.0000.0000.000
76A146LYS10.8830.93332.7728.6698.6690.0000.0000.0000.000
77A147ILE00.0150.01425.109-0.011-0.0110.0000.0000.0000.000
78A148GLN00.0610.01529.624-0.421-0.4210.0000.0000.0000.000
79A149GLU-1-0.846-0.91531.285-8.738-8.7380.0000.0000.0000.000
80A150VAL0-0.0190.01828.9370.1150.1150.0000.0000.0000.000
81A151ILE00.0280.02824.478-0.357-0.3570.0000.0000.0000.000
82A152ARG10.8730.92926.65710.42010.4200.0000.0000.0000.000
83A153ARG10.9510.95724.63211.05811.0580.0000.0000.0000.000
84A154ARG10.9090.94022.74412.37912.3790.0000.0000.0000.000
85A155GLN00.0320.04122.7880.1410.1410.0000.0000.0000.000
86A156ILE00.0250.00517.971-0.499-0.4990.0000.0000.0000.000
87A157MET0-0.045-0.01518.1021.0401.0400.0000.0000.0000.000
88A158LEU00.0360.03213.713-1.021-1.0210.0000.0000.0000.000
89A159VAL0-0.070-0.03712.4301.2751.2750.0000.0000.0000.000
90A160GLN00.0310.00511.3140.1410.1410.0000.0000.0000.000
91A161VAL0-0.025-0.0088.1632.5322.5320.0000.0000.0000.000
92A162VAL00.0030.01011.1610.0340.0340.0000.0000.0000.000
93A163LYS10.7980.88812.66520.88520.8850.0000.0000.0000.000
94A164GLU-1-0.741-0.8767.043-34.984-34.9840.0000.0000.0000.000
95A165GLU-1-0.833-0.9068.320-24.298-24.2980.0000.0000.0000.000
96A166ARG10.9470.9608.75418.76418.7640.0000.0000.0000.000
97A167GLY00.0430.02310.0871.5061.5060.0000.0000.0000.000
98A168ASN00.0520.01911.890-1.207-1.2070.0000.0000.0000.000
99A169LYS10.9290.96514.03615.85715.8570.0000.0000.0000.000
100A170GLY00.1100.06312.507-1.073-1.0730.0000.0000.0000.000
101A171ALA00.0020.00110.1381.0511.0510.0000.0000.0000.000
102A172VAL0-0.047-0.02212.1591.4231.4230.0000.0000.0000.000
103A173LEU00.0270.02412.087-1.469-1.4690.0000.0000.0000.000
104A174THR0-0.002-0.01015.3251.6391.6390.0000.0000.0000.000
105A175THR00.0160.00116.045-0.854-0.8540.0000.0000.0000.000
106A176TYR0-0.034-0.01418.3910.4670.4670.0000.0000.0000.000
107A177LEU00.0080.01314.497-0.362-0.3620.0000.0000.0000.000
108A178SER0-0.075-0.05315.5641.3611.3610.0000.0000.0000.000
109A179LEU00.0730.04713.736-1.367-1.3670.0000.0000.0000.000
110A180ALA0-0.006-0.01114.9161.9051.9050.0000.0000.0000.000
111A181GLY00.0780.05615.827-0.850-0.8500.0000.0000.0000.000
112A182ARG10.9210.94418.43314.01714.0170.0000.0000.0000.000
113A183TYR0-0.079-0.08820.1410.2290.2290.0000.0000.0000.000
114A184GLY0-0.009-0.00321.6200.6840.6840.0000.0000.0000.000
115A185VAL0-0.0110.01618.122-0.794-0.7940.0000.0000.0000.000
116A186LEU00.0370.02219.4181.0231.0230.0000.0000.0000.000
117A187MET0-0.028-0.01019.144-1.068-1.0680.0000.0000.0000.000
118A188PRO00.0200.00818.4520.9430.9430.0000.0000.0000.000
119A189ASN00.0340.00720.3040.7350.7350.0000.0000.0000.000
120A190THR0-0.0010.00022.3110.3320.3320.0000.0000.0000.000
121A191ALA00.0340.02624.8210.0430.0430.0000.0000.0000.000
122A192ARG10.8050.88025.75912.39912.3990.0000.0000.0000.000
123A193GLY00.0340.02228.7960.2300.2300.0000.0000.0000.000
124A194GLY0-0.085-0.01527.8190.0230.0230.0000.0000.0000.000
125A195GLY0-0.011-0.02328.3380.5430.5430.0000.0000.0000.000
126A196ILE0-0.031-0.00628.408-0.354-0.3540.0000.0000.0000.000
127A197SER00.0450.02825.5470.0750.0750.0000.0000.0000.000
128A198ARG10.8730.89127.17411.39111.3910.0000.0000.0000.000
129A199LYS10.9320.98925.86711.92911.9290.0000.0000.0000.000
130A200ILE0-0.031-0.01629.5560.0930.0930.0000.0000.0000.000
131A201THR0-0.003-0.02232.1620.2270.2270.0000.0000.0000.000
132A202ALA00.0470.02534.8140.2690.2690.0000.0000.0000.000
133A203VAL00.0580.01136.879-0.135-0.1350.0000.0000.0000.000
134A204THR00.0390.01738.904-0.039-0.0390.0000.0000.0000.000
135A205ASP-1-0.781-0.87533.795-9.258-9.2580.0000.0000.0000.000
136A206ARG10.9631.01234.5828.6618.6610.0000.0000.0000.000
137A207LYS10.9820.98635.6417.5307.5300.0000.0000.0000.000
138A208ARG10.9130.97132.7539.4639.4630.0000.0000.0000.000
139A209LEU0-0.011-0.01630.633-0.062-0.0620.0000.0000.0000.000
140A210LYS10.9200.97433.5929.3259.3250.0000.0000.0000.000
141A211SER00.0030.00535.178-0.045-0.0450.0000.0000.0000.000
142A212VAL0-0.006-0.01931.5550.0040.0040.0000.0000.0000.000
143A213VAL00.001-0.02229.605-0.073-0.0730.0000.0000.0000.000
144A214GLN00.0090.02131.908-0.171-0.1710.0000.0000.0000.000
145A215SER0-0.029-0.02234.668-0.021-0.0210.0000.0000.0000.000
146A216LEU0-0.097-0.04828.2750.0310.0310.0000.0000.0000.000
147A217ASP-1-0.870-0.91231.394-9.332-9.3320.0000.0000.0000.000
148A218VAL0-0.079-0.04027.154-0.222-0.2220.0000.0000.0000.000
149A219PRO00.0400.00927.4500.2550.2550.0000.0000.0000.000
150A220GLN0-0.0020.00127.631-0.473-0.4730.0000.0000.0000.000
151A221GLY00.0390.01628.2150.2370.2370.0000.0000.0000.000
152A222MET0-0.0400.00623.721-0.540-0.5400.0000.0000.0000.000
153A223GLY00.0340.01724.4640.5990.5990.0000.0000.0000.000
154A224LEU00.0180.00323.059-0.511-0.5110.0000.0000.0000.000
155A225ILE0-0.007-0.00523.6210.6440.6440.0000.0000.0000.000
156A226VAL0-0.0070.00223.911-0.546-0.5460.0000.0000.0000.000
157A227ARG10.8950.90018.64316.70616.7060.0000.0000.0000.000
158A228THR00.009-0.01224.4140.2200.2200.0000.0000.0000.000
159A229ALA00.0090.01922.9300.4260.4260.0000.0000.0000.000
160A230GLY00.040-0.00224.9760.2110.2110.0000.0000.0000.000
161A231ALA0-0.0100.00227.1450.3930.3930.0000.0000.0000.000
162A232LYS10.8180.89730.1399.5619.5610.0000.0000.0000.000
163A233ARG10.8810.95927.11011.53711.5370.0000.0000.0000.000
164A234THR00.0490.00230.3560.2310.2310.0000.0000.0000.000
165A235LYS11.0031.00931.6048.4818.4810.0000.0000.0000.000
166A236ALA00.0200.00331.634-0.101-0.1010.0000.0000.0000.000
167A237GLU-1-0.777-0.86126.468-12.243-12.2430.0000.0000.0000.000
168A238ILE00.0080.00226.538-0.530-0.5300.0000.0000.0000.000
169A239LYS10.9020.94626.6799.5929.5920.0000.0000.0000.000
170A240ARG10.8830.92225.68910.94810.9480.0000.0000.0000.000
171A241ASP-1-0.797-0.87521.524-15.562-15.5620.0000.0000.0000.000
172A242TYR00.0680.02522.059-0.766-0.7660.0000.0000.0000.000
173A243GLU-1-0.794-0.88223.187-11.854-11.8540.0000.0000.0000.000
174A244TYR0-0.036-0.01714.8590.1760.1760.0000.0000.0000.000
175A245LEU00.0140.00417.541-0.574-0.5740.0000.0000.0000.000
176A246LEU0-0.010-0.00719.450-0.458-0.4580.0000.0000.0000.000
177A247ARG10.9250.96120.83113.48513.4850.0000.0000.0000.000
178A248LEU00.0240.03913.202-0.159-0.1590.0000.0000.0000.000
179A249TRP00.023-0.01116.468-1.149-1.1490.0000.0000.0000.000
180A250GLU-1-0.848-0.91418.342-14.063-14.0630.0000.0000.0000.000
181A251ASN00.0250.01015.8900.6830.6830.0000.0000.0000.000
182A252ILE0-0.024-0.00312.942-0.505-0.5050.0000.0000.0000.000
183A253ARG10.8440.90315.40413.92113.9210.0000.0000.0000.000
184A254GLU-1-0.909-0.94118.533-14.837-14.8370.0000.0000.0000.000
185A255ASN0-0.004-0.01212.2781.1411.1410.0000.0000.0000.000
186A256THR0-0.097-0.05515.020-0.132-0.1320.0000.0000.0000.000
187A257LEU0-0.040-0.01416.5360.3800.3800.0000.0000.0000.000
188A258HIS0-0.0230.00417.5650.6960.6960.0000.0000.0000.000
189A259SER0-0.030-0.01514.263-1.337-1.3370.0000.0000.0000.000
190A260ILE0-0.003-0.01915.3811.1481.1480.0000.0000.0000.000
191A261ALA0-0.087-0.01514.785-1.126-1.1260.0000.0000.0000.000
192A262PRO0-0.054-0.03011.740-0.062-0.0620.0000.0000.0000.000
193A263ALA00.1010.03910.356-0.404-0.4040.0000.0000.0000.000
194A264LEU0-0.019-0.0093.7631.1701.3480.002-0.030-0.1500.000
195A265ILE0-0.050-0.0257.8561.4391.4390.0000.0000.0000.000
196A266TYR0-0.008-0.0468.4932.1062.1060.0000.0000.0000.000
197A267GLU-1-0.758-0.8481.805-166.695-169.03724.737-13.645-8.750-0.178
198A268GLU-1-0.903-0.9346.094-23.478-23.4780.0000.0000.0000.000
199A269GLU-1-1.006-0.9886.762-36.509-36.5090.0000.0000.0000.000
200A270ASP-1-0.997-0.9917.693-28.147-28.1470.0000.0000.0000.000