Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 5JQ5Z

Calculation Name: 1UXO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UXO

Chain ID: A

ChEMBL ID:

UniProt ID: P96671

Base Structure: X-ray

Registration Date: 2023-09-23

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2149649.055697
FMO2-HF: Nuclear repulsion 2076854.239327
FMO2-HF: Total energy -72794.816371
FMO2-MP2: Total energy -73011.660367


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:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-6.935-2.8780.466-1.825-2.698-0.011
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.022
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].
3A4GLN0-0.017-0.0022.741-5.219-2.3120.459-1.544-1.822-0.010
4A5VAL0-0.0110.0005.2370.8120.830-0.001-0.003-0.0140.000
5A6TYR00.015-0.0138.782-0.104-0.1040.0000.0000.0000.000
6A7ILE0-0.030-0.02111.6260.1460.1460.0000.0000.0000.000
7A8ILE00.0140.01114.912-0.017-0.0170.0000.0000.0000.000
8A9HIS00.0170.01118.1820.0280.0280.0000.0000.0000.000
9A10GLY00.0750.03021.5770.0040.0040.0000.0000.0000.000
10A11TYR00.0220.00125.133-0.010-0.0100.0000.0000.0000.000
11A12ARG10.8750.95128.5640.1790.1790.0000.0000.0000.000
12A13ALA0-0.0030.00624.9760.0090.0090.0000.0000.0000.000
13A14SER00.0420.02123.238-0.016-0.0160.0000.0000.0000.000
14A15SER00.040-0.01418.5230.0060.0060.0000.0000.0000.000
15A16THR0-0.066-0.03920.008-0.020-0.0200.0000.0000.0000.000
16A17ASN0-0.041-0.01622.5180.0090.0090.0000.0000.0000.000
17A18HIS00.0470.02322.552-0.023-0.0230.0000.0000.0000.000
18A19TRP00.0360.02218.236-0.021-0.0210.0000.0000.0000.000
19A20PHE0-0.0240.00317.760-0.025-0.0250.0000.0000.0000.000
20A21PRO00.015-0.00316.867-0.059-0.0590.0000.0000.0000.000
21A22TRP00.0040.00417.209-0.036-0.0360.0000.0000.0000.000
22A23LEU00.0340.01414.2260.0060.0060.0000.0000.0000.000
23A24LYS10.9640.98612.0150.8780.8780.0000.0000.0000.000
24A25LYS10.9320.95612.4550.3160.3160.0000.0000.0000.000
25A26ARG10.8450.94014.5350.1260.1260.0000.0000.0000.000
26A27LEU00.0400.0149.8580.0690.0690.0000.0000.0000.000
27A28LEU00.0220.0249.9550.0340.0340.0000.0000.0000.000
28A29ALA0-0.055-0.02511.0540.0650.0650.0000.0000.0000.000
29A30ASP-1-0.809-0.84910.5840.0530.0530.0000.0000.0000.000
30A31GLY0-0.050-0.0237.9560.1910.1910.0000.0000.0000.000
31A32VAL0-0.088-0.0475.787-0.106-0.1060.0000.0000.0000.000
32A33GLN0-0.029-0.0114.1670.2490.356-0.001-0.008-0.0980.000
33A34ALA00.009-0.0076.028-0.150-0.1500.0000.0000.0000.000
34A35ASP-1-0.873-0.9148.661-1.802-1.8020.0000.0000.0000.000
35A36ILE0-0.045-0.01411.3230.0500.0500.0000.0000.0000.000
36A37LEU0-0.0140.00413.5140.0060.0060.0000.0000.0000.000
37A38ASN00.001-0.01516.6100.0930.0930.0000.0000.0000.000
38A39MET0-0.0070.00718.959-0.019-0.0190.0000.0000.0000.000
39A40PRO00.0160.01022.6990.0210.0210.0000.0000.0000.000
40A41ASN00.005-0.00325.9360.0160.0160.0000.0000.0000.000
41A42PRO00.0600.03826.4140.0160.0160.0000.0000.0000.000
42A43LEU00.004-0.02128.3410.0140.0140.0000.0000.0000.000
43A44GLN0-0.061-0.03231.6960.0130.0130.0000.0000.0000.000
44A45PRO0-0.0110.01728.516-0.003-0.0030.0000.0000.0000.000
45A46ARG10.8660.92129.3070.2020.2020.0000.0000.0000.000
46A47LEU00.0210.00726.535-0.022-0.0220.0000.0000.0000.000
47A48GLU-1-0.896-0.96726.770-0.247-0.2470.0000.0000.0000.000
48A49ASP-1-0.849-0.91326.643-0.276-0.2760.0000.0000.0000.000
49A50TRP0-0.050-0.04823.692-0.039-0.0390.0000.0000.0000.000
50A51LEU0-0.022-0.02022.185-0.055-0.0550.0000.0000.0000.000
51A52ASP-1-0.861-0.91721.776-0.351-0.3510.0000.0000.0000.000
52A53THR0-0.059-0.03619.526-0.043-0.0430.0000.0000.0000.000
53A54LEU0-0.021-0.01717.413-0.080-0.0800.0000.0000.0000.000
54A55SER0-0.051-0.01816.867-0.090-0.0900.0000.0000.0000.000
55A56LEU0-0.030-0.01417.533-0.032-0.0320.0000.0000.0000.000
56A57TYR0-0.021-0.01612.324-0.089-0.0890.0000.0000.0000.000
57A58GLN00.0290.03712.407-0.154-0.1540.0000.0000.0000.000
58A59HIS0-0.042-0.03011.767-0.073-0.0730.0000.0000.0000.000
59A60THR0-0.046-0.0238.061-0.117-0.1170.0000.0000.0000.000
60A61LEU0-0.0290.0027.830-0.450-0.4500.0000.0000.0000.000
61A62HIS00.001-0.0023.6470.8761.4650.005-0.190-0.404-0.001
62A63GLU-1-0.879-0.9506.3590.3680.3680.0000.0000.0000.000
63A64ASN0-0.071-0.0313.749-0.3890.0470.004-0.080-0.3600.000
64A65THR00.003-0.0025.890-1.347-1.3470.0000.0000.0000.000
65A66TYR0-0.015-0.0067.6600.5050.5050.0000.0000.0000.000
66A67LEU00.0140.01011.005-0.209-0.2090.0000.0000.0000.000
67A68VAL00.0000.00413.6810.1280.1280.0000.0000.0000.000
68A69ALA00.0200.01215.984-0.053-0.0530.0000.0000.0000.000
69A70HIS0-0.005-0.01119.2290.0210.0210.0000.0000.0000.000
70A71SER00.0280.00022.467-0.008-0.0080.0000.0000.0000.000
71A72LEU0-0.011-0.00225.379-0.002-0.0020.0000.0000.0000.000
72A73GLY00.0410.01821.934-0.003-0.0030.0000.0000.0000.000
73A74CYS0-0.093-0.02021.789-0.021-0.0210.0000.0000.0000.000
74A75PRO00.0140.01523.163-0.006-0.0060.0000.0000.0000.000
75A76ALA00.0280.01922.7970.0020.0020.0000.0000.0000.000
76A77ILE00.008-0.00517.814-0.011-0.0110.0000.0000.0000.000
77A78LEU0-0.022-0.00520.4110.0050.0050.0000.0000.0000.000
78A79ARG10.8320.89522.6720.1680.1680.0000.0000.0000.000
79A80PHE00.0020.00815.826-0.003-0.0030.0000.0000.0000.000
80A81LEU0-0.029-0.02616.226-0.002-0.0020.0000.0000.0000.000
81A82GLU-1-0.812-0.88219.634-0.120-0.1200.0000.0000.0000.000
82A83HIS00.0190.00922.4910.0260.0260.0000.0000.0000.000
83A84LEU0-0.0260.01714.930-0.012-0.0120.0000.0000.0000.000
84A85GLN0-0.0120.00018.6500.0720.0720.0000.0000.0000.000
85A86LEU0-0.011-0.00813.119-0.050-0.0500.0000.0000.0000.000
86A87ARG10.9330.9579.9290.0330.0330.0000.0000.0000.000
87A88ALA0-0.002-0.01211.7790.0880.0880.0000.0000.0000.000
88A89ALA00.0070.02812.955-0.089-0.0890.0000.0000.0000.000
89A90LEU00.0460.01610.5820.0500.0500.0000.0000.0000.000
90A91GLY00.0260.0259.8930.1760.1760.0000.0000.0000.000
91A92GLY0-0.035-0.04010.7340.1200.1200.0000.0000.0000.000
92A93ILE00.0080.00813.732-0.148-0.1480.0000.0000.0000.000
93A94ILE0-0.045-0.02316.1020.0730.0730.0000.0000.0000.000
94A95LEU0-0.007-0.01318.484-0.053-0.0530.0000.0000.0000.000
95A96VAL00.0180.00220.4480.0360.0360.0000.0000.0000.000
96A97SER00.0340.00623.131-0.018-0.0180.0000.0000.0000.000
97A98GLY00.0580.02225.505-0.007-0.0070.0000.0000.0000.000
98A99PHE0-0.026-0.01626.1540.0210.0210.0000.0000.0000.000
99A100ALA00.0520.02228.117-0.016-0.0160.0000.0000.0000.000
100A101LYS10.8660.93930.1320.0820.0820.0000.0000.0000.000
101A102SER0-0.007-0.01233.529-0.004-0.0040.0000.0000.0000.000
102A103LEU00.0430.01431.5020.0080.0080.0000.0000.0000.000
103A104PRO00.018-0.00235.845-0.002-0.0020.0000.0000.0000.000
104A105THR0-0.023-0.01537.432-0.001-0.0010.0000.0000.0000.000
105A106LEU0-0.026-0.01533.042-0.004-0.0040.0000.0000.0000.000
106A107GLN00.0760.04135.775-0.002-0.0020.0000.0000.0000.000
107A108MET0-0.072-0.02234.3790.0000.0000.0000.0000.0000.000
108A109LEU0-0.001-0.00330.863-0.010-0.0100.0000.0000.0000.000
109A110ASP-1-0.817-0.90432.781-0.124-0.1240.0000.0000.0000.000
110A111GLU-1-0.822-0.89631.948-0.182-0.1820.0000.0000.0000.000
111A112PHE0-0.013-0.01626.201-0.004-0.0040.0000.0000.0000.000
112A113THR0-0.072-0.02729.4400.0000.0000.0000.0000.0000.000
113A114GLN0-0.0340.00631.7560.0080.0080.0000.0000.0000.000
114A115GLY00.0290.01333.023-0.006-0.0060.0000.0000.0000.000
115A116SER0-0.013-0.02032.636-0.005-0.0050.0000.0000.0000.000
116A117PHE00.0030.01426.314-0.008-0.0080.0000.0000.0000.000
117A118ASP-1-0.892-0.95426.494-0.048-0.0480.0000.0000.0000.000
118A119HIS00.013-0.01825.677-0.012-0.0120.0000.0000.0000.000
119A120GLN0-0.0230.00324.855-0.003-0.0030.0000.0000.0000.000
120A121LYS10.8800.95119.4530.1680.1680.0000.0000.0000.000
121A122ILE0-0.020-0.00720.932-0.010-0.0100.0000.0000.0000.000
122A123ILE0-0.034-0.01619.961-0.003-0.0030.0000.0000.0000.000
123A124GLU-1-0.937-0.97519.6460.0540.0540.0000.0000.0000.000
124A125SER0-0.030-0.02116.8850.0060.0060.0000.0000.0000.000
125A126ALA0-0.033-0.01614.843-0.059-0.0590.0000.0000.0000.000
126A127LYS10.9420.99012.987-0.637-0.6370.0000.0000.0000.000
127A128HIS0-0.077-0.03313.4650.0510.0510.0000.0000.0000.000
128A129ARG10.8820.93616.689-0.095-0.0950.0000.0000.0000.000
129A130ALA00.0130.01019.4190.0330.0330.0000.0000.0000.000
130A131VAL00.0150.01821.432-0.040-0.0400.0000.0000.0000.000
131A132ILE0-0.0060.00621.0120.0230.0230.0000.0000.0000.000
132A133ALA00.006-0.00224.846-0.020-0.0200.0000.0000.0000.000
133A134SER00.0270.02128.2370.0170.0170.0000.0000.0000.000
134A135LYS10.9030.95431.0070.0430.0430.0000.0000.0000.000
135A136ASP-1-0.842-0.94334.504-0.077-0.0770.0000.0000.0000.000
136A137ASP-1-0.715-0.83830.859-0.134-0.1340.0000.0000.0000.000
137A138GLN0-0.081-0.04534.1520.0070.0070.0000.0000.0000.000
138A139ILE0-0.068-0.02732.4470.0000.0000.0000.0000.0000.000
139A140VAL0-0.032-0.01329.5240.0000.0000.0000.0000.0000.000
140A141PRO00.0160.02032.7220.0060.0060.0000.0000.0000.000
141A142PHE00.0870.02931.0200.0010.0010.0000.0000.0000.000
142A143SER0-0.043-0.03432.902-0.001-0.0010.0000.0000.0000.000
143A144PHE00.023-0.00432.6450.0070.0070.0000.0000.0000.000
144A145SER00.0090.00028.635-0.004-0.0040.0000.0000.0000.000
145A146LYS10.9070.95929.3670.0220.0220.0000.0000.0000.000
146A147ASP-1-0.900-0.94731.236-0.052-0.0520.0000.0000.0000.000
147A148LEU00.0550.03425.6300.0040.0040.0000.0000.0000.000
148A149ALA0-0.030-0.03026.6230.0030.0030.0000.0000.0000.000
149A150GLN0-0.037-0.02227.4670.0100.0100.0000.0000.0000.000
150A151GLN0-0.020-0.00729.1180.0010.0010.0000.0000.0000.000
151A152ILE0-0.003-0.00522.4630.0010.0010.0000.0000.0000.000
152A153ASP-1-0.925-0.95224.0050.0630.0630.0000.0000.0000.000
153A154ALA0-0.0300.00323.1660.0110.0110.0000.0000.0000.000
154A155ALA0-0.008-0.00222.8610.0040.0040.0000.0000.0000.000
155A156LEU0-0.016-0.01224.425-0.021-0.0210.0000.0000.0000.000
156A157TYR0-0.042-0.02621.9720.0210.0210.0000.0000.0000.000
157A158GLU-1-0.903-0.95526.928-0.050-0.0500.0000.0000.0000.000
158A159VAL0-0.024-0.00827.2910.0070.0070.0000.0000.0000.000
159A160GLN0-0.010-0.00930.369-0.005-0.0050.0000.0000.0000.000
160A161HIS0-0.045-0.03833.3950.0050.0050.0000.0000.0000.000
161A162GLY00.0140.00230.395-0.001-0.0010.0000.0000.0000.000
162A163GLY00.0310.04530.365-0.013-0.0130.0000.0000.0000.000
163A164HIS0-0.074-0.06428.877-0.010-0.0100.0000.0000.0000.000
164A165PHE0-0.047-0.03225.542-0.016-0.0160.0000.0000.0000.000
165A166LEU00.0100.00726.166-0.027-0.0270.0000.0000.0000.000
166A167GLU-1-0.803-0.91927.102-0.221-0.2210.0000.0000.0000.000
167A168ASP-1-0.932-0.96428.568-0.148-0.1480.0000.0000.0000.000
168A169GLU-1-0.922-0.95731.160-0.123-0.1230.0000.0000.0000.000
169A170GLY0-0.0010.00430.5720.0100.0100.0000.0000.0000.000
170A171PHE0-0.035-0.01025.914-0.003-0.0030.0000.0000.0000.000
171A172THR00.018-0.00324.631-0.018-0.0180.0000.0000.0000.000
172A173SER0-0.092-0.05122.062-0.017-0.0170.0000.0000.0000.000
173A174LEU00.0270.01021.1310.0140.0140.0000.0000.0000.000
174A175PRO00.015-0.00320.493-0.016-0.0160.0000.0000.0000.000
175A176ILE00.0620.04320.2100.0050.0050.0000.0000.0000.000
176A177VAL00.0320.01816.8310.0150.0150.0000.0000.0000.000
177A178TYR0-0.093-0.09313.359-0.011-0.0110.0000.0000.0000.000
178A179ASP-1-0.870-0.94415.8200.0130.0130.0000.0000.0000.000
179A180VAL0-0.040-0.02017.6030.0500.0500.0000.0000.0000.000
180A181LEU00.0110.01611.4320.0370.0370.0000.0000.0000.000
181A182THR00.0200.00312.7710.0620.0620.0000.0000.0000.000
182A183SER0-0.074-0.04513.5290.1330.1330.0000.0000.0000.000
183A184TYR0-0.013-0.03112.7660.1030.1030.0000.0000.0000.000
184A185PHE0-0.018-0.0079.3390.1180.1180.0000.0000.0000.000
185A186SER0-0.059-0.00410.7420.2240.2240.0000.0000.0000.000
186A187LYS10.9100.96812.022-0.202-0.2020.0000.0000.0000.000