FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 175VZ

Calculation Name: 5T0O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5T0O

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RTE4

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 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 1033
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -29059875.818529
FMO2-HF: Nuclear repulsion 28665109.839984
FMO2-HF: Total energy -394765.978546
FMO2-MP2: Total energy -395923.004828


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-4.516-3.2834.812-1.731-4.3140.006
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.057 / 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].
3A3SER00.0610.0113.890-1.4440.028-0.005-0.573-0.8940.001
4A4LYS10.9060.9462.952-4.023-4.5124.818-1.127-3.2020.005
5A5PHE0-0.040-0.0154.2630.0790.329-0.001-0.031-0.2180.000
6A6PHE00.0730.0255.6510.1060.1060.0000.0000.0000.000
7A7ILE00.0110.0317.1100.0220.0220.0000.0000.0000.000
8A8GLU-1-0.827-0.8967.2611.4951.4950.0000.0000.0000.000
9A9ARG10.8290.9197.170-0.592-0.5920.0000.0000.0000.000
10A10PRO00.1000.04611.941-0.061-0.0610.0000.0000.0000.000
11A11VAL00.0000.01214.744-0.030-0.0300.0000.0000.0000.000
12A12PHE00.0040.00711.405-0.020-0.0200.0000.0000.0000.000
13A13ALA00.0450.01812.731-0.017-0.0170.0000.0000.0000.000
14A14SER0-0.016-0.01914.483-0.015-0.0150.0000.0000.0000.000
15A15VAL0-0.008-0.00418.045-0.012-0.0120.0000.0000.0000.000
16A16VAL00.0100.01014.941-0.010-0.0100.0000.0000.0000.000
17A17ALA00.0370.02318.034-0.007-0.0070.0000.0000.0000.000
18A18ILE00.0050.01019.717-0.009-0.0090.0000.0000.0000.000
19A19ILE0-0.007-0.00420.448-0.008-0.0080.0000.0000.0000.000
20A20ILE0-0.0050.00218.472-0.006-0.0060.0000.0000.0000.000
21A21SER0-0.008-0.02222.944-0.006-0.0060.0000.0000.0000.000
22A22LEU0-0.031-0.00825.443-0.005-0.0050.0000.0000.0000.000
23A23ALA00.0250.00425.836-0.005-0.0050.0000.0000.0000.000
24A24GLY00.0240.01526.855-0.004-0.0040.0000.0000.0000.000
25A25ALA0-0.014-0.01328.171-0.004-0.0040.0000.0000.0000.000
26A26ILE0-0.016-0.00230.356-0.004-0.0040.0000.0000.0000.000
27A27GLY00.0240.00931.156-0.003-0.0030.0000.0000.0000.000
28A28LEU0-0.061-0.04232.106-0.003-0.0030.0000.0000.0000.000
29A29THR0-0.072-0.03633.777-0.003-0.0030.0000.0000.0000.000
30A30ASN0-0.024-0.00935.841-0.003-0.0030.0000.0000.0000.000
31A31LEU0-0.0330.00432.545-0.001-0.0010.0000.0000.0000.000
32A32PRO0-0.0020.01836.962-0.001-0.0010.0000.0000.0000.000
33A33ILE00.0210.00339.1130.0020.0020.0000.0000.0000.000
34A34GLU-1-0.870-0.90941.0630.0350.0350.0000.0000.0000.000
35A35GLN00.006-0.00642.1220.0010.0010.0000.0000.0000.000
36A36TYR0-0.011-0.02641.5950.0010.0010.0000.0000.0000.000
37A37PRO00.0930.06938.854-0.001-0.0010.0000.0000.0000.000
38A38SER00.0200.00441.400-0.002-0.0020.0000.0000.0000.000
39A39LEU0-0.066-0.03140.8560.0000.0000.0000.0000.0000.000
40A40THR00.015-0.01244.716-0.001-0.0010.0000.0000.0000.000
41A41PRO00.0140.00548.4330.0000.0000.0000.0000.0000.000
42A42PRO0-0.0190.01848.818-0.001-0.0010.0000.0000.0000.000
43A43THR0-0.003-0.02951.641-0.001-0.0010.0000.0000.0000.000
44A44VAL00.000-0.00455.4680.0000.0000.0000.0000.0000.000
45A45LYS10.8310.91558.278-0.016-0.0160.0000.0000.0000.000
46A46VAL00.0320.00761.8440.0000.0000.0000.0000.0000.000
47A47SER0-0.007-0.01364.8670.0000.0000.0000.0000.0000.000
48A48ALA0-0.018-0.00768.3000.0000.0000.0000.0000.0000.000
49A49THR00.0120.00071.9030.0000.0000.0000.0000.0000.000
50A50TYR0-0.001-0.01475.4960.0000.0000.0000.0000.0000.000
51A51THR00.008-0.00478.7660.0000.0000.0000.0000.0000.000
52A52GLY00.0060.00981.0470.0000.0000.0000.0000.0000.000
53A53ALA0-0.043-0.00480.1980.0000.0000.0000.0000.0000.000
54A54ASP-1-0.772-0.87980.6230.0090.0090.0000.0000.0000.000
55A55ALA00.0260.01675.7400.0000.0000.0000.0000.0000.000
56A56GLN00.0300.00575.9800.0000.0000.0000.0000.0000.000
57A57THR0-0.019-0.02377.2490.0000.0000.0000.0000.0000.000
58A58ILE0-0.0350.00273.9750.0000.0000.0000.0000.0000.000
59A59ALA00.0390.01572.7440.0000.0000.0000.0000.0000.000
60A60SER0-0.046-0.03772.9400.0000.0000.0000.0000.0000.000
61A61THR0-0.095-0.06075.5090.0000.0000.0000.0000.0000.000
62A62VAL0-0.044-0.02972.4910.0000.0000.0000.0000.0000.000
63A63ALA00.0310.01269.4570.0000.0000.0000.0000.0000.000
64A64SER0-0.011-0.01469.1290.0000.0000.0000.0000.0000.000
65A65PRO0-0.020-0.01669.1130.0000.0000.0000.0000.0000.000
66A66ILE00.0010.00466.2280.0000.0000.0000.0000.0000.000
67A67GLU-1-0.754-0.85664.8580.0120.0120.0000.0000.0000.000
68A68ASP-1-0.852-0.93264.3170.0110.0110.0000.0000.0000.000
69A69ALA0-0.065-0.01865.2240.0000.0000.0000.0000.0000.000
70A70ILE0-0.012-0.01360.2950.0000.0000.0000.0000.0000.000
71A71ASN0-0.031-0.02360.1760.0010.0010.0000.0000.0000.000
72A72GLY00.0460.02357.3430.0000.0000.0000.0000.0000.000
73A73ALA00.0050.00456.7100.0000.0000.0000.0000.0000.000
74A74ASP-1-0.882-0.93951.9410.0180.0180.0000.0000.0000.000
75A75ASN0-0.042-0.02048.3310.0010.0010.0000.0000.0000.000
76A76MET0-0.069-0.01751.0600.0000.0000.0000.0000.0000.000
77A77ILE0-0.021-0.00550.2500.0000.0000.0000.0000.0000.000
78A78TYR0-0.054-0.03353.516-0.001-0.0010.0000.0000.0000.000
79A79MET0-0.0200.00257.0950.0000.0000.0000.0000.0000.000
80A80ASP-1-0.796-0.85260.1380.0150.0150.0000.0000.0000.000
81A81SER0-0.030-0.01962.5520.0000.0000.0000.0000.0000.000
82A82THR00.003-0.01066.0970.0000.0000.0000.0000.0000.000
83A83SER00.0100.01068.9630.0000.0000.0000.0000.0000.000
84A84SER00.006-0.00572.5540.0000.0000.0000.0000.0000.000
85A85SER00.017-0.00775.2210.0000.0000.0000.0000.0000.000
86A86SER0-0.027-0.00775.6630.0000.0000.0000.0000.0000.000
87A87GLY0-0.0020.00478.1860.0000.0000.0000.0000.0000.000
88A88THR0-0.042-0.03372.8810.0000.0000.0000.0000.0000.000
89A89MET00.0070.01168.3150.0000.0000.0000.0000.0000.000
90A90SER00.0060.00966.4030.0000.0000.0000.0000.0000.000
91A91LEU00.0480.01763.2120.0000.0000.0000.0000.0000.000
92A92THR0-0.040-0.03959.1480.0000.0000.0000.0000.0000.000
93A93VAL00.0280.01357.0220.0000.0000.0000.0000.0000.000
94A94TYR0-0.051-0.04054.3040.0010.0010.0000.0000.0000.000
95A95PHE00.006-0.00551.075-0.001-0.0010.0000.0000.0000.000
96A96ASP-1-0.833-0.91546.9340.0240.0240.0000.0000.0000.000
97A97ILE0-0.086-0.04643.9840.0000.0000.0000.0000.0000.000
98A98GLY00.0240.00743.5420.0010.0010.0000.0000.0000.000
99A99THR0-0.081-0.03344.3870.0000.0000.0000.0000.0000.000
100A100ASP-1-0.832-0.90947.1980.0240.0240.0000.0000.0000.000
101A101PRO00.0510.00348.306-0.001-0.0010.0000.0000.0000.000
102A102ASP-1-0.842-0.89451.2080.0210.0210.0000.0000.0000.000
103A103GLN00.0420.01350.512-0.001-0.0010.0000.0000.0000.000
104A104ALA00.0260.01452.430-0.001-0.0010.0000.0000.0000.000
105A105THR0-0.045-0.05054.140-0.001-0.0010.0000.0000.0000.000
106A106ILE0-0.051-0.03055.193-0.001-0.0010.0000.0000.0000.000
107A107ASP-1-0.820-0.88255.5420.0150.0150.0000.0000.0000.000
108A108VAL00.0360.01257.606-0.001-0.0010.0000.0000.0000.000
109A109ASN0-0.005-0.00560.142-0.001-0.0010.0000.0000.0000.000
110A110ASN00.0030.00858.986-0.001-0.0010.0000.0000.0000.000
111A111ARG10.8000.88756.566-0.016-0.0160.0000.0000.0000.000
112A112ILE00.0270.01163.605-0.001-0.0010.0000.0000.0000.000
113A113SER0-0.0250.00365.795-0.001-0.0010.0000.0000.0000.000
114A114ALA0-0.0140.00266.357-0.001-0.0010.0000.0000.0000.000
115A115ALA00.0190.01467.813-0.001-0.0010.0000.0000.0000.000
116A116THR00.004-0.02469.5510.0000.0000.0000.0000.0000.000
117A117ALA0-0.033-0.02271.9480.0000.0000.0000.0000.0000.000
118A118LYS10.8440.90571.086-0.010-0.0100.0000.0000.0000.000
119A119MET0-0.0180.03772.4450.0000.0000.0000.0000.0000.000
120A120PRO00.0740.02875.6210.0000.0000.0000.0000.0000.000
121A121ASP-1-0.822-0.90378.6780.0080.0080.0000.0000.0000.000
122A122ALA0-0.070-0.03380.7810.0000.0000.0000.0000.0000.000
123A123VAL00.0340.01674.5240.0000.0000.0000.0000.0000.000
124A124LYS10.8190.89776.179-0.009-0.0090.0000.0000.0000.000
125A125LYS10.8880.94977.213-0.009-0.0090.0000.0000.0000.000
126A126LEU0-0.065-0.02476.0500.0000.0000.0000.0000.0000.000
127A127GLY0-0.0020.02173.5980.0000.0000.0000.0000.0000.000
128A128VAL0-0.027-0.01768.4570.0000.0000.0000.0000.0000.000
129A129THR0-0.053-0.01967.4690.0000.0000.0000.0000.0000.000
130A130VAL00.0380.00261.4010.0000.0000.0000.0000.0000.000
131A131ARG10.8430.92760.735-0.017-0.0170.0000.0000.0000.000
132A132LYS10.9050.96752.555-0.022-0.0220.0000.0000.0000.000
133A133THR0-0.056-0.04257.4980.0000.0000.0000.0000.0000.000
134A134SER00.0760.06454.2710.0000.0000.0000.0000.0000.000
135A135SER0-0.0050.00956.3540.0000.0000.0000.0000.0000.000
136A136THR00.000-0.01552.8890.0000.0000.0000.0000.0000.000
137A137THR0-0.030-0.02156.1350.0000.0000.0000.0000.0000.000
138A138LEU00.0110.03055.0090.0000.0000.0000.0000.0000.000
139A139ALA00.0380.02256.5500.0000.0000.0000.0000.0000.000
140A140ALA0-0.004-0.00359.5540.0000.0000.0000.0000.0000.000
141A141ILE00.0230.01763.3620.0000.0000.0000.0000.0000.000
142A142SER00.0460.00565.558-0.001-0.0010.0000.0000.0000.000
143A143MET0-0.028-0.00168.9440.0000.0000.0000.0000.0000.000
144A144TYR00.0550.02570.8610.0000.0000.0000.0000.0000.000
145A145SER00.0250.01675.4080.0000.0000.0000.0000.0000.000
146A146SER0-0.102-0.06475.8730.0000.0000.0000.0000.0000.000
147A147ASP-1-0.766-0.85377.7920.0120.0120.0000.0000.0000.000
148A148GLY00.0080.00281.0630.0000.0000.0000.0000.0000.000
149A149SER0-0.077-0.05682.3270.0000.0000.0000.0000.0000.000
150A150MET0-0.048-0.02679.0530.0000.0000.0000.0000.0000.000
151A151SER00.045-0.02581.6270.0000.0000.0000.0000.0000.000
152A152ALA00.0150.01179.9010.0000.0000.0000.0000.0000.000
153A153VAL0-0.031-0.00579.5870.0000.0000.0000.0000.0000.000
154A154ASP-1-0.843-0.89080.8420.0110.0110.0000.0000.0000.000
155A155VAL0-0.0040.00175.6320.0000.0000.0000.0000.0000.000
156A156TYR00.0290.02375.1530.0000.0000.0000.0000.0000.000
157A157ASN00.014-0.00376.9250.0000.0000.0000.0000.0000.000
158A158TYR00.012-0.00973.8880.0000.0000.0000.0000.0000.000
159A159ILE00.0230.00071.6450.0000.0000.0000.0000.0000.000
160A160THR0-0.041-0.02273.2280.0000.0000.0000.0000.0000.000
161A161LEU0-0.036-0.00575.1710.0000.0000.0000.0000.0000.000
162A162ASN0-0.010-0.01073.6550.0000.0000.0000.0000.0000.000
163A163VAL00.0120.01668.9420.0000.0000.0000.0000.0000.000
164A164LEU0-0.003-0.00468.6630.0010.0010.0000.0000.0000.000
165A165ASP-1-0.800-0.89567.9560.0140.0140.0000.0000.0000.000
166A166GLU-1-0.809-0.87766.2790.0170.0170.0000.0000.0000.000
167A167LEU0-0.014-0.01163.8590.0010.0010.0000.0000.0000.000
168A168LYS10.7930.87863.139-0.016-0.0160.0000.0000.0000.000
169A169ARG10.8220.90163.455-0.016-0.0160.0000.0000.0000.000
170A170VAL0-0.0270.01158.5140.0000.0000.0000.0000.0000.000
171A171PRO00.023-0.00955.4170.0000.0000.0000.0000.0000.000
172A172GLY00.0360.01654.6550.0010.0010.0000.0000.0000.000
173A173VAL00.0200.01855.4510.0000.0000.0000.0000.0000.000
174A174GLY00.0020.01358.4720.0000.0000.0000.0000.0000.000
175A175ASP-1-0.874-0.93159.6930.0160.0160.0000.0000.0000.000
176A176ALA00.0310.01562.5740.0000.0000.0000.0000.0000.000
177A177ASN0-0.046-0.02664.950-0.001-0.0010.0000.0000.0000.000
178A178ALA00.0520.03568.2050.0000.0000.0000.0000.0000.000
179A179ILE0-0.008-0.01068.5790.0000.0000.0000.0000.0000.000
180A180GLY00.0620.02372.1860.0000.0000.0000.0000.0000.000
181A181ASN0-0.095-0.03075.0610.0000.0000.0000.0000.0000.000
182A182ARG10.9940.99272.374-0.012-0.0120.0000.0000.0000.000
183A183ASN00.0060.00073.954-0.001-0.0010.0000.0000.0000.000
184A184TYR00.0350.02975.5400.0000.0000.0000.0000.0000.000
185A185SER0-0.024-0.01379.3230.0000.0000.0000.0000.0000.000
186A186LEU00.0260.03082.6670.0000.0000.0000.0000.0000.000
187A187ARG10.8680.94684.281-0.010-0.0100.0000.0000.0000.000
188A188ILE00.0290.01788.3750.0000.0000.0000.0000.0000.000
189A189TRP00.014-0.02487.9820.0000.0000.0000.0000.0000.000
190A190LEU00.0120.00193.2570.0000.0000.0000.0000.0000.000
191A191LYS10.8680.94896.535-0.007-0.0070.0000.0000.0000.000
192A192PRO0-0.001-0.00398.4430.0000.0000.0000.0000.0000.000
193A193ASP-1-0.818-0.913101.0830.0070.0070.0000.0000.0000.000
194A194LEU0-0.013-0.017102.9020.0000.0000.0000.0000.0000.000
195A195LEU0-0.002-0.00299.1170.0000.0000.0000.0000.0000.000
196A196ASN0-0.014-0.006103.6780.0000.0000.0000.0000.0000.000
197A197LYS10.8700.961106.404-0.006-0.0060.0000.0000.0000.000
198A198PHE0-0.030-0.024106.2320.0000.0000.0000.0000.0000.000
199A199GLY00.0300.021108.1130.0000.0000.0000.0000.0000.000
200A200ILE0-0.042-0.012101.9570.0000.0000.0000.0000.0000.000
201A201THR00.023-0.001100.7410.0000.0000.0000.0000.0000.000
202A202ALA00.0620.01396.2670.0000.0000.0000.0000.0000.000
203A203THR0-0.017-0.01096.6680.0000.0000.0000.0000.0000.000
204A204ASP-1-0.752-0.84998.1320.0060.0060.0000.0000.0000.000
205A205VAL0-0.021-0.01095.6790.0000.0000.0000.0000.0000.000
206A206ILE0-0.027-0.01192.8420.0000.0000.0000.0000.0000.000
207A207SER0-0.049-0.02394.3630.0000.0000.0000.0000.0000.000
208A208ALA00.0270.02595.9390.0000.0000.0000.0000.0000.000
209A209VAL0-0.020-0.02391.3600.0000.0000.0000.0000.0000.000
210A210ASN0-0.037-0.02390.9620.0000.0000.0000.0000.0000.000
211A211ASP-1-0.882-0.94992.3950.0070.0070.0000.0000.0000.000
212A212GLN0-0.028-0.01995.1350.0000.0000.0000.0000.0000.000
213A213ASN0-0.049-0.02687.7600.0000.0000.0000.0000.0000.000
214A214ALA00.0380.03990.0640.0000.0000.0000.0000.0000.000
215A215GLN00.013-0.00784.7220.0000.0000.0000.0000.0000.000
216A216TYR00.0300.00884.8030.0000.0000.0000.0000.0000.000
217A217ALA00.0030.01389.0990.0000.0000.0000.0000.0000.000
218A218THR0-0.050-0.04686.9400.0000.0000.0000.0000.0000.000
219A219GLY00.0460.03789.9650.0000.0000.0000.0000.0000.000
220A220LYS10.7910.87486.837-0.008-0.0080.0000.0000.0000.000
221A221ILE0-0.0210.00792.4110.0000.0000.0000.0000.0000.000
222A222GLY00.028-0.00394.5210.0000.0000.0000.0000.0000.000
223A223GLU-1-0.781-0.85789.8010.0080.0080.0000.0000.0000.000
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