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: N97MQ

Calculation Name: 5U15-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5U15

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2100606.421403
FMO2-HF: Nuclear repulsion 2018641.846125
FMO2-HF: Total energy -81964.575278
FMO2-MP2: Total energy -82201.984745


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:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
0.5624.3060.467-1.238-2.9720
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.014
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].
3A3GLN0-0.0100.0002.556-1.3421.4880.463-1.037-2.2560.000
4A4LEU0-0.023-0.0095.1330.8690.950-0.001-0.005-0.0740.000
5A5VAL00.0240.0117.9910.2030.2030.0000.0000.0000.000
6A6GLN00.012-0.02510.6860.1150.1150.0000.0000.0000.000
7A7SER00.0320.03214.4680.0020.0020.0000.0000.0000.000
8A8GLY00.0100.00417.388-0.004-0.0040.0000.0000.0000.000
9A9ALA0-0.028-0.01819.6650.0140.0140.0000.0000.0000.000
10A10GLU-1-0.777-0.88922.468-0.362-0.3620.0000.0000.0000.000
11A11VAL0-0.008-0.00325.5650.0130.0130.0000.0000.0000.000
12A12LYS10.8140.90527.3630.3430.3430.0000.0000.0000.000
13A13LYS10.9350.97131.7110.1890.1890.0000.0000.0000.000
14A14PRO00.019-0.01034.775-0.007-0.0070.0000.0000.0000.000
15A15GLY0-0.033-0.00736.2370.0080.0080.0000.0000.0000.000
16A16ALA0-0.025-0.00333.3340.0000.0000.0000.0000.0000.000
17A17SER00.0370.00530.1160.0060.0060.0000.0000.0000.000
18A18VAL0-0.032-0.01024.8970.0010.0010.0000.0000.0000.000
19A19LYS10.8830.93122.9880.3870.3870.0000.0000.0000.000
20A20VAL0-0.0110.01218.608-0.012-0.0120.0000.0000.0000.000
21A21SER00.0140.00017.039-0.001-0.0010.0000.0000.0000.000
22A22CYS0-0.039-0.00813.431-0.067-0.0670.0000.0000.0000.000
23A23LYS10.9000.9599.9981.6251.6250.0000.0000.0000.000
24A24ALA00.0150.0118.808-0.372-0.3720.0000.0000.0000.000
25A25SER0-0.046-0.0345.199-0.409-0.263-0.001-0.007-0.1380.000
26A26GLY00.0820.0343.763-2.064-1.7650.008-0.158-0.1490.000
27A27TYR0-0.001-0.0084.3812.8153.069-0.001-0.025-0.2290.000
28A28THR00.0220.0117.418-0.358-0.3580.0000.0000.0000.000
29A29PHE00.0460.02411.1540.0380.0380.0000.0000.0000.000
30A30THR0-0.003-0.01112.7700.0100.0100.0000.0000.0000.000
31A31GLY00.0280.02014.0540.0580.0580.0000.0000.0000.000
32A32TYR0-0.017-0.01110.7000.0890.0890.0000.0000.0000.000
33A33TYR0-0.032-0.00714.555-0.060-0.0600.0000.0000.0000.000
34A34MET0-0.0340.00712.351-0.071-0.0710.0000.0000.0000.000
35A35HIS00.0320.01616.5880.0820.0820.0000.0000.0000.000
36A36TRP00.014-0.00517.761-0.105-0.1050.0000.0000.0000.000
37A37VAL0-0.003-0.00119.5400.0700.0700.0000.0000.0000.000
38A38ARG10.8240.89920.5220.2590.2590.0000.0000.0000.000
39A39GLN00.004-0.00222.113-0.012-0.0120.0000.0000.0000.000
40A40ALA00.0370.02924.402-0.011-0.0110.0000.0000.0000.000
41A41PRO00.016-0.01127.0860.0000.0000.0000.0000.0000.000
42A42GLY00.0020.01127.3670.0190.0190.0000.0000.0000.000
43A43GLN0-0.0230.00328.1840.0190.0190.0000.0000.0000.000
44A44GLY00.0220.00926.508-0.015-0.0150.0000.0000.0000.000
45A45LEU0-0.014-0.01120.453-0.009-0.0090.0000.0000.0000.000
46A46GLU-1-0.773-0.87924.295-0.235-0.2350.0000.0000.0000.000
47A47TRP0-0.033-0.01722.016-0.010-0.0100.0000.0000.0000.000
48A48MET0-0.004-0.00223.6900.0150.0150.0000.0000.0000.000
49A49GLY00.0210.00523.7350.0310.0310.0000.0000.0000.000
50A50TRP0-0.0220.01220.709-0.054-0.0540.0000.0000.0000.000
51A51ILE00.020-0.01319.2450.0310.0310.0000.0000.0000.000
52A52ASN00.0310.01919.553-0.044-0.0440.0000.0000.0000.000
53A53PRO00.0320.01816.1240.0350.0350.0000.0000.0000.000
54A54ASN00.0560.02919.064-0.001-0.0010.0000.0000.0000.000
55A55SER0-0.026-0.01220.4440.0100.0100.0000.0000.0000.000
56A56GLY0-0.033-0.02722.9080.0100.0100.0000.0000.0000.000
57A57GLY0-0.0040.01024.0890.0040.0040.0000.0000.0000.000
58A58THR0-0.016-0.01223.969-0.025-0.0250.0000.0000.0000.000
59A59ASN0-0.005-0.00325.8620.0320.0320.0000.0000.0000.000
60A60TYR00.0690.01925.863-0.004-0.0040.0000.0000.0000.000
61A61ALA0-0.0060.01227.9230.0220.0220.0000.0000.0000.000
62A62GLN00.043-0.00129.493-0.002-0.0020.0000.0000.0000.000
63A63LYS10.8640.93331.3250.2250.2250.0000.0000.0000.000
64A64PHE0-0.041-0.01928.0530.0010.0010.0000.0000.0000.000
65A65GLN00.0690.04931.458-0.017-0.0170.0000.0000.0000.000
66A66GLY00.0080.00433.0640.0120.0120.0000.0000.0000.000
67A67ARG10.7010.80332.2310.2460.2460.0000.0000.0000.000
68A68VAL00.0080.00826.319-0.012-0.0120.0000.0000.0000.000
69A69THR0-0.0170.00526.5690.0200.0200.0000.0000.0000.000
70A70MET0-0.0430.00122.336-0.031-0.0310.0000.0000.0000.000
71A71THR00.001-0.00422.3290.0250.0250.0000.0000.0000.000
72A72ARG10.8420.91518.6640.2890.2890.0000.0000.0000.000
73A73ASP-1-0.809-0.88418.251-0.435-0.4350.0000.0000.0000.000
74A74THR0-0.011-0.02516.734-0.088-0.0880.0000.0000.0000.000
75A75SER0-0.046-0.02416.191-0.035-0.0350.0000.0000.0000.000
76A76ILE00.0440.02514.694-0.044-0.0440.0000.0000.0000.000
77A77SER0-0.050-0.01311.508-0.181-0.1810.0000.0000.0000.000
78A78THR0-0.013-0.00312.439-0.262-0.2620.0000.0000.0000.000
79A79ALA0-0.0040.00114.9490.1450.1450.0000.0000.0000.000
80A80TYR0-0.002-0.02317.174-0.072-0.0720.0000.0000.0000.000
81A81MET0-0.0150.01720.1380.0580.0580.0000.0000.0000.000
82A82GLU-1-0.838-0.91422.563-0.344-0.3440.0000.0000.0000.000
83A83LEU00.0010.00225.9270.0210.0210.0000.0000.0000.000
84A84SER00.0280.00128.5020.0070.0070.0000.0000.0000.000
85A85ARG10.9160.95732.0530.1990.1990.0000.0000.0000.000
86A86LEU0-0.0300.00829.3970.0060.0060.0000.0000.0000.000
87A87ARG10.8930.90833.4100.2210.2210.0000.0000.0000.000
88A88SER00.0740.02433.331-0.011-0.0110.0000.0000.0000.000
89A89ASP-1-0.836-0.88333.073-0.220-0.2200.0000.0000.0000.000
90A90ASP-1-0.741-0.82229.703-0.264-0.2640.0000.0000.0000.000
91A91THR0-0.0100.01728.287-0.030-0.0300.0000.0000.0000.000
92A92ALA0-0.010-0.00925.1260.0140.0140.0000.0000.0000.000
93A93VAL00.0000.01319.393-0.012-0.0120.0000.0000.0000.000
94A94TYR0-0.027-0.04820.6920.0170.0170.0000.0000.0000.000
95A95TYR00.0310.02715.776-0.066-0.0660.0000.0000.0000.000
96A97ALA00.0660.01613.318-0.119-0.1190.0000.0000.0000.000
97A98ARG10.7860.8868.1280.6470.6470.0000.0000.0000.000
98A99GLY00.0250.01512.7120.0520.0520.0000.0000.0000.000
99A100GLY00.0320.00913.8070.0050.0050.0000.0000.0000.000
100A101TRP0-0.005-0.01814.011-0.038-0.0380.0000.0000.0000.000
101A102ILE0-0.051-0.02615.6840.0030.0030.0000.0000.0000.000
102A103SER0-0.035-0.02418.5970.0380.0380.0000.0000.0000.000
103A104LEU00.0380.02521.450-0.018-0.0180.0000.0000.0000.000
104A105TYR0-0.022-0.01024.5140.0100.0100.0000.0000.0000.000
105A106TYR00.0110.00923.5220.0080.0080.0000.0000.0000.000
106A107ASP-1-0.775-0.87024.042-0.198-0.1980.0000.0000.0000.000
107A108SER0-0.026-0.01819.9990.0110.0110.0000.0000.0000.000
108A109SER0-0.079-0.05520.355-0.032-0.0320.0000.0000.0000.000
109A110GLY00.005-0.00921.653-0.033-0.0330.0000.0000.0000.000
110A111TYR0-0.028-0.01218.8950.0080.0080.0000.0000.0000.000
111A112PRO0-0.0120.00919.385-0.040-0.0400.0000.0000.0000.000
112A113ASN0-0.026-0.02015.847-0.003-0.0030.0000.0000.0000.000
113A114PHE00.004-0.00914.273-0.010-0.0100.0000.0000.0000.000
114A115ASP-1-0.762-0.8509.718-0.694-0.6940.0000.0000.0000.000
115A116TYR0-0.009-0.0044.767-0.437-0.303-0.001-0.006-0.1260.000
116A117TRP0-0.008-0.0239.5710.1870.1870.0000.0000.0000.000
117A118GLY00.0290.00610.052-0.300-0.3000.0000.0000.0000.000
118A119GLN0-0.0110.00311.649-0.046-0.0460.0000.0000.0000.000
119A120GLY0-0.0060.00413.0110.1510.1510.0000.0000.0000.000
120A121THR0-0.035-0.03316.466-0.029-0.0290.0000.0000.0000.000
121A122LEU0-0.040-0.01119.1860.0410.0410.0000.0000.0000.000
122A123VAL00.0250.02422.5550.0010.0010.0000.0000.0000.000
123A124THR0-0.015-0.01325.6010.0180.0180.0000.0000.0000.000
124A125VAL0-0.022-0.01128.9450.0070.0070.0000.0000.0000.000
125A126SER00.0390.00832.0550.0150.0150.0000.0000.0000.000
126A127GLY0-0.005-0.02635.432-0.001-0.0010.0000.0000.0000.000
127A128ALA0-0.0210.01138.6570.0090.0090.0000.0000.0000.000
128A129SER0-0.014-0.00739.708-0.006-0.0060.0000.0000.0000.000
129A130THR0-0.007-0.01342.268-0.001-0.0010.0000.0000.0000.000
130A131LYS10.9270.98143.3030.1170.1170.0000.0000.0000.000
131A132GLY00.0460.02345.289-0.003-0.0030.0000.0000.0000.000
132A133PRO00.0010.00146.3920.0000.0000.0000.0000.0000.000
133A134SER0-0.0250.00448.1650.0060.0060.0000.0000.0000.000
134A135VAL00.006-0.01050.252-0.002-0.0020.0000.0000.0000.000
135A136PHE0-0.033-0.01852.1490.0040.0040.0000.0000.0000.000
136A137PRO0-0.041-0.00553.111-0.002-0.0020.0000.0000.0000.000
137A138LEU00.0200.00250.1860.0000.0000.0000.0000.0000.000
138A149THR00.000-0.00855.2840.0010.0010.0000.0000.0000.000
139A150ALA0-0.052-0.02957.5280.0000.0000.0000.0000.0000.000
140A151ALA00.0050.00753.171-0.001-0.0010.0000.0000.0000.000
141A152LEU0-0.0110.00553.6220.0010.0010.0000.0000.0000.000
142A153GLY00.0850.02151.314-0.002-0.0020.0000.0000.0000.000
143A154CYS0-0.121-0.03650.6500.0010.0010.0000.0000.0000.000
144A155LEU00.0030.01248.001-0.003-0.0030.0000.0000.0000.000
145A156VAL00.018-0.00745.7220.0020.0020.0000.0000.0000.000
146A157LYS10.9540.97646.4600.0880.0880.0000.0000.0000.000
147A158ASP-1-0.853-0.93845.148-0.111-0.1110.0000.0000.0000.000
148A159TYR0-0.053-0.02240.2670.0060.0060.0000.0000.0000.000
149A160PHE00.0290.01936.768-0.008-0.0080.0000.0000.0000.000
150A161PRO0-0.004-0.00237.0110.0060.0060.0000.0000.0000.000
151A162GLU-1-0.765-0.87235.433-0.138-0.1380.0000.0000.0000.000
152A163PRO0-0.016-0.01536.703-0.003-0.0030.0000.0000.0000.000
153A164VAL00.016-0.00838.4830.0050.0050.0000.0000.0000.000
154A165THR0-0.046-0.02541.498-0.001-0.0010.0000.0000.0000.000
155A166VAL00.0390.01443.5600.0030.0030.0000.0000.0000.000
156A167SER0-0.029-0.01446.2360.0020.0020.0000.0000.0000.000
157A168TRP00.0660.02348.8610.0010.0010.0000.0000.0000.000
158A169ASN0-0.018-0.03652.1120.0000.0000.0000.0000.0000.000
159A170SER0-0.016-0.01552.8870.0010.0010.0000.0000.0000.000
160A171GLY00.0110.00750.3070.0010.0010.0000.0000.0000.000
161A172ALA0-0.0090.01751.2100.0010.0010.0000.0000.0000.000
162A173LEU0-0.022-0.00152.1350.0020.0020.0000.0000.0000.000
163A174THR00.029-0.00247.411-0.002-0.0020.0000.0000.0000.000
164A175SER00.0150.00847.912-0.003-0.0030.0000.0000.0000.000
165A176GLY00.0700.03248.4370.0010.0010.0000.0000.0000.000
166A177VAL0-0.060-0.02046.703-0.001-0.0010.0000.0000.0000.000
167A178HIS00.0110.00840.6550.0000.0000.0000.0000.0000.000
168A179THR00.0070.02841.7220.0030.0030.0000.0000.0000.000
169A180PHE0-0.023-0.00941.165-0.004-0.0040.0000.0000.0000.000
170A181PRO00.020-0.00536.2870.0000.0000.0000.0000.0000.000
171A182ALA0-0.0140.00937.8800.0040.0040.0000.0000.0000.000
172A183VAL0-0.024-0.00637.597-0.008-0.0080.0000.0000.0000.000
173A184LEU0-0.026-0.01734.1840.0020.0020.0000.0000.0000.000
174A185GLN0-0.034-0.02137.9090.0030.0030.0000.0000.0000.000
175A186SER0-0.004-0.00739.207-0.006-0.0060.0000.0000.0000.000
176A187SER00.0140.00440.284-0.004-0.0040.0000.0000.0000.000
177A188GLY0-0.020-0.01338.375-0.001-0.0010.0000.0000.0000.000
178A189LEU0-0.065-0.02439.324-0.002-0.0020.0000.0000.0000.000
179A190TYR00.0430.01734.358-0.004-0.0040.0000.0000.0000.000
180A191SER0-0.011-0.01540.9860.0100.0100.0000.0000.0000.000
181A192LEU00.0440.05141.332-0.004-0.0040.0000.0000.0000.000
182A193SER00.010-0.00943.6000.0060.0060.0000.0000.0000.000
183A194SER00.013-0.00144.936-0.004-0.0040.0000.0000.0000.000
184A195VAL0-0.022-0.03746.9970.0030.0030.0000.0000.0000.000
185A196VAL00.0230.01348.356-0.001-0.0010.0000.0000.0000.000
186A197THR0-0.054-0.02250.0160.0010.0010.0000.0000.0000.000
187A198VAL00.0290.01252.5230.0020.0020.0000.0000.0000.000
188A199PRO00.0310.02056.1290.0000.0000.0000.0000.0000.000
189A200SER00.047-0.00359.5350.0000.0000.0000.0000.0000.000
190A201SER0-0.049-0.01962.0230.0000.0000.0000.0000.0000.000
191A202SER00.0130.02562.4730.0020.0020.0000.0000.0000.000
192A203LEU00.010-0.00663.849-0.002-0.0020.0000.0000.0000.000
193A204GLY00.0110.00265.606-0.001-0.0010.0000.0000.0000.000
194A205THR0-0.055-0.02665.7890.0010.0010.0000.0000.0000.000
195A206GLN00.0510.03060.3490.0000.0000.0000.0000.0000.000
196A207THR0-0.046-0.00161.303-0.001-0.0010.0000.0000.0000.000
197A208TYR00.0410.01656.5430.0000.0000.0000.0000.0000.000
198A209ILE0-0.001-0.00755.794-0.001-0.0010.0000.0000.0000.000
199A211ASN00.001-0.01050.620-0.001-0.0010.0000.0000.0000.000
200A212VAL00.0220.01547.972-0.003-0.0030.0000.0000.0000.000
201A213ASN0-0.009-0.02146.0360.0040.0040.0000.0000.0000.000
202A214HIS0-0.0040.02141.5310.0020.0020.0000.0000.0000.000
203A215LYS10.9600.97141.9000.1060.1060.0000.0000.0000.000
204A216PRO00.0230.01640.2980.0030.0030.0000.0000.0000.000
205A217SER0-0.018-0.01842.9290.0010.0010.0000.0000.0000.000
206A218ASN0-0.039-0.01746.2650.0020.0020.0000.0000.0000.000
207A219THR00.0150.00947.6530.0060.0060.0000.0000.0000.000
208A220LYS10.8440.90248.8000.0680.0680.0000.0000.0000.000
209A221VAL00.0110.01251.2490.0030.0030.0000.0000.0000.000
210A222ASP-1-0.819-0.89152.887-0.067-0.0670.0000.0000.0000.000
211A223LYS10.9500.97754.5960.0650.0650.0000.0000.0000.000
212A224ARG10.9731.00655.7470.0540.0540.0000.0000.0000.000