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: 856ZY

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2101241.228218
FMO2-HF: Nuclear repulsion 2019277.602188
FMO2-HF: Total energy -81963.62603
FMO2-MP2: Total energy -82201.102872


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.
1.5785.4421.388-1.72-3.5330
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 : 0.036 / q_NPA : 0.003
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].
3A3GLN0-0.020-0.0032.224-0.4252.7451.370-1.546-2.9950.000
4A4LEU0-0.026-0.0164.9951.1131.202-0.001-0.008-0.0800.000
5A5VAL00.0200.0118.143-0.076-0.0760.0000.0000.0000.000
6A6GLN0-0.008-0.04710.6720.2460.2460.0000.0000.0000.000
7A7SER00.0340.03114.389-0.095-0.0950.0000.0000.0000.000
8A8GLY00.0210.01117.317-0.023-0.0230.0000.0000.0000.000
9A9ALA0-0.018-0.01219.2450.0510.0510.0000.0000.0000.000
10A10GLU-1-0.923-0.96122.263-0.498-0.4980.0000.0000.0000.000
11A11VAL00.001-0.00225.4170.0180.0180.0000.0000.0000.000
12A12LYS10.9140.96228.2700.3830.3830.0000.0000.0000.000
13A13LYS10.9870.98931.6390.2340.2340.0000.0000.0000.000
14A14PRO00.019-0.00634.690-0.002-0.0020.0000.0000.0000.000
15A15GLY0-0.031-0.00536.1510.0070.0070.0000.0000.0000.000
16A16ALA0-0.029-0.00533.2280.0050.0050.0000.0000.0000.000
17A17SER00.0530.01230.2200.0110.0110.0000.0000.0000.000
18A18VAL0-0.040-0.01724.818-0.012-0.0120.0000.0000.0000.000
19A19LYS10.9770.99123.3580.3430.3430.0000.0000.0000.000
20A20VAL00.0070.01918.536-0.030-0.0300.0000.0000.0000.000
21A21SER0-0.009-0.00617.2080.0290.0290.0000.0000.0000.000
22A22CYS0-0.0320.00113.403-0.074-0.0740.0000.0000.0000.000
23A23LYS10.9460.99210.7091.2651.2650.0000.0000.0000.000
24A24ALA00.007-0.0029.351-0.397-0.3970.0000.0000.0000.000
25A25SER0-0.057-0.0286.063-0.229-0.2290.0000.0000.0000.000
26A26GLY00.0930.0373.307-1.499-1.1910.020-0.144-0.1840.000
27A27TYR0-0.010-0.0143.9172.9553.252-0.001-0.022-0.2740.000
28A28THR00.0260.0127.094-0.498-0.4980.0000.0000.0000.000
29A29PHE00.0420.02410.773-0.090-0.0900.0000.0000.0000.000
30A30THR0-0.009-0.01412.427-0.032-0.0320.0000.0000.0000.000
31A31GLY00.0470.02514.000-0.024-0.0240.0000.0000.0000.000
32A32TYR0-0.015-0.01310.9530.1800.1800.0000.0000.0000.000
33A33TYR00.0110.01514.574-0.090-0.0900.0000.0000.0000.000
34A34MET0-0.0200.01112.484-0.037-0.0370.0000.0000.0000.000
35A35HIS00.0350.02716.594-0.005-0.0050.0000.0000.0000.000
36A36TRP00.019-0.00117.634-0.115-0.1150.0000.0000.0000.000
37A37VAL00.001-0.00119.5030.0670.0670.0000.0000.0000.000
38A38ARG10.8590.92820.4470.2110.2110.0000.0000.0000.000
39A39GLN00.0030.00122.135-0.008-0.0080.0000.0000.0000.000
40A40ALA00.0390.03024.366-0.030-0.0300.0000.0000.0000.000
41A41PRO00.006-0.01427.093-0.003-0.0030.0000.0000.0000.000
42A42GLY00.0080.01627.3760.0230.0230.0000.0000.0000.000
43A43GLN0-0.026-0.00528.1900.0280.0280.0000.0000.0000.000
44A44GLY00.0180.00526.528-0.021-0.0210.0000.0000.0000.000
45A45LEU0-0.022-0.01620.612-0.012-0.0120.0000.0000.0000.000
46A46GLU-1-0.807-0.91424.298-0.176-0.1760.0000.0000.0000.000
47A47TRP0-0.042-0.02721.763-0.026-0.0260.0000.0000.0000.000
48A48MET0-0.014-0.00623.583-0.002-0.0020.0000.0000.0000.000
49A49GLY00.0350.00423.6740.0220.0220.0000.0000.0000.000
50A50TRP0-0.0130.01520.702-0.037-0.0370.0000.0000.0000.000
51A51ILE00.026-0.01519.4100.0030.0030.0000.0000.0000.000
52A52ASN00.0230.01619.5660.0320.0320.0000.0000.0000.000
53A53PRO00.0320.01616.180-0.017-0.0170.0000.0000.0000.000
54A54ASN00.0540.03418.9890.0090.0090.0000.0000.0000.000
55A55SER0-0.029-0.00620.152-0.018-0.0180.0000.0000.0000.000
56A56GLY0-0.029-0.02622.820-0.018-0.0180.0000.0000.0000.000
57A57GLY0-0.0140.00224.129-0.023-0.0230.0000.0000.0000.000
58A58THR0-0.014-0.01123.9840.0010.0010.0000.0000.0000.000
59A59ASN00.0030.00125.8730.0180.0180.0000.0000.0000.000
60A60TYR00.0470.01825.796-0.014-0.0140.0000.0000.0000.000
61A61ALA00.0180.01927.9250.0190.0190.0000.0000.0000.000
62A62GLN00.0480.00129.490-0.016-0.0160.0000.0000.0000.000
63A63LYS10.8700.94831.1940.1600.1600.0000.0000.0000.000
64A64PHE0-0.035-0.02328.126-0.011-0.0110.0000.0000.0000.000
65A65GLN00.0670.04631.336-0.006-0.0060.0000.0000.0000.000
66A66GLY00.0010.00133.0050.0030.0030.0000.0000.0000.000
67A67ARG10.6820.78631.6500.2100.2100.0000.0000.0000.000
68A68VAL00.0030.01026.269-0.020-0.0200.0000.0000.0000.000
69A69THR00.0160.01527.0950.0320.0320.0000.0000.0000.000
70A70MET0-0.067-0.00522.543-0.029-0.0290.0000.0000.0000.000
71A71THR00.0010.00122.7500.0260.0260.0000.0000.0000.000
72A72ARG10.8370.90218.993-0.036-0.0360.0000.0000.0000.000
73A73ASP-1-0.821-0.89018.978-0.183-0.1830.0000.0000.0000.000
74A74THR0-0.017-0.02416.988-0.066-0.0660.0000.0000.0000.000
75A75SER0-0.023-0.01316.3810.0300.0300.0000.0000.0000.000
76A76ILE00.0180.01415.525-0.025-0.0250.0000.0000.0000.000
77A77SER0-0.060-0.03011.936-0.106-0.1060.0000.0000.0000.000
78A78THR0-0.015-0.00313.309-0.240-0.2400.0000.0000.0000.000
79A79ALA0-0.0040.00015.8360.1320.1320.0000.0000.0000.000
80A80TYR0-0.017-0.02817.749-0.095-0.0950.0000.0000.0000.000
81A81MET0-0.0120.02020.5640.0760.0760.0000.0000.0000.000
82A82GLU-1-0.919-0.96922.682-0.300-0.3000.0000.0000.0000.000
83A83LEU0-0.013-0.00226.0860.0330.0330.0000.0000.0000.000
84A84SER00.0340.00328.433-0.007-0.0070.0000.0000.0000.000
85A85ARG10.9020.95232.0560.1570.1570.0000.0000.0000.000
86A86LEU0-0.0230.00829.3510.0070.0070.0000.0000.0000.000
87A87ARG11.0100.99933.3190.1930.1930.0000.0000.0000.000
88A88SER00.0640.01533.259-0.011-0.0110.0000.0000.0000.000
89A89ASP-1-0.928-0.96233.023-0.225-0.2250.0000.0000.0000.000
90A90ASP-1-0.743-0.81929.626-0.244-0.2440.0000.0000.0000.000
91A91THR0-0.0060.03428.218-0.035-0.0350.0000.0000.0000.000
92A92ALA0-0.006-0.00625.0600.0180.0180.0000.0000.0000.000
93A93VAL00.0060.02019.392-0.025-0.0250.0000.0000.0000.000
94A94TYR0-0.021-0.04420.6200.0560.0560.0000.0000.0000.000
95A95TYR00.0280.03715.456-0.102-0.1020.0000.0000.0000.000
96A97ALA00.0720.01813.210-0.149-0.1490.0000.0000.0000.000
97A98ARG10.8080.8987.702-0.954-0.9540.0000.0000.0000.000
98A99GLY00.0290.01612.7120.0190.0190.0000.0000.0000.000
99A100GLY00.0260.01013.8130.1030.1030.0000.0000.0000.000
100A101TRP00.010-0.01313.852-0.069-0.0690.0000.0000.0000.000
101A102ILE0-0.066-0.02515.702-0.081-0.0810.0000.0000.0000.000
102A103SER0-0.191-0.11418.6180.0460.0460.0000.0000.0000.000
103A104LEU00.1140.03021.473-0.048-0.0480.0000.0000.0000.000
104A105TYR00.0370.07324.5380.0200.0200.0000.0000.0000.000
105A106TYR00.0230.00523.576-0.008-0.0080.0000.0000.0000.000
106A107ASP-1-0.840-0.89524.0600.1460.1460.0000.0000.0000.000
107A108SER0-0.018-0.01820.0820.0050.0050.0000.0000.0000.000
108A109SER0-0.077-0.05320.362-0.009-0.0090.0000.0000.0000.000
109A110GLY00.003-0.00821.657-0.039-0.0390.0000.0000.0000.000
110A111TYR0-0.031-0.01619.092-0.020-0.0200.0000.0000.0000.000
111A112PRO0-0.0050.01219.383-0.013-0.0130.0000.0000.0000.000
112A113ASN0-0.025-0.02115.948-0.057-0.0570.0000.0000.0000.000
113A114PHE0-0.005-0.01414.2490.0440.0440.0000.0000.0000.000
114A115ASP-1-0.768-0.8559.7060.3640.3640.0000.0000.0000.000
115A116TYR0-0.021-0.0144.897-0.009-0.0090.0000.0000.0000.000
116A117TRP00.000-0.0149.5910.1460.1460.0000.0000.0000.000
117A118GLY00.0250.00010.001-0.364-0.3640.0000.0000.0000.000
118A119GLN0-0.0020.00811.691-0.029-0.0290.0000.0000.0000.000
119A120GLY0-0.0030.00312.9920.1490.1490.0000.0000.0000.000
120A121THR0-0.033-0.03216.424-0.075-0.0750.0000.0000.0000.000
121A122LEU0-0.032-0.00819.1310.0740.0740.0000.0000.0000.000
122A123VAL00.0290.02622.517-0.005-0.0050.0000.0000.0000.000
123A124THR0-0.022-0.01925.5450.0250.0250.0000.0000.0000.000
124A125VAL0-0.036-0.02628.9020.0080.0080.0000.0000.0000.000
125A126SER00.024-0.00331.9980.0190.0190.0000.0000.0000.000
126A127GLY0-0.016-0.02835.384-0.002-0.0020.0000.0000.0000.000
127A128ALA0-0.0290.01038.5990.0110.0110.0000.0000.0000.000
128A129SER0-0.010-0.00539.667-0.010-0.0100.0000.0000.0000.000
129A130THR0-0.010-0.01341.902-0.001-0.0010.0000.0000.0000.000
130A131LYS10.9300.97743.0970.1700.1700.0000.0000.0000.000
131A132GLY00.0300.01945.211-0.007-0.0070.0000.0000.0000.000
132A133PRO0-0.014-0.00646.2160.0040.0040.0000.0000.0000.000
133A134SER0-0.0050.01848.1790.0080.0080.0000.0000.0000.000
134A135VAL00.012-0.00150.106-0.003-0.0030.0000.0000.0000.000
135A136PHE0-0.031-0.02152.1790.0070.0070.0000.0000.0000.000
136A137PRO0-0.059-0.02053.151-0.004-0.0040.0000.0000.0000.000
137A138LEU00.0190.00950.2300.0020.0020.0000.0000.0000.000
138A149THR0-0.019-0.02355.0390.0020.0020.0000.0000.0000.000
139A150ALA0-0.030-0.00257.3800.0020.0020.0000.0000.0000.000
140A151ALA00.0150.00753.157-0.004-0.0040.0000.0000.0000.000
141A152LEU0-0.0090.00453.6060.0030.0030.0000.0000.0000.000
142A153GLY00.0900.02151.373-0.006-0.0060.0000.0000.0000.000
143A154CYS0-0.102-0.03550.7060.0010.0010.0000.0000.0000.000
144A155LEU0-0.0080.00047.978-0.006-0.0060.0000.0000.0000.000
145A156VAL00.0110.00245.9200.0040.0040.0000.0000.0000.000
146A157LYS10.9760.97546.4830.1220.1220.0000.0000.0000.000
147A158ASP-1-0.871-0.95145.173-0.153-0.1530.0000.0000.0000.000
148A159TYR0-0.0200.00940.9400.0020.0020.0000.0000.0000.000
149A160PHE00.0350.01836.619-0.010-0.0100.0000.0000.0000.000
150A161PRO0-0.009-0.00636.8660.0090.0090.0000.0000.0000.000
151A162GLU-1-0.815-0.90135.322-0.243-0.2430.0000.0000.0000.000
152A163PRO0-0.022-0.02136.326-0.008-0.0080.0000.0000.0000.000
153A164VAL00.026-0.00438.3270.0090.0090.0000.0000.0000.000
154A165THR0-0.045-0.03541.167-0.006-0.0060.0000.0000.0000.000
155A166VAL00.0270.01743.3710.0080.0080.0000.0000.0000.000
156A167SER0-0.017-0.00546.159-0.001-0.0010.0000.0000.0000.000
157A168TRP00.0700.02248.7480.0070.0070.0000.0000.0000.000
158A169ASN0-0.005-0.02552.063-0.001-0.0010.0000.0000.0000.000
159A170SER0-0.026-0.01952.6320.0010.0010.0000.0000.0000.000
160A171GLY00.0090.00850.112-0.002-0.0020.0000.0000.0000.000
161A172ALA0-0.0070.01551.059-0.002-0.0020.0000.0000.0000.000
162A173LEU0-0.0240.00151.7640.0020.0020.0000.0000.0000.000
163A174THR00.029-0.00247.365-0.003-0.0030.0000.0000.0000.000
164A175SER00.0090.00347.820-0.005-0.0050.0000.0000.0000.000
165A176GLY00.0600.02648.3480.0050.0050.0000.0000.0000.000
166A177VAL0-0.052-0.01646.4030.0030.0030.0000.0000.0000.000
167A178HIS00.0170.01040.656-0.007-0.0070.0000.0000.0000.000
168A179THR0-0.0060.01141.9520.0080.0080.0000.0000.0000.000
169A180PHE0-0.043-0.02541.239-0.009-0.0090.0000.0000.0000.000
170A181PRO00.017-0.00836.358-0.001-0.0010.0000.0000.0000.000
171A182ALA0-0.0060.01537.9950.0110.0110.0000.0000.0000.000
172A183VAL0-0.018-0.00137.626-0.009-0.0090.0000.0000.0000.000
173A184LEU0-0.020-0.01634.3860.0010.0010.0000.0000.0000.000
174A185GLN0-0.019-0.00837.9080.0110.0110.0000.0000.0000.000
175A186SER00.007-0.00339.171-0.009-0.0090.0000.0000.0000.000
176A187SER0-0.003-0.00740.249-0.002-0.0020.0000.0000.0000.000
177A188GLY0-0.015-0.00838.346-0.001-0.0010.0000.0000.0000.000
178A189LEU0-0.068-0.02439.305-0.008-0.0080.0000.0000.0000.000
179A190TYR00.0530.02134.309-0.003-0.0030.0000.0000.0000.000
180A191SER0-0.005-0.01340.9930.0150.0150.0000.0000.0000.000
181A192LEU00.0050.04041.429-0.005-0.0050.0000.0000.0000.000
182A193SER00.020-0.00943.6360.0130.0130.0000.0000.0000.000
183A194SER00.0010.01244.993-0.010-0.0100.0000.0000.0000.000
184A195VAL0-0.001-0.01947.0660.0070.0070.0000.0000.0000.000
185A196VAL00.0420.02448.303-0.006-0.0060.0000.0000.0000.000
186A197THR0-0.065-0.03150.0010.0060.0060.0000.0000.0000.000
187A198VAL00.0370.01252.475-0.001-0.0010.0000.0000.0000.000
188A199PRO00.0270.01956.0800.0020.0020.0000.0000.0000.000
189A200SER00.032-0.01559.504-0.001-0.0010.0000.0000.0000.000
190A201SER0-0.031-0.00961.9280.0000.0000.0000.0000.0000.000
191A202SER00.0000.01762.4410.0020.0020.0000.0000.0000.000
192A203LEU00.004-0.00163.759-0.003-0.0030.0000.0000.0000.000
193A204GLY00.0160.00565.5870.0000.0000.0000.0000.0000.000
194A205THR0-0.052-0.01865.7730.0010.0010.0000.0000.0000.000
195A206GLN00.0400.00560.370-0.004-0.0040.0000.0000.0000.000
196A207THR0-0.0570.00361.3270.0000.0000.0000.0000.0000.000
197A208TYR00.0440.00956.452-0.003-0.0030.0000.0000.0000.000
198A209ILE0-0.0010.00455.5540.0010.0010.0000.0000.0000.000
199A211ASN00.0020.00050.9270.0020.0020.0000.0000.0000.000
200A212VAL00.0120.01347.670-0.008-0.0080.0000.0000.0000.000
201A213ASN00.007-0.02245.5320.0080.0080.0000.0000.0000.000
202A214HIS0-0.0070.00941.2720.0020.0020.0000.0000.0000.000
203A215LYS10.9420.97041.4460.2240.2240.0000.0000.0000.000
204A216PRO00.0270.01739.8960.0060.0060.0000.0000.0000.000
205A217SER0-0.0070.00442.5040.0050.0050.0000.0000.0000.000
206A218ASN0-0.042-0.01845.7930.0050.0050.0000.0000.0000.000
207A219THR00.010-0.00247.2720.0110.0110.0000.0000.0000.000
208A220LYS10.9480.96448.4690.1340.1340.0000.0000.0000.000
209A221VAL0-0.022-0.01050.8930.0060.0060.0000.0000.0000.000
210A222ASP-1-0.848-0.92052.725-0.136-0.1360.0000.0000.0000.000
211A223LYS10.9030.95854.6250.1130.1130.0000.0000.0000.000
212A224ARG10.9981.01255.8050.0980.0980.0000.0000.0000.000