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: R8Q18

Calculation Name: 3U5R-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U5R

Chain ID: E

ChEMBL ID:

UniProt ID: Q92MN6

Base Structure: X-ray

Registration Date: 2023-09-22

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1876865.768211
FMO2-HF: Nuclear repulsion 1809208.548815
FMO2-HF: Total energy -67657.219396
FMO2-MP2: Total energy -67857.426679


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(E:26:LYS)


Summations of interaction energy for fragment #1(E:26: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.
-26.743-18.2174.133-5.151-7.509-0.042
Interaction energy analysis for fragmet #1(E:26:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.913 / q_NPA : 0.952
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].
3E28GLN00.0300.0153.735-3.170-0.802-0.011-1.272-1.0850.001
4E29SER00.0590.0186.3210.6200.6200.0000.0000.0000.000
5E30ASN0-0.032-0.0149.717-0.452-0.4520.0000.0000.0000.000
6E31SER00.0060.00412.5070.1520.1520.0000.0000.0000.000
7E32ILE0-0.043-0.01115.3640.9110.9110.0000.0000.0000.000
8E33THR00.0100.00617.726-0.139-0.1390.0000.0000.0000.000
9E34LEU00.0440.03819.9380.1860.1860.0000.0000.0000.000
10E35GLY0-0.008-0.00722.6370.3340.3340.0000.0000.0000.000
11E36THR0-0.057-0.04722.7600.5380.5380.0000.0000.0000.000
12E37ARG10.8280.87424.6989.5069.5060.0000.0000.0000.000
13E38ALA00.0070.01223.796-0.425-0.4250.0000.0000.0000.000
14E39ALA0-0.0160.00323.0400.4700.4700.0000.0000.0000.000
15E40ASP-1-0.797-0.90824.635-10.424-10.4240.0000.0000.0000.000
16E41PHE0-0.088-0.04423.772-0.365-0.3650.0000.0000.0000.000
17E42VAL00.0360.01426.0410.3390.3390.0000.0000.0000.000
18E43LEU0-0.042-0.01221.372-0.299-0.2990.0000.0000.0000.000
19E44PRO00.0230.02624.4120.2580.2580.0000.0000.0000.000
20E45ASP-1-0.721-0.86224.424-11.001-11.0010.0000.0000.0000.000
21E46ALA0-0.034-0.03424.6190.1490.1490.0000.0000.0000.000
22E47GLY0-0.065-0.02026.2790.1620.1620.0000.0000.0000.000
23E48GLY0-0.030-0.00828.8100.3230.3230.0000.0000.0000.000
24E49ASN0-0.088-0.05630.0300.4740.4740.0000.0000.0000.000
25E50LEU0-0.022-0.01728.796-0.403-0.4030.0000.0000.0000.000
26E51PHE0-0.005-0.00326.7710.2120.2120.0000.0000.0000.000
27E52THR0-0.012-0.03227.524-0.263-0.2630.0000.0000.0000.000
28E53LEU0-0.012-0.01825.442-0.046-0.0460.0000.0000.0000.000
29E54ALA0-0.024-0.00328.8970.1500.1500.0000.0000.0000.000
30E55GLU-1-0.830-0.89730.247-9.112-9.1120.0000.0000.0000.000
31E56PHE00.004-0.00526.392-0.069-0.0690.0000.0000.0000.000
32E57LYS10.8530.92130.3238.2018.2010.0000.0000.0000.000
33E58ASP-1-0.838-0.90632.997-8.334-8.3340.0000.0000.0000.000
34E59SER00.0010.02830.1080.1430.1430.0000.0000.0000.000
35E60PRO0-0.027-0.01231.132-0.119-0.1190.0000.0000.0000.000
36E61ALA00.0350.02126.251-0.111-0.1110.0000.0000.0000.000
37E62LEU0-0.006-0.00324.2050.1970.1970.0000.0000.0000.000
38E63LEU0-0.0080.00318.037-0.309-0.3090.0000.0000.0000.000
39E64VAL00.0260.01818.4400.2000.2000.0000.0000.0000.000
40E65ALA0-0.007-0.01015.971-0.649-0.6490.0000.0000.0000.000
41E66PHE00.0300.02512.8450.2580.2580.0000.0000.0000.000
42E67ILE0-0.002-0.02911.731-1.955-1.9550.0000.0000.0000.000
43E68SER0-0.030-0.05610.370-0.498-0.4980.0000.0000.0000.000
44E69ASN00.0480.00812.2980.0230.0230.0000.0000.0000.000
45E70ARG10.8230.88912.09421.61521.6150.0000.0000.0000.000
46E71CYS0-0.0540.0106.245-3.254-3.2540.0000.0000.0000.000
47E72PRO00.0360.0046.1510.9720.9720.0000.0000.0000.000
48E73PHE00.034-0.0052.516-2.855-1.2411.553-0.819-2.348-0.011
49E74VAL00.0040.0066.9631.4371.4370.0000.0000.0000.000
50E75VAL0-0.018-0.01410.1981.5701.5700.0000.0000.0000.000
51E76LEU0-0.037-0.0089.6351.0341.0340.0000.0000.0000.000
52E77ILE00.008-0.00311.4840.9950.9950.0000.0000.0000.000
53E78ARG10.8470.93913.83918.19318.1930.0000.0000.0000.000
54E79GLU-1-0.840-0.93815.825-15.211-15.2110.0000.0000.0000.000
55E80ALA0-0.017-0.00416.8290.7390.7390.0000.0000.0000.000
56E81LEU00.006-0.00115.5990.5480.5480.0000.0000.0000.000
57E82ALA00.0030.00818.4660.5720.5720.0000.0000.0000.000
58E83LYS10.8800.95021.39811.78411.7840.0000.0000.0000.000
59E84PHE00.004-0.00720.4800.4310.4310.0000.0000.0000.000
60E85ALA0-0.010-0.01122.3090.3840.3840.0000.0000.0000.000
61E86GLY00.0010.00223.9320.4490.4490.0000.0000.0000.000
62E87ASP-1-0.824-0.90425.124-10.972-10.9720.0000.0000.0000.000
63E88TYR0-0.036-0.03823.8680.2120.2120.0000.0000.0000.000
64E89ALA00.0370.02428.1970.2070.2070.0000.0000.0000.000
65E90GLY0-0.034-0.01629.8110.2260.2260.0000.0000.0000.000
66E91GLN0-0.057-0.03930.2910.3150.3150.0000.0000.0000.000
67E92GLY0-0.002-0.00331.3000.1440.1440.0000.0000.0000.000
68E93LEU0-0.028-0.01423.357-0.094-0.0940.0000.0000.0000.000
69E94ALA00.0020.01727.2700.0580.0580.0000.0000.0000.000
70E95VAL0-0.002-0.01721.222-0.387-0.3870.0000.0000.0000.000
71E96VAL00.0060.01221.7650.3460.3460.0000.0000.0000.000
72E97ALA00.0070.01017.982-0.611-0.6110.0000.0000.0000.000
73E98ILE00.0190.00217.0710.6110.6110.0000.0000.0000.000
74E99ASN00.001-0.00714.711-1.494-1.4940.0000.0000.0000.000
75E100SER00.016-0.03313.9880.5340.5340.0000.0000.0000.000
76E101ASN0-0.028-0.0089.616-0.512-0.5120.0000.0000.0000.000
77E102ASP-1-0.788-0.90113.199-15.573-15.5730.0000.0000.0000.000
78E103ALA0-0.004-0.01315.242-0.563-0.5630.0000.0000.0000.000
79E104GLN0-0.047-0.01917.6020.5810.5810.0000.0000.0000.000
80E105ALA0-0.022-0.00714.0870.1380.1380.0000.0000.0000.000
81E106PHE0-0.023-0.01310.108-1.362-1.3620.0000.0000.0000.000
82E107PRO00.0870.04715.1230.2260.2260.0000.0000.0000.000
83E108GLU-1-0.825-0.89514.107-19.093-19.0930.0000.0000.0000.000
84E109GLU-1-0.727-0.79511.852-21.559-21.5590.0000.0000.0000.000
85E110THR0-0.002-0.00916.2600.5980.5980.0000.0000.0000.000
86E111LEU00.0220.00720.012-0.218-0.2180.0000.0000.0000.000
87E112GLU-1-0.788-0.85222.439-12.063-12.0630.0000.0000.0000.000
88E113ARG10.8360.88019.57413.16413.1640.0000.0000.0000.000
89E114VAL00.0000.00918.510-0.218-0.2180.0000.0000.0000.000
90E115GLY00.0420.01020.7360.1410.1410.0000.0000.0000.000
91E116ALA0-0.072-0.03722.4070.3050.3050.0000.0000.0000.000
92E117GLU-1-0.820-0.89117.034-16.435-16.4350.0000.0000.0000.000
93E118VAL0-0.0070.00020.7940.1250.1250.0000.0000.0000.000
94E119LYS10.8980.94523.31910.57010.5700.0000.0000.0000.000
95E120ALA0-0.033-0.00521.9470.3120.3120.0000.0000.0000.000
96E121TYR0-0.021-0.01418.998-0.039-0.0390.0000.0000.0000.000
97E122GLY00.0100.01722.143-0.119-0.1190.0000.0000.0000.000
98E123TYR0-0.052-0.04217.117-0.082-0.0820.0000.0000.0000.000
99E124GLY00.0130.01823.1380.2830.2830.0000.0000.0000.000
100E125PHE0-0.037-0.03119.1470.1980.1980.0000.0000.0000.000
101E126PRO00.0120.02224.187-0.203-0.2030.0000.0000.0000.000
102E127TYR0-0.011-0.02516.103-0.733-0.7330.0000.0000.0000.000
103E128LEU0-0.0060.00020.6720.3630.3630.0000.0000.0000.000
104E129LYS10.7570.86216.38515.70815.7080.0000.0000.0000.000
105E130ASP-1-0.702-0.82618.110-14.372-14.3720.0000.0000.0000.000
106E131ALA00.003-0.00818.543-0.700-0.7000.0000.0000.0000.000
107E132SER00.0110.01319.756-0.427-0.4270.0000.0000.0000.000
108E133GLN0-0.024-0.02714.284-0.090-0.0900.0000.0000.0000.000
109E134SER0-0.027-0.00417.743-0.194-0.1940.0000.0000.0000.000
110E135VAL00.0470.01919.7070.0790.0790.0000.0000.0000.000
111E136ALA00.0120.00014.228-0.148-0.1480.0000.0000.0000.000
112E137LYS10.8400.92416.10815.56715.5670.0000.0000.0000.000
113E138ALA0-0.025-0.00717.4850.0420.0420.0000.0000.0000.000
114E139TYR0-0.046-0.04317.6100.2930.2930.0000.0000.0000.000
115E140GLY00.0130.01916.077-0.210-0.2100.0000.0000.0000.000
116E141ALA0-0.0130.01112.773-1.021-1.0210.0000.0000.0000.000
117E142ALA0-0.012-0.0079.0150.0090.0090.0000.0000.0000.000
118E143CYS0-0.110-0.0645.817-2.555-2.5550.0000.0000.0000.000
119E144THR0-0.0040.0316.6253.2553.2550.0000.0000.0000.000
120E145PRO00.0270.0087.045-3.436-3.4360.0000.0000.0000.000
121E146ASP-1-0.768-0.8968.945-24.126-24.1260.0000.0000.0000.000
122E147PHE00.0190.02011.4111.0871.0870.0000.0000.0000.000
123E148PHE00.0100.00514.396-0.213-0.2130.0000.0000.0000.000
124E149LEU00.0140.02118.1160.4430.4430.0000.0000.0000.000
125E150TYR00.009-0.00121.003-0.099-0.0990.0000.0000.0000.000
126E151ASP-1-0.752-0.87524.533-10.054-10.0540.0000.0000.0000.000
127E152ARG10.8960.94227.9938.8248.8240.0000.0000.0000.000
128E153GLU-1-0.798-0.84330.834-8.822-8.8220.0000.0000.0000.000
129E154ARG10.7810.86627.16110.08210.0820.0000.0000.0000.000
130E155ARG10.8550.91826.7299.3259.3250.0000.0000.0000.000
131E156LEU0-0.036-0.00118.942-0.076-0.0760.0000.0000.0000.000
132E157VAL00.005-0.00622.8630.1060.1060.0000.0000.0000.000
133E158TYR0-0.023-0.03415.5680.1420.1420.0000.0000.0000.000
134E159HIS10.7860.88213.62318.58218.5820.0000.0000.0000.000
135E160GLY00.0540.03413.007-0.337-0.3370.0000.0000.0000.000
136E161GLN0-0.049-0.02611.507-2.172-2.1720.0000.0000.0000.000
137E162PHE00.0280.03412.5401.2051.2050.0000.0000.0000.000
138E163ASP-1-0.744-0.86313.650-17.238-17.2380.0000.0000.0000.000
139E164ASP-1-0.768-0.87712.993-20.534-20.5340.0000.0000.0000.000
140E165ALA0-0.0070.02412.213-0.977-0.9770.0000.0000.0000.000
141E166ARG10.7680.8426.58324.39524.3950.0000.0000.0000.000
142E167PRO0-0.010-0.0075.9191.7591.7590.0000.0000.0000.000
143E168GLY00.0090.0137.472-2.158-2.1580.0000.0000.0000.000
144E169ASN0-0.065-0.0469.2391.8701.8700.0000.0000.0000.000
145E170GLY00.0170.00811.0171.0161.0160.0000.0000.0000.000
146E171LYS10.8420.92713.50920.08220.0820.0000.0000.0000.000
147E172ASP-1-0.891-0.94315.118-14.921-14.9210.0000.0000.0000.000
148E173VAL0-0.035-0.01813.903-0.139-0.1390.0000.0000.0000.000
149E174THR0-0.054-0.03816.5790.9010.9010.0000.0000.0000.000
150E175GLY0-0.011-0.01617.3970.7570.7570.0000.0000.0000.000
151E176ALA0-0.016-0.00718.3840.4300.4300.0000.0000.0000.000
152E177ASP-1-0.814-0.89816.793-15.984-15.9840.0000.0000.0000.000
153E178LEU00.0170.00116.3420.5530.5530.0000.0000.0000.000
154E179ARG10.8040.88819.30913.12313.1230.0000.0000.0000.000
155E180ALA00.0080.01222.3980.5600.5600.0000.0000.0000.000
156E181ALA0-0.010-0.00521.2810.4730.4730.0000.0000.0000.000
157E182VAL00.0180.00422.6500.4610.4610.0000.0000.0000.000
158E183ASP-1-0.814-0.87925.043-10.001-10.0010.0000.0000.0000.000
159E184ALA0-0.0140.00226.6420.4710.4710.0000.0000.0000.000
160E185VAL00.0240.01025.7500.3950.3950.0000.0000.0000.000
161E186LEU0-0.058-0.03228.5650.3700.3700.0000.0000.0000.000
162E187LYS10.7470.86030.5249.9809.9800.0000.0000.0000.000
163E188GLY0-0.0330.00032.3380.2260.2260.0000.0000.0000.000
164E189LYS10.8970.94231.0318.9378.9370.0000.0000.0000.000
165E190ASP-1-0.891-0.94028.565-9.858-9.8580.0000.0000.0000.000
166E191VAL0-0.035-0.01122.165-0.086-0.0860.0000.0000.0000.000
167E192GLY0-0.0050.00323.4070.1050.1050.0000.0000.0000.000
168E193THR00.033-0.00322.118-0.469-0.4690.0000.0000.0000.000
169E194THR0-0.027-0.01418.560-0.351-0.3510.0000.0000.0000.000
170E195GLN00.0170.01116.922-0.492-0.4920.0000.0000.0000.000
171E196VAL00.0320.02811.586-0.451-0.4510.0000.0000.0000.000
172E197PRO00.0360.0169.410-0.047-0.0470.0000.0000.0000.000
173E198SER0-0.023-0.0109.012-0.710-0.7100.0000.0000.0000.000
174E199ILE0-0.004-0.0183.108-2.699-2.2260.055-0.116-0.412-0.001
175E200GLY00.0360.0143.5222.7763.1900.009-0.133-0.289-0.001
176E201CYS0-0.056-0.0402.516-15.370-12.0902.518-2.777-3.022-0.030
177E202ASN00.0500.0433.308-0.428-0.1190.010-0.032-0.2880.000
178E203ILE00.0380.0255.1210.8120.880-0.001-0.002-0.0650.000
179E204LYS10.7680.8925.79335.12935.1290.0000.0000.0000.000
180E205TRP00.029-0.00310.3052.3402.3400.0000.0000.0000.000
181E206THR00.0200.00713.016-0.401-0.4010.0000.0000.0000.000
182E207ALA0-0.015-0.00715.806-0.303-0.3030.0000.0000.0000.000
183E208GLY0-0.040-0.00316.7030.8630.8630.0000.0000.0000.000