FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 6YZ3Z

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 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 183
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1872640.00112
FMO2-HF: Nuclear repulsion 1804984.471301
FMO2-HF: Total energy -67655.52982
FMO2-MP2: Total energy -67855.902517


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.
-25.492-20.7528.754-6.048-7.448-0.039
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 : 0.936 / q_NPA : 0.947
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].
3E28GLN0-0.034-0.0103.886-2.675-1.089-0.019-0.767-0.8010.001
4E29SER00.0190.0176.6331.7631.7630.0000.0000.0000.000
5E30ASN0-0.008-0.0159.689-1.015-1.0150.0000.0000.0000.000
6E31SER00.000-0.00312.5730.0370.0370.0000.0000.0000.000
7E32ILE0-0.0330.00215.5880.6020.6020.0000.0000.0000.000
8E33THR00.001-0.00118.085-0.199-0.1990.0000.0000.0000.000
9E34LEU00.0440.03220.7260.1910.1910.0000.0000.0000.000
10E35GLY00.0100.00123.1670.3920.3920.0000.0000.0000.000
11E36THR0-0.058-0.03822.1550.4830.4830.0000.0000.0000.000
12E37ARG10.9300.95324.4759.4839.4830.0000.0000.0000.000
13E38ALA00.0160.02323.171-0.303-0.3030.0000.0000.0000.000
14E39ALA0-0.0040.01022.4920.4450.4450.0000.0000.0000.000
15E40ASP-1-0.819-0.91324.224-9.891-9.8910.0000.0000.0000.000
16E41PHE0-0.086-0.04023.351-0.352-0.3520.0000.0000.0000.000
17E42VAL00.0350.01225.4720.3010.3010.0000.0000.0000.000
18E43LEU0-0.062-0.02621.070-0.243-0.2430.0000.0000.0000.000
19E44PRO00.0370.02523.8570.2090.2090.0000.0000.0000.000
20E45ASP-1-0.731-0.87324.252-10.504-10.5040.0000.0000.0000.000
21E46ALA0-0.050-0.04224.7430.1890.1890.0000.0000.0000.000
22E47GLY0-0.057-0.02226.3830.1800.1800.0000.0000.0000.000
23E48GLY0-0.027-0.00828.7360.3120.3120.0000.0000.0000.000
24E49ASN0-0.077-0.03029.9010.4980.4980.0000.0000.0000.000
25E50LEU0-0.026-0.02828.608-0.370-0.3700.0000.0000.0000.000
26E51PHE0-0.0120.00026.3940.1500.1500.0000.0000.0000.000
27E52THR00.002-0.01827.255-0.213-0.2130.0000.0000.0000.000
28E53LEU00.006-0.00825.180-0.017-0.0170.0000.0000.0000.000
29E54ALA0-0.0330.00128.4670.0910.0910.0000.0000.0000.000
30E55GLU-1-0.820-0.90029.902-8.726-8.7260.0000.0000.0000.000
31E56PHE0-0.025-0.02426.484-0.043-0.0430.0000.0000.0000.000
32E57LYS10.9050.95530.1488.0118.0110.0000.0000.0000.000
33E58ASP-1-0.898-0.94932.664-7.988-7.9880.0000.0000.0000.000
34E59SER0-0.066-0.00829.7100.0390.0390.0000.0000.0000.000
35E60PRO0-0.012-0.00430.649-0.138-0.1380.0000.0000.0000.000
36E61ALA00.0420.02226.340-0.141-0.1410.0000.0000.0000.000
37E62LEU00.0010.00223.6620.1050.1050.0000.0000.0000.000
38E63LEU00.0020.00118.160-0.333-0.3330.0000.0000.0000.000
39E64VAL00.0190.01317.9920.2090.2090.0000.0000.0000.000
40E65ALA0-0.033-0.01015.581-0.681-0.6810.0000.0000.0000.000
41E66PHE00.0180.01112.3010.4050.4050.0000.0000.0000.000
42E67ILE00.015-0.02011.551-1.795-1.7950.0000.0000.0000.000
43E68SER0-0.064-0.06810.227-0.304-0.3040.0000.0000.0000.000
44E69ASN00.0500.01212.278-0.008-0.0080.0000.0000.0000.000
45E70ARG10.9210.96511.82020.27920.2790.0000.0000.0000.000
46E71CYS0-0.102-0.0015.848-2.664-2.6640.0000.0000.0000.000
47E72PRO00.0580.0056.0680.6130.6130.0000.0000.0000.000
48E73PHE00.017-0.0222.062-2.723-2.2642.600-0.823-2.236-0.011
49E74VAL00.0120.0047.4911.6321.6320.0000.0000.0000.000
50E75VAL0-0.013-0.00910.5451.3381.3380.0000.0000.0000.000
51E76LEU0-0.030-0.0099.3000.9980.9980.0000.0000.0000.000
52E77ILE00.0310.01111.8861.1121.1120.0000.0000.0000.000
53E78ARG10.8880.96414.30218.30918.3090.0000.0000.0000.000
54E79GLU-1-0.877-0.95016.350-15.771-15.7710.0000.0000.0000.000
55E80ALA0-0.017-0.01217.3950.7170.7170.0000.0000.0000.000
56E81LEU00.0200.02216.0410.5550.5550.0000.0000.0000.000
57E82ALA00.0250.01719.0720.6290.6290.0000.0000.0000.000
58E83LYS10.8870.95622.02712.45812.4580.0000.0000.0000.000
59E84PHE0-0.024-0.01921.2290.4660.4660.0000.0000.0000.000
60E85ALA00.019-0.00322.6450.4310.4310.0000.0000.0000.000
61E86GLY00.0000.00224.3240.4410.4410.0000.0000.0000.000
62E87ASP-1-0.828-0.91426.329-11.017-11.0170.0000.0000.0000.000
63E88TYR0-0.041-0.04225.0870.1420.1420.0000.0000.0000.000
64E89ALA0-0.0050.01628.7100.2540.2540.0000.0000.0000.000
65E90GLY0-0.005-0.01030.1400.2220.2220.0000.0000.0000.000
66E91GLN0-0.068-0.04630.985-0.003-0.0030.0000.0000.0000.000
67E92GLY0-0.001-0.00331.7130.0940.0940.0000.0000.0000.000
68E93LEU0-0.013-0.00323.816-0.086-0.0860.0000.0000.0000.000
69E94ALA0-0.0130.01426.8330.1130.1130.0000.0000.0000.000
70E95VAL00.008-0.00920.686-0.345-0.3450.0000.0000.0000.000
71E96VAL00.0090.01021.1100.3090.3090.0000.0000.0000.000
72E97ALA0-0.0040.00717.549-0.557-0.5570.0000.0000.0000.000
73E98ILE00.0260.01016.7760.6050.6050.0000.0000.0000.000
74E99ASN00.000-0.00114.632-1.130-1.1300.0000.0000.0000.000
75E100SER00.021-0.03513.7170.5730.5730.0000.0000.0000.000
76E101ASN0-0.0080.0149.6100.0850.0850.0000.0000.0000.000
77E102ASP-1-0.804-0.90413.374-13.960-13.9600.0000.0000.0000.000
78E103ALA0-0.014-0.01715.232-0.452-0.4520.0000.0000.0000.000
79E104GLN0-0.052-0.01417.6200.3880.3880.0000.0000.0000.000
80E105ALA0-0.014-0.00414.1460.0260.0260.0000.0000.0000.000
81E106PHE0-0.040-0.01710.059-1.002-1.0020.0000.0000.0000.000
82E107PRO00.0780.05215.0390.2060.2060.0000.0000.0000.000
83E108GLU-1-0.904-0.97313.690-17.977-17.9770.0000.0000.0000.000
84E109GLU-1-0.711-0.81812.093-19.285-19.2850.0000.0000.0000.000
85E110THR00.0270.01216.4750.3980.3980.0000.0000.0000.000
86E111LEU00.0410.02620.156-0.228-0.2280.0000.0000.0000.000
87E112GLU-1-0.814-0.88222.272-11.620-11.6200.0000.0000.0000.000
88E113ARG10.8540.89519.52412.58012.5800.0000.0000.0000.000
89E114VAL0-0.0120.02118.403-0.209-0.2090.0000.0000.0000.000
90E115GLY00.0470.00720.5490.0690.0690.0000.0000.0000.000
91E116ALA0-0.073-0.03722.8190.2520.2520.0000.0000.0000.000
92E117GLU-1-0.871-0.95217.013-16.049-16.0490.0000.0000.0000.000
93E118VAL0-0.011-0.00321.059-0.038-0.0380.0000.0000.0000.000
94E119LYS10.8990.94523.46210.15710.1570.0000.0000.0000.000
95E120ALA0-0.032-0.00522.1510.2090.2090.0000.0000.0000.000
96E121TYR0-0.018-0.01919.069-0.272-0.2720.0000.0000.0000.000
97E122GLY00.0060.02022.356-0.069-0.0690.0000.0000.0000.000
98E123TYR0-0.063-0.03316.843-0.126-0.1260.0000.0000.0000.000
99E124GLY00.0460.01823.7320.3150.3150.0000.0000.0000.000
100E125PHE0-0.065-0.01819.6820.3210.3210.0000.0000.0000.000
101E126PRO00.0460.02524.167-0.153-0.1530.0000.0000.0000.000
102E127TYR0-0.025-0.03016.072-0.706-0.7060.0000.0000.0000.000
103E128LEU00.0000.00220.5910.2880.2880.0000.0000.0000.000
104E129LYS10.8000.88316.63114.07014.0700.0000.0000.0000.000
105E130ASP-1-0.765-0.87717.701-13.255-13.2550.0000.0000.0000.000
106E131ALA0-0.022-0.01318.490-0.449-0.4490.0000.0000.0000.000
107E132SER00.0140.00219.946-0.329-0.3290.0000.0000.0000.000
108E133GLN0-0.011-0.00914.1410.0010.0010.0000.0000.0000.000
109E134SER0-0.054-0.02217.900-0.179-0.1790.0000.0000.0000.000
110E135VAL00.0770.03419.088-0.015-0.0150.0000.0000.0000.000
111E136ALA00.0150.00014.096-0.198-0.1980.0000.0000.0000.000
112E137LYS10.9030.94415.79912.91712.9170.0000.0000.0000.000
113E138ALA0-0.037-0.00917.331-0.003-0.0030.0000.0000.0000.000
114E139TYR0-0.054-0.04617.0350.1630.1630.0000.0000.0000.000
115E140GLY00.0220.02015.602-0.161-0.1610.0000.0000.0000.000
116E141ALA0-0.029-0.00312.053-0.889-0.8890.0000.0000.0000.000
117E142ALA0-0.007-0.0088.6110.2720.2720.0000.0000.0000.000
118E143CYS0-0.107-0.0435.134-0.733-0.7330.0000.0000.0000.000
119E144THR0-0.0180.0176.2232.4492.4490.0000.0000.0000.000
120E145PRO00.009-0.0136.745-3.074-3.0740.0000.0000.0000.000
121E146ASP-1-0.791-0.9249.437-22.531-22.5310.0000.0000.0000.000
122E147PHE00.0110.00611.4691.2131.2130.0000.0000.0000.000
123E148PHE00.0060.00014.042-0.197-0.1970.0000.0000.0000.000
124E149LEU00.0210.01617.9790.4080.4080.0000.0000.0000.000
125E150TYR0-0.008-0.00419.9740.1110.1110.0000.0000.0000.000
126E151ASP-1-0.778-0.88724.622-9.956-9.9560.0000.0000.0000.000
127E152ARG11.0030.99528.2068.5398.5390.0000.0000.0000.000
128E153GLU-1-0.952-0.95630.966-8.302-8.3020.0000.0000.0000.000
129E154ARG10.7450.84526.8189.9169.9160.0000.0000.0000.000
130E155ARG10.9200.96026.6109.2709.2700.0000.0000.0000.000
131E156LEU0-0.053-0.02019.046-0.097-0.0970.0000.0000.0000.000
132E157VAL00.0200.00023.2630.1070.1070.0000.0000.0000.000
133E158TYR0-0.026-0.03916.0440.1760.1760.0000.0000.0000.000
134E159HIS10.8120.91713.58518.08518.0850.0000.0000.0000.000
135E160GLY00.0390.02713.476-0.240-0.2400.0000.0000.0000.000
136E161GLN0-0.059-0.05011.659-2.269-2.2690.0000.0000.0000.000
137E162PHE00.0390.04112.8491.5151.5150.0000.0000.0000.000
138E163ASP-1-0.740-0.85713.521-18.425-18.4250.0000.0000.0000.000
139E164ASP-1-0.819-0.89712.635-20.750-20.7500.0000.0000.0000.000
140E165ALA0-0.0270.00411.789-1.762-1.7620.0000.0000.0000.000
141E166ARG10.7670.8466.18827.08227.0820.0000.0000.0000.000
142E167PRO00.0150.0055.6751.8251.8250.0000.0000.0000.000
143E168GLY00.0000.0097.211-3.603-3.6030.0000.0000.0000.000
144E169ASN0-0.050-0.0379.5301.8131.8130.0000.0000.0000.000
145E170GLY00.000-0.00710.9601.3881.3880.0000.0000.0000.000
146E171LYS10.9150.98013.62221.57321.5730.0000.0000.0000.000
147E172ASP-1-0.873-0.93114.829-16.041-16.0410.0000.0000.0000.000
148E173VAL0-0.040-0.02413.722-0.416-0.4160.0000.0000.0000.000
149E174THR0-0.031-0.00916.3871.0581.0580.0000.0000.0000.000
150E175GLY0-0.014-0.03717.4930.8180.8180.0000.0000.0000.000
151E176ALA0-0.031-0.02018.6270.5270.5270.0000.0000.0000.000
152E177ASP-1-0.812-0.88216.506-16.651-16.6510.0000.0000.0000.000
153E178LEU0-0.009-0.01117.8610.6360.6360.0000.0000.0000.000
154E179ARG10.8000.90019.83513.40613.4060.0000.0000.0000.000
155E180ALA00.0330.03022.5610.5590.5590.0000.0000.0000.000
156E181ALA00.001-0.00321.8080.5550.5550.0000.0000.0000.000
157E182VAL00.0270.00423.1420.5110.5110.0000.0000.0000.000
158E183ASP-1-0.862-0.90525.619-10.395-10.3950.0000.0000.0000.000
159E184ALA0-0.061-0.02227.0200.4850.4850.0000.0000.0000.000
160E185VAL00.0330.01626.1960.4110.4110.0000.0000.0000.000
161E186LEU0-0.056-0.02729.1540.4210.4210.0000.0000.0000.000
162E187LYS10.8340.91731.3419.9849.9840.0000.0000.0000.000
163E188GLY0-0.018-0.00232.8780.2600.2600.0000.0000.0000.000
164E189LYS10.8670.93031.1289.1589.1580.0000.0000.0000.000
165E190ASP-1-0.866-0.92729.292-9.828-9.8280.0000.0000.0000.000
166E191VAL0-0.050-0.02422.959-0.137-0.1370.0000.0000.0000.000
167E192GLY0-0.0010.00924.0830.1280.1280.0000.0000.0000.000
168E193THR00.003-0.02222.957-0.483-0.4830.0000.0000.0000.000
169E194THR0-0.0140.00318.068-0.338-0.3380.0000.0000.0000.000
170E195GLN00.0210.00717.479-0.429-0.4290.0000.0000.0000.000
171E196VAL00.0110.01411.398-0.357-0.3570.0000.0000.0000.000
172E197PRO00.0580.0289.856-0.021-0.0210.0000.0000.0000.000
173E198SER0-0.0230.0019.562-1.351-1.3510.0000.0000.0000.000
174E199ILE0-0.016-0.0203.099-3.109-2.4130.092-0.158-0.631-0.002
175E200GLY00.0460.0124.1941.6521.934-0.001-0.106-0.1750.000
176E201CYS0-0.045-0.0122.186-9.454-8.3796.064-4.020-3.119-0.029
177E202ASN00.0710.0523.408-0.0770.5080.019-0.171-0.4330.002
178E203ILE00.0460.0175.1590.6550.712-0.001-0.003-0.0530.000
179E204LYS10.7670.8985.56725.66225.6620.0000.0000.0000.000
180E205TRP00.0160.0019.5921.5531.5530.0000.0000.0000.000
181E206THR00.007-0.00112.577-0.078-0.0780.0000.0000.0000.000
182E207ALA0-0.044-0.01715.359-0.085-0.0850.0000.0000.0000.000
183E208GLY0-0.0050.00716.0870.5450.5450.0000.0000.0000.000