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: ZV72N

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1873324.474681
FMO2-HF: Nuclear repulsion 1805667.83853
FMO2-HF: Total energy -67656.636151
FMO2-MP2: Total energy -67856.910733


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.
-24.631-18.5928.021-6.327-7.731-0.039
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 : 0.942 / q_NPA : 0.967
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].
3E28GLN00.0180.0093.886-2.906-0.559-0.021-1.229-1.0970.004
4E29SER00.0410.0206.7451.0951.0950.0000.0000.0000.000
5E30ASN0-0.030-0.0259.687-0.699-0.6990.0000.0000.0000.000
6E31SER00.0010.00312.5590.0190.0190.0000.0000.0000.000
7E32ILE0-0.0090.00915.5260.5910.5910.0000.0000.0000.000
8E33THR0-0.002-0.00418.074-0.143-0.1430.0000.0000.0000.000
9E34LEU00.0450.03020.7260.1780.1780.0000.0000.0000.000
10E35GLY00.0100.00423.1770.3880.3880.0000.0000.0000.000
11E36THR0-0.061-0.03522.1540.4510.4510.0000.0000.0000.000
12E37ARG10.8910.92924.4619.4069.4060.0000.0000.0000.000
13E38ALA00.0040.01623.151-0.354-0.3540.0000.0000.0000.000
14E39ALA0-0.0060.00922.4370.4500.4500.0000.0000.0000.000
15E40ASP-1-0.815-0.91724.188-10.075-10.0750.0000.0000.0000.000
16E41PHE0-0.079-0.03923.292-0.377-0.3770.0000.0000.0000.000
17E42VAL00.0340.01125.4260.3270.3270.0000.0000.0000.000
18E43LEU0-0.058-0.02520.997-0.282-0.2820.0000.0000.0000.000
19E44PRO00.0270.02723.9060.2210.2210.0000.0000.0000.000
20E45ASP-1-0.712-0.85524.209-10.636-10.6360.0000.0000.0000.000
21E46ALA0-0.053-0.04524.6210.1810.1810.0000.0000.0000.000
22E47GLY0-0.053-0.01926.3450.1800.1800.0000.0000.0000.000
23E48GLY0-0.028-0.00828.6980.3200.3200.0000.0000.0000.000
24E49ASN0-0.088-0.04729.9650.4530.4530.0000.0000.0000.000
25E50LEU0-0.020-0.02228.546-0.387-0.3870.0000.0000.0000.000
26E51PHE0-0.016-0.00726.3940.1710.1710.0000.0000.0000.000
27E52THR00.004-0.02427.215-0.235-0.2350.0000.0000.0000.000
28E53LEU0-0.003-0.01025.0530.0040.0040.0000.0000.0000.000
29E54ALA0-0.029-0.00128.4370.1000.1000.0000.0000.0000.000
30E55GLU-1-0.813-0.88629.885-8.837-8.8370.0000.0000.0000.000
31E56PHE0-0.031-0.02826.104-0.033-0.0330.0000.0000.0000.000
32E57LYS10.8630.92430.1328.0538.0530.0000.0000.0000.000
33E58ASP-1-0.888-0.94032.648-8.064-8.0640.0000.0000.0000.000
34E59SER0-0.0280.01629.7540.0740.0740.0000.0000.0000.000
35E60PRO0-0.029-0.01230.647-0.130-0.1300.0000.0000.0000.000
36E61ALA00.0430.01726.480-0.139-0.1390.0000.0000.0000.000
37E62LEU0-0.0020.00423.8040.1230.1230.0000.0000.0000.000
38E63LEU00.0010.00118.299-0.321-0.3210.0000.0000.0000.000
39E64VAL00.0180.01818.0910.2030.2030.0000.0000.0000.000
40E65ALA0-0.026-0.01415.592-0.676-0.6760.0000.0000.0000.000
41E66PHE00.0230.01712.3400.3280.3280.0000.0000.0000.000
42E67ILE00.010-0.02411.527-1.820-1.8200.0000.0000.0000.000
43E68SER0-0.040-0.06210.273-0.473-0.4730.0000.0000.0000.000
44E69ASN00.0430.00712.2520.0880.0880.0000.0000.0000.000
45E70ARG10.9070.95611.73120.53820.5380.0000.0000.0000.000
46E71CYS0-0.0600.0186.514-3.077-3.0770.0000.0000.0000.000
47E72PRO00.0350.0065.9340.6230.6230.0000.0000.0000.000
48E73PHE00.023-0.0162.409-2.721-1.6311.919-0.759-2.251-0.009
49E74VAL00.0200.0047.3311.6141.6140.0000.0000.0000.000
50E75VAL0-0.017-0.00910.3491.4051.4050.0000.0000.0000.000
51E76LEU0-0.036-0.0089.4981.0881.0880.0000.0000.0000.000
52E77ILE00.0180.00311.9911.0731.0730.0000.0000.0000.000
53E78ARG10.8450.92414.34518.05918.0590.0000.0000.0000.000
54E79GLU-1-0.863-0.94516.170-15.313-15.3130.0000.0000.0000.000
55E80ALA0-0.025-0.01017.4520.7030.7030.0000.0000.0000.000
56E81LEU00.0300.01816.0290.5130.5130.0000.0000.0000.000
57E82ALA00.0210.01918.9130.6000.6000.0000.0000.0000.000
58E83LYS10.8800.95121.85111.94911.9490.0000.0000.0000.000
59E84PHE0-0.013-0.01421.0490.4600.4600.0000.0000.0000.000
60E85ALA00.003-0.00722.5570.4200.4200.0000.0000.0000.000
61E86GLY00.0060.00624.1920.4300.4300.0000.0000.0000.000
62E87ASP-1-0.828-0.91525.929-10.941-10.9410.0000.0000.0000.000
63E88TYR0-0.030-0.03424.4810.1260.1260.0000.0000.0000.000
64E89ALA00.0040.02128.6210.2410.2410.0000.0000.0000.000
65E90GLY0-0.008-0.00830.1540.2240.2240.0000.0000.0000.000
66E91GLN0-0.062-0.04531.0170.0520.0520.0000.0000.0000.000
67E92GLY00.0040.00331.7050.0950.0950.0000.0000.0000.000
68E93LEU0-0.016-0.00623.680-0.098-0.0980.0000.0000.0000.000
69E94ALA0-0.0130.01226.8330.1120.1120.0000.0000.0000.000
70E95VAL00.006-0.01220.763-0.346-0.3460.0000.0000.0000.000
71E96VAL00.0070.00621.2950.3090.3090.0000.0000.0000.000
72E97ALA0-0.0050.00717.569-0.563-0.5630.0000.0000.0000.000
73E98ILE00.0300.01616.7440.5890.5890.0000.0000.0000.000
74E99ASN00.0160.00814.589-1.270-1.2700.0000.0000.0000.000
75E100SER00.010-0.04913.6710.6290.6290.0000.0000.0000.000
76E101ASN0-0.022-0.0069.656-0.282-0.2820.0000.0000.0000.000
77E102ASP-1-0.787-0.89412.700-14.617-14.6170.0000.0000.0000.000
78E103ALA0-0.008-0.01414.435-0.521-0.5210.0000.0000.0000.000
79E104GLN0-0.046-0.01616.8520.4090.4090.0000.0000.0000.000
80E105ALA0-0.015-0.00513.3870.0400.0400.0000.0000.0000.000
81E106PHE0-0.025-0.0149.530-1.182-1.1820.0000.0000.0000.000
82E107PRO00.0870.05114.4100.1940.1940.0000.0000.0000.000
83E108GLU-1-0.892-0.95914.159-18.308-18.3080.0000.0000.0000.000
84E109GLU-1-0.730-0.80211.996-20.065-20.0650.0000.0000.0000.000
85E110THR00.0290.01616.2890.5040.5040.0000.0000.0000.000
86E111LEU00.0450.02319.869-0.221-0.2210.0000.0000.0000.000
87E112GLU-1-0.819-0.87022.225-11.781-11.7810.0000.0000.0000.000
88E113ARG10.8490.88519.47912.77512.7750.0000.0000.0000.000
89E114VAL0-0.0200.01318.204-0.193-0.1930.0000.0000.0000.000
90E115GLY00.0530.01020.5180.1020.1020.0000.0000.0000.000
91E116ALA0-0.074-0.03622.6230.2740.2740.0000.0000.0000.000
92E117GLU-1-0.865-0.93417.135-16.099-16.0990.0000.0000.0000.000
93E118VAL00.0110.01320.8320.0110.0110.0000.0000.0000.000
94E119LYS10.9040.94623.25810.24810.2480.0000.0000.0000.000
95E120ALA0-0.035-0.00421.9580.2340.2340.0000.0000.0000.000
96E121TYR0-0.020-0.02018.947-0.141-0.1410.0000.0000.0000.000
97E122GLY00.0040.02122.152-0.050-0.0500.0000.0000.0000.000
98E123TYR0-0.069-0.03816.950-0.069-0.0690.0000.0000.0000.000
99E124GLY00.0440.01923.5280.3040.3040.0000.0000.0000.000
100E125PHE0-0.065-0.01919.4480.3220.3220.0000.0000.0000.000
101E126PRO00.0520.02824.157-0.157-0.1570.0000.0000.0000.000
102E127TYR0-0.029-0.03915.879-0.719-0.7190.0000.0000.0000.000
103E128LEU0-0.009-0.00120.5330.2890.2890.0000.0000.0000.000
104E129LYS10.7640.86116.02814.85114.8510.0000.0000.0000.000
105E130ASP-1-0.756-0.86617.601-13.784-13.7840.0000.0000.0000.000
106E131ALA0-0.018-0.01618.097-0.519-0.5190.0000.0000.0000.000
107E132SER00.0280.01719.147-0.376-0.3760.0000.0000.0000.000
108E133GLN0-0.020-0.01813.373-0.085-0.0850.0000.0000.0000.000
109E134SER0-0.032-0.01317.379-0.205-0.2050.0000.0000.0000.000
110E135VAL00.0600.03019.326-0.006-0.0060.0000.0000.0000.000
111E136ALA00.0190.00213.952-0.202-0.2020.0000.0000.0000.000
112E137LYS10.8720.93815.74614.30114.3010.0000.0000.0000.000
113E138ALA0-0.031-0.00916.9890.0240.0240.0000.0000.0000.000
114E139TYR0-0.035-0.03517.0360.1960.1960.0000.0000.0000.000
115E140GLY00.0200.02515.554-0.127-0.1270.0000.0000.0000.000
116E141ALA0-0.0270.00512.132-0.949-0.9490.0000.0000.0000.000
117E142ALA00.007-0.0038.6030.1710.1710.0000.0000.0000.000
118E143CYS0-0.066-0.0305.077-2.131-2.1310.0000.0000.0000.000
119E144THR0-0.0290.0306.1612.6642.6640.0000.0000.0000.000
120E145PRO00.013-0.0096.748-3.189-3.1890.0000.0000.0000.000
121E146ASP-1-0.826-0.9389.449-22.324-22.3240.0000.0000.0000.000
122E147PHE00.0300.01311.4661.1281.1280.0000.0000.0000.000
123E148PHE00.004-0.00213.912-0.148-0.1480.0000.0000.0000.000
124E149LEU00.0130.00917.9780.4210.4210.0000.0000.0000.000
125E150TYR0-0.006-0.00520.565-0.079-0.0790.0000.0000.0000.000
126E151ASP-1-0.759-0.86924.621-9.960-9.9600.0000.0000.0000.000
127E152ARG11.0050.99628.2108.5758.5750.0000.0000.0000.000
128E153GLU-1-0.855-0.89630.940-8.555-8.5550.0000.0000.0000.000
129E154ARG10.7830.87626.7779.9669.9660.0000.0000.0000.000
130E155ARG10.8370.89526.6279.2229.2220.0000.0000.0000.000
131E156LEU0-0.063-0.02019.114-0.080-0.0800.0000.0000.0000.000
132E157VAL00.016-0.00423.2590.1170.1170.0000.0000.0000.000
133E158TYR0-0.017-0.02516.3890.1190.1190.0000.0000.0000.000
134E159HIS10.8090.90913.51218.21118.2110.0000.0000.0000.000
135E160GLY00.0410.02913.468-0.219-0.2190.0000.0000.0000.000
136E161GLN0-0.049-0.03111.968-2.084-2.0840.0000.0000.0000.000
137E162PHE00.0300.03513.0081.3611.3610.0000.0000.0000.000
138E163ASP-1-0.758-0.86713.635-17.574-17.5740.0000.0000.0000.000
139E164ASP-1-0.747-0.86012.775-20.628-20.6280.0000.0000.0000.000
140E165ALA0-0.0280.01211.844-1.462-1.4620.0000.0000.0000.000
141E166ARG10.7560.8356.28325.25525.2550.0000.0000.0000.000
142E167PRO00.0220.0125.8011.7431.7430.0000.0000.0000.000
143E168GLY0-0.0020.0067.589-2.768-2.7680.0000.0000.0000.000
144E169ASN0-0.049-0.0389.6201.5961.5960.0000.0000.0000.000
145E170GLY00.002-0.00211.3131.1741.1740.0000.0000.0000.000
146E171LYS10.8360.93113.77220.54220.5420.0000.0000.0000.000
147E172ASP-1-0.885-0.93915.094-15.369-15.3690.0000.0000.0000.000
148E173VAL0-0.038-0.01913.957-0.370-0.3700.0000.0000.0000.000
149E174THR0-0.035-0.02816.5630.9740.9740.0000.0000.0000.000
150E175GLY0-0.008-0.02917.4620.7480.7480.0000.0000.0000.000
151E176ALA0-0.028-0.01518.6210.4780.4780.0000.0000.0000.000
152E177ASP-1-0.806-0.88816.922-16.148-16.1480.0000.0000.0000.000
153E178LEU00.003-0.00617.2380.5770.5770.0000.0000.0000.000
154E179ARG10.8010.89520.03013.13713.1370.0000.0000.0000.000
155E180ALA00.0140.01622.7450.5540.5540.0000.0000.0000.000
156E181ALA00.0030.00122.0410.5250.5250.0000.0000.0000.000
157E182VAL00.0300.00623.2240.4750.4750.0000.0000.0000.000
158E183ASP-1-0.792-0.85925.730-9.950-9.9500.0000.0000.0000.000
159E184ALA0-0.026-0.00527.2390.4610.4610.0000.0000.0000.000
160E185VAL00.0230.01126.1820.3920.3920.0000.0000.0000.000
161E186LEU0-0.062-0.02729.1630.3990.3990.0000.0000.0000.000
162E187LYS10.7330.84531.0119.9599.9590.0000.0000.0000.000
163E188GLY0-0.020-0.00232.9150.2570.2570.0000.0000.0000.000
164E189LYS10.8710.93231.5798.9298.9290.0000.0000.0000.000
165E190ASP-1-0.880-0.93329.381-9.690-9.6900.0000.0000.0000.000
166E191VAL0-0.043-0.02322.986-0.122-0.1220.0000.0000.0000.000
167E192GLY0-0.0010.00924.4250.1220.1220.0000.0000.0000.000
168E193THR00.011-0.02023.075-0.424-0.4240.0000.0000.0000.000
169E194THR0-0.018-0.00218.648-0.222-0.2220.0000.0000.0000.000
170E195GLN00.0160.00917.518-0.438-0.4380.0000.0000.0000.000
171E196VAL00.0110.01611.868-0.380-0.3800.0000.0000.0000.000
172E197PRO00.0570.0269.964-0.015-0.0150.0000.0000.0000.000
173E198SER0-0.036-0.0029.574-1.102-1.1020.0000.0000.0000.000
174E199ILE0-0.004-0.0173.475-2.695-2.2090.027-0.122-0.391-0.001
175E200GLY00.0490.0184.2531.9702.2540.000-0.102-0.1810.000
176E201CYS0-0.045-0.0282.191-10.681-9.5256.048-4.014-3.188-0.032
177E202ASN00.0360.0342.7760.1520.7410.049-0.094-0.544-0.001
178E203ILE00.0490.0224.6420.9641.051-0.001-0.007-0.0790.000
179E204LYS10.7570.8874.89129.88129.8810.0000.0000.0000.000
180E205TRP00.0230.0029.3271.9201.9200.0000.0000.0000.000
181E206THR00.0110.01311.878-0.160-0.1600.0000.0000.0000.000
182E207ALA0-0.034-0.01714.925-0.088-0.0880.0000.0000.0000.000
183E208GLY0-0.021-0.00115.7360.5250.5250.0000.0000.0000.000