Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: Q1LJY

Calculation Name: 3K5B-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K5B

Chain ID: E

ChEMBL ID:

UniProt ID: P74901

Base Structure: X-ray

Registration Date: 2023-03-14

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1330550.742402
FMO2-HF: Nuclear repulsion 1259576.478658
FMO2-HF: Total energy -70974.263744
FMO2-MP2: Total energy -71183.81661


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:3:LYS)


Summations of interaction energy for fragment #1(E:3: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.
-147.047-135.8263.539-7.081-7.682-0.08
Interaction energy analysis for fragmet #1(E:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.915 / q_NPA : 0.954
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].
3E5GLU-1-0.911-0.9502.181-121.514-112.2702.976-6.474-5.747-0.077
4E6ALA00.015-0.0082.7607.8279.2960.562-0.517-1.515-0.003
5E7ILE00.0170.0164.0146.7667.2740.001-0.090-0.4200.000
6E8LEU00.0220.0106.0053.5733.5730.0000.0000.0000.000
7E9SER0-0.010-0.0247.1314.1054.1050.0000.0000.0000.000
8E10GLN0-0.065-0.0267.5361.8631.8630.0000.0000.0000.000
9E11GLU-1-0.935-0.9659.366-20.527-20.5270.0000.0000.0000.000
10E12VAL0-0.0280.00011.7591.8481.8480.0000.0000.0000.000
11E13GLU-1-0.908-0.95012.926-17.053-17.0530.0000.0000.0000.000
12E14ALA00.017-0.01114.131-0.139-0.1390.0000.0000.0000.000
13E15GLU-1-0.902-0.93816.030-14.714-14.7140.0000.0000.0000.000
14E16ILE0-0.094-0.05116.1991.1191.1190.0000.0000.0000.000
15E17GLN00.0200.00317.667-0.090-0.0900.0000.0000.0000.000
16E18ALA00.0220.02320.1830.8580.8580.0000.0000.0000.000
17E19LEU00.009-0.00222.0970.7890.7890.0000.0000.0000.000
18E20LEU0-0.028-0.01722.2910.6800.6800.0000.0000.0000.000
19E21GLN0-0.039-0.00922.3980.0080.0080.0000.0000.0000.000
20E22GLU-1-0.949-0.97825.928-10.688-10.6880.0000.0000.0000.000
21E23ALA0-0.090-0.06327.7380.5150.5150.0000.0000.0000.000
22E24GLU-1-0.909-0.94929.084-9.743-9.7430.0000.0000.0000.000
23E25ALA00.0030.00730.3740.2440.2440.0000.0000.0000.000
24E26LYS10.8830.94030.33510.59910.5990.0000.0000.0000.000
25E27ALA00.0220.01833.6360.3310.3310.0000.0000.0000.000
26E28GLU-1-0.940-0.94534.258-8.513-8.5130.0000.0000.0000.000
27E29ALA00.0270.00536.4870.2980.2980.0000.0000.0000.000
28E30VAL00.012-0.00638.1720.2460.2460.0000.0000.0000.000
29E31LYS10.8390.91339.4937.6867.6860.0000.0000.0000.000
30E32ARG10.8720.93839.7977.7687.7680.0000.0000.0000.000
31E33GLU-1-0.915-0.94142.497-7.047-7.0470.0000.0000.0000.000
32E34ALA00.0460.01943.9480.2110.2110.0000.0000.0000.000
33E35GLU-1-0.849-0.91944.504-6.927-6.9270.0000.0000.0000.000
34E36GLU-1-0.948-1.00444.787-6.851-6.8510.0000.0000.0000.000
35E37LYS10.9220.99548.2096.3366.3360.0000.0000.0000.000
36E38ALA00.023-0.00649.8140.1830.1830.0000.0000.0000.000
37E39LYS11.0091.00751.1936.1756.1750.0000.0000.0000.000
38E40ALA00.015-0.00152.7790.1550.1550.0000.0000.0000.000
39E41LEU0-0.098-0.04454.0770.1220.1220.0000.0000.0000.000
40E42LEU0-0.006-0.00455.8040.0970.0970.0000.0000.0000.000
41E43GLN00.0480.03656.5690.1650.1650.0000.0000.0000.000
42E44ALA0-0.007-0.00458.7980.1070.1070.0000.0000.0000.000
43E45ARG10.9490.97360.3325.3875.3870.0000.0000.0000.000
44E46GLU-1-0.878-0.94759.305-5.276-5.2760.0000.0000.0000.000
45E47ARG10.9000.93559.8425.3085.3080.0000.0000.0000.000
46E48ALA0-0.033-0.00664.8790.0910.0910.0000.0000.0000.000
47E49LEU00.0200.00365.6800.0870.0870.0000.0000.0000.000
48E50GLU-1-0.828-0.90267.698-4.536-4.5360.0000.0000.0000.000
49E51ALA00.0100.01569.7570.0930.0930.0000.0000.0000.000
50E52GLN0-0.031-0.03868.8630.0250.0250.0000.0000.0000.000
51E53TYR00.0220.02272.4970.0660.0660.0000.0000.0000.000
52E54ARG10.8460.91771.8364.4654.4650.0000.0000.0000.000
53E55ALA0-0.039-0.01875.5310.0690.0690.0000.0000.0000.000
54E56ALA00.000-0.00676.8290.0670.0670.0000.0000.0000.000
55E57LEU00.0580.01877.8310.0550.0550.0000.0000.0000.000
56E58ARG11.0181.02679.1544.0634.0630.0000.0000.0000.000
57E59ARG10.8880.95381.5043.9033.9030.0000.0000.0000.000
58E60ALA00.006-0.01382.6800.0560.0560.0000.0000.0000.000
59E61GLU-1-0.901-0.93082.295-3.868-3.8680.0000.0000.0000.000
60E62SER00.0120.00485.9310.0520.0520.0000.0000.0000.000
61E63ALA0-0.034-0.00487.3330.0500.0500.0000.0000.0000.000
62E64GLY00.0450.01888.3930.0470.0470.0000.0000.0000.000
63E65GLU-1-0.902-0.96489.456-3.555-3.5550.0000.0000.0000.000
64E66LEU0-0.088-0.05391.7390.0550.0550.0000.0000.0000.000
65E67LEU0-0.056-0.03391.8460.0460.0460.0000.0000.0000.000
66E68VAL00.0280.03594.0340.0420.0420.0000.0000.0000.000
67E69ALA0-0.007-0.00896.2840.0480.0480.0000.0000.0000.000
68E70THR0-0.0030.00997.3860.0530.0530.0000.0000.0000.000
69E71ALA00.0930.05598.9820.0400.0400.0000.0000.0000.000
70E72ARG10.9250.96099.8733.2413.2410.0000.0000.0000.000
71E73THR0-0.073-0.048101.7190.0400.0400.0000.0000.0000.000
72E74GLN0-0.039-0.017103.5690.0020.0020.0000.0000.0000.000
73E75ALA00.0530.039105.0010.0320.0320.0000.0000.0000.000
74E76ARG10.8930.933104.3523.1083.1080.0000.0000.0000.000
75E77GLY0-0.003-0.007107.8490.0320.0320.0000.0000.0000.000
76E78GLU-1-0.828-0.918108.069-2.983-2.9830.0000.0000.0000.000
77E79VAL0-0.0010.010111.2190.0330.0330.0000.0000.0000.000
78E80LEU0-0.034-0.020111.6550.0340.0340.0000.0000.0000.000
79E81GLU-1-0.950-0.985113.252-2.857-2.8570.0000.0000.0000.000
80E82GLU-1-0.849-0.928115.553-2.718-2.7180.0000.0000.0000.000
81E83VAL0-0.039-0.027117.1860.0340.0340.0000.0000.0000.000
82E84ARG10.8790.947118.4572.7542.7540.0000.0000.0000.000
83E85ARG10.9090.964119.6102.7222.7220.0000.0000.0000.000
84E86ARG10.9220.963121.1722.7192.7190.0000.0000.0000.000
85E87VAL00.0150.014122.7970.0260.0260.0000.0000.0000.000
86E88ARG10.9910.971120.8412.6932.6930.0000.0000.0000.000
87E89GLU-1-0.976-0.972125.868-2.568-2.5680.0000.0000.0000.000
88E90ALA0-0.031-0.013127.7070.0240.0240.0000.0000.0000.000
89E91LEU0-0.023-0.029128.6270.0230.0230.0000.0000.0000.000
90E92GLU-1-0.848-0.922129.530-2.503-2.5030.0000.0000.0000.000
91E93ALA0-0.0060.005131.6510.0180.0180.0000.0000.0000.000
92E94LEU0-0.083-0.044133.4430.0140.0140.0000.0000.0000.000
93E95PRO00.046-0.003135.5150.0170.0170.0000.0000.0000.000
94E96GLN0-0.039-0.006137.1230.0090.0090.0000.0000.0000.000
95E97LYS10.9140.962135.0862.4122.4120.0000.0000.0000.000
96E98PRO00.0400.029140.3800.0090.0090.0000.0000.0000.000
97E99GLU-1-0.900-0.952138.781-2.363-2.3630.0000.0000.0000.000
98E100TRP00.0110.010137.246-0.019-0.0190.0000.0000.0000.000
99E101PRO00.000-0.010140.685-0.003-0.0030.0000.0000.0000.000
100E102GLU-1-0.942-0.988142.404-2.259-2.2590.0000.0000.0000.000
101E103VAL0-0.039-0.006136.661-0.008-0.0080.0000.0000.0000.000
102E104VAL00.0250.012139.685-0.006-0.0060.0000.0000.0000.000
103E105ARG10.9220.969140.9622.2182.2180.0000.0000.0000.000
104E106LYS10.8750.946138.6532.3552.3550.0000.0000.0000.000
105E107LEU0-0.030-0.017134.891-0.013-0.0130.0000.0000.0000.000
106E108ALA00.0180.001138.823-0.006-0.0060.0000.0000.0000.000
107E109LEU0-0.022-0.010141.5880.0080.0080.0000.0000.0000.000
108E110GLU-1-0.829-0.914135.795-2.402-2.4020.0000.0000.0000.000
109E111ALA0-0.047-0.024138.977-0.008-0.0080.0000.0000.0000.000
110E112LEU0-0.064-0.033139.9560.0020.0020.0000.0000.0000.000
111E113GLU-1-0.976-0.970140.797-2.311-2.3110.0000.0000.0000.000
112E114ALA0-0.054-0.018137.148-0.007-0.0070.0000.0000.0000.000
113E115LEU0-0.042-0.034134.7090.0090.0090.0000.0000.0000.000
114E116PRO0-0.040-0.021138.1260.0100.0100.0000.0000.0000.000
115E117GLY00.0520.050141.2170.0090.0090.0000.0000.0000.000
116E118ALA00.0200.000144.665-0.008-0.0080.0000.0000.0000.000
117E119LYS10.9000.949146.4852.2092.2090.0000.0000.0000.000
118E120ALA0-0.044-0.015145.9940.0190.0190.0000.0000.0000.000
119E121LEU0-0.0170.015141.553-0.020-0.0200.0000.0000.0000.000
120E122VAL0-0.0120.000140.9560.0130.0130.0000.0000.0000.000
121E123ALA00.0570.012140.727-0.018-0.0180.0000.0000.0000.000
122E124ASN00.0430.033138.385-0.003-0.0030.0000.0000.0000.000
123E125PRO00.0650.016141.8600.0100.0100.0000.0000.0000.000
124E126GLU-1-0.937-0.985142.930-2.238-2.2380.0000.0000.0000.000
125E127ASP-1-0.879-0.954140.972-2.334-2.3340.0000.0000.0000.000
126E128LEU0-0.045-0.004144.1950.0130.0130.0000.0000.0000.000
127E129PRO0-0.021-0.004147.3700.0140.0140.0000.0000.0000.000
128E130HIS0-0.067-0.020144.9610.0210.0210.0000.0000.0000.000
129E131LEU0-0.023-0.011143.897-0.010-0.0100.0000.0000.0000.000
130E132GLU-1-0.736-0.863147.901-2.148-2.1480.0000.0000.0000.000
131E133ALA0-0.057-0.032150.1300.0160.0160.0000.0000.0000.000
132E134MET00.0400.002148.9520.0150.0150.0000.0000.0000.000
133E135ALA0-0.0300.012150.7210.0010.0010.0000.0000.0000.000
134E136ARG10.8370.884151.9532.1272.1270.0000.0000.0000.000
135E137GLU-1-0.896-0.922152.733-2.087-2.0870.0000.0000.0000.000
136E138ARG10.8020.888153.0962.0852.0850.0000.0000.0000.000
137E139GLY00.0410.034150.119-0.010-0.0100.0000.0000.0000.000
138E140VAL0-0.076-0.041149.928-0.002-0.0020.0000.0000.0000.000
139E141GLU-1-0.776-0.895144.946-2.272-2.2720.0000.0000.0000.000
140E142LEU0-0.048-0.041144.5320.0150.0150.0000.0000.0000.000
141E143GLN0-0.024-0.028146.690-0.019-0.0190.0000.0000.0000.000
142E144ALA00.0550.022145.905-0.009-0.0090.0000.0000.0000.000
143E145GLU-1-0.948-0.964139.401-2.365-2.3650.0000.0000.0000.000
144E146PRO0-0.028-0.019138.781-0.009-0.0090.0000.0000.0000.000
145E147ALA0-0.019-0.003135.811-0.020-0.0200.0000.0000.0000.000
146E148LEU0-0.010-0.003135.524-0.020-0.0200.0000.0000.0000.000
147E149ARG10.8280.918130.5082.4712.4710.0000.0000.0000.000
148E150LEU00.0050.001132.3800.0110.0110.0000.0000.0000.000
149E151GLY0-0.008-0.014134.571-0.018-0.0180.0000.0000.0000.000
150E152VAL00.0200.030136.2460.0110.0110.0000.0000.0000.000
151E153ARG10.8350.915135.9162.3922.3920.0000.0000.0000.000
152E154ALA00.0630.021138.6290.0180.0180.0000.0000.0000.000
153E155VAL0-0.074-0.036140.036-0.019-0.0190.0000.0000.0000.000
154E156GLY00.0660.022141.6700.0150.0150.0000.0000.0000.000
155E157ALA0-0.016-0.016143.0850.0170.0170.0000.0000.0000.000
156E158GLU-1-0.885-0.935144.813-2.234-2.2340.0000.0000.0000.000
157E159GLY0-0.019-0.004142.274-0.014-0.0140.0000.0000.0000.000
158E160LYS10.9370.936138.7662.3412.3410.0000.0000.0000.000
159E161THR0-0.0190.019138.1390.0090.0090.0000.0000.0000.000
160E162GLN0-0.040-0.035135.269-0.007-0.0070.0000.0000.0000.000
161E163VAL00.0460.038135.326-0.019-0.0190.0000.0000.0000.000
162E164GLU-1-0.860-0.918132.943-2.441-2.4410.0000.0000.0000.000
163E165ASN0-0.019-0.012133.492-0.019-0.0190.0000.0000.0000.000
164E166SER00.0790.020131.6390.0110.0110.0000.0000.0000.000
165E167LEU00.0510.024131.293-0.020-0.0200.0000.0000.0000.000
166E168LEU00.0260.016127.758-0.022-0.0220.0000.0000.0000.000
167E169ALA00.0580.027126.752-0.021-0.0210.0000.0000.0000.000
168E170ARG10.8970.944126.6742.4562.4560.0000.0000.0000.000
169E171MET0-0.0360.013124.079-0.021-0.0210.0000.0000.0000.000
170E172ASP-1-0.851-0.942122.360-2.690-2.6900.0000.0000.0000.000
171E173ARG10.8490.936121.7652.5432.5430.0000.0000.0000.000
172E174ALA00.025-0.011122.2390.0160.0160.0000.0000.0000.000
173E175TRP0-0.034-0.021115.927-0.006-0.0060.0000.0000.0000.000
174E176ASP-1-0.918-0.951115.833-2.843-2.8430.0000.0000.0000.000
175E177ALA0-0.0250.010117.468-0.011-0.0110.0000.0000.0000.000
176E178MET0-0.032-0.028118.629-0.003-0.0030.0000.0000.0000.000
177E179SER00.0450.027114.093-0.007-0.0070.0000.0000.0000.000
178E180SER00.0200.008113.250-0.006-0.0060.0000.0000.0000.000
179E181LYS10.9490.974114.1902.7522.7520.0000.0000.0000.000
180E182VAL00.0610.033115.9740.0040.0040.0000.0000.0000.000
181E183ALA00.0480.016111.627-0.007-0.0070.0000.0000.0000.000
182E184GLN0-0.082-0.054113.064-0.014-0.0140.0000.0000.0000.000
183E185ALA0-0.042-0.022114.078-0.002-0.0020.0000.0000.0000.000
184E186LEU0-0.0440.000113.5860.0050.0050.0000.0000.0000.000
185E187TRP0-0.045-0.022109.286-0.011-0.0110.0000.0000.0000.000
186E188GLY0-0.0010.011110.131-0.004-0.0040.0000.0000.0000.000