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: LJ979

Calculation Name: 1K4N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K4N

Chain ID: A

ChEMBL ID:

UniProt ID: P52007

Base Structure: X-ray

Registration Date: 2023-06-19

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 -2012576.572096
FMO2-HF: Nuclear repulsion 1939891.384983
FMO2-HF: Total energy -72685.187113
FMO2-MP2: Total energy -72897.837691


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-1.565-0.192-0.003-0.677-0.6930.004
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.005
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].
3A3MET00.001-0.0083.798-0.4520.921-0.003-0.677-0.6930.004
4A4ILE0-0.011-0.0115.9640.6980.6980.0000.0000.0000.000
5A5MET0-0.0060.0178.1870.1440.1440.0000.0000.0000.000
6A6ALA00.0050.01111.6510.0430.0430.0000.0000.0000.000
7A7ASN00.0350.01314.4500.0730.0730.0000.0000.0000.000
8A8TRP00.0950.01416.7210.0720.0720.0000.0000.0000.000
9A9GLN0-0.082-0.04720.1200.0270.0270.0000.0000.0000.000
10A10SER0-0.068-0.03817.1680.0080.0080.0000.0000.0000.000
11A11ILE0-0.0280.00718.0890.0180.0180.0000.0000.0000.000
12A12ASP-1-0.828-0.90920.941-0.163-0.1630.0000.0000.0000.000
13A13GLU-1-0.914-0.96223.636-0.210-0.2100.0000.0000.0000.000
14A14LEU0-0.046-0.02322.6140.0120.0120.0000.0000.0000.000
15A15GLN00.0220.01024.2980.0120.0120.0000.0000.0000.000
16A16ASP-1-0.769-0.83426.743-0.159-0.1590.0000.0000.0000.000
17A17ILE00.0340.00026.5260.0060.0060.0000.0000.0000.000
18A18ALA00.0030.01025.089-0.003-0.0030.0000.0000.0000.000
19A19SER0-0.051-0.03726.9910.0070.0070.0000.0000.0000.000
20A20ASP-1-0.761-0.84629.926-0.134-0.1340.0000.0000.0000.000
21A21LEU0-0.0190.00527.0670.0070.0070.0000.0000.0000.000
22A22PRO00.0270.00529.8410.0050.0050.0000.0000.0000.000
23A23ARG10.7980.86432.4310.1380.1380.0000.0000.0000.000
24A24PHE0-0.005-0.00832.4880.0070.0070.0000.0000.0000.000
25A25ILE00.0200.01629.9470.0020.0020.0000.0000.0000.000
26A26HIS00.0150.01534.0220.0030.0030.0000.0000.0000.000
27A27ALA0-0.0020.00137.3740.0050.0050.0000.0000.0000.000
28A28LEU0-0.012-0.01333.9630.0050.0050.0000.0000.0000.000
29A29ASP-1-0.848-0.87936.837-0.113-0.1130.0000.0000.0000.000
30A30GLU-1-0.848-0.92338.597-0.085-0.0850.0000.0000.0000.000
31A31LEU0-0.050-0.02141.1500.0050.0050.0000.0000.0000.000
32A32SER0-0.002-0.02939.4120.0020.0020.0000.0000.0000.000
33A33ARG10.7730.86740.1230.1040.1040.0000.0000.0000.000
34A34ARG10.9040.95344.0200.0870.0870.0000.0000.0000.000
35A35LEU0-0.014-0.00943.7920.0040.0040.0000.0000.0000.000
36A36GLY00.0150.03446.0790.0010.0010.0000.0000.0000.000
37A37LEU0-0.020-0.00940.923-0.001-0.0010.0000.0000.0000.000
38A38ASN0-0.015-0.01539.768-0.008-0.0080.0000.0000.0000.000
39A39ILE00.0560.01435.024-0.003-0.0030.0000.0000.0000.000
40A40THR0-0.010-0.00834.316-0.009-0.0090.0000.0000.0000.000
41A41PRO0-0.023-0.00734.522-0.009-0.0090.0000.0000.0000.000
42A42LEU0-0.0240.00736.193-0.003-0.0030.0000.0000.0000.000
43A43THR00.0280.01831.359-0.011-0.0110.0000.0000.0000.000
44A44ALA0-0.0030.00129.7550.0080.0080.0000.0000.0000.000
45A45ASP-1-0.750-0.84630.306-0.220-0.2200.0000.0000.0000.000
46A46HIS10.7430.84629.3230.1790.1790.0000.0000.0000.000
47A47ILE00.0110.01828.2760.0180.0180.0000.0000.0000.000
48A48SER0-0.052-0.07330.834-0.010-0.0100.0000.0000.0000.000
49A49LEU00.0280.03829.3290.0090.0090.0000.0000.0000.000
50A50ARG10.7950.90133.7210.1430.1430.0000.0000.0000.000
51A51CYS0-0.0020.01235.488-0.001-0.0010.0000.0000.0000.000
52A52HIS0-0.068-0.05637.5470.0020.0020.0000.0000.0000.000
53A53GLN0-0.0060.01038.1010.0070.0070.0000.0000.0000.000
54A54ASN00.0580.00037.395-0.010-0.0100.0000.0000.0000.000
55A55ALA0-0.008-0.00335.559-0.007-0.0070.0000.0000.0000.000
56A56THR0-0.042-0.03833.396-0.006-0.0060.0000.0000.0000.000
57A57ALA00.0590.02632.295-0.010-0.0100.0000.0000.0000.000
58A58GLU-1-0.871-0.94731.326-0.166-0.1660.0000.0000.0000.000
59A59ARG10.7860.87429.0700.1440.1440.0000.0000.0000.000
60A60TRP00.016-0.03227.679-0.012-0.0120.0000.0000.0000.000
61A61ARG10.7580.86426.6550.1760.1760.0000.0000.0000.000
62A62ARG10.8060.88425.4350.1790.1790.0000.0000.0000.000
63A63GLY00.0420.02523.248-0.021-0.0210.0000.0000.0000.000
64A64PHE00.045-0.02521.932-0.030-0.0300.0000.0000.0000.000
65A65GLU-1-0.850-0.90021.713-0.270-0.2700.0000.0000.0000.000
66A66GLN0-0.073-0.04118.437-0.035-0.0350.0000.0000.0000.000
67A67CYS0-0.096-0.02417.038-0.041-0.0410.0000.0000.0000.000
68A68GLY00.0510.02218.288-0.026-0.0260.0000.0000.0000.000
69A69GLU-1-0.910-0.92617.918-0.571-0.5710.0000.0000.0000.000
70A70LEU0-0.068-0.03621.6610.0160.0160.0000.0000.0000.000
71A71LEU0-0.017-0.00524.503-0.004-0.0040.0000.0000.0000.000
72A72SER00.013-0.00427.0060.0150.0150.0000.0000.0000.000
73A73GLU-1-0.808-0.88230.474-0.181-0.1810.0000.0000.0000.000
74A74ASN00.0150.01832.8150.0110.0110.0000.0000.0000.000
75A75MET00.0010.00436.4880.0010.0010.0000.0000.0000.000
76A76ILE0-0.0020.00538.8170.0060.0060.0000.0000.0000.000
77A77ASN0-0.043-0.04241.525-0.001-0.0010.0000.0000.0000.000
78A78GLY00.0230.01144.2040.0030.0030.0000.0000.0000.000
79A79ARG10.8650.93339.2590.1220.1220.0000.0000.0000.000
80A80PRO00.0410.02835.4030.0000.0000.0000.0000.0000.000
81A81ILE0-0.044-0.02534.4320.0020.0020.0000.0000.0000.000
82A82CYS0-0.0130.01629.706-0.001-0.0010.0000.0000.0000.000
83A83LEU0-0.0110.00429.5370.0030.0030.0000.0000.0000.000
84A84PHE00.0490.01923.9230.0010.0010.0000.0000.0000.000
85A85LYS10.8990.93221.4270.4140.4140.0000.0000.0000.000
86A86LEU0-0.021-0.02320.225-0.018-0.0180.0000.0000.0000.000
87A87HIS0-0.048-0.03914.851-0.041-0.0410.0000.0000.0000.000
88A88GLU-1-0.884-0.92413.884-0.880-0.8800.0000.0000.0000.000
89A89PRO0-0.037-0.02017.7390.0480.0480.0000.0000.0000.000
90A90VAL00.0020.02021.4360.0020.0020.0000.0000.0000.000
91A91GLN0-0.019-0.02723.511-0.017-0.0170.0000.0000.0000.000
92A92VAL0-0.003-0.01425.3250.0200.0200.0000.0000.0000.000
93A93ALA00.0200.01329.1250.0040.0040.0000.0000.0000.000
94A94HIS00.000-0.00128.331-0.016-0.0160.0000.0000.0000.000
95A95TRP0-0.015-0.01627.858-0.011-0.0110.0000.0000.0000.000
96A96GLN0-0.008-0.00421.697-0.020-0.0200.0000.0000.0000.000
97A97PHE0-0.0060.00025.211-0.003-0.0030.0000.0000.0000.000
98A98SER00.0580.02522.484-0.029-0.0290.0000.0000.0000.000
99A99ILE0-0.0120.01123.677-0.015-0.0150.0000.0000.0000.000
100A100VAL00.0270.01325.5550.0210.0210.0000.0000.0000.000
101A101GLU-1-0.811-0.87328.107-0.165-0.1650.0000.0000.0000.000
102A102LEU00.000-0.01129.3630.0060.0060.0000.0000.0000.000
103A103PRO0-0.040-0.02032.1140.0050.0050.0000.0000.0000.000
104A104TRP00.0420.01131.3380.0020.0020.0000.0000.0000.000
105A105PRO00.0040.01337.4260.0020.0020.0000.0000.0000.000
106A106GLY00.0070.00340.6190.0010.0010.0000.0000.0000.000
107A107GLU-1-0.897-0.93843.340-0.075-0.0750.0000.0000.0000.000
108A108LYS10.9050.96044.5050.1020.1020.0000.0000.0000.000
109A109ARG10.8840.93844.5030.0750.0750.0000.0000.0000.000
110A110TYR0-0.057-0.06341.2820.0050.0050.0000.0000.0000.000
111A111PRO00.006-0.01642.180-0.002-0.0020.0000.0000.0000.000
112A112HIS0-0.050-0.00235.8390.0080.0080.0000.0000.0000.000
113A113GLU-1-0.749-0.83635.935-0.121-0.1210.0000.0000.0000.000
114A114GLY00.0460.01633.422-0.002-0.0020.0000.0000.0000.000
115A115TRP0-0.045-0.02927.1770.0010.0010.0000.0000.0000.000
116A116GLU-1-0.786-0.84934.035-0.119-0.1190.0000.0000.0000.000
117A117HIS10.7330.82335.7330.1610.1610.0000.0000.0000.000
118A118ILE00.0360.04632.649-0.010-0.0100.0000.0000.0000.000
119A119GLU-1-0.838-0.90633.982-0.143-0.1430.0000.0000.0000.000
120A120ILE00.0350.01334.021-0.012-0.0120.0000.0000.0000.000
121A121VAL00.0430.02333.6390.0090.0090.0000.0000.0000.000
122A122LEU0-0.038-0.01636.4850.0000.0000.0000.0000.0000.000
123A123PRO00.0410.01836.5970.0070.0070.0000.0000.0000.000
124A124GLY00.004-0.00239.3900.0060.0060.0000.0000.0000.000
125A125ASP-1-0.785-0.88342.810-0.098-0.0980.0000.0000.0000.000
126A126PRO0-0.019-0.00443.0040.0010.0010.0000.0000.0000.000
127A127GLU-1-0.924-0.95945.276-0.091-0.0910.0000.0000.0000.000
128A128THR0-0.046-0.03348.0320.0020.0020.0000.0000.0000.000
129A129LEU0-0.069-0.01242.1280.0000.0000.0000.0000.0000.000
130A130ASN00.033-0.01346.002-0.004-0.0040.0000.0000.0000.000
131A131ALA00.0130.00748.0570.0010.0010.0000.0000.0000.000
132A132ARG10.8400.89942.4930.1140.1140.0000.0000.0000.000
133A133ALA00.005-0.00144.306-0.001-0.0010.0000.0000.0000.000
134A134LEU0-0.021-0.02245.5700.0000.0000.0000.0000.0000.000
135A135ALA0-0.0130.00248.5080.0020.0020.0000.0000.0000.000
136A136LEU0-0.052-0.01742.2410.0000.0000.0000.0000.0000.000
137A137LEU0-0.067-0.02244.926-0.002-0.0020.0000.0000.0000.000
138A138SER00.0180.00547.8370.0040.0040.0000.0000.0000.000
139A139ASP-1-0.879-0.95550.456-0.069-0.0690.0000.0000.0000.000
140A140GLU-1-0.955-0.96852.688-0.066-0.0660.0000.0000.0000.000
141A141GLY00.0520.02349.8240.0000.0000.0000.0000.0000.000
142A142LEU0-0.068-0.03950.0950.0000.0000.0000.0000.0000.000
143A143SER0-0.074-0.04452.1200.0020.0020.0000.0000.0000.000
144A144LEU0-0.0090.01350.2740.0030.0030.0000.0000.0000.000
145A145PRO00.0220.01253.479-0.001-0.0010.0000.0000.0000.000
146A146GLY0-0.065-0.04251.637-0.002-0.0020.0000.0000.0000.000
147A147ILE0-0.031-0.00847.408-0.004-0.0040.0000.0000.0000.000
148A148SER0-0.049-0.01849.0240.0030.0030.0000.0000.0000.000
149A149VAL00.0480.01047.953-0.005-0.0050.0000.0000.0000.000
150A150LYS10.9110.96146.8790.0930.0930.0000.0000.0000.000
151A151THR00.0630.03847.483-0.003-0.0030.0000.0000.0000.000
152A152SER0-0.0200.00244.8020.0010.0010.0000.0000.0000.000
153A160ARG11.0171.00540.3790.1100.1100.0000.0000.0000.000
154A161LEU00.0110.00337.9460.0060.0060.0000.0000.0000.000
155A162PRO0-0.028-0.00441.783-0.001-0.0010.0000.0000.0000.000
156A163ASN00.1150.05939.315-0.008-0.0080.0000.0000.0000.000
157A164PRO0-0.0170.01242.316-0.001-0.0010.0000.0000.0000.000
158A165THR00.004-0.03040.906-0.007-0.0070.0000.0000.0000.000
159A166LEU0-0.0250.00943.4110.0050.0050.0000.0000.0000.000
160A167ALA0-0.033-0.03043.176-0.007-0.0070.0000.0000.0000.000
161A168VAL00.0660.03843.4920.0060.0060.0000.0000.0000.000
162A169THR0-0.015-0.03043.604-0.004-0.0040.0000.0000.0000.000
163A170ASP-1-0.690-0.83544.529-0.091-0.0910.0000.0000.0000.000
164A171GLY0-0.041-0.01446.1750.0050.0050.0000.0000.0000.000
165A172LYS10.7140.83742.7850.0880.0880.0000.0000.0000.000
166A173THR00.0320.03538.730-0.007-0.0070.0000.0000.0000.000
167A174THR0-0.059-0.03139.8240.0080.0080.0000.0000.0000.000
168A175ILE00.0450.03438.276-0.009-0.0090.0000.0000.0000.000
169A176LYS10.8290.90138.7040.1460.1460.0000.0000.0000.000
170A177PHE00.0440.03138.725-0.008-0.0080.0000.0000.0000.000
171A178HIS10.8130.87535.2480.1730.1730.0000.0000.0000.000
172A179PRO0-0.015-0.01239.130-0.004-0.0040.0000.0000.0000.000
173A180TRP0-0.0240.00436.2580.0010.0010.0000.0000.0000.000
174A181SER00.002-0.01631.146-0.002-0.0020.0000.0000.0000.000
175A182ILE0-0.008-0.02529.7600.0080.0080.0000.0000.0000.000
176A183GLU-1-0.785-0.89125.996-0.304-0.3040.0000.0000.0000.000
177A184GLU-1-0.845-0.89529.648-0.188-0.1880.0000.0000.0000.000
178A185ILE0-0.035-0.01832.8940.0110.0110.0000.0000.0000.000
179A186VAL00.0180.01329.1640.0080.0080.0000.0000.0000.000
180A187ALA00.0060.00231.2100.0060.0060.0000.0000.0000.000
181A188SER0-0.134-0.07832.6470.0130.0130.0000.0000.0000.000
182A189GLU-1-1.015-1.00235.150-0.137-0.1370.0000.0000.0000.000
183A190GLN0-0.050-0.00530.246-0.015-0.0150.0000.0000.0000.000