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: JQN29

Calculation Name: 5CDK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CDK

Chain ID: A

ChEMBL ID:

UniProt ID: A8JE91

Base Structure: X-ray

Registration Date: 2023-09-23

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1908137.055008
FMO2-HF: Nuclear repulsion 1837466.447918
FMO2-HF: Total energy -70670.607091
FMO2-MP2: Total energy -70876.096322


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:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-25.525-15.35512.271-9.379-13.061-0.053
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.012
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].
3A3PHE00.011-0.0052.609-1.5091.6930.232-1.603-1.8300.008
4A4GLU-1-0.820-0.8986.4680.2680.2680.0000.0000.0000.000
5A5ARG10.8150.9048.532-0.436-0.4360.0000.0000.0000.000
6A6GLY00.0580.0569.443-0.192-0.1920.0000.0000.0000.000
7A7TYR0-0.078-0.05111.9550.0520.0520.0000.0000.0000.000
8A8THR0-0.059-0.05114.1800.0720.0720.0000.0000.0000.000
9A9SER00.013-0.00616.7080.0280.0280.0000.0000.0000.000
10A10PRO00.0460.02718.323-0.038-0.0380.0000.0000.0000.000
11A11TYR00.0330.00820.008-0.024-0.0240.0000.0000.0000.000
12A12PHE00.0310.00616.395-0.014-0.0140.0000.0000.0000.000
13A13VAL0-0.0500.00417.299-0.054-0.0540.0000.0000.0000.000
14A14THR00.0130.00116.9580.0060.0060.0000.0000.0000.000
15A15ASP-1-0.799-0.87118.762-0.233-0.2330.0000.0000.0000.000
16A16PRO00.012-0.01020.011-0.002-0.0020.0000.0000.0000.000
17A17GLU-1-0.917-0.95622.680-0.111-0.1110.0000.0000.0000.000
18A18ARG10.8210.88318.5440.2500.2500.0000.0000.0000.000
19A19MET0-0.0370.00618.8400.0000.0000.0000.0000.0000.000
20A20ILE00.0090.02014.4170.0000.0000.0000.0000.0000.000
21A21CYS0-0.026-0.01213.4530.0210.0210.0000.0000.0000.000
22A22GLU-1-0.877-0.92612.511-0.829-0.8290.0000.0000.0000.000
23A23TYR0-0.009-0.02212.2850.1500.1500.0000.0000.0000.000
24A24GLU-1-0.842-0.92511.785-1.004-1.0040.0000.0000.0000.000
25A25ASN0-0.026-0.02212.9790.0910.0910.0000.0000.0000.000
26A26CYS0-0.055-0.00410.7400.1440.1440.0000.0000.0000.000
27A27LYS10.9300.95811.5650.4630.4630.0000.0000.0000.000
28A28ILE0-0.001-0.0047.671-0.076-0.0760.0000.0000.0000.000
29A29LEU00.0410.02710.8500.1100.1100.0000.0000.0000.000
30A30LEU0-0.017-0.0087.8950.0230.0230.0000.0000.0000.000
31A31VAL00.0120.00911.880-0.005-0.0050.0000.0000.0000.000
32A32ASP-1-0.785-0.88314.2860.4880.4880.0000.0000.0000.000
33A33LYS10.8080.90515.579-0.090-0.0900.0000.0000.0000.000
34A34LYS10.8170.88517.463-0.108-0.1080.0000.0000.0000.000
35A35ILE00.0060.00816.427-0.011-0.0110.0000.0000.0000.000
36A36SER0-0.011-0.01520.466-0.005-0.0050.0000.0000.0000.000
37A37THR0-0.034-0.05323.965-0.011-0.0110.0000.0000.0000.000
38A38ALA00.017-0.01323.189-0.004-0.0040.0000.0000.0000.000
39A39ARG10.9200.95124.2760.0130.0130.0000.0000.0000.000
40A40ASP-1-0.759-0.83222.876-0.015-0.0150.0000.0000.0000.000
41A41ILE00.0650.02718.9230.0030.0030.0000.0000.0000.000
42A42ILE00.0080.01121.920-0.025-0.0250.0000.0000.0000.000
43A43THR00.0480.01923.458-0.016-0.0160.0000.0000.0000.000
44A44ILE0-0.0050.00517.365-0.021-0.0210.0000.0000.0000.000
45A45LEU0-0.035-0.01719.570-0.036-0.0360.0000.0000.0000.000
46A46GLU-1-0.896-0.94921.705-0.149-0.1490.0000.0000.0000.000
47A47SER0-0.063-0.05521.371-0.017-0.0170.0000.0000.0000.000
48A48ALA00.0020.00018.716-0.021-0.0210.0000.0000.0000.000
49A49ILE0-0.010-0.00720.352-0.017-0.0170.0000.0000.0000.000
50A50ARG10.8580.93323.5330.1570.1570.0000.0000.0000.000
51A51GLY00.0060.00722.3140.0090.0090.0000.0000.0000.000
52A52ASN0-0.020-0.00921.941-0.037-0.0370.0000.0000.0000.000
53A53TYR00.0340.03216.923-0.040-0.0400.0000.0000.0000.000
54A54PRO0-0.050-0.02214.7170.0490.0490.0000.0000.0000.000
55A55LEU00.002-0.00213.913-0.031-0.0310.0000.0000.0000.000
56A56LEU00.0060.0077.0650.0250.0250.0000.0000.0000.000
57A57ILE0-0.007-0.00411.5780.0530.0530.0000.0000.0000.000
58A58MET0-0.038-0.0064.8300.2090.2090.0000.0000.0000.000
59A59ALA00.0510.03710.9380.0400.0400.0000.0000.0000.000
60A60GLU-1-0.847-0.90213.6350.2720.2720.0000.0000.0000.000
61A61GLU-1-0.837-0.91715.8440.1050.1050.0000.0000.0000.000
62A62VAL00.0120.01816.060-0.010-0.0100.0000.0000.0000.000
63A63GLU-1-0.829-0.90918.8540.0500.0500.0000.0000.0000.000
64A64GLN00.0270.00122.472-0.013-0.0130.0000.0000.0000.000
65A65GLU-1-0.880-0.93624.884-0.040-0.0400.0000.0000.0000.000
66A66ALA00.0210.02421.469-0.016-0.0160.0000.0000.0000.000
67A67LEU0-0.032-0.01019.047-0.026-0.0260.0000.0000.0000.000
68A68ALA00.0210.00721.766-0.022-0.0220.0000.0000.0000.000
69A69THR0-0.012-0.01524.828-0.012-0.0120.0000.0000.0000.000
70A70LEU0-0.015-0.00518.204-0.016-0.0160.0000.0000.0000.000
71A71VAL0-0.003-0.00321.181-0.021-0.0210.0000.0000.0000.000
72A72VAL00.0070.00322.812-0.009-0.0090.0000.0000.0000.000
73A73ASN0-0.038-0.03624.3520.0000.0000.0000.0000.0000.000
74A74LYS10.8400.93519.2220.2720.2720.0000.0000.0000.000
75A75LEU0-0.050-0.03222.858-0.007-0.0070.0000.0000.0000.000
76A76ARG10.8780.94425.7050.1200.1200.0000.0000.0000.000
77A77GLY0-0.0080.00924.7300.0030.0030.0000.0000.0000.000
78A78THR0-0.055-0.02725.139-0.009-0.0090.0000.0000.0000.000
79A79LEU00.0300.00820.103-0.005-0.0050.0000.0000.0000.000
80A80LYS10.8520.92918.5300.4040.4040.0000.0000.0000.000
81A81VAL00.0190.01316.139-0.055-0.0550.0000.0000.0000.000
82A82VAL00.000-0.00911.9340.0160.0160.0000.0000.0000.000
83A83ALA00.0340.02713.308-0.025-0.0250.0000.0000.0000.000
84A84ILE0-0.0100.0127.5190.0190.0190.0000.0000.0000.000
85A85LYS10.8950.92812.169-0.083-0.0830.0000.0000.0000.000
86A86ALA00.0580.0249.4160.0150.0150.0000.0000.0000.000
87A87PRO0-0.0030.0126.127-0.150-0.1500.0000.0000.0000.000
88A88GLY00.0170.0029.3390.0340.0340.0000.0000.0000.000
89A89PHE00.000-0.02212.301-0.102-0.1020.0000.0000.0000.000
90A90GLY00.0670.03315.6850.0370.0370.0000.0000.0000.000
91A91GLU-1-0.806-0.91415.6640.4330.4330.0000.0000.0000.000
92A92ARG10.7630.85512.783-0.580-0.5800.0000.0000.0000.000
93A93ARG10.7650.87511.330-0.175-0.1750.0000.0000.0000.000
94A94SER00.037-0.00511.1000.1320.1320.0000.0000.0000.000
95A95SER0-0.080-0.05111.708-0.035-0.0350.0000.0000.0000.000
96A96TYR0-0.029-0.0256.848-0.010-0.0100.0000.0000.0000.000
97A97LEU00.0030.0026.8210.5230.5230.0000.0000.0000.000
98A98GLU-1-0.793-0.8838.8670.2020.2020.0000.0000.0000.000
99A99ASP-1-0.781-0.8405.8881.2581.2580.0000.0000.0000.000
100A100ILE0-0.006-0.0083.235-1.227-0.3650.072-0.359-0.5750.003
101A101ALA00.0170.0255.675-0.912-0.885-0.0010.000-0.0260.000
102A102ILE00.0230.0148.676-0.257-0.2570.0000.0000.0000.000
103A103LEU0-0.055-0.0262.452-0.818-1.0642.497-0.852-1.399-0.001
104A104THR0-0.073-0.0526.044-0.449-0.4490.0000.0000.0000.000
105A105GLY00.0570.0348.6060.0430.0430.0000.0000.0000.000
106A106GLY00.0250.02411.1220.0240.0240.0000.0000.0000.000
107A107THR0-0.086-0.05112.7570.0690.0690.0000.0000.0000.000
108A108VAL0-0.049-0.01611.464-0.010-0.0100.0000.0000.0000.000
109A109VAL00.0190.01814.094-0.009-0.0090.0000.0000.0000.000
110A110ARG10.8290.88813.993-0.270-0.2700.0000.0000.0000.000
111A111ASP-1-0.774-0.86619.2050.0780.0780.0000.0000.0000.000
112A112GLU-1-0.942-0.95422.6290.1080.1080.0000.0000.0000.000
113A113MET0-0.049-0.03220.848-0.002-0.0020.0000.0000.0000.000
114A114GLY0-0.006-0.01620.9090.0110.0110.0000.0000.0000.000
115A115VAL0-0.049-0.01220.577-0.005-0.0050.0000.0000.0000.000
116A116SER00.0380.01221.5830.0140.0140.0000.0000.0000.000
117A117LEU00.003-0.02219.142-0.014-0.0140.0000.0000.0000.000
118A118GLU-1-0.888-0.92422.075-0.024-0.0240.0000.0000.0000.000
119A119GLN0-0.064-0.03924.914-0.004-0.0040.0000.0000.0000.000
120A120ALA0-0.032-0.00320.042-0.008-0.0080.0000.0000.0000.000
121A121THR00.014-0.00222.188-0.012-0.0120.0000.0000.0000.000
122A122ASP-1-0.809-0.90419.595-0.203-0.2030.0000.0000.0000.000
123A123ALA0-0.024-0.00518.536-0.034-0.0340.0000.0000.0000.000
124A124VAL0-0.0190.00116.3220.0000.0000.0000.0000.0000.000
125A125LEU0-0.084-0.03714.2270.0060.0060.0000.0000.0000.000
126A126GLY00.0850.05110.8530.0000.0000.0000.0000.0000.000
127A127THR0-0.103-0.05310.7720.0740.0740.0000.0000.0000.000
128A128ALA00.0380.0177.262-0.223-0.2230.0000.0000.0000.000
129A129ALA00.0110.0158.9710.2610.2610.0000.0000.0000.000
130A130LYS10.8060.8938.6461.2031.2030.0000.0000.0000.000
131A131ILE0-0.042-0.0096.772-0.786-0.7860.0000.0000.0000.000
132A132THR00.0330.0047.7420.4020.4020.0000.0000.0000.000
133A133ILE0-0.062-0.0228.013-0.249-0.2490.0000.0000.0000.000
134A134THR00.012-0.00410.4460.1690.1690.0000.0000.0000.000
135A135LYS10.8790.91413.123-0.025-0.0250.0000.0000.0000.000
136A136GLU-1-0.800-0.88513.5600.0870.0870.0000.0000.0000.000
137A137ARG10.7780.8857.597-0.633-0.6330.0000.0000.0000.000
138A138THR00.0400.0044.495-0.191-0.103-0.001-0.004-0.0830.000
139A139THR0-0.050-0.0294.4260.1930.312-0.001-0.048-0.0700.000
140A140VAL0-0.005-0.0092.456-0.1381.5250.577-0.782-1.4580.001
141A141VAL0-0.0020.0032.612-6.769-4.4950.877-1.466-1.686-0.019
142A142GLY00.0870.0304.8701.1191.1190.0000.0000.0000.000
143A143ASP-1-0.867-0.9316.749-1.014-1.0140.0000.0000.0000.000
144A144GLY00.0040.0079.7410.1600.1600.0000.0000.0000.000
145A145SER0-0.060-0.05811.3040.1820.1820.0000.0000.0000.000
146A146THR0-0.009-0.0049.4760.0350.0350.0000.0000.0000.000
147A147ALA00.0080.00911.0330.0230.0230.0000.0000.0000.000
148A148ALA0-0.013-0.00612.0670.0640.0640.0000.0000.0000.000
149A149ASP-1-0.835-0.92111.801-0.266-0.2660.0000.0000.0000.000
150A150VAL00.0140.0107.3800.1420.1420.0000.0000.0000.000
151A151ALA0-0.0020.0019.7380.1490.1490.0000.0000.0000.000
152A152ALA0-0.041-0.02712.5080.1020.1020.0000.0000.0000.000
153A153ARG10.8490.9139.232-0.517-0.5170.0000.0000.0000.000
154A154VAL00.0420.0149.2080.1420.1420.0000.0000.0000.000
155A155LYS10.9110.95811.5850.0900.0900.0000.0000.0000.000
156A156GLN00.0210.02214.0040.0620.0620.0000.0000.0000.000
157A157ILE0-0.006-0.0059.6200.0240.0240.0000.0000.0000.000
158A158ARG10.9710.99113.153-0.266-0.2660.0000.0000.0000.000
159A159ASN00.002-0.01616.139-0.009-0.0090.0000.0000.0000.000
160A160LEU0-0.0120.01414.948-0.007-0.0070.0000.0000.0000.000
161A161GLN0-0.067-0.03914.288-0.054-0.0540.0000.0000.0000.000
162A162MET0-0.040-0.01218.147-0.023-0.0230.0000.0000.0000.000
163A163GLN0-0.065-0.03020.682-0.032-0.0320.0000.0000.0000.000
164A164THR0-0.038-0.02419.7690.0140.0140.0000.0000.0000.000
165A165ASP-1-0.792-0.90622.3470.2360.2360.0000.0000.0000.000
166A166GLN0-0.036-0.00422.0020.0020.0020.0000.0000.0000.000
167A167ASP-1-0.809-0.90320.4140.3550.3550.0000.0000.0000.000
168A168TYR0-0.017-0.00116.8340.0750.0750.0000.0000.0000.000
169A169GLU-1-0.732-0.83816.3310.6810.6810.0000.0000.0000.000
170A170ARG10.7810.88915.454-0.239-0.2390.0000.0000.0000.000
171A171GLU-1-0.872-0.93113.7540.7600.7600.0000.0000.0000.000
172A172LYS10.8390.90111.893-0.800-0.8000.0000.0000.0000.000
173A173LEU0-0.036-0.02310.6690.2390.2390.0000.0000.0000.000
174A174GLN00.0820.03710.696-0.011-0.0110.0000.0000.0000.000
175A175GLU-1-0.795-0.8767.7071.6471.6470.0000.0000.0000.000
176A176ARG10.7780.8596.231-0.561-0.5610.0000.0000.0000.000
177A177ILE00.0110.0046.343-0.122-0.1220.0000.0000.0000.000
178A178ALA0-0.0280.0006.612-0.396-0.3960.0000.0000.0000.000
179A179ARG10.7840.8672.300-4.704-3.3432.257-1.599-2.0190.000
180A180LEU00.0040.0092.040-11.991-11.2805.763-2.655-3.819-0.045
181A181SER0-0.072-0.0334.475-0.303-0.194-0.001-0.011-0.0960.000