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: 89RNY

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1901517.370506
FMO2-HF: Nuclear repulsion 1830848.178947
FMO2-HF: Total energy -70669.191559
FMO2-MP2: Total energy -70874.822453


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.
-28.482-15.6716.366-7.935-11.239-0.046
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 : -0.032 / q_NPA : -0.006
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].
3A3PHE0-0.021-0.0353.347-2.8990.210-0.008-1.487-1.6140.010
4A4GLU-1-0.827-0.9046.5300.9810.9810.0000.0000.0000.000
5A5ARG10.8380.9329.587-0.919-0.9190.0000.0000.0000.000
6A6GLY00.0820.06110.3560.0680.0680.0000.0000.0000.000
7A7TYR0-0.076-0.03312.974-0.042-0.0420.0000.0000.0000.000
8A8THR0-0.043-0.02815.0500.0320.0320.0000.0000.0000.000
9A9SER00.0260.00617.621-0.011-0.0110.0000.0000.0000.000
10A10PRO00.0370.02219.342-0.008-0.0080.0000.0000.0000.000
11A11TYR00.0230.00521.112-0.015-0.0150.0000.0000.0000.000
12A12PHE0-0.003-0.01817.253-0.024-0.0240.0000.0000.0000.000
13A13VAL0-0.0550.00217.897-0.032-0.0320.0000.0000.0000.000
14A14THR00.008-0.01717.451-0.015-0.0150.0000.0000.0000.000
15A15ASP-1-0.793-0.87518.8400.0180.0180.0000.0000.0000.000
16A16PRO0-0.006-0.02420.5710.0280.0280.0000.0000.0000.000
17A17GLU-1-0.899-0.95223.1630.0770.0770.0000.0000.0000.000
18A18ARG10.8210.90318.221-0.037-0.0370.0000.0000.0000.000
19A19MET0-0.069-0.01419.1390.0310.0310.0000.0000.0000.000
20A20ILE00.007-0.00614.5960.0610.0610.0000.0000.0000.000
21A21CYS0-0.0220.00714.047-0.061-0.0610.0000.0000.0000.000
22A22GLU-1-0.945-0.97712.727-0.129-0.1290.0000.0000.0000.000
23A23TYR00.006-0.01112.2360.0470.0470.0000.0000.0000.000
24A24GLU-1-0.906-0.96111.783-0.669-0.6690.0000.0000.0000.000
25A25ASN0-0.041-0.01912.6060.0070.0070.0000.0000.0000.000
26A26CYS0-0.048-0.00910.7170.1820.1820.0000.0000.0000.000
27A27LYS10.9490.97811.5280.5400.5400.0000.0000.0000.000
28A28ILE0-0.024-0.0187.3410.0530.0530.0000.0000.0000.000
29A29LEU00.0540.03110.6740.0100.0100.0000.0000.0000.000
30A30LEU0-0.020-0.0037.5220.0820.0820.0000.0000.0000.000
31A31VAL00.0180.00311.477-0.004-0.0040.0000.0000.0000.000
32A32ASP-1-0.869-0.91814.3740.2020.2020.0000.0000.0000.000
33A33LYS10.9460.97915.3830.0330.0330.0000.0000.0000.000
34A34LYS10.8450.91917.502-0.136-0.1360.0000.0000.0000.000
35A35ILE0-0.0140.00216.788-0.025-0.0250.0000.0000.0000.000
36A36SER00.0350.02620.7180.0160.0160.0000.0000.0000.000
37A37THR0-0.007-0.02624.273-0.001-0.0010.0000.0000.0000.000
38A38ALA00.037-0.00223.360-0.010-0.0100.0000.0000.0000.000
39A39ARG10.9580.97624.4500.0310.0310.0000.0000.0000.000
40A40ASP-1-0.812-0.90222.899-0.053-0.0530.0000.0000.0000.000
41A41ILE00.011-0.00418.988-0.014-0.0140.0000.0000.0000.000
42A42ILE00.0090.00621.981-0.024-0.0240.0000.0000.0000.000
43A43THR00.0720.04023.531-0.008-0.0080.0000.0000.0000.000
44A44ILE00.0050.01117.321-0.021-0.0210.0000.0000.0000.000
45A45LEU0-0.046-0.03119.588-0.024-0.0240.0000.0000.0000.000
46A46GLU-1-0.931-0.96921.602-0.168-0.1680.0000.0000.0000.000
47A47SER0-0.083-0.05120.907-0.012-0.0120.0000.0000.0000.000
48A48ALA00.0010.00018.572-0.017-0.0170.0000.0000.0000.000
49A49ILE0-0.005-0.00620.258-0.004-0.0040.0000.0000.0000.000
50A50ARG10.9060.96023.5230.2090.2090.0000.0000.0000.000
51A51GLY0-0.024-0.02321.9740.0070.0070.0000.0000.0000.000
52A52ASN0-0.028-0.00921.844-0.012-0.0120.0000.0000.0000.000
53A53TYR0-0.016-0.01016.714-0.035-0.0350.0000.0000.0000.000
54A54PRO0-0.063-0.03114.7000.0500.0500.0000.0000.0000.000
55A55LEU00.0300.01513.926-0.072-0.0720.0000.0000.0000.000
56A56LEU0-0.012-0.0037.7420.0860.0860.0000.0000.0000.000
57A57ILE00.003-0.00211.564-0.078-0.0780.0000.0000.0000.000
58A58MET0-0.042-0.0115.0640.2420.2420.0000.0000.0000.000
59A59ALA00.0450.03411.227-0.062-0.0620.0000.0000.0000.000
60A60GLU-1-0.942-0.96414.2230.2520.2520.0000.0000.0000.000
61A61GLU-1-0.924-0.98816.1130.2150.2150.0000.0000.0000.000
62A62VAL0-0.0130.01116.530-0.036-0.0360.0000.0000.0000.000
63A63GLU-1-0.900-0.94919.2710.0740.0740.0000.0000.0000.000
64A64GLN00.017-0.01022.984-0.006-0.0060.0000.0000.0000.000
65A65GLU-1-0.875-0.92825.415-0.007-0.0070.0000.0000.0000.000
66A66ALA00.0110.00822.205-0.012-0.0120.0000.0000.0000.000
67A67LEU0-0.019-0.00819.750-0.017-0.0170.0000.0000.0000.000
68A68ALA00.0190.01322.554-0.009-0.0090.0000.0000.0000.000
69A69THR00.0030.00125.179-0.011-0.0110.0000.0000.0000.000
70A70LEU00.0060.00918.730-0.015-0.0150.0000.0000.0000.000
71A71VAL0-0.011-0.01122.407-0.012-0.0120.0000.0000.0000.000
72A72VAL0-0.014-0.00223.826-0.007-0.0070.0000.0000.0000.000
73A73ASN0-0.052-0.04824.429-0.010-0.0100.0000.0000.0000.000
74A74LYS10.8870.96820.5150.0480.0480.0000.0000.0000.000
75A75LEU0-0.078-0.04523.526-0.003-0.0030.0000.0000.0000.000
76A76ARG10.9260.96126.5780.0580.0580.0000.0000.0000.000
77A77GLY00.0040.01925.508-0.002-0.0020.0000.0000.0000.000
78A78THR0-0.070-0.02526.039-0.009-0.0090.0000.0000.0000.000
79A79LEU00.0150.00620.143-0.018-0.0180.0000.0000.0000.000
80A80LYS10.8890.96818.4290.3370.3370.0000.0000.0000.000
81A81VAL00.0160.00416.584-0.045-0.0450.0000.0000.0000.000
82A82VAL00.0000.00112.7010.0490.0490.0000.0000.0000.000
83A83ALA00.0290.02313.965-0.054-0.0540.0000.0000.0000.000
84A84ILE00.003-0.0098.2830.0520.0520.0000.0000.0000.000
85A85LYS10.9680.98012.886-0.336-0.3360.0000.0000.0000.000
86A86ALA00.0550.02510.1090.1510.1510.0000.0000.0000.000
87A87PRO0-0.0060.0056.799-0.095-0.0950.0000.0000.0000.000
88A88GLY00.0280.00810.077-0.098-0.0980.0000.0000.0000.000
89A89PHE00.014-0.01712.783-0.082-0.0820.0000.0000.0000.000
90A90GLY00.0340.01315.9890.0210.0210.0000.0000.0000.000
91A91GLU-1-0.797-0.90116.1250.1790.1790.0000.0000.0000.000
92A92ARG10.7490.84013.170-0.492-0.4920.0000.0000.0000.000
93A93ARG10.9320.98411.826-0.202-0.2020.0000.0000.0000.000
94A94SER00.045-0.01711.3470.0210.0210.0000.0000.0000.000
95A95SER0-0.089-0.04111.855-0.110-0.1100.0000.0000.0000.000
96A96TYR0-0.061-0.0437.373-0.013-0.0130.0000.0000.0000.000
97A97LEU00.0250.0156.863-0.080-0.0800.0000.0000.0000.000
98A98GLU-1-0.838-0.9328.365-0.745-0.7450.0000.0000.0000.000
99A99ASP-1-0.788-0.8626.0280.1690.1690.0000.0000.0000.000
100A100ILE0-0.005-0.0102.931-1.164-0.6630.040-0.146-0.3940.000
101A101ALA00.0010.0104.968-0.586-0.565-0.0010.000-0.0200.000
102A102ILE00.0130.0078.462-0.122-0.1220.0000.0000.0000.000
103A103LEU0-0.060-0.0402.472-1.426-0.8200.993-0.474-1.124-0.002
104A104THR0-0.094-0.0595.3000.2310.2310.0000.0000.0000.000
105A105GLY00.0740.0477.9290.2890.2890.0000.0000.0000.000
106A106GLY00.0050.01410.1080.1520.1520.0000.0000.0000.000
107A107THR0-0.057-0.02811.6080.0450.0450.0000.0000.0000.000
108A108VAL0-0.047-0.02111.0810.0300.0300.0000.0000.0000.000
109A109VAL0-0.0020.00113.4990.0300.0300.0000.0000.0000.000
110A110ARG10.9110.95213.9250.2080.2080.0000.0000.0000.000
111A111ASP-1-0.877-0.94118.595-0.017-0.0170.0000.0000.0000.000
112A112GLU-1-0.942-0.95421.880-0.014-0.0140.0000.0000.0000.000
113A113MET0-0.038-0.03420.495-0.018-0.0180.0000.0000.0000.000
114A114GLY0-0.0070.00220.655-0.021-0.0210.0000.0000.0000.000
115A115VAL0-0.035-0.01019.8600.0130.0130.0000.0000.0000.000
116A116SER00.032-0.03621.0450.0020.0020.0000.0000.0000.000
117A117LEU00.000-0.03118.878-0.018-0.0180.0000.0000.0000.000
118A118GLU-1-0.909-0.94421.668-0.092-0.0920.0000.0000.0000.000
119A119GLN0-0.0250.03724.575-0.012-0.0120.0000.0000.0000.000
120A120ALA0-0.0150.01619.564-0.016-0.0160.0000.0000.0000.000
121A121THR00.011-0.00821.341-0.001-0.0010.0000.0000.0000.000
122A122ASP-1-0.840-0.92318.825-0.370-0.3700.0000.0000.0000.000
123A123ALA0-0.0010.00717.896-0.055-0.0550.0000.0000.0000.000
124A124VAL0-0.056-0.02015.680-0.041-0.0410.0000.0000.0000.000
125A125LEU0-0.053-0.02213.640-0.060-0.0600.0000.0000.0000.000
126A126GLY00.0750.04310.153-0.014-0.0140.0000.0000.0000.000
127A127THR0-0.065-0.04710.4660.2570.2570.0000.0000.0000.000
128A128ALA00.0020.0147.080-0.368-0.3680.0000.0000.0000.000
129A129ALA00.0230.0138.5130.4110.4110.0000.0000.0000.000
130A130LYS10.9680.9838.2000.8270.8270.0000.0000.0000.000
131A131ILE0-0.032-0.0017.016-0.604-0.6040.0000.0000.0000.000
132A132THR00.012-0.0097.9380.1370.1370.0000.0000.0000.000
133A133ILE0-0.057-0.0149.0500.1630.1630.0000.0000.0000.000
134A134THR00.0520.01411.446-0.049-0.0490.0000.0000.0000.000
135A135LYS10.9670.97114.016-0.286-0.2860.0000.0000.0000.000
136A136GLU-1-0.918-0.96514.1690.5140.5140.0000.0000.0000.000
137A137ARG10.8170.9097.454-1.858-1.8580.0000.0000.0000.000
138A138THR00.0290.0035.578-0.460-0.4600.0000.0000.0000.000
139A139THR0-0.057-0.0343.7331.0021.2080.000-0.101-0.1060.000
140A140VAL00.0200.0092.606-1.3440.4850.411-0.835-1.4040.003
141A141VAL0-0.015-0.0052.394-7.682-5.6552.052-1.846-2.232-0.026
142A142GLY00.0690.0185.0360.7380.7380.0000.0000.0000.000
143A143ASP-1-0.868-0.9456.563-1.109-1.1090.0000.0000.0000.000
144A144GLY0-0.029-0.0109.6310.2560.2560.0000.0000.0000.000
145A145SER0-0.015-0.01511.5140.2420.2420.0000.0000.0000.000
146A146THR00.0030.0089.2200.1500.1500.0000.0000.0000.000
147A147ALA00.0160.01411.231-0.018-0.0180.0000.0000.0000.000
148A148ALA0-0.005-0.01112.2470.0480.0480.0000.0000.0000.000
149A149ASP-1-0.847-0.91412.010-0.740-0.7400.0000.0000.0000.000
150A150VAL00.0080.0037.3890.0960.0960.0000.0000.0000.000
151A151ALA0-0.026-0.0139.9610.1860.1860.0000.0000.0000.000
152A152ALA0-0.025-0.02112.6330.1490.1490.0000.0000.0000.000
153A153ARG10.8870.9369.6100.3550.3550.0000.0000.0000.000
154A154VAL00.0450.0229.3600.1870.1870.0000.0000.0000.000
155A155LYS10.8730.92411.6630.3900.3900.0000.0000.0000.000
156A156GLN00.0530.03714.4430.0240.0240.0000.0000.0000.000
157A157ILE0-0.0260.00210.0040.0680.0680.0000.0000.0000.000
158A158ARG10.9890.99513.7630.0770.0770.0000.0000.0000.000
159A159ASN0-0.010-0.01916.4640.0320.0320.0000.0000.0000.000
160A160LEU0-0.038-0.01415.3630.0130.0130.0000.0000.0000.000
161A161GLN0-0.053-0.04615.023-0.034-0.0340.0000.0000.0000.000
162A162MET0-0.055-0.03018.3440.0030.0030.0000.0000.0000.000
163A163GLN0-0.0310.00721.3070.0030.0030.0000.0000.0000.000
164A164THR0-0.078-0.02320.0730.0230.0230.0000.0000.0000.000
165A165ASP-1-0.842-0.92722.3500.1420.1420.0000.0000.0000.000
166A166GLN0-0.032-0.01721.8790.0030.0030.0000.0000.0000.000
167A167ASP-1-0.877-0.94920.6370.2780.2780.0000.0000.0000.000
168A168TYR00.001-0.00416.7540.0600.0600.0000.0000.0000.000
169A169GLU-1-0.763-0.85216.7380.4900.4900.0000.0000.0000.000
170A170ARG10.9540.98715.891-0.202-0.2020.0000.0000.0000.000
171A171GLU-1-0.896-0.94114.0310.6830.6830.0000.0000.0000.000
172A172LYS10.9410.96412.194-0.757-0.7570.0000.0000.0000.000
173A173LEU0-0.047-0.02510.8660.1710.1710.0000.0000.0000.000
174A174GLN00.0630.03810.987-0.075-0.0750.0000.0000.0000.000
175A175GLU-1-0.917-0.9658.3631.2741.2740.0000.0000.0000.000
176A176ARG10.7480.8516.6430.0190.0190.0000.0000.0000.000
177A177ILE0-0.0090.0046.579-0.227-0.2270.0000.0000.0000.000
178A178ALA0-0.014-0.0036.999-0.397-0.3970.0000.0000.0000.000
179A179ARG10.8760.9402.285-4.550-3.5601.206-0.884-1.311-0.001
180A180LEU0-0.0040.0022.405-9.888-6.4821.674-2.154-2.926-0.030
181A181SER0-0.079-0.0274.760-0.810-0.694-0.001-0.008-0.1080.000