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: NNK2Q

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1903268.869843
FMO2-HF: Nuclear repulsion 1832598.575754
FMO2-HF: Total energy -70670.294088
FMO2-MP2: Total energy -70875.90991


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.
-23.738-10.4085.402-7.64-11.085-0.044
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 : -0.009 / q_NPA : 0.002
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].
3A3PHE00.002-0.0142.695-1.6961.6290.093-1.576-1.8400.008
4A4GLU-1-0.823-0.9066.3590.0200.0200.0000.0000.0000.000
5A5ARG10.8170.9198.687-0.228-0.2280.0000.0000.0000.000
6A6GLY00.0690.0559.388-0.208-0.2080.0000.0000.0000.000
7A7TYR0-0.091-0.04811.9800.0450.0450.0000.0000.0000.000
8A8THR0-0.049-0.03614.0330.0770.0770.0000.0000.0000.000
9A9SER00.0140.00116.6550.0360.0360.0000.0000.0000.000
10A10PRO00.0410.02518.322-0.038-0.0380.0000.0000.0000.000
11A11TYR00.0350.01220.078-0.016-0.0160.0000.0000.0000.000
12A12PHE00.004-0.00816.397-0.010-0.0100.0000.0000.0000.000
13A13VAL0-0.0370.01017.194-0.059-0.0590.0000.0000.0000.000
14A14THR00.020-0.00317.1530.0120.0120.0000.0000.0000.000
15A15ASP-1-0.805-0.86818.770-0.235-0.2350.0000.0000.0000.000
16A16PRO00.005-0.01720.2290.0000.0000.0000.0000.0000.000
17A17GLU-1-0.911-0.95522.705-0.114-0.1140.0000.0000.0000.000
18A18ARG10.8210.88518.3660.2430.2430.0000.0000.0000.000
19A19MET0-0.053-0.00619.0130.0000.0000.0000.0000.0000.000
20A20ILE00.0140.00914.446-0.016-0.0160.0000.0000.0000.000
21A21CYS0-0.028-0.00313.3400.0230.0230.0000.0000.0000.000
22A22GLU-1-0.878-0.93212.655-0.790-0.7900.0000.0000.0000.000
23A23TYR0-0.004-0.01712.2850.1600.1600.0000.0000.0000.000
24A24GLU-1-0.841-0.92811.832-0.929-0.9290.0000.0000.0000.000
25A25ASN0-0.042-0.01912.6350.0780.0780.0000.0000.0000.000
26A26CYS0-0.041-0.00910.7210.1310.1310.0000.0000.0000.000
27A27LYS10.9450.97211.5660.3980.3980.0000.0000.0000.000
28A28ILE0-0.018-0.0177.875-0.090-0.0900.0000.0000.0000.000
29A29LEU00.0480.03011.1120.1010.1010.0000.0000.0000.000
30A30LEU0-0.0120.0027.967-0.002-0.0020.0000.0000.0000.000
31A31VAL00.0250.00711.9340.0090.0090.0000.0000.0000.000
32A32ASP-1-0.818-0.89614.5410.4020.4020.0000.0000.0000.000
33A33LYS10.8610.91715.674-0.078-0.0780.0000.0000.0000.000
34A34LYS10.8200.89517.488-0.079-0.0790.0000.0000.0000.000
35A35ILE0-0.014-0.00116.683-0.008-0.0080.0000.0000.0000.000
36A36SER0-0.006-0.00320.603-0.005-0.0050.0000.0000.0000.000
37A37THR0-0.041-0.05024.059-0.011-0.0110.0000.0000.0000.000
38A38ALA00.041-0.00223.257-0.003-0.0030.0000.0000.0000.000
39A39ARG10.9210.95924.3410.0220.0220.0000.0000.0000.000
40A40ASP-1-0.764-0.86222.956-0.024-0.0240.0000.0000.0000.000
41A41ILE00.0370.01319.1130.0010.0010.0000.0000.0000.000
42A42ILE00.0100.00922.215-0.023-0.0230.0000.0000.0000.000
43A43THR00.0710.03623.910-0.014-0.0140.0000.0000.0000.000
44A44ILE00.0120.01317.695-0.018-0.0180.0000.0000.0000.000
45A45LEU0-0.051-0.02919.596-0.034-0.0340.0000.0000.0000.000
46A46GLU-1-0.935-0.96821.771-0.133-0.1330.0000.0000.0000.000
47A47SER0-0.076-0.06021.373-0.018-0.0180.0000.0000.0000.000
48A48ALA0-0.002-0.00218.833-0.018-0.0180.0000.0000.0000.000
49A49ILE0-0.008-0.00920.540-0.016-0.0160.0000.0000.0000.000
50A50ARG10.9120.96323.6780.1460.1460.0000.0000.0000.000
51A51GLY0-0.020-0.01722.1410.0060.0060.0000.0000.0000.000
52A52ASN00.0050.01321.828-0.034-0.0340.0000.0000.0000.000
53A53TYR00.0130.01416.810-0.036-0.0360.0000.0000.0000.000
54A54PRO0-0.060-0.02614.7330.0400.0400.0000.0000.0000.000
55A55LEU00.0250.01213.912-0.025-0.0250.0000.0000.0000.000
56A56LEU0-0.009-0.0017.246-0.003-0.0030.0000.0000.0000.000
57A57ILE0-0.001-0.00411.5850.0550.0550.0000.0000.0000.000
58A58MET0-0.032-0.0054.9690.1520.1520.0000.0000.0000.000
59A59ALA00.0440.03011.0140.0570.0570.0000.0000.0000.000
60A60GLU-1-0.858-0.90513.9080.2010.2010.0000.0000.0000.000
61A61GLU-1-0.838-0.92415.8440.0590.0590.0000.0000.0000.000
62A62VAL0-0.0050.01916.088-0.005-0.0050.0000.0000.0000.000
63A63GLU-1-0.852-0.92518.8080.0260.0260.0000.0000.0000.000
64A64GLN00.016-0.00722.469-0.015-0.0150.0000.0000.0000.000
65A65GLU-1-0.867-0.92824.774-0.047-0.0470.0000.0000.0000.000
66A66ALA00.0300.01921.852-0.013-0.0130.0000.0000.0000.000
67A67LEU0-0.026-0.01219.069-0.024-0.0240.0000.0000.0000.000
68A68ALA00.0260.01621.957-0.019-0.0190.0000.0000.0000.000
69A69THR0-0.010-0.00724.664-0.008-0.0080.0000.0000.0000.000
70A70LEU00.0040.00718.258-0.014-0.0140.0000.0000.0000.000
71A71VAL0-0.007-0.01021.599-0.021-0.0210.0000.0000.0000.000
72A72VAL0-0.0090.00123.147-0.006-0.0060.0000.0000.0000.000
73A73ASN0-0.049-0.04624.0510.0000.0000.0000.0000.0000.000
74A74LYS10.8510.93819.5930.2700.2700.0000.0000.0000.000
75A75LEU0-0.066-0.03922.966-0.004-0.0040.0000.0000.0000.000
76A76ARG10.9190.96325.8880.1180.1180.0000.0000.0000.000
77A77GLY00.0050.01825.1080.0050.0050.0000.0000.0000.000
78A78THR0-0.072-0.03125.736-0.004-0.0040.0000.0000.0000.000
79A79LEU00.0120.00219.921-0.006-0.0060.0000.0000.0000.000
80A80LYS10.8310.92218.3710.3860.3860.0000.0000.0000.000
81A81VAL00.0320.00516.201-0.034-0.0340.0000.0000.0000.000
82A82VAL0-0.009-0.00712.1080.0230.0230.0000.0000.0000.000
83A83ALA00.0270.02413.410-0.025-0.0250.0000.0000.0000.000
84A84ILE00.0110.0057.4900.0010.0010.0000.0000.0000.000
85A85LYS10.8840.92412.0720.0000.0000.0000.0000.0000.000
86A86ALA00.0450.0239.662-0.008-0.0080.0000.0000.0000.000
87A87PRO00.0090.0126.384-0.092-0.0920.0000.0000.0000.000
88A88GLY00.0290.0119.6160.0750.0750.0000.0000.0000.000
89A89PHE00.018-0.02012.514-0.096-0.0960.0000.0000.0000.000
90A90GLY00.0490.02315.8230.0470.0470.0000.0000.0000.000
91A91GLU-1-0.807-0.90516.0720.3740.3740.0000.0000.0000.000
92A92ARG10.7590.83613.055-0.495-0.4950.0000.0000.0000.000
93A93ARG10.7870.89411.681-0.148-0.1480.0000.0000.0000.000
94A94SER00.038-0.01111.4340.1080.1080.0000.0000.0000.000
95A95SER0-0.090-0.04311.9750.0050.0050.0000.0000.0000.000
96A96TYR0-0.044-0.0317.2450.0370.0370.0000.0000.0000.000
97A97LEU00.0170.0107.1460.4900.4900.0000.0000.0000.000
98A98GLU-1-0.818-0.9009.0090.3300.3300.0000.0000.0000.000
99A99ASP-1-0.789-0.8446.3001.3541.3540.0000.0000.0000.000
100A100ILE00.003-0.0023.431-0.749-0.1150.028-0.246-0.4150.002
101A101ALA0-0.0040.0085.788-0.814-0.797-0.0010.001-0.0160.000
102A102ILE00.0190.0068.935-0.232-0.2320.0000.0000.0000.000
103A103LEU0-0.054-0.0362.560-1.114-0.6180.905-0.412-0.989-0.001
104A104THR0-0.078-0.0506.102-0.415-0.4150.0000.0000.0000.000
105A105GLY00.0620.0428.572-0.036-0.0360.0000.0000.0000.000
106A106GLY00.0070.01511.155-0.011-0.0110.0000.0000.0000.000
107A107THR0-0.065-0.03112.6510.0750.0750.0000.0000.0000.000
108A108VAL0-0.050-0.02211.704-0.012-0.0120.0000.0000.0000.000
109A109VAL00.0000.00514.264-0.020-0.0200.0000.0000.0000.000
110A110ARG10.8720.91114.379-0.275-0.2750.0000.0000.0000.000
111A111ASP-1-0.789-0.88619.1770.0600.0600.0000.0000.0000.000
112A112GLU-1-0.969-0.96222.3670.1030.1030.0000.0000.0000.000
113A113MET0-0.036-0.03121.1300.0000.0000.0000.0000.0000.000
114A114GLY00.0010.00621.3400.0090.0090.0000.0000.0000.000
115A115VAL0-0.033-0.01420.746-0.006-0.0060.0000.0000.0000.000
116A116SER00.0390.00021.8040.0120.0120.0000.0000.0000.000
117A117LEU00.020-0.02119.160-0.012-0.0120.0000.0000.0000.000
118A118GLU-1-0.900-0.93222.141-0.020-0.0200.0000.0000.0000.000
119A119GLN0-0.064-0.01625.151-0.004-0.0040.0000.0000.0000.000
120A120ALA0-0.0290.00920.260-0.004-0.0040.0000.0000.0000.000
121A121THR00.018-0.00922.185-0.012-0.0120.0000.0000.0000.000
122A122ASP-1-0.825-0.90619.543-0.173-0.1730.0000.0000.0000.000
123A123ALA0-0.0170.00118.766-0.026-0.0260.0000.0000.0000.000
124A124VAL0-0.046-0.01716.2620.0000.0000.0000.0000.0000.000
125A125LEU0-0.056-0.02114.4180.0090.0090.0000.0000.0000.000
126A126GLY00.0770.04311.0880.0130.0130.0000.0000.0000.000
127A127THR0-0.077-0.04610.9250.0320.0320.0000.0000.0000.000
128A128ALA00.0120.0197.073-0.136-0.1360.0000.0000.0000.000
129A129ALA00.0160.0128.5520.2680.2680.0000.0000.0000.000
130A130LYS10.8310.9078.2531.1431.1430.0000.0000.0000.000
131A131ILE0-0.041-0.0056.918-0.752-0.7520.0000.0000.0000.000
132A132THR00.030-0.0027.9320.3960.3960.0000.0000.0000.000
133A133ILE0-0.062-0.0168.184-0.247-0.2470.0000.0000.0000.000
134A134THR00.0360.01210.6210.1830.1830.0000.0000.0000.000
135A135LYS10.9130.93313.0740.0210.0210.0000.0000.0000.000
136A136GLU-1-0.858-0.92313.3640.0360.0360.0000.0000.0000.000
137A137ARG10.7980.8937.614-0.623-0.6230.0000.0000.0000.000
138A138THR00.0410.0104.475-0.127-0.020-0.001-0.005-0.1010.000
139A139THR0-0.047-0.0273.948-0.211-0.040-0.001-0.088-0.0820.000
140A140VAL00.0150.0032.6130.1811.8350.375-0.688-1.3400.001
141A141VAL0-0.0100.0002.484-7.274-4.9251.450-1.747-2.052-0.024
142A142GLY00.0710.0195.0720.9570.9570.0000.0000.0000.000
143A143ASP-1-0.860-0.9306.577-0.839-0.8390.0000.0000.0000.000
144A144GLY0-0.024-0.0089.6430.1760.1760.0000.0000.0000.000
145A145SER0-0.031-0.03411.5370.1730.1730.0000.0000.0000.000
146A146THR0-0.0090.0039.2360.0500.0500.0000.0000.0000.000
147A147ALA00.0150.01411.2900.0440.0440.0000.0000.0000.000
148A148ALA0-0.004-0.00912.3030.0540.0540.0000.0000.0000.000
149A149ASP-1-0.837-0.92011.952-0.136-0.1360.0000.0000.0000.000
150A150VAL00.0210.0107.3800.1420.1420.0000.0000.0000.000
151A151ALA0-0.021-0.0099.9530.1260.1260.0000.0000.0000.000
152A152ALA0-0.035-0.02412.6390.0860.0860.0000.0000.0000.000
153A153ARG10.8680.9239.577-0.633-0.6330.0000.0000.0000.000
154A154VAL00.0500.0219.2540.1160.1160.0000.0000.0000.000
155A155LYS10.8870.93611.6180.0110.0110.0000.0000.0000.000
156A156GLN00.0380.02414.3500.0510.0510.0000.0000.0000.000
157A157ILE0-0.0200.0039.9260.0140.0140.0000.0000.0000.000
158A158ARG10.9971.00113.538-0.265-0.2650.0000.0000.0000.000
159A159ASN0-0.010-0.02216.394-0.019-0.0190.0000.0000.0000.000
160A160LEU0-0.025-0.00515.314-0.008-0.0080.0000.0000.0000.000
161A161GLN0-0.055-0.03514.637-0.044-0.0440.0000.0000.0000.000
162A162MET0-0.057-0.02718.348-0.025-0.0250.0000.0000.0000.000
163A163GLN0-0.048-0.00521.122-0.020-0.0200.0000.0000.0000.000
164A164THR0-0.060-0.02120.0030.0090.0090.0000.0000.0000.000
165A165ASP-1-0.798-0.91022.3530.2250.2250.0000.0000.0000.000
166A166GLN0-0.039-0.01322.004-0.003-0.0030.0000.0000.0000.000
167A167ASP-1-0.794-0.90120.6380.3180.3180.0000.0000.0000.000
168A168TYR0-0.010-0.00616.8510.0650.0650.0000.0000.0000.000
169A169GLU-1-0.749-0.84116.7380.5780.5780.0000.0000.0000.000
170A170ARG10.8270.91615.896-0.221-0.2210.0000.0000.0000.000
171A171GLU-1-0.911-0.95014.1890.6710.6710.0000.0000.0000.000
172A172LYS10.8470.90312.169-0.727-0.7270.0000.0000.0000.000
173A173LEU0-0.034-0.02210.8710.2270.2270.0000.0000.0000.000
174A174GLN00.0780.03810.9880.0240.0240.0000.0000.0000.000
175A175GLU-1-0.787-0.8718.1051.3601.3600.0000.0000.0000.000
176A176ARG10.7860.8586.632-0.691-0.6910.0000.0000.0000.000
177A177ILE0-0.0040.0046.5830.0030.0030.0000.0000.0000.000
178A178ALA0-0.020-0.0027.014-0.318-0.3180.0000.0000.0000.000
179A179ARG10.7860.8842.372-4.018-2.9470.955-0.752-1.2730.000
180A180LEU0-0.009-0.0012.408-9.677-6.2841.600-2.120-2.872-0.030
181A181SER0-0.076-0.0304.762-0.838-0.725-0.001-0.007-0.1050.000