Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: JQNY9

Calculation Name: 5KBC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KBC

Chain ID: A

ChEMBL ID:

UniProt ID: G4NNC6

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2237354.667914
FMO2-HF: Nuclear repulsion 2159155.724687
FMO2-HF: Total energy -78198.943227
FMO2-MP2: Total energy -78426.323431


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:6:PRO)


Summations of interaction energy for fragment #1(A:6:PRO)
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.
-0.4911.565-0.013-1.09-0.9530.005
Interaction energy analysis for fragmet #1(A:6:PRO)
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 : 0.011
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].
3A8LYS10.9640.9773.821-0.1071.949-0.013-1.090-0.9530.005
4A9THR00.0240.0136.1660.2430.2430.0000.0000.0000.000
5A10HIS00.0160.0008.316-0.126-0.1260.0000.0000.0000.000
6A11ILE00.003-0.00110.609-0.033-0.0330.0000.0000.0000.000
7A12PRO0-0.037-0.02414.4090.0480.0480.0000.0000.0000.000
8A13THR0-0.022-0.01617.647-0.030-0.0300.0000.0000.0000.000
9A14THR00.0350.02718.6040.0040.0040.0000.0000.0000.000
10A15ALA00.0230.01620.4460.0040.0040.0000.0000.0000.000
11A16LYS10.9740.98921.5260.0240.0240.0000.0000.0000.000
12A17TYR0-0.034-0.03815.708-0.002-0.0020.0000.0000.0000.000
13A18PHE0-0.058-0.00420.4020.0190.0190.0000.0000.0000.000
14A19PRO00.0220.01322.474-0.005-0.0050.0000.0000.0000.000
15A20THR00.029-0.00724.342-0.009-0.0090.0000.0000.0000.000
16A21ILE0-0.030-0.01426.1520.0090.0090.0000.0000.0000.000
17A22GLY00.0790.02528.874-0.007-0.0070.0000.0000.0000.000
18A23ASP-1-0.841-0.89328.7560.0320.0320.0000.0000.0000.000
19A24PRO0-0.050-0.02825.083-0.004-0.0040.0000.0000.0000.000
20A25TYR0-0.095-0.07627.081-0.009-0.0090.0000.0000.0000.000
21A26ALA00.0090.02729.419-0.004-0.0040.0000.0000.0000.000
22A27PRO0-0.023-0.00531.381-0.003-0.0030.0000.0000.0000.000
23A28ILE0-0.0040.00533.317-0.004-0.0040.0000.0000.0000.000
24A29ASN00.001-0.00228.8250.0080.0080.0000.0000.0000.000
25A30ILE00.0220.00931.769-0.003-0.0030.0000.0000.0000.000
26A31THR0-0.040-0.01227.8860.0030.0030.0000.0000.0000.000
27A32VAL00.0390.01630.642-0.004-0.0040.0000.0000.0000.000
28A33PHE0-0.023-0.00427.0320.0060.0060.0000.0000.0000.000
29A34GLU-1-0.741-0.91430.6920.0430.0430.0000.0000.0000.000
30A35GLU-1-0.699-0.82430.9300.0630.0630.0000.0000.0000.000
31A36PRO0-0.020-0.01330.515-0.001-0.0010.0000.0000.0000.000
32A37SER0-0.045-0.05633.3710.0010.0010.0000.0000.0000.000
33A38CYS0-0.0670.00536.327-0.006-0.0060.0000.0000.0000.000
34A39SER0-0.002-0.01138.0780.0010.0010.0000.0000.0000.000
35A40ALA00.0630.04041.0010.0000.0000.0000.0000.0000.000
36A42GLU-1-0.952-0.95839.0990.0440.0440.0000.0000.0000.000
37A43GLU-1-0.894-0.93641.1430.0290.0290.0000.0000.0000.000
38A44PHE00.0440.01935.9030.0000.0000.0000.0000.0000.000
39A45SER00.003-0.02237.3230.0010.0010.0000.0000.0000.000
40A46SER0-0.085-0.05739.0440.0030.0030.0000.0000.0000.000
41A47GLU-1-0.932-0.96042.3720.0310.0310.0000.0000.0000.000
42A48VAL0-0.023-0.01040.633-0.001-0.0010.0000.0000.0000.000
43A49PHE0-0.014-0.01832.6870.0000.0000.0000.0000.0000.000
44A50PRO0-0.008-0.00838.5140.0000.0000.0000.0000.0000.000
45A51LEU0-0.006-0.00240.0980.0000.0000.0000.0000.0000.000
46A52ILE0-0.0150.00236.587-0.002-0.0020.0000.0000.0000.000
47A53LYS10.8310.89534.417-0.051-0.0510.0000.0000.0000.000
48A54LYS10.9450.99237.530-0.030-0.0300.0000.0000.0000.000
49A55HIS00.004-0.00540.632-0.001-0.0010.0000.0000.0000.000
50A56PHE00.0120.01938.089-0.003-0.0030.0000.0000.0000.000
51A57VAL0-0.025-0.00132.912-0.001-0.0010.0000.0000.0000.000
52A58ASP-1-0.841-0.92035.1260.0440.0440.0000.0000.0000.000
53A59THR0-0.078-0.04837.2210.0000.0000.0000.0000.0000.000
54A60GLY00.0320.02935.093-0.002-0.0020.0000.0000.0000.000
55A61GLU-1-0.879-0.91535.5930.0040.0040.0000.0000.0000.000
56A62ALA0-0.047-0.03734.295-0.004-0.0040.0000.0000.0000.000
57A63SER0-0.004-0.00929.0350.0020.0020.0000.0000.0000.000
58A64LEU00.0050.00230.313-0.003-0.0030.0000.0000.0000.000
59A65THR0-0.028-0.00725.6530.0090.0090.0000.0000.0000.000
60A66LEU00.0220.04227.815-0.004-0.0040.0000.0000.0000.000
61A67VAL0-0.016-0.00324.9180.0120.0120.0000.0000.0000.000
62A68PRO0-0.0410.00324.840-0.004-0.0040.0000.0000.0000.000
63A69VAL00.008-0.00526.1910.0020.0020.0000.0000.0000.000
64A70CYS0-0.098-0.05227.8890.0060.0060.0000.0000.0000.000
65A71PHE00.0440.02229.586-0.002-0.0020.0000.0000.0000.000
66A72ILE0-0.0140.00832.363-0.002-0.0020.0000.0000.0000.000
67A73ARG10.9320.94634.241-0.043-0.0430.0000.0000.0000.000
68A74GLY00.0570.01633.952-0.002-0.0020.0000.0000.0000.000
69A75SER00.022-0.00631.8370.0030.0030.0000.0000.0000.000
70A76MET0-0.0080.01825.5840.0110.0110.0000.0000.0000.000
71A77PRO00.004-0.00527.7690.0110.0110.0000.0000.0000.000
72A78ALA00.0670.02728.8720.0090.0090.0000.0000.0000.000
73A79ALA00.0320.01926.5540.0050.0050.0000.0000.0000.000
74A80GLN0-0.022-0.03422.4920.0280.0280.0000.0000.0000.000
75A81ALA00.0180.00724.4140.0180.0180.0000.0000.0000.000
76A82LEU00.0260.04526.4770.0100.0100.0000.0000.0000.000
77A83LEU00.0050.00020.6390.0070.0070.0000.0000.0000.000
78A84CYS0-0.112-0.06021.7710.0410.0410.0000.0000.0000.000
79A85VAL0-0.0020.00623.0000.0170.0170.0000.0000.0000.000
80A86TYR0-0.007-0.00220.0080.0080.0080.0000.0000.0000.000
81A87HIS0-0.046-0.02117.6310.0220.0220.0000.0000.0000.000
82A88HIS0-0.085-0.04520.2630.0440.0440.0000.0000.0000.000
83A89ASP-1-0.858-0.93621.3160.2730.2730.0000.0000.0000.000
84A90PRO0-0.040-0.03016.5630.0100.0100.0000.0000.0000.000
85A91LYS10.9000.96516.657-0.229-0.2290.0000.0000.0000.000
86A92ARG10.9680.96517.311-0.169-0.1690.0000.0000.0000.000
87A93PRO00.0700.04317.935-0.008-0.0080.0000.0000.0000.000
88A94ASP-1-0.772-0.90020.9370.1440.1440.0000.0000.0000.000
89A95PRO0-0.040-0.01923.8790.0020.0020.0000.0000.0000.000
90A96GLU-1-0.884-0.93626.3630.0790.0790.0000.0000.0000.000
91A97ALA00.0210.03227.599-0.006-0.0060.0000.0000.0000.000
92A98TYR0-0.096-0.08325.8950.0010.0010.0000.0000.0000.000
93A99MET0-0.010-0.00928.085-0.006-0.0060.0000.0000.0000.000
94A100GLU-1-0.770-0.86830.8930.0730.0730.0000.0000.0000.000
95A101TYR0-0.061-0.05928.8840.0000.0000.0000.0000.0000.000
96A102PHE00.015-0.02329.200-0.001-0.0010.0000.0000.0000.000
97A103HIS00.0690.05632.241-0.004-0.0040.0000.0000.0000.000
98A104ARG10.7410.84135.065-0.090-0.0900.0000.0000.0000.000
99A105ILE0-0.067-0.03331.581-0.002-0.0020.0000.0000.0000.000
100A106LEU0-0.0130.00034.492-0.002-0.0020.0000.0000.0000.000
101A107THR00.0190.01537.333-0.003-0.0030.0000.0000.0000.000
102A108TYR0-0.058-0.00238.801-0.001-0.0010.0000.0000.0000.000
103A109LYS11.0311.00540.630-0.042-0.0420.0000.0000.0000.000
104A110LYS10.8160.89937.093-0.055-0.0550.0000.0000.0000.000
105A111THR00.011-0.00142.072-0.001-0.0010.0000.0000.0000.000
106A112LYS10.8560.94039.987-0.069-0.0690.0000.0000.0000.000
107A113GLY00.0530.04141.7980.0000.0000.0000.0000.0000.000
108A114SER0-0.004-0.02137.3710.0030.0030.0000.0000.0000.000
109A115HIS0-0.0060.01036.9870.0070.0070.0000.0000.0000.000
110A116TRP00.0410.00735.0340.0010.0010.0000.0000.0000.000
111A117ALA00.0330.02933.5740.0020.0020.0000.0000.0000.000
112A118THR0-0.050-0.05433.9910.0040.0040.0000.0000.0000.000
113A119PRO00.0580.01231.6710.0010.0010.0000.0000.0000.000
114A120GLU-1-0.830-0.90533.3460.1010.1010.0000.0000.0000.000
115A121VAL0-0.0110.01136.5060.0000.0000.0000.0000.0000.000
116A122LEU00.0330.02030.7910.0000.0000.0000.0000.0000.000
117A123ALA0-0.0050.00432.8390.0050.0050.0000.0000.0000.000
118A124LYS10.8150.89533.751-0.083-0.0830.0000.0000.0000.000
119A125LEU0-0.024-0.01635.057-0.003-0.0030.0000.0000.0000.000
120A126ALA0-0.0200.00331.325-0.001-0.0010.0000.0000.0000.000
121A127GLU-1-0.839-0.89833.2140.0960.0960.0000.0000.0000.000
122A128LYS10.9330.96735.961-0.085-0.0850.0000.0000.0000.000
123A129ILE00.0090.02431.566-0.006-0.0060.0000.0000.0000.000
124A130PRO00.0020.01032.8210.0070.0070.0000.0000.0000.000
125A131THR0-0.031-0.01428.7680.0060.0060.0000.0000.0000.000
126A132HIS0-0.217-0.03227.2190.0010.0010.0000.0000.0000.000
127A133SER00.1750.00923.410-0.019-0.0190.0000.0000.0000.000
128A134GLY00.0690.05324.8950.0020.0020.0000.0000.0000.000
129A135ARG10.8140.87623.533-0.239-0.2390.0000.0000.0000.000
130A136GLU-1-0.875-0.91227.2000.1160.1160.0000.0000.0000.000
131A137ILE0-0.0090.01627.4090.0150.0150.0000.0000.0000.000
132A138ASN00.017-0.00528.230-0.008-0.0080.0000.0000.0000.000
133A139PRO00.0910.03429.1320.0080.0080.0000.0000.0000.000
134A140LYS10.9820.99230.084-0.136-0.1360.0000.0000.0000.000
135A141GLY00.0080.01026.2190.0070.0070.0000.0000.0000.000
136A142LEU00.0210.01925.3530.0170.0170.0000.0000.0000.000
137A143ILE00.022-0.00826.9010.0020.0020.0000.0000.0000.000
138A144GLN0-0.029-0.00523.8520.0120.0120.0000.0000.0000.000
139A146ILE00.0260.01123.5510.0020.0020.0000.0000.0000.000
140A147ASN0-0.068-0.04426.034-0.012-0.0120.0000.0000.0000.000
141A148SER0-0.067-0.01620.9480.0120.0120.0000.0000.0000.000
142A149GLN0-0.041-0.02022.104-0.003-0.0030.0000.0000.0000.000
143A150ARG10.9981.00016.269-0.406-0.4060.0000.0000.0000.000
144A151PHE00.023-0.01017.2020.0080.0080.0000.0000.0000.000
145A152THR00.0230.01319.966-0.025-0.0250.0000.0000.0000.000
146A153GLU-1-0.831-0.90517.6360.0710.0710.0000.0000.0000.000
147A154GLN0-0.029-0.00616.744-0.005-0.0050.0000.0000.0000.000
148A155LEU00.0530.01719.002-0.020-0.0200.0000.0000.0000.000
149A156LYS10.8720.93821.812-0.104-0.1040.0000.0000.0000.000
150A157LYS10.8970.94114.833-0.112-0.1120.0000.0000.0000.000
151A158ASN00.0090.00621.114-0.011-0.0110.0000.0000.0000.000
152A159ASN0-0.006-0.00923.295-0.006-0.0060.0000.0000.0000.000
153A160ILE0-0.028-0.00822.371-0.007-0.0070.0000.0000.0000.000
154A161TYR00.004-0.00722.816-0.003-0.0030.0000.0000.0000.000
155A162GLY00.0480.01324.858-0.005-0.0050.0000.0000.0000.000
156A163SER0-0.0040.00328.153-0.003-0.0030.0000.0000.0000.000
157A164GLN00.0120.00126.3420.0010.0010.0000.0000.0000.000
158A165ILE0-0.056-0.02526.692-0.004-0.0040.0000.0000.0000.000
159A166MET0-0.0210.00530.1760.0000.0000.0000.0000.0000.000
160A167GLY00.0210.02932.2020.0000.0000.0000.0000.0000.000
161A168GLY0-0.082-0.04432.7050.0000.0000.0000.0000.0000.000
162A169GLN0-0.087-0.05534.0860.0020.0020.0000.0000.0000.000
163A170LEU0-0.056-0.03830.8100.0020.0020.0000.0000.0000.000
164A171ALA00.0190.02834.8300.0030.0030.0000.0000.0000.000
165A172THR0-0.117-0.04233.4350.0020.0020.0000.0000.0000.000
166A173PRO00.1020.02135.8890.0010.0010.0000.0000.0000.000
167A174THR00.011-0.01934.481-0.004-0.0040.0000.0000.0000.000
168A175ALA0-0.025-0.01034.1130.0040.0040.0000.0000.0000.000
169A176VAL0-0.032-0.02132.071-0.003-0.0030.0000.0000.0000.000
170A177VAL00.0320.02333.4910.0020.0020.0000.0000.0000.000
171A178GLY00.0230.00533.831-0.003-0.0030.0000.0000.0000.000
172A179ASP-1-0.981-0.99733.078-0.034-0.0340.0000.0000.0000.000
173A180TYR0-0.047-0.01334.862-0.001-0.0010.0000.0000.0000.000
174A181LEU0-0.022-0.01135.1030.0030.0030.0000.0000.0000.000
175A182ILE0-0.004-0.00637.198-0.001-0.0010.0000.0000.0000.000
176A183GLU-1-0.847-0.92538.2920.0090.0090.0000.0000.0000.000
177A184ASP-1-0.916-0.95239.5700.0200.0200.0000.0000.0000.000
178A185PRO0-0.058-0.01238.248-0.001-0.0010.0000.0000.0000.000
179A186THR00.020-0.02741.5430.0030.0030.0000.0000.0000.000
180A187PHE0-0.012-0.03342.346-0.001-0.0010.0000.0000.0000.000
181A188ASP-1-0.903-0.94844.3440.0060.0060.0000.0000.0000.000
182A189GLU-1-0.817-0.88643.6550.0070.0070.0000.0000.0000.000
183A190ILE0-0.016-0.01738.734-0.002-0.0020.0000.0000.0000.000
184A191GLU-1-0.910-0.94541.7740.0090.0090.0000.0000.0000.000
185A192ARG10.9660.98144.124-0.002-0.0020.0000.0000.0000.000
186A193VAL0-0.029-0.00739.767-0.002-0.0020.0000.0000.0000.000
187A194ILE0-0.0010.00937.793-0.003-0.0030.0000.0000.0000.000
188A195THR0-0.025-0.02641.314-0.002-0.0020.0000.0000.0000.000
189A196GLN00.0070.01543.809-0.001-0.0010.0000.0000.0000.000
190A197LEU0-0.010-0.01437.337-0.003-0.0030.0000.0000.0000.000
191A198ARG10.8100.88741.076-0.006-0.0060.0000.0000.0000.000
192A199HIS0-0.050-0.02242.0320.0000.0000.0000.0000.0000.000
193A200LEU0-0.062-0.02440.451-0.002-0.0020.0000.0000.0000.000
194A201GLN0-0.001-0.01537.447-0.003-0.0030.0000.0000.0000.000
195A202ALA0-0.0320.02141.079-0.001-0.0010.0000.0000.0000.000
196A203ILE0-0.051-0.03342.045-0.001-0.0010.0000.0000.0000.000