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: 765LK

Calculation Name: 4B9X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4B9X

Chain ID: A

ChEMBL ID:

UniProt ID: Q99MV1

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 196
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2138727.063408
FMO2-HF: Nuclear repulsion 2060028.57122
FMO2-HF: Total energy -78698.492188
FMO2-MP2: Total energy -78923.952579


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:697:LEU)


Summations of interaction energy for fragment #1(A:697:LEU)
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.
-10.924-2.4045.104-3.913-9.712-0.008
Interaction energy analysis for fragmet #1(A:697:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.020
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].
3A699TRP00.014-0.0063.880-1.0341.344-0.015-1.208-1.1550.004
4A700THR00.0250.0226.472-0.018-0.0180.0000.0000.0000.000
5A701TRP00.0100.00410.2580.0350.0350.0000.0000.0000.000
6A702VAL00.001-0.00713.247-0.021-0.0210.0000.0000.0000.000
7A703GLU-1-0.886-0.93314.641-0.635-0.6350.0000.0000.0000.000
8A704PHE0-0.024-0.02018.0410.0460.0460.0000.0000.0000.000
9A705THR0-0.058-0.03921.843-0.005-0.0050.0000.0000.0000.000
10A706VAL00.015-0.01025.1670.0050.0050.0000.0000.0000.000
11A707ASP-1-0.850-0.91828.097-0.143-0.1430.0000.0000.0000.000
12A708GLU-1-0.797-0.86724.336-0.243-0.2430.0000.0000.0000.000
13A709THR0-0.032-0.01728.3890.0010.0010.0000.0000.0000.000
14A710VAL0-0.011-0.00724.6450.0010.0010.0000.0000.0000.000
15A711ASP-1-0.819-0.90228.042-0.120-0.1200.0000.0000.0000.000
16A712VAL0-0.018-0.01125.014-0.015-0.0150.0000.0000.0000.000
17A713VAL00.0220.00825.1140.0160.0160.0000.0000.0000.000
18A714VAL00.0120.00625.274-0.014-0.0140.0000.0000.0000.000
19A715CYS0-0.071-0.02221.2700.0090.0090.0000.0000.0000.000
20A716MET00.0210.01821.4680.0180.0180.0000.0000.0000.000
21A717MET0-0.049-0.02424.316-0.012-0.0120.0000.0000.0000.000
22A718TYR0-0.048-0.00821.7280.0180.0180.0000.0000.0000.000
23A719SER0-0.057-0.03728.4570.0090.0090.0000.0000.0000.000
24A720PRO00.029-0.00229.759-0.008-0.0080.0000.0000.0000.000
25A721GLY00.000-0.00529.604-0.005-0.0050.0000.0000.0000.000
26A722GLU-1-0.846-0.89322.698-0.183-0.1830.0000.0000.0000.000
27A723PHE0-0.002-0.00725.4340.0170.0170.0000.0000.0000.000
28A724TYR0-0.025-0.01618.586-0.022-0.0220.0000.0000.0000.000
29A725CYS0-0.009-0.00321.9030.0270.0270.0000.0000.0000.000
30A726HIS00.0180.00518.554-0.009-0.0090.0000.0000.0000.000
31A727PHE00.033-0.00821.0650.0170.0170.0000.0000.0000.000
32A728LEU0-0.047-0.02222.021-0.007-0.0070.0000.0000.0000.000
33A729LYS10.8080.88720.6050.3050.3050.0000.0000.0000.000
34A730ASP-1-0.874-0.94719.768-0.278-0.2780.0000.0000.0000.000
35A731ASP-1-0.853-0.91320.149-0.173-0.1730.0000.0000.0000.000
36A732ALA0-0.0110.00818.6220.0080.0080.0000.0000.0000.000
37A733LEU00.020-0.00318.569-0.005-0.0050.0000.0000.0000.000
38A734GLU-1-0.927-0.95320.275-0.098-0.0980.0000.0000.0000.000
39A735LYS10.8130.87516.3780.2130.2130.0000.0000.0000.000
40A736LEU0-0.0100.00014.533-0.009-0.0090.0000.0000.0000.000
41A737ASP-1-0.846-0.91916.189-0.089-0.0890.0000.0000.0000.000
42A738ASP-1-0.902-0.94717.499-0.047-0.0470.0000.0000.0000.000
43A739LEU0-0.086-0.02410.1800.0230.0230.0000.0000.0000.000
44A740ASN0-0.003-0.02813.7540.0160.0160.0000.0000.0000.000
45A741GLN0-0.033-0.01315.5770.0270.0270.0000.0000.0000.000
46A742SER0-0.036-0.03213.1730.0300.0300.0000.0000.0000.000
47A743LEU0-0.031-0.0248.9450.0440.0440.0000.0000.0000.000
48A744ALA00.0300.03112.7790.0420.0420.0000.0000.0000.000
49A745ASP-1-0.909-0.95616.1020.1040.1040.0000.0000.0000.000
50A746TYR0-0.134-0.0847.2750.0690.0690.0000.0000.0000.000
51A747CYS0-0.038-0.02311.7130.0460.0460.0000.0000.0000.000
52A748ALA00.0000.02013.4950.0100.0100.0000.0000.0000.000
53A749GLN0-0.074-0.04414.6030.0320.0320.0000.0000.0000.000
54A750LYS10.9090.93416.336-0.239-0.2390.0000.0000.0000.000
55A751PRO00.0250.01213.8130.0330.0330.0000.0000.0000.000
56A752PRO00.0370.0239.2660.0300.0300.0000.0000.0000.000
57A753ASN0-0.067-0.02710.340-0.006-0.0060.0000.0000.0000.000
58A754GLY0-0.0070.00010.7770.0980.0980.0000.0000.0000.000
59A755PHE00.0510.0184.675-0.0100.067-0.001-0.004-0.0720.000
60A756LYS10.8650.9389.081-0.616-0.6160.0000.0000.0000.000
61A757ALA00.0340.0188.1400.1320.1320.0000.0000.0000.000
62A758GLU-1-0.836-0.9188.3650.4520.4520.0000.0000.0000.000
63A759ILE0-0.012-0.0028.868-0.024-0.0240.0000.0000.0000.000
64A760GLY00.0270.0198.924-0.043-0.0430.0000.0000.0000.000
65A761ARG10.8050.9043.880-1.729-1.4860.002-0.029-0.2150.000
66A762PRO00.0200.0112.530-1.347-0.0490.946-0.465-1.7800.003
67A763CYS0-0.085-0.0423.7240.2320.7160.013-0.160-0.338-0.001
68A764CYS00.0130.0265.874-0.235-0.2350.0000.0000.0000.000
69A765ALA00.018-0.0048.6310.0840.0840.0000.0000.0000.000
70A766PHE0-0.007-0.00311.920-0.035-0.0350.0000.0000.0000.000
71A767PHE00.0300.02015.511-0.004-0.0040.0000.0000.0000.000
72A768SER0-0.010-0.01917.848-0.002-0.0020.0000.0000.0000.000
73A769GLY0-0.031-0.00621.1700.0010.0010.0000.0000.0000.000
74A770ASP-1-0.826-0.89320.125-0.022-0.0220.0000.0000.0000.000
75A771GLY0-0.0370.00021.1240.0040.0040.0000.0000.0000.000
76A772ASN0-0.058-0.03517.8350.0250.0250.0000.0000.0000.000
77A773TRP0-0.025-0.01812.2180.0190.0190.0000.0000.0000.000
78A774TYR0-0.020-0.02012.652-0.017-0.0170.0000.0000.0000.000
79A775ARG10.7210.8067.8760.5680.5680.0000.0000.0000.000
80A776ALA0-0.003-0.0078.189-0.009-0.0090.0000.0000.0000.000
81A777LEU0-0.0120.0156.9260.0190.0190.0000.0000.0000.000
82A778VAL0-0.009-0.0088.2430.0370.0370.0000.0000.0000.000
83A779LYS10.8650.92710.1650.0900.0900.0000.0000.0000.000
84A780GLU-1-0.872-0.94613.428-0.101-0.1010.0000.0000.0000.000
85A781ILE00.0010.00412.2370.0290.0290.0000.0000.0000.000
86A782LEU0-0.0240.00516.246-0.022-0.0220.0000.0000.0000.000
87A783PRO0-0.010-0.01119.8930.0140.0140.0000.0000.0000.000
88A784SER0-0.011-0.00121.8660.0060.0060.0000.0000.0000.000
89A785GLY00.0080.01519.3140.0060.0060.0000.0000.0000.000
90A786ASN0-0.066-0.05417.9520.0280.0280.0000.0000.0000.000
91A787VAL0-0.008-0.01311.9320.0040.0040.0000.0000.0000.000
92A788LYS10.8680.93415.3980.0120.0120.0000.0000.0000.000
93A789VAL00.003-0.00211.4230.0040.0040.0000.0000.0000.000
94A790HIS00.0150.01512.735-0.026-0.0260.0000.0000.0000.000
95A791PHE00.0700.02312.168-0.031-0.0310.0000.0000.0000.000
96A792VAL00.0100.0049.3050.0090.0090.0000.0000.0000.000
97A793ASP-1-0.729-0.82012.016-0.437-0.4370.0000.0000.0000.000
98A794TYR00.009-0.00214.6550.0190.0190.0000.0000.0000.000
99A795GLY00.0360.01416.5600.0130.0130.0000.0000.0000.000
100A796ASN0-0.067-0.03918.191-0.012-0.0120.0000.0000.0000.000
101A797VAL0-0.042-0.03716.986-0.017-0.0170.0000.0000.0000.000
102A798GLU-1-0.839-0.89317.170-0.041-0.0410.0000.0000.0000.000
103A799GLU-1-0.890-0.94917.5480.0240.0240.0000.0000.0000.000
104A800VAL00.0160.02114.090-0.001-0.0010.0000.0000.0000.000
105A801THR0-0.020-0.04617.0010.0030.0030.0000.0000.0000.000
106A802THR00.012-0.01014.2790.0050.0050.0000.0000.0000.000
107A803ASP-1-0.906-0.92713.8440.2410.2410.0000.0000.0000.000
108A804GLN0-0.0220.00615.389-0.004-0.0040.0000.0000.0000.000
109A805LEU00.0070.00310.160-0.023-0.0230.0000.0000.0000.000
110A806GLN0-0.026-0.0219.0230.0590.0590.0000.0000.0000.000
111A807ALA00.0180.0094.373-0.0410.023-0.001-0.006-0.0570.000
112A808ILE00.0350.0312.479-0.825-0.2480.674-0.239-1.012-0.001
113A809LEU0-0.0110.0023.020-1.879-0.1460.611-0.934-1.410-0.009
114A810PRO00.0540.0072.487-1.610-0.5780.732-0.313-1.4510.002
115A811GLN00.0250.0163.807-0.415-0.3640.0080.007-0.0660.000
116A812PHE00.002-0.0076.349-0.048-0.0480.0000.0000.0000.000
117A813LEU0-0.019-0.0122.503-1.257-0.6742.135-0.562-2.156-0.006
118A814LEU0-0.0310.0036.487-0.082-0.0820.0000.0000.0000.000
119A815LEU0-0.0050.0239.2810.0210.0210.0000.0000.0000.000
120A816PRO00.0330.02410.406-0.078-0.0780.0000.0000.0000.000
121A817PHE0-0.035-0.0146.0670.0560.0560.0000.0000.0000.000
122A818GLN00.049-0.01111.7790.0480.0480.0000.0000.0000.000
123A819GLY0-0.0190.00814.9400.0420.0420.0000.0000.0000.000
124A820MET0-0.054-0.01615.080-0.022-0.0220.0000.0000.0000.000
125A821GLN0-0.0040.00318.5140.0120.0120.0000.0000.0000.000
126A822CYS0-0.072-0.04020.511-0.016-0.0160.0000.0000.0000.000
127A823TRP0-0.061-0.02922.5830.0120.0120.0000.0000.0000.000
128A824LEU0-0.011-0.00627.500-0.003-0.0030.0000.0000.0000.000
129A825VAL00.0230.01430.1810.0000.0000.0000.0000.0000.000
130A826ASP-1-0.915-0.96232.256-0.116-0.1160.0000.0000.0000.000
131A827ILE0-0.022-0.01133.6420.0110.0110.0000.0000.0000.000
132A828GLN0-0.041-0.02335.060-0.007-0.0070.0000.0000.0000.000
133A829PRO0-0.009-0.01535.2730.0050.0050.0000.0000.0000.000
134A830PRO00.0030.01538.0360.0010.0010.0000.0000.0000.000
135A831ASN0-0.026-0.01840.6440.0060.0060.0000.0000.0000.000
136A832LYS10.9220.94838.2980.0680.0680.0000.0000.0000.000
137A833HIS00.0280.02533.856-0.006-0.0060.0000.0000.0000.000
138A834TRP00.0970.04331.4550.0080.0080.0000.0000.0000.000
139A835THR00.0450.02936.3110.0020.0020.0000.0000.0000.000
140A836LYS10.9960.97535.0270.0520.0520.0000.0000.0000.000
141A837GLU-1-0.922-0.94837.657-0.054-0.0540.0000.0000.0000.000
142A838ALA00.0380.01937.790-0.001-0.0010.0000.0000.0000.000
143A839THR0-0.016-0.01332.635-0.005-0.0050.0000.0000.0000.000
144A840ALA0-0.021-0.00834.884-0.002-0.0020.0000.0000.0000.000
145A841ARG10.8240.86037.1480.0660.0660.0000.0000.0000.000
146A842PHE00.0220.00830.2290.0010.0010.0000.0000.0000.000
147A843GLN00.0310.01030.009-0.005-0.0050.0000.0000.0000.000
148A844ALA0-0.026-0.02134.0170.0000.0000.0000.0000.0000.000
149A845CYM-1-0.854-0.84636.866-0.071-0.0710.0000.0000.0000.000
150A846VAL00.031-0.00231.115-0.003-0.0030.0000.0000.0000.000
151A847VAL0-0.0140.00031.698-0.003-0.0030.0000.0000.0000.000
152A848GLY0-0.027-0.01131.0720.0040.0040.0000.0000.0000.000
153A849LEU0-0.042-0.00232.0330.0040.0040.0000.0000.0000.000
154A850LYS10.8690.93330.0100.1040.1040.0000.0000.0000.000
155A851LEU0-0.053-0.02030.6980.0070.0070.0000.0000.0000.000
156A852GLN0-0.0040.00530.613-0.004-0.0040.0000.0000.0000.000
157A853ALA0-0.002-0.00827.7350.0040.0040.0000.0000.0000.000
158A854ARG10.8590.91729.8590.1370.1370.0000.0000.0000.000
159A855VAL00.0230.00924.2310.0030.0030.0000.0000.0000.000
160A856VAL0-0.024-0.00327.397-0.001-0.0010.0000.0000.0000.000
161A857GLU-1-0.881-0.92326.777-0.189-0.1890.0000.0000.0000.000
162A858ILE00.0070.00121.205-0.006-0.0060.0000.0000.0000.000
163A859THR0-0.040-0.02221.1610.0020.0020.0000.0000.0000.000
164A860ALA00.005-0.00416.288-0.019-0.0190.0000.0000.0000.000
165A861ASN0-0.077-0.05115.792-0.065-0.0650.0000.0000.0000.000
166A862GLY00.1100.06618.0680.0330.0330.0000.0000.0000.000
167A863VAL0-0.041-0.01220.109-0.009-0.0090.0000.0000.0000.000
168A864GLY00.0370.02923.2360.0140.0140.0000.0000.0000.000
169A865VAL0-0.025-0.03725.9370.0000.0000.0000.0000.0000.000
170A866GLU-1-0.815-0.86328.701-0.106-0.1060.0000.0000.0000.000
171A867LEU00.002-0.00628.659-0.005-0.0050.0000.0000.0000.000
172A868THR0-0.041-0.04332.5970.0080.0080.0000.0000.0000.000
173A869ASP-1-0.792-0.86534.827-0.082-0.0820.0000.0000.0000.000
174A870LEU00.000-0.01436.0100.0030.0030.0000.0000.0000.000
175A871SER0-0.049-0.03338.7040.0040.0040.0000.0000.0000.000
176A872THR0-0.020-0.01340.1130.0060.0060.0000.0000.0000.000
177A873PRO0-0.013-0.02542.977-0.003-0.0030.0000.0000.0000.000
178A874TYR0-0.062-0.01544.6070.0000.0000.0000.0000.0000.000
179A875PRO00.010-0.00340.315-0.001-0.0010.0000.0000.0000.000
180A876LYS10.8300.91537.8920.0770.0770.0000.0000.0000.000
181A877ILE0-0.004-0.00837.167-0.003-0.0030.0000.0000.0000.000
182A878ILE0-0.006-0.00534.2550.0050.0050.0000.0000.0000.000
183A879SER00.017-0.02935.2780.0070.0070.0000.0000.0000.000
184A880ASP-1-0.807-0.89836.857-0.075-0.0750.0000.0000.0000.000
185A881VAL0-0.036-0.01339.6210.0060.0060.0000.0000.0000.000
186A882LEU0-0.0030.00235.5300.0050.0050.0000.0000.0000.000
187A883ILE0-0.027-0.00839.2610.0040.0040.0000.0000.0000.000
188A884ARG10.8450.91642.1210.0750.0750.0000.0000.0000.000
189A885GLU-1-0.873-0.92243.499-0.058-0.0580.0000.0000.0000.000
190A886GLN0-0.096-0.05444.8550.0020.0020.0000.0000.0000.000
191A887LEU0-0.0110.00840.7080.0000.0000.0000.0000.0000.000
192A888VAL0-0.037-0.02536.960-0.002-0.0020.0000.0000.0000.000
193A889LEU0-0.0040.01340.1240.0030.0030.0000.0000.0000.000
194A890ARG10.9690.97239.4840.0810.0810.0000.0000.0000.000
195A891CYS0-0.038-0.01336.9630.0030.0030.0000.0000.0000.000
196A892GLY0-0.046-0.01639.073-0.001-0.0010.0000.0000.0000.000