Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6GG6Z

Calculation Name: 3K5R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K5R

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WTR5

Base Structure: X-ray

Registration Date: 2023-09-27

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2371180.268281
FMO2-HF: Nuclear repulsion 2287434.683897
FMO2-HF: Total energy -83745.584383
FMO2-MP2: Total energy -83990.623092


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:0:SER)


Summations of interaction energy for fragment #1(A:0: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.
-40.013-44.28228.763-13.501-10.992-0.051
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.064 / q_NPA : -0.039
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].
3A2ILE0-0.078-0.0293.693-2.577-1.114-0.009-0.901-0.5540.000
4A3VAL0-0.020-0.0034.1201.0011.130-0.001-0.012-0.1160.000
5A4VAL00.0120.0006.936-0.136-0.1360.0000.0000.0000.000
6A5SER00.007-0.02110.5380.2360.2360.0000.0000.0000.000
7A6PRO0-0.0040.00313.672-0.066-0.0660.0000.0000.0000.000
8A7ILE00.0170.01715.5730.0190.0190.0000.0000.0000.000
9A8LEU00.0050.00518.762-0.014-0.0140.0000.0000.0000.000
10A9ILE0-0.035-0.02022.083-0.004-0.0040.0000.0000.0000.000
11A10PRO00.0230.01724.591-0.002-0.0020.0000.0000.0000.000
12A11GLU-1-0.763-0.89628.1200.0020.0020.0000.0000.0000.000
13A12ASN0-0.064-0.03530.789-0.003-0.0030.0000.0000.0000.000
14A13GLN0-0.040-0.00425.936-0.007-0.0070.0000.0000.0000.000
15A14ARG10.9680.98231.554-0.006-0.0060.0000.0000.0000.000
16A15GLN00.0350.02031.9310.0010.0010.0000.0000.0000.000
17A16PRO0-0.035-0.01930.3620.0070.0070.0000.0000.0000.000
18A17PHE0-0.0280.00328.0950.0050.0050.0000.0000.0000.000
19A18PRO0-0.001-0.01424.8150.0000.0000.0000.0000.0000.000
20A19ARG10.8640.93624.8450.0410.0410.0000.0000.0000.000
21A20ASP-1-0.828-0.90019.093-0.168-0.1680.0000.0000.0000.000
22A21VAL0-0.069-0.03719.8120.0250.0250.0000.0000.0000.000
23A22GLY00.0530.03016.6850.0390.0390.0000.0000.0000.000
24A23LYS10.7810.89911.576-0.265-0.2650.0000.0000.0000.000
25A24VAL0-0.010-0.0028.8770.0770.0770.0000.0000.0000.000
26A25VAL0-0.016-0.0064.1020.0510.150-0.001-0.008-0.0900.000
27A26ASP-1-0.790-0.9083.955-5.705-5.636-0.001-0.030-0.0370.000
28A27SER0-0.104-0.0681.751-5.420-10.37214.082-5.617-3.5120.036
29A28ASP-1-0.832-0.9162.020-28.515-29.68114.691-6.932-6.593-0.087
30A29ARG10.8050.8973.8762.8172.9060.002-0.001-0.0900.000
31A30PRO0-0.033-0.0086.6940.6960.6960.0000.0000.0000.000
32A31GLU-1-0.844-0.9389.466-0.658-0.6580.0000.0000.0000.000
33A32GLY0-0.072-0.03513.052-0.013-0.0130.0000.0000.0000.000
34A33SER0-0.040-0.01010.1740.2050.2050.0000.0000.0000.000
35A34LYS10.8060.90512.9430.6050.6050.0000.0000.0000.000
36A35PHE00.0280.0048.301-0.005-0.0050.0000.0000.0000.000
37A36ARG10.7470.84813.4860.6440.6440.0000.0000.0000.000
38A37LEU00.0130.00415.380-0.039-0.0390.0000.0000.0000.000
39A38THR0-0.031-0.01217.6210.0240.0240.0000.0000.0000.000
40A39GLY00.0590.02320.2100.0070.0070.0000.0000.0000.000
41A40LYS10.8990.95322.9640.0430.0430.0000.0000.0000.000
42A41GLY00.0510.02124.9440.0080.0080.0000.0000.0000.000
43A42VAL0-0.035-0.00721.014-0.003-0.0030.0000.0000.0000.000
44A43ASP-1-0.783-0.90023.999-0.212-0.2120.0000.0000.0000.000
45A44GLN0-0.007-0.00725.8390.0210.0210.0000.0000.0000.000
46A45ASP-1-0.849-0.90227.717-0.102-0.1020.0000.0000.0000.000
47A46PRO00.0130.01028.9100.0040.0040.0000.0000.0000.000
48A47LYS10.8410.89827.9780.1130.1130.0000.0000.0000.000
49A48GLY0-0.018-0.00726.3770.0080.0080.0000.0000.0000.000
50A49THR0-0.0050.02726.1700.0060.0060.0000.0000.0000.000
51A50PHE00.0190.01521.3730.0110.0110.0000.0000.0000.000
52A51ARG10.8890.94621.0800.2350.2350.0000.0000.0000.000
53A52ILE00.0780.04313.0530.0200.0200.0000.0000.0000.000
54A53ASN0-0.028-0.00616.058-0.051-0.0510.0000.0000.0000.000
55A54GLU-1-0.806-0.89614.926-0.618-0.6180.0000.0000.0000.000
56A55ASN00.0420.03114.130-0.235-0.2350.0000.0000.0000.000
57A56THR0-0.026-0.01812.453-0.105-0.1050.0000.0000.0000.000
58A57GLY00.0650.04811.1680.0200.0200.0000.0000.0000.000
59A58SER0-0.027-0.03912.2330.0840.0840.0000.0000.0000.000
60A59VAL0-0.004-0.00714.805-0.049-0.0490.0000.0000.0000.000
61A60SER00.0170.01417.3420.0450.0450.0000.0000.0000.000
62A61VAL0-0.0030.00121.103-0.016-0.0160.0000.0000.0000.000
63A62THR0-0.038-0.06524.4230.0100.0100.0000.0000.0000.000
64A63ARG10.8190.91327.4650.0750.0750.0000.0000.0000.000
65A64THR00.028-0.00329.1710.0020.0020.0000.0000.0000.000
66A65LEU0-0.050-0.03126.204-0.008-0.0080.0000.0000.0000.000
67A66ASP-1-0.783-0.87030.977-0.003-0.0030.0000.0000.0000.000
68A67ARG10.8660.93129.957-0.043-0.0430.0000.0000.0000.000
69A68GLU-1-0.926-0.96532.4770.0200.0200.0000.0000.0000.000
70A69THR0-0.117-0.06933.712-0.003-0.0030.0000.0000.0000.000
71A70ILE0-0.108-0.06528.582-0.005-0.0050.0000.0000.0000.000
72A71ALA00.0750.05529.736-0.001-0.0010.0000.0000.0000.000
73A72THR0-0.089-0.06024.5370.0040.0040.0000.0000.0000.000
74A73TYR00.031-0.00523.607-0.012-0.0120.0000.0000.0000.000
75A74GLN0-0.025-0.01319.640-0.019-0.0190.0000.0000.0000.000
76A75LEU0-0.034-0.00418.531-0.012-0.0120.0000.0000.0000.000
77A76TYR0-0.004-0.00616.5580.0380.0380.0000.0000.0000.000
78A77VAL0-0.004-0.00111.565-0.008-0.0080.0000.0000.0000.000
79A78GLU-1-0.774-0.83712.189-0.538-0.5380.0000.0000.0000.000
80A79THR00.019-0.0038.9170.1250.1250.0000.0000.0000.000
81A80THR0-0.023-0.01812.0860.1360.1360.0000.0000.0000.000
82A81ASP-1-0.760-0.86914.351-0.887-0.8870.0000.0000.0000.000
83A82ALA00.0390.02315.6020.0730.0730.0000.0000.0000.000
84A83SER0-0.058-0.04018.6020.0410.0410.0000.0000.0000.000
85A84GLY0-0.0010.01118.8420.0570.0570.0000.0000.0000.000
86A85LYS10.7820.88214.2450.7890.7890.0000.0000.0000.000
87A86THR0-0.012-0.01613.597-0.044-0.0440.0000.0000.0000.000
88A87LEU0-0.087-0.0459.7980.0730.0730.0000.0000.0000.000
89A88GLU-1-0.834-0.8896.620-1.121-1.1210.0000.0000.0000.000
90A89GLY0-0.002-0.0189.5460.0830.0830.0000.0000.0000.000
91A90PRO0-0.045-0.03712.290-0.036-0.0360.0000.0000.0000.000
92A91VAL00.0530.0429.9710.1400.1400.0000.0000.0000.000
93A92PRO0-0.047-0.03613.345-0.039-0.0390.0000.0000.0000.000
94A93LEU00.0220.00713.8850.0070.0070.0000.0000.0000.000
95A94GLU-1-0.875-0.92116.1290.0120.0120.0000.0000.0000.000
96A95VAL00.0110.01418.8800.0130.0130.0000.0000.0000.000
97A96ILE0-0.016-0.02021.1850.0020.0020.0000.0000.0000.000
98A97VAL0-0.0070.00524.1430.0020.0020.0000.0000.0000.000
99A98ILE0-0.021-0.00425.2620.0060.0060.0000.0000.0000.000
100A99ASP-1-0.784-0.89928.1920.0310.0310.0000.0000.0000.000
101A100GLN0-0.011-0.01031.8300.0010.0010.0000.0000.0000.000
102A101ASN0-0.094-0.05533.747-0.001-0.0010.0000.0000.0000.000
103A102ASP-1-0.845-0.88029.7750.0970.0970.0000.0000.0000.000
104A103ASN0-0.058-0.04130.261-0.001-0.0010.0000.0000.0000.000
105A104ARG10.8050.86827.233-0.110-0.1100.0000.0000.0000.000
106A105PRO0-0.0150.01525.773-0.004-0.0040.0000.0000.0000.000
107A106ILE0-0.006-0.01621.2220.0150.0150.0000.0000.0000.000
108A107PHE0-0.030-0.02018.322-0.005-0.0050.0000.0000.0000.000
109A108ARG10.8550.90818.236-0.043-0.0430.0000.0000.0000.000
110A109GLU-1-0.873-0.91515.5370.1040.1040.0000.0000.0000.000
111A110GLY00.0070.02112.8580.0780.0780.0000.0000.0000.000
112A111PRO0-0.042-0.0268.319-0.093-0.0930.0000.0000.0000.000
113A112TYR00.0460.0189.9480.0890.0890.0000.0000.0000.000
114A113ILE0-0.012-0.0134.8980.1010.1010.0000.0000.0000.000
115A114GLY00.0290.0128.6240.0330.0330.0000.0000.0000.000
116A115HIS10.8090.8705.327-2.913-2.9130.0000.0000.0000.000
117A116VAL00.0090.00910.701-0.213-0.2130.0000.0000.0000.000
118A117MET0-0.0010.03313.2700.0450.0450.0000.0000.0000.000
119A118GLU-1-0.727-0.82714.7520.3890.3890.0000.0000.0000.000
120A119GLY0-0.032-0.01516.662-0.050-0.0500.0000.0000.0000.000
121A120SER0-0.079-0.06817.408-0.044-0.0440.0000.0000.0000.000
122A121PRO0-0.031-0.02020.0830.0050.0050.0000.0000.0000.000
123A122THR0-0.016-0.01622.5390.0230.0230.0000.0000.0000.000
124A123GLY0-0.0120.00023.853-0.028-0.0280.0000.0000.0000.000
125A124THR0-0.059-0.04118.617-0.018-0.0180.0000.0000.0000.000
126A125THR0-0.010-0.01318.8220.0270.0270.0000.0000.0000.000
127A126VAL0-0.044-0.00913.6710.0150.0150.0000.0000.0000.000
128A127MET0-0.0030.00612.2380.1200.1200.0000.0000.0000.000
129A128ARG10.8300.88715.674-0.305-0.3050.0000.0000.0000.000
130A129MET0-0.074-0.02616.1130.0620.0620.0000.0000.0000.000
131A130THR00.0390.01718.769-0.007-0.0070.0000.0000.0000.000
132A131ALA0-0.035-0.02020.7700.0120.0120.0000.0000.0000.000
133A132PHE0-0.005-0.00223.286-0.010-0.0100.0000.0000.0000.000
134A133ASP-1-0.889-0.91823.3670.0750.0750.0000.0000.0000.000
135A134ALA0-0.020-0.02124.5400.0140.0140.0000.0000.0000.000
136A135ASP-1-0.942-0.96927.0480.0740.0740.0000.0000.0000.000
137A136ASP-1-0.787-0.84928.5130.0690.0690.0000.0000.0000.000
138A137PRO0-0.095-0.06530.523-0.001-0.0010.0000.0000.0000.000
139A138ALA0-0.0040.00233.3440.0010.0010.0000.0000.0000.000
140A139THR00.050-0.00727.8200.0020.0020.0000.0000.0000.000
141A140ASP-1-0.938-0.97431.1840.0980.0980.0000.0000.0000.000
142A141ASN0-0.115-0.07133.2710.0010.0010.0000.0000.0000.000
143A142ALA00.0400.03731.536-0.002-0.0020.0000.0000.0000.000
144A143LEU0-0.068-0.04033.4020.0060.0060.0000.0000.0000.000
145A144LEU00.0140.01926.5240.0070.0070.0000.0000.0000.000
146A145ARG10.7960.88828.895-0.152-0.1520.0000.0000.0000.000
147A146TYR0-0.0030.00623.7880.0050.0050.0000.0000.0000.000
148A147ASN0-0.011-0.01524.6510.0000.0000.0000.0000.0000.000
149A148ILE00.0150.01220.6720.0220.0220.0000.0000.0000.000
150A149ARG10.8420.91323.034-0.258-0.2580.0000.0000.0000.000
151A150GLN0-0.028-0.02120.534-0.050-0.0500.0000.0000.0000.000
152A151GLN0-0.019-0.01418.8290.0290.0290.0000.0000.0000.000
153A152THR0-0.0050.01816.907-0.079-0.0790.0000.0000.0000.000
154A153PRO00.0300.00615.9280.0900.0900.0000.0000.0000.000
155A154ASP-1-0.851-0.93418.8150.4030.4030.0000.0000.0000.000
156A155LYS10.8290.91421.037-0.443-0.4430.0000.0000.0000.000
157A156PRO00.0550.03420.2260.0510.0510.0000.0000.0000.000
158A157SER00.016-0.00122.757-0.042-0.0420.0000.0000.0000.000
159A158PRO00.0160.02222.7090.0400.0400.0000.0000.0000.000
160A159ASN0-0.032-0.02023.299-0.003-0.0030.0000.0000.0000.000
161A160MET0-0.0050.00519.216-0.050-0.0500.0000.0000.0000.000
162A161PHE0-0.003-0.01315.8910.0020.0020.0000.0000.0000.000
163A162TYR0-0.013-0.00320.953-0.033-0.0330.0000.0000.0000.000
164A163ILE00.0210.01520.5210.0360.0360.0000.0000.0000.000
165A164ASP-1-0.772-0.86523.0550.1860.1860.0000.0000.0000.000
166A165PRO0-0.001-0.00925.4390.0010.0010.0000.0000.0000.000
167A166GLU-1-0.883-0.91927.7360.1390.1390.0000.0000.0000.000
168A167LYS10.7910.86525.199-0.193-0.1930.0000.0000.0000.000
169A168GLY00.0830.04622.1750.0040.0040.0000.0000.0000.000
170A169ASP-1-0.855-0.89620.4140.3250.3250.0000.0000.0000.000
171A170ILE00.0180.00816.551-0.019-0.0190.0000.0000.0000.000
172A171VAL0-0.004-0.00419.0210.0180.0180.0000.0000.0000.000
173A172THR00.0370.01518.9020.0080.0080.0000.0000.0000.000
174A173VAL0-0.028-0.02021.136-0.041-0.0410.0000.0000.0000.000
175A174VAL0-0.0040.01621.950-0.030-0.0300.0000.0000.0000.000
176A175SER00.0020.01024.382-0.001-0.0010.0000.0000.0000.000
177A176PRO00.0580.03122.4110.0210.0210.0000.0000.0000.000
178A177ALA0-0.029-0.02222.2260.0170.0170.0000.0000.0000.000
179A178LEU0-0.029-0.01122.847-0.008-0.0080.0000.0000.0000.000
180A179LEU0-0.042-0.00917.3350.0380.0380.0000.0000.0000.000
181A180ASP-1-0.774-0.88018.4540.3610.3610.0000.0000.0000.000
182A181ARG10.8030.8529.775-0.769-0.7690.0000.0000.0000.000
183A182GLU-1-0.981-0.97216.1950.3100.3100.0000.0000.0000.000
184A183THR0-0.098-0.06518.845-0.020-0.0200.0000.0000.0000.000
185A184LEU0-0.083-0.04115.935-0.003-0.0030.0000.0000.0000.000
186A185GLU-1-0.876-0.91517.0330.4770.4770.0000.0000.0000.000
187A186ASN0-0.027-0.03512.6030.1430.1430.0000.0000.0000.000
188A187PRO00.0060.03111.5940.0010.0010.0000.0000.0000.000
189A188LYS10.9220.9616.948-2.436-2.4360.0000.0000.0000.000
190A189TYR00.019-0.01711.200-0.099-0.0990.0000.0000.0000.000
191A190GLU-1-0.882-0.93812.3020.9590.9590.0000.0000.0000.000
192A191LEU0-0.042-0.01714.269-0.115-0.1150.0000.0000.0000.000
193A192ILE0-0.005-0.00516.8800.0140.0140.0000.0000.0000.000
194A193ILE0-0.007-0.00517.717-0.030-0.0300.0000.0000.0000.000
195A194GLU-1-0.831-0.90120.4640.2020.2020.0000.0000.0000.000
196A195ALA00.0170.00923.7250.0080.0080.0000.0000.0000.000
197A196GLN0-0.028-0.02925.805-0.013-0.0130.0000.0000.0000.000
198A197ASP-1-0.785-0.90029.5960.1270.1270.0000.0000.0000.000
199A198MET0-0.046-0.01032.269-0.002-0.0020.0000.0000.0000.000
200A199ALA0-0.060-0.03634.942-0.007-0.0070.0000.0000.0000.000
201A200GLY00.0710.03736.1380.0020.0020.0000.0000.0000.000
202A201LEU0-0.076-0.05738.1880.0000.0000.0000.0000.0000.000
203A202ASP-1-0.821-0.88934.2830.0720.0720.0000.0000.0000.000
204A203VAL0-0.043-0.00934.9510.0080.0080.0000.0000.0000.000
205A204GLY0-0.028-0.01834.976-0.004-0.0040.0000.0000.0000.000
206A205LEU0-0.047-0.00531.3280.0070.0070.0000.0000.0000.000
207A206THR0-0.057-0.05328.2330.0050.0050.0000.0000.0000.000
208A207GLY00.0410.01925.449-0.014-0.0140.0000.0000.0000.000
209A208THR0-0.031-0.02421.7650.0110.0110.0000.0000.0000.000
210A209ALA0-0.0030.00016.752-0.025-0.0250.0000.0000.0000.000
211A210THR0-0.052-0.02614.342-0.015-0.0150.0000.0000.0000.000
212A211ALA00.0160.00312.740-0.010-0.0100.0000.0000.0000.000
213A212THR0-0.0120.0018.7930.1660.1660.0000.0000.0000.000
214A213ILE0-0.017-0.01211.0070.0160.0160.0000.0000.0000.000
215A214VAL0-0.063-0.0196.6640.0020.0020.0000.0000.0000.000
216A215ILE00.0260.01910.092-0.142-0.1420.0000.0000.0000.000
217A216ASP-1-0.837-0.9108.1821.6491.6490.0000.0000.0000.000
218A217ASP-1-0.884-0.95610.7150.3170.3170.0000.0000.0000.000