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: JQN79

Calculation Name: 1G61-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G61

Chain ID: A

ChEMBL ID:

UniProt ID: Q60357

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2673182.408293
FMO2-HF: Nuclear repulsion 2589397.930558
FMO2-HF: Total energy -83784.477735
FMO2-MP2: Total energy -84031.916705


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:2003:MET)


Summations of interaction energy for fragment #1(A:2003:MET)
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.
-16.371-8.2056.602-4.691-10.077-0.032
Interaction energy analysis for fragmet #1(A:2003:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.005
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].
3A2005ILE0-0.0110.0133.8920.8052.446-0.018-0.863-0.7600.001
4A2006ARG10.8070.9097.115-0.170-0.1700.0000.0000.0000.000
5A2007LYS10.8140.89310.547-0.023-0.0230.0000.0000.0000.000
6A2008TYR0-0.037-0.05313.287-0.038-0.0380.0000.0000.0000.000
7A2009PHE00.0420.03914.0670.0190.0190.0000.0000.0000.000
8A2010SER00.0040.00118.286-0.005-0.0050.0000.0000.0000.000
9A2011GLY0-0.015-0.00920.1680.0020.0020.0000.0000.0000.000
10A2012ILE0-0.037-0.02120.435-0.006-0.0060.0000.0000.0000.000
11A2013PRO00.0240.01717.158-0.007-0.0070.0000.0000.0000.000
12A2014THR0-0.028-0.01316.941-0.032-0.0320.0000.0000.0000.000
13A2015ILE00.012-0.00212.7680.0190.0190.0000.0000.0000.000
14A2016GLY00.0640.04016.2050.0070.0070.0000.0000.0000.000
15A2017VAL0-0.037-0.01616.6810.0200.0200.0000.0000.0000.000
16A2018LEU0-0.047-0.03118.9700.0180.0180.0000.0000.0000.000
17A2019ALA0-0.0210.00315.9120.0150.0150.0000.0000.0000.000
18A2020LEU00.0110.01215.553-0.015-0.0150.0000.0000.0000.000
19A2021THR0-0.021-0.02910.680-0.006-0.0060.0000.0000.0000.000
20A2022THR00.0570.01613.5790.0160.0160.0000.0000.0000.000
21A2023GLU-1-0.745-0.83010.153-0.133-0.1330.0000.0000.0000.000
22A2024GLU-1-0.835-0.86912.325-0.061-0.0610.0000.0000.0000.000
23A2025ILE0-0.029-0.02414.9470.0070.0070.0000.0000.0000.000
24A2026THR00.0420.00512.704-0.057-0.0570.0000.0000.0000.000
25A2027LEU0-0.047-0.00415.3860.0360.0360.0000.0000.0000.000
26A2028LEU00.0420.00614.789-0.019-0.0190.0000.0000.0000.000
27A2029PRO00.0600.04318.8660.0150.0150.0000.0000.0000.000
28A2030ILE00.006-0.01421.6590.0060.0060.0000.0000.0000.000
29A2031PHE0-0.032-0.01721.3710.0060.0060.0000.0000.0000.000
30A2032LEU0-0.0340.01417.0520.0060.0060.0000.0000.0000.000
31A2033ASP-1-0.824-0.91619.4650.0430.0430.0000.0000.0000.000
32A2034LYS10.8190.87919.385-0.013-0.0130.0000.0000.0000.000
33A2035ASP-1-0.843-0.90516.5860.1060.1060.0000.0000.0000.000
34A2036ASP-1-0.826-0.93514.7810.0330.0330.0000.0000.0000.000
35A2037VAL0-0.069-0.02914.317-0.031-0.0310.0000.0000.0000.000
36A2038ASN0-0.060-0.03713.731-0.044-0.0440.0000.0000.0000.000
37A2039GLU-1-0.799-0.89510.2580.2470.2470.0000.0000.0000.000
38A2040VAL0-0.017-0.0038.910-0.039-0.0390.0000.0000.0000.000
39A2041SER0-0.056-0.0529.662-0.108-0.1080.0000.0000.0000.000
40A2042GLU-1-0.960-0.9847.6050.4260.4260.0000.0000.0000.000
41A2043VAL0-0.016-0.0073.683-0.277-0.0400.009-0.052-0.1940.000
42A2044LEU0-0.0300.0074.720-1.080-1.015-0.001-0.005-0.0580.000
43A2045GLU-1-0.897-0.9437.059-0.073-0.0730.0000.0000.0000.000
44A2046THR0-0.0400.0119.5090.0720.0720.0000.0000.0000.000
45A2047LYS10.8810.94612.6240.0480.0480.0000.0000.0000.000
46A2048CYS0-0.0050.01214.125-0.022-0.0220.0000.0000.0000.000
47A2049LEU0-0.0090.00216.8160.0220.0220.0000.0000.0000.000
48A2050GLN0-0.032-0.00720.041-0.001-0.0010.0000.0000.0000.000
49A2051THR0-0.022-0.03921.7690.0140.0140.0000.0000.0000.000
50A2052ASN0-0.0070.01424.218-0.007-0.0070.0000.0000.0000.000
51A2053ILE00.009-0.00224.195-0.001-0.0010.0000.0000.0000.000
52A2054GLY00.0010.00027.933-0.002-0.0020.0000.0000.0000.000
53A2055GLY00.0190.01231.2750.0000.0000.0000.0000.0000.000
54A2056SER0-0.090-0.04528.6890.0000.0000.0000.0000.0000.000
55A2057SER00.0620.02024.2870.0000.0000.0000.0000.0000.000
56A2058LEU0-0.064-0.02223.380-0.009-0.0090.0000.0000.0000.000
57A2059VAL00.0420.00020.999-0.001-0.0010.0000.0000.0000.000
58A2060GLY00.0020.02619.3930.0000.0000.0000.0000.0000.000
59A2061SER00.021-0.02920.1360.0010.0010.0000.0000.0000.000
60A2062LEU0-0.078-0.03522.9220.0080.0080.0000.0000.0000.000
61A2063SER0-0.067-0.03622.5280.0080.0080.0000.0000.0000.000
62A2064VAL00.0280.00020.265-0.012-0.0120.0000.0000.0000.000
63A2065ALA0-0.021-0.00318.3160.0120.0120.0000.0000.0000.000
64A2066ASN0-0.011-0.03017.643-0.011-0.0110.0000.0000.0000.000
65A2067LYS10.8080.87915.930-0.009-0.0090.0000.0000.0000.000
66A2068TYR0-0.033-0.01119.4120.0110.0110.0000.0000.0000.000
67A2069GLY00.0500.04122.3500.0050.0050.0000.0000.0000.000
68A2070LEU0-0.040-0.01921.793-0.010-0.0100.0000.0000.0000.000
69A2071LEU00.0100.02323.8280.0070.0070.0000.0000.0000.000
70A2072LEU00.0250.01524.997-0.009-0.0090.0000.0000.0000.000
71A2073PRO00.0360.02427.4430.0040.0040.0000.0000.0000.000
72A2074LYS10.8680.92230.2710.0370.0370.0000.0000.0000.000
73A2075ILE0-0.072-0.04331.0340.0020.0020.0000.0000.0000.000
74A2076VAL0-0.036-0.00329.3050.0000.0000.0000.0000.0000.000
75A2077GLU-1-0.902-0.95631.775-0.024-0.0240.0000.0000.0000.000
76A2078ASP-1-0.910-0.96632.939-0.020-0.0200.0000.0000.0000.000
77A2079GLU-1-0.945-0.96932.483-0.016-0.0160.0000.0000.0000.000
78A2080GLU-1-0.747-0.87028.919-0.040-0.0400.0000.0000.0000.000
79A2081LEU00.001-0.00228.790-0.002-0.0020.0000.0000.0000.000
80A2082ASP-1-0.845-0.92130.083-0.016-0.0160.0000.0000.0000.000
81A2083ARG10.8420.92224.9510.0290.0290.0000.0000.0000.000
82A2084ILE00.0060.00224.805-0.001-0.0010.0000.0000.0000.000
83A2085LYS10.8890.94026.1040.0190.0190.0000.0000.0000.000
84A2086ASN0-0.074-0.03828.2680.0020.0020.0000.0000.0000.000
85A2087PHE00.0140.00318.8500.0050.0050.0000.0000.0000.000
86A2088LEU00.0190.02222.3580.0000.0000.0000.0000.0000.000
87A2089LYS10.8540.91724.7160.0050.0050.0000.0000.0000.000
88A2090GLU-1-0.844-0.90825.6100.0020.0020.0000.0000.0000.000
89A2091ASN0-0.068-0.03720.7990.0050.0050.0000.0000.0000.000
90A2092ASN0-0.088-0.04422.5440.0030.0030.0000.0000.0000.000
91A2093LEU0-0.033-0.01619.5200.0020.0020.0000.0000.0000.000
92A2094ASP-1-0.930-0.96323.583-0.008-0.0080.0000.0000.0000.000
93A2095LEU0-0.0050.00021.603-0.002-0.0020.0000.0000.0000.000
94A2096ASN0-0.027-0.01025.7410.0030.0030.0000.0000.0000.000
95A2097VAL0-0.061-0.03426.262-0.005-0.0050.0000.0000.0000.000
96A2098GLU-1-0.795-0.88427.964-0.023-0.0230.0000.0000.0000.000
97A2099ILE0-0.051-0.01928.993-0.005-0.0050.0000.0000.0000.000
98A2100ILE00.0350.02228.7660.0030.0030.0000.0000.0000.000
99A2101LYS10.7690.85931.6970.0250.0250.0000.0000.0000.000
100A2102SER00.0090.00632.1940.0020.0020.0000.0000.0000.000
101A2103LYS10.8870.92234.6120.0280.0280.0000.0000.0000.000
102A2104ASN00.0350.00930.935-0.001-0.0010.0000.0000.0000.000
103A2105THR00.0280.01330.5860.0010.0010.0000.0000.0000.000
104A2106ALA00.0080.02526.823-0.002-0.0020.0000.0000.0000.000
105A2107LEU00.035-0.00225.520-0.004-0.0040.0000.0000.0000.000
106A2108GLY00.0700.04821.7270.0000.0000.0000.0000.0000.000
107A2109ASN0-0.018-0.00921.181-0.022-0.0220.0000.0000.0000.000
108A2110LEU0-0.076-0.03223.520-0.001-0.0010.0000.0000.0000.000
109A2111ILE0-0.008-0.00322.1100.0090.0090.0000.0000.0000.000
110A2112LEU00.0030.02016.881-0.013-0.0130.0000.0000.0000.000
111A2113THR00.011-0.01018.0860.0190.0190.0000.0000.0000.000
112A2114ASN0-0.003-0.00214.926-0.020-0.0200.0000.0000.0000.000
113A2115ASP-1-0.782-0.87415.956-0.023-0.0230.0000.0000.0000.000
114A2116LYS10.7550.85814.836-0.096-0.0960.0000.0000.0000.000
115A2117GLY00.0370.02619.6080.0030.0030.0000.0000.0000.000
116A2118ALA0-0.023-0.01620.018-0.011-0.0110.0000.0000.0000.000
117A2119LEU00.0150.02222.2380.0060.0060.0000.0000.0000.000
118A2120ILE0-0.030-0.02023.686-0.008-0.0080.0000.0000.0000.000
119A2121SER00.0930.04526.4370.0040.0040.0000.0000.0000.000
120A2122PRO00.016-0.01028.7750.0040.0040.0000.0000.0000.000
121A2123GLU-1-0.939-0.95431.588-0.048-0.0480.0000.0000.0000.000
122A2124LEU0-0.013-0.01528.0450.0030.0030.0000.0000.0000.000
123A2125LYS10.8870.93431.9830.0290.0290.0000.0000.0000.000
124A2126ASP-1-0.899-0.93933.812-0.025-0.0250.0000.0000.0000.000
125A2127PHE0-0.014-0.01332.0870.0010.0010.0000.0000.0000.000
126A2128LYS10.8310.92030.1340.0230.0230.0000.0000.0000.000
127A2129LYS10.8880.92730.6760.0130.0130.0000.0000.0000.000
128A2130ASP-1-0.849-0.91931.908-0.024-0.0240.0000.0000.0000.000
129A2131ILE0-0.019-0.01926.061-0.001-0.0010.0000.0000.0000.000
130A2132GLU-1-0.873-0.93627.116-0.021-0.0210.0000.0000.0000.000
131A2133ASP-1-0.866-0.91528.222-0.011-0.0110.0000.0000.0000.000
132A2134SER0-0.057-0.02526.7750.0000.0000.0000.0000.0000.000
133A2135LEU00.0270.00621.8860.0010.0010.0000.0000.0000.000
134A2136ASN0-0.034-0.01123.5530.0030.0030.0000.0000.0000.000
135A2137VAL0-0.0270.00021.2080.0070.0070.0000.0000.0000.000
136A2138GLU-1-0.846-0.91224.505-0.008-0.0080.0000.0000.0000.000
137A2139VAL00.0090.01424.510-0.005-0.0050.0000.0000.0000.000
138A2140GLU-1-0.860-0.94326.045-0.022-0.0220.0000.0000.0000.000
139A2141ILE0-0.047-0.01727.136-0.005-0.0050.0000.0000.0000.000
140A2142GLY0-0.011-0.01327.8280.0030.0030.0000.0000.0000.000
141A2143THR0-0.074-0.03526.9010.0010.0010.0000.0000.0000.000
142A2144ILE0-0.001-0.00220.807-0.002-0.0020.0000.0000.0000.000
143A2145ALA0-0.009-0.01424.136-0.003-0.0030.0000.0000.0000.000
144A2146GLU-1-0.944-0.96726.017-0.060-0.0600.0000.0000.0000.000
145A2147LEU0-0.066-0.02225.0220.0050.0050.0000.0000.0000.000
146A2148PRO00.0310.00626.663-0.002-0.0020.0000.0000.0000.000
147A2149THR0-0.051-0.02224.9070.0000.0000.0000.0000.0000.000
148A2150VAL00.0590.01622.740-0.012-0.0120.0000.0000.0000.000
149A2151GLY00.0250.03619.804-0.011-0.0110.0000.0000.0000.000
150A2152SER0-0.011-0.02518.947-0.015-0.0150.0000.0000.0000.000
151A2153ASN0-0.067-0.05019.761-0.021-0.0210.0000.0000.0000.000
152A2154ALA00.0180.00817.0480.0000.0000.0000.0000.0000.000
153A2155VAL00.0140.01810.789-0.010-0.0100.0000.0000.0000.000
154A2156VAL0-0.0180.00213.0100.0200.0200.0000.0000.0000.000
155A2157THR00.0650.0598.1920.0110.0110.0000.0000.0000.000
156A2158ASN0-0.049-0.05911.4820.0370.0370.0000.0000.0000.000
157A2159LYS10.8070.9174.394-3.808-3.5800.005-0.055-0.1780.000
158A2160GLY00.0600.01810.7210.0240.0240.0000.0000.0000.000
159A2161CYS0-0.059-0.02911.555-0.043-0.0430.0000.0000.0000.000
160A2162LEU00.0330.02711.801-0.015-0.0150.0000.0000.0000.000
161A2163THR00.021-0.00514.1690.0090.0090.0000.0000.0000.000
162A2164HIS00.1090.04317.697-0.021-0.0210.0000.0000.0000.000
163A2165PRO0-0.036-0.01620.3430.0070.0070.0000.0000.0000.000
164A2166LEU0-0.057-0.03621.3030.0060.0060.0000.0000.0000.000
165A2167VAL00.0060.02421.4770.0090.0090.0000.0000.0000.000
166A2168GLU-1-0.911-0.94623.736-0.074-0.0740.0000.0000.0000.000
167A2169ASP-1-0.873-0.95223.597-0.094-0.0940.0000.0000.0000.000
168A2170ASP-1-0.905-0.94424.309-0.052-0.0520.0000.0000.0000.000
169A2171GLU-1-0.775-0.89024.246-0.077-0.0770.0000.0000.0000.000
170A2172LEU0-0.015-0.01318.5630.0000.0000.0000.0000.0000.000
171A2173GLU-1-0.893-0.95521.047-0.022-0.0220.0000.0000.0000.000
172A2174PHE0-0.045-0.02322.7650.0110.0110.0000.0000.0000.000
173A2175LEU00.0050.00019.5800.0050.0050.0000.0000.0000.000
174A2176LYS10.8200.91516.866-0.008-0.0080.0000.0000.0000.000
175A2177SER0-0.011-0.00519.4040.0190.0190.0000.0000.0000.000
176A2178LEU0-0.0060.01422.0680.0100.0100.0000.0000.0000.000
177A2179PHE0-0.006-0.01216.9630.0040.0040.0000.0000.0000.000
178A2180LYS10.7960.88817.6850.0140.0140.0000.0000.0000.000
179A2181VAL0-0.0470.00814.0030.0340.0340.0000.0000.0000.000
180A2182GLU-1-0.849-0.93213.4280.0490.0490.0000.0000.0000.000
181A2183TYR0-0.056-0.0047.8330.1100.1100.0000.0000.0000.000
182A2184ILE00.004-0.00112.114-0.005-0.0050.0000.0000.0000.000
183A2185GLY00.0040.00614.499-0.019-0.0190.0000.0000.0000.000
184A2186LYS10.8090.90415.6060.1210.1210.0000.0000.0000.000
185A2187GLY0-0.017-0.01716.403-0.011-0.0110.0000.0000.0000.000
186A2188THR0-0.067-0.04916.7790.0200.0200.0000.0000.0000.000
187A2189ALA00.0350.01814.288-0.050-0.0500.0000.0000.0000.000
188A2190ASN0-0.017-0.03515.6090.0280.0280.0000.0000.0000.000
189A2191LYS10.9160.96117.3750.1210.1210.0000.0000.0000.000
190A2192GLY00.0100.00619.0860.0200.0200.0000.0000.0000.000
191A2193THR0-0.069-0.02819.4080.0180.0180.0000.0000.0000.000
192A2194THR00.0400.00419.210-0.020-0.0200.0000.0000.0000.000
193A2195SER0-0.0210.00720.0910.0000.0000.0000.0000.0000.000
194A2196VAL00.0450.01114.860-0.002-0.0020.0000.0000.0000.000
195A2197GLY00.0610.05515.230-0.036-0.0360.0000.0000.0000.000
196A2198ALA0-0.037-0.02816.430-0.006-0.0060.0000.0000.0000.000
197A2199CYS0-0.113-0.06015.5500.0250.0250.0000.0000.0000.000
198A2200ILE0-0.009-0.0109.733-0.031-0.0310.0000.0000.0000.000
199A2201ILE00.0000.01710.6880.0820.0820.0000.0000.0000.000
200A2202ALA00.016-0.0067.246-0.206-0.2060.0000.0000.0000.000
201A2203ASN0-0.002-0.0167.0390.0320.0320.0000.0000.0000.000
202A2204SER0-0.073-0.0796.613-0.027-0.0270.0000.0000.0000.000
203A2205LYS10.8110.8984.5441.1491.439-0.001-0.025-0.2640.000
204A2206GLY00.0550.0242.502-5.658-3.3680.914-1.391-1.813-0.012
205A2207ALA0-0.020-0.0233.4961.4791.7670.0030.029-0.3200.000
206A2208VAL00.0070.0095.945-0.012-0.0120.0000.0000.0000.000
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208A2210GLY00.0460.03110.9350.1050.1050.0000.0000.0000.000
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