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: NNKJQ

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 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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2671048.211217
FMO2-HF: Nuclear repulsion 2587264.239194
FMO2-HF: Total energy -83783.972022
FMO2-MP2: Total energy -84031.550074


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.
-12.24-4.5943.944-3.841-7.747-0.022
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 : 0.007 / q_NPA : -0.003
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].
3A2005ILE0-0.0190.0113.821-0.0711.790-0.028-0.970-0.8620.002
4A2006ARG10.8510.9256.425-0.026-0.0260.0000.0000.0000.000
5A2007LYS10.8120.88210.0010.5090.5090.0000.0000.0000.000
6A2008TYR0-0.073-0.05812.7000.0350.0350.0000.0000.0000.000
7A2009PHE00.0560.02113.888-0.022-0.0220.0000.0000.0000.000
8A2010SER00.0380.00818.2080.0260.0260.0000.0000.0000.000
9A2011GLY0-0.013-0.00719.9610.0210.0210.0000.0000.0000.000
10A2012ILE0-0.026-0.00220.7050.0200.0200.0000.0000.0000.000
11A2013PRO00.0390.02117.600-0.035-0.0350.0000.0000.0000.000
12A2014THR0-0.034-0.01117.103-0.017-0.0170.0000.0000.0000.000
13A2015ILE00.0260.00112.9250.0160.0160.0000.0000.0000.000
14A2016GLY00.0390.03216.165-0.017-0.0170.0000.0000.0000.000
15A2017VAL0-0.013-0.01916.8210.0210.0210.0000.0000.0000.000
16A2018LEU0-0.055-0.03318.7610.0140.0140.0000.0000.0000.000
17A2019ALA0-0.032-0.00515.760-0.008-0.0080.0000.0000.0000.000
18A2020LEU00.0250.02815.7310.0150.0150.0000.0000.0000.000
19A2021THR0-0.050-0.04710.576-0.041-0.0410.0000.0000.0000.000
20A2022THR00.0480.02813.9080.0410.0410.0000.0000.0000.000
21A2023GLU-1-0.732-0.84410.249-0.221-0.2210.0000.0000.0000.000
22A2024GLU-1-0.878-0.92312.503-0.238-0.2380.0000.0000.0000.000
23A2025ILE0-0.030-0.02015.071-0.028-0.0280.0000.0000.0000.000
24A2026THR00.029-0.00112.570-0.030-0.0300.0000.0000.0000.000
25A2027LEU0-0.050-0.00215.2400.0250.0250.0000.0000.0000.000
26A2028LEU00.0370.01014.389-0.016-0.0160.0000.0000.0000.000
27A2029PRO00.0460.01618.5120.0340.0340.0000.0000.0000.000
28A2030ILE00.0260.00621.128-0.017-0.0170.0000.0000.0000.000
29A2031PHE0-0.047-0.02021.1490.0030.0030.0000.0000.0000.000
30A2032LEU0-0.0250.01116.4640.0060.0060.0000.0000.0000.000
31A2033ASP-1-0.833-0.91219.055-0.278-0.2780.0000.0000.0000.000
32A2034LYS10.8440.89718.5750.2480.2480.0000.0000.0000.000
33A2035ASP-1-0.865-0.92216.166-0.353-0.3530.0000.0000.0000.000
34A2036ASP-1-0.822-0.91014.514-0.458-0.4580.0000.0000.0000.000
35A2037VAL0-0.093-0.05313.566-0.088-0.0880.0000.0000.0000.000
36A2038ASN0-0.030-0.02113.407-0.057-0.0570.0000.0000.0000.000
37A2039GLU-1-0.807-0.88610.215-0.686-0.6860.0000.0000.0000.000
38A2040VAL0-0.028-0.0198.791-0.270-0.2700.0000.0000.0000.000
39A2041SER0-0.068-0.0439.051-0.168-0.1680.0000.0000.0000.000
40A2042GLU-1-0.977-0.9907.223-1.070-1.0700.0000.0000.0000.000
41A2043VAL0-0.024-0.0103.133-0.682-0.3240.073-0.096-0.335-0.001
42A2044LEU0-0.035-0.0134.712-0.681-0.570-0.001-0.006-0.1030.000
43A2045GLU-1-0.889-0.9386.367-0.654-0.6540.0000.0000.0000.000
44A2046THR0-0.0390.0129.1370.2300.2300.0000.0000.0000.000
45A2047LYS10.8690.93112.3370.2630.2630.0000.0000.0000.000
46A2048CYS00.0000.01613.830-0.011-0.0110.0000.0000.0000.000
47A2049LEU00.0100.01416.5230.0330.0330.0000.0000.0000.000
48A2050GLN0-0.048-0.02419.784-0.008-0.0080.0000.0000.0000.000
49A2051THR00.011-0.02121.5270.0260.0260.0000.0000.0000.000
50A2052ASN0-0.0070.01824.017-0.020-0.0200.0000.0000.0000.000
51A2053ILE00.005-0.01124.0050.0000.0000.0000.0000.0000.000
52A2054GLY0-0.014-0.00827.8300.0010.0010.0000.0000.0000.000
53A2055GLY00.0060.00330.7760.0050.0050.0000.0000.0000.000
54A2056SER0-0.104-0.05028.324-0.005-0.0050.0000.0000.0000.000
55A2057SER00.0600.01923.999-0.003-0.0030.0000.0000.0000.000
56A2058LEU0-0.052-0.01823.148-0.019-0.0190.0000.0000.0000.000
57A2059VAL00.0570.00820.6140.0130.0130.0000.0000.0000.000
58A2060GLY00.0100.01719.3700.0060.0060.0000.0000.0000.000
59A2061SER0-0.001-0.02920.1260.0160.0160.0000.0000.0000.000
60A2062LEU0-0.074-0.03023.2310.0190.0190.0000.0000.0000.000
61A2063SER0-0.072-0.03522.6320.0080.0080.0000.0000.0000.000
62A2064VAL00.0230.00920.532-0.009-0.0090.0000.0000.0000.000
63A2065ALA0-0.016-0.00618.7260.0060.0060.0000.0000.0000.000
64A2066ASN00.005-0.00817.593-0.015-0.0150.0000.0000.0000.000
65A2067LYS10.8830.93817.1920.0080.0080.0000.0000.0000.000
66A2068TYR0-0.047-0.01819.1380.0010.0010.0000.0000.0000.000
67A2069GLY00.0790.05922.2140.0030.0030.0000.0000.0000.000
68A2070LEU0-0.058-0.02621.905-0.016-0.0160.0000.0000.0000.000
69A2071LEU00.0120.01423.8850.0110.0110.0000.0000.0000.000
70A2072LEU00.0230.00925.253-0.013-0.0130.0000.0000.0000.000
71A2073PRO00.0530.03027.4750.0120.0120.0000.0000.0000.000
72A2074LYS10.9310.94930.3640.0530.0530.0000.0000.0000.000
73A2075ILE0-0.065-0.03230.8520.0030.0030.0000.0000.0000.000
74A2076VAL0-0.046-0.00229.494-0.003-0.0030.0000.0000.0000.000
75A2077GLU-1-0.893-0.95731.902-0.085-0.0850.0000.0000.0000.000
76A2078ASP-1-0.919-0.96732.980-0.074-0.0740.0000.0000.0000.000
77A2079GLU-1-0.942-0.97432.548-0.102-0.1020.0000.0000.0000.000
78A2080GLU-1-0.717-0.84828.973-0.123-0.1230.0000.0000.0000.000
79A2081LEU0-0.010-0.01228.915-0.008-0.0080.0000.0000.0000.000
80A2082ASP-1-0.895-0.94029.993-0.089-0.0890.0000.0000.0000.000
81A2083ARG10.8270.90624.4270.1700.1700.0000.0000.0000.000
82A2084ILE0-0.003-0.00724.636-0.011-0.0110.0000.0000.0000.000
83A2085LYS10.9760.98625.8450.0770.0770.0000.0000.0000.000
84A2086ASN0-0.057-0.01728.020-0.004-0.0040.0000.0000.0000.000
85A2087PHE00.0180.00418.6220.0020.0020.0000.0000.0000.000
86A2088LEU00.0160.02122.272-0.010-0.0100.0000.0000.0000.000
87A2089LYS10.8690.92324.5610.1050.1050.0000.0000.0000.000
88A2090GLU-1-0.876-0.93425.227-0.110-0.1100.0000.0000.0000.000
89A2091ASN0-0.092-0.04220.576-0.023-0.0230.0000.0000.0000.000
90A2092ASN0-0.078-0.03422.5780.0040.0040.0000.0000.0000.000
91A2093LEU0-0.034-0.01819.5960.0040.0040.0000.0000.0000.000
92A2094ASP-1-0.944-0.96823.743-0.065-0.0650.0000.0000.0000.000
93A2095LEU0-0.017-0.00121.2940.0020.0020.0000.0000.0000.000
94A2096ASN0-0.023-0.02025.2940.0030.0030.0000.0000.0000.000
95A2097VAL0-0.060-0.03326.405-0.004-0.0040.0000.0000.0000.000
96A2098GLU-1-0.796-0.90428.021-0.046-0.0460.0000.0000.0000.000
97A2099ILE0-0.059-0.01829.125-0.006-0.0060.0000.0000.0000.000
98A2100ILE00.0520.02928.8810.0080.0080.0000.0000.0000.000
99A2101LYS10.8230.91531.7920.0460.0460.0000.0000.0000.000
100A2102SER00.0160.00131.8900.0040.0040.0000.0000.0000.000
101A2103LYS10.8650.90334.5740.0320.0320.0000.0000.0000.000
102A2104ASN00.000-0.00131.103-0.008-0.0080.0000.0000.0000.000
103A2105THR00.0240.01030.8600.0010.0010.0000.0000.0000.000
104A2106ALA00.0080.02326.942-0.008-0.0080.0000.0000.0000.000
105A2107LEU00.042-0.00125.6950.0030.0030.0000.0000.0000.000
106A2108GLY00.0430.03322.1000.0060.0060.0000.0000.0000.000
107A2109ASN00.000-0.00421.642-0.009-0.0090.0000.0000.0000.000
108A2110LEU0-0.061-0.02323.8590.0110.0110.0000.0000.0000.000
109A2111ILE0-0.0150.00022.4250.0130.0130.0000.0000.0000.000
110A2112LEU0-0.0030.02017.240-0.017-0.0170.0000.0000.0000.000
111A2113THR00.009-0.01518.6500.0210.0210.0000.0000.0000.000
112A2114ASN00.0030.00615.228-0.034-0.0340.0000.0000.0000.000
113A2115ASP-1-0.818-0.91016.264-0.061-0.0610.0000.0000.0000.000
114A2116LYS10.7410.84715.274-0.191-0.1910.0000.0000.0000.000
115A2117GLY00.0480.03920.0290.0050.0050.0000.0000.0000.000
116A2118ALA0-0.016-0.01220.463-0.011-0.0110.0000.0000.0000.000
117A2119LEU00.0230.03022.4940.0070.0070.0000.0000.0000.000
118A2120ILE0-0.025-0.02124.043-0.013-0.0130.0000.0000.0000.000
119A2121SER00.0810.04326.7480.0090.0090.0000.0000.0000.000
120A2122PRO00.026-0.00728.930-0.001-0.0010.0000.0000.0000.000
121A2123GLU-1-0.963-0.96832.027-0.041-0.0410.0000.0000.0000.000
122A2124LEU0-0.011-0.01328.349-0.002-0.0020.0000.0000.0000.000
123A2125LYS10.9260.97132.3360.0120.0120.0000.0000.0000.000
124A2126ASP-1-0.937-0.97334.145-0.016-0.0160.0000.0000.0000.000
125A2127PHE0-0.025-0.02132.282-0.001-0.0010.0000.0000.0000.000
126A2128LYS10.8390.92130.587-0.004-0.0040.0000.0000.0000.000
127A2129LYS10.8780.92231.1610.0150.0150.0000.0000.0000.000
128A2130ASP-1-0.890-0.95332.214-0.035-0.0350.0000.0000.0000.000
129A2131ILE0-0.028-0.01726.351-0.005-0.0050.0000.0000.0000.000
130A2132GLU-1-0.846-0.92727.436-0.006-0.0060.0000.0000.0000.000
131A2133ASP-1-0.859-0.89928.346-0.017-0.0170.0000.0000.0000.000
132A2134SER0-0.074-0.03226.855-0.003-0.0030.0000.0000.0000.000
133A2135LEU00.0280.00322.044-0.005-0.0050.0000.0000.0000.000
134A2136ASN0-0.031-0.01223.6340.0070.0070.0000.0000.0000.000
135A2137VAL0-0.049-0.01321.4160.0090.0090.0000.0000.0000.000
136A2138GLU-1-0.836-0.89724.8810.0460.0460.0000.0000.0000.000
137A2139VAL00.001-0.00925.050-0.002-0.0020.0000.0000.0000.000
138A2140GLU-1-0.891-0.94826.5540.0190.0190.0000.0000.0000.000
139A2141ILE0-0.054-0.02527.482-0.007-0.0070.0000.0000.0000.000
140A2142GLY00.002-0.00628.5000.0060.0060.0000.0000.0000.000
141A2143THR0-0.042-0.02827.416-0.008-0.0080.0000.0000.0000.000
142A2144ILE00.003-0.00321.5890.0050.0050.0000.0000.0000.000
143A2145ALA0-0.012-0.00424.737-0.007-0.0070.0000.0000.0000.000
144A2146GLU-1-0.940-0.96826.4880.0030.0030.0000.0000.0000.000
145A2147LEU0-0.074-0.03025.581-0.006-0.0060.0000.0000.0000.000
146A2148PRO00.0250.00127.1960.0010.0010.0000.0000.0000.000
147A2149THR0-0.045-0.02225.0800.0000.0000.0000.0000.0000.000
148A2150VAL00.0450.01022.994-0.005-0.0050.0000.0000.0000.000
149A2151GLY00.0250.04020.1560.0020.0020.0000.0000.0000.000
150A2152SER0-0.007-0.02219.370-0.013-0.0130.0000.0000.0000.000
151A2153ASN0-0.072-0.04920.125-0.006-0.0060.0000.0000.0000.000
152A2154ALA00.015-0.00117.4270.0210.0210.0000.0000.0000.000
153A2155VAL00.0230.03011.193-0.028-0.0280.0000.0000.0000.000
154A2156VAL0-0.017-0.00313.6540.0510.0510.0000.0000.0000.000
155A2157THR00.0790.0628.789-0.015-0.0150.0000.0000.0000.000
156A2158ASN0-0.040-0.05111.9750.0540.0540.0000.0000.0000.000
157A2159LYS10.8680.9465.091-3.089-2.996-0.001-0.009-0.0820.000
158A2160GLY00.0480.01211.1320.0570.0570.0000.0000.0000.000
159A2161CYS0-0.061-0.02511.952-0.089-0.0890.0000.0000.0000.000
160A2162LEU00.0410.03112.2450.0290.0290.0000.0000.0000.000
161A2163THR00.0370.00014.435-0.031-0.0310.0000.0000.0000.000
162A2164HIS00.0890.03518.0880.0110.0110.0000.0000.0000.000
163A2165PRO00.0010.00620.3550.0110.0110.0000.0000.0000.000
164A2166LEU0-0.060-0.04521.4810.0090.0090.0000.0000.0000.000
165A2167VAL00.0100.02022.002-0.002-0.0020.0000.0000.0000.000
166A2168GLU-1-0.920-0.94323.8750.0430.0430.0000.0000.0000.000
167A2169ASP-1-0.910-0.97224.0420.0800.0800.0000.0000.0000.000
168A2170ASP-1-0.927-0.96024.8270.0520.0520.0000.0000.0000.000
169A2171GLU-1-0.816-0.90924.4370.0240.0240.0000.0000.0000.000
170A2172LEU0-0.004-0.01418.8990.0010.0010.0000.0000.0000.000
171A2173GLU-1-0.914-0.95521.6150.1350.1350.0000.0000.0000.000
172A2174PHE0-0.036-0.02123.5170.0040.0040.0000.0000.0000.000
173A2175LEU00.010-0.00220.137-0.001-0.0010.0000.0000.0000.000
174A2176LYS10.8770.95717.084-0.206-0.2060.0000.0000.0000.000
175A2177SER0-0.0010.00020.0280.0120.0120.0000.0000.0000.000
176A2178LEU0-0.016-0.00122.4440.0010.0010.0000.0000.0000.000
177A2179PHE0-0.012-0.01017.360-0.008-0.0080.0000.0000.0000.000
178A2180LYS10.7940.89117.953-0.062-0.0620.0000.0000.0000.000
179A2181VAL0-0.0340.01514.3280.0300.0300.0000.0000.0000.000
180A2182GLU-1-0.853-0.94513.6680.2370.2370.0000.0000.0000.000
181A2183TYR0-0.088-0.0258.7520.1000.1000.0000.0000.0000.000
182A2184ILE0-0.003-0.00912.834-0.030-0.0300.0000.0000.0000.000
183A2185GLY00.0080.01014.7740.0090.0090.0000.0000.0000.000
184A2186LYS10.8330.92815.594-0.077-0.0770.0000.0000.0000.000
185A2187GLY00.002-0.01116.3110.0150.0150.0000.0000.0000.000
186A2188THR0-0.071-0.04817.227-0.009-0.0090.0000.0000.0000.000
187A2189ALA00.0220.00814.6270.0060.0060.0000.0000.0000.000
188A2190ASN0-0.025-0.04315.628-0.002-0.0020.0000.0000.0000.000
189A2191LYS10.9200.95617.6030.0260.0260.0000.0000.0000.000
190A2192GLY00.0170.01219.2010.0010.0010.0000.0000.0000.000
191A2193THR0-0.067-0.02519.5900.0010.0010.0000.0000.0000.000
192A2194THR00.0490.00319.5980.0010.0010.0000.0000.0000.000
193A2195SER0-0.0200.00920.5780.0080.0080.0000.0000.0000.000
194A2196VAL00.0450.01115.309-0.023-0.0230.0000.0000.0000.000
195A2197GLY00.0440.04315.682-0.035-0.0350.0000.0000.0000.000
196A2198ALA0-0.029-0.02317.046-0.030-0.0300.0000.0000.0000.000
197A2199CYS0-0.111-0.06015.799-0.009-0.0090.0000.0000.0000.000
198A2200ILE0-0.005-0.0049.953-0.030-0.0300.0000.0000.0000.000
199A2201ILE00.0010.02710.6890.0730.0730.0000.0000.0000.000
200A2202ALA00.006-0.0177.507-0.211-0.2110.0000.0000.0000.000
201A2203ASN00.004-0.0097.1820.0220.0220.0000.0000.0000.000
202A2204SER0-0.095-0.0756.7250.0490.0490.0000.0000.0000.000
203A2205LYS10.8020.9004.8311.5981.5980.0000.0000.0000.000
204A2206GLY00.0620.0352.497-4.326-2.4820.512-1.074-1.282-0.007
205A2207ALA0-0.026-0.0233.5031.5931.8350.0030.048-0.2930.000
206A2208VAL00.0010.0085.991-0.466-0.4660.0000.0000.0000.000
207A2209VAL0-0.018-0.0168.6150.2200.2200.0000.0000.0000.000
208A2210GLY00.0560.02910.8320.0000.0000.0000.0000.0000.000
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