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: 89R4Y

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 OptH
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 -2668030.432935
FMO2-HF: Nuclear repulsion 2584247.690425
FMO2-HF: Total energy -83782.74251
FMO2-MP2: Total energy -84030.358893


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.
-13.723-5.6464.425-3.953-8.547-0.024
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 : 0.005 / q_NPA : -0.004
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].
3A2005ILE0-0.0140.0113.821-0.0961.724-0.028-0.949-0.8420.002
4A2006ARG10.8510.9256.4400.1340.1340.0000.0000.0000.000
5A2007LYS10.7760.86010.0180.5370.5370.0000.0000.0000.000
6A2008TYR0-0.060-0.05812.7130.0370.0370.0000.0000.0000.000
7A2009PHE00.0390.01513.662-0.023-0.0230.0000.0000.0000.000
8A2010SER00.0420.01118.2160.0370.0370.0000.0000.0000.000
9A2011GLY0-0.015-0.00919.9800.0220.0220.0000.0000.0000.000
10A2012ILE0-0.025-0.00120.5010.0190.0190.0000.0000.0000.000
11A2013PRO00.0460.02017.600-0.037-0.0370.0000.0000.0000.000
12A2014THR0-0.027-0.00517.103-0.018-0.0180.0000.0000.0000.000
13A2015ILE00.0300.00412.9380.0180.0180.0000.0000.0000.000
14A2016GLY00.0370.02616.129-0.016-0.0160.0000.0000.0000.000
15A2017VAL0-0.016-0.01716.7870.0230.0230.0000.0000.0000.000
16A2018LEU0-0.060-0.03018.6660.0130.0130.0000.0000.0000.000
17A2019ALA0-0.0190.00115.695-0.011-0.0110.0000.0000.0000.000
18A2020LEU00.0340.03115.6920.0170.0170.0000.0000.0000.000
19A2021THR0-0.040-0.02610.515-0.076-0.0760.0000.0000.0000.000
20A2022THR00.0410.05113.8730.0390.0390.0000.0000.0000.000
21A2023GLU-1-0.714-0.84010.371-0.150-0.1500.0000.0000.0000.000
22A2024GLU-1-0.916-0.95512.256-0.195-0.1950.0000.0000.0000.000
23A2025ILE0-0.022-0.01214.910-0.034-0.0340.0000.0000.0000.000
24A2026THR00.0220.00712.798-0.052-0.0520.0000.0000.0000.000
25A2027LEU0-0.038-0.00215.2180.0220.0220.0000.0000.0000.000
26A2028LEU00.0350.00714.406-0.015-0.0150.0000.0000.0000.000
27A2029PRO00.0480.01018.4800.0360.0360.0000.0000.0000.000
28A2030ILE00.0240.00421.098-0.019-0.0190.0000.0000.0000.000
29A2031PHE0-0.071-0.03021.0920.0030.0030.0000.0000.0000.000
30A2032LEU0-0.0340.00016.4210.0060.0060.0000.0000.0000.000
31A2033ASP-1-0.832-0.90118.775-0.310-0.3100.0000.0000.0000.000
32A2034LYS10.9290.93818.5490.2380.2380.0000.0000.0000.000
33A2035ASP-1-0.889-0.92716.127-0.385-0.3850.0000.0000.0000.000
34A2036ASP-1-0.794-0.89614.511-0.481-0.4810.0000.0000.0000.000
35A2037VAL0-0.079-0.04213.538-0.095-0.0950.0000.0000.0000.000
36A2038ASN0-0.027-0.02813.383-0.058-0.0580.0000.0000.0000.000
37A2039GLU-1-0.806-0.88710.077-0.713-0.7130.0000.0000.0000.000
38A2040VAL0-0.042-0.0278.766-0.283-0.2830.0000.0000.0000.000
39A2041SER0-0.062-0.0359.026-0.180-0.1800.0000.0000.0000.000
40A2042GLU-1-0.975-0.9887.223-1.148-1.1480.0000.0000.0000.000
41A2043VAL0-0.038-0.0213.099-0.713-0.3620.079-0.099-0.332-0.001
42A2044LEU0-0.036-0.0104.695-0.774-0.665-0.001-0.006-0.1010.000
43A2045GLU-1-0.900-0.9475.679-1.079-1.0790.0000.0000.0000.000
44A2046THR0-0.042-0.0189.1290.1980.1980.0000.0000.0000.000
45A2047LYS10.9120.95612.3240.2980.2980.0000.0000.0000.000
46A2048CYS00.0090.01013.8720.0010.0010.0000.0000.0000.000
47A2049LEU00.0090.01816.5020.0340.0340.0000.0000.0000.000
48A2050GLN0-0.080-0.03719.759-0.009-0.0090.0000.0000.0000.000
49A2051THR0-0.002-0.03221.5010.0270.0270.0000.0000.0000.000
50A2052ASN00.0080.02723.989-0.019-0.0190.0000.0000.0000.000
51A2053ILE0-0.007-0.01623.9630.0010.0010.0000.0000.0000.000
52A2054GLY0-0.019-0.01027.8030.0010.0010.0000.0000.0000.000
53A2055GLY00.0110.00530.8430.0050.0050.0000.0000.0000.000
54A2056SER0-0.109-0.04528.058-0.007-0.0070.0000.0000.0000.000
55A2057SER00.0540.00923.868-0.004-0.0040.0000.0000.0000.000
56A2058LEU0-0.034-0.01223.118-0.019-0.0190.0000.0000.0000.000
57A2059VAL00.0500.00920.3250.0140.0140.0000.0000.0000.000
58A2060GLY00.0040.00919.3370.0080.0080.0000.0000.0000.000
59A2061SER0-0.002-0.01620.0900.0170.0170.0000.0000.0000.000
60A2062LEU0-0.078-0.03323.1970.0200.0200.0000.0000.0000.000
61A2063SER0-0.070-0.02822.6300.0080.0080.0000.0000.0000.000
62A2064VAL00.0330.02020.503-0.008-0.0080.0000.0000.0000.000
63A2065ALA0-0.018-0.01018.6980.0030.0030.0000.0000.0000.000
64A2066ASN00.006-0.00817.568-0.017-0.0170.0000.0000.0000.000
65A2067LYS10.9130.96017.843-0.042-0.0420.0000.0000.0000.000
66A2068TYR0-0.046-0.02219.115-0.001-0.0010.0000.0000.0000.000
67A2069GLY00.0880.06122.2000.0000.0000.0000.0000.0000.000
68A2070LEU0-0.064-0.02821.864-0.014-0.0140.0000.0000.0000.000
69A2071LEU00.0100.01123.8520.0090.0090.0000.0000.0000.000
70A2072LEU00.0170.00025.219-0.014-0.0140.0000.0000.0000.000
71A2073PRO00.0500.03327.4040.0120.0120.0000.0000.0000.000
72A2074LYS10.9310.94730.3300.0460.0460.0000.0000.0000.000
73A2075ILE0-0.066-0.03430.8370.0030.0030.0000.0000.0000.000
74A2076VAL0-0.0430.00229.454-0.004-0.0040.0000.0000.0000.000
75A2077GLU-1-0.899-0.95931.865-0.085-0.0850.0000.0000.0000.000
76A2078ASP-1-0.906-0.96132.956-0.072-0.0720.0000.0000.0000.000
77A2079GLU-1-0.945-0.97432.711-0.102-0.1020.0000.0000.0000.000
78A2080GLU-1-0.723-0.84628.979-0.121-0.1210.0000.0000.0000.000
79A2081LEU0-0.011-0.00828.892-0.008-0.0080.0000.0000.0000.000
80A2082ASP-1-0.897-0.94229.972-0.087-0.0870.0000.0000.0000.000
81A2083ARG10.8220.90324.2000.1780.1780.0000.0000.0000.000
82A2084ILE0-0.003-0.00724.496-0.012-0.0120.0000.0000.0000.000
83A2085LYS10.9720.98325.8260.0710.0710.0000.0000.0000.000
84A2086ASN0-0.053-0.02128.004-0.007-0.0070.0000.0000.0000.000
85A2087PHE00.0320.01318.6290.0020.0020.0000.0000.0000.000
86A2088LEU00.0170.01522.250-0.009-0.0090.0000.0000.0000.000
87A2089LYS10.9660.98024.5470.0860.0860.0000.0000.0000.000
88A2090GLU-1-0.995-0.99725.171-0.127-0.1270.0000.0000.0000.000
89A2091ASN0-0.107-0.05120.740-0.021-0.0210.0000.0000.0000.000
90A2092ASN0-0.086-0.04022.3810.0060.0060.0000.0000.0000.000
91A2093LEU0-0.036-0.01819.4630.0060.0060.0000.0000.0000.000
92A2094ASP-1-0.962-0.97623.495-0.050-0.0500.0000.0000.0000.000
93A2095LEU0-0.0130.00221.2630.0030.0030.0000.0000.0000.000
94A2096ASN0-0.024-0.02325.267-0.001-0.0010.0000.0000.0000.000
95A2097VAL0-0.079-0.04226.314-0.004-0.0040.0000.0000.0000.000
96A2098GLU-1-0.874-0.93527.985-0.034-0.0340.0000.0000.0000.000
97A2099ILE0-0.071-0.03529.093-0.006-0.0060.0000.0000.0000.000
98A2100ILE00.0870.05128.7960.0070.0070.0000.0000.0000.000
99A2101LYS10.9100.95331.7610.0350.0350.0000.0000.0000.000
100A2102SER00.0190.00631.8030.0040.0040.0000.0000.0000.000
101A2103LYS10.8580.89934.5430.0270.0270.0000.0000.0000.000
102A2104ASN00.0070.01531.007-0.009-0.0090.0000.0000.0000.000
103A2105THR00.0230.00630.8610.0020.0020.0000.0000.0000.000
104A2106ALA00.0170.02526.842-0.008-0.0080.0000.0000.0000.000
105A2107LEU00.042-0.00325.6100.0040.0040.0000.0000.0000.000
106A2108GLY00.0400.03022.0710.0090.0090.0000.0000.0000.000
107A2109ASN00.017-0.00721.612-0.009-0.0090.0000.0000.0000.000
108A2110LEU0-0.073-0.03023.8300.0130.0130.0000.0000.0000.000
109A2111ILE0-0.0110.00422.3680.0140.0140.0000.0000.0000.000
110A2112LEU00.0000.01817.117-0.017-0.0170.0000.0000.0000.000
111A2113THR00.001-0.01918.6330.0210.0210.0000.0000.0000.000
112A2114ASN00.0080.01215.238-0.042-0.0420.0000.0000.0000.000
113A2115ASP-1-0.813-0.90916.176-0.019-0.0190.0000.0000.0000.000
114A2116LYS10.7400.85115.028-0.308-0.3080.0000.0000.0000.000
115A2117GLY00.0610.04320.0040.0020.0020.0000.0000.0000.000
116A2118ALA0-0.017-0.01220.447-0.008-0.0080.0000.0000.0000.000
117A2119LEU00.0280.03122.4840.0060.0060.0000.0000.0000.000
118A2120ILE0-0.032-0.02424.022-0.014-0.0140.0000.0000.0000.000
119A2121SER00.0730.04126.7270.0090.0090.0000.0000.0000.000
120A2122PRO00.028-0.00528.908-0.001-0.0010.0000.0000.0000.000
121A2123GLU-1-0.972-0.98132.098-0.031-0.0310.0000.0000.0000.000
122A2124LEU0-0.012-0.01028.319-0.003-0.0030.0000.0000.0000.000
123A2125LYS10.9871.00432.311-0.004-0.0040.0000.0000.0000.000
124A2126ASP-1-0.988-0.99934.123-0.005-0.0050.0000.0000.0000.000
125A2127PHE0-0.042-0.03232.220-0.002-0.0020.0000.0000.0000.000
126A2128LYS10.8580.92430.739-0.025-0.0250.0000.0000.0000.000
127A2129LYS10.8770.93831.1390.0000.0000.0000.0000.0000.000
128A2130ASP-1-0.878-0.94132.064-0.022-0.0220.0000.0000.0000.000
129A2131ILE0-0.032-0.02226.325-0.004-0.0040.0000.0000.0000.000
130A2132GLU-1-0.851-0.92027.4130.0170.0170.0000.0000.0000.000
131A2133ASP-1-0.849-0.91328.3250.0020.0020.0000.0000.0000.000
132A2134SER0-0.080-0.03226.744-0.002-0.0020.0000.0000.0000.000
133A2135LEU00.022-0.00722.090-0.005-0.0050.0000.0000.0000.000
134A2136ASN0-0.025-0.00523.6140.0080.0080.0000.0000.0000.000
135A2137VAL0-0.066-0.02321.4070.0120.0120.0000.0000.0000.000
136A2138GLU-1-0.904-0.94424.8650.0740.0740.0000.0000.0000.000
137A2139VAL0-0.026-0.01825.0360.0000.0000.0000.0000.0000.000
138A2140GLU-1-0.887-0.93826.5350.0480.0480.0000.0000.0000.000
139A2141ILE0-0.078-0.04827.465-0.007-0.0070.0000.0000.0000.000
140A2142GLY00.003-0.00428.4840.0070.0070.0000.0000.0000.000
141A2143THR0-0.037-0.03027.373-0.009-0.0090.0000.0000.0000.000
142A2144ILE00.0150.00621.2910.0080.0080.0000.0000.0000.000
143A2145ALA00.0020.01024.751-0.009-0.0090.0000.0000.0000.000
144A2146GLU-1-0.935-0.96626.4780.0110.0110.0000.0000.0000.000
145A2147LEU0-0.080-0.03325.501-0.008-0.0080.0000.0000.0000.000
146A2148PRO00.025-0.00227.1780.0030.0030.0000.0000.0000.000
147A2149THR0-0.048-0.02325.1470.0010.0010.0000.0000.0000.000
148A2150VAL00.0550.01222.995-0.006-0.0060.0000.0000.0000.000
149A2151GLY00.0300.04320.1320.0050.0050.0000.0000.0000.000
150A2152SER0-0.016-0.02619.344-0.014-0.0140.0000.0000.0000.000
151A2153ASN0-0.067-0.04220.102-0.009-0.0090.0000.0000.0000.000
152A2154ALA00.013-0.00217.4080.0210.0210.0000.0000.0000.000
153A2155VAL00.0210.03011.141-0.033-0.0330.0000.0000.0000.000
154A2156VAL0-0.024-0.00813.6270.0610.0610.0000.0000.0000.000
155A2157THR00.0790.0668.819-0.023-0.0230.0000.0000.0000.000
156A2158ASN0-0.006-0.02811.9590.0320.0320.0000.0000.0000.000
157A2159LYS10.8860.9625.375-3.376-3.302-0.001-0.002-0.0700.000
158A2160GLY00.0470.00710.9270.0700.0700.0000.0000.0000.000
159A2161CYS0-0.044-0.00911.952-0.112-0.1120.0000.0000.0000.000
160A2162LEU00.0470.02912.3890.0300.0300.0000.0000.0000.000
161A2163THR00.027-0.00714.428-0.036-0.0360.0000.0000.0000.000
162A2164HIS00.0800.03818.0790.0070.0070.0000.0000.0000.000
163A2165PRO00.0010.00520.3000.0150.0150.0000.0000.0000.000
164A2166LEU0-0.064-0.05621.2370.0080.0080.0000.0000.0000.000
165A2167VAL00.0020.01421.928-0.002-0.0020.0000.0000.0000.000
166A2168GLU-1-0.953-0.96923.7540.0570.0570.0000.0000.0000.000
167A2169ASP-1-0.903-0.96623.9690.1100.1100.0000.0000.0000.000
168A2170ASP-1-0.919-0.95324.8240.0810.0810.0000.0000.0000.000
169A2171GLU-1-0.842-0.92924.2110.0540.0540.0000.0000.0000.000
170A2172LEU00.003-0.01418.9180.0060.0060.0000.0000.0000.000
171A2173GLU-1-0.945-0.96521.6850.1970.1970.0000.0000.0000.000
172A2174PHE0-0.030-0.02123.5180.0090.0090.0000.0000.0000.000
173A2175LEU00.0210.00320.0840.0020.0020.0000.0000.0000.000
174A2176LYS10.9380.98917.146-0.276-0.2760.0000.0000.0000.000
175A2177SER0-0.033-0.01619.8660.0200.0200.0000.0000.0000.000
176A2178LEU00.0250.01822.4260.0050.0050.0000.0000.0000.000
177A2179PHE0-0.0030.00117.325-0.006-0.0060.0000.0000.0000.000
178A2180LYS10.8700.92917.949-0.137-0.1370.0000.0000.0000.000
179A2181VAL0-0.0300.01414.1140.0400.0400.0000.0000.0000.000
180A2182GLU-1-0.934-0.97913.4590.3570.3570.0000.0000.0000.000
181A2183TYR0-0.088-0.0339.5380.1260.1260.0000.0000.0000.000
182A2184ILE0-0.004-0.01213.006-0.035-0.0350.0000.0000.0000.000
183A2185GLY00.0010.00714.6860.0030.0030.0000.0000.0000.000
184A2186LYS10.8900.97715.520-0.093-0.0930.0000.0000.0000.000
185A2187GLY0-0.002-0.01616.0190.0080.0080.0000.0000.0000.000
186A2188THR0-0.070-0.05416.937-0.004-0.0040.0000.0000.0000.000
187A2189ALA00.0210.01114.6990.0020.0020.0000.0000.0000.000
188A2190ASN0-0.017-0.03715.741-0.005-0.0050.0000.0000.0000.000
189A2191LYS10.9130.94817.7120.0590.0590.0000.0000.0000.000
190A2192GLY00.0070.00619.2290.0030.0030.0000.0000.0000.000
191A2193THR0-0.071-0.02819.6920.0060.0060.0000.0000.0000.000
192A2194THR00.0470.00019.7030.0010.0010.0000.0000.0000.000
193A2195SER0-0.0060.01720.5620.0120.0120.0000.0000.0000.000
194A2196VAL00.0310.00415.341-0.025-0.0250.0000.0000.0000.000
195A2197GLY00.0450.04215.659-0.033-0.0330.0000.0000.0000.000
196A2198ALA0-0.027-0.02217.016-0.032-0.0320.0000.0000.0000.000
197A2199CYS0-0.106-0.05415.692-0.015-0.0150.0000.0000.0000.000
198A2200ILE0-0.006-0.0069.979-0.039-0.0390.0000.0000.0000.000
199A2201ILE00.0000.02310.5820.0800.0800.0000.0000.0000.000
200A2202ALA00.005-0.0127.517-0.213-0.2130.0000.0000.0000.000
201A2203ASN0-0.020-0.0227.1460.0120.0120.0000.0000.0000.000
202A2204SER0-0.126-0.0996.7060.1190.1190.0000.0000.0000.000
203A2205LYS10.8130.9144.6321.4751.747-0.001-0.012-0.2590.000
204A2206GLY00.0650.0362.462-5.411-3.2020.658-1.295-1.573-0.009
205A2207ALA0-0.029-0.0223.4671.7111.9440.0040.072-0.3080.000
206A2208VAL0-0.0030.0045.970-0.499-0.4990.0000.0000.0000.000
207A2209VAL0-0.026-0.0108.8190.2270.2270.0000.0000.0000.000
208A2210GLY00.0500.02110.832-0.011-0.0110.0000.0000.0000.000
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