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: 2NJGR

Calculation Name: 2R6Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2R6Z

Chain ID: A

ChEMBL ID:

UniProt ID: P72077

Base Structure: X-ray

Registration Date: 2023-09-21

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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2532539.154868
FMO2-HF: Nuclear repulsion 2447108.521847
FMO2-HF: Total energy -85430.633021
FMO2-MP2: Total energy -85683.53301


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:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-14.428-4.4774.302-4.799-9.4560.01
Interaction energy analysis for fragmet #1(A:2:THR)
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].
3A4ILE0-0.044-0.0322.733-1.9851.3190.519-1.843-1.981-0.007
4A5LEU00.0100.0184.8020.2610.297-0.001-0.008-0.0270.000
5A6ILE0-0.041-0.0428.3820.2590.2590.0000.0000.0000.000
6A7ASP-1-0.771-0.84710.815-0.498-0.4980.0000.0000.0000.000
7A8ASP-1-0.916-0.97013.962-0.634-0.6340.0000.0000.0000.000
8A9THR0-0.089-0.07616.8640.0510.0510.0000.0000.0000.000
9A10ALA0-0.070-0.01713.4840.0600.0600.0000.0000.0000.000
10A11THR00.018-0.03015.429-0.024-0.0240.0000.0000.0000.000
11A12GLU-1-0.856-0.94216.170-0.518-0.5180.0000.0000.0000.000
12A13ALA0-0.0130.00117.084-0.020-0.0200.0000.0000.0000.000
13A14VAL00.0110.01811.6540.0110.0110.0000.0000.0000.000
14A15ARG10.8680.92512.4180.5880.5880.0000.0000.0000.000
15A16THR0-0.056-0.05013.308-0.096-0.0960.0000.0000.0000.000
16A17LEU0-0.0380.00510.038-0.032-0.0320.0000.0000.0000.000
17A18ILE00.019-0.0088.1750.0770.0770.0000.0000.0000.000
18A19ARG10.8590.9488.7900.4620.4620.0000.0000.0000.000
19A20ALA0-0.0360.00311.024-0.032-0.0320.0000.0000.0000.000
20A21PHE0-0.005-0.0065.9300.4140.4140.0000.0000.0000.000
21A22PRO0-0.0250.0035.401-0.460-0.4600.0000.0000.0000.000
22A23LEU0-0.026-0.0302.712-2.455-1.2190.247-0.302-1.182-0.001
23A24VAL00.0060.0023.0491.3402.3900.033-0.395-0.6890.000
24A25PRO0-0.028-0.0025.157-0.353-0.327-0.001-0.004-0.0210.000
25A26VAL00.0010.0027.1720.2740.2740.0000.0000.0000.000
26A27SER0-0.011-0.0219.5770.2060.2060.0000.0000.0000.000
27A28GLN0-0.010-0.00511.7830.2960.2960.0000.0000.0000.000
28A29PRO0-0.023-0.0109.523-0.284-0.2840.0000.0000.0000.000
29A30PRO00.0360.0336.8620.1230.1230.0000.0000.0000.000
30A31GLU-1-0.882-0.9429.621-0.199-0.1990.0000.0000.0000.000
31A32GLN0-0.093-0.06510.6350.2510.2510.0000.0000.0000.000
32A33GLY00.0280.0268.413-0.116-0.1160.0000.0000.0000.000
33A34SER0-0.019-0.0265.259-0.225-0.2250.0000.0000.0000.000
34A35TYR00.0190.0043.492-0.491-0.2610.009-0.057-0.1820.000
35A36LEU00.0030.0012.6460.2761.0250.798-0.246-1.301-0.001
36A37LEU00.0020.0104.866-0.674-0.665-0.001-0.002-0.0050.000
37A38ALA0-0.009-0.0058.2950.2540.2540.0000.0000.0000.000
38A39GLU-1-0.896-0.95710.280-0.392-0.3920.0000.0000.0000.000
39A40HIS00.0370.01813.8350.0870.0870.0000.0000.0000.000
40A41ASP-1-0.799-0.87516.056-0.151-0.1510.0000.0000.0000.000
41A42THR0-0.064-0.02413.7870.0970.0970.0000.0000.0000.000
42A43VAL00.0310.0127.140-0.137-0.1370.0000.0000.0000.000
43A44SER0-0.045-0.0169.1990.2050.2050.0000.0000.0000.000
44A45LEU0-0.016-0.0204.510-0.198-0.112-0.001-0.007-0.0780.000
45A46ARG10.8690.9327.0090.0080.0080.0000.0000.0000.000
46A47LEU00.0220.0157.5900.2050.2050.0000.0000.0000.000
47A48VAL0-0.0070.0029.809-0.060-0.0600.0000.0000.0000.000
48A49GLY00.0110.01111.9840.0760.0760.0000.0000.0000.000
49A50GLU-1-0.940-0.97013.9360.2110.2110.0000.0000.0000.000
50A51LYS10.9220.93914.630-0.033-0.0330.0000.0000.0000.000
51A52SER0-0.0200.01315.176-0.030-0.0300.0000.0000.0000.000
52A53ASN0-0.018-0.01511.9860.0100.0100.0000.0000.0000.000
53A54VAL00.0060.01410.0080.0050.0050.0000.0000.0000.000
54A55ILE00.0470.01810.4210.0530.0530.0000.0000.0000.000
55A56VAL0-0.0240.01011.2350.0220.0220.0000.0000.0000.000
56A57ASP-1-0.822-0.93413.7330.1840.1840.0000.0000.0000.000
57A58PHE0-0.063-0.03216.3730.0240.0240.0000.0000.0000.000
58A59THR0-0.0540.00020.027-0.024-0.0240.0000.0000.0000.000
59A73GLU-1-0.828-0.92631.3420.2390.2390.0000.0000.0000.000
60A74LEU0-0.126-0.05831.237-0.009-0.0090.0000.0000.0000.000
61A75ILE00.0690.03125.505-0.010-0.0100.0000.0000.0000.000
62A76ALA00.0710.03929.8170.0000.0000.0000.0000.0000.000
63A77LYS10.9050.95231.783-0.216-0.2160.0000.0000.0000.000
64A78ALA0-0.0120.00730.540-0.008-0.0080.0000.0000.0000.000
65A79VAL0-0.003-0.00428.025-0.002-0.0020.0000.0000.0000.000
66A80ASN0-0.022-0.03131.395-0.017-0.0170.0000.0000.0000.000
67A81HIS00.0860.02032.346-0.007-0.0070.0000.0000.0000.000
68A82THR0-0.0190.01133.712-0.010-0.0100.0000.0000.0000.000
69A83ALA0-0.039-0.01036.264-0.011-0.0110.0000.0000.0000.000
70A84HIS10.8340.92431.821-0.185-0.1850.0000.0000.0000.000
71A85PRO0-0.0250.00031.065-0.007-0.0070.0000.0000.0000.000
72A86THR00.0110.00128.1200.0150.0150.0000.0000.0000.000
73A87VAL0-0.012-0.01424.5160.0030.0030.0000.0000.0000.000
74A88TRP00.0190.00222.5260.0160.0160.0000.0000.0000.000
75A89ASP-1-0.801-0.90319.2580.6990.6990.0000.0000.0000.000
76A90ALA0-0.001-0.03318.6190.0430.0430.0000.0000.0000.000
77A91THR0-0.029-0.01015.8200.0320.0320.0000.0000.0000.000
78A92ALA00.0420.04314.3640.0190.0190.0000.0000.0000.000
79A93GLY00.0800.05512.175-0.076-0.0760.0000.0000.0000.000
80A94LEU0-0.041-0.04410.3780.0240.0240.0000.0000.0000.000
81A95GLY00.0300.01213.149-0.144-0.1440.0000.0000.0000.000
82A96ARG10.8790.93916.117-0.754-0.7540.0000.0000.0000.000
83A97ASP-1-0.782-0.90618.8930.4870.4870.0000.0000.0000.000
84A98SER00.003-0.00818.443-0.043-0.0430.0000.0000.0000.000
85A99PHE00.0920.04720.038-0.051-0.0510.0000.0000.0000.000
86A100VAL0-0.0040.02021.674-0.049-0.0490.0000.0000.0000.000
87A101LEU0-0.023-0.02423.042-0.041-0.0410.0000.0000.0000.000
88A102ALA00.0410.03123.436-0.031-0.0310.0000.0000.0000.000
89A103SER0-0.012-0.03425.232-0.037-0.0370.0000.0000.0000.000
90A104LEU0-0.124-0.04327.408-0.022-0.0220.0000.0000.0000.000
91A105GLY00.0170.00329.059-0.016-0.0160.0000.0000.0000.000
92A106LEU0-0.091-0.04428.053-0.016-0.0160.0000.0000.0000.000
93A107THR0-0.024-0.00526.2400.0180.0180.0000.0000.0000.000
94A108VAL00.020-0.00920.9410.0040.0040.0000.0000.0000.000
95A109THR0-0.033-0.00420.175-0.022-0.0220.0000.0000.0000.000
96A110ALA00.012-0.00616.2180.0180.0180.0000.0000.0000.000
97A111PHE00.0190.00115.651-0.025-0.0250.0000.0000.0000.000
98A112GLU-1-0.820-0.9159.5932.2882.2880.0000.0000.0000.000
99A113GLN00.0300.0149.771-0.168-0.1680.0000.0000.0000.000
100A114HIS00.0250.0173.066-1.236-0.1070.100-0.488-0.7420.005
101A115PRO00.0420.0093.010-2.049-0.5660.156-0.682-0.9570.005
102A116ALA00.0390.0232.185-4.081-3.3522.395-1.085-2.0380.009
103A117VAL0-0.0220.0033.250-2.179-2.2950.0490.320-0.2530.000
104A118ALA00.0400.0196.976-0.803-0.8030.0000.0000.0000.000
105A119CYS0-0.0540.0005.238-0.706-0.7060.0000.0000.0000.000
106A120LEU0-0.003-0.0066.081-0.428-0.4280.0000.0000.0000.000
107A121LEU0-0.015-0.0018.425-0.285-0.2850.0000.0000.0000.000
108A122SER0-0.007-0.00910.561-0.201-0.2010.0000.0000.0000.000
109A123ASP-1-0.698-0.85410.735-0.053-0.0530.0000.0000.0000.000
110A124GLY00.0140.00912.508-0.071-0.0710.0000.0000.0000.000
111A125ILE0-0.018-0.01314.588-0.058-0.0580.0000.0000.0000.000
112A126ARG10.7520.86614.463-0.029-0.0290.0000.0000.0000.000
113A127ARG10.8160.87912.862-0.290-0.2900.0000.0000.0000.000
114A128ALA00.0010.01218.346-0.019-0.0190.0000.0000.0000.000
115A129LEU0-0.028-0.00720.142-0.020-0.0200.0000.0000.0000.000
116A130LEU0-0.033-0.01320.180-0.021-0.0210.0000.0000.0000.000
117A131ASN00.0110.00923.122-0.036-0.0360.0000.0000.0000.000
118A132PRO00.0530.00224.7400.0140.0140.0000.0000.0000.000
119A133GLU-1-0.957-0.97226.5860.1560.1560.0000.0000.0000.000
120A134THR0-0.038-0.01923.1250.0170.0170.0000.0000.0000.000
121A135GLN0-0.065-0.00724.4150.0190.0190.0000.0000.0000.000
122A136ASP-1-0.847-0.93425.4340.1660.1660.0000.0000.0000.000
123A137THR0-0.029-0.02023.690-0.001-0.0010.0000.0000.0000.000
124A138ALA00.0280.00620.8920.0250.0250.0000.0000.0000.000
125A139ALA0-0.0130.00321.7890.0130.0130.0000.0000.0000.000
126A140ARG10.7390.89524.252-0.213-0.2130.0000.0000.0000.000
127A141ILE0-0.022-0.00218.4420.0300.0300.0000.0000.0000.000
128A142ASN0-0.025-0.00219.510-0.041-0.0410.0000.0000.0000.000
129A143LEU00.0000.00411.5150.0340.0340.0000.0000.0000.000
130A144HIS0-0.040-0.03715.744-0.092-0.0920.0000.0000.0000.000
131A145PHE00.015-0.0027.5410.0340.0340.0000.0000.0000.000
132A146GLY00.0350.00411.939-0.171-0.1710.0000.0000.0000.000
133A147ASN00.0450.01212.836-0.034-0.0340.0000.0000.0000.000
134A148ALA00.0390.02114.341-0.136-0.1360.0000.0000.0000.000
135A149ALA00.004-0.00717.603-0.086-0.0860.0000.0000.0000.000
136A150GLU-1-0.917-0.95515.9360.5550.5550.0000.0000.0000.000
137A151GLN0-0.0110.00615.835-0.119-0.1190.0000.0000.0000.000
138A152MET0-0.0200.02018.961-0.064-0.0640.0000.0000.0000.000
139A153PRO00.003-0.00121.705-0.054-0.0540.0000.0000.0000.000
140A154ALA00.0630.03221.547-0.041-0.0410.0000.0000.0000.000
141A155LEU00.0570.03821.233-0.036-0.0360.0000.0000.0000.000
142A156VAL0-0.048-0.02823.828-0.029-0.0290.0000.0000.0000.000
143A157LYS10.7680.87526.975-0.222-0.2220.0000.0000.0000.000
144A158THR0-0.0090.01125.187-0.025-0.0250.0000.0000.0000.000
145A159GLN00.001-0.00524.317-0.008-0.0080.0000.0000.0000.000
146A160GLY00.0000.01528.476-0.004-0.0040.0000.0000.0000.000
147A161LYS10.8890.93328.556-0.193-0.1930.0000.0000.0000.000
148A162PRO00.0190.04726.110-0.019-0.0190.0000.0000.0000.000
149A163ASP-1-0.854-0.94528.9090.1960.1960.0000.0000.0000.000
150A164ILE0-0.031-0.01727.609-0.003-0.0030.0000.0000.0000.000
151A165VAL0-0.0020.01923.4050.0090.0090.0000.0000.0000.000
152A166TYR0-0.040-0.04721.810-0.050-0.0500.0000.0000.0000.000
153A167LEU0-0.002-0.01521.2490.0390.0390.0000.0000.0000.000
154A168ASP-1-0.894-0.97120.1840.6190.6190.0000.0000.0000.000
155A169PRO00.0320.03017.8140.0710.0710.0000.0000.0000.000
156A170MET00.0580.06517.523-0.033-0.0330.0000.0000.0000.000
157A184MET00.0450.00926.381-0.011-0.0110.0000.0000.0000.000
158A185ALA00.0300.01026.8180.0200.0200.0000.0000.0000.000
159A186TYR00.017-0.00327.2830.0240.0240.0000.0000.0000.000
160A187PHE00.0290.00722.7660.0070.0070.0000.0000.0000.000
161A188HIS00.0700.03023.0760.0280.0280.0000.0000.0000.000
162A189ARG10.9280.98023.154-0.264-0.2640.0000.0000.0000.000
163A190LEU0-0.042-0.03225.2220.0080.0080.0000.0000.0000.000
164A191VAL0-0.030-0.01121.223-0.005-0.0050.0000.0000.0000.000
165A192GLY00.0170.02419.4800.0420.0420.0000.0000.0000.000
166A193GLU-1-0.873-0.94617.2470.8420.8420.0000.0000.0000.000
167A194ALA0-0.031-0.01119.619-0.019-0.0190.0000.0000.0000.000
168A195GLN00.0190.01322.016-0.034-0.0340.0000.0000.0000.000
169A196ASP-1-0.857-0.93417.3300.7590.7590.0000.0000.0000.000
170A197GLU-1-0.886-0.95720.0930.5360.5360.0000.0000.0000.000
171A198VAL0-0.053-0.02622.333-0.032-0.0320.0000.0000.0000.000
172A199VAL0-0.009-0.00421.239-0.032-0.0320.0000.0000.0000.000
173A200LEU00.0100.01619.132-0.027-0.0270.0000.0000.0000.000
174A201LEU00.0060.00321.936-0.030-0.0300.0000.0000.0000.000
175A202HIS00.0250.03425.457-0.032-0.0320.0000.0000.0000.000
176A203THR00.0350.00722.605-0.036-0.0360.0000.0000.0000.000
177A204ALA00.0070.02624.258-0.024-0.0240.0000.0000.0000.000
178A205ARG10.8950.94925.730-0.294-0.2940.0000.0000.0000.000
179A206GLN0-0.030-0.01228.138-0.016-0.0160.0000.0000.0000.000
180A207THR0-0.096-0.06325.103-0.020-0.0200.0000.0000.0000.000
181A208ALA00.0200.00428.067-0.016-0.0160.0000.0000.0000.000
182A209LYS10.8550.93029.663-0.195-0.1950.0000.0000.0000.000
183A210LYS10.9100.95732.484-0.194-0.1940.0000.0000.0000.000
184A211ARG10.9480.98231.828-0.231-0.2310.0000.0000.0000.000
185A212VAL00.0270.03826.5410.0120.0120.0000.0000.0000.000
186A213VAL0-0.031-0.01727.441-0.017-0.0170.0000.0000.0000.000
187A214VAL00.0400.01324.6440.0330.0330.0000.0000.0000.000
188A215LYS10.8820.97123.353-0.553-0.5530.0000.0000.0000.000
189A216ARG10.8130.88823.279-0.478-0.4780.0000.0000.0000.000
190A217PRO00.0690.02725.748-0.026-0.0260.0000.0000.0000.000
191A218ARG10.9560.98828.165-0.264-0.2640.0000.0000.0000.000
192A219LEU0-0.025-0.02231.909-0.010-0.0100.0000.0000.0000.000
193A220GLY0-0.0020.01629.067-0.001-0.0010.0000.0000.0000.000
194A221GLU-1-0.860-0.91927.6290.3740.3740.0000.0000.0000.000
195A222HIS0-0.035-0.03328.8390.0060.0060.0000.0000.0000.000
196A223LEU00.0320.02123.1630.0070.0070.0000.0000.0000.000
197A224ALA00.0140.01326.048-0.030-0.0300.0000.0000.0000.000
198A225GLY0-0.031-0.01027.322-0.027-0.0270.0000.0000.0000.000
199A226GLN0-0.050-0.02230.366-0.040-0.0400.0000.0000.0000.000
200A227ALA00.0130.01332.1020.0140.0140.0000.0000.0000.000
201A228PRO0-0.060-0.01232.598-0.004-0.0040.0000.0000.0000.000
202A229ALA0-0.034-0.01334.351-0.015-0.0150.0000.0000.0000.000
203A230TYR0-0.028-0.02335.904-0.010-0.0100.0000.0000.0000.000
204A231GLN0-0.016-0.00634.0720.0020.0020.0000.0000.0000.000
205A232TYR00.0020.02233.708-0.016-0.0160.0000.0000.0000.000
206A233THR00.019-0.00533.6480.0230.0230.0000.0000.0000.000
207A234GLY00.0090.00533.763-0.014-0.0140.0000.0000.0000.000
208A235LYS10.9390.96632.255-0.252-0.2520.0000.0000.0000.000
209A236SER0-0.011-0.02830.071-0.009-0.0090.0000.0000.0000.000
210A237THR00.0230.00728.5250.0320.0320.0000.0000.0000.000
211A238ARG10.7040.82629.465-0.356-0.3560.0000.0000.0000.000
212A239PHE00.0330.00726.4610.0210.0210.0000.0000.0000.000
213A240ASP-1-0.710-0.83229.6770.3000.3000.0000.0000.0000.000
214A241VAL00.006-0.00530.1030.0210.0210.0000.0000.0000.000
215A242TYR0-0.003-0.02129.273-0.012-0.0120.0000.0000.0000.000
216A243LEU00.0000.00432.6180.0020.0020.0000.0000.0000.000
217A244PRO00.0090.00332.5580.0090.0090.0000.0000.0000.000
218A245TYR0-0.067-0.06030.204-0.014-0.0140.0000.0000.0000.000
219A246GLY0-0.020-0.01035.034-0.006-0.0060.0000.0000.0000.000
220A247ALA0-0.0240.00837.351-0.009-0.0090.0000.0000.0000.000
221A248ASP-1-0.847-0.92339.2150.1400.1400.0000.0000.0000.000
222A249LYS10.9820.96040.800-0.161-0.1610.0000.0000.0000.000
223A250GLY0-0.058-0.02141.8800.0000.0000.0000.0000.0000.000
224A251LEU0-0.026-0.01143.400-0.005-0.0050.0000.0000.0000.000
225A252GLU-1-0.963-0.97337.6870.1960.1960.0000.0000.0000.000