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

tag_button

FMODB ID: 6YN5Z

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 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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2533505.54392
FMO2-HF: Nuclear repulsion 2448074.083085
FMO2-HF: Total energy -85431.460835
FMO2-MP2: Total energy -85684.308795


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.
-14.476-4.9144.825-4.522-9.8670.006
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 : -0.034 / q_NPA : -0.033
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].
3A4ILE0-0.043-0.0312.757-2.6540.0980.449-1.480-1.721-0.011
4A5LEU00.0040.0164.8260.3920.432-0.001-0.007-0.0320.000
5A6ILE0-0.032-0.0378.4000.1170.1170.0000.0000.0000.000
6A7ASP-1-0.776-0.85010.826-0.281-0.2810.0000.0000.0000.000
7A8ASP-1-0.887-0.96013.966-0.433-0.4330.0000.0000.0000.000
8A9THR0-0.100-0.07916.8440.0220.0220.0000.0000.0000.000
9A10ALA0-0.079-0.02213.4700.0310.0310.0000.0000.0000.000
10A11THR00.023-0.02315.418-0.020-0.0200.0000.0000.0000.000
11A12GLU-1-0.784-0.89116.158-0.526-0.5260.0000.0000.0000.000
12A13ALA0-0.028-0.00817.072-0.034-0.0340.0000.0000.0000.000
13A14VAL00.0150.01511.595-0.024-0.0240.0000.0000.0000.000
14A15ARG10.8530.92312.3650.4060.4060.0000.0000.0000.000
15A16THR0-0.050-0.04313.308-0.095-0.0950.0000.0000.0000.000
16A17LEU0-0.037-0.0049.946-0.052-0.0520.0000.0000.0000.000
17A18ILE00.028-0.0058.097-0.007-0.0070.0000.0000.0000.000
18A19ARG10.7940.9018.7200.3740.3740.0000.0000.0000.000
19A20ALA0-0.0410.00110.969-0.026-0.0260.0000.0000.0000.000
20A21PHE0-0.010-0.0105.9610.2660.2660.0000.0000.0000.000
21A22PRO0-0.0250.0065.584-0.188-0.1880.0000.0000.0000.000
22A23LEU0-0.040-0.0352.439-3.278-1.9570.637-0.420-1.538-0.002
23A24VAL00.0160.0053.1671.3672.2850.017-0.310-0.6260.000
24A25PRO0-0.022-0.0015.184-0.236-0.214-0.001-0.003-0.0170.000
25A26VAL0-0.008-0.0027.1590.3650.3650.0000.0000.0000.000
26A27SER0-0.004-0.0149.6290.0510.0510.0000.0000.0000.000
27A28GLN0-0.026-0.01311.8310.1080.1080.0000.0000.0000.000
28A29PRO0-0.005-0.0029.546-0.118-0.1180.0000.0000.0000.000
29A30PRO00.0330.0316.7200.0340.0340.0000.0000.0000.000
30A31GLU-1-0.900-0.9479.6430.2390.2390.0000.0000.0000.000
31A32GLN0-0.075-0.05810.6620.0410.0410.0000.0000.0000.000
32A33GLY00.0270.0248.4210.0900.0900.0000.0000.0000.000
33A34SER0-0.004-0.0214.690-0.183-0.136-0.001-0.005-0.0400.000
34A35TYR0-0.012-0.0083.681-0.0190.2010.004-0.046-0.1780.000
35A36LEU00.0000.0002.777-0.0640.7170.737-0.226-1.293-0.001
36A37LEU0-0.0090.0064.831-0.451-0.437-0.001-0.002-0.0110.000
37A38ALA0-0.001-0.0038.2720.1520.1520.0000.0000.0000.000
38A39GLU-1-0.836-0.93110.260-0.214-0.2140.0000.0000.0000.000
39A40HIS00.0020.00013.8130.0500.0500.0000.0000.0000.000
40A41ASP-1-0.793-0.85716.031-0.226-0.2260.0000.0000.0000.000
41A42THR0-0.046-0.02013.6390.0640.0640.0000.0000.0000.000
42A43VAL00.0120.0027.147-0.095-0.0950.0000.0000.0000.000
43A44SER0-0.032-0.0099.1710.1590.1590.0000.0000.0000.000
44A45LEU0-0.020-0.0204.501-0.182-0.098-0.001-0.007-0.0770.000
45A46ARG10.8690.9327.053-0.133-0.1330.0000.0000.0000.000
46A47LEU00.0220.0117.6830.2260.2260.0000.0000.0000.000
47A48VAL00.0060.0079.976-0.111-0.1110.0000.0000.0000.000
48A49GLY00.0140.01712.1510.0450.0450.0000.0000.0000.000
49A50GLU-1-0.869-0.93614.2190.2210.2210.0000.0000.0000.000
50A51LYS10.8450.90214.730-0.208-0.2080.0000.0000.0000.000
51A52SER0-0.0240.00915.197-0.027-0.0270.0000.0000.0000.000
52A53ASN0-0.001-0.01011.9620.0050.0050.0000.0000.0000.000
53A54VAL0-0.0100.00410.053-0.009-0.0090.0000.0000.0000.000
54A55ILE00.0580.02610.4930.0280.0280.0000.0000.0000.000
55A56VAL0-0.0230.00911.2490.0220.0220.0000.0000.0000.000
56A57ASP-1-0.801-0.91013.7270.0510.0510.0000.0000.0000.000
57A58PHE0-0.060-0.02116.1750.0200.0200.0000.0000.0000.000
58A59THR0-0.088-0.03319.999-0.011-0.0110.0000.0000.0000.000
59A73GLU-1-0.858-0.94231.9330.1200.1200.0000.0000.0000.000
60A74LEU0-0.103-0.05131.246-0.006-0.0060.0000.0000.0000.000
61A75ILE00.0700.03425.314-0.006-0.0060.0000.0000.0000.000
62A76ALA00.0640.03429.784-0.004-0.0040.0000.0000.0000.000
63A77LYS10.9040.95531.734-0.105-0.1050.0000.0000.0000.000
64A78ALA0-0.0060.00830.528-0.006-0.0060.0000.0000.0000.000
65A79VAL0-0.009-0.00427.908-0.003-0.0030.0000.0000.0000.000
66A80ASN0-0.032-0.03031.326-0.013-0.0130.0000.0000.0000.000
67A81HIS00.0870.02032.265-0.006-0.0060.0000.0000.0000.000
68A82THR0-0.0090.01333.633-0.006-0.0060.0000.0000.0000.000
69A83ALA0-0.023-0.00336.173-0.006-0.0060.0000.0000.0000.000
70A84HIS10.8280.91231.992-0.049-0.0490.0000.0000.0000.000
71A85PRO0-0.0130.00231.158-0.007-0.0070.0000.0000.0000.000
72A86THR00.017-0.00428.0330.0050.0050.0000.0000.0000.000
73A87VAL0-0.012-0.01724.5440.0040.0040.0000.0000.0000.000
74A88TRP00.015-0.00422.4300.0000.0000.0000.0000.0000.000
75A89ASP-1-0.799-0.88919.2020.3100.3100.0000.0000.0000.000
76A90ALA00.002-0.02618.5350.0080.0080.0000.0000.0000.000
77A91THR0-0.011-0.00315.7730.0000.0000.0000.0000.0000.000
78A92ALA00.0420.04114.3280.0340.0340.0000.0000.0000.000
79A93GLY00.0710.05312.141-0.016-0.0160.0000.0000.0000.000
80A94LEU0-0.036-0.04210.5150.0090.0090.0000.0000.0000.000
81A95GLY00.0320.01313.133-0.089-0.0890.0000.0000.0000.000
82A96ARG10.8200.90516.068-0.444-0.4440.0000.0000.0000.000
83A97ASP-1-0.723-0.84218.8730.2390.2390.0000.0000.0000.000
84A98SER00.005-0.01718.306-0.036-0.0360.0000.0000.0000.000
85A99PHE00.0840.04319.917-0.032-0.0320.0000.0000.0000.000
86A100VAL00.0000.01821.610-0.026-0.0260.0000.0000.0000.000
87A101LEU0-0.023-0.02323.084-0.021-0.0210.0000.0000.0000.000
88A102ALA00.0400.02623.378-0.016-0.0160.0000.0000.0000.000
89A103SER0-0.019-0.02725.209-0.018-0.0180.0000.0000.0000.000
90A104LEU0-0.129-0.04427.338-0.009-0.0090.0000.0000.0000.000
91A105GLY00.0320.01828.973-0.008-0.0080.0000.0000.0000.000
92A106LEU0-0.092-0.03528.070-0.011-0.0110.0000.0000.0000.000
93A107THR00.0110.00626.0180.0030.0030.0000.0000.0000.000
94A108VAL0-0.015-0.01820.9870.0020.0020.0000.0000.0000.000
95A109THR0-0.032-0.00919.983-0.019-0.0190.0000.0000.0000.000
96A110ALA00.008-0.00216.2830.0170.0170.0000.0000.0000.000
97A111PHE00.0330.00515.508-0.036-0.0360.0000.0000.0000.000
98A112GLU-1-0.820-0.9099.5481.0891.0890.0000.0000.0000.000
99A113GLN00.0410.0299.546-0.222-0.2220.0000.0000.0000.000
100A114HIS00.0170.0053.035-2.252-1.0450.115-0.525-0.7970.005
101A115PRO00.0410.0082.882-1.4850.1410.242-0.761-1.1070.006
102A116ALA00.0380.0232.239-3.024-2.2602.565-1.171-2.1590.009
103A117VAL0-0.023-0.0053.183-1.598-1.8320.0640.441-0.2710.000
104A118ALA00.0440.0236.937-0.530-0.5300.0000.0000.0000.000
105A119CYS0-0.0150.0115.072-0.519-0.5190.0000.0000.0000.000
106A120LEU0-0.033-0.0136.114-0.224-0.2240.0000.0000.0000.000
107A121LEU0-0.012-0.0018.362-0.169-0.1690.0000.0000.0000.000
108A122SER0-0.002-0.00510.441-0.094-0.0940.0000.0000.0000.000
109A123ASP-1-0.706-0.84510.698-0.165-0.1650.0000.0000.0000.000
110A124GLY00.0180.01512.406-0.022-0.0220.0000.0000.0000.000
111A125ILE0-0.017-0.01714.518-0.022-0.0220.0000.0000.0000.000
112A126ARG10.7240.83614.4040.1470.1470.0000.0000.0000.000
113A127ARG10.8180.87812.892-0.068-0.0680.0000.0000.0000.000
114A128ALA0-0.0010.00718.263-0.001-0.0010.0000.0000.0000.000
115A129LEU0-0.026-0.00719.850-0.004-0.0040.0000.0000.0000.000
116A130LEU0-0.040-0.01620.178-0.008-0.0080.0000.0000.0000.000
117A131ASN00.0140.01523.044-0.012-0.0120.0000.0000.0000.000
118A132PRO00.0600.00824.6700.0060.0060.0000.0000.0000.000
119A133GLU-1-0.956-0.97226.4790.0630.0630.0000.0000.0000.000
120A134THR0-0.036-0.02623.0560.0140.0140.0000.0000.0000.000
121A135GLN0-0.064-0.00124.3300.0050.0050.0000.0000.0000.000
122A136ASP-1-0.820-0.90025.3260.0370.0370.0000.0000.0000.000
123A137THR00.000-0.01023.477-0.004-0.0040.0000.0000.0000.000
124A138ALA00.0240.00420.7600.0090.0090.0000.0000.0000.000
125A139ALA0-0.0160.00121.667-0.004-0.0040.0000.0000.0000.000
126A140ARG10.7120.85424.124-0.061-0.0610.0000.0000.0000.000
127A141ILE0-0.031-0.00818.3290.0180.0180.0000.0000.0000.000
128A142ASN0-0.039-0.01019.362-0.035-0.0350.0000.0000.0000.000
129A143LEU0-0.0030.00311.3960.0280.0280.0000.0000.0000.000
130A144HIS0-0.031-0.02915.595-0.051-0.0510.0000.0000.0000.000
131A145PHE00.007-0.0037.3320.0210.0210.0000.0000.0000.000
132A146GLY00.0390.00211.582-0.111-0.1110.0000.0000.0000.000
133A147ASN00.0400.00912.4120.0850.0850.0000.0000.0000.000
134A148ALA00.0520.02514.007-0.057-0.0570.0000.0000.0000.000
135A149ALA0-0.002-0.00417.267-0.034-0.0340.0000.0000.0000.000
136A150GLU-1-0.923-0.96115.365-0.048-0.0480.0000.0000.0000.000
137A151GLN0-0.011-0.00315.423-0.038-0.0380.0000.0000.0000.000
138A152MET0-0.0140.02218.547-0.012-0.0120.0000.0000.0000.000
139A153PRO00.0090.00021.326-0.013-0.0130.0000.0000.0000.000
140A154ALA00.0410.02421.084-0.007-0.0070.0000.0000.0000.000
141A155LEU00.0510.03521.063-0.010-0.0100.0000.0000.0000.000
142A156VAL0-0.040-0.02523.528-0.002-0.0020.0000.0000.0000.000
143A157LYS10.7750.88426.5440.0110.0110.0000.0000.0000.000
144A158THR0-0.0200.00225.180-0.011-0.0110.0000.0000.0000.000
145A159GLN00.0100.00524.675-0.009-0.0090.0000.0000.0000.000
146A160GLY00.0100.01928.4490.0060.0060.0000.0000.0000.000
147A161LYS10.8530.92428.239-0.037-0.0370.0000.0000.0000.000
148A162PRO00.0420.06025.846-0.005-0.0050.0000.0000.0000.000
149A163ASP-1-0.829-0.91828.7220.0450.0450.0000.0000.0000.000
150A164ILE0-0.004-0.00527.5620.0020.0020.0000.0000.0000.000
151A165VAL00.0040.02123.195-0.001-0.0010.0000.0000.0000.000
152A166TYR0-0.051-0.06721.737-0.015-0.0150.0000.0000.0000.000
153A167LEU00.005-0.00621.2400.0110.0110.0000.0000.0000.000
154A168ASP-1-0.847-0.94420.1710.3320.3320.0000.0000.0000.000
155A169PRO00.0400.02617.8400.0410.0410.0000.0000.0000.000
156A170MET00.0400.06317.648-0.004-0.0040.0000.0000.0000.000
157A184MET00.0430.00826.118-0.007-0.0070.0000.0000.0000.000
158A185ALA00.0250.01626.9110.0070.0070.0000.0000.0000.000
159A186TYR00.0250.00027.4390.0090.0090.0000.0000.0000.000
160A187PHE00.0250.00522.348-0.002-0.0020.0000.0000.0000.000
161A188HIS00.0670.01823.3190.0010.0010.0000.0000.0000.000
162A189ARG10.9300.98223.256-0.133-0.1330.0000.0000.0000.000
163A190LEU0-0.030-0.02625.261-0.002-0.0020.0000.0000.0000.000
164A191VAL0-0.030-0.01421.322-0.010-0.0100.0000.0000.0000.000
165A192GLY00.0160.02719.5630.0120.0120.0000.0000.0000.000
166A193GLU-1-0.872-0.94917.2070.4580.4580.0000.0000.0000.000
167A194ALA0-0.038-0.01719.663-0.015-0.0150.0000.0000.0000.000
168A195GLN00.0160.01222.076-0.015-0.0150.0000.0000.0000.000
169A196ASP-1-0.855-0.93017.0190.2760.2760.0000.0000.0000.000
170A197GLU-1-0.887-0.94920.0120.2520.2520.0000.0000.0000.000
171A198VAL0-0.058-0.03222.250-0.018-0.0180.0000.0000.0000.000
172A199VAL0-0.002-0.00120.883-0.017-0.0170.0000.0000.0000.000
173A200LEU00.0160.02518.740-0.020-0.0200.0000.0000.0000.000
174A201LEU00.0060.00321.738-0.016-0.0160.0000.0000.0000.000
175A202HIS00.0160.02725.265-0.010-0.0100.0000.0000.0000.000
176A203THR00.027-0.01122.347-0.019-0.0190.0000.0000.0000.000
177A204ALA00.0100.01423.945-0.014-0.0140.0000.0000.0000.000
178A205ARG10.8740.93525.449-0.104-0.1040.0000.0000.0000.000
179A206GLN0-0.007-0.00127.814-0.010-0.0100.0000.0000.0000.000
180A207THR0-0.070-0.03624.613-0.017-0.0170.0000.0000.0000.000
181A208ALA00.0150.00727.720-0.008-0.0080.0000.0000.0000.000
182A209LYS10.7690.88629.420-0.040-0.0400.0000.0000.0000.000
183A210LYS10.8630.91532.310-0.051-0.0510.0000.0000.0000.000
184A211ARG10.8380.91231.771-0.082-0.0820.0000.0000.0000.000
185A212VAL00.0230.03026.3280.0010.0010.0000.0000.0000.000
186A213VAL0-0.031-0.01427.401-0.003-0.0030.0000.0000.0000.000
187A214VAL00.0410.01524.6240.0140.0140.0000.0000.0000.000
188A215LYS10.8140.91623.318-0.290-0.2900.0000.0000.0000.000
189A216ARG10.8320.89723.055-0.245-0.2450.0000.0000.0000.000
190A217PRO00.0770.02825.745-0.012-0.0120.0000.0000.0000.000
191A218ARG10.9530.98928.234-0.153-0.1530.0000.0000.0000.000
192A219LEU0-0.024-0.02131.978-0.008-0.0080.0000.0000.0000.000
193A220GLY0-0.0020.01629.1290.0010.0010.0000.0000.0000.000
194A221GLU-1-0.870-0.92527.9260.2010.2010.0000.0000.0000.000
195A222HIS0-0.046-0.05128.8940.0020.0020.0000.0000.0000.000
196A223LEU00.0380.02622.9360.0050.0050.0000.0000.0000.000
197A224ALA00.0210.00725.920-0.019-0.0190.0000.0000.0000.000
198A225GLY0-0.031-0.00727.264-0.015-0.0150.0000.0000.0000.000
199A226GLN0-0.068-0.02730.074-0.021-0.0210.0000.0000.0000.000
200A227ALA00.0110.00732.0150.0080.0080.0000.0000.0000.000
201A228PRO0-0.054-0.01132.553-0.005-0.0050.0000.0000.0000.000
202A229ALA0-0.049-0.02134.270-0.006-0.0060.0000.0000.0000.000
203A230TYR0-0.081-0.08035.886-0.003-0.0030.0000.0000.0000.000
204A231GLN0-0.029-0.01934.0090.0010.0010.0000.0000.0000.000
205A232TYR00.0100.02333.710-0.008-0.0080.0000.0000.0000.000
206A233THR00.013-0.00433.6650.0120.0120.0000.0000.0000.000
207A234GLY00.0150.01233.795-0.008-0.0080.0000.0000.0000.000
208A235LYS10.9330.96132.465-0.138-0.1380.0000.0000.0000.000
209A236SER00.002-0.01930.256-0.006-0.0060.0000.0000.0000.000
210A237THR00.0150.00328.2940.0200.0200.0000.0000.0000.000
211A238ARG10.7240.83529.504-0.182-0.1820.0000.0000.0000.000
212A239PHE00.0410.01226.2910.0110.0110.0000.0000.0000.000
213A240ASP-1-0.716-0.82029.6960.1420.1420.0000.0000.0000.000
214A241VAL00.0160.00030.0930.0070.0070.0000.0000.0000.000
215A242TYR00.009-0.01429.273-0.005-0.0050.0000.0000.0000.000
216A243LEU00.0240.01332.498-0.001-0.0010.0000.0000.0000.000
217A244PRO00.0180.01332.2850.0040.0040.0000.0000.0000.000
218A245TYR0-0.073-0.05729.847-0.001-0.0010.0000.0000.0000.000
219A246GLY0-0.016-0.00634.761-0.005-0.0050.0000.0000.0000.000
220A247ALA0-0.0280.00637.060-0.004-0.0040.0000.0000.0000.000
221A248ASP-1-0.830-0.91738.9340.0480.0480.0000.0000.0000.000
222A249LYS10.9700.95840.524-0.066-0.0660.0000.0000.0000.000
223A250GLY0-0.052-0.02041.7250.0010.0010.0000.0000.0000.000
224A251LEU0-0.028-0.01143.165-0.002-0.0020.0000.0000.0000.000
225A252GLU-1-0.819-0.84837.9080.0710.0710.0000.0000.0000.000