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: ZV69N

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 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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2535335.686735
FMO2-HF: Nuclear repulsion 2449903.827164
FMO2-HF: Total energy -85431.859571
FMO2-MP2: Total energy -85684.654289


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.
-14.964-5.3426.534-4.828-11.3290.006
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 : -0.020 / q_NPA : -0.029
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].
3A4ILE0-0.048-0.0292.812-2.804-0.4180.406-1.242-1.551-0.009
4A5LEU00.0220.0314.7980.4950.543-0.001-0.007-0.0400.000
5A6ILE0-0.024-0.0288.412-0.019-0.0190.0000.0000.0000.000
6A7ASP-1-0.770-0.85310.738-0.283-0.2830.0000.0000.0000.000
7A8ASP-1-0.836-0.92114.048-0.475-0.4750.0000.0000.0000.000
8A9THR0-0.091-0.07116.8830.0240.0240.0000.0000.0000.000
9A10ALA0-0.050-0.00713.4110.0270.0270.0000.0000.0000.000
10A11THR00.021-0.01815.350-0.019-0.0190.0000.0000.0000.000
11A12GLU-1-0.789-0.88115.993-0.566-0.5660.0000.0000.0000.000
12A13ALA0-0.032-0.00316.924-0.032-0.0320.0000.0000.0000.000
13A14VAL00.0100.01311.506-0.039-0.0390.0000.0000.0000.000
14A15ARG10.7800.86612.1120.4000.4000.0000.0000.0000.000
15A16THR0-0.044-0.03513.117-0.092-0.0920.0000.0000.0000.000
16A17LEU0-0.047-0.0139.757-0.071-0.0710.0000.0000.0000.000
17A18ILE00.023-0.0077.793-0.012-0.0120.0000.0000.0000.000
18A19ARG10.7910.8848.2110.3740.3740.0000.0000.0000.000
19A20ALA0-0.042-0.00110.662-0.002-0.0020.0000.0000.0000.000
20A21PHE0-0.003-0.0025.7680.3100.3100.0000.0000.0000.000
21A22PRO0-0.029-0.0055.109-0.180-0.1800.0000.0000.0000.000
22A23LEU0-0.031-0.0222.279-4.921-2.9951.404-0.918-2.412-0.005
23A24VAL00.0070.0002.8381.2962.4330.091-0.360-0.8680.000
24A25PRO0-0.0130.0015.090-0.186-0.159-0.001-0.005-0.0210.000
25A26VAL0-0.016-0.0057.0900.4140.4140.0000.0000.0000.000
26A27SER00.000-0.0139.7200.0170.0170.0000.0000.0000.000
27A28GLN0-0.052-0.02711.7770.1060.1060.0000.0000.0000.000
28A29PRO00.0040.0029.750-0.132-0.1320.0000.0000.0000.000
29A30PRO00.0360.0337.0350.0390.0390.0000.0000.0000.000
30A31GLU-1-0.897-0.94510.0820.2600.2600.0000.0000.0000.000
31A32GLN0-0.075-0.05311.1340.0190.0190.0000.0000.0000.000
32A33GLY00.0320.0228.8930.0770.0770.0000.0000.0000.000
33A34SER0-0.036-0.0245.289-0.093-0.0930.0000.0000.0000.000
34A35TYR00.019-0.0014.2520.2830.406-0.001-0.014-0.1080.000
35A36LEU00.005-0.0042.5430.0180.4311.476-0.293-1.5960.000
36A37LEU0-0.023-0.0124.862-0.283-0.279-0.001-0.002-0.0010.000
37A38ALA0-0.0030.0098.2960.1720.1720.0000.0000.0000.000
38A39GLU-1-0.828-0.92610.115-0.236-0.2360.0000.0000.0000.000
39A40HIS0-0.006-0.00213.7630.0450.0450.0000.0000.0000.000
40A41ASP-1-0.813-0.86115.998-0.283-0.2830.0000.0000.0000.000
41A42THR0-0.060-0.04113.5170.0580.0580.0000.0000.0000.000
42A43VAL00.0140.0017.134-0.114-0.1140.0000.0000.0000.000
43A44SER0-0.034-0.0119.1010.1800.1800.0000.0000.0000.000
44A45LEU00.001-0.0034.593-0.214-0.143-0.001-0.004-0.0650.000
45A46ARG10.8740.9297.4300.0160.0160.0000.0000.0000.000
46A47LEU00.0140.0088.0720.1640.1640.0000.0000.0000.000
47A48VAL00.0060.01010.147-0.105-0.1050.0000.0000.0000.000
48A49GLY00.0210.02112.4670.0470.0470.0000.0000.0000.000
49A50GLU-1-0.857-0.92714.5510.1770.1770.0000.0000.0000.000
50A51LYS10.8280.89915.088-0.181-0.1810.0000.0000.0000.000
51A52SER0-0.0120.00615.637-0.032-0.0320.0000.0000.0000.000
52A53ASN0-0.010-0.01311.859-0.006-0.0060.0000.0000.0000.000
53A54VAL0-0.020-0.00310.2370.0150.0150.0000.0000.0000.000
54A55ILE00.0510.01710.3380.0180.0180.0000.0000.0000.000
55A56VAL0-0.0240.01311.1050.0270.0270.0000.0000.0000.000
56A57ASP-1-0.774-0.88213.481-0.035-0.0350.0000.0000.0000.000
57A58PHE0-0.027-0.00816.2020.0350.0350.0000.0000.0000.000
58A59THR0-0.102-0.04120.198-0.006-0.0060.0000.0000.0000.000
59A73GLU-1-0.788-0.90431.2260.0950.0950.0000.0000.0000.000
60A74LEU0-0.065-0.03131.644-0.006-0.0060.0000.0000.0000.000
61A75ILE00.0640.03625.265-0.005-0.0050.0000.0000.0000.000
62A76ALA00.0540.02929.729-0.003-0.0030.0000.0000.0000.000
63A77LYS10.8230.90831.694-0.087-0.0870.0000.0000.0000.000
64A78ALA00.0000.00730.733-0.005-0.0050.0000.0000.0000.000
65A79VAL0-0.029-0.01727.869-0.003-0.0030.0000.0000.0000.000
66A80ASN0-0.010-0.01331.285-0.011-0.0110.0000.0000.0000.000
67A81HIS00.0550.01332.291-0.006-0.0060.0000.0000.0000.000
68A82THR00.0140.00733.536-0.005-0.0050.0000.0000.0000.000
69A83ALA0-0.0230.00135.894-0.005-0.0050.0000.0000.0000.000
70A84HIS10.8310.90731.512-0.024-0.0240.0000.0000.0000.000
71A85PRO0-0.0170.00130.647-0.006-0.0060.0000.0000.0000.000
72A86THR00.020-0.01227.7600.0010.0010.0000.0000.0000.000
73A87VAL0-0.027-0.02524.6110.0040.0040.0000.0000.0000.000
74A88TRP00.020-0.00722.2230.0000.0000.0000.0000.0000.000
75A89ASP-1-0.757-0.86618.9760.2610.2610.0000.0000.0000.000
76A90ALA0-0.014-0.02718.3330.0010.0010.0000.0000.0000.000
77A91THR0-0.026-0.00615.7780.0100.0100.0000.0000.0000.000
78A92ALA00.0350.03914.5180.0380.0380.0000.0000.0000.000
79A93GLY00.0520.03311.802-0.012-0.0120.0000.0000.0000.000
80A94LEU0-0.032-0.03610.671-0.007-0.0070.0000.0000.0000.000
81A95GLY00.0450.01413.047-0.084-0.0840.0000.0000.0000.000
82A96ARG10.7710.85915.843-0.384-0.3840.0000.0000.0000.000
83A97ASP-1-0.710-0.80918.6540.1980.1980.0000.0000.0000.000
84A98SER00.014-0.02718.248-0.034-0.0340.0000.0000.0000.000
85A99PHE00.0790.04519.668-0.026-0.0260.0000.0000.0000.000
86A100VAL0-0.0200.00421.419-0.020-0.0200.0000.0000.0000.000
87A101LEU0-0.030-0.03322.890-0.017-0.0170.0000.0000.0000.000
88A102ALA00.0410.03123.251-0.012-0.0120.0000.0000.0000.000
89A103SER00.007-0.00425.041-0.017-0.0170.0000.0000.0000.000
90A104LEU0-0.122-0.04527.263-0.005-0.0050.0000.0000.0000.000
91A105GLY00.0480.02929.180-0.005-0.0050.0000.0000.0000.000
92A106LEU0-0.076-0.02228.176-0.008-0.0080.0000.0000.0000.000
93A107THR0-0.0030.00026.0090.0000.0000.0000.0000.0000.000
94A108VAL00.009-0.00420.9740.0050.0050.0000.0000.0000.000
95A109THR0-0.0140.00919.447-0.015-0.0150.0000.0000.0000.000
96A110ALA0-0.006-0.00716.5010.0220.0220.0000.0000.0000.000
97A111PHE00.017-0.00115.086-0.030-0.0300.0000.0000.0000.000
98A112GLU-1-0.820-0.9059.3950.9970.9970.0000.0000.0000.000
99A113GLN00.0280.0119.496-0.232-0.2320.0000.0000.0000.000
100A114HIS00.0330.0093.229-1.603-0.6140.056-0.403-0.6420.003
101A115PRO00.017-0.0012.551-1.9180.0370.783-1.069-1.6690.010
102A116ALA00.0330.0212.301-3.053-1.9812.227-1.198-2.1020.006
103A117VAL0-0.027-0.0043.069-1.225-1.7540.0960.687-0.2540.001
104A118ALA00.0440.0226.901-0.473-0.4730.0000.0000.0000.000
105A119CYS00.0040.0195.044-0.457-0.4570.0000.0000.0000.000
106A120LEU0-0.027-0.0086.114-0.176-0.1760.0000.0000.0000.000
107A121LEU0-0.0140.0048.367-0.133-0.1330.0000.0000.0000.000
108A122SER0-0.003-0.00310.376-0.063-0.0630.0000.0000.0000.000
109A123ASP-1-0.696-0.83710.756-0.256-0.2560.0000.0000.0000.000
110A124GLY00.0150.01412.437-0.005-0.0050.0000.0000.0000.000
111A125ILE0-0.030-0.02314.450-0.007-0.0070.0000.0000.0000.000
112A126ARG10.7310.83814.4020.2280.2280.0000.0000.0000.000
113A127ARG10.8080.86812.9440.0330.0330.0000.0000.0000.000
114A128ALA00.0020.00718.2610.0050.0050.0000.0000.0000.000
115A129LEU0-0.031-0.02019.5080.0020.0020.0000.0000.0000.000
116A130LEU0-0.042-0.01619.850-0.007-0.0070.0000.0000.0000.000
117A131ASN0-0.032-0.01422.897-0.007-0.0070.0000.0000.0000.000
118A132PRO00.012-0.01324.5910.0080.0080.0000.0000.0000.000
119A133GLU-1-0.902-0.93726.3020.0290.0290.0000.0000.0000.000
120A134THR0-0.026-0.02322.7750.0120.0120.0000.0000.0000.000
121A135GLN0-0.047-0.00224.0750.0030.0030.0000.0000.0000.000
122A136ASP-1-0.820-0.89525.1220.0050.0050.0000.0000.0000.000
123A137THR0-0.005-0.01522.944-0.005-0.0050.0000.0000.0000.000
124A138ALA00.0210.00520.6030.0060.0060.0000.0000.0000.000
125A139ALA0-0.030-0.00821.517-0.007-0.0070.0000.0000.0000.000
126A140ARG10.7000.83523.773-0.025-0.0250.0000.0000.0000.000
127A141ILE0-0.025-0.00717.8980.0200.0200.0000.0000.0000.000
128A142ASN0-0.043-0.02219.193-0.032-0.0320.0000.0000.0000.000
129A143LEU00.0010.00111.2440.0240.0240.0000.0000.0000.000
130A144HIS0-0.029-0.02415.356-0.051-0.0510.0000.0000.0000.000
131A145PHE00.007-0.0056.8760.0040.0040.0000.0000.0000.000
132A146GLY00.0430.01211.171-0.094-0.0940.0000.0000.0000.000
133A147ASN00.0180.00412.0640.0750.0750.0000.0000.0000.000
134A148ALA00.0460.01313.885-0.053-0.0530.0000.0000.0000.000
135A149ALA00.002-0.00717.287-0.028-0.0280.0000.0000.0000.000
136A150GLU-1-0.891-0.94414.612-0.069-0.0690.0000.0000.0000.000
137A151GLN0-0.023-0.00915.011-0.034-0.0340.0000.0000.0000.000
138A152MET0-0.0210.01918.316-0.011-0.0110.0000.0000.0000.000
139A153PRO00.0110.00321.169-0.013-0.0130.0000.0000.0000.000
140A154ALA00.0280.02620.596-0.006-0.0060.0000.0000.0000.000
141A155LEU00.0540.03620.680-0.006-0.0060.0000.0000.0000.000
142A156VAL0-0.023-0.02423.074-0.001-0.0010.0000.0000.0000.000
143A157LYS10.7690.87625.9150.0260.0260.0000.0000.0000.000
144A158THR0-0.0300.00224.408-0.010-0.0100.0000.0000.0000.000
145A159GLN00.009-0.00424.552-0.011-0.0110.0000.0000.0000.000
146A160GLY00.0010.01928.1790.0070.0070.0000.0000.0000.000
147A161LYS10.8280.90727.830-0.028-0.0280.0000.0000.0000.000
148A162PRO00.0570.06025.574-0.004-0.0040.0000.0000.0000.000
149A163ASP-1-0.827-0.90328.3150.0260.0260.0000.0000.0000.000
150A164ILE0-0.017-0.01127.6660.0030.0030.0000.0000.0000.000
151A165VAL00.0140.02423.016-0.003-0.0030.0000.0000.0000.000
152A166TYR0-0.056-0.07121.797-0.013-0.0130.0000.0000.0000.000
153A167LEU00.0150.00921.2130.0110.0110.0000.0000.0000.000
154A168ASP-1-0.801-0.90720.1440.2820.2820.0000.0000.0000.000
155A169PRO00.0360.02417.9960.0410.0410.0000.0000.0000.000
156A170MET00.0290.05317.928-0.015-0.0150.0000.0000.0000.000
157A184MET00.0410.00726.131-0.008-0.0080.0000.0000.0000.000
158A185ALA00.0230.01427.1750.0060.0060.0000.0000.0000.000
159A186TYR00.0160.00427.7250.0060.0060.0000.0000.0000.000
160A187PHE00.0260.00822.373-0.004-0.0040.0000.0000.0000.000
161A188HIS00.0510.00423.2910.0000.0000.0000.0000.0000.000
162A189ARG10.9400.98323.286-0.131-0.1310.0000.0000.0000.000
163A190LEU0-0.028-0.02525.029-0.001-0.0010.0000.0000.0000.000
164A191VAL0-0.051-0.02021.433-0.013-0.0130.0000.0000.0000.000
165A192GLY00.0650.04719.3370.0190.0190.0000.0000.0000.000
166A193GLU-1-0.890-0.94717.4110.4260.4260.0000.0000.0000.000
167A194ALA0-0.023-0.01019.783-0.018-0.0180.0000.0000.0000.000
168A195GLN0-0.020-0.00622.522-0.023-0.0230.0000.0000.0000.000
169A196ASP-1-0.860-0.93717.6970.2670.2670.0000.0000.0000.000
170A197GLU-1-0.859-0.93820.1070.2240.2240.0000.0000.0000.000
171A198VAL0-0.042-0.01722.375-0.019-0.0190.0000.0000.0000.000
172A199VAL00.0060.00620.848-0.017-0.0170.0000.0000.0000.000
173A200LEU00.0190.02718.649-0.022-0.0220.0000.0000.0000.000
174A201LEU0-0.002-0.00221.667-0.017-0.0170.0000.0000.0000.000
175A202HIS00.0110.02425.209-0.010-0.0100.0000.0000.0000.000
176A203THR00.013-0.01622.226-0.018-0.0180.0000.0000.0000.000
177A204ALA00.0090.01323.873-0.014-0.0140.0000.0000.0000.000
178A205ARG10.8750.93225.296-0.091-0.0910.0000.0000.0000.000
179A206GLN0-0.0020.00227.461-0.009-0.0090.0000.0000.0000.000
180A207THR0-0.050-0.02324.384-0.015-0.0150.0000.0000.0000.000
181A208ALA00.0170.00927.371-0.009-0.0090.0000.0000.0000.000
182A209LYS10.7720.89929.393-0.021-0.0210.0000.0000.0000.000
183A210LYS10.8630.92732.383-0.033-0.0330.0000.0000.0000.000
184A211ARG10.8130.88131.738-0.065-0.0650.0000.0000.0000.000
185A212VAL00.0320.02126.291-0.001-0.0010.0000.0000.0000.000
186A213VAL0-0.029-0.01227.490-0.001-0.0010.0000.0000.0000.000
187A214VAL00.0300.00824.9820.0110.0110.0000.0000.0000.000
188A215LYS10.8150.91522.967-0.244-0.2440.0000.0000.0000.000
189A216ARG10.8360.90123.457-0.211-0.2110.0000.0000.0000.000
190A217PRO00.0940.03425.791-0.011-0.0110.0000.0000.0000.000
191A218ARG10.8860.95728.483-0.128-0.1280.0000.0000.0000.000
192A219LEU00.000-0.00932.283-0.009-0.0090.0000.0000.0000.000
193A220GLY00.0140.02529.2110.0000.0000.0000.0000.0000.000
194A221GLU-1-0.885-0.93628.1700.1870.1870.0000.0000.0000.000
195A222HIS0-0.051-0.05328.7040.0050.0050.0000.0000.0000.000
196A223LEU00.0420.02822.8330.0020.0020.0000.0000.0000.000
197A224ALA00.0220.00425.928-0.018-0.0180.0000.0000.0000.000
198A225GLY0-0.0240.00027.260-0.013-0.0130.0000.0000.0000.000
199A226GLN0-0.089-0.03929.820-0.020-0.0200.0000.0000.0000.000
200A227ALA00.0320.01532.0670.0050.0050.0000.0000.0000.000
201A228PRO0-0.049-0.01032.747-0.004-0.0040.0000.0000.0000.000
202A229ALA0-0.048-0.02534.392-0.006-0.0060.0000.0000.0000.000
203A230TYR0-0.098-0.08735.786-0.003-0.0030.0000.0000.0000.000
204A231GLN0-0.032-0.02234.1550.0000.0000.0000.0000.0000.000
205A232TYR00.0110.02233.693-0.007-0.0070.0000.0000.0000.000
206A233THR00.0170.00233.5860.0110.0110.0000.0000.0000.000
207A234GLY00.0350.01634.037-0.007-0.0070.0000.0000.0000.000
208A235LYS10.9230.95232.436-0.110-0.1100.0000.0000.0000.000
209A236SER00.018-0.00330.107-0.004-0.0040.0000.0000.0000.000
210A237THR0-0.017-0.00527.9970.0110.0110.0000.0000.0000.000
211A238ARG10.7340.82229.647-0.159-0.1590.0000.0000.0000.000
212A239PHE00.0400.02126.4790.0110.0110.0000.0000.0000.000
213A240ASP-1-0.677-0.79929.8430.1230.1230.0000.0000.0000.000
214A241VAL0-0.015-0.01230.1310.0060.0060.0000.0000.0000.000
215A242TYR00.006-0.01229.366-0.004-0.0040.0000.0000.0000.000
216A243LEU00.0330.02232.0600.0000.0000.0000.0000.0000.000
217A244PRO00.0230.00932.1510.0040.0040.0000.0000.0000.000
218A245TYR0-0.063-0.04629.6210.0000.0000.0000.0000.0000.000
219A246GLY0-0.002-0.00134.586-0.005-0.0050.0000.0000.0000.000
220A247ALA0-0.044-0.01036.983-0.003-0.0030.0000.0000.0000.000
221A248ASP-1-0.828-0.91338.7190.0420.0420.0000.0000.0000.000
222A249LYS10.9720.96340.224-0.058-0.0580.0000.0000.0000.000
223A250GLY0-0.049-0.01941.5330.0010.0010.0000.0000.0000.000
224A251LEU0-0.028-0.01042.636-0.002-0.0020.0000.0000.0000.000
225A252GLU-1-0.816-0.84437.8720.0570.0570.0000.0000.0000.000