Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: XYV42

Calculation Name: 3U6G-A-Xray21

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U6G

Chain ID: A

ChEMBL ID:

UniProt ID: A6L6K5

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1153276.554717
FMO2-HF: Nuclear repulsion 1099488.734628
FMO2-HF: Total energy -53787.820089
FMO2-MP2: Total energy -53940.369836


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:29:ACE)


Summations of interaction energy for fragment #1(A:29:ACE)
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.
0.342.247-0.012-0.716-1.176-0.001
Interaction energy analysis for fragmet #1(A:29:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / 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].
3A31SER00.004-0.0033.8440.1821.519-0.012-0.593-0.731-0.001
4A32ASP-1-0.887-0.9184.1940.0380.435-0.001-0.082-0.3140.000
5A33PHE0-0.048-0.0223.8520.0440.2070.002-0.040-0.1230.000
6A34GLN00.0530.0657.943-0.014-0.0140.0000.0000.0000.000
7A35THR0-0.059-0.04111.4190.0130.0130.0000.0000.0000.000
8A36GLY00.0360.02614.0420.0340.0340.0000.0000.0000.000
9A37ILE0-0.045-0.00717.378-0.010-0.0100.0000.0000.0000.000
10A38HIS00.0060.05712.5410.0510.0510.0000.0000.0000.000
11A39LYS10.8660.90518.0340.1230.1230.0000.0000.0000.000
12A40ILE00.0180.00618.0720.0000.0000.0000.0000.0000.000
13A41VAL0-0.032-0.01521.6680.0040.0040.0000.0000.0000.000
14A42ILE0-0.001-0.00724.4600.0030.0030.0000.0000.0000.000
15A43GLN0-0.034-0.02226.7960.0010.0010.0000.0000.0000.000
16A44GLN00.0230.02429.7520.0050.0050.0000.0000.0000.000
17A45SER0-0.038-0.01932.2790.0000.0000.0000.0000.0000.000
18A46GLY00.0610.04135.2320.0020.0020.0000.0000.0000.000
19A47ASP-1-0.848-0.92038.006-0.006-0.0060.0000.0000.0000.000
20A48THR0-0.005-0.02136.0460.0000.0000.0000.0000.0000.000
21A49ASP-1-0.897-0.94738.094-0.016-0.0160.0000.0000.0000.000
22A50SER0-0.039-0.00939.9610.0010.0010.0000.0000.0000.000
23A51PHE0-0.040-0.00534.6070.0020.0020.0000.0000.0000.000
24A52GLU-1-0.843-0.88534.649-0.013-0.0130.0000.0000.0000.000
25A53VAL0-0.009-0.01329.2550.0020.0020.0000.0000.0000.000
26A54SER0-0.045-0.02829.379-0.005-0.0050.0000.0000.0000.000
27A55VAL0-0.011-0.01124.4630.0020.0020.0000.0000.0000.000
28A56SER0-0.012-0.02322.983-0.002-0.0020.0000.0000.0000.000
29A57ILE0-0.009-0.01320.405-0.001-0.0010.0000.0000.0000.000
30A58GLY00.0410.03319.1220.0080.0080.0000.0000.0000.000
31A59GLY00.0500.02015.609-0.005-0.0050.0000.0000.0000.000
32A60ALA0-0.0180.03712.7790.0290.0290.0000.0000.0000.000
33A61ASP-1-0.691-0.82114.278-0.319-0.3190.0000.0000.0000.000
34A62LYS10.9050.94110.2770.8420.8420.0000.0000.0000.000
35A63GLY00.0220.02614.4380.0120.0120.0000.0000.0000.000
36A64GLY00.0350.03816.7430.0390.0390.0000.0000.0000.000
37A65PRO00.0360.02916.987-0.036-0.0360.0000.0000.0000.000
38A66ALA00.0020.01817.4000.0070.0070.0000.0000.0000.000
39A67LYS10.9420.98019.2430.1620.1620.0000.0000.0000.000
40A68LEU00.0200.01920.489-0.015-0.0150.0000.0000.0000.000
41A69TYR0-0.040-0.03323.9320.0060.0060.0000.0000.0000.000
42A70ASN00.0800.04126.251-0.004-0.0040.0000.0000.0000.000
43A71ASP-1-0.860-0.92128.900-0.066-0.0660.0000.0000.0000.000
44A72LYS10.8350.92830.2630.0570.0570.0000.0000.0000.000
45A73GLY00.0200.02129.3110.0000.0000.0000.0000.0000.000
46A74GLU-1-0.983-0.97230.395-0.069-0.0690.0000.0000.0000.000
47A75TYR0-0.060-0.06125.933-0.008-0.0080.0000.0000.0000.000
48A76ILE0-0.016-0.02226.4240.0080.0080.0000.0000.0000.000
49A77GLY00.0030.00827.3960.0060.0060.0000.0000.0000.000
50A78ASP-1-0.793-0.85722.220-0.133-0.1330.0000.0000.0000.000
51A79SER0-0.0080.00422.207-0.006-0.0060.0000.0000.0000.000
52A80TYR00.0320.00824.0560.0060.0060.0000.0000.0000.000
53A81SER00.0510.04824.8200.0020.0020.0000.0000.0000.000
54A82ALA00.0210.03027.3910.0010.0010.0000.0000.0000.000
55A83GLN00.0750.05129.5810.0030.0030.0000.0000.0000.000
56A84ILE0-0.034-0.01828.203-0.003-0.0030.0000.0000.0000.000
57A85ARG10.9970.99532.1770.0360.0360.0000.0000.0000.000
58A86THR0-0.025-0.00934.1800.0010.0010.0000.0000.0000.000
59A87ALA00.0670.02734.3040.0000.0000.0000.0000.0000.000
60A88THR0-0.007-0.01029.9660.0000.0000.0000.0000.0000.000
61A89MET0-0.0120.04626.018-0.001-0.0010.0000.0000.0000.000
62A90SER00.019-0.01726.149-0.002-0.0020.0000.0000.0000.000
63A91CYS0-0.0090.01323.5380.0000.0000.0000.0000.0000.000
64A92CYS00.000-0.00121.818-0.004-0.0040.0000.0000.0000.000
65A93THR00.0300.00517.9280.0040.0040.0000.0000.0000.000
66A94ASN00.010-0.00620.469-0.011-0.0110.0000.0000.0000.000
67A95GLY00.0430.02119.861-0.016-0.0160.0000.0000.0000.000
68A96ASN00.0110.00917.754-0.024-0.0240.0000.0000.0000.000
69A97ALA0-0.0040.01915.688-0.053-0.0530.0000.0000.0000.000
70A98PHE0-0.012-0.0199.677-0.036-0.0360.0000.0000.0000.000
71A99PHE00.0280.00110.379-0.082-0.0820.0000.0000.0000.000
72A100MET0-0.0030.02112.2550.0380.0380.0000.0000.0000.000
73A101THR0-0.0060.00514.0810.0150.0150.0000.0000.0000.000
74A102CYS0-0.011-0.00816.3880.0050.0050.0000.0000.0000.000
75A103ALA00.0110.01719.5100.0100.0100.0000.0000.0000.000
76A104GLY00.038-0.00221.168-0.006-0.0060.0000.0000.0000.000
77A105SER0-0.0180.00024.6880.0070.0070.0000.0000.0000.000
78A106VAL00.000-0.00127.688-0.005-0.0050.0000.0000.0000.000
79A107SER00.0200.00630.6050.0040.0040.0000.0000.0000.000
80A108SER00.016-0.00933.849-0.002-0.0020.0000.0000.0000.000
81A109ILE0-0.014-0.00937.4750.0020.0020.0000.0000.0000.000
82A110SER0-0.029-0.00240.6130.0000.0000.0000.0000.0000.000
83A111GLU-1-0.947-0.97042.4870.0020.0020.0000.0000.0000.000
84A112ALA0-0.012-0.02042.3000.0000.0000.0000.0000.0000.000
85A113GLY0-0.066-0.04341.605-0.001-0.0010.0000.0000.0000.000
86A114LYS10.9080.97140.2610.0020.0020.0000.0000.0000.000
87A115ARG10.9400.96237.358-0.002-0.0020.0000.0000.0000.000
88A116LEU0-0.0050.01532.166-0.002-0.0020.0000.0000.0000.000
89A117HIS0-0.028-0.02529.6900.0000.0000.0000.0000.0000.000
90A118ILE0-0.018-0.00626.427-0.004-0.0040.0000.0000.0000.000
91A119THR00.0170.01625.7120.0040.0040.0000.0000.0000.000
92A120VAL0-0.024-0.01321.371-0.005-0.0050.0000.0000.0000.000
93A121ILE0-0.0090.00721.3620.0040.0040.0000.0000.0000.000
94A122GLY00.0360.01517.822-0.007-0.0070.0000.0000.0000.000
95A123TYR0-0.014-0.00518.5190.0100.0100.0000.0000.0000.000
96A124ILE00.0410.02012.923-0.018-0.0180.0000.0000.0000.000
97A125ASP-1-0.775-0.83117.431-0.218-0.2180.0000.0000.0000.000
98A126ASP-1-0.867-0.91020.438-0.104-0.1040.0000.0000.0000.000
99A127LYS10.9490.99116.6790.1460.1460.0000.0000.0000.000
100A128GLU-1-0.768-0.83818.917-0.064-0.0640.0000.0000.0000.000
101A129VAL0-0.020-0.02414.2020.0090.0090.0000.0000.0000.000
102A130ASN0-0.0110.00512.8130.0440.0440.0000.0000.0000.000
103A131ARG10.8210.88017.0980.0240.0240.0000.0000.0000.000
104A132LEU0-0.066-0.01220.3280.0140.0140.0000.0000.0000.000
105A133GLU-1-0.849-0.93522.047-0.019-0.0190.0000.0000.0000.000
106A134LYS10.8700.94123.134-0.012-0.0120.0000.0000.0000.000
107A135GLU-1-0.762-0.87027.694-0.004-0.0040.0000.0000.0000.000
108A136TYR0-0.0030.03227.0160.0060.0060.0000.0000.0000.000
109A137ILE00.014-0.01433.193-0.002-0.0020.0000.0000.0000.000
110A138THR0-0.0130.00036.8100.0020.0020.0000.0000.0000.000
111A139ASP-1-0.840-0.91738.6470.0150.0150.0000.0000.0000.000
112A140GLY0-0.0120.00740.6200.0010.0010.0000.0000.0000.000
113A141ASN0-0.059-0.01339.255-0.001-0.0010.0000.0000.0000.000
114A142THR0-0.020-0.02436.834-0.001-0.0010.0000.0000.0000.000
115A143LEU0-0.0220.01532.6410.0020.0020.0000.0000.0000.000
116A144ILE0-0.010-0.01829.716-0.004-0.0040.0000.0000.0000.000
117A145GLU-1-0.832-0.85228.1760.0270.0270.0000.0000.0000.000
118A146THR0-0.035-0.04124.109-0.005-0.0050.0000.0000.0000.000
119A147PHE0-0.008-0.00122.0060.0060.0060.0000.0000.0000.000
120A148SER0-0.033-0.02316.953-0.014-0.0140.0000.0000.0000.000
121A149VAL00.0210.01916.6100.0140.0140.0000.0000.0000.000
122A150SER0-0.011-0.01112.282-0.032-0.0320.0000.0000.0000.000
123A151THR0-0.006-0.05213.4610.0200.0200.0000.0000.0000.000
124A152LYS10.8940.9685.246-0.237-0.2370.0000.0000.0000.000
125A153GLU-1-0.902-0.9408.204-0.158-0.1580.0000.0000.0000.000
126A154ILE-1-0.983-0.9818.3570.2100.2100.0000.0000.0000.000
127A157HOH0-0.015-0.01920.012-0.005-0.0050.0000.0000.0000.000
128A160HOH00.0380.03628.170-0.003-0.0030.0000.0000.0000.000
129A164HOH0-0.0120.00530.8270.0010.0010.0000.0000.0000.000
130A170HOH00.0050.00420.0450.0020.0020.0000.0000.0000.000
131A175HOH0-0.048-0.03328.3330.0000.0000.0000.0000.0000.000
132A178HOH0-0.032-0.04025.4380.0010.0010.0000.0000.0000.000
133A181HOH00.000-0.00534.4260.0000.0000.0000.0000.0000.000
134A190HOH0-0.026-0.02020.5890.0040.0040.0000.0000.0000.000
135A194HOH0-0.028-0.02029.028-0.001-0.0010.0000.0000.0000.000
136A196HOH00.0340.01619.868-0.003-0.0030.0000.0000.0000.000
137A198HOH0-0.074-0.07220.1940.0020.0020.0000.0000.0000.000
138A199HOH0-0.019-0.02318.8820.0050.0050.0000.0000.0000.000
139A201HOH00.0320.02826.959-0.001-0.0010.0000.0000.0000.000
140A203HOH0-0.035-0.02421.3140.0070.0070.0000.0000.0000.000
141A204HOH0-0.009-0.00432.294-0.001-0.0010.0000.0000.0000.000
142A206HOH0-0.020-0.01821.8680.0040.0040.0000.0000.0000.000
143A207HOH0-0.012-0.01521.3420.0070.0070.0000.0000.0000.000
144A209HOH0-0.012-0.00924.2020.0000.0000.0000.0000.0000.000
145A212HOH0-0.0010.00625.089-0.006-0.0060.0000.0000.0000.000
146A213HOH00.0210.02418.9840.0040.0040.0000.0000.0000.000
147A224HOH00.006-0.00715.207-0.018-0.0180.0000.0000.0000.000
148A225HOH0-0.042-0.02635.5760.0000.0000.0000.0000.0000.000
149A228HOH0-0.006-0.00323.705-0.003-0.0030.0000.0000.0000.000
150A236HOH0-0.057-0.06710.403-0.046-0.0460.0000.0000.0000.000
151A238HOH0-0.010-0.01825.6680.0020.0020.0000.0000.0000.000
152A240HOH00.020-0.01026.043-0.001-0.0010.0000.0000.0000.000
153A243HOH0-0.015-0.01420.3740.0030.0030.0000.0000.0000.000
154A244HOH0-0.019-0.02328.7770.0000.0000.0000.0000.0000.000
155A246HOH0-0.0010.01625.9220.0000.0000.0000.0000.0000.000
156A247HOH0-0.076-0.05021.4230.0000.0000.0000.0000.0000.000
157A248HOH0-0.053-0.04343.3210.0000.0000.0000.0000.0000.000
158A253HOH0-0.043-0.02518.2410.0060.0060.0000.0000.0000.000
159A256HOH00.0450.04228.125-0.002-0.0020.0000.0000.0000.000
160A259HOH00.0280.0154.658-0.071-0.061-0.001-0.001-0.0080.000
161A266HOH0-0.057-0.03817.345-0.001-0.0010.0000.0000.0000.000
162A268HOH0-0.018-0.03529.5050.0010.0010.0000.0000.0000.000
163A271HOH0-0.029-0.03322.1300.0000.0000.0000.0000.0000.000
164A273HOH0-0.042-0.04416.8040.0000.0000.0000.0000.0000.000
165A275HOH0-0.030-0.01824.2650.0000.0000.0000.0000.0000.000
166A280HOH0-0.031-0.02034.895-0.001-0.0010.0000.0000.0000.000
167A281HOH0-0.062-0.05717.2810.0070.0070.0000.0000.0000.000
168A294HOH0-0.028-0.02632.7880.0010.0010.0000.0000.0000.000
169A298HOH0-0.058-0.03619.2390.0010.0010.0000.0000.0000.000
170A299HOH0-0.057-0.04527.5300.0000.0000.0000.0000.0000.000
171A300HOH00.009-0.00437.8630.0000.0000.0000.0000.0000.000
172A301HOH00.0100.00513.1480.0050.0050.0000.0000.0000.000
173A303HOH00.000-0.00232.395-0.001-0.0010.0000.0000.0000.000
174A305HOH0-0.041-0.07016.5830.0090.0090.0000.0000.0000.000
175A312HOH0-0.041-0.03019.9010.0050.0050.0000.0000.0000.000
176A314HOH00.0350.02427.962-0.003-0.0030.0000.0000.0000.000
177A317HOH0-0.015-0.02024.8300.0010.0010.0000.0000.0000.000
178A319HOH0-0.028-0.02122.256-0.001-0.0010.0000.0000.0000.000
179A320HOH00.0090.01226.662-0.001-0.0010.0000.0000.0000.000
180A322HOH0-0.048-0.03718.905-0.005-0.0050.0000.0000.0000.000
181A323HOH0-0.031-0.02027.6000.0010.0010.0000.0000.0000.000
182A327HOH00.0460.02332.873-0.003-0.0030.0000.0000.0000.000
183A331HOH0-0.023-0.01931.0610.0000.0000.0000.0000.0000.000
184A333HOH00.0300.02746.2680.0000.0000.0000.0000.0000.000
185A336HOH0-0.013-0.02211.4330.0010.0010.0000.0000.0000.000
186A337HOH0-0.012-0.00342.1290.0000.0000.0000.0000.0000.000
187A339HOH0-0.036-0.02119.7170.0000.0000.0000.0000.0000.000
188A343HOH00.0220.0359.470-0.025-0.0250.0000.0000.0000.000
189A350HOH0-0.027-0.01838.323-0.001-0.0010.0000.0000.0000.000
190A354HOH0-0.040-0.05631.7180.0000.0000.0000.0000.0000.000
191A355HOH0-0.096-0.09023.417-0.001-0.0010.0000.0000.0000.000
192A366HOH0-0.041-0.03343.3710.0000.0000.0000.0000.0000.000
193A368HOH00.0260.02345.6430.0000.0000.0000.0000.0000.000
194A369HOH0-0.048-0.03820.1560.0090.0090.0000.0000.0000.000
195A370HOH0-0.029-0.01822.1450.0020.0020.0000.0000.0000.000
196A378HOH00.0350.02039.8590.0010.0010.0000.0000.0000.000
197A379HOH0-0.080-0.06735.8000.0000.0000.0000.0000.0000.000
198A389HOH00.000-0.00433.343-0.001-0.0010.0000.0000.0000.000
199A392HOH0-0.027-0.01737.1070.0000.0000.0000.0000.0000.000
200B158HOH0-0.072-0.06830.2060.0000.0000.0000.0000.0000.000
201B205HOH0-0.029-0.01814.0780.0020.0020.0000.0000.0000.000
202B231HOH0-0.035-0.02212.816-0.041-0.0410.0000.0000.0000.000