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: G6GG1

Calculation Name: 1DOW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DOW

Chain ID: A

ChEMBL ID:

UniProt ID: P26231

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1957176.978115
FMO2-HF: Nuclear repulsion 1878383.009453
FMO2-HF: Total energy -78793.968663
FMO2-MP2: Total energy -79023.181047


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:57:LYS)


Summations of interaction energy for fragment #1(A:57:LYS)
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.
-7.13-1.9623.923-3.911-5.181-0.039
Interaction energy analysis for fragmet #1(A:57:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.003 / q_NPA : 0.990
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].
3A59HIS00.057-0.0042.267-11.728-7.8593.840-3.518-4.192-0.039
4A60VAL0-0.0020.0083.0033.2634.3970.085-0.383-0.8360.000
5A61LEU0-0.0100.0075.2984.4494.565-0.001-0.007-0.1080.000
6A62ALA00.0200.0117.3962.8332.8330.0000.0000.0000.000
7A63ALA00.0590.0247.9802.2822.2820.0000.0000.0000.000
8A64SER0-0.021-0.0189.2492.1582.1580.0000.0000.0000.000
9A65VAL0-0.027-0.01611.3881.8051.8050.0000.0000.0000.000
10A66GLU-1-0.853-0.90412.496-19.203-19.2030.0000.0000.0000.000
11A67GLN00.0370.01713.4820.3120.3120.0000.0000.0000.000
12A68ALA0-0.037-0.02215.2511.1771.1770.0000.0000.0000.000
13A69THR0-0.023-0.02317.0321.2271.2270.0000.0000.0000.000
14A70GLU-1-0.868-0.93617.320-15.654-15.6540.0000.0000.0000.000
15A71ASN00.0000.00219.2761.0951.0950.0000.0000.0000.000
16A72PHE0-0.012-0.00121.1390.6950.6950.0000.0000.0000.000
17A73LEU00.0180.00721.7520.6060.6060.0000.0000.0000.000
18A74GLU-1-0.798-0.85723.834-11.236-11.2360.0000.0000.0000.000
19A75LYS10.7600.85423.87112.55112.5510.0000.0000.0000.000
20A76GLY00.0440.01827.1880.4230.4230.0000.0000.0000.000
21A77ASP-1-0.755-0.85227.193-10.479-10.4790.0000.0000.0000.000
22A78LYS10.8230.90028.13510.96610.9660.0000.0000.0000.000
23A79ILE00.0190.01730.8620.3240.3240.0000.0000.0000.000
24A80ALA00.0220.01033.0070.3140.3140.0000.0000.0000.000
25A81LYS10.7890.88134.1668.9158.9150.0000.0000.0000.000
26A82GLU-1-0.805-0.89835.320-8.298-8.2980.0000.0000.0000.000
27A83SER0-0.035-0.00437.6040.2830.2830.0000.0000.0000.000
28A84GLN0-0.021-0.02039.3540.0660.0660.0000.0000.0000.000
29A85PHE0-0.003-0.00841.6510.2070.2070.0000.0000.0000.000
30A86LEU00.0180.02139.697-0.178-0.1780.0000.0000.0000.000
31A87LYS10.8970.95738.6787.5417.5410.0000.0000.0000.000
32A88GLU-1-0.903-0.94937.851-7.347-7.3470.0000.0000.0000.000
33A89GLU-1-0.851-0.94237.501-7.614-7.6140.0000.0000.0000.000
34A90LEU0-0.038-0.02134.299-0.291-0.2910.0000.0000.0000.000
35A91VAL00.0030.00233.267-0.337-0.3370.0000.0000.0000.000
36A92VAL00.0400.03032.677-0.314-0.3140.0000.0000.0000.000
37A93ALA0-0.041-0.01831.790-0.278-0.2780.0000.0000.0000.000
38A94VAL0-0.017-0.01028.144-0.431-0.4310.0000.0000.0000.000
39A95GLU-1-0.922-0.96027.901-9.482-9.4820.0000.0000.0000.000
40A96ASP-1-0.863-0.92127.758-10.545-10.5450.0000.0000.0000.000
41A97VAL0-0.027-0.02724.298-0.446-0.4460.0000.0000.0000.000
42A98ARG10.8420.88823.66210.86710.8670.0000.0000.0000.000
43A99LYS10.9640.99322.8889.5839.5830.0000.0000.0000.000
44A100GLN0-0.084-0.06822.857-0.629-0.6290.0000.0000.0000.000
45A101GLY00.0340.02019.931-0.584-0.5840.0000.0000.0000.000
46A102ASP-1-0.867-0.93818.372-14.587-14.5870.0000.0000.0000.000
47A103LEU0-0.056-0.01718.169-0.571-0.5710.0000.0000.0000.000
48A104MET0-0.047-0.01814.409-0.552-0.5520.0000.0000.0000.000
49A105LYS10.8240.92014.15916.53516.5350.0000.0000.0000.000
50A106SER0-0.015-0.01213.127-1.243-1.2430.0000.0000.0000.000
51A107ALA0-0.048-0.02413.472-0.799-0.7990.0000.0000.0000.000
52A108ALA0-0.023-0.02711.132-0.722-0.7220.0000.0000.0000.000
53A109GLY00.0360.0248.974-2.080-2.0800.0000.0000.0000.000
54A110GLU-1-0.795-0.9028.695-19.994-19.9940.0000.0000.0000.000
55A111PHE0-0.051-0.0289.741-0.287-0.2870.0000.0000.0000.000
56A112ALA0-0.014-0.0135.066-1.138-1.1380.0000.0000.0000.000
57A113ASP-1-0.850-0.9124.935-34.382-34.333-0.001-0.003-0.0450.000
58A114ASP-1-0.888-0.9456.856-19.387-19.3870.0000.0000.0000.000
59A115PRO0-0.011-0.0056.0152.0102.0100.0000.0000.0000.000
60A116CYS0-0.016-0.0179.1051.0871.0870.0000.0000.0000.000
61A117SER00.0460.03712.0001.8781.8780.0000.0000.0000.000
62A118SER00.011-0.01314.3750.0230.0230.0000.0000.0000.000
63A119VAL0-0.0200.00116.7830.3820.3820.0000.0000.0000.000
64A120LYS10.8170.91212.61419.40619.4060.0000.0000.0000.000
65A121ARG10.9660.99012.44118.41718.4170.0000.0000.0000.000
66A122GLY00.0100.00114.5780.2800.2800.0000.0000.0000.000
67A123ASN00.008-0.00217.1181.0111.0110.0000.0000.0000.000
68A124MET00.0020.03012.6200.6350.6350.0000.0000.0000.000
69A125VAL00.0240.00215.8120.4130.4130.0000.0000.0000.000
70A126ARG10.8400.90718.35713.27113.2710.0000.0000.0000.000
71A127ALA00.0370.02317.9020.5070.5070.0000.0000.0000.000
72A128ALA00.0460.02117.4480.3220.3220.0000.0000.0000.000
73A129ARG10.9450.97119.37111.78511.7850.0000.0000.0000.000
74A130ALA00.0020.01722.8370.4860.4860.0000.0000.0000.000
75A131LEU00.0440.01919.0650.4280.4280.0000.0000.0000.000
76A132LEU00.0240.00520.6780.3330.3330.0000.0000.0000.000
77A133SER0-0.054-0.02623.9670.5530.5530.0000.0000.0000.000
78A134ALA00.0000.00125.7920.3820.3820.0000.0000.0000.000
79A135VAL0-0.001-0.00423.2310.2880.2880.0000.0000.0000.000
80A136THR0-0.033-0.02626.6430.3060.3060.0000.0000.0000.000
81A137ARG10.8720.93229.3949.9479.9470.0000.0000.0000.000
82A138LEU00.0410.02528.1060.2640.2640.0000.0000.0000.000
83A139LEU0-0.018-0.01327.4450.1900.1900.0000.0000.0000.000
84A140ILE0-0.0060.00131.5730.2360.2360.0000.0000.0000.000
85A141LEU00.0170.00334.3600.2350.2350.0000.0000.0000.000
86A142ALA00.0000.00433.5100.1940.1940.0000.0000.0000.000
87A143ASP-1-0.824-0.87535.504-7.777-7.7770.0000.0000.0000.000
88A144MET00.008-0.00237.3010.1910.1910.0000.0000.0000.000
89A145ALA00.0020.01438.4780.2350.2350.0000.0000.0000.000
90A146ASP-1-0.893-0.95237.643-7.788-7.7880.0000.0000.0000.000
91A147VAL0-0.030-0.01340.7960.2340.2340.0000.0000.0000.000
92A148TYR0-0.010-0.01443.2700.2120.2120.0000.0000.0000.000
93A149LYS10.9050.95642.1957.2747.2740.0000.0000.0000.000
94A150LEU0-0.034-0.02544.8500.1610.1610.0000.0000.0000.000
95A151LEU00.010-0.00246.5950.1790.1790.0000.0000.0000.000
96A152VAL0-0.0040.00348.6180.1680.1680.0000.0000.0000.000
97A153GLN0-0.042-0.03649.0640.0840.0840.0000.0000.0000.000
98A154LEU0-0.022-0.01350.7880.1260.1260.0000.0000.0000.000
99A155LYS10.8190.90252.6605.4395.4390.0000.0000.0000.000
100A156VAL0-0.0030.00053.3890.1350.1350.0000.0000.0000.000
101A157VAL0-0.019-0.00854.3780.1170.1170.0000.0000.0000.000
102A158GLU-1-0.810-0.88156.726-5.204-5.2040.0000.0000.0000.000
103A159ASP-1-0.818-0.90958.824-5.129-5.1290.0000.0000.0000.000
104A160GLY0-0.024-0.00359.7310.0950.0950.0000.0000.0000.000
105A161ILE00.004-0.01059.0050.1020.1020.0000.0000.0000.000
106A162LEU0-0.007-0.00162.6130.1050.1050.0000.0000.0000.000
107A163LYS10.8840.93561.8485.1345.1340.0000.0000.0000.000
108A164LEU0-0.029-0.01864.3850.0740.0740.0000.0000.0000.000
109A165ARG10.8110.89566.6894.5764.5760.0000.0000.0000.000
110A166ASN00.004-0.00368.8000.1130.1130.0000.0000.0000.000
111A167ALA00.0080.02469.8160.0470.0470.0000.0000.0000.000
112A168GLY00.0310.01371.5720.0370.0370.0000.0000.0000.000
113A169ASN0-0.024-0.02674.4640.0540.0540.0000.0000.0000.000
114A170GLU-1-0.773-0.90073.865-4.225-4.2250.0000.0000.0000.000
115A171GLN00.0100.02272.754-0.082-0.0820.0000.0000.0000.000
116A172ASP-1-0.860-0.92970.748-4.503-4.5030.0000.0000.0000.000
117A173LEU0-0.055-0.01169.281-0.090-0.0900.0000.0000.0000.000
118A174GLY00.0250.01268.207-0.082-0.0820.0000.0000.0000.000
119A175ILE0-0.027-0.01366.285-0.100-0.1000.0000.0000.0000.000
120A176GLN00.018-0.00464.909-0.163-0.1630.0000.0000.0000.000
121A177TYR0-0.019-0.00262.741-0.128-0.1280.0000.0000.0000.000
122A178LYS10.9170.94762.3974.7774.7770.0000.0000.0000.000
123A179ALA00.0020.01060.558-0.097-0.0970.0000.0000.0000.000
124A180LEU0-0.0150.00958.628-0.105-0.1050.0000.0000.0000.000
125A181LYS10.8270.89256.4725.4655.4650.0000.0000.0000.000
126A182PRO00.0470.01355.099-0.096-0.0960.0000.0000.0000.000
127A183GLU-1-0.759-0.84453.569-6.053-6.0530.0000.0000.0000.000
128A184VAL00.0300.00853.287-0.103-0.1030.0000.0000.0000.000
129A185ASP-1-0.821-0.88452.449-5.832-5.8320.0000.0000.0000.000
130A186LYS10.7870.87748.6075.9465.9460.0000.0000.0000.000
131A187LEU00.0310.01748.489-0.149-0.1490.0000.0000.0000.000
132A188ASN0-0.0020.01248.921-0.158-0.1580.0000.0000.0000.000
133A189ILE0-0.003-0.00544.911-0.130-0.1300.0000.0000.0000.000
134A190MET0-0.055-0.01544.357-0.158-0.1580.0000.0000.0000.000
135A191ALA00.0530.01844.351-0.124-0.1240.0000.0000.0000.000
136A192ALA0-0.048-0.02645.373-0.050-0.0500.0000.0000.0000.000
137A193LYS10.9180.95940.5467.4107.4100.0000.0000.0000.000
138A194ARG10.8560.89838.5927.5337.5330.0000.0000.0000.000
139A195GLN00.0310.02641.7880.0140.0140.0000.0000.0000.000
140A196GLN0-0.047-0.02337.4530.0300.0300.0000.0000.0000.000
141A197GLU-1-0.888-0.93136.737-8.122-8.1220.0000.0000.0000.000
142A198LEU0-0.046-0.00638.457-0.084-0.0840.0000.0000.0000.000
143A199LYS10.9960.99233.7608.6718.6710.0000.0000.0000.000
144A200ASP-1-0.797-0.88539.667-6.686-6.6860.0000.0000.0000.000
145A201VAL00.007-0.00243.031-0.002-0.0020.0000.0000.0000.000
146A202GLY00.0460.03245.2840.0950.0950.0000.0000.0000.000
147A203ASN00.008-0.00645.492-0.018-0.0180.0000.0000.0000.000
148A204ARG10.8610.93241.2117.2897.2890.0000.0000.0000.000
149A205ASP-1-0.880-0.94845.881-6.382-6.3820.0000.0000.0000.000
150A206GLN0-0.042-0.01949.1930.0390.0390.0000.0000.0000.000
151A207MET00.0040.01646.4510.1540.1540.0000.0000.0000.000
152A208ALA0-0.040-0.00948.8020.0600.0600.0000.0000.0000.000
153A209ALA00.0080.00250.2310.0980.0980.0000.0000.0000.000
154A210ALA0-0.0230.00052.5500.1110.1110.0000.0000.0000.000
155A211ARG10.8870.91747.8186.5006.5000.0000.0000.0000.000
156A212GLY00.0110.02652.9760.0560.0560.0000.0000.0000.000
157A213ILE0-0.039-0.02855.3530.1050.1050.0000.0000.0000.000
158A214LEU00.0300.01254.0170.1070.1070.0000.0000.0000.000
159A215GLN0-0.046-0.04352.7070.0580.0580.0000.0000.0000.000
160A216LYS10.8930.95557.5195.0845.0840.0000.0000.0000.000
161A217ASN00.015-0.00760.3800.1750.1750.0000.0000.0000.000
162A218VAL00.0290.03259.6400.0880.0880.0000.0000.0000.000
163A219PRO00.0340.01261.4940.0790.0790.0000.0000.0000.000
164A220ILE0-0.0030.01664.6920.0920.0920.0000.0000.0000.000
165A221LEU00.0190.01564.9500.0830.0830.0000.0000.0000.000
166A222TYR0-0.0140.00166.6580.0520.0520.0000.0000.0000.000
167A223THR00.002-0.00768.3490.0810.0810.0000.0000.0000.000
168A224ALA00.0220.00870.5480.0760.0760.0000.0000.0000.000
169A225SER0-0.008-0.02969.9810.0760.0760.0000.0000.0000.000
170A226GLN00.0000.01472.498-0.007-0.0070.0000.0000.0000.000
171A227ALA0-0.0020.00674.3370.0650.0650.0000.0000.0000.000
172A228CYS0-0.098-0.06075.1990.0620.0620.0000.0000.0000.000
173A229LEU0-0.058-0.01274.4460.0480.0480.0000.0000.0000.000
174A230GLN0-0.023-0.02877.2470.0600.0600.0000.0000.0000.000
175A231HIS0-0.031-0.00680.0150.0910.0910.0000.0000.0000.000
176A232PRO00.0490.03381.544-0.005-0.0050.0000.0000.0000.000
177A233ASP-1-0.833-0.89782.609-3.715-3.7150.0000.0000.0000.000
178A234VAL0-0.037-0.01681.582-0.003-0.0030.0000.0000.0000.000
179A235ALA00.0050.00281.181-0.059-0.0590.0000.0000.0000.000
180A236ALA00.0140.00479.526-0.054-0.0540.0000.0000.0000.000
181A237TYR00.0590.01876.717-0.069-0.0690.0000.0000.0000.000
182A238LYS10.8300.89475.3703.8593.8590.0000.0000.0000.000
183A239ALA00.0140.01274.715-0.060-0.0600.0000.0000.0000.000
184A240ASN0-0.040-0.01872.349-0.082-0.0820.0000.0000.0000.000
185A241ARG10.9610.96470.6894.2554.2550.0000.0000.0000.000
186A242ASP-1-0.851-0.90969.733-4.568-4.5680.0000.0000.0000.000
187A243LEU0-0.022-0.00168.354-0.075-0.0750.0000.0000.0000.000
188A244ILE00.005-0.00865.821-0.082-0.0820.0000.0000.0000.000
189A245TYR00.0130.00063.975-0.064-0.0640.0000.0000.0000.000
190A246LYS10.9760.98764.4424.5074.5070.0000.0000.0000.000
191A247GLN0-0.019-0.02362.561-0.093-0.0930.0000.0000.0000.000
192A248LEU0-0.0030.00560.233-0.107-0.1070.0000.0000.0000.000
193A249GLN00.012-0.00259.731-0.082-0.0820.0000.0000.0000.000
194A250GLN0-0.0230.00559.480-0.056-0.0560.0000.0000.0000.000
195A251ALA0-0.0100.00956.775-0.091-0.0910.0000.0000.0000.000
196A252VAL00.0240.00755.287-0.127-0.1270.0000.0000.0000.000
197A253THR0-0.003-0.02854.655-0.112-0.1120.0000.0000.0000.000
198A254GLY00.0120.01954.223-0.085-0.0850.0000.0000.0000.000
199A255ILE00.013-0.01549.738-0.123-0.1230.0000.0000.0000.000
200A256SER0-0.004-0.00249.796-0.177-0.1770.0000.0000.0000.000
201A257ASN0-0.039-0.02749.814-0.127-0.1270.0000.0000.0000.000
202A258ALA00.0050.00848.153-0.102-0.1020.0000.0000.0000.000
203A259ALA0-0.016-0.02245.597-0.157-0.1570.0000.0000.0000.000
204A260GLN0-0.058-0.03444.327-0.207-0.2070.0000.0000.0000.000
205A261ALA0-0.053-0.02742.535-0.194-0.1940.0000.0000.0000.000