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: 497GN

Calculation Name: 1X9G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1X9G

Chain ID: A

ChEMBL ID:

UniProt ID: D0VWV0

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2227066.835791
FMO2-HF: Nuclear repulsion 2150203.640995
FMO2-HF: Total energy -76863.194796
FMO2-MP2: Total energy -77083.456017


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-12.224-16.56215.135-5.695-5.1020.044
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.103 / q_NPA : 0.054
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].
3A3ARG10.8900.9222.261-11.246-15.76015.135-5.669-4.9520.044
4A4LEU0-0.0040.0386.1900.0110.0110.0000.0000.0000.000
5A5MET00.0530.0408.6440.1430.1430.0000.0000.0000.000
6A6PRO0-0.0210.00410.4140.0050.0050.0000.0000.0000.000
7A7HIS00.0260.01911.847-0.034-0.0340.0000.0000.0000.000
8A8TYR0-0.039-0.05015.1330.0180.0180.0000.0000.0000.000
9A9SER0-0.012-0.01217.711-0.005-0.0050.0000.0000.0000.000
10A10LYS10.8100.8999.813-0.734-0.7340.0000.0000.0000.000
11A11GLY0-0.034-0.01213.7360.0900.0900.0000.0000.0000.000
12A12LYS10.9090.94815.421-0.265-0.2650.0000.0000.0000.000
13A13THR0-0.026-0.01315.5800.0900.0900.0000.0000.0000.000
14A14ALA00.0230.01717.420-0.040-0.0400.0000.0000.0000.000
15A15PHE0-0.014-0.01819.3210.0210.0210.0000.0000.0000.000
16A16LEU0-0.004-0.00520.713-0.019-0.0190.0000.0000.0000.000
17A17CYS00.0300.01922.9160.0030.0030.0000.0000.0000.000
18A18VAL00.019-0.00723.847-0.011-0.0110.0000.0000.0000.000
19A19ASP-1-0.741-0.84026.9670.1060.1060.0000.0000.0000.000
20A20LEU00.0040.01928.477-0.005-0.0050.0000.0000.0000.000
21A21GLN0-0.010-0.02031.9000.0020.0020.0000.0000.0000.000
22A22GLU-1-0.831-0.90735.4620.0790.0790.0000.0000.0000.000
23A23ALA0-0.0120.00338.583-0.001-0.0010.0000.0000.0000.000
24A24PHE0-0.026-0.02533.701-0.001-0.0010.0000.0000.0000.000
25A25SER0-0.028-0.02536.0320.0020.0020.0000.0000.0000.000
26A26LYS10.8510.93137.145-0.074-0.0740.0000.0000.0000.000
27A27ARG10.8480.91636.893-0.071-0.0710.0000.0000.0000.000
28A28ILE0-0.0030.00230.8990.0000.0000.0000.0000.0000.000
29A29GLU-1-0.812-0.88133.6020.1060.1060.0000.0000.0000.000
30A30ASN00.035-0.00427.971-0.009-0.0090.0000.0000.0000.000
31A31PHE00.0510.02931.2040.0090.0090.0000.0000.0000.000
32A32ALA00.0390.01632.3090.0040.0040.0000.0000.0000.000
33A33ASN00.0320.00929.116-0.005-0.0050.0000.0000.0000.000
34A34CYS0-0.029-0.00727.8840.0110.0110.0000.0000.0000.000
35A35VAL0-0.0020.00628.7040.0070.0070.0000.0000.0000.000
36A36PHE0-0.0050.01028.5130.0030.0030.0000.0000.0000.000
37A37VAL0-0.004-0.00124.2130.0070.0070.0000.0000.0000.000
38A38ALA00.0240.01126.5320.0100.0100.0000.0000.0000.000
39A39ASN00.0330.00927.9420.0010.0010.0000.0000.0000.000
40A40ARG10.8780.93725.341-0.196-0.1960.0000.0000.0000.000
41A41LEU0-0.022-0.02421.3720.0110.0110.0000.0000.0000.000
42A42ALA0-0.0200.00825.2470.0030.0030.0000.0000.0000.000
43A43ARG10.7730.83028.307-0.138-0.1380.0000.0000.0000.000
44A44LEU00.008-0.00521.1210.0000.0000.0000.0000.0000.000
45A45HIS0-0.0290.00224.796-0.009-0.0090.0000.0000.0000.000
46A46GLU-1-0.799-0.86925.8220.1310.1310.0000.0000.0000.000
47A47VAL0-0.103-0.05426.040-0.009-0.0090.0000.0000.0000.000
48A48VAL0-0.0170.00621.634-0.003-0.0030.0000.0000.0000.000
49A49PRO00.0230.02823.9170.0130.0130.0000.0000.0000.000
50A50GLU-1-0.800-0.89624.2570.1930.1930.0000.0000.0000.000
51A51ASN0-0.082-0.04219.3210.0080.0080.0000.0000.0000.000
52A52THR0-0.041-0.03819.5980.0320.0320.0000.0000.0000.000
53A53LYS10.8530.90521.646-0.207-0.2070.0000.0000.0000.000
54A54TYR0-0.022-0.02523.0450.0150.0150.0000.0000.0000.000
55A55ILE00.0150.01722.546-0.014-0.0140.0000.0000.0000.000
56A56VAL0-0.023-0.01326.1760.0080.0080.0000.0000.0000.000
57A57THR00.024-0.01326.866-0.004-0.0040.0000.0000.0000.000
58A58GLU-1-0.766-0.87929.6390.0830.0830.0000.0000.0000.000
59A59HIS00.0250.01531.8300.0000.0000.0000.0000.0000.000
60A60TYR0-0.014-0.00833.548-0.003-0.0030.0000.0000.0000.000
61A61PRO00.0910.06036.016-0.003-0.0030.0000.0000.0000.000
62A62LYS10.9110.95938.442-0.048-0.0480.0000.0000.0000.000
63A63GLY0-0.068-0.03640.908-0.003-0.0030.0000.0000.0000.000
64A64LEU0-0.018-0.01540.4660.0000.0000.0000.0000.0000.000
65A65GLY00.000-0.01039.3900.0030.0030.0000.0000.0000.000
66A66ARG10.8310.90437.974-0.071-0.0710.0000.0000.0000.000
67A67ILE0-0.022-0.01732.2540.0010.0010.0000.0000.0000.000
68A68VAL0-0.022-0.01535.259-0.003-0.0030.0000.0000.0000.000
69A69PRO00.003-0.00836.0240.0050.0050.0000.0000.0000.000
70A70GLU-1-0.921-0.94935.8750.1040.1040.0000.0000.0000.000
71A71ILE0-0.036-0.00431.0000.0070.0070.0000.0000.0000.000
72A72THR00.0100.00633.955-0.003-0.0030.0000.0000.0000.000
73A73LEU00.0020.00331.5440.0070.0070.0000.0000.0000.000
74A74PRO00.0040.01729.067-0.007-0.0070.0000.0000.0000.000
75A75LYS10.8980.93932.315-0.099-0.0990.0000.0000.0000.000
76A76THR00.007-0.01429.183-0.009-0.0090.0000.0000.0000.000
77A77ALA0-0.055-0.01729.3930.0060.0060.0000.0000.0000.000
78A78HIS00.0350.01327.612-0.011-0.0110.0000.0000.0000.000
79A79LEU0-0.032-0.01229.1120.0060.0060.0000.0000.0000.000
80A80ILE0-0.0100.00528.506-0.005-0.0050.0000.0000.0000.000
81A81GLU-1-0.851-0.92031.7870.0720.0720.0000.0000.0000.000
82A82LYS10.7900.87828.465-0.102-0.1020.0000.0000.0000.000
83A83THR00.004-0.01932.7230.0000.0000.0000.0000.0000.000
84A84ARG10.7950.88323.990-0.076-0.0760.0000.0000.0000.000
85A85PHE00.023-0.00528.3310.0050.0050.0000.0000.0000.000
86A86SER0-0.027-0.03423.0120.0130.0130.0000.0000.0000.000
87A87CYS0-0.031-0.03023.352-0.007-0.0070.0000.0000.0000.000
88A88VAL0-0.0050.00920.6370.0010.0010.0000.0000.0000.000
89A89VAL00.0090.00823.969-0.016-0.0160.0000.0000.0000.000
90A90PRO00.0790.03626.5800.0100.0100.0000.0000.0000.000
91A91GLN00.0360.02027.1270.0030.0030.0000.0000.0000.000
92A92VAL0-0.067-0.03822.8390.0080.0080.0000.0000.0000.000
93A93GLU-1-0.935-0.98122.5050.0890.0890.0000.0000.0000.000
94A94GLU-1-0.842-0.92322.5130.0870.0870.0000.0000.0000.000
95A95LEU0-0.065-0.01723.9870.0100.0100.0000.0000.0000.000
96A96LEU0-0.033-0.02718.9820.0270.0270.0000.0000.0000.000
97A97GLU-1-0.885-0.93518.6460.1180.1180.0000.0000.0000.000
98A98ASP-1-0.872-0.91018.4310.1980.1980.0000.0000.0000.000
99A99VAL0-0.040-0.02516.4830.0230.0230.0000.0000.0000.000
100A100ASP-1-0.799-0.86311.3660.6270.6270.0000.0000.0000.000
101A101ASN0-0.037-0.03411.3410.2070.2070.0000.0000.0000.000
102A102ALA00.0490.03113.667-0.075-0.0750.0000.0000.0000.000
103A103VAL0-0.021-0.02115.3430.0370.0370.0000.0000.0000.000
104A104VAL00.0220.01017.733-0.032-0.0320.0000.0000.0000.000
105A105PHE00.017-0.00320.0950.0070.0070.0000.0000.0000.000
106A106GLY00.0440.02423.267-0.009-0.0090.0000.0000.0000.000
107A107ILE0-0.051-0.01726.4370.0040.0040.0000.0000.0000.000
108A108GLU-1-0.720-0.85428.2000.0890.0890.0000.0000.0000.000
109A109GLY00.010-0.02524.3110.0020.0020.0000.0000.0000.000
110A110HIS0-0.001-0.00423.6150.0150.0150.0000.0000.0000.000
111A111ALA00.0070.00725.845-0.009-0.0090.0000.0000.0000.000
112A112CYS0-0.014-0.00525.2220.0000.0000.0000.0000.0000.000
113A113ILE00.0200.04321.1800.0080.0080.0000.0000.0000.000
114A114LEU0-0.009-0.00120.0270.0130.0130.0000.0000.0000.000
115A115GLN00.000-0.01720.3950.0040.0040.0000.0000.0000.000
116A116THR00.0430.01720.149-0.004-0.0040.0000.0000.0000.000
117A117VAL0-0.021-0.02716.1240.0120.0120.0000.0000.0000.000
118A118ALA0-0.0060.00316.1230.0180.0180.0000.0000.0000.000
119A119ASP-1-0.695-0.79617.0720.0850.0850.0000.0000.0000.000
120A120LEU0-0.004-0.01715.4040.0020.0020.0000.0000.0000.000
121A121LEU0-0.055-0.01611.1210.0530.0530.0000.0000.0000.000
122A122ASP-1-0.877-0.92313.2030.0220.0220.0000.0000.0000.000
123A123MET0-0.095-0.04215.878-0.012-0.0120.0000.0000.0000.000
124A124ASN0-0.084-0.04911.321-0.001-0.0010.0000.0000.0000.000
125A125LYS10.8350.92911.087-0.172-0.1720.0000.0000.0000.000
126A126ARG10.8030.9206.230-1.275-1.2750.0000.0000.0000.000
127A127VAL00.017-0.00410.216-0.099-0.0990.0000.0000.0000.000
128A128PHE0-0.018-0.0159.5890.0220.0220.0000.0000.0000.000
129A129LEU00.0190.01114.399-0.043-0.0430.0000.0000.0000.000
130A130PRO00.0220.01517.5770.0080.0080.0000.0000.0000.000
131A131LYS10.9710.97520.125-0.243-0.2430.0000.0000.0000.000
132A132ASP-1-0.809-0.89021.9770.2070.2070.0000.0000.0000.000
133A133GLY00.0140.01223.914-0.015-0.0150.0000.0000.0000.000
134A134LEU0-0.0030.00620.579-0.002-0.0020.0000.0000.0000.000
135A135GLY00.0570.03025.228-0.002-0.0020.0000.0000.0000.000
136A136SER0-0.048-0.03827.9630.0030.0030.0000.0000.0000.000
137A137GLN0-0.027-0.01730.162-0.005-0.0050.0000.0000.0000.000
138A138LYS10.9220.96732.398-0.076-0.0760.0000.0000.0000.000
139A139LYS10.8820.90930.747-0.099-0.0990.0000.0000.0000.000
140A140THR0-0.020-0.01229.5660.0090.0090.0000.0000.0000.000
141A141ASP-1-0.832-0.91928.8040.0860.0860.0000.0000.0000.000
142A142PHE00.0270.02024.5260.0040.0040.0000.0000.0000.000
143A143LYS10.9300.95424.895-0.107-0.1070.0000.0000.0000.000
144A144ALA00.0040.00724.1820.0100.0100.0000.0000.0000.000
145A145ALA00.0670.04322.8900.0020.0020.0000.0000.0000.000
146A146ILE00.0040.00820.1940.0130.0130.0000.0000.0000.000
147A147LYS10.9080.96219.229-0.153-0.1530.0000.0000.0000.000
148A148LEU00.0170.02018.8460.0080.0080.0000.0000.0000.000
149A149MET00.0370.04016.6650.0070.0070.0000.0000.0000.000
150A150SER0-0.047-0.04314.8150.0370.0370.0000.0000.0000.000
151A151SER0-0.111-0.05813.8010.0280.0280.0000.0000.0000.000
152A152TRP00.0400.01512.426-0.025-0.0250.0000.0000.0000.000
153A153GLY00.0290.0418.9430.0470.0470.0000.0000.0000.000
154A154PRO0-0.041-0.0323.941-0.275-0.0990.000-0.026-0.1500.000
155A155ASN00.023-0.0056.0390.4610.4610.0000.0000.0000.000
156A156CYS0-0.0120.0157.8680.0170.0170.0000.0000.0000.000
157A157GLH0-0.040-0.0568.0730.0270.0270.0000.0000.0000.000
158A158ILE00.0030.00012.209-0.033-0.0330.0000.0000.0000.000
159A159THR0-0.027-0.01314.7070.0070.0070.0000.0000.0000.000
160A160THR00.000-0.00417.596-0.025-0.0250.0000.0000.0000.000
161A161SER0-0.003-0.03619.8030.0210.0210.0000.0000.0000.000
162A162GLU-1-0.912-0.95321.5740.2630.2630.0000.0000.0000.000
163A163SER00.0020.00617.1390.0290.0290.0000.0000.0000.000
164A164ILE00.019-0.00316.1190.0310.0310.0000.0000.0000.000
165A165LEU00.0110.00117.8940.0170.0170.0000.0000.0000.000
166A166LEU00.0270.02219.570-0.001-0.0010.0000.0000.0000.000
167A167GLN0-0.044-0.01812.9250.0760.0760.0000.0000.0000.000
168A168MET00.0310.03115.3950.0250.0250.0000.0000.0000.000
169A169THR0-0.062-0.03817.334-0.019-0.0190.0000.0000.0000.000
170A170LYS10.7930.86611.826-0.629-0.6290.0000.0000.0000.000
171A171ASP-1-0.803-0.89617.5140.2590.2590.0000.0000.0000.000
172A172ALA00.0030.00120.805-0.009-0.0090.0000.0000.0000.000
173A173MET0-0.064-0.04024.065-0.024-0.0240.0000.0000.0000.000
174A174ASP-1-0.767-0.84221.8470.2390.2390.0000.0000.0000.000
175A175PRO00.009-0.00324.121-0.008-0.0080.0000.0000.0000.000
176A176ASN00.0220.00324.645-0.024-0.0240.0000.0000.0000.000
177A177PHE00.0400.03423.581-0.002-0.0020.0000.0000.0000.000
178A178LYS10.9480.97025.966-0.136-0.1360.0000.0000.0000.000
179A179ARG10.8310.92228.657-0.166-0.1660.0000.0000.0000.000
180A180ILE00.0680.02423.039-0.006-0.0060.0000.0000.0000.000
181A181SER00.0210.00726.845-0.005-0.0050.0000.0000.0000.000
182A182LYS10.7930.88728.170-0.153-0.1530.0000.0000.0000.000
183A183LEU00.0030.01126.703-0.008-0.0080.0000.0000.0000.000
184A184LEU0-0.002-0.00624.261-0.002-0.0020.0000.0000.0000.000
185A185LYS10.8560.93828.296-0.170-0.1700.0000.0000.0000.000
186A186GLU-1-0.864-0.90231.2250.1440.1440.0000.0000.0000.000
187A187GLU-1-0.863-0.95131.2270.1600.1600.0000.0000.0000.000
188A188PRO0-0.052-0.02529.503-0.004-0.0040.0000.0000.0000.000
189A189PRO0-0.035-0.01532.231-0.005-0.0050.0000.0000.0000.000
190A190ILE0-0.0180.00433.161-0.007-0.0070.0000.0000.0000.000
191A191PRO00.0270.01632.2710.0090.0090.0000.0000.0000.000
192A192LEU0-0.0280.00126.2220.0020.0020.0000.0000.0000.000