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: QYQ5Y

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 OptH
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 -2217467.91684
FMO2-HF: Nuclear repulsion 2140607.393687
FMO2-HF: Total energy -76860.523154
FMO2-MP2: Total energy -77080.907919


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.
-5.418-3.4220.177-0.791-1.380.004
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 : 0.041 / q_NPA : 0.011
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].
3A3ARG11.0441.0193.790-4.570-2.7270.177-0.774-1.2450.004
4A4LEU0-0.0230.0876.326-0.081-0.0810.0000.0000.0000.000
5A5MET00.0570.0459.3210.1760.1760.0000.0000.0000.000
6A6PRO0-0.042-0.01410.3830.0170.0170.0000.0000.0000.000
7A7HIS00.0220.03111.842-0.040-0.0400.0000.0000.0000.000
8A8TYR0-0.030-0.06515.1460.0190.0190.0000.0000.0000.000
9A9SER0-0.043-0.02517.827-0.010-0.0100.0000.0000.0000.000
10A10LYS10.9130.9648.561-1.191-1.1910.0000.0000.0000.000
11A11GLY0-0.0040.00214.2750.0720.0720.0000.0000.0000.000
12A12LYS10.9470.99515.482-0.305-0.3050.0000.0000.0000.000
13A13THR0-0.024-0.01815.8030.0840.0840.0000.0000.0000.000
14A14ALA00.0070.01417.596-0.041-0.0410.0000.0000.0000.000
15A15PHE0-0.011-0.01819.4660.0230.0230.0000.0000.0000.000
16A16LEU00.0250.00921.198-0.016-0.0160.0000.0000.0000.000
17A17CYS0-0.038-0.02223.325-0.005-0.0050.0000.0000.0000.000
18A18VAL0-0.002-0.02123.884-0.010-0.0100.0000.0000.0000.000
19A19ASP-1-0.726-0.85927.0920.0780.0780.0000.0000.0000.000
20A20LEU0-0.0060.00728.696-0.007-0.0070.0000.0000.0000.000
21A21GLN0-0.019-0.01232.1570.0020.0020.0000.0000.0000.000
22A22GLU-1-0.879-0.92335.7260.0550.0550.0000.0000.0000.000
23A23ALA0-0.024-0.00638.233-0.002-0.0020.0000.0000.0000.000
24A24PHE0-0.024-0.02834.303-0.004-0.0040.0000.0000.0000.000
25A25SER00.007-0.00836.613-0.001-0.0010.0000.0000.0000.000
26A26LYS10.9330.96337.550-0.045-0.0450.0000.0000.0000.000
27A27ARG10.8560.94136.782-0.039-0.0390.0000.0000.0000.000
28A28ILE00.0260.00931.748-0.003-0.0030.0000.0000.0000.000
29A29GLU-1-0.929-0.94934.1140.0530.0530.0000.0000.0000.000
30A30ASN0-0.004-0.03328.211-0.004-0.0040.0000.0000.0000.000
31A31PHE00.0310.02431.5020.0080.0080.0000.0000.0000.000
32A32ALA00.0490.02132.7170.0050.0050.0000.0000.0000.000
33A33ASN00.030-0.00729.4430.0010.0010.0000.0000.0000.000
34A34CYS0-0.033-0.01128.2090.0110.0110.0000.0000.0000.000
35A35VAL00.0020.01629.0050.0090.0090.0000.0000.0000.000
36A36PHE00.0250.01628.6260.0070.0070.0000.0000.0000.000
37A37VAL0-0.0060.00724.3600.0090.0090.0000.0000.0000.000
38A38ALA00.0220.01026.6920.0140.0140.0000.0000.0000.000
39A39ASN00.0240.00628.3220.0080.0080.0000.0000.0000.000
40A40ARG10.9140.96525.219-0.160-0.1600.0000.0000.0000.000
41A41LEU0-0.014-0.03321.4200.0120.0120.0000.0000.0000.000
42A42ALA0-0.0240.00625.5150.0090.0090.0000.0000.0000.000
43A43ARG10.7940.86328.544-0.127-0.1270.0000.0000.0000.000
44A44LEU0-0.006-0.00821.6840.0010.0010.0000.0000.0000.000
45A45HIS0-0.020-0.01524.719-0.006-0.0060.0000.0000.0000.000
46A46GLU-1-0.842-0.91325.7220.1360.1360.0000.0000.0000.000
47A47VAL0-0.133-0.06026.442-0.007-0.0070.0000.0000.0000.000
48A48VAL0-0.033-0.00721.9420.0010.0010.0000.0000.0000.000
49A49PRO00.0490.03423.8730.0160.0160.0000.0000.0000.000
50A50GLU-1-0.892-0.95324.6660.2180.2180.0000.0000.0000.000
51A51ASN0-0.048-0.02619.8370.0310.0310.0000.0000.0000.000
52A52THR0-0.0190.00419.9050.0270.0270.0000.0000.0000.000
53A53LYS10.8830.94421.939-0.241-0.2410.0000.0000.0000.000
54A54TYR0-0.018-0.02323.2900.0120.0120.0000.0000.0000.000
55A55ILE00.0190.01323.205-0.012-0.0120.0000.0000.0000.000
56A56VAL00.0190.02726.6890.0040.0040.0000.0000.0000.000
57A57THR00.0210.00726.936-0.001-0.0010.0000.0000.0000.000
58A58GLU-1-0.843-0.94029.9510.0720.0720.0000.0000.0000.000
59A59HIS0-0.033-0.02531.9690.0010.0010.0000.0000.0000.000
60A60TYR0-0.051-0.03133.754-0.003-0.0030.0000.0000.0000.000
61A61PRO00.0520.03936.483-0.003-0.0030.0000.0000.0000.000
62A62LYS10.9540.97138.616-0.038-0.0380.0000.0000.0000.000
63A63GLY0-0.062-0.03541.573-0.002-0.0020.0000.0000.0000.000
64A64LEU0-0.047-0.04040.8950.0000.0000.0000.0000.0000.000
65A65GLY00.0450.02938.7010.0020.0020.0000.0000.0000.000
66A66ARG10.9791.00438.309-0.060-0.0600.0000.0000.0000.000
67A67ILE0-0.032-0.02232.334-0.001-0.0010.0000.0000.0000.000
68A68VAL00.0100.00135.8850.0000.0000.0000.0000.0000.000
69A69PRO00.0220.01136.6540.0040.0040.0000.0000.0000.000
70A70GLU-1-0.968-0.98936.3150.0900.0900.0000.0000.0000.000
71A71ILE00.0180.02531.7300.0060.0060.0000.0000.0000.000
72A72THR0-0.009-0.00134.803-0.001-0.0010.0000.0000.0000.000
73A73LEU0-0.009-0.00431.5520.0080.0080.0000.0000.0000.000
74A74PRO00.0200.03029.225-0.005-0.0050.0000.0000.0000.000
75A75LYS10.9260.94632.453-0.096-0.0960.0000.0000.0000.000
76A76THR0-0.017-0.02329.156-0.008-0.0080.0000.0000.0000.000
77A77ALA0-0.063-0.01029.5620.0050.0050.0000.0000.0000.000
78A78HIS00.0160.00527.474-0.013-0.0130.0000.0000.0000.000
79A79LEU0-0.022-0.01129.5150.0040.0040.0000.0000.0000.000
80A80ILE00.0060.00428.361-0.004-0.0040.0000.0000.0000.000
81A81GLU-1-0.893-0.94432.1370.0620.0620.0000.0000.0000.000
82A82LYS10.8380.92628.469-0.080-0.0800.0000.0000.0000.000
83A83THR00.018-0.01033.282-0.001-0.0010.0000.0000.0000.000
84A84ARG10.9571.00125.923-0.047-0.0470.0000.0000.0000.000
85A85PHE00.009-0.00828.5600.0050.0050.0000.0000.0000.000
86A86SER0-0.029-0.02623.4400.0110.0110.0000.0000.0000.000
87A87CYS0-0.044-0.03723.695-0.005-0.0050.0000.0000.0000.000
88A88VAL00.0460.02320.6500.0070.0070.0000.0000.0000.000
89A89VAL0-0.049-0.02123.996-0.017-0.0170.0000.0000.0000.000
90A90PRO00.0820.01526.2660.0110.0110.0000.0000.0000.000
91A91GLN00.0320.01527.1770.0040.0040.0000.0000.0000.000
92A92VAL0-0.043-0.01423.9800.0080.0080.0000.0000.0000.000
93A93GLU-1-0.933-0.97122.3290.1040.1040.0000.0000.0000.000
94A94GLU-1-0.823-0.90322.2350.1070.1070.0000.0000.0000.000
95A95LEU0-0.094-0.03423.9290.0140.0140.0000.0000.0000.000
96A96LEU0-0.092-0.06618.9430.0300.0300.0000.0000.0000.000
97A97GLU-1-0.893-0.95018.7300.1550.1550.0000.0000.0000.000
98A98ASP-1-0.879-0.91718.4140.2430.2430.0000.0000.0000.000
99A99VAL0-0.063-0.03316.6330.0250.0250.0000.0000.0000.000
100A100ASP-1-0.868-0.94011.6680.6290.6290.0000.0000.0000.000
101A101ASN0-0.078-0.04411.3880.2710.2710.0000.0000.0000.000
102A102ALA00.0540.03013.837-0.076-0.0760.0000.0000.0000.000
103A103VAL0-0.011-0.00615.7310.0210.0210.0000.0000.0000.000
104A104VAL00.004-0.00518.046-0.029-0.0290.0000.0000.0000.000
105A105PHE0-0.010-0.01920.163-0.002-0.0020.0000.0000.0000.000
106A106GLY00.0550.02123.182-0.003-0.0030.0000.0000.0000.000
107A107ILE0-0.046-0.00126.349-0.004-0.0040.0000.0000.0000.000
108A108GLU-1-0.741-0.89528.2130.0490.0490.0000.0000.0000.000
109A109GLY0-0.009-0.02524.3070.0010.0010.0000.0000.0000.000
110A110HIS00.0360.02023.7320.0060.0060.0000.0000.0000.000
111A111ALA0-0.0060.00325.942-0.008-0.0080.0000.0000.0000.000
112A112CYS00.000-0.01325.672-0.002-0.0020.0000.0000.0000.000
113A113ILE0-0.0230.06021.3850.0090.0090.0000.0000.0000.000
114A114LEU00.0180.00420.4040.0110.0110.0000.0000.0000.000
115A115GLN0-0.042-0.02620.733-0.001-0.0010.0000.0000.0000.000
116A116THR00.020-0.03020.7010.0010.0010.0000.0000.0000.000
117A117VAL0-0.029-0.02216.2460.0160.0160.0000.0000.0000.000
118A118ALA0-0.006-0.00316.5860.0190.0190.0000.0000.0000.000
119A119ASP-1-0.780-0.86417.3130.0640.0640.0000.0000.0000.000
120A120LEU0-0.013-0.02915.7410.0150.0150.0000.0000.0000.000
121A121LEU0-0.092-0.03911.1160.0500.0500.0000.0000.0000.000
122A122ASP-1-0.900-0.94813.1040.0250.0250.0000.0000.0000.000
123A123MET0-0.076-0.02115.589-0.006-0.0060.0000.0000.0000.000
124A124ASN0-0.070-0.03010.458-0.001-0.0010.0000.0000.0000.000
125A125LYS10.8860.96110.855-0.179-0.1790.0000.0000.0000.000
126A126ARG10.8490.9306.955-1.496-1.4960.0000.0000.0000.000
127A127VAL00.012-0.00210.678-0.095-0.0950.0000.0000.0000.000
128A128PHE0-0.041-0.0259.9440.0060.0060.0000.0000.0000.000
129A129LEU00.0100.00514.513-0.029-0.0290.0000.0000.0000.000
130A130PRO00.0080.01817.662-0.003-0.0030.0000.0000.0000.000
131A131LYS10.9780.95920.291-0.108-0.1080.0000.0000.0000.000
132A132ASP-1-0.761-0.86721.9730.1450.1450.0000.0000.0000.000
133A133GLY0-0.0330.00723.836-0.010-0.0100.0000.0000.0000.000
134A134LEU0-0.0150.00620.660-0.001-0.0010.0000.0000.0000.000
135A135GLY00.0500.02425.355-0.005-0.0050.0000.0000.0000.000
136A136SER0-0.014-0.04328.3450.0030.0030.0000.0000.0000.000
137A137GLN0-0.053-0.02630.227-0.004-0.0040.0000.0000.0000.000
138A138LYS10.9370.97832.881-0.028-0.0280.0000.0000.0000.000
139A139LYS11.0130.99030.732-0.039-0.0390.0000.0000.0000.000
140A140THR0-0.014-0.00929.4180.0030.0030.0000.0000.0000.000
141A141ASP-1-0.825-0.90628.9170.0170.0170.0000.0000.0000.000
142A142PHE00.0040.00924.732-0.001-0.0010.0000.0000.0000.000
143A143LYS10.9130.93424.947-0.024-0.0240.0000.0000.0000.000
144A144ALA00.0100.01424.109-0.002-0.0020.0000.0000.0000.000
145A145ALA00.0680.05322.888-0.007-0.0070.0000.0000.0000.000
146A146ILE0-0.023-0.01219.9890.0030.0030.0000.0000.0000.000
147A147LYS10.9040.94419.037-0.002-0.0020.0000.0000.0000.000
148A148LEU00.0420.03018.442-0.012-0.0120.0000.0000.0000.000
149A149MET00.0290.04716.535-0.009-0.0090.0000.0000.0000.000
150A150SER0-0.047-0.02614.6230.0170.0170.0000.0000.0000.000
151A151SER0-0.147-0.08313.690-0.023-0.0230.0000.0000.0000.000
152A152TRP00.0660.02512.562-0.036-0.0360.0000.0000.0000.000
153A153GLY0-0.0010.0188.9630.0800.0800.0000.0000.0000.000
154A154PRO0-0.021-0.0284.018-0.306-0.1530.000-0.017-0.1350.000
155A155ASN00.004-0.0126.0521.0261.0260.0000.0000.0000.000
156A156CYS00.0280.0457.9010.0260.0260.0000.0000.0000.000
157A157GLH0-0.074-0.1278.246-0.033-0.0330.0000.0000.0000.000
158A158ILE00.0150.01812.2030.0160.0160.0000.0000.0000.000
159A159THR0-0.023-0.01514.642-0.001-0.0010.0000.0000.0000.000
160A160THR0-0.014-0.01317.360-0.020-0.0200.0000.0000.0000.000
161A161SER00.018-0.04319.6970.0250.0250.0000.0000.0000.000
162A162GLU-1-0.902-0.93721.9680.2010.2010.0000.0000.0000.000
163A163SER0-0.003-0.00117.4340.0330.0330.0000.0000.0000.000
164A164ILE00.012-0.01216.3450.0320.0320.0000.0000.0000.000
165A165LEU0-0.007-0.00618.1850.0290.0290.0000.0000.0000.000
166A166LEU00.0380.01719.5160.0140.0140.0000.0000.0000.000
167A167GLN0-0.037-0.00813.6600.0820.0820.0000.0000.0000.000
168A168MET00.0200.02615.1020.0500.0500.0000.0000.0000.000
169A169THR0-0.0280.00217.136-0.006-0.0060.0000.0000.0000.000
170A170LYS10.7890.86711.508-0.677-0.6770.0000.0000.0000.000
171A171ASP-1-0.814-0.90517.3360.3010.3010.0000.0000.0000.000
172A172ALA00.0010.00020.661-0.012-0.0120.0000.0000.0000.000
173A173MET0-0.081-0.04323.897-0.027-0.0270.0000.0000.0000.000
174A174ASP-1-0.740-0.83421.4360.2870.2870.0000.0000.0000.000
175A175PRO00.0050.00423.915-0.016-0.0160.0000.0000.0000.000
176A176ASN0-0.009-0.02824.538-0.031-0.0310.0000.0000.0000.000
177A177PHE00.0430.03524.269-0.009-0.0090.0000.0000.0000.000
178A178LYS10.9760.98326.177-0.137-0.1370.0000.0000.0000.000
179A179ARG10.9570.97229.042-0.170-0.1700.0000.0000.0000.000
180A180ILE00.0550.02423.198-0.009-0.0090.0000.0000.0000.000
181A181SER0-0.049-0.02727.048-0.008-0.0080.0000.0000.0000.000
182A182LYS10.9080.94528.218-0.148-0.1480.0000.0000.0000.000
183A183LEU0-0.0090.00927.157-0.007-0.0070.0000.0000.0000.000
184A184LEU0-0.031-0.02824.305-0.004-0.0040.0000.0000.0000.000
185A185LYS10.9100.97728.622-0.145-0.1450.0000.0000.0000.000
186A186GLU-1-0.955-0.96631.7850.1210.1210.0000.0000.0000.000
187A187GLU-1-0.918-0.96231.4560.1150.1150.0000.0000.0000.000
188A188PRO0-0.064-0.03129.978-0.003-0.0030.0000.0000.0000.000
189A189PRO0-0.019-0.00532.728-0.005-0.0050.0000.0000.0000.000
190A190ILE0-0.0240.00033.133-0.006-0.0060.0000.0000.0000.000
191A191PRO00.0240.02232.3690.0070.0070.0000.0000.0000.000
192A192LEU0-0.0170.00226.246-0.003-0.0030.0000.0000.0000.000