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: R5VG8

Calculation Name: 1YXY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YXY

Chain ID: A

ChEMBL ID:

UniProt ID: P65522

Base Structure: X-ray

Registration Date: 2023-06-19

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2698116.732608
FMO2-HF: Nuclear repulsion 2611329.904743
FMO2-HF: Total energy -86786.827865
FMO2-MP2: Total energy -87038.463204


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:4:LYS)


Summations of interaction energy for fragment #1(A:4: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.
-147.791-142.7296.661-4.552-7.167-0.046
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.930 / q_NPA : 0.962
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].
3A6THR00.0750.0223.822-1.916-0.561-0.012-0.567-0.7750.003
4A7LYS10.9870.9836.21819.84319.8430.0000.0000.0000.000
5A8GLU-1-0.945-0.9658.720-16.737-16.7370.0000.0000.0000.000
6A9LYS10.9710.9777.88121.63121.6310.0000.0000.0000.000
7A10LEU00.0050.0106.6860.6830.6830.0000.0000.0000.000
8A11MET0-0.024-0.0248.8881.1301.1300.0000.0000.0000.000
9A12GLU-1-0.994-0.98912.349-15.648-15.6480.0000.0000.0000.000
10A13GLN0-0.052-0.02510.7140.8340.8340.0000.0000.0000.000
11A14LEU0-0.037-0.03110.8310.6210.6210.0000.0000.0000.000
12A15LYS10.9840.99414.12113.37513.3750.0000.0000.0000.000
13A16GLY0-0.045-0.01317.1990.1880.1880.0000.0000.0000.000
14A17GLY00.0260.02518.4960.4560.4560.0000.0000.0000.000
15A18ILE0-0.043-0.02219.2960.1220.1220.0000.0000.0000.000
16A19ILE0-0.0050.00813.880-0.433-0.4330.0000.0000.0000.000
17A20VAL00.0450.01016.8170.6350.6350.0000.0000.0000.000
18A21SER00.0100.00517.449-0.940-0.9400.0000.0000.0000.000
19A22CYS0-0.065-0.00718.3480.9350.9350.0000.0000.0000.000
20A23GLN00.026-0.00319.260-0.388-0.3880.0000.0000.0000.000
21A24ALA00.0710.02621.7840.5560.5560.0000.0000.0000.000
22A25LEU0-0.041-0.01723.391-0.372-0.3720.0000.0000.0000.000
23A26PRO00.0370.00525.3680.3720.3720.0000.0000.0000.000
24A27GLY00.0230.01728.5490.1240.1240.0000.0000.0000.000
25A28GLH0-0.030-0.09627.001-0.118-0.1180.0000.0000.0000.000
26A29PRO00.001-0.00630.785-0.064-0.0640.0000.0000.0000.000
27A30LEU0-0.004-0.00427.0940.0860.0860.0000.0000.0000.000
28A31TYR0-0.0100.00924.603-0.355-0.3550.0000.0000.0000.000
29A32SER00.0220.02126.4070.4920.4920.0000.0000.0000.000
30A33GLU-1-0.898-0.95425.961-10.634-10.6340.0000.0000.0000.000
31A34THR0-0.060-0.03926.078-0.399-0.3990.0000.0000.0000.000
32A35GLY0-0.0080.01923.171-0.352-0.3520.0000.0000.0000.000
33A36GLY00.032-0.01122.5270.5900.5900.0000.0000.0000.000
34A37ILE0-0.040-0.02123.8410.2480.2480.0000.0000.0000.000
35A38MET0-0.002-0.00419.9030.0560.0560.0000.0000.0000.000
36A39PRO00.0490.03318.606-0.169-0.1690.0000.0000.0000.000
37A40LEU0-0.0010.00019.6160.0180.0180.0000.0000.0000.000
38A41MET0-0.019-0.00421.5070.3590.3590.0000.0000.0000.000
39A42ALA00.0480.01116.6770.0930.0930.0000.0000.0000.000
40A43LYS10.9120.96218.67312.07912.0790.0000.0000.0000.000
41A44ALA0-0.0030.00020.1140.1780.1780.0000.0000.0000.000
42A45ALA00.0050.00019.0000.2500.2500.0000.0000.0000.000
43A46GLN00.0540.02816.161-0.803-0.8030.0000.0000.0000.000
44A47GLU-1-0.963-0.98318.679-11.572-11.5720.0000.0000.0000.000
45A48ALA0-0.058-0.01922.0680.4000.4000.0000.0000.0000.000
46A49GLY0-0.0140.00320.1970.3470.3470.0000.0000.0000.000
47A50ALA0-0.079-0.03017.826-0.123-0.1230.0000.0000.0000.000
48A51VAL00.0210.01314.596-0.401-0.4010.0000.0000.0000.000
49A52GLY00.0410.00812.643-1.250-1.2500.0000.0000.0000.000
50A53ILE0-0.0200.00512.5041.2401.2400.0000.0000.0000.000
51A54ARG10.7730.88412.74514.71514.7150.0000.0000.0000.000
52A55ALA00.0160.00114.3591.0481.0480.0000.0000.0000.000
53A56ASN00.1020.03715.258-1.138-1.1380.0000.0000.0000.000
54A57SER0-0.034-0.01116.4200.5480.5480.0000.0000.0000.000
55A58VAL00.0730.01813.128-0.552-0.5520.0000.0000.0000.000
56A59ARG10.7860.88714.73313.20513.2050.0000.0000.0000.000
57A60ASP-1-0.808-0.90117.169-15.192-15.1920.0000.0000.0000.000
58A61ILE0-0.027-0.00610.803-0.242-0.2420.0000.0000.0000.000
59A62LYS10.9520.97711.33124.70924.7090.0000.0000.0000.000
60A63GLU-1-0.857-0.92213.911-14.720-14.7200.0000.0000.0000.000
61A64ILE0-0.013-0.01513.3220.5350.5350.0000.0000.0000.000
62A65GLN0-0.026-0.0377.7321.5931.5930.0000.0000.0000.000
63A66ALA0-0.046-0.00312.044-0.189-0.1890.0000.0000.0000.000
64A67ILE0-0.094-0.04814.9240.9020.9020.0000.0000.0000.000
65A68THR0-0.061-0.03212.6390.6480.6480.0000.0000.0000.000
66A69ASP-1-0.873-0.92510.073-22.845-22.8450.0000.0000.0000.000
67A70LEU0-0.088-0.0359.419-0.832-0.8320.0000.0000.0000.000
68A71PRO0-0.025-0.0017.602-1.486-1.4860.0000.0000.0000.000
69A72ILE00.011-0.0108.0131.4411.4410.0000.0000.0000.000
70A73ILE0-0.017-0.0108.381-1.937-1.9370.0000.0000.0000.000
71A74GLY00.018-0.00710.4371.3891.3890.0000.0000.0000.000
72A75ILE0-0.044-0.02112.124-0.059-0.0590.0000.0000.0000.000
73A76ILE00.007-0.01013.755-0.056-0.0560.0000.0000.0000.000
74A77LYS10.8320.92816.94713.88713.8870.0000.0000.0000.000
75A78LYS10.8760.94020.64813.94313.9430.0000.0000.0000.000
76A79ASP-1-0.861-0.92422.550-11.578-11.5780.0000.0000.0000.000
77A80TYR0-0.111-0.10320.286-0.038-0.0380.0000.0000.0000.000
78A81PRO00.0340.04426.3360.1290.1290.0000.0000.0000.000
79A82PRO0-0.052-0.04930.093-0.072-0.0720.0000.0000.0000.000
80A83GLN00.0160.00928.0620.0050.0050.0000.0000.0000.000
81A84GLU-1-0.897-0.95728.893-9.954-9.9540.0000.0000.0000.000
82A85PRO0-0.058-0.01123.428-0.177-0.1770.0000.0000.0000.000
83A86PHE00.0690.02723.219-0.130-0.1300.0000.0000.0000.000
84A87ILE0-0.051-0.02217.905-0.448-0.4480.0000.0000.0000.000
85A88THR0-0.019-0.02814.164-0.092-0.0920.0000.0000.0000.000
86A89ALA00.0220.02317.399-0.242-0.2420.0000.0000.0000.000
87A90THR0-0.011-0.02018.7790.3260.3260.0000.0000.0000.000
88A91MET00.0450.00214.031-1.351-1.3510.0000.0000.0000.000
89A92THR00.0160.02814.573-1.530-1.5300.0000.0000.0000.000
90A93GLU-1-0.758-0.83314.763-17.554-17.5540.0000.0000.0000.000
91A94VAL00.0250.00810.934-1.598-1.5980.0000.0000.0000.000
92A95ASP-1-0.771-0.86310.220-26.436-26.4360.0000.0000.0000.000
93A96GLN0-0.051-0.0329.718-2.267-2.2670.0000.0000.0000.000
94A97LEU0-0.028-0.0159.598-1.633-1.6330.0000.0000.0000.000
95A98ALA00.0300.0226.037-3.459-3.4590.0000.0000.0000.000
96A99ALA0-0.067-0.0304.983-9.679-9.600-0.001-0.001-0.0760.000
97A100LEU0-0.058-0.0286.721-0.616-0.6160.0000.0000.0000.000
98A101ASN0-0.044-0.0132.223-27.368-26.0166.629-3.397-4.584-0.046
99A102ILE00.0320.0303.9004.3364.551-0.001-0.010-0.2040.000
100A103ALA00.007-0.0013.486-4.163-3.6980.007-0.083-0.3890.000
101A104VAL0-0.021-0.0094.570-1.195-1.095-0.001-0.006-0.0930.000
102A105ILE00.0190.0307.4790.7970.7970.0000.0000.0000.000
103A106ALA00.0030.00210.0620.8180.8180.0000.0000.0000.000
104A107MET00.006-0.00612.381-0.139-0.1390.0000.0000.0000.000
105A108ASP-1-0.783-0.84916.482-12.509-12.5090.0000.0000.0000.000
106A109CYS0-0.053-0.03018.146-0.488-0.4880.0000.0000.0000.000
107A110THR0-0.038-0.03420.9240.6020.6020.0000.0000.0000.000
108A111LYS10.9000.94124.5979.5379.5370.0000.0000.0000.000
109A112ARG10.7960.89025.35811.69711.6970.0000.0000.0000.000
110A113ASP-1-0.865-0.92227.178-10.233-10.2330.0000.0000.0000.000
111A114ARG10.8200.88219.78514.39514.3950.0000.0000.0000.000
112A115HIS0-0.035-0.02024.9100.0590.0590.0000.0000.0000.000
113A116ASP-1-0.814-0.88721.448-13.934-13.9340.0000.0000.0000.000
114A117GLY0-0.021-0.00424.8480.0420.0420.0000.0000.0000.000
115A118LEU0-0.065-0.01521.0750.2170.2170.0000.0000.0000.000
116A119ASP-1-0.775-0.84824.826-12.209-12.2090.0000.0000.0000.000
117A120ILE00.0440.00620.009-0.513-0.5130.0000.0000.0000.000
118A121ALA00.0190.00820.478-0.770-0.7700.0000.0000.0000.000
119A122SER0-0.075-0.09720.004-0.705-0.7050.0000.0000.0000.000
120A123PHE00.0110.01416.487-0.758-0.7580.0000.0000.0000.000
121A124ILE00.0210.01015.298-1.105-1.1050.0000.0000.0000.000
122A125ARG10.9460.97415.01812.67712.6770.0000.0000.0000.000
123A126GLN0-0.0110.00015.625-1.214-1.2140.0000.0000.0000.000
124A127VAL0-0.021-0.00711.120-1.239-1.2390.0000.0000.0000.000
125A128LYS10.8320.8978.76523.77023.7700.0000.0000.0000.000
126A129GLU-1-0.950-0.96411.228-20.294-20.2940.0000.0000.0000.000
127A130LYS10.7940.90310.68322.49122.4910.0000.0000.0000.000
128A131TYR0-0.085-0.0866.539-3.386-3.3860.0000.0000.0000.000
129A132PRO00.0610.0427.711-1.481-1.4810.0000.0000.0000.000
130A133ASN0-0.096-0.0563.3862.4352.7030.011-0.055-0.2240.000
131A134GLN0-0.062-0.0183.414-12.442-11.2700.030-0.426-0.775-0.003
132A135LEU0-0.028-0.0075.1975.2215.277-0.001-0.007-0.0470.000
133A136LEU00.013-0.0067.153-0.711-0.7110.0000.0000.0000.000
134A137MET0-0.024-0.01610.4750.9260.9260.0000.0000.0000.000
135A138ALA00.0280.00513.179-0.033-0.0330.0000.0000.0000.000
136A139ASP-1-0.779-0.87016.814-15.344-15.3440.0000.0000.0000.000
137A140ILE0-0.045-0.02219.1440.3020.3020.0000.0000.0000.000
138A141SER0-0.042-0.05222.4370.2950.2950.0000.0000.0000.000
139A142THR0-0.001-0.01226.0140.4370.4370.0000.0000.0000.000
140A143PHE00.0650.00425.864-0.349-0.3490.0000.0000.0000.000
141A144ASP-1-0.901-0.95326.121-10.545-10.5450.0000.0000.0000.000
142A145GLU-1-0.677-0.79824.193-11.480-11.4800.0000.0000.0000.000
143A146GLY00.0250.01621.783-0.547-0.5470.0000.0000.0000.000
144A147LEU0-0.013-0.00721.663-0.524-0.5240.0000.0000.0000.000
145A148VAL00.0000.00223.178-0.358-0.3580.0000.0000.0000.000
146A149ALA00.018-0.00118.720-0.426-0.4260.0000.0000.0000.000
147A150HIS00.000-0.00418.174-1.080-1.0800.0000.0000.0000.000
148A151GLN0-0.043-0.02518.971-0.529-0.5290.0000.0000.0000.000
149A152ALA0-0.063-0.01819.169-0.010-0.0100.0000.0000.0000.000
150A153GLY00.0000.00215.906-0.606-0.6060.0000.0000.0000.000
151A154ILE0-0.052-0.01513.843-1.409-1.4090.0000.0000.0000.000
152A155ASP-1-0.820-0.89110.152-23.791-23.7910.0000.0000.0000.000
153A156PHE0-0.014-0.0309.0210.8300.8300.0000.0000.0000.000
154A157VAL00.0190.02314.158-0.206-0.2060.0000.0000.0000.000
155A158GLY00.0580.02817.5670.1910.1910.0000.0000.0000.000
156A159THR0-0.017-0.02618.6390.1850.1850.0000.0000.0000.000
157A160THR0-0.046-0.01620.0040.7470.7470.0000.0000.0000.000
158A161LEU00.000-0.00222.2030.3360.3360.0000.0000.0000.000
159A162SER0-0.062-0.04624.6680.4910.4910.0000.0000.0000.000
160A163GLY0-0.030-0.01327.287-0.020-0.0200.0000.0000.0000.000
161A164TYR0-0.065-0.03226.6680.2900.2900.0000.0000.0000.000
162A165THR0-0.0040.00027.620-0.042-0.0420.0000.0000.0000.000
163A166PRO00.024-0.00330.4400.1340.1340.0000.0000.0000.000
164A167TYR0-0.061-0.05627.9980.2930.2930.0000.0000.0000.000
165A168SER0-0.0140.01229.7390.0370.0370.0000.0000.0000.000
166A169ARG10.8820.94131.2899.1819.1810.0000.0000.0000.000
167A170GLN0-0.002-0.01032.258-0.127-0.1270.0000.0000.0000.000
168A171GLU-1-0.940-0.96034.819-8.002-8.0020.0000.0000.0000.000
169A172ALA00.0100.00233.520-0.291-0.2910.0000.0000.0000.000
170A173GLY00.0420.02431.7550.0980.0980.0000.0000.0000.000
171A174PRO00.0470.02627.435-0.087-0.0870.0000.0000.0000.000
172A175ASP-1-0.819-0.90027.383-9.422-9.4220.0000.0000.0000.000
173A176VAL0-0.008-0.03227.682-0.215-0.2150.0000.0000.0000.000
174A177ALA00.0290.02628.863-0.074-0.0740.0000.0000.0000.000
175A178LEU0-0.0190.01325.392-0.073-0.0730.0000.0000.0000.000
176A179ILE00.020-0.00123.353-0.271-0.2710.0000.0000.0000.000
177A180GLU-1-0.897-0.94424.898-9.308-9.3080.0000.0000.0000.000
178A181ALA0-0.015-0.00827.209-0.057-0.0570.0000.0000.0000.000
179A182LEU0-0.016-0.01722.106-0.074-0.0740.0000.0000.0000.000
180A183CYS0-0.0070.00222.850-0.375-0.3750.0000.0000.0000.000
181A184LYS10.8870.93923.8979.1069.1060.0000.0000.0000.000
182A185ALA0-0.046-0.01324.9500.1470.1470.0000.0000.0000.000
183A186GLY0-0.0210.00823.059-0.083-0.0830.0000.0000.0000.000
184A187ILE0-0.022-0.00318.831-0.551-0.5510.0000.0000.0000.000
185A188ALA0-0.018-0.00915.1930.2020.2020.0000.0000.0000.000
186A189VAL00.004-0.00216.695-0.558-0.5580.0000.0000.0000.000
187A190ILE0-0.0020.00112.715-0.071-0.0710.0000.0000.0000.000
188A191ALA00.0110.01017.3560.1730.1730.0000.0000.0000.000
189A192GLU-1-0.795-0.92617.928-15.089-15.0890.0000.0000.0000.000
190A193GLY00.0570.03721.3580.1990.1990.0000.0000.0000.000
191A194LYS10.8230.90924.5269.8859.8850.0000.0000.0000.000
192A195ILE0-0.0070.01923.1090.3480.3480.0000.0000.0000.000
193A196HIS00.008-0.02026.855-0.361-0.3610.0000.0000.0000.000
194A197SER0-0.0020.01429.6360.1280.1280.0000.0000.0000.000
195A198PRO00.0630.01628.344-0.250-0.2500.0000.0000.0000.000
196A199GLU-1-0.885-0.94629.190-8.689-8.6890.0000.0000.0000.000
197A200GLU-1-0.920-0.96929.142-9.270-9.2700.0000.0000.0000.000
198A201ALA00.0300.01224.989-0.175-0.1750.0000.0000.0000.000
199A202LYS10.9030.95125.8208.7008.7000.0000.0000.0000.000
200A203LYS10.9590.98427.9568.6938.6930.0000.0000.0000.000
201A204ILE00.008-0.00723.504-0.011-0.0110.0000.0000.0000.000
202A205ASN00.001-0.00122.469-0.593-0.5930.0000.0000.0000.000
203A206ASP-1-0.898-0.94824.479-9.581-9.5810.0000.0000.0000.000
204A207LEU0-0.090-0.03925.4590.1590.1590.0000.0000.0000.000
205A208GLY0-0.043-0.00423.195-0.007-0.0070.0000.0000.0000.000
206A209VAL0-0.024-0.01119.957-0.277-0.2770.0000.0000.0000.000
207A210ALA0-0.043-0.02514.976-0.085-0.0850.0000.0000.0000.000
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209A212ILE00.0060.00517.0070.4640.4640.0000.0000.0000.000
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