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: K3ML3

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2707182.668407
FMO2-HF: Nuclear repulsion 2620394.55163
FMO2-HF: Total energy -86788.116777
FMO2-MP2: Total energy -87039.692352


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.
-184.552-179.58515.418-9.247-11.137-0.096
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 : 0.888 / q_NPA : 0.928
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].
3A6THR00.0600.0183.886-2.728-1.396-0.007-0.619-0.7070.002
4A7LYS10.8500.9146.17721.84821.8480.0000.0000.0000.000
5A8GLU-1-0.904-0.9548.393-17.713-17.7130.0000.0000.0000.000
6A9LYS10.8450.9038.46219.24219.2420.0000.0000.0000.000
7A10LEU0-0.0180.0066.6230.5300.5300.0000.0000.0000.000
8A11MET0-0.011-0.0198.7761.0601.0600.0000.0000.0000.000
9A12GLU-1-0.901-0.93412.301-16.117-16.1170.0000.0000.0000.000
10A13GLN0-0.045-0.02210.5680.9460.9460.0000.0000.0000.000
11A14LEU0-0.020-0.01810.6700.5800.5800.0000.0000.0000.000
12A15LYS10.9510.97813.97813.65013.6500.0000.0000.0000.000
13A16GLY00.0010.01017.1120.2680.2680.0000.0000.0000.000
14A17GLY00.0070.00918.5260.4640.4640.0000.0000.0000.000
15A18ILE0-0.052-0.02618.722-0.088-0.0880.0000.0000.0000.000
16A19ILE00.0020.01413.576-0.356-0.3560.0000.0000.0000.000
17A20VAL00.0380.00516.5870.5950.5950.0000.0000.0000.000
18A21SER00.0160.00617.204-0.944-0.9440.0000.0000.0000.000
19A22CYS0-0.0350.01517.8791.0351.0350.0000.0000.0000.000
20A23GLN00.021-0.00818.816-0.614-0.6140.0000.0000.0000.000
21A24ALA00.0470.02221.0910.6310.6310.0000.0000.0000.000
22A25LEU0-0.010-0.00421.948-0.415-0.4150.0000.0000.0000.000
23A26PRO00.012-0.00824.8380.4260.4260.0000.0000.0000.000
24A27GLY00.0330.02627.9970.1380.1380.0000.0000.0000.000
25A28GLH0-0.080-0.08426.1920.1430.1430.0000.0000.0000.000
26A29PRO0-0.002-0.01130.097-0.102-0.1020.0000.0000.0000.000
27A30LEU0-0.0030.00026.9230.1040.1040.0000.0000.0000.000
28A31TYR0-0.010-0.00324.207-0.614-0.6140.0000.0000.0000.000
29A32SER0-0.007-0.00825.9470.5510.5510.0000.0000.0000.000
30A33GLU-1-0.917-0.95325.425-11.081-11.0810.0000.0000.0000.000
31A34THR0-0.026-0.02425.189-0.349-0.3490.0000.0000.0000.000
32A35GLY00.0120.02922.958-0.251-0.2510.0000.0000.0000.000
33A36GLY0-0.007-0.01422.5790.6840.6840.0000.0000.0000.000
34A37ILE0-0.025-0.02123.9010.0850.0850.0000.0000.0000.000
35A38MET00.0110.00919.5310.0360.0360.0000.0000.0000.000
36A39PRO00.0360.02818.463-0.246-0.2460.0000.0000.0000.000
37A40LEU00.0100.00419.4650.0840.0840.0000.0000.0000.000
38A41MET0-0.0280.00221.4980.3030.3030.0000.0000.0000.000
39A42ALA00.0570.00516.6200.1060.1060.0000.0000.0000.000
40A43LYS10.7910.88518.56412.03012.0300.0000.0000.0000.000
41A44ALA00.0180.01020.1370.1870.1870.0000.0000.0000.000
42A45ALA0-0.017-0.01118.8860.2770.2770.0000.0000.0000.000
43A46GLN00.0260.02415.951-0.560-0.5600.0000.0000.0000.000
44A47GLU-1-0.856-0.91118.851-11.769-11.7690.0000.0000.0000.000
45A48ALA0-0.060-0.02222.3930.4330.4330.0000.0000.0000.000
46A49GLY0-0.0110.00320.2750.2830.2830.0000.0000.0000.000
47A50ALA0-0.066-0.02917.598-0.100-0.1000.0000.0000.0000.000
48A51VAL00.0200.01714.542-0.470-0.4700.0000.0000.0000.000
49A52GLY00.0530.01012.426-1.245-1.2450.0000.0000.0000.000
50A53ILE0-0.036-0.00512.1741.2731.2730.0000.0000.0000.000
51A54ARG10.7300.82612.37316.14916.1490.0000.0000.0000.000
52A55ALA00.0090.00213.9031.0681.0680.0000.0000.0000.000
53A56ASN00.027-0.00314.687-1.027-1.0270.0000.0000.0000.000
54A57SER0-0.021-0.02115.3620.5960.5960.0000.0000.0000.000
55A58VAL00.0660.01512.346-0.702-0.7020.0000.0000.0000.000
56A59ARG10.8020.88613.94013.66813.6680.0000.0000.0000.000
57A60ASP-1-0.776-0.85416.273-15.910-15.9100.0000.0000.0000.000
58A61ILE00.0070.01510.113-0.244-0.2440.0000.0000.0000.000
59A62LYS10.8890.9389.34528.71028.7100.0000.0000.0000.000
60A63GLU-1-0.834-0.92313.484-14.721-14.7210.0000.0000.0000.000
61A64ILE0-0.017-0.01413.2620.5310.5310.0000.0000.0000.000
62A65GLN00.008-0.0167.7241.4221.4220.0000.0000.0000.000
63A66ALA0-0.049-0.00212.222-0.130-0.1300.0000.0000.0000.000
64A67ILE0-0.094-0.04315.1751.0371.0370.0000.0000.0000.000
65A68THR0-0.034-0.03812.7700.6910.6910.0000.0000.0000.000
66A69ASP-1-0.888-0.93110.092-21.899-21.8990.0000.0000.0000.000
67A70LEU0-0.059-0.0149.325-0.968-0.9680.0000.0000.0000.000
68A71PRO0-0.030-0.0167.477-1.611-1.6110.0000.0000.0000.000
69A72ILE00.0090.0007.9991.3161.3160.0000.0000.0000.000
70A73ILE00.0100.0018.069-2.673-2.6730.0000.0000.0000.000
71A74GLY00.015-0.0089.9641.6491.6490.0000.0000.0000.000
72A75ILE0-0.032-0.02111.423-0.257-0.2570.0000.0000.0000.000
73A76ILE00.012-0.00813.0110.1050.1050.0000.0000.0000.000
74A77LYS10.8480.93216.06014.54814.5480.0000.0000.0000.000
75A78LYS10.8260.91619.69214.48214.4820.0000.0000.0000.000
76A79ASP-1-0.857-0.92621.299-12.392-12.3920.0000.0000.0000.000
77A80TYR0-0.066-0.07119.223-0.035-0.0350.0000.0000.0000.000
78A81PRO00.0420.04825.2430.1410.1410.0000.0000.0000.000
79A82PRO0-0.030-0.03828.999-0.042-0.0420.0000.0000.0000.000
80A83GLN00.0110.00926.7500.1280.1280.0000.0000.0000.000
81A84GLU-1-0.841-0.90827.527-10.492-10.4920.0000.0000.0000.000
82A85PRO0-0.049-0.01422.293-0.206-0.2060.0000.0000.0000.000
83A86PHE00.0540.01722.037-0.158-0.1580.0000.0000.0000.000
84A87ILE0-0.036-0.01717.018-0.493-0.4930.0000.0000.0000.000
85A88THR0-0.030-0.04312.798-0.212-0.2120.0000.0000.0000.000
86A89ALA00.0170.03616.117-0.344-0.3440.0000.0000.0000.000
87A90THR00.003-0.00817.5450.4170.4170.0000.0000.0000.000
88A91MET00.0510.00713.311-1.765-1.7650.0000.0000.0000.000
89A92THR00.0020.01013.457-1.692-1.6920.0000.0000.0000.000
90A93GLU-1-0.746-0.83013.678-18.657-18.6570.0000.0000.0000.000
91A94VAL00.0200.0109.840-1.877-1.8770.0000.0000.0000.000
92A95ASP-1-0.750-0.8429.210-29.955-29.9550.0000.0000.0000.000
93A96GLN0-0.047-0.0278.638-2.791-2.7910.0000.0000.0000.000
94A97LEU0-0.015-0.0048.641-1.330-1.3300.0000.0000.0000.000
95A98ALA00.0250.0145.011-4.160-4.1600.0000.0000.0000.000
96A99ALA0-0.055-0.0233.930-13.399-13.196-0.001-0.077-0.1250.000
97A100LEU0-0.050-0.0206.1291.0581.0580.0000.0000.0000.000
98A101ASN0-0.0300.0051.718-39.584-42.27814.182-6.099-5.388-0.072
99A102ILE00.0210.0283.8106.1856.5370.000-0.021-0.3310.000
100A103ALA00.0110.0103.304-7.109-6.3370.021-0.212-0.582-0.001
101A104VAL0-0.034-0.0174.375-1.800-1.635-0.001-0.015-0.1490.000
102A105ILE00.0080.0236.1650.8170.8170.0000.0000.0000.000
103A106ALA00.0060.0029.0091.0161.0160.0000.0000.0000.000
104A107MET00.0140.00311.721-0.153-0.1530.0000.0000.0000.000
105A108ASP-1-0.760-0.83715.687-13.093-13.0930.0000.0000.0000.000
106A109CYS0-0.066-0.02417.318-0.567-0.5670.0000.0000.0000.000
107A110THR0-0.032-0.03720.0690.6180.6180.0000.0000.0000.000
108A111LYS10.8480.93523.84210.02810.0280.0000.0000.0000.000
109A112ARG10.7570.84824.55012.27712.2770.0000.0000.0000.000
110A113ASP-1-0.888-0.94126.132-10.705-10.7050.0000.0000.0000.000
111A114ARG10.7970.86419.16615.01615.0160.0000.0000.0000.000
112A115HIS0-0.045-0.02423.7930.1360.1360.0000.0000.0000.000
113A116ASP-1-0.799-0.88520.026-15.008-15.0080.0000.0000.0000.000
114A117GLY0-0.027-0.01123.3650.0180.0180.0000.0000.0000.000
115A118LEU0-0.053-0.00619.7320.2430.2430.0000.0000.0000.000
116A119ASP-1-0.761-0.84723.560-12.940-12.9400.0000.0000.0000.000
117A120ILE00.0430.00319.179-0.587-0.5870.0000.0000.0000.000
118A121ALA00.0230.01319.552-0.846-0.8460.0000.0000.0000.000
119A122SER0-0.055-0.07119.049-0.806-0.8060.0000.0000.0000.000
120A123PHE0-0.0120.01315.546-0.790-0.7900.0000.0000.0000.000
121A124ILE00.0190.00814.372-1.238-1.2380.0000.0000.0000.000
122A125ARG10.9090.94214.13413.06713.0670.0000.0000.0000.000
123A126GLN0-0.009-0.00214.757-1.229-1.2290.0000.0000.0000.000
124A127VAL0-0.013-0.00810.136-1.479-1.4790.0000.0000.0000.000
125A128LYS10.8210.8957.74626.41726.4170.0000.0000.0000.000
126A129GLU-1-0.938-0.96310.699-20.716-20.7160.0000.0000.0000.000
127A130LYS10.7580.8789.86724.50824.5080.0000.0000.0000.000
128A131TYR0-0.090-0.0835.639-4.313-4.3130.0000.0000.0000.000
129A132PRO00.0590.0446.939-1.863-1.8630.0000.0000.0000.000
130A133ASN0-0.075-0.0513.8813.8654.0880.000-0.038-0.1840.000
131A134GLN0-0.047-0.0132.585-28.135-23.6801.223-2.142-3.536-0.025
132A135LEU0-0.0030.0134.0396.8857.0440.001-0.024-0.1350.000
133A136LEU00.0200.0006.684-1.228-1.2280.0000.0000.0000.000
134A137MET0-0.010-0.0199.6951.2971.2970.0000.0000.0000.000
135A138ALA00.0440.00612.962-0.048-0.0480.0000.0000.0000.000
136A139ASP-1-0.787-0.86116.465-16.433-16.4330.0000.0000.0000.000
137A140ILE0-0.030-0.01718.8410.3190.3190.0000.0000.0000.000
138A141SER0-0.043-0.05422.2330.3200.3200.0000.0000.0000.000
139A142THR0-0.014-0.03325.8330.5270.5270.0000.0000.0000.000
140A143PHE00.0480.00025.648-0.382-0.3820.0000.0000.0000.000
141A144ASP-1-0.895-0.94425.781-11.002-11.0020.0000.0000.0000.000
142A145GLU-1-0.671-0.78223.645-11.980-11.9800.0000.0000.0000.000
143A146GLY00.0330.02021.535-0.630-0.6300.0000.0000.0000.000
144A147LEU0-0.012-0.00721.373-0.544-0.5440.0000.0000.0000.000
145A148VAL0-0.017-0.01122.376-0.426-0.4260.0000.0000.0000.000
146A149ALA00.0280.00318.201-0.464-0.4640.0000.0000.0000.000
147A150HIS0-0.012-0.01417.342-1.272-1.2720.0000.0000.0000.000
148A151GLN0-0.034-0.02118.150-0.640-0.6400.0000.0000.0000.000
149A152ALA0-0.048-0.00518.2880.1200.1200.0000.0000.0000.000
150A153GLY0-0.0010.00415.037-0.605-0.6050.0000.0000.0000.000
151A154ILE0-0.044-0.01813.086-1.740-1.7400.0000.0000.0000.000
152A155ASP-1-0.819-0.8949.055-25.353-25.3530.0000.0000.0000.000
153A156PHE00.0440.0048.9170.8090.8090.0000.0000.0000.000
154A157VAL00.0050.01413.972-0.214-0.2140.0000.0000.0000.000
155A158GLY00.0820.04117.3150.2350.2350.0000.0000.0000.000
156A159THR0-0.039-0.04018.6670.0600.0600.0000.0000.0000.000
157A160THR0-0.075-0.05419.6470.8250.8250.0000.0000.0000.000
158A161LEU00.0230.01321.8820.3160.3160.0000.0000.0000.000
159A162SER0-0.041-0.05224.6580.4990.4990.0000.0000.0000.000
160A163GLY0-0.042-0.02627.2840.0760.0760.0000.0000.0000.000
161A164TYR0-0.053-0.02326.6970.1760.1760.0000.0000.0000.000
162A165THR00.0370.02727.186-0.118-0.1180.0000.0000.0000.000
163A166PRO00.0330.00229.9170.1830.1830.0000.0000.0000.000
164A167TYR0-0.057-0.05227.4170.3670.3670.0000.0000.0000.000
165A168SER00.0040.01229.445-0.032-0.0320.0000.0000.0000.000
166A169ARG10.8740.94030.7959.5139.5130.0000.0000.0000.000
167A170GLN0-0.030-0.03231.738-0.155-0.1550.0000.0000.0000.000
168A171GLU-1-0.921-0.95634.134-8.456-8.4560.0000.0000.0000.000
169A172ALA00.0260.01632.968-0.307-0.3070.0000.0000.0000.000
170A173GLY00.0470.03731.2010.0860.0860.0000.0000.0000.000
171A174PRO00.0130.01826.824-0.089-0.0890.0000.0000.0000.000
172A175ASP-1-0.786-0.88626.971-9.782-9.7820.0000.0000.0000.000
173A176VAL0-0.001-0.02427.242-0.245-0.2450.0000.0000.0000.000
174A177ALA00.0190.02728.398-0.066-0.0660.0000.0000.0000.000
175A178LEU0-0.0180.00824.966-0.073-0.0730.0000.0000.0000.000
176A179ILE00.0190.00222.860-0.306-0.3060.0000.0000.0000.000
177A180GLU-1-0.828-0.89524.511-9.514-9.5140.0000.0000.0000.000
178A181ALA0-0.022-0.01027.010-0.030-0.0300.0000.0000.0000.000
179A182LEU0-0.010-0.01321.894-0.052-0.0520.0000.0000.0000.000
180A183CYS0-0.017-0.00322.814-0.410-0.4100.0000.0000.0000.000
181A184LYS10.8170.88923.8269.4259.4250.0000.0000.0000.000
182A185ALA0-0.047-0.01624.6960.1800.1800.0000.0000.0000.000
183A186GLY0-0.0150.00422.867-0.151-0.1510.0000.0000.0000.000
184A187ILE0-0.036-0.00618.788-0.586-0.5860.0000.0000.0000.000
185A188ALA00.0140.00614.8600.2650.2650.0000.0000.0000.000
186A189VAL0-0.027-0.02216.110-0.762-0.7620.0000.0000.0000.000
187A190ILE0-0.009-0.00112.429-0.082-0.0820.0000.0000.0000.000
188A191ALA00.0040.01216.9520.0990.0990.0000.0000.0000.000
189A192GLU-1-0.789-0.86817.604-15.846-15.8460.0000.0000.0000.000
190A193GLY00.0550.04520.9240.2690.2690.0000.0000.0000.000
191A194LYS10.8090.89524.06810.14710.1470.0000.0000.0000.000
192A195ILE00.0000.01322.8040.4080.4080.0000.0000.0000.000
193A196HIS0-0.019-0.02226.659-0.238-0.2380.0000.0000.0000.000
194A197SER0-0.023-0.01129.2310.2130.2130.0000.0000.0000.000
195A198PRO00.0430.01427.881-0.313-0.3130.0000.0000.0000.000
196A199GLU-1-0.855-0.93228.615-8.999-8.9990.0000.0000.0000.000
197A200GLU-1-0.890-0.94728.548-9.479-9.4790.0000.0000.0000.000
198A201ALA00.0380.02124.434-0.195-0.1950.0000.0000.0000.000
199A202LYS10.8260.89225.3089.1489.1480.0000.0000.0000.000
200A203LYS10.9480.96927.5679.0149.0140.0000.0000.0000.000
201A204ILE00.003-0.01223.017-0.011-0.0110.0000.0000.0000.000
202A205ASN0-0.037-0.01523.001-0.621-0.6210.0000.0000.0000.000
203A206ASP-1-0.827-0.89824.130-9.799-9.7990.0000.0000.0000.000
204A207LEU0-0.070-0.02324.9880.1800.1800.0000.0000.0000.000
205A208GLY0-0.026-0.00623.244-0.008-0.0080.0000.0000.0000.000
206A209VAL0-0.044-0.02019.517-0.377-0.3770.0000.0000.0000.000
207A210ALA0-0.017-0.00614.7430.0050.0050.0000.0000.0000.000
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