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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: 3J44L

Calculation Name: 1YK9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YK9

Chain ID: A

ChEMBL ID:

UniProt ID: P9WQ35

Base Structure: X-ray

Registration Date: 2023-09-23

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1844184.488615
FMO2-HF: Nuclear repulsion 1773211.66308
FMO2-HF: Total energy -70972.825535
FMO2-MP2: Total energy -71180.269285


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:245:ASP)


Summations of interaction energy for fragment #1(A:245:ASP)
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.
12.96519.4862.923-4.577-4.8660.045
Interaction energy analysis for fragmet #1(A:245:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.906 / q_NPA : -0.959
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].
3A247TYR00.007-0.0113.8550.6822.896-0.011-1.227-0.9750.004
4A248ASP-1-0.805-0.9116.50228.16428.1640.0000.0000.0000.000
5A249GLU-1-0.787-0.8379.97016.01016.0100.0000.0000.0000.000
6A250ALA0-0.038-0.00310.9380.6870.6870.0000.0000.0000.000
7A251SER00.0330.00212.958-1.196-1.1960.0000.0000.0000.000
8A252VAL0-0.061-0.03114.8281.0831.0830.0000.0000.0000.000
9A253LEU00.0400.02716.718-0.985-0.9850.0000.0000.0000.000
10A254PHE00.001-0.00918.7130.8710.8710.0000.0000.0000.000
11A255ALA00.0340.01421.012-0.645-0.6450.0000.0000.0000.000
12A256ASP-1-0.796-0.89624.05011.71611.7160.0000.0000.0000.000
13A257ILE00.0220.04026.844-0.392-0.3920.0000.0000.0000.000
14A258VAL00.0850.06030.447-0.200-0.2000.0000.0000.0000.000
15A259GLY0-0.056-0.06332.873-0.411-0.4110.0000.0000.0000.000
16A260PHE00.0040.01530.978-0.306-0.3060.0000.0000.0000.000
17A261THR0-0.024-0.01833.740-0.021-0.0210.0000.0000.0000.000
18A262GLU-1-0.927-0.97134.6228.7928.7920.0000.0000.0000.000
19A263ARG10.8120.91636.431-8.646-8.6460.0000.0000.0000.000
20A264ALA00.027-0.00439.844-0.157-0.1570.0000.0000.0000.000
21A265SER0-0.035-0.00239.829-0.233-0.2330.0000.0000.0000.000
22A266SER00.0220.00041.9210.0630.0630.0000.0000.0000.000
23A267THR00.0080.01238.6090.1090.1090.0000.0000.0000.000
24A268ALA0-0.005-0.00240.519-0.194-0.1940.0000.0000.0000.000
25A269PRO00.0230.01939.2130.1950.1950.0000.0000.0000.000
26A270ALA00.010-0.00639.6270.1450.1450.0000.0000.0000.000
27A271ASP-1-0.866-0.92840.5297.4677.4670.0000.0000.0000.000
28A272LEU0-0.021-0.03637.9000.1690.1690.0000.0000.0000.000
29A273VAL0-0.041-0.00833.798-0.021-0.0210.0000.0000.0000.000
30A274ARG10.8970.95334.384-8.520-8.5200.0000.0000.0000.000
31A275PHE0-0.012-0.02434.9610.1400.1400.0000.0000.0000.000
32A276LEU00.0110.01633.0340.0160.0160.0000.0000.0000.000
33A277ASP-1-0.819-0.92130.37910.39610.3960.0000.0000.0000.000
34A278ARG10.9020.95630.207-8.378-8.3780.0000.0000.0000.000
35A279LEU0-0.0150.00531.5240.0190.0190.0000.0000.0000.000
36A280TYR0-0.013-0.02125.5490.1920.1920.0000.0000.0000.000
37A281SER0-0.071-0.03426.5390.3330.3330.0000.0000.0000.000
38A282ALA00.0440.02027.6220.2730.2730.0000.0000.0000.000
39A283PHE0-0.020-0.01025.1820.0120.0120.0000.0000.0000.000
40A284ASP-1-0.776-0.86422.60014.52614.5260.0000.0000.0000.000
41A285GLU-1-0.943-0.97123.96811.01211.0120.0000.0000.0000.000
42A286LEU0-0.046-0.01925.850-0.324-0.3240.0000.0000.0000.000
43A287VAL0-0.0020.00419.3670.1540.1540.0000.0000.0000.000
44A288ASP-1-0.932-0.95621.46614.26014.2600.0000.0000.0000.000
45A289GLN0-0.057-0.03022.190-0.326-0.3260.0000.0000.0000.000
46A290HIS00.013-0.00619.6240.2760.2760.0000.0000.0000.000
47A291GLY0-0.060-0.02815.8910.4550.4550.0000.0000.0000.000
48A292LEU0-0.038-0.01615.1571.1041.1040.0000.0000.0000.000
49A293GLU-1-0.834-0.91913.46819.79019.7900.0000.0000.0000.000
50A294LYS10.8270.90915.164-14.756-14.7560.0000.0000.0000.000
51A295ILE0-0.069-0.03010.5191.4231.4230.0000.0000.0000.000
52A296GLU-1-0.772-0.87412.89423.65323.6530.0000.0000.0000.000
53A297VAL00.0200.00715.230-0.699-0.6990.0000.0000.0000.000
54A298SER0-0.051-0.02419.0150.2060.2060.0000.0000.0000.000
55A299GLY0-0.012-0.02121.447-0.422-0.4220.0000.0000.0000.000
56A300ASP-1-0.881-0.92124.53411.82211.8220.0000.0000.0000.000
57A301SER0-0.048-0.00122.6300.1600.1600.0000.0000.0000.000
58A302TYR0-0.020-0.03421.2610.5970.5970.0000.0000.0000.000
59A303MET0-0.050-0.01914.0430.2350.2350.0000.0000.0000.000
60A304VAL00.0380.01916.2680.6050.6050.0000.0000.0000.000
61A305VAL0-0.034-0.01111.054-0.230-0.2300.0000.0000.0000.000
62A306SER00.0810.03414.151-0.328-0.3280.0000.0000.0000.000
63A307GLY0-0.062-0.03210.206-0.127-0.1270.0000.0000.0000.000
64A308VAL00.0160.0178.6973.5983.5980.0000.0000.0000.000
65A309PRO0-0.001-0.0226.637-0.406-0.4060.0000.0000.0000.000
66A310ARG10.8810.9617.805-19.717-19.7170.0000.0000.0000.000
67A311PRO00.0960.0559.264-1.802-1.8020.0000.0000.0000.000
68A312ARG10.9240.94112.192-19.051-19.0510.0000.0000.0000.000
69A313PRO00.018-0.00315.9090.3960.3960.0000.0000.0000.000
70A314ASP-1-0.884-0.94618.29114.14814.1480.0000.0000.0000.000
71A315HIS0-0.0020.02115.291-0.274-0.2740.0000.0000.0000.000
72A316THR00.0210.00717.2410.0190.0190.0000.0000.0000.000
73A317GLN00.0180.00819.830-0.187-0.1870.0000.0000.0000.000
74A318ALA00.0300.01719.089-0.388-0.3880.0000.0000.0000.000
75A319LEU0-0.014-0.00717.1340.2600.2600.0000.0000.0000.000
76A320ALA0-0.024-0.00421.427-0.427-0.4270.0000.0000.0000.000
77A321ASP-1-0.843-0.92924.64611.63211.6320.0000.0000.0000.000
78A322PHE00.0420.03222.690-0.268-0.2680.0000.0000.0000.000
79A323ALA0-0.001-0.01424.733-0.223-0.2230.0000.0000.0000.000
80A324LEU0-0.073-0.02826.096-0.417-0.4170.0000.0000.0000.000
81A325ASP-1-0.817-0.91828.2259.9779.9770.0000.0000.0000.000
82A326MET0-0.051-0.00625.179-0.110-0.1100.0000.0000.0000.000
83A327THR0-0.004-0.01528.617-0.115-0.1150.0000.0000.0000.000
84A328ASN0-0.070-0.03132.112-0.578-0.5780.0000.0000.0000.000
85A329VAL00.0390.01230.493-0.339-0.3390.0000.0000.0000.000
86A330ALA0-0.007-0.00331.902-0.231-0.2310.0000.0000.0000.000
87A331ALA0-0.060-0.02233.797-0.252-0.2520.0000.0000.0000.000
88A332GLN0-0.028-0.00936.754-0.459-0.4590.0000.0000.0000.000
89A333LEU00.0050.01235.705-0.255-0.2550.0000.0000.0000.000
90A334LYS10.7880.89338.192-8.206-8.2060.0000.0000.0000.000
91A335ASP-1-0.898-0.93641.6066.7766.7760.0000.0000.0000.000
92A336PRO00.0260.00942.8740.0910.0910.0000.0000.0000.000
93A337ARG10.8890.93742.448-7.092-7.0920.0000.0000.0000.000
94A338GLY00.0820.05142.5450.1710.1710.0000.0000.0000.000
95A339ASN0-0.044-0.02238.7810.1300.1300.0000.0000.0000.000
96A340PRO00.0100.00839.3090.0060.0060.0000.0000.0000.000
97A341VAL00.0580.01534.3030.1160.1160.0000.0000.0000.000
98A342PRO0-0.0320.00035.1950.0570.0570.0000.0000.0000.000
99A343LEU00.006-0.01328.0690.1560.1560.0000.0000.0000.000
100A344ARG10.7460.86028.566-11.135-11.1350.0000.0000.0000.000
101A345VAL00.0160.00024.6740.4410.4410.0000.0000.0000.000
102A346GLY0-0.0020.00824.042-0.438-0.4380.0000.0000.0000.000
103A347LEU0-0.003-0.00521.2510.6260.6260.0000.0000.0000.000
104A348ALA0-0.016-0.01518.301-0.399-0.3990.0000.0000.0000.000
105A349THR0-0.014-0.02416.4980.7190.7190.0000.0000.0000.000
106A350GLY00.0290.01615.053-0.819-0.8190.0000.0000.0000.000
107A351PRO00.0000.01210.7970.8280.8280.0000.0000.0000.000
108A352VAL0-0.054-0.0388.469-0.772-0.7720.0000.0000.0000.000
109A353VAL0-0.031-0.0033.6291.2691.3300.004-0.039-0.0260.000
110A354ALA00.0080.0082.404-9.646-7.7262.047-1.898-2.0700.026
111A355GLY0-0.003-0.0034.351-0.396-0.2830.000-0.053-0.0600.000
112A356VAL0-0.038-0.0242.851-6.723-4.5110.884-1.359-1.7360.015
113A357VAL0-0.0090.0045.659-1.049-1.048-0.001-0.0010.0010.000
114A358GLY00.0520.0428.220-2.642-2.6420.0000.0000.0000.000
115A359SER0-0.040-0.0329.798-3.053-3.0530.0000.0000.0000.000
116A360ARG10.9950.99911.797-22.913-22.9130.0000.0000.0000.000
117A361ARG10.8920.91814.291-18.370-18.3700.0000.0000.0000.000
118A362PHE00.0520.04012.8991.8001.8000.0000.0000.0000.000
119A363ARG10.8050.88711.334-24.566-24.5660.0000.0000.0000.000
120A364TYR00.0340.0157.4802.6342.6340.0000.0000.0000.000
121A365CYS0-0.063-0.0426.9204.9224.9220.0000.0000.0000.000
122A366VAL00.0580.0267.8533.2823.2820.0000.0000.0000.000
123A367TRP0-0.021-0.0058.569-3.614-3.6140.0000.0000.0000.000
124A368GLY00.0860.0419.2331.8521.8520.0000.0000.0000.000
125A369ASP-1-0.838-0.91311.32015.12915.1290.0000.0000.0000.000
126A370ALA00.0670.03513.745-1.052-1.0520.0000.0000.0000.000
127A371VAL00.0420.01312.045-0.956-0.9560.0000.0000.0000.000
128A372ASN0-0.054-0.02415.148-1.421-1.4210.0000.0000.0000.000
129A373VAL0-0.036-0.03217.302-1.182-1.1820.0000.0000.0000.000
130A374ALA00.0480.03518.088-0.769-0.7690.0000.0000.0000.000
131A375SER00.0230.02219.974-0.704-0.7040.0000.0000.0000.000
132A376ARG10.8360.91720.558-14.708-14.7080.0000.0000.0000.000
133A377MET0-0.0260.02523.547-0.781-0.7810.0000.0000.0000.000
134A378GLU-1-0.662-0.80924.66411.60811.6080.0000.0000.0000.000
135A379SER0-0.111-0.07125.741-0.458-0.4580.0000.0000.0000.000
136A380THR0-0.087-0.05127.998-0.449-0.4490.0000.0000.0000.000
137A381ASP-1-0.778-0.88429.6419.8659.8650.0000.0000.0000.000
138A382SER0-0.090-0.06131.362-0.354-0.3540.0000.0000.0000.000
139A383VAL0-0.037-0.01334.8810.0760.0760.0000.0000.0000.000
140A384GLY0-0.025-0.01033.499-0.119-0.1190.0000.0000.0000.000
141A385GLN0-0.031-0.01732.514-0.128-0.1280.0000.0000.0000.000
142A386ILE00.0490.02426.9440.2920.2920.0000.0000.0000.000
143A387GLN0-0.0050.00827.643-0.521-0.5210.0000.0000.0000.000
144A388VAL0-0.024-0.02325.3470.5880.5880.0000.0000.0000.000
145A389PRO00.0210.01622.301-0.468-0.4680.0000.0000.0000.000
146A390ASP-1-0.718-0.89025.50111.31111.3110.0000.0000.0000.000
147A391GLU-1-0.877-0.91420.82613.34613.3460.0000.0000.0000.000
148A392VAL0-0.031-0.02121.1280.4280.4280.0000.0000.0000.000
149A393TYR0-0.047-0.00423.455-0.205-0.2050.0000.0000.0000.000
150A394GLU-1-0.891-0.95524.76910.49910.4990.0000.0000.0000.000
151A395ARG10.7100.83217.944-15.245-15.2450.0000.0000.0000.000
152A396LEU00.0060.01124.2810.2580.2580.0000.0000.0000.000
153A397LYS10.8510.90421.887-13.179-13.1790.0000.0000.0000.000
154A398ASP-1-0.885-0.93728.2899.3049.3040.0000.0000.0000.000
155A399ASP-1-0.897-0.94828.45610.23410.2340.0000.0000.0000.000
156A400PHE0-0.030-0.02826.3660.0520.0520.0000.0000.0000.000
157A401VAL0-0.0180.00131.085-0.204-0.2040.0000.0000.0000.000
158A402LEU00.0330.01128.5520.1730.1730.0000.0000.0000.000
159A403ARG10.8560.92433.185-8.544-8.5440.0000.0000.0000.000
160A404GLU-1-0.859-0.93133.7808.8708.8700.0000.0000.0000.000
161A405ARG10.8280.90231.979-9.659-9.6590.0000.0000.0000.000
162A406GLY00.0160.01834.412-0.222-0.2220.0000.0000.0000.000
163A407HIS0-0.023-0.00932.9910.3710.3710.0000.0000.0000.000
164A408ILE00.022-0.01232.729-0.205-0.2050.0000.0000.0000.000
165A409ASN0-0.034-0.02333.052-0.210-0.2100.0000.0000.0000.000
166A410VAL00.0450.02126.5790.2500.2500.0000.0000.0000.000
167A411LYS10.9720.98828.600-9.885-9.8850.0000.0000.0000.000
168A412GLY00.0400.00924.4680.0070.0070.0000.0000.0000.000
169A413LYS10.8700.90719.467-14.033-14.0330.0000.0000.0000.000
170A414GLY0-0.0250.01725.505-0.098-0.0980.0000.0000.0000.000
171A415VAL0-0.014-0.00628.365-0.408-0.4080.0000.0000.0000.000
172A416MET0-0.0510.00128.5630.3230.3230.0000.0000.0000.000
173A417ARG10.7730.84823.384-12.152-12.1520.0000.0000.0000.000
174A418THR00.0160.02529.971-0.082-0.0820.0000.0000.0000.000
175A419TRP0-0.0060.00325.5210.4950.4950.0000.0000.0000.000
176A420TYR00.0530.00928.991-0.553-0.5530.0000.0000.0000.000
177A421LEU00.0010.00830.0260.2520.2520.0000.0000.0000.000
178A422ILE0-0.0010.00927.651-0.262-0.2620.0000.0000.0000.000
179A423GLY00.0050.00530.771-0.087-0.0870.0000.0000.0000.000
180A424ARG10.8760.91632.639-8.765-8.7650.0000.0000.0000.000
181A425LYS10.9060.96826.977-11.102-11.1020.0000.0000.0000.000
182A426VAL0-0.055-0.02131.910-0.350-0.3500.0000.0000.0000.000
183A427ALA00.0230.00033.4120.2090.2090.0000.0000.0000.000
184A428ALA0-0.0190.00735.881-0.324-0.3240.0000.0000.0000.000