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: G5LQ1

Calculation Name: 1ULY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ULY

Chain ID: A

ChEMBL ID:

UniProt ID: O59595

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2127252.334178
FMO2-HF: Nuclear repulsion 2049154.960095
FMO2-HF: Total energy -78097.374084
FMO2-MP2: Total energy -78327.556058


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-19.18-22.01725.557-12.147-10.573-0.085
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.016
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].
3A4LYS10.8600.9322.874-0.4863.1200.016-1.989-1.6330.010
4A5VAL0-0.085-0.0413.3021.6152.1620.003-0.212-0.3380.001
5A6LYS10.9801.0032.280-4.772-4.6312.614-1.365-1.390-0.013
6A7VAL0-0.051-0.0234.1870.7280.813-0.001-0.019-0.0650.000
7A8ILE0-0.053-0.0347.1460.3300.3300.0000.0000.0000.000
8A9THR00.008-0.0239.8540.0140.0140.0000.0000.0000.000
9A10ASP-1-0.863-0.92312.6380.1000.1000.0000.0000.0000.000
10A11PRO00.034-0.00514.591-0.065-0.0650.0000.0000.0000.000
11A12GLU-1-0.802-0.89917.756-0.049-0.0490.0000.0000.0000.000
12A13VAL00.0300.01012.195-0.038-0.0380.0000.0000.0000.000
13A14ILE0-0.044-0.03414.149-0.064-0.0640.0000.0000.0000.000
14A15LYS10.8360.92615.9330.0100.0100.0000.0000.0000.000
15A16VAL0-0.0140.01417.448-0.012-0.0120.0000.0000.0000.000
16A17MET0-0.075-0.03612.332-0.015-0.0150.0000.0000.0000.000
17A18LEU0-0.050-0.02517.115-0.028-0.0280.0000.0000.0000.000
18A19GLU-1-0.866-0.91919.750-0.179-0.1790.0000.0000.0000.000
19A20ASP-1-0.858-0.94221.408-0.235-0.2350.0000.0000.0000.000
20A21THR0-0.054-0.03522.680-0.021-0.0210.0000.0000.0000.000
21A22ARG10.9210.94318.9670.1630.1630.0000.0000.0000.000
22A23ARG10.9360.98818.0010.2820.2820.0000.0000.0000.000
23A24LYS10.9210.95818.4120.1920.1920.0000.0000.0000.000
24A25ILE00.0310.03118.158-0.019-0.0190.0000.0000.0000.000
25A26LEU00.0280.02113.487-0.040-0.0400.0000.0000.0000.000
26A27LYS10.9140.95415.4850.3740.3740.0000.0000.0000.000
27A28LEU00.0270.00417.380-0.029-0.0290.0000.0000.0000.000
28A29LEU0-0.023-0.01915.174-0.003-0.0030.0000.0000.0000.000
29A30ARG10.8790.95213.2500.8130.8130.0000.0000.0000.000
30A31ASN0-0.051-0.00915.096-0.018-0.0180.0000.0000.0000.000
31A32LYS10.9660.98616.5380.2850.2850.0000.0000.0000.000
32A33GLU-1-0.884-0.93916.295-0.304-0.3040.0000.0000.0000.000
33A34MET0-0.068-0.04017.7960.0490.0490.0000.0000.0000.000
34A35THR00.0290.01720.805-0.006-0.0060.0000.0000.0000.000
35A36ILE00.019-0.00423.504-0.012-0.0120.0000.0000.0000.000
36A37SER0-0.027-0.03425.126-0.001-0.0010.0000.0000.0000.000
37A38GLN00.0140.01624.042-0.014-0.0140.0000.0000.0000.000
38A39LEU00.0050.00420.709-0.005-0.0050.0000.0000.0000.000
39A40SER0-0.085-0.05124.7250.0030.0030.0000.0000.0000.000
40A41GLU-1-0.886-0.95028.084-0.128-0.1280.0000.0000.0000.000
41A42ILE0-0.026-0.00824.843-0.003-0.0030.0000.0000.0000.000
42A43LEU0-0.070-0.05923.104-0.004-0.0040.0000.0000.0000.000
43A44GLY00.0340.04427.4840.0060.0060.0000.0000.0000.000
44A45LYS10.8770.94627.9480.1650.1650.0000.0000.0000.000
45A46THR00.0410.04130.145-0.002-0.0020.0000.0000.0000.000
46A47PRO00.0890.02829.270-0.006-0.0060.0000.0000.0000.000
47A48GLN00.0510.01628.669-0.009-0.0090.0000.0000.0000.000
48A49THR00.0290.01327.8250.0000.0000.0000.0000.0000.000
49A50ILE0-0.009-0.00423.714-0.008-0.0080.0000.0000.0000.000
50A51TYR00.0120.00524.082-0.013-0.0130.0000.0000.0000.000
51A52HIS00.0410.01924.4160.0000.0000.0000.0000.0000.000
52A53HIS00.0070.02022.070-0.005-0.0050.0000.0000.0000.000
53A54ILE0-0.002-0.00919.136-0.017-0.0170.0000.0000.0000.000
54A55GLU-1-0.950-0.96719.460-0.081-0.0810.0000.0000.0000.000
55A56LYS10.9900.99520.2810.0940.0940.0000.0000.0000.000
56A57LEU0-0.014-0.01015.768-0.003-0.0030.0000.0000.0000.000
57A58LYS10.8980.95015.3820.0440.0440.0000.0000.0000.000
58A59GLU-1-0.968-0.97816.020-0.015-0.0150.0000.0000.0000.000
59A60ALA0-0.0170.00615.3380.0270.0270.0000.0000.0000.000
60A61GLY00.0340.01512.193-0.009-0.0090.0000.0000.0000.000
61A62LEU0-0.057-0.03310.710-0.136-0.1360.0000.0000.0000.000
62A63VAL0-0.044-0.02011.752-0.149-0.1490.0000.0000.0000.000
63A64GLU-1-0.837-0.92510.793-0.142-0.1420.0000.0000.0000.000
64A65VAL0-0.079-0.05514.429-0.035-0.0350.0000.0000.0000.000
65A66LYS10.8750.97011.3980.5540.5540.0000.0000.0000.000
66A67ARG10.9590.98716.2480.2080.2080.0000.0000.0000.000
67A68THR0-0.035-0.01919.821-0.017-0.0170.0000.0000.0000.000
68A69GLU-1-0.838-0.92023.342-0.106-0.1060.0000.0000.0000.000
69A70MET00.0050.01226.5150.0000.0000.0000.0000.0000.000
70A71LYS10.9160.97526.7010.1340.1340.0000.0000.0000.000
71A72GLY00.0220.01831.285-0.001-0.0010.0000.0000.0000.000
72A73ASN0-0.013-0.01334.9980.0010.0010.0000.0000.0000.000
73A74LEU00.0150.01030.4620.0040.0040.0000.0000.0000.000
74A75VAL00.0000.00427.296-0.006-0.0060.0000.0000.0000.000
75A76GLU-1-0.855-0.91325.946-0.124-0.1240.0000.0000.0000.000
76A77LYS10.9380.96221.2080.0690.0690.0000.0000.0000.000
77A78TYR0-0.063-0.04319.596-0.017-0.0170.0000.0000.0000.000
78A79TYR00.0350.00617.2040.0200.0200.0000.0000.0000.000
79A80GLY00.040-0.00614.157-0.016-0.0160.0000.0000.0000.000
80A81ARG10.8280.9019.8721.2311.2310.0000.0000.0000.000
81A82THR00.0150.0036.8430.0240.0240.0000.0000.0000.000
82A83ALA00.0440.0204.968-0.302-0.3020.0000.0000.0000.000
83A84ASP-1-0.850-0.8986.676-1.263-1.2630.0000.0000.0000.000
84A85VAL0-0.083-0.0447.2560.6110.6110.0000.0000.0000.000
85A86PHE0-0.035-0.0186.932-0.447-0.4470.0000.0000.0000.000
86A87TYR00.0510.0218.0590.1690.1690.0000.0000.0000.000
87A88ILE00.0010.00310.2030.0620.0620.0000.0000.0000.000
88A89ASN00.0830.02812.945-0.022-0.0220.0000.0000.0000.000
89A90LEU0-0.059-0.02615.6550.0250.0250.0000.0000.0000.000
90A91TYR0-0.055-0.05818.7360.0160.0160.0000.0000.0000.000
91A92LEU0-0.0180.00715.0720.0110.0110.0000.0000.0000.000
92A93GLY0-0.0030.00019.2460.0210.0210.0000.0000.0000.000
93A94ASP-1-0.794-0.88921.340-0.029-0.0290.0000.0000.0000.000
94A95GLU-1-0.873-0.94723.067-0.028-0.0280.0000.0000.0000.000
95A96GLU-1-0.883-0.95324.689-0.069-0.0690.0000.0000.0000.000
96A97LEU0-0.038-0.02918.591-0.020-0.0200.0000.0000.0000.000
97A98ARG10.8740.94722.9650.0400.0400.0000.0000.0000.000
98A99TYR00.0320.01325.119-0.012-0.0120.0000.0000.0000.000
99A100ILE00.0150.06022.792-0.011-0.0110.0000.0000.0000.000
100A101ALA0-0.023-0.01523.117-0.013-0.0130.0000.0000.0000.000
101A102ARG10.9410.96024.6500.0640.0640.0000.0000.0000.000
102A103SER0-0.038-0.04227.8570.0040.0040.0000.0000.0000.000
103A104ARG10.8920.94419.8820.2270.2270.0000.0000.0000.000
104A105LEU0-0.003-0.00825.953-0.004-0.0040.0000.0000.0000.000
105A106LYS10.9890.99428.8050.0780.0780.0000.0000.0000.000
106A107THR00.0020.01929.9520.0010.0010.0000.0000.0000.000
107A108LYS10.8940.93726.6080.1670.1670.0000.0000.0000.000
108A109ILE00.0560.04131.7760.0030.0030.0000.0000.0000.000
109A110ASP-1-0.901-0.94634.719-0.085-0.0850.0000.0000.0000.000
110A111ILE0-0.075-0.03932.0620.0030.0030.0000.0000.0000.000
111A112PHE00.0360.01431.6910.0020.0020.0000.0000.0000.000
112A113LYS10.9590.99137.2360.0720.0720.0000.0000.0000.000
113A114ARG10.8600.94038.9930.0890.0890.0000.0000.0000.000
114A115LEU0-0.045-0.02836.4040.0010.0010.0000.0000.0000.000
115A116GLY00.0090.01640.6500.0010.0010.0000.0000.0000.000
116A117TYR0-0.046-0.01138.5520.0020.0020.0000.0000.0000.000
117A118GLN0-0.034-0.02841.5270.0010.0010.0000.0000.0000.000
118A119PHE0-0.004-0.00937.573-0.001-0.0010.0000.0000.0000.000
119A120GLU-1-0.734-0.85040.611-0.052-0.0520.0000.0000.0000.000
120A121GLU-1-0.924-0.98137.888-0.062-0.0620.0000.0000.0000.000
121A122ASN0-0.050-0.04036.718-0.004-0.0040.0000.0000.0000.000
122A123GLU-1-0.875-0.94136.381-0.057-0.0570.0000.0000.0000.000
123A124LEU00.010-0.01033.416-0.004-0.0040.0000.0000.0000.000
124A125LEU0-0.0090.00330.820-0.007-0.0070.0000.0000.0000.000
125A126ASN0-0.033-0.01831.107-0.006-0.0060.0000.0000.0000.000
126A127ILE00.0090.00730.920-0.001-0.0010.0000.0000.0000.000
127A128MET0-0.009-0.01028.959-0.005-0.0050.0000.0000.0000.000
128A129ASP-1-0.804-0.89026.627-0.099-0.0990.0000.0000.0000.000
129A130ARG10.9710.99525.9080.0430.0430.0000.0000.0000.000
130A131MET0-0.0100.01825.7060.0010.0010.0000.0000.0000.000
131A132SER00.0630.02622.900-0.018-0.0180.0000.0000.0000.000
132A133GLN0-0.025-0.01521.508-0.020-0.0200.0000.0000.0000.000
133A134LYS10.7750.85820.9310.0540.0540.0000.0000.0000.000
134A135GLU-1-0.887-0.95120.505-0.207-0.2070.0000.0000.0000.000
135A136PHE0-0.086-0.05216.248-0.047-0.0470.0000.0000.0000.000
136A137ASP-1-0.875-0.94015.963-0.102-0.1020.0000.0000.0000.000
137A138ALA00.0050.00916.4020.0150.0150.0000.0000.0000.000
138A139THR00.015-0.00713.121-0.033-0.0330.0000.0000.0000.000
139A140VAL0-0.0120.00111.382-0.095-0.0950.0000.0000.0000.000
140A141ARG10.9010.96311.2480.0330.0330.0000.0000.0000.000
141A142ILE0-0.020-0.00211.4600.0530.0530.0000.0000.0000.000
142A143SER0-0.025-0.0218.663-0.068-0.0680.0000.0000.0000.000
143A144LYS10.9730.9897.121-0.678-0.6780.0000.0000.0000.000
144A145TYR00.0080.0117.1880.2490.2490.0000.0000.0000.000
145A146ILE0-0.014-0.0186.6040.0540.0540.0000.0000.0000.000
146A147GLU-1-0.873-0.9432.383-2.198-1.2391.332-1.012-1.279-0.003
147A148GLU-1-0.929-0.9563.4110.2751.0440.031-0.318-0.481-0.002
148A149LYS10.8670.9345.946-0.242-0.2420.0000.0000.0000.000
149A150GLU-1-0.689-0.8511.767-14.958-23.90221.562-7.232-5.387-0.078
150A151ASP-1-0.910-0.9445.4660.3400.3400.0000.0000.0000.000
151A152ALA0-0.092-0.0477.4130.0650.0650.0000.0000.0000.000
152A153LEU00.012-0.0058.3410.0210.0210.0000.0000.0000.000
153A154LYS10.8990.9508.4980.2080.2080.0000.0000.0000.000
154A155ASP-1-0.956-0.9709.456-0.427-0.4270.0000.0000.0000.000
155A156PHE00.0350.03211.6350.0510.0510.0000.0000.0000.000
156A157SER0-0.034-0.03711.591-0.162-0.1620.0000.0000.0000.000
157A158ASN00.047-0.0189.271-0.209-0.2090.0000.0000.0000.000
158A159GLU-1-0.943-0.96211.842-0.507-0.5070.0000.0000.0000.000
159A160ASP-1-0.798-0.88115.062-0.480-0.4800.0000.0000.0000.000
160A161ILE0-0.012-0.0038.9410.0050.0050.0000.0000.0000.000
161A162ILE0-0.065-0.02911.8710.0210.0210.0000.0000.0000.000
162A163HIS10.9200.94613.2460.5460.5460.0000.0000.0000.000
163A164ALA0-0.0140.01113.8760.0700.0700.0000.0000.0000.000
164A165ILE0-0.014-0.0179.4740.0650.0650.0000.0000.0000.000
165A166GLU-1-0.868-0.93514.031-0.383-0.3830.0000.0000.0000.000
166A167TRP00.0090.01617.3340.0670.0670.0000.0000.0000.000
167A168LEU0-0.018-0.01414.0220.0450.0450.0000.0000.0000.000
168A169SER0-0.027-0.01616.1470.0620.0620.0000.0000.0000.000
169A170THR00.003-0.00917.8480.0420.0420.0000.0000.0000.000
170A171ALA0-0.046-0.03320.7840.0290.0290.0000.0000.0000.000
171A172GLU-1-0.922-0.97818.240-0.052-0.0520.0000.0000.0000.000
172A173LEU00.0360.02621.3250.0230.0230.0000.0000.0000.000
173A174ALA0-0.039-0.01523.5370.0160.0160.0000.0000.0000.000
174A175ARG10.8520.92920.7120.1050.1050.0000.0000.0000.000
175A176ASP-1-0.767-0.84325.329-0.046-0.0460.0000.0000.0000.000
176A177GLU-1-0.881-0.96727.267-0.041-0.0410.0000.0000.0000.000
177A178GLU-1-0.851-0.90429.121-0.044-0.0440.0000.0000.0000.000
178A179TYR0-0.029-0.02025.502-0.004-0.0040.0000.0000.0000.000
179A180LEU00.0380.02428.683-0.006-0.0060.0000.0000.0000.000
180A181GLU-1-1.017-1.00631.088-0.045-0.0450.0000.0000.0000.000
181A182LEU0-0.030-0.02328.828-0.001-0.0010.0000.0000.0000.000
182A183LEU00.009-0.00229.271-0.002-0.0020.0000.0000.0000.000
183A184LYS10.8790.92931.7070.0640.0640.0000.0000.0000.000
184A185ARG10.9030.95535.1410.0580.0580.0000.0000.0000.000
185A186LEU00.0410.03030.7440.0020.0020.0000.0000.0000.000
186A187GLY00.0030.00734.716-0.001-0.0010.0000.0000.0000.000
187A188SER0-0.099-0.05736.6850.0040.0040.0000.0000.0000.000
188A189ILE0-0.003-0.01336.5590.0020.0020.0000.0000.0000.000
189A190LEU0-0.031-0.01233.9510.0020.0020.0000.0000.0000.000
190A191LYS10.8860.97438.0330.0670.0670.0000.0000.0000.000