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: 898JY

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 OptHSide
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 -2128618.736121
FMO2-HF: Nuclear repulsion 2050519.604787
FMO2-HF: Total energy -78099.131334
FMO2-MP2: Total energy -78329.279659


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.
-16.911-10.7279.57-7.514-8.242-0.047
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 : 0.037 / q_NPA : 0.026
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].
3A4LYS10.8340.9243.415-0.7682.864-0.019-2.063-1.5490.011
4A5VAL0-0.066-0.0453.2171.5382.0820.003-0.213-0.3350.001
5A6LYS10.9721.0012.372-4.217-3.9462.325-1.230-1.367-0.013
6A7VAL0-0.047-0.0284.2180.5780.668-0.001-0.020-0.0700.000
7A8ILE0-0.062-0.0387.1560.2820.2820.0000.0000.0000.000
8A9THR00.026-0.0139.8360.0180.0180.0000.0000.0000.000
9A10ASP-1-0.842-0.91612.5920.0640.0640.0000.0000.0000.000
10A11PRO00.040-0.00314.544-0.062-0.0620.0000.0000.0000.000
11A12GLU-1-0.778-0.88117.673-0.060-0.0600.0000.0000.0000.000
12A13VAL0-0.0120.00012.184-0.040-0.0400.0000.0000.0000.000
13A14ILE0-0.040-0.02714.054-0.060-0.0600.0000.0000.0000.000
14A15LYS10.7850.88115.9220.0110.0110.0000.0000.0000.000
15A16VAL0-0.0270.00517.589-0.012-0.0120.0000.0000.0000.000
16A17MET0-0.051-0.02312.459-0.016-0.0160.0000.0000.0000.000
17A18LEU0-0.038-0.02017.089-0.028-0.0280.0000.0000.0000.000
18A19GLU-1-0.786-0.86719.765-0.185-0.1850.0000.0000.0000.000
19A20ASP-1-0.804-0.90621.430-0.235-0.2350.0000.0000.0000.000
20A21THR0-0.052-0.05422.713-0.018-0.0180.0000.0000.0000.000
21A22ARG10.8960.93618.8660.1670.1670.0000.0000.0000.000
22A23ARG10.9080.98218.0330.2580.2580.0000.0000.0000.000
23A24LYS10.8280.90118.4550.1760.1760.0000.0000.0000.000
24A25ILE00.0300.02418.165-0.018-0.0180.0000.0000.0000.000
25A26LEU00.0220.01613.364-0.040-0.0400.0000.0000.0000.000
26A27LYS10.9290.96215.5350.3330.3330.0000.0000.0000.000
27A28LEU00.0260.00617.440-0.026-0.0260.0000.0000.0000.000
28A29LEU0-0.018-0.01315.170-0.003-0.0030.0000.0000.0000.000
29A30ARG10.8760.94912.2500.8240.8240.0000.0000.0000.000
30A31ASN0-0.082-0.03115.161-0.010-0.0100.0000.0000.0000.000
31A32LYS10.9370.97716.9140.2960.2960.0000.0000.0000.000
32A33GLU-1-0.828-0.90516.048-0.322-0.3220.0000.0000.0000.000
33A34MET0-0.073-0.04017.7960.0520.0520.0000.0000.0000.000
34A35THR0-0.024-0.02320.797-0.008-0.0080.0000.0000.0000.000
35A36ILE00.013-0.00923.504-0.009-0.0090.0000.0000.0000.000
36A37SER0-0.015-0.02825.1310.0030.0030.0000.0000.0000.000
37A38GLN00.0290.01124.187-0.019-0.0190.0000.0000.0000.000
38A39LEU00.0240.01220.732-0.004-0.0040.0000.0000.0000.000
39A40SER0-0.097-0.05824.7530.0040.0040.0000.0000.0000.000
40A41GLU-1-0.892-0.95028.108-0.130-0.1300.0000.0000.0000.000
41A42ILE0-0.034-0.01424.808-0.001-0.0010.0000.0000.0000.000
42A43LEU0-0.060-0.04823.473-0.002-0.0020.0000.0000.0000.000
43A44GLY00.0280.04027.5240.0070.0070.0000.0000.0000.000
44A45LYS10.8830.95027.4890.1700.1700.0000.0000.0000.000
45A46THR00.0500.03530.169-0.003-0.0030.0000.0000.0000.000
46A47PRO00.0890.03329.271-0.007-0.0070.0000.0000.0000.000
47A48GLN00.0510.01128.666-0.012-0.0120.0000.0000.0000.000
48A49THR0-0.0130.00928.171-0.003-0.0030.0000.0000.0000.000
49A50ILE00.0260.00523.742-0.008-0.0080.0000.0000.0000.000
50A51TYR00.0120.01024.077-0.015-0.0150.0000.0000.0000.000
51A52HIS00.0300.01224.397-0.004-0.0040.0000.0000.0000.000
52A53HIS00.0070.01622.145-0.007-0.0070.0000.0000.0000.000
53A54ILE0-0.004-0.00719.238-0.017-0.0170.0000.0000.0000.000
54A55GLU-1-0.799-0.89019.437-0.116-0.1160.0000.0000.0000.000
55A56LYS10.8930.93520.2430.0960.0960.0000.0000.0000.000
56A57LEU0-0.005-0.00815.698-0.003-0.0030.0000.0000.0000.000
57A58LYS10.7680.87515.3510.0670.0670.0000.0000.0000.000
58A59GLU-1-0.885-0.92215.902-0.064-0.0640.0000.0000.0000.000
59A60ALA0-0.0020.00815.3560.0280.0280.0000.0000.0000.000
60A61GLY00.0430.02012.133-0.012-0.0120.0000.0000.0000.000
61A62LEU0-0.081-0.02910.668-0.153-0.1530.0000.0000.0000.000
62A63VAL0-0.014-0.01611.746-0.139-0.1390.0000.0000.0000.000
63A64GLU-1-0.807-0.88710.253-0.383-0.3830.0000.0000.0000.000
64A65VAL0-0.051-0.03914.347-0.031-0.0310.0000.0000.0000.000
65A66LYS10.8500.92110.9290.6150.6150.0000.0000.0000.000
66A67ARG10.8820.93216.2190.2220.2220.0000.0000.0000.000
67A68THR00.003-0.00419.710-0.013-0.0130.0000.0000.0000.000
68A69GLU-1-0.817-0.88323.313-0.137-0.1370.0000.0000.0000.000
69A70MET00.0340.01926.4090.0000.0000.0000.0000.0000.000
70A71LYS10.8270.93325.9970.1530.1530.0000.0000.0000.000
71A72GLY00.0250.01831.2000.0000.0000.0000.0000.0000.000
72A73ASN0-0.016-0.01534.9200.0010.0010.0000.0000.0000.000
73A74LEU00.0020.00230.3560.0030.0030.0000.0000.0000.000
74A75VAL00.0120.00827.188-0.006-0.0060.0000.0000.0000.000
75A76GLU-1-0.756-0.83825.762-0.150-0.1500.0000.0000.0000.000
76A77LYS10.9400.96921.1620.1140.1140.0000.0000.0000.000
77A78TYR0-0.093-0.07719.574-0.012-0.0120.0000.0000.0000.000
78A79TYR00.0140.00017.0980.0140.0140.0000.0000.0000.000
79A80GLY00.0530.01814.090-0.006-0.0060.0000.0000.0000.000
80A81ARG10.7900.8919.6661.2071.2070.0000.0000.0000.000
81A82THR0-0.024-0.0236.988-0.019-0.0190.0000.0000.0000.000
82A83ALA00.0440.0194.920-0.365-0.3650.0000.0000.0000.000
83A84ASP-1-0.794-0.8666.711-0.976-0.9760.0000.0000.0000.000
84A85VAL0-0.082-0.0397.3320.5930.5930.0000.0000.0000.000
85A86PHE0-0.031-0.0177.004-0.403-0.4030.0000.0000.0000.000
86A87TYR00.0620.0278.1480.1520.1520.0000.0000.0000.000
87A88ILE0-0.0030.00210.2260.0520.0520.0000.0000.0000.000
88A89ASN00.0740.01212.967-0.017-0.0170.0000.0000.0000.000
89A90LEU0-0.064-0.02515.6690.0160.0160.0000.0000.0000.000
90A91TYR0-0.060-0.04418.7380.0110.0110.0000.0000.0000.000
91A92LEU0-0.0020.01714.9530.0150.0150.0000.0000.0000.000
92A93GLY0-0.0050.00019.2300.0190.0190.0000.0000.0000.000
93A94ASP-1-0.803-0.89321.306-0.025-0.0250.0000.0000.0000.000
94A95GLU-1-0.832-0.91623.041-0.024-0.0240.0000.0000.0000.000
95A96GLU-1-0.865-0.93724.778-0.064-0.0640.0000.0000.0000.000
96A97LEU0-0.024-0.02118.622-0.019-0.0190.0000.0000.0000.000
97A98ARG10.8520.92922.9590.0270.0270.0000.0000.0000.000
98A99TYR0-0.030-0.02725.121-0.011-0.0110.0000.0000.0000.000
99A100ILE00.0100.03123.159-0.011-0.0110.0000.0000.0000.000
100A101ALA0-0.018-0.00923.028-0.012-0.0120.0000.0000.0000.000
101A102ARG10.8690.90324.6730.0490.0490.0000.0000.0000.000
102A103SER0-0.030-0.01827.9620.0030.0030.0000.0000.0000.000
103A104ARG10.8770.94220.1190.1980.1980.0000.0000.0000.000
104A105LEU00.0090.00225.904-0.004-0.0040.0000.0000.0000.000
105A106LYS11.0091.00228.8470.0680.0680.0000.0000.0000.000
106A107THR00.0110.01130.197-0.002-0.0020.0000.0000.0000.000
107A108LYS10.8630.92326.6320.1450.1450.0000.0000.0000.000
108A109ILE00.0440.04131.8300.0030.0030.0000.0000.0000.000
109A110ASP-1-0.918-0.95334.770-0.075-0.0750.0000.0000.0000.000
110A111ILE0-0.069-0.03632.1180.0020.0020.0000.0000.0000.000
111A112PHE00.0380.01331.6350.0020.0020.0000.0000.0000.000
112A113LYS10.8910.94837.2980.0600.0600.0000.0000.0000.000
113A114ARG10.8630.94439.0630.0800.0800.0000.0000.0000.000
114A115LEU0-0.041-0.02836.5820.0010.0010.0000.0000.0000.000
115A116GLY00.0050.01440.7180.0010.0010.0000.0000.0000.000
116A117TYR0-0.049-0.01338.4120.0020.0020.0000.0000.0000.000
117A118GLN0-0.031-0.02541.5920.0010.0010.0000.0000.0000.000
118A119PHE00.011-0.00237.513-0.001-0.0010.0000.0000.0000.000
119A120GLU-1-0.754-0.86140.929-0.042-0.0420.0000.0000.0000.000
120A121GLU-1-0.839-0.93237.922-0.054-0.0540.0000.0000.0000.000
121A122ASN0-0.066-0.05136.755-0.003-0.0030.0000.0000.0000.000
122A123GLU-1-0.819-0.89636.413-0.042-0.0420.0000.0000.0000.000
123A124LEU00.008-0.00233.643-0.002-0.0020.0000.0000.0000.000
124A125LEU00.0060.00730.832-0.005-0.0050.0000.0000.0000.000
125A126ASN0-0.009-0.00531.143-0.004-0.0040.0000.0000.0000.000
126A127ILE00.0230.01430.9540.0000.0000.0000.0000.0000.000
127A128MET00.002-0.00228.980-0.004-0.0040.0000.0000.0000.000
128A129ASP-1-0.781-0.85826.578-0.076-0.0760.0000.0000.0000.000
129A130ARG10.9030.96025.9400.0250.0250.0000.0000.0000.000
130A131MET0-0.0260.00925.7440.0030.0030.0000.0000.0000.000
131A132SER00.0530.01523.176-0.016-0.0160.0000.0000.0000.000
132A133GLN00.0110.00121.550-0.017-0.0170.0000.0000.0000.000
133A134LYS10.8160.89220.9620.0260.0260.0000.0000.0000.000
134A135GLU-1-0.809-0.89120.511-0.151-0.1510.0000.0000.0000.000
135A136PHE0-0.065-0.03316.129-0.038-0.0380.0000.0000.0000.000
136A137ASP-1-0.846-0.92216.002-0.046-0.0460.0000.0000.0000.000
137A138ALA0-0.0100.00616.4350.0240.0240.0000.0000.0000.000
138A139THR00.010-0.01913.295-0.016-0.0160.0000.0000.0000.000
139A140VAL0-0.0180.01711.626-0.074-0.0740.0000.0000.0000.000
140A141ARG10.8350.90311.2830.0010.0010.0000.0000.0000.000
141A142ILE0-0.033-0.01711.6830.0640.0640.0000.0000.0000.000
142A143SER0-0.017-0.0308.501-0.026-0.0260.0000.0000.0000.000
143A144LYS10.8830.9306.978-1.145-1.1450.0000.0000.0000.000
144A145TYR00.0090.0107.2500.3210.3210.0000.0000.0000.000
145A146ILE00.001-0.0136.6610.0550.0550.0000.0000.0000.000
146A147GLU-1-0.806-0.8962.611-0.721-0.1140.777-0.532-0.8530.001
147A148GLU-1-0.880-0.9193.5151.2271.8600.022-0.215-0.440-0.001
148A149LYS10.8190.8986.132-0.610-0.6100.0000.0000.0000.000
149A150GLU-1-0.727-0.8682.126-14.438-14.0856.464-3.240-3.577-0.046
150A151ASP-1-0.906-0.9455.3250.2560.310-0.001-0.001-0.0510.000
151A152ALA0-0.086-0.0407.2700.0200.0200.0000.0000.0000.000
152A153LEU00.000-0.0168.3690.0090.0090.0000.0000.0000.000
153A154LYS10.8190.8898.7150.1420.1420.0000.0000.0000.000
154A155ASP-1-0.871-0.9089.669-0.301-0.3010.0000.0000.0000.000
155A156PHE00.0190.02211.8820.0550.0550.0000.0000.0000.000
156A157SER0-0.022-0.04211.943-0.151-0.1510.0000.0000.0000.000
157A158ASN00.029-0.0319.748-0.110-0.1100.0000.0000.0000.000
158A159GLU-1-0.907-0.94311.954-0.461-0.4610.0000.0000.0000.000
159A160ASP-1-0.809-0.86915.160-0.428-0.4280.0000.0000.0000.000
160A161ILE0-0.011-0.0038.8820.0120.0120.0000.0000.0000.000
161A162ILE0-0.055-0.02511.6000.0200.0200.0000.0000.0000.000
162A163HIS10.8740.92913.1910.4880.4880.0000.0000.0000.000
163A164ALA0-0.0080.01213.9140.0640.0640.0000.0000.0000.000
164A165ILE0-0.001-0.0099.4040.0630.0630.0000.0000.0000.000
165A166GLU-1-0.865-0.93214.013-0.329-0.3290.0000.0000.0000.000
166A167TRP00.0090.02417.3040.0600.0600.0000.0000.0000.000
167A168LEU0-0.016-0.01214.3320.0400.0400.0000.0000.0000.000
168A169SER0-0.022-0.02016.0890.0570.0570.0000.0000.0000.000
169A170THR0-0.008-0.02417.8420.0330.0330.0000.0000.0000.000
170A171ALA0-0.046-0.03020.8070.0240.0240.0000.0000.0000.000
171A172GLU-1-0.799-0.86318.2710.0080.0080.0000.0000.0000.000
172A173LEU00.0120.01721.1150.0180.0180.0000.0000.0000.000
173A174ALA0-0.038-0.01523.5370.0110.0110.0000.0000.0000.000
174A175ARG10.8330.90120.8050.0540.0540.0000.0000.0000.000
175A176ASP-1-0.809-0.88325.277-0.014-0.0140.0000.0000.0000.000
176A177GLU-1-0.878-0.95727.280-0.020-0.0200.0000.0000.0000.000
177A178GLU-1-0.828-0.89729.269-0.024-0.0240.0000.0000.0000.000
178A179TYR0-0.060-0.06025.356-0.003-0.0030.0000.0000.0000.000
179A180LEU00.0330.02228.679-0.007-0.0070.0000.0000.0000.000
180A181GLU-1-1.012-0.99831.082-0.029-0.0290.0000.0000.0000.000
181A182LEU0-0.022-0.01929.183-0.002-0.0020.0000.0000.0000.000
182A183LEU00.012-0.00429.017-0.003-0.0030.0000.0000.0000.000
183A184LYS10.8880.93431.7010.0420.0420.0000.0000.0000.000
184A185ARG10.8810.93035.1900.0420.0420.0000.0000.0000.000
185A186LEU00.0340.02530.7070.0000.0000.0000.0000.0000.000
186A187GLY00.0070.01034.777-0.001-0.0010.0000.0000.0000.000
187A188SER0-0.102-0.06636.7030.0030.0030.0000.0000.0000.000
188A189ILE0-0.046-0.03836.5370.0010.0010.0000.0000.0000.000
189A190LEU0-0.023-0.00334.0560.0010.0010.0000.0000.0000.000
190A191LYS10.9030.98638.0990.0540.0540.0000.0000.0000.000