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: YNQ72

Calculation Name: 1O65-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O65

Chain ID: A

ChEMBL ID:

UniProt ID: P32157

Base Structure: X-ray

Registration Date: 2023-09-26

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2775030.108843
FMO2-HF: Nuclear repulsion 2686194.552638
FMO2-HF: Total energy -88835.556205
FMO2-MP2: Total energy -89094.495111


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:3:LYS)


Summations of interaction energy for fragment #1(A:3: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.
-80.513-75.851.408-2.356-3.716-0.003
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.000 / q_NPA : 0.999
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].
3A5LEU00.0090.0022.470-0.9423.5321.409-2.342-3.542-0.003
4A6VAL00.0410.0105.0343.8184.007-0.001-0.014-0.1740.000
5A7GLU-1-0.849-0.9097.271-24.664-24.6640.0000.0000.0000.000
6A8ARG10.8750.9308.40126.49226.4920.0000.0000.0000.000
7A9GLU-1-0.947-0.9728.316-28.528-28.5280.0000.0000.0000.000
8A10GLN0-0.024-0.00111.1492.3972.3970.0000.0000.0000.000
9A11MET00.0120.01410.9680.6010.6010.0000.0000.0000.000
10A12ARG10.8460.91713.94516.38116.3810.0000.0000.0000.000
11A13TYR0-0.003-0.00414.376-0.425-0.4250.0000.0000.0000.000
12A14PRO00.0160.00320.2150.3150.3150.0000.0000.0000.000
13A15VAL0-0.023-0.01023.451-0.391-0.3910.0000.0000.0000.000
14A16ASP-1-0.788-0.85525.338-10.634-10.6340.0000.0000.0000.000
15A17VAL00.010-0.00428.182-0.218-0.2180.0000.0000.0000.000
16A18TYR0-0.015-0.02929.9250.2700.2700.0000.0000.0000.000
17A19THR0-0.039-0.02631.899-0.119-0.1190.0000.0000.0000.000
18A20GLY00.0540.01934.6450.1550.1550.0000.0000.0000.000
19A21LYS10.7310.83137.4957.7957.7950.0000.0000.0000.000
20A34ALA0-0.013-0.01637.710-0.054-0.0540.0000.0000.0000.000
21A35LYS10.7490.88431.2089.5299.5290.0000.0000.0000.000
22A36ILE00.010-0.00436.383-0.002-0.0020.0000.0000.0000.000
23A37GLN00.003-0.00333.627-0.320-0.3200.0000.0000.0000.000
24A38VAL0-0.031-0.01833.7010.2750.2750.0000.0000.0000.000
25A39ASP-1-0.891-0.93033.810-8.865-8.8650.0000.0000.0000.000
26A40GLY00.0200.00634.9820.1300.1300.0000.0000.0000.000
27A41GLU-1-0.880-0.93033.212-8.900-8.9000.0000.0000.0000.000
28A42LEU0-0.021-0.01031.5190.2900.2900.0000.0000.0000.000
29A43MET0-0.041-0.00531.768-0.227-0.2270.0000.0000.0000.000
30A44LEU00.0130.01825.3810.0580.0580.0000.0000.0000.000
31A45THR00.0240.00329.758-0.128-0.1280.0000.0000.0000.000
32A46GLU-1-0.916-0.97228.603-9.510-9.5100.0000.0000.0000.000
33A47LEU0-0.037-0.04528.455-0.248-0.2480.0000.0000.0000.000
34A48GLY00.0610.03629.0860.0030.0030.0000.0000.0000.000
35A49LEU0-0.039-0.00928.7770.0610.0610.0000.0000.0000.000
36A50GLU-1-0.892-0.95431.686-8.028-8.0280.0000.0000.0000.000
37A51GLY00.0410.02935.2660.0200.0200.0000.0000.0000.000
38A52ASP-1-0.749-0.83932.310-9.000-9.0000.0000.0000.0000.000
39A53GLU-1-0.852-0.88635.212-7.485-7.4850.0000.0000.0000.000
40A54GLN0-0.036-0.02334.742-0.062-0.0620.0000.0000.0000.000
41A55ALA0-0.028-0.01036.7450.0000.0000.0000.0000.0000.000
42A56GLU-1-0.713-0.83338.150-7.183-7.1830.0000.0000.0000.000
43A57LYS10.8170.88538.3777.2337.2330.0000.0000.0000.000
44A58LYS10.8520.90037.6957.3467.3460.0000.0000.0000.000
45A59VAL0-0.0330.00232.258-0.014-0.0140.0000.0000.0000.000
46A60HIS00.0740.03332.565-0.217-0.2170.0000.0000.0000.000
47A61GLY00.0120.01229.014-0.150-0.1500.0000.0000.0000.000
48A62GLY00.0110.00628.553-0.197-0.1970.0000.0000.0000.000
49A63PRO00.0910.03526.924-0.181-0.1810.0000.0000.0000.000
50A64ASP-1-0.835-0.90023.947-11.335-11.3350.0000.0000.0000.000
51A65ARG10.8240.91723.7678.9938.9930.0000.0000.0000.000
52A66ALA00.0250.04326.0010.2080.2080.0000.0000.0000.000
53A67LEU00.0060.02123.9670.1760.1760.0000.0000.0000.000
54A68CYS0-0.029-0.01124.567-0.432-0.4320.0000.0000.0000.000
55A69HIS00.0730.04621.3900.3290.3290.0000.0000.0000.000
56A70TYR0-0.025-0.03023.706-0.109-0.1090.0000.0000.0000.000
57A71PRO0-0.0230.00420.4050.2190.2190.0000.0000.0000.000
58A72ARG10.8200.87122.90912.13412.1340.0000.0000.0000.000
59A73GLU-1-0.830-0.92521.088-14.205-14.2050.0000.0000.0000.000
60A74HIS10.7200.83520.95513.72613.7260.0000.0000.0000.000
61A75TYR00.013-0.01525.9240.3720.3720.0000.0000.0000.000
62A76LEU0-0.0030.00826.4640.3020.3020.0000.0000.0000.000
63A77TYR0-0.103-0.07026.689-0.197-0.1970.0000.0000.0000.000
64A78TRP00.045-0.00828.0400.2680.2680.0000.0000.0000.000
65A79ALA00.0250.01831.6840.2890.2890.0000.0000.0000.000
66A80ARG10.8210.91128.95710.88610.8860.0000.0000.0000.000
67A81GLU-1-0.895-0.92231.550-9.982-9.9820.0000.0000.0000.000
68A82PHE0-0.016-0.01334.0310.1540.1540.0000.0000.0000.000
69A83PRO00.0090.00737.4040.0280.0280.0000.0000.0000.000
70A84GLU-1-0.938-0.98139.053-7.562-7.5620.0000.0000.0000.000
71A85GLN0-0.039-0.00539.0340.1740.1740.0000.0000.0000.000
72A86ALA00.0090.00437.177-0.194-0.1940.0000.0000.0000.000
73A87GLU-1-0.910-0.96336.922-7.877-7.8770.0000.0000.0000.000
74A88LEU0-0.022-0.00337.814-0.063-0.0630.0000.0000.0000.000
75A89PHE0-0.072-0.04532.618-0.302-0.3020.0000.0000.0000.000
76A90VAL00.0110.00732.747-0.243-0.2430.0000.0000.0000.000
77A91ALA00.0000.01529.8740.0140.0140.0000.0000.0000.000
78A92PRO0-0.0370.00131.2360.2070.2070.0000.0000.0000.000
79A93ALA00.0390.01932.2650.1020.1020.0000.0000.0000.000
80A94PHE00.013-0.00529.3260.1350.1350.0000.0000.0000.000
81A95GLY0-0.019-0.01230.647-0.086-0.0860.0000.0000.0000.000
82A96GLU-1-0.815-0.90426.923-10.514-10.5140.0000.0000.0000.000
83A97ASN0-0.033-0.04327.2290.1680.1680.0000.0000.0000.000
84A98LEU0-0.0040.01523.4110.1320.1320.0000.0000.0000.000
85A99SER00.0230.01425.404-0.221-0.2210.0000.0000.0000.000
86A100THR00.0630.03121.541-0.049-0.0490.0000.0000.0000.000
87A101ASP-1-0.831-0.88422.405-12.381-12.3810.0000.0000.0000.000
88A102GLY00.005-0.00818.636-0.315-0.3150.0000.0000.0000.000
89A103LEU0-0.042-0.00615.325-1.375-1.3750.0000.0000.0000.000
90A104THR00.017-0.02415.8560.9190.9190.0000.0000.0000.000
91A105GLU-1-0.698-0.84215.305-15.665-15.6650.0000.0000.0000.000
92A106SER00.0030.00813.836-0.321-0.3210.0000.0000.0000.000
93A107ASN0-0.049-0.02111.041-1.285-1.2850.0000.0000.0000.000
94A108VAL00.0470.04311.054-1.666-1.6660.0000.0000.0000.000
95A109TYR0-0.047-0.0356.858-1.180-1.1800.0000.0000.0000.000
96A110MET0-0.0330.00111.2191.4651.4650.0000.0000.0000.000
97A111GLY00.0560.04311.609-1.076-1.0760.0000.0000.0000.000
98A112ASP-1-0.731-0.82910.289-24.292-24.2920.0000.0000.0000.000
99A113ILE0-0.029-0.01612.5681.5121.5120.0000.0000.0000.000
100A114PHE00.0320.00114.462-1.193-1.1930.0000.0000.0000.000
101A115ARG10.8610.91017.13415.01415.0140.0000.0000.0000.000
102A116TRP0-0.009-0.01820.133-0.384-0.3840.0000.0000.0000.000
103A117GLY00.0480.02623.2240.4880.4880.0000.0000.0000.000
104A118GLU-1-0.956-0.98024.958-10.669-10.6690.0000.0000.0000.000
105A119ALA0-0.0410.00225.2120.0370.0370.0000.0000.0000.000
106A120LEU0-0.025-0.01819.567-0.635-0.6350.0000.0000.0000.000
107A121ILE0-0.017-0.00519.3770.5630.5630.0000.0000.0000.000
108A122GLN0-0.036-0.02714.336-0.113-0.1130.0000.0000.0000.000
109A123VAL0-0.0250.00115.0490.9190.9190.0000.0000.0000.000
110A124SER00.000-0.02016.497-0.506-0.5060.0000.0000.0000.000
111A125GLN0-0.022-0.02218.8820.3900.3900.0000.0000.0000.000
112A126PRO00.0510.02818.2230.0490.0490.0000.0000.0000.000
113A127ARG10.8140.92620.47711.06711.0670.0000.0000.0000.000
114A128SER0-0.010-0.02624.052-0.098-0.0980.0000.0000.0000.000
115A129PRO00.0150.03926.1320.3290.3290.0000.0000.0000.000
116A130CYS0-0.059-0.04329.0590.2500.2500.0000.0000.0000.000
117A131TYR00.0730.03032.7200.1080.1080.0000.0000.0000.000
118A132LYS10.8790.94135.8787.9627.9620.0000.0000.0000.000
119A133LEU00.0310.01331.0250.1240.1240.0000.0000.0000.000
120A134ASN00.0100.00435.550-0.184-0.1840.0000.0000.0000.000
121A135TYR0-0.015-0.01937.7600.1360.1360.0000.0000.0000.000
122A136HIS0-0.073-0.01835.9740.2810.2810.0000.0000.0000.000
123A137PHE00.000-0.00833.0100.0220.0220.0000.0000.0000.000
124A138ASP-1-0.924-0.94838.419-7.094-7.0940.0000.0000.0000.000
125A139ILE00.0090.01636.565-0.019-0.0190.0000.0000.0000.000
126A140SER0-0.028-0.04138.362-0.078-0.0780.0000.0000.0000.000
127A141ASP-1-0.858-0.92136.319-8.402-8.4020.0000.0000.0000.000
128A142ILE00.0440.03832.427-0.318-0.3180.0000.0000.0000.000
129A143ALA0-0.004-0.00231.405-0.393-0.3930.0000.0000.0000.000
130A144GLN0-0.017-0.01530.351-0.124-0.1240.0000.0000.0000.000
131A145LEU00.0480.03030.217-0.414-0.4140.0000.0000.0000.000
132A146MET0-0.0170.01727.479-0.338-0.3380.0000.0000.0000.000
133A147GLN00.0480.03726.024-0.401-0.4010.0000.0000.0000.000
134A148ASN00.0090.01325.408-0.534-0.5340.0000.0000.0000.000
135A149THR0-0.033-0.02625.522-0.453-0.4530.0000.0000.0000.000
136A150GLY00.0150.00521.854-0.561-0.5610.0000.0000.0000.000
137A151LYS10.8170.94321.65212.34612.3460.0000.0000.0000.000
138A152VAL0-0.0080.00021.8060.6000.6000.0000.0000.0000.000
139A153GLY00.0530.03121.8210.4610.4610.0000.0000.0000.000
140A154TRP0-0.072-0.05018.588-0.225-0.2250.0000.0000.0000.000
141A155LEU0-0.038-0.01620.8860.5660.5660.0000.0000.0000.000
142A156TYR00.017-0.01217.941-0.991-0.9910.0000.0000.0000.000
143A157SER0-0.044-0.00720.6420.6300.6300.0000.0000.0000.000
144A158VAL00.0360.00421.812-0.532-0.5320.0000.0000.0000.000
145A159ILE0-0.044-0.01419.0940.3120.3120.0000.0000.0000.000
146A160ALA00.001-0.00922.5950.2840.2840.0000.0000.0000.000
147A161PRO0-0.006-0.01125.198-0.109-0.1090.0000.0000.0000.000
148A162GLY00.0240.01728.3010.0480.0480.0000.0000.0000.000
149A163LYS10.8490.90529.5628.7508.7500.0000.0000.0000.000
150A164VAL0-0.0180.00426.882-0.357-0.3570.0000.0000.0000.000
151A165SER0-0.015-0.05328.5680.2800.2800.0000.0000.0000.000
152A166ALA00.0690.03228.400-0.381-0.3810.0000.0000.0000.000
153A167ASP-1-0.877-0.89828.522-9.972-9.9720.0000.0000.0000.000
154A168ALA0-0.063-0.01826.293-0.357-0.3570.0000.0000.0000.000
155A169PRO0-0.011-0.00421.620-0.104-0.1040.0000.0000.0000.000
156A170LEU00.0170.00819.318-0.019-0.0190.0000.0000.0000.000
157A171GLU-1-0.810-0.89617.520-15.296-15.2960.0000.0000.0000.000
158A172LEU0-0.050-0.0069.9820.1700.1700.0000.0000.0000.000
159A173VAL0-0.029-0.01913.684-0.335-0.3350.0000.0000.0000.000
160A174SER0-0.047-0.03510.6350.3330.3330.0000.0000.0000.000
161A175ARG10.7570.8506.09529.18429.1840.0000.0000.0000.000
162A176VAL00.000-0.0026.956-2.164-2.1640.0000.0000.0000.000
163A177SER0-0.061-0.0577.9061.5421.5420.0000.0000.0000.000
164A178ASP-1-0.818-0.9015.825-26.447-26.4470.0000.0000.0000.000
165A179VAL0-0.020-0.0016.753-0.341-0.3410.0000.0000.0000.000
166A180THR00.011-0.01910.0081.2861.2860.0000.0000.0000.000
167A181VAL00.0170.00011.7071.3791.3790.0000.0000.0000.000
168A182GLN00.018-0.00414.8900.3160.3160.0000.0000.0000.000
169A183GLU-1-0.774-0.84711.076-22.220-22.2200.0000.0000.0000.000
170A184ALA00.0200.01615.2520.9360.9360.0000.0000.0000.000
171A185ALA00.002-0.01016.9420.8850.8850.0000.0000.0000.000
172A186ALA00.0170.01418.2180.7050.7050.0000.0000.0000.000
173A187ILE00.000-0.02115.6530.7130.7130.0000.0000.0000.000
174A188ALA0-0.016-0.00919.9540.6590.6590.0000.0000.0000.000
175A189TRP0-0.052-0.04922.6730.5800.5800.0000.0000.0000.000
176A190HIS0-0.045-0.02622.104-0.083-0.0830.0000.0000.0000.000
177A191MET0-0.0590.02120.908-0.076-0.0760.0000.0000.0000.000
178A192PRO00.005-0.00123.8130.3570.3570.0000.0000.0000.000
179A193PHE0-0.025-0.02424.741-0.343-0.3430.0000.0000.0000.000
180A194ASP-1-0.783-0.89120.433-13.519-13.5190.0000.0000.0000.000
181A195ASP-1-0.810-0.88422.054-11.596-11.5960.0000.0000.0000.000
182A196ASP-1-0.866-0.91818.484-13.552-13.5520.0000.0000.0000.000
183A197GLN0-0.052-0.04415.756-1.584-1.5840.0000.0000.0000.000
184A198TYR0-0.007-0.00817.736-0.090-0.0900.0000.0000.0000.000
185A199HIS00.0270.02416.8270.5180.5180.0000.0000.0000.000
186A200ARG10.7660.8709.31521.82121.8210.0000.0000.0000.000
187A201LEU0-0.004-0.00714.410-0.449-0.4490.0000.0000.0000.000
188A202LEU0-0.071-0.04716.3150.0900.0900.0000.0000.0000.000
189A203SER0-0.056-0.02414.0970.4180.4180.0000.0000.0000.000
190A204ALA0-0.032-0.00212.721-0.827-0.8270.0000.0000.0000.000
191A205ALA00.0320.00912.4941.0301.0300.0000.0000.0000.000
192A206GLY00.0160.00014.248-0.280-0.2800.0000.0000.0000.000
193A207LEU0-0.054-0.00316.9240.6600.6600.0000.0000.0000.000
194A208SER00.0210.00518.5090.5060.5060.0000.0000.0000.000
195A209LYS10.8730.91022.14011.06011.0600.0000.0000.0000.000
196A210SER0-0.032-0.01425.0280.1140.1140.0000.0000.0000.000
197A211TRP00.0670.03719.7180.1670.1670.0000.0000.0000.000
198A212THR00.0260.01122.063-0.046-0.0460.0000.0000.0000.000
199A213ARG10.9090.94923.2319.1709.1700.0000.0000.0000.000
200A214THR0-0.061-0.04325.6310.3690.3690.0000.0000.0000.000
201A215MET00.0500.02921.1040.2390.2390.0000.0000.0000.000
202A216GLN00.0600.02624.179-0.023-0.0230.0000.0000.0000.000
203A217LYS10.8840.93425.7529.0419.0410.0000.0000.0000.000
204A218ARG10.7840.89224.71611.33811.3380.0000.0000.0000.000
205A219ARG10.8310.88021.47812.21212.2120.0000.0000.0000.000
206A220LEU0-0.073-0.03527.0440.2750.2750.0000.0000.0000.000
207A221SER0-0.103-0.06830.3530.3670.3670.0000.0000.0000.000
208A222GLY00.0100.01330.0780.2560.2560.0000.0000.0000.000
209A223LYS10.8930.95330.6628.3158.3150.0000.0000.0000.000
210A224ILE00.0430.01827.035-0.241-0.2410.0000.0000.0000.000
211A225GLU-1-0.831-0.88828.046-9.939-9.9390.0000.0000.0000.000
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