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: 6NZQZ

Calculation Name: 1O63-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O63

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0D2

Base Structure: X-ray

Registration Date: 2023-06-22

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2262854.335298
FMO2-HF: Nuclear repulsion 2182658.03731
FMO2-HF: Total energy -80196.297988
FMO2-MP2: Total energy -80430.803632


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:LEU)


Summations of interaction energy for fragment #1(A:2:LEU)
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.
-39.444-20.93112.168-11.705-18.977-0.094
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.011
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].
3A4LEU00.0470.0153.044-1.6240.8270.242-1.021-1.6730.005
4A5ALA0-0.028-0.0055.502-0.050-0.0500.0000.0000.0000.000
5A6ILE00.019-0.0218.136-0.034-0.0340.0000.0000.0000.000
6A7PRO0-0.0150.01011.3520.0330.0330.0000.0000.0000.000
7A8LYS10.8680.91514.996-0.133-0.1330.0000.0000.0000.000
8A9GLY0-0.051-0.03117.6690.0150.0150.0000.0000.0000.000
9A10ARG10.8380.88120.3770.0290.0290.0000.0000.0000.000
10A11LEU00.0330.00517.026-0.011-0.0110.0000.0000.0000.000
11A12GLU-1-0.896-0.93115.776-0.081-0.0810.0000.0000.0000.000
12A13GLU-1-0.894-0.96615.799-0.179-0.1790.0000.0000.0000.000
13A14LYS10.9861.00217.1310.0940.0940.0000.0000.0000.000
14A15VAL00.0170.01311.237-0.035-0.0350.0000.0000.0000.000
15A16MET0-0.009-0.00211.506-0.089-0.0890.0000.0000.0000.000
16A17THR0-0.006-0.00113.324-0.085-0.0850.0000.0000.0000.000
17A18TYR00.001-0.00511.770-0.034-0.0340.0000.0000.0000.000
18A19LEU00.0220.0047.264-0.079-0.0790.0000.0000.0000.000
19A20LYS10.9831.0019.9720.2140.2140.0000.0000.0000.000
20A21LYS10.8350.90612.7950.2750.2750.0000.0000.0000.000
21A22THR0-0.0490.0008.152-0.102-0.1020.0000.0000.0000.000
22A23GLY00.000-0.0149.747-0.120-0.1200.0000.0000.0000.000
23A24VAL0-0.073-0.0236.656-0.096-0.0960.0000.0000.0000.000
24A25ILE00.0040.0009.3960.2450.2450.0000.0000.0000.000
25A26PHE0-0.028-0.0438.255-0.109-0.1090.0000.0000.0000.000
26A27GLU-1-0.954-0.96511.541-0.198-0.1980.0000.0000.0000.000
27A28ARG10.9290.97212.598-0.017-0.0170.0000.0000.0000.000
28A29GLU-1-0.881-0.94512.906-0.287-0.2870.0000.0000.0000.000
29A30SER0-0.0070.00815.1570.0350.0350.0000.0000.0000.000
30A31SER0-0.006-0.02316.480-0.018-0.0180.0000.0000.0000.000
31A32ILE0-0.010-0.02315.788-0.013-0.0130.0000.0000.0000.000
32A33LEU0-0.0270.00410.2370.0570.0570.0000.0000.0000.000
33A34ARG10.9000.94910.5890.1510.1510.0000.0000.0000.000
34A35GLU-1-0.878-0.9378.2930.1200.1200.0000.0000.0000.000
35A36GLY00.0680.0247.1720.0560.0560.0000.0000.0000.000
36A37LYS10.9450.9856.5081.1601.1600.0000.0000.0000.000
37A38ASP-1-0.895-0.9463.922-2.705-2.2950.001-0.126-0.2850.000
38A39ILE0-0.017-0.0042.146-10.871-8.5543.957-3.132-3.143-0.035
39A40VAL0-0.0100.0073.5271.4321.9070.004-0.109-0.3700.000
40A41CYS0-0.045-0.0175.860-0.144-0.1440.0000.0000.0000.000
41A42PHE00.0220.0037.9470.0750.0750.0000.0000.0000.000
42A43MET0-0.0120.01510.752-0.043-0.0430.0000.0000.0000.000
43A44VAL00.0190.01313.1940.0130.0130.0000.0000.0000.000
44A45ARG10.9690.97915.530-0.126-0.1260.0000.0000.0000.000
45A46PRO00.0820.03916.8770.0320.0320.0000.0000.0000.000
46A47PHE00.0560.02317.1500.0220.0220.0000.0000.0000.000
47A48ASP-1-0.949-0.97816.8310.2460.2460.0000.0000.0000.000
48A49VAL0-0.0120.00411.6460.0630.0630.0000.0000.0000.000
49A50PRO00.0470.00912.9200.0860.0860.0000.0000.0000.000
50A51THR00.0060.01914.6540.0340.0340.0000.0000.0000.000
51A52TYR00.0240.00811.1450.0390.0390.0000.0000.0000.000
52A53LEU0-0.033-0.0068.2320.1280.1280.0000.0000.0000.000
53A54VAL0-0.004-0.00311.1740.0670.0670.0000.0000.0000.000
54A55HIS0-0.075-0.03614.174-0.030-0.0300.0000.0000.0000.000
55A56GLY0-0.019-0.00110.5140.0100.0100.0000.0000.0000.000
56A57VAL0-0.045-0.0189.4470.2180.2180.0000.0000.0000.000
57A58ALA0-0.025-0.0196.4550.2320.2320.0000.0000.0000.000
58A59ASP-1-0.738-0.7882.6263.3565.6851.378-1.469-2.238-0.013
59A60ILE00.0200.0032.640-1.191-0.4420.302-0.149-0.9010.000
60A61GLY00.0140.0096.089-0.088-0.0880.0000.0000.0000.000
61A62PHE00.0220.0127.827-0.044-0.0440.0000.0000.0000.000
62A63CYS0-0.064-0.02612.0960.0180.0180.0000.0000.0000.000
63A64GLY00.1030.04215.742-0.018-0.0180.0000.0000.0000.000
64A65THR00.025-0.01219.2420.0130.0130.0000.0000.0000.000
65A66ASP-1-0.881-0.93921.4770.0720.0720.0000.0000.0000.000
66A67VAL0-0.051-0.03117.9640.0120.0120.0000.0000.0000.000
67A68LEU0-0.010-0.02316.4530.0180.0180.0000.0000.0000.000
68A69LEU00.0390.02720.2980.0050.0050.0000.0000.0000.000
69A70GLU-1-0.837-0.89723.7230.0960.0960.0000.0000.0000.000
70A71LYS10.8310.91618.932-0.255-0.2550.0000.0000.0000.000
71A72GLU-1-0.874-0.92420.9540.1450.1450.0000.0000.0000.000
72A73THR0-0.077-0.04216.7390.0350.0350.0000.0000.0000.000
73A74SER00.0210.00416.894-0.011-0.0110.0000.0000.0000.000
74A75LEU0-0.055-0.03111.7500.0190.0190.0000.0000.0000.000
75A76ILE00.0410.03011.349-0.054-0.0540.0000.0000.0000.000
76A77GLN00.0500.02211.9860.0190.0190.0000.0000.0000.000
77A78PRO0-0.087-0.0239.090-0.024-0.0240.0000.0000.0000.000
78A79PHE00.0630.0229.416-0.031-0.0310.0000.0000.0000.000
79A80PHE00.0050.01514.2580.0300.0300.0000.0000.0000.000
80A81ILE0-0.004-0.00412.527-0.026-0.0260.0000.0000.0000.000
81A82PRO00.0430.01616.7860.0240.0240.0000.0000.0000.000
82A83THR0-0.015-0.01719.7620.0110.0110.0000.0000.0000.000
83A84ASN00.0030.00521.7720.0130.0130.0000.0000.0000.000
84A85ILE0-0.061-0.02820.388-0.008-0.0080.0000.0000.0000.000
85A86SER0-0.014-0.00624.3220.0010.0010.0000.0000.0000.000
86A87ARG10.8480.92327.0560.0090.0090.0000.0000.0000.000
87A88MET00.0160.02927.3350.0010.0010.0000.0000.0000.000
88A89VAL0-0.032-0.01430.194-0.003-0.0030.0000.0000.0000.000
89A90LEU00.0580.03434.0400.0050.0050.0000.0000.0000.000
90A91ALA0-0.019-0.02637.132-0.004-0.0040.0000.0000.0000.000
91A92GLY00.0610.02639.4910.0040.0040.0000.0000.0000.000
92A93PRO0-0.0060.01042.872-0.003-0.0030.0000.0000.0000.000
93A94LYS10.9840.98145.9630.0020.0020.0000.0000.0000.000
94A95GLY0-0.0100.01147.1030.0000.0000.0000.0000.0000.000
95A96ARG10.9040.96048.370-0.017-0.0170.0000.0000.0000.000
96A97GLY00.0520.03547.2840.0000.0000.0000.0000.0000.000
97A98ILE0-0.027-0.02443.4390.0020.0020.0000.0000.0000.000
98A99PRO00.0100.00546.302-0.001-0.0010.0000.0000.0000.000
99A100GLU-1-0.890-0.95348.3210.0200.0200.0000.0000.0000.000
100A101GLY0-0.037-0.00850.1060.0010.0010.0000.0000.0000.000
101A102GLU-1-0.955-0.98545.6080.0420.0420.0000.0000.0000.000
102A103LYS10.8730.95443.267-0.031-0.0310.0000.0000.0000.000
103A104ARG10.8690.94542.903-0.030-0.0300.0000.0000.0000.000
104A105ILE00.0130.00437.369-0.003-0.0030.0000.0000.0000.000
105A106ALA00.0240.02437.7780.0040.0040.0000.0000.0000.000
106A107THR00.025-0.00432.530-0.001-0.0010.0000.0000.0000.000
107A108LYS10.9280.97427.854-0.047-0.0470.0000.0000.0000.000
108A109PHE0-0.073-0.03125.3770.0080.0080.0000.0000.0000.000
109A110PRO00.0510.00829.338-0.006-0.0060.0000.0000.0000.000
110A111ASN00.003-0.03027.104-0.009-0.0090.0000.0000.0000.000
111A112VAL0-0.011-0.00227.392-0.005-0.0050.0000.0000.0000.000
112A113THR0-0.065-0.01030.045-0.008-0.0080.0000.0000.0000.000
113A114GLN0-0.027-0.04233.323-0.006-0.0060.0000.0000.0000.000
114A115ARG10.9280.96527.242-0.092-0.0920.0000.0000.0000.000
115A116TYR0-0.076-0.08433.318-0.004-0.0040.0000.0000.0000.000
116A117CYS0-0.020-0.01535.240-0.008-0.0080.0000.0000.0000.000
117A118GLU-1-0.828-0.88735.0110.0650.0650.0000.0000.0000.000
118A119SER0-0.116-0.05635.666-0.004-0.0040.0000.0000.0000.000
119A120LYS10.9330.95037.770-0.028-0.0280.0000.0000.0000.000
120A121GLY0-0.0300.00340.861-0.002-0.0020.0000.0000.0000.000
121A122TRP0-0.047-0.03140.563-0.001-0.0010.0000.0000.0000.000
122A123HIS00.0470.03142.2640.0040.0040.0000.0000.0000.000
123A125ARG10.9640.98341.636-0.045-0.0450.0000.0000.0000.000
124A126ILE00.0080.00135.134-0.003-0.0030.0000.0000.0000.000
125A127ILE0-0.038-0.01838.1830.0040.0040.0000.0000.0000.000
126A128PRO00.0150.00133.073-0.002-0.0020.0000.0000.0000.000
127A129LEU00.0050.00933.594-0.001-0.0010.0000.0000.0000.000
128A130LYS10.9370.94828.227-0.094-0.0940.0000.0000.0000.000
129A131GLY0-0.019-0.02030.3000.0010.0010.0000.0000.0000.000
130A132SER00.0210.02032.3780.0000.0000.0000.0000.0000.000
131A133VAL00.0180.00833.2290.0000.0000.0000.0000.0000.000
132A134GLU-1-0.871-0.93935.9360.0210.0210.0000.0000.0000.000
133A135LEU0-0.0050.00038.458-0.002-0.0020.0000.0000.0000.000
134A136ALA0-0.011-0.00639.7520.0000.0000.0000.0000.0000.000
135A137PRO00.0180.00340.7410.0000.0000.0000.0000.0000.000
136A138ILE0-0.0040.00444.0740.0000.0000.0000.0000.0000.000
137A139ALA0-0.024-0.00144.467-0.001-0.0010.0000.0000.0000.000
138A140GLY0-0.0060.00246.3000.0010.0010.0000.0000.0000.000
139A141LEU0-0.056-0.01940.3130.0020.0020.0000.0000.0000.000
140A142SER0-0.073-0.06441.0200.0020.0020.0000.0000.0000.000
141A143ASP-1-0.874-0.93943.4860.0270.0270.0000.0000.0000.000
142A144LEU0-0.016-0.01540.688-0.003-0.0030.0000.0000.0000.000
143A145ILE0-0.0260.00136.3790.0030.0030.0000.0000.0000.000
144A146VAL00.0240.01332.173-0.003-0.0030.0000.0000.0000.000
145A147ASP-1-0.866-0.93931.2160.0400.0400.0000.0000.0000.000
146A148ILE0-0.020-0.00825.851-0.004-0.0040.0000.0000.0000.000
147A149THR0-0.0260.00230.167-0.003-0.0030.0000.0000.0000.000
148A150GLU-1-0.774-0.87227.069-0.029-0.0290.0000.0000.0000.000
149A151THR00.012-0.01030.806-0.001-0.0010.0000.0000.0000.000
150A152GLY00.0190.01134.1850.0000.0000.0000.0000.0000.000
151A153ARG10.9090.96836.1390.0150.0150.0000.0000.0000.000
152A154THR00.0640.03234.823-0.001-0.0010.0000.0000.0000.000
153A155LEU00.0300.04035.9470.0020.0020.0000.0000.0000.000
154A156LYS10.9840.99039.0330.0080.0080.0000.0000.0000.000
155A157GLU-1-0.966-0.99439.361-0.004-0.0040.0000.0000.0000.000
156A158ASN0-0.021-0.02639.9420.0020.0020.0000.0000.0000.000
157A159ASN0-0.057-0.02443.0690.0000.0000.0000.0000.0000.000
158A160LEU0-0.025-0.00639.6910.0020.0020.0000.0000.0000.000
159A161GLU-1-0.950-0.99442.1830.0010.0010.0000.0000.0000.000
160A162ILE0-0.045-0.03536.3460.0020.0020.0000.0000.0000.000
161A163LEU0-0.017-0.01239.784-0.001-0.0010.0000.0000.0000.000
162A164ASP-1-0.796-0.85937.7590.0160.0160.0000.0000.0000.000
163A165GLU-1-0.854-0.91133.422-0.001-0.0010.0000.0000.0000.000
164A166ILE0-0.048-0.01931.0010.0020.0020.0000.0000.0000.000
165A167PHE00.018-0.01125.5270.0040.0040.0000.0000.0000.000
166A168VAL0-0.0320.00025.277-0.001-0.0010.0000.0000.0000.000
167A169ILE0-0.027-0.01522.6120.0070.0070.0000.0000.0000.000
168A170ARG10.9450.97120.1860.0140.0140.0000.0000.0000.000
169A171THR00.002-0.00314.6390.0150.0150.0000.0000.0000.000
170A172HIS00.0350.05215.232-0.019-0.0190.0000.0000.0000.000
171A173VAL00.0570.0228.5390.0160.0160.0000.0000.0000.000
172A174VAL0-0.023-0.01610.500-0.002-0.0020.0000.0000.0000.000
173A175VAL00.021-0.0016.4210.0870.0870.0000.0000.0000.000
174A176ASN00.0160.0147.368-0.327-0.3270.0000.0000.0000.000
175A177PRO00.0760.0208.3280.1020.1020.0000.0000.0000.000
176A178VAL0-0.026-0.0119.914-0.069-0.0690.0000.0000.0000.000
177A179SER0-0.025-0.0714.665-0.293-0.230-0.001-0.002-0.0600.000
178A180TYR00.0220.0246.145-0.051-0.0510.0000.0000.0000.000
179A181ARG10.9430.9718.079-0.726-0.7260.0000.0000.0000.000
180A182THR0-0.077-0.0687.6740.0180.0180.0000.0000.0000.000
181A183LYS10.8940.9322.552-8.660-7.4900.978-0.540-1.6080.002
182A184ARG10.9420.9984.583-0.637-0.533-0.001-0.006-0.0970.000
183A185GLU-1-0.873-0.9536.586-0.603-0.6030.0000.0000.0000.000
184A186GLU-1-0.892-0.9412.269-14.594-9.7183.734-3.702-4.908-0.045
185A187VAL0-0.034-0.0322.755-2.857-0.8170.595-0.919-1.716-0.006
186A188VAL0-0.006-0.0093.8930.0120.1160.0050.017-0.1260.000
187A189SER00.0500.0445.657-0.020-0.0200.0000.0000.0000.000
188A190PHE00.002-0.0092.732-1.2250.1210.975-0.535-1.786-0.002
189A191LEU0-0.052-0.0524.5870.2340.313-0.001-0.012-0.0660.000
190A192GLU-1-0.940-0.9577.019-0.478-0.4780.0000.0000.0000.000
191A193LYS10.9720.9897.2701.3881.3880.0000.0000.0000.000
192A194LEU0-0.044-0.0196.9490.1050.1050.0000.0000.0000.000
193A195GLN00.012-0.0019.4970.1160.1160.0000.0000.0000.000
194A196GLU-1-0.893-0.93612.279-0.471-0.4710.0000.0000.0000.000
195A197VAL0-0.056-0.02511.9440.0440.0440.0000.0000.0000.000
196A198ILE0-0.062-0.05111.0920.0560.0560.0000.0000.0000.000
197A199GLU-1-0.946-0.96514.773-0.164-0.1640.0000.0000.0000.000
198A200HIS00.0000.00117.4900.0240.0240.0000.0000.0000.000
199A201ASP-1-0.924-0.96117.417-0.212-0.2120.0000.0000.0000.000
200A202SER0-0.031-0.03818.6440.0200.0200.0000.0000.0000.000
201A203ASN0-0.090-0.03220.4020.0320.0320.0000.0000.0000.000
202A204GLU-1-1.007-0.98122.246-0.141-0.1410.0000.0000.0000.000