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: 72VJK

Calculation Name: 1F6F-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1F6F

Chain ID: B

ChEMBL ID:

UniProt ID: P16038

Base Structure: X-ray

Registration Date: 2023-09-19

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2156242.392504
FMO2-HF: Nuclear repulsion 2074028.908988
FMO2-HF: Total energy -82213.483516
FMO2-MP2: Total energy -82452.139954


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(B:5:GLY)


Summations of interaction energy for fragment #1(B:5:GLY)
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.
-16.626-11.937.469-6.412-5.75-0.045
Interaction energy analysis for fragmet #1(B:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.015
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].
3B7PRO00.0140.0283.476-2.0401.476-0.003-2.039-1.4740.002
4B8GLU-1-0.806-0.8805.640-3.224-3.2240.0000.0000.0000.000
5B9ILE00.003-0.0088.2380.4450.4450.0000.0000.0000.000
6B10HIS00.008-0.0059.3710.1770.1770.0000.0000.0000.000
7B11LYS10.8230.90413.2970.4940.4940.0000.0000.0000.000
8B12CYS00.0020.02515.381-0.020-0.0200.0000.0000.0000.000
9B13ARG10.7840.87018.6760.3500.3500.0000.0000.0000.000
10B14SER00.0410.02322.5530.0100.0100.0000.0000.0000.000
11B15PRO00.0060.00625.763-0.002-0.0020.0000.0000.0000.000
12B16ASP-1-0.726-0.85529.199-0.144-0.1440.0000.0000.0000.000
13B17LYS10.8350.94028.8090.1200.1200.0000.0000.0000.000
14B18GLU-1-0.886-0.93029.500-0.084-0.0840.0000.0000.0000.000
15B19THR0-0.085-0.06726.8480.0040.0040.0000.0000.0000.000
16B20PHE0-0.001-0.01118.774-0.009-0.0090.0000.0000.0000.000
17B21THR0-0.0170.00920.0900.0200.0200.0000.0000.0000.000
18B23TRP00.0330.00316.1170.0400.0400.0000.0000.0000.000
19B24TRP0-0.025-0.01011.021-0.060-0.0600.0000.0000.0000.000
20B25ASN0-0.016-0.00411.4010.2640.2640.0000.0000.0000.000
21B26PRO00.003-0.01210.003-0.280-0.2800.0000.0000.0000.000
22B27GLY00.0350.0247.514-0.198-0.1980.0000.0000.0000.000
23B28THR0-0.071-0.0396.9820.1420.1420.0000.0000.0000.000
24B29ASP-1-0.826-0.9028.082-0.312-0.3120.0000.0000.0000.000
25B30GLY0-0.010-0.00910.7910.1350.1350.0000.0000.0000.000
26B31GLY0-0.027-0.02013.6760.0420.0420.0000.0000.0000.000
27B32LEU0-0.045-0.00513.7430.0280.0280.0000.0000.0000.000
28B33PRO0-0.0030.00114.664-0.047-0.0470.0000.0000.0000.000
29B34THR00.000-0.00910.0960.0680.0680.0000.0000.0000.000
30B35ASN0-0.024-0.00413.396-0.082-0.0820.0000.0000.0000.000
31B36TYR00.016-0.0179.029-0.059-0.0590.0000.0000.0000.000
32B37SER0-0.0130.00511.5020.0580.0580.0000.0000.0000.000
33B38LEU0-0.015-0.01111.475-0.116-0.1160.0000.0000.0000.000
34B39THR00.0050.00311.2640.0780.0780.0000.0000.0000.000
35B40TYR0-0.026-0.02312.533-0.085-0.0850.0000.0000.0000.000
36B41SER0-0.005-0.01114.7500.0660.0660.0000.0000.0000.000
37B42LYS10.8480.90616.9060.0160.0160.0000.0000.0000.000
38B43GLU-1-0.814-0.89119.912-0.061-0.0610.0000.0000.0000.000
39B44GLY0-0.023-0.00921.691-0.004-0.0040.0000.0000.0000.000
40B45GLU-1-0.817-0.87922.604-0.025-0.0250.0000.0000.0000.000
41B46LYS10.9190.96521.117-0.094-0.0940.0000.0000.0000.000
42B47THR00.008-0.00120.7090.0290.0290.0000.0000.0000.000
43B48THR0-0.0150.00914.671-0.002-0.0020.0000.0000.0000.000
44B49TYR0-0.072-0.05117.2460.0260.0260.0000.0000.0000.000
45B50GLU-1-0.752-0.85316.001-0.079-0.0790.0000.0000.0000.000
46B51CYS0-0.054-0.01016.7330.0270.0270.0000.0000.0000.000
47B52PRO0-0.025-0.00318.3920.0200.0200.0000.0000.0000.000
48B53ASP-1-0.783-0.89121.462-0.136-0.1360.0000.0000.0000.000
49B54TYR0-0.032-0.04115.856-0.043-0.0430.0000.0000.0000.000
50B55LYS10.8980.95020.9240.0860.0860.0000.0000.0000.000
51B56THR0-0.044-0.04524.290-0.005-0.0050.0000.0000.0000.000
52B57SER0-0.032-0.02622.1570.0140.0140.0000.0000.0000.000
53B58GLY00.0070.01922.719-0.025-0.0250.0000.0000.0000.000
54B59PRO00.0050.00319.555-0.007-0.0070.0000.0000.0000.000
55B60ASN0-0.028-0.01414.982-0.002-0.0020.0000.0000.0000.000
56B61SER00.000-0.00816.205-0.059-0.0590.0000.0000.0000.000
57B63PHE0-0.009-0.00418.670-0.012-0.0120.0000.0000.0000.000
58B64PHE00.0280.00817.3540.0190.0190.0000.0000.0000.000
59B65SER00.0670.02323.3710.0020.0020.0000.0000.0000.000
60B66LYS10.8700.90926.8210.0960.0960.0000.0000.0000.000
61B67GLN0-0.0430.00228.2510.0000.0000.0000.0000.0000.000
62B68TYR0-0.013-0.01223.3360.0110.0110.0000.0000.0000.000
63B69THR0-0.0090.01623.714-0.022-0.0220.0000.0000.0000.000
64B70SER0-0.033-0.02024.9220.0170.0170.0000.0000.0000.000
65B71ILE0-0.004-0.00525.004-0.010-0.0100.0000.0000.0000.000
66B72TRP0-0.036-0.02326.5210.0180.0180.0000.0000.0000.000
67B73LYS10.8870.94423.2750.0770.0770.0000.0000.0000.000
68B74ILE0-0.012-0.00417.747-0.026-0.0260.0000.0000.0000.000
69B75TYR0-0.032-0.04017.2240.0370.0370.0000.0000.0000.000
70B76ILE0-0.020-0.01112.158-0.036-0.0360.0000.0000.0000.000
71B77ILE00.007-0.01111.9680.0830.0830.0000.0000.0000.000
72B78THR0-0.0110.0077.196-0.075-0.0750.0000.0000.0000.000
73B79VAL00.0400.0147.5730.2090.2090.0000.0000.0000.000
74B80ASN0-0.044-0.0226.676-0.353-0.3530.0000.0000.0000.000
75B81ALA00.0360.0186.853-0.086-0.0860.0000.0000.0000.000
76B82THR00.0270.0167.7370.3570.3570.0000.0000.0000.000
77B83ASN00.0070.00210.376-0.028-0.0280.0000.0000.0000.000
78B84GLN0-0.011-0.01612.8580.0630.0630.0000.0000.0000.000
79B85MET0-0.0250.00012.7910.0130.0130.0000.0000.0000.000
80B86GLY0-0.0040.0089.7070.1060.1060.0000.0000.0000.000
81B87SER0-0.003-0.0227.573-0.256-0.2560.0000.0000.0000.000
82B88SER0-0.022-0.0152.539-1.428-0.5631.647-1.292-1.220-0.012
83B89SER00.0170.0022.405-1.352-0.6580.350-0.496-0.548-0.002
84B90SER0-0.0190.0002.062-6.366-7.0385.474-2.540-2.261-0.033
85B91ASP-1-0.900-0.9433.894-3.205-2.9220.002-0.045-0.2390.000
86B92PRO0-0.033-0.0185.2200.2730.283-0.0010.000-0.0080.000
87B93LEU00.0010.0198.5820.0210.0210.0000.0000.0000.000
88B94TYR0-0.012-0.01311.3520.1440.1440.0000.0000.0000.000
89B95VAL00.001-0.01814.737-0.020-0.0200.0000.0000.0000.000
90B96ASP-1-0.716-0.81617.811-0.127-0.1270.0000.0000.0000.000
91B97VAL0-0.001-0.01521.508-0.015-0.0150.0000.0000.0000.000
92B98THR0-0.083-0.06923.2090.0070.0070.0000.0000.0000.000
93B99TYR0-0.052-0.03122.8230.0110.0110.0000.0000.0000.000
94B100ILE0-0.039-0.00220.161-0.023-0.0230.0000.0000.0000.000
95B101VAL00.0190.00523.539-0.005-0.0050.0000.0000.0000.000
96B102GLU-1-0.793-0.87425.022-0.310-0.3100.0000.0000.0000.000
97B103PRO0-0.0050.01327.943-0.001-0.0010.0000.0000.0000.000
98B104GLU-1-0.898-0.96331.351-0.175-0.1750.0000.0000.0000.000
99B105PRO0-0.044-0.02533.7510.0050.0050.0000.0000.0000.000
100B106PRO0-0.040-0.00436.9400.0040.0040.0000.0000.0000.000
101B107ARG10.8670.92940.2000.0890.0890.0000.0000.0000.000
102B108ASN0-0.025-0.03442.8950.0000.0000.0000.0000.0000.000
103B109LEU00.0070.02345.1330.0030.0030.0000.0000.0000.000
104B110THR0-0.011-0.00447.3380.0030.0030.0000.0000.0000.000
105B111LEU00.002-0.00250.553-0.001-0.0010.0000.0000.0000.000
106B112GLU-1-0.816-0.88753.671-0.052-0.0520.0000.0000.0000.000
107B113VAL00.0310.01557.117-0.001-0.0010.0000.0000.0000.000
108B114LYS10.8490.93459.7320.0480.0480.0000.0000.0000.000
109B115GLN0-0.037-0.02559.9840.0000.0000.0000.0000.0000.000
110B116LEU0-0.029-0.02963.0300.0010.0010.0000.0000.0000.000
111B117LYS10.8940.93465.9370.0400.0400.0000.0000.0000.000
112B118ASP-1-0.807-0.87067.761-0.041-0.0410.0000.0000.0000.000
113B119LYS11.0010.98867.9250.0390.0390.0000.0000.0000.000
114B120LYS10.9020.94860.5900.0520.0520.0000.0000.0000.000
115B121THR00.0040.00661.6770.0000.0000.0000.0000.0000.000
116B122TYR0-0.049-0.04057.1780.0000.0000.0000.0000.0000.000
117B123LEU00.0400.03552.9240.0010.0010.0000.0000.0000.000
118B124TRP0-0.027-0.04053.2030.0000.0000.0000.0000.0000.000
119B125VAL00.0340.02048.2020.0000.0000.0000.0000.0000.000
120B126LYS10.8710.92949.5570.0600.0600.0000.0000.0000.000
121B127TRP00.0110.01442.9040.0000.0000.0000.0000.0000.000
122B128SER0-0.033-0.01344.3230.0040.0040.0000.0000.0000.000
123B129PRO00.0810.04439.262-0.004-0.0040.0000.0000.0000.000
124B130PRO00.0610.03035.7950.0070.0070.0000.0000.0000.000
125B131THR0-0.029-0.01838.5010.0010.0010.0000.0000.0000.000
126B132ILE00.0140.01033.4050.0050.0050.0000.0000.0000.000
127B133THR00.0130.02433.845-0.005-0.0050.0000.0000.0000.000
128B134ASP-1-0.746-0.84436.220-0.073-0.0730.0000.0000.0000.000
129B135VAL00.018-0.01238.3860.0020.0020.0000.0000.0000.000
130B136LYS10.7850.88440.1970.0760.0760.0000.0000.0000.000
131B137THR0-0.031-0.03540.1520.0040.0040.0000.0000.0000.000
132B138GLY0-0.0060.00840.5090.0030.0030.0000.0000.0000.000
133B139TRP0-0.0030.00431.5580.0010.0010.0000.0000.0000.000
134B140PHE0-0.004-0.01931.927-0.007-0.0070.0000.0000.0000.000
135B141THR00.006-0.00935.5940.0070.0070.0000.0000.0000.000
136B142MET0-0.0040.00534.998-0.010-0.0100.0000.0000.0000.000
137B143GLU-1-0.838-0.88636.316-0.118-0.1180.0000.0000.0000.000
138B144TYR00.007-0.01438.115-0.008-0.0080.0000.0000.0000.000
139B145GLU-1-0.812-0.87838.836-0.129-0.1290.0000.0000.0000.000
140B146ILE0-0.022-0.00741.321-0.002-0.0020.0000.0000.0000.000
141B147ARG10.8710.94241.3450.1190.1190.0000.0000.0000.000
142B148LEU0-0.016-0.02044.8460.0020.0020.0000.0000.0000.000
143B149LYS10.8600.93647.4150.0890.0890.0000.0000.0000.000
144B150PRO00.0570.03450.3430.0000.0000.0000.0000.0000.000
145B151GLU-1-0.829-0.92451.682-0.077-0.0770.0000.0000.0000.000
146B152GLU-1-0.922-0.95152.066-0.066-0.0660.0000.0000.0000.000
147B153ALA0-0.018-0.01751.5500.0020.0020.0000.0000.0000.000
148B154GLU-1-0.945-0.95347.081-0.095-0.0950.0000.0000.0000.000
149B155GLU-1-0.869-0.90546.524-0.094-0.0940.0000.0000.0000.000
150B156TRP0-0.038-0.02744.1270.0020.0020.0000.0000.0000.000
151B157GLH0-0.045-0.04445.538-0.002-0.0020.0000.0000.0000.000
152B158ILE0-0.018-0.02541.098-0.001-0.0010.0000.0000.0000.000
153B159HIS00.0240.00944.4780.0030.0030.0000.0000.0000.000
154B160PHE00.0220.01138.478-0.001-0.0010.0000.0000.0000.000
155B161THR0-0.017-0.01642.9470.0030.0030.0000.0000.0000.000
156B162GLY00.0480.03141.6550.0050.0050.0000.0000.0000.000
157B163HIS0-0.028-0.04439.2930.0000.0000.0000.0000.0000.000
158B164GLN0-0.0260.01242.9920.0030.0030.0000.0000.0000.000
159B165THR00.0180.00843.827-0.003-0.0030.0000.0000.0000.000
160B166GLN0-0.009-0.01546.0100.0030.0030.0000.0000.0000.000
161B167PHE00.0110.00648.3130.0000.0000.0000.0000.0000.000
162B168LYS10.8760.95250.4040.0610.0610.0000.0000.0000.000
163B169VAL00.0410.03451.166-0.001-0.0010.0000.0000.0000.000
164B170PHE0-0.029-0.02854.1340.0030.0030.0000.0000.0000.000
165B171ASP-1-0.867-0.94453.996-0.066-0.0660.0000.0000.0000.000
166B172LEU0-0.0190.00653.0160.0000.0000.0000.0000.0000.000
167B173TYR00.0440.01856.8900.0030.0030.0000.0000.0000.000
168B174PRO0-0.009-0.02859.429-0.001-0.0010.0000.0000.0000.000
169B175GLY0-0.0070.00762.3720.0000.0000.0000.0000.0000.000
170B176GLN0-0.011-0.00357.419-0.001-0.0010.0000.0000.0000.000
171B177LYS10.8220.90655.2490.0670.0670.0000.0000.0000.000
172B178TYR0-0.003-0.00452.307-0.001-0.0010.0000.0000.0000.000
173B179LEU00.0120.02548.1070.0010.0010.0000.0000.0000.000
174B180VAL0-0.011-0.02247.3990.0000.0000.0000.0000.0000.000
175B181GLN00.0060.01640.629-0.002-0.0020.0000.0000.0000.000
176B182THR00.014-0.00342.1350.0020.0020.0000.0000.0000.000
177B183ARG10.8310.89134.2190.1450.1450.0000.0000.0000.000
178B184CYS0-0.013-0.01735.2960.0090.0090.0000.0000.0000.000
179B185LYS10.8300.91632.0260.1350.1350.0000.0000.0000.000
180B186PRO00.0490.03430.3990.0110.0110.0000.0000.0000.000
181B187ASP-1-0.823-0.89732.745-0.133-0.1330.0000.0000.0000.000
182B188HIS10.8070.89328.7440.1360.1360.0000.0000.0000.000
183B189GLY00.0160.01527.878-0.014-0.0140.0000.0000.0000.000
184B190TYR0-0.008-0.01622.533-0.011-0.0110.0000.0000.0000.000
185B191TRP0-0.022-0.02528.5910.0130.0130.0000.0000.0000.000
186B192SER00.0230.01330.708-0.009-0.0090.0000.0000.0000.000
187B193ARG10.9560.96929.4370.2000.2000.0000.0000.0000.000
188B194TRP00.0310.01634.0890.0070.0070.0000.0000.0000.000
189B195SER00.0100.00837.850-0.003-0.0030.0000.0000.0000.000
190B196GLN0-0.022-0.01640.312-0.002-0.0020.0000.0000.0000.000
191B197GLU-1-0.837-0.93842.609-0.104-0.1040.0000.0000.0000.000
192B198SER0-0.066-0.03045.3920.0030.0030.0000.0000.0000.000
193B199SER00.0120.00048.923-0.001-0.0010.0000.0000.0000.000
194B200VAL0-0.063-0.02752.2270.0020.0020.0000.0000.0000.000
195B201GLU-1-0.835-0.90555.319-0.061-0.0610.0000.0000.0000.000
196B202MET0-0.0340.00557.7010.0010.0010.0000.0000.0000.000
197B203PRO0-0.014-0.00560.2150.0010.0010.0000.0000.0000.000