FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: VK711

Calculation Name: 4A9A-C-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4A9A

Chain ID: C

ChEMBL ID:

UniProt ID: P39729

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -595574.008255
FMO2-HF: Nuclear repulsion 553991.644744
FMO2-HF: Total energy -41582.363511
FMO2-MP2: Total energy -41705.275625


3D Structure Molmil
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(C:214:LEU)


Summations of interaction energy for fragment #1(C:214: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.
-4.471-7.91312.479-5.01-4.027-0.042
Interaction energy analysis for fragmet #1(C:214:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.092 / 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].
4C215GLU-1-0.959-0.8821.813-5.324-9.80512.484-4.520-3.483-0.045
5C216LYS00.167-0.0823.868-1.301-0.480-0.008-0.507-0.3060.003
6C216LYS10.7411.0107.8881.1461.1460.0000.0000.0000.000
7C217GLN00.085-0.1166.0290.1320.1320.0000.0000.0000.000
8C217GLN0-0.0240.1363.9540.5740.7920.0030.017-0.2380.000
9C218PRO0-0.029-0.0956.7150.3190.3190.0000.0000.0000.000
10C219LYS00.1270.06410.184-0.095-0.0950.0000.0000.0000.000
11C219LYS10.8601.03311.9520.5820.5820.0000.0000.0000.000
12C220ILE00.026-0.10012.4890.0150.0150.0000.0000.0000.000
13C220ILE0-0.0390.10312.036-0.003-0.0030.0000.0000.0000.000
14C221THR0-0.009-0.11814.551-0.007-0.0070.0000.0000.0000.000
15C221THR0-0.0590.05218.8120.0150.0150.0000.0000.0000.000
16C222LEU00.131-0.10317.306-0.033-0.0330.0000.0000.0000.000
17C222LEU0-0.0880.10819.3240.0010.0010.0000.0000.0000.000
18C223GLU00.039-0.12919.2420.0040.0040.0000.0000.0000.000
19C223GLU-1-0.876-0.79621.665-0.225-0.2250.0000.0000.0000.000
20C224GLU00.157-0.09817.5430.0270.0270.0000.0000.0000.000
21C224GLU-1-0.868-0.75016.716-0.386-0.3860.0000.0000.0000.000
22C225PHE00.098-0.07315.953-0.006-0.0060.0000.0000.0000.000
23C225PHE0-0.1250.05014.3720.0030.0030.0000.0000.0000.000
24C226ILE0-0.017-0.13216.8600.0010.0010.0000.0000.0000.000
25C226ILE0-0.1030.09320.4900.0040.0040.0000.0000.0000.000
26C227GLU00.068-0.13620.2460.0150.0150.0000.0000.0000.000
27C227GLU-1-1.000-0.83021.337-0.181-0.1810.0000.0000.0000.000
28C228THR0-0.046-0.12618.4580.0250.0250.0000.0000.0000.000
29C228THR0-0.0370.07517.766-0.012-0.0120.0000.0000.0000.000
30C229GLU00.057-0.10914.1690.0310.0310.0000.0000.0000.000
31C229GLU-1-0.883-0.78212.639-0.511-0.5110.0000.0000.0000.000
32C230ARG00.116-0.10114.291-0.016-0.0160.0000.0000.0000.000
33C230ARG10.8391.08316.8300.1770.1770.0000.0000.0000.000
34C231GLY0-0.057-0.13916.0870.0250.0250.0000.0000.0000.000
35C232LYS00.1230.00314.0930.0430.0430.0000.0000.0000.000
36C232LYS10.7410.99612.7210.4190.4190.0000.0000.0000.000
37C233LEU0-0.023-0.10913.6510.0190.0190.0000.0000.0000.000
38C233LEU0-0.0920.09311.1310.0010.0010.0000.0000.0000.000
39C234ASP00.175-0.08014.5200.0060.0060.0000.0000.0000.000
40C234ASP-1-0.902-0.78515.811-0.007-0.0070.0000.0000.0000.000
41C235LYS00.082-0.12216.5630.0070.0070.0000.0000.0000.000
42C235LYS10.9071.07619.5280.0910.0910.0000.0000.0000.000
43C236SER0-0.020-0.09018.9360.0000.0000.0000.0000.0000.000
44C236SER0-0.0600.04019.8000.0080.0080.0000.0000.0000.000
45C237LYS00.033-0.11615.7920.0190.0190.0000.0000.0000.000
46C237LYS10.8771.08115.136-0.045-0.0450.0000.0000.0000.000
47C238LEU00.021-0.08715.2960.0220.0220.0000.0000.0000.000
48C238LEU0-0.0860.10314.558-0.005-0.0050.0000.0000.0000.000
49C239THR00.048-0.10615.3400.0180.0180.0000.0000.0000.000
50C239THR0-0.0390.09414.9190.0170.0170.0000.0000.0000.000
51C240PRO0-0.023-0.09216.677-0.024-0.0240.0000.0000.0000.000
52C241ILE00.1740.03519.0000.0230.0230.0000.0000.0000.000
53C241ILE0-0.0730.12717.535-0.003-0.0030.0000.0000.0000.000
54C242THR00.004-0.09319.706-0.010-0.0100.0000.0000.0000.000
55C242THR0-0.0150.05922.2500.0030.0030.0000.0000.0000.000
56C243ILE00.139-0.06721.413-0.002-0.0020.0000.0000.0000.000
57C243ILE0-0.0270.12725.1020.0000.0000.0000.0000.0000.000
58C244ALA00.090-0.09822.3950.0000.0000.0000.0000.0000.000
59C244ALA0-0.0550.11722.8630.0010.0010.0000.0000.0000.000
60C245ASN00.111-0.09918.6460.0190.0190.0000.0000.0000.000
61C245ASN0-0.1560.06417.7300.0160.0160.0000.0000.0000.000
62C246PHE00.130-0.08717.2530.0130.0130.0000.0000.0000.000
63C246PHE0-0.0820.10017.828-0.003-0.0030.0000.0000.0000.000
64C247ALA00.099-0.10217.911-0.004-0.0040.0000.0000.0000.000
65C247ALA0-0.0620.12021.4630.0000.0000.0000.0000.0000.000
66C248GLN00.067-0.10517.3990.0040.0040.0000.0000.0000.000
67C248GLN0-0.0580.10314.345-0.022-0.0220.0000.0000.0000.000
68C249TRP00.120-0.07913.7650.0530.0530.0000.0000.0000.000
69C249TRP0-0.0880.09211.0000.0030.0030.0000.0000.0000.000
70C250LYS00.101-0.11514.021-0.001-0.0010.0000.0000.0000.000
71C250LYS10.8551.09017.6680.0280.0280.0000.0000.0000.000
72C251LYS00.092-0.10316.513-0.016-0.0160.0000.0000.0000.000
73C251LYS10.7421.02016.153-0.271-0.2710.0000.0000.0000.000
74C252ASP00.075-0.12412.712-0.010-0.0100.0000.0000.0000.000
75C252ASP-1-0.897-0.77111.8460.3730.3730.0000.0000.0000.000
76C253HIS00.138-0.06612.3350.0370.0370.0000.0000.0000.000
77C253HIS0-0.1160.08112.287-0.007-0.0070.0000.0000.0000.000
78C254VAL00.055-0.13913.369-0.023-0.0230.0000.0000.0000.000
79C254VAL0-0.0680.11617.661-0.004-0.0040.0000.0000.0000.000
80C255ILE00.092-0.09815.516-0.036-0.0360.0000.0000.0000.000
81C255ILE0-0.0670.12014.2620.0070.0070.0000.0000.0000.000
82C256ALA00.098-0.11211.4240.0420.0420.0000.0000.0000.000
83C256ALA0-0.0600.12510.813-0.005-0.0050.0000.0000.0000.000
84C257LYS0-0.003-0.11812.731-0.019-0.0190.0000.0000.0000.000
85C257LYS10.8471.04614.0300.1220.1220.0000.0000.0000.000
86C258ILE00.123-0.06715.283-0.025-0.0250.0000.0000.0000.000
87C258ILE0-0.0780.10717.6710.0020.0020.0000.0000.0000.000
88C259ASN00.077-0.06614.724-0.033-0.0330.0000.0000.0000.000
89C259ASN0-0.0740.08413.917-0.030-0.0300.0000.0000.0000.000
90C260ALA00.111-0.11714.2980.0240.0240.0000.0000.0000.000
91C260ALA0-0.0780.10213.251-0.016-0.0160.0000.0000.0000.000
92C261GLU00.057-0.12815.035-0.025-0.0250.0000.0000.0000.000
93C261GLU-1-0.859-0.78119.118-0.024-0.0240.0000.0000.0000.000
94C262LYS00.154-0.07918.654-0.019-0.0190.0000.0000.0000.000
95C262LYS10.7901.05818.178-0.183-0.1830.0000.0000.0000.000
96C263LYS00.082-0.08616.675-0.001-0.0010.0000.0000.0000.000
97C263LYS10.8321.04312.757-0.046-0.0460.0000.0000.0000.000
98C264LEU00.050-0.11318.166-0.005-0.0050.0000.0000.0000.000
99C264LEU0-0.0280.13217.802-0.005-0.0050.0000.0000.0000.000
100C265SER00.009-0.10320.170-0.013-0.0130.0000.0000.0000.000
101C265SER0-0.0020.06922.6790.0050.0050.0000.0000.0000.000
102C266SER0-0.006-0.03822.004-0.004-0.0040.0000.0000.0000.000
103C266SER0-0.0820.04121.1610.0020.0020.0000.0000.0000.000
104C267LYS00.045-0.10422.4710.0050.0050.0000.0000.0000.000
105C267LYS10.7671.01218.502-0.014-0.0140.0000.0000.0000.000
106C268ARG00.107-0.05723.721-0.009-0.0090.0000.0000.0000.000
107C268ARG10.7140.98024.2990.0110.0110.0000.0000.0000.000
108C269LYS00.086-0.10925.8850.0090.0090.0000.0000.0000.000
109C269LYS10.8971.07929.8770.0340.0340.0000.0000.0000.000
110C270PRO0-0.038-0.10229.587-0.001-0.0010.0000.0000.0000.000
111C271THR00.0580.01331.238-0.004-0.0040.0000.0000.0000.000
112C271THR0-0.0840.03630.3980.0010.0010.0000.0000.0000.000
113C272GLY00.061-0.07433.0040.0040.0040.0000.0000.0000.000
114C273ARG00.1890.04835.2580.0020.0020.0000.0000.0000.000
115C273ARG10.8641.07132.049-0.007-0.0070.0000.0000.0000.000
116C274GLU00.081-0.10532.6030.0030.0030.0000.0000.0000.000
117C274GLU-1-0.866-0.77629.105-0.001-0.0010.0000.0000.0000.000
118C275ILE00.014-0.09234.0200.0050.0050.0000.0000.0000.000
119C275ILE0-0.0590.08234.9820.0000.0000.0000.0000.0000.000
120C276ILE00.102-0.07636.5640.0030.0030.0000.0000.0000.000
121C276ILE0-0.0720.10639.2480.0000.0000.0000.0000.0000.000
122C277LEU00.141-0.07336.3340.0010.0010.0000.0000.0000.000
123C277LEU0-0.1090.06734.4560.0000.0000.0000.0000.0000.000
124C278LYS00.153-0.02536.5150.0040.0040.0000.0000.0000.000
125C278LYS10.8151.01531.155-0.014-0.0140.0000.0000.0000.000
126C279MET00.089-0.08837.2340.0030.0030.0000.0000.0000.000
127C279MET0-0.1300.05739.962-0.002-0.0020.0000.0000.0000.000
128C280SER00.036-0.04040.4310.0000.0000.0000.0000.0000.000
129C280SER0-0.0660.02840.436-0.001-0.0010.0000.0000.0000.000
130C281ALA00.036-0.07538.5030.0000.0000.0000.0000.0000.000
131C281ALA0-0.1200.06038.0040.0010.0010.0000.0000.0000.000
132C282GLU0-0.128-0.17940.0190.0020.0020.0000.0000.0000.000
133C282GLU-1-0.898-0.91239.5240.0180.0180.0000.0000.0000.000
134C302ALA00.1650.00355.199-0.001-0.0010.0000.0000.0000.000
135C302ALA0-0.1300.08956.3240.0000.0000.0000.0000.0000.000
136C303TRP00.080-0.08854.5380.0000.0000.0000.0000.0000.000
137C303TRP0-0.1430.06953.840-0.001-0.0010.0000.0000.0000.000
138C304ASP00.099-0.12754.0260.0000.0000.0000.0000.0000.000
139C304ASP-1-0.895-0.76455.799-0.005-0.0050.0000.0000.0000.000
140C305LEU00.089-0.08852.4680.0000.0000.0000.0000.0000.000
141C305LEU0-0.1020.08349.5090.0000.0000.0000.0000.0000.000
142C306THR0-0.016-0.11752.817-0.001-0.0010.0000.0000.0000.000
143C306THR00.0100.07853.5280.0000.0000.0000.0000.0000.000
144C307GLU00.183-0.08053.5110.0000.0000.0000.0000.0000.000
145C307GLU-1-1.004-0.83957.232-0.008-0.0080.0000.0000.0000.000
146C308PHE00.044-0.10353.7090.0000.0000.0000.0000.0000.000
147C308PHE0-0.0990.08753.0610.0000.0000.0000.0000.0000.000
148C309THR00.045-0.07049.751-0.001-0.0010.0000.0000.0000.000
149C309THR0-0.0840.04848.7290.0000.0000.0000.0000.0000.000
150C310ASP00.071-0.14049.896-0.001-0.0010.0000.0000.0000.000
151C310ASP-1-0.902-0.77651.584-0.006-0.0060.0000.0000.0000.000
152C311ALA00.062-0.12851.3880.0000.0000.0000.0000.0000.000
153C311ALA0-0.0630.12153.7240.0000.0000.0000.0000.0000.000
154C312LEU00.090-0.09449.073-0.001-0.0010.0000.0000.0000.000
155C312LEU0-0.1210.09745.7470.0000.0000.0000.0000.0000.000
156C313LYS00.120-0.07046.609-0.002-0.0020.0000.0000.0000.000
157C313LYS10.7510.99646.4700.0090.0090.0000.0000.0000.000
158C314LYS00.114-0.05847.5240.0000.0000.0000.0000.0000.000
159C314LYS10.8601.04751.7810.0090.0090.0000.0000.0000.000
160C315ALA00.085-0.10649.6860.0000.0000.0000.0000.0000.000
161C315ALA0-0.0980.09449.8390.0000.0000.0000.0000.0000.000
162C316ASP00.077-0.09945.419-0.001-0.0010.0000.0000.0000.000
163C316ASP-1-1.008-0.87643.277-0.021-0.0210.0000.0000.0000.000
164C317HIS00.057-0.06244.945-0.002-0.0020.0000.0000.0000.000
165C317HIS10.6340.92241.6150.0160.0160.0000.0000.0000.000
166C318GLN00.111-0.08646.3150.0010.0010.0000.0000.0000.000
167C318GLN0-0.1730.04049.5350.0010.0010.0000.0000.0000.000
168C319ASP00.038-0.10347.2380.0020.0020.0000.0000.0000.000
169C319ASP-1-0.940-0.82646.567-0.020-0.0200.0000.0000.0000.000
170C320ASP00.087-0.14144.012-0.002-0.0020.0000.0000.0000.000
171C320ASP-1-0.882-0.76743.733-0.014-0.0140.0000.0000.0000.000
172C321GLY0-0.077-0.11543.8590.0000.0000.0000.0000.0000.000
173C322GLY0-0.080-0.04544.6150.0010.0010.0000.0000.0000.000
174C323ILE00.035-0.03940.880-0.003-0.0030.0000.0000.0000.000
175C323ILE0-0.0350.13939.573-0.001-0.0010.0000.0000.0000.000
176C324LYS00.074-0.08137.3890.0030.0030.0000.0000.0000.000
177C324LYS10.7310.97833.1770.0230.0230.0000.0000.0000.000
178C325ASP00.049-0.14736.931-0.004-0.0040.0000.0000.0000.000
179C325ASP-1-0.904-0.77036.796-0.014-0.0140.0000.0000.0000.000
180C326TYR00.022-0.10832.3820.0040.0040.0000.0000.0000.000
181C326TYR0-0.1090.07831.372-0.001-0.0010.0000.0000.0000.000
182C327GLY00.083-0.07632.3410.0030.0030.0000.0000.0000.000
183C328ASP00.003-0.03331.546-0.006-0.0060.0000.0000.0000.000
184C328ASP-1-0.882-0.79030.6010.0070.0070.0000.0000.0000.000
185C329GLY0-0.042-0.11328.468-0.003-0.0030.0000.0000.0000.000
186C330SER0-0.009-0.02526.731-0.005-0.0050.0000.0000.0000.000
187C330SER0-0.0760.04127.4600.0040.0040.0000.0000.0000.000
188C331ASN0-0.082-0.10426.541-0.003-0.0030.0000.0000.0000.000
189C331ASN0-0.1040.05426.6740.0040.0040.0000.0000.0000.000
190C332PRO00.090-0.06926.4840.0010.0010.0000.0000.0000.000
191C333THR0-0.022-0.01029.1040.0010.0010.0000.0000.0000.000
192C333THR00.0180.09331.7300.0000.0000.0000.0000.0000.000
193C334PHE00.015-0.07231.379-0.003-0.0030.0000.0000.0000.000
194C334PHE0-0.0980.07927.556-0.002-0.0020.0000.0000.0000.000
195C335ASP00.198-0.08932.628-0.003-0.0030.0000.0000.0000.000
196C335ASP-1-0.941-0.82935.640-0.004-0.0040.0000.0000.0000.000
197C336ILE00.018-0.11836.139-0.001-0.0010.0000.0000.0000.000
198C336ILE0-0.0560.11735.2100.0000.0000.0000.0000.0000.000
199C337LYS00.041-0.10238.2800.0020.0020.0000.0000.0000.000
200C337LYS10.9251.07240.6730.0130.0130.0000.0000.0000.000
201C338LYS0-0.030-0.09141.912-0.001-0.0010.0000.0000.0000.000
202C338LYS11.0301.01344.8020.0160.0160.0000.0000.0000.000