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: LNVJ9

Calculation Name: 2FXT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FXT

Chain ID: A

ChEMBL ID:

UniProt ID: Q01852

Base Structure: X-ray

Registration Date: 2023-09-23

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2115371.040883
FMO2-HF: Nuclear repulsion 2038775.035729
FMO2-HF: Total energy -76596.005153
FMO2-MP2: Total energy -76821.136278


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:234:SER)


Summations of interaction energy for fragment #1(A:234:SER)
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.
-6.908-3.1430.094-1.599-2.260.003
Interaction energy analysis for fragmet #1(A:234:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.027
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].
3A236GLN0-0.016-0.0062.928-3.523-0.9520.082-1.187-1.4660.002
4A237SER00.0360.0033.331-0.3880.5580.013-0.377-0.5820.001
5A238LEU0-0.006-0.0014.776-0.0720.176-0.001-0.035-0.2120.000
6A239LYS10.9650.9867.217-1.335-1.3350.0000.0000.0000.000
7A240ASN0-0.055-0.0318.325-0.112-0.1120.0000.0000.0000.000
8A241LYS10.9750.9905.820-1.612-1.6120.0000.0000.0000.000
9A242LEU00.0020.01710.993-0.069-0.0690.0000.0000.0000.000
10A243TRP0-0.003-0.02513.029-0.084-0.0840.0000.0000.0000.000
11A244ASP-1-0.856-0.93112.4260.2040.2040.0000.0000.0000.000
12A245GLU-1-0.899-0.95514.8530.2350.2350.0000.0000.0000.000
13A246SER0-0.068-0.02716.428-0.035-0.0350.0000.0000.0000.000
14A247GLU-1-0.889-0.94219.8280.1160.1160.0000.0000.0000.000
15A248ASN0-0.047-0.02617.450-0.038-0.0380.0000.0000.0000.000
16A249PRO00.018-0.01020.9100.0160.0160.0000.0000.0000.000
17A250LEU00.0450.02720.1840.0040.0040.0000.0000.0000.000
18A251ILE0-0.006-0.00315.5860.0060.0060.0000.0000.0000.000
19A252VAL00.0130.02219.0070.0130.0130.0000.0000.0000.000
20A253VAL00.0140.00821.3480.0010.0010.0000.0000.0000.000
21A254MET00.0020.00619.2910.0050.0050.0000.0000.0000.000
22A255ARG10.8950.95816.997-0.267-0.2670.0000.0000.0000.000
23A256LYS10.7660.88920.233-0.142-0.1420.0000.0000.0000.000
24A257ILE0-0.015-0.00423.794-0.013-0.0130.0000.0000.0000.000
25A258THR0-0.089-0.03619.070-0.002-0.0020.0000.0000.0000.000
26A259ASN0-0.040-0.03217.7450.0280.0280.0000.0000.0000.000
27A260LYS10.9110.98321.356-0.150-0.1500.0000.0000.0000.000
28A261VAL0-0.001-0.02024.575-0.010-0.0100.0000.0000.0000.000
29A262GLY00.0410.01525.6010.0010.0010.0000.0000.0000.000
30A263GLY00.0140.03024.690-0.010-0.0100.0000.0000.0000.000
31A264PHE00.010-0.01221.2530.0200.0200.0000.0000.0000.000
32A265PHE00.0170.00519.878-0.013-0.0130.0000.0000.0000.000
33A266ALA00.0090.00721.7530.0180.0180.0000.0000.0000.000
34A267GLU-1-0.934-0.96820.1090.1780.1780.0000.0000.0000.000
35A268THR0-0.010-0.01022.684-0.014-0.0140.0000.0000.0000.000
36A269GLU-1-0.849-0.90324.0220.0730.0730.0000.0000.0000.000
37A270SER00.0010.02224.793-0.009-0.0090.0000.0000.0000.000
38A271SER0-0.007-0.03027.053-0.006-0.0060.0000.0000.0000.000
39A272ARG10.9020.95629.582-0.081-0.0810.0000.0000.0000.000
40A273VAL00.0220.02728.830-0.004-0.0040.0000.0000.0000.000
41A274TYR0-0.006-0.02328.593-0.003-0.0030.0000.0000.0000.000
42A275SER0-0.055-0.04633.079-0.005-0.0050.0000.0000.0000.000
43A276GLN00.0070.00733.833-0.005-0.0050.0000.0000.0000.000
44A277PHE00.0480.00232.141-0.002-0.0020.0000.0000.0000.000
45A278LYS10.7980.89537.078-0.051-0.0510.0000.0000.0000.000
46A279LEU0-0.063-0.03439.196-0.003-0.0030.0000.0000.0000.000
47A280MET0-0.0600.00337.121-0.002-0.0020.0000.0000.0000.000
48A281ASP-1-0.743-0.87041.2190.0460.0460.0000.0000.0000.000
49A282PRO00.0110.00641.7550.0010.0010.0000.0000.0000.000
50A283THR0-0.0030.00143.267-0.002-0.0020.0000.0000.0000.000
51A284PHE0-0.0160.01434.1570.0000.0000.0000.0000.0000.000
52A285SER0-0.013-0.02537.273-0.001-0.0010.0000.0000.0000.000
53A286ASN00.0770.04231.5210.0060.0060.0000.0000.0000.000
54A287GLU-1-0.910-0.94034.6890.0470.0470.0000.0000.0000.000
55A288SER0-0.042-0.00737.1420.0000.0000.0000.0000.0000.000
56A289PHE00.0700.02233.1160.0000.0000.0000.0000.0000.000
57A290THR00.004-0.01933.2700.0030.0030.0000.0000.0000.000
58A291ARG10.8410.90735.342-0.038-0.0380.0000.0000.0000.000
59A292HIS0-0.007-0.01838.9030.0000.0000.0000.0000.0000.000
60A293LEU0-0.0070.00532.9610.0000.0000.0000.0000.0000.000
61A294ARG10.9090.94035.264-0.048-0.0480.0000.0000.0000.000
62A295GLU-1-0.831-0.91537.5180.0390.0390.0000.0000.0000.000
63A296TYR0-0.094-0.04940.526-0.002-0.0020.0000.0000.0000.000
64A297ILE00.0270.02237.8290.0010.0010.0000.0000.0000.000
65A298VAL0-0.013-0.01333.8100.0020.0020.0000.0000.0000.000
66A299PRO0-0.001-0.00136.9010.0010.0010.0000.0000.0000.000
67A300GLU-1-0.805-0.86739.4310.0460.0460.0000.0000.0000.000
68A301ILE00.015-0.01135.3190.0000.0000.0000.0000.0000.000
69A302LEU0-0.029-0.01533.7360.0020.0020.0000.0000.0000.000
70A303GLU-1-0.831-0.92537.8110.0390.0390.0000.0000.0000.000
71A304ALA0-0.0240.00441.208-0.002-0.0020.0000.0000.0000.000
72A305TYR0-0.052-0.01633.5940.0020.0020.0000.0000.0000.000
73A306VAL0-0.025-0.01437.3100.0000.0000.0000.0000.0000.000
74A307LYS10.7710.88639.648-0.044-0.0440.0000.0000.0000.000
75A308GLY0-0.008-0.00542.7400.0020.0020.0000.0000.0000.000
76A309ASP-1-0.895-0.93744.1130.0410.0410.0000.0000.0000.000
77A310VAL0-0.019-0.03143.7570.0020.0020.0000.0000.0000.000
78A311LYS10.9290.96744.713-0.035-0.0350.0000.0000.0000.000
79A312VAL00.0670.03842.8630.0010.0010.0000.0000.0000.000
80A313LEU00.0250.00738.6900.0020.0020.0000.0000.0000.000
81A314LYS10.7460.86541.191-0.053-0.0530.0000.0000.0000.000
82A315LYS10.7990.90343.629-0.046-0.0460.0000.0000.0000.000
83A316TRP00.0300.02638.8460.0040.0040.0000.0000.0000.000
84A317PHE0-0.067-0.05135.5270.0050.0050.0000.0000.0000.000
85A318SER00.0800.02736.082-0.004-0.0040.0000.0000.0000.000
86A319GLU-1-0.815-0.91737.8760.0610.0610.0000.0000.0000.000
87A320ALA0-0.0090.01033.566-0.001-0.0010.0000.0000.0000.000
88A321PRO0-0.025-0.01333.6930.0000.0000.0000.0000.0000.000
89A322PHE00.0230.03034.963-0.003-0.0030.0000.0000.0000.000
90A323ASN0-0.005-0.01238.253-0.006-0.0060.0000.0000.0000.000
91A324VAL00.0150.00932.547-0.002-0.0020.0000.0000.0000.000
92A325TYR00.0430.04036.012-0.002-0.0020.0000.0000.0000.000
93A326ALA00.001-0.01137.668-0.004-0.0040.0000.0000.0000.000
94A327ALA0-0.049-0.02337.603-0.003-0.0030.0000.0000.0000.000
95A328GLN0-0.007-0.01733.974-0.003-0.0030.0000.0000.0000.000
96A329GLN00.0410.01538.656-0.005-0.0050.0000.0000.0000.000
97A330LYS10.9170.95741.995-0.054-0.0540.0000.0000.0000.000
98A331ILE00.0540.03937.836-0.002-0.0020.0000.0000.0000.000
99A332PHE0-0.015-0.00537.526-0.002-0.0020.0000.0000.0000.000
100A333LYS10.7860.88843.181-0.044-0.0440.0000.0000.0000.000
101A334GLU-1-0.890-0.94144.1680.0390.0390.0000.0000.0000.000
102A335GLN0-0.0140.00640.562-0.001-0.0010.0000.0000.0000.000
103A336ASP-1-0.818-0.88446.1870.0270.0270.0000.0000.0000.000
104A337VAL00.0250.00143.970-0.001-0.0010.0000.0000.0000.000
105A338TYR0-0.044-0.02045.3680.0020.0020.0000.0000.0000.000
106A339ALA00.0710.04441.502-0.001-0.0010.0000.0000.0000.000
107A340ASP-1-0.804-0.89343.4180.0330.0330.0000.0000.0000.000
108A341GLY00.0750.04142.0760.0000.0000.0000.0000.0000.000
109A342ARG10.8180.89542.119-0.035-0.0350.0000.0000.0000.000
110A343ILE00.0260.02238.0370.0010.0010.0000.0000.0000.000
111A344LEU00.007-0.00538.809-0.003-0.0030.0000.0000.0000.000
112A345ASP-1-0.837-0.90735.5050.0480.0480.0000.0000.0000.000
113A346ILE0-0.037-0.02635.0720.0000.0000.0000.0000.0000.000
114A347ARG10.8560.92432.320-0.039-0.0390.0000.0000.0000.000
115A348GLY00.0010.00530.1990.0050.0050.0000.0000.0000.000
116A349VAL0-0.044-0.03030.522-0.004-0.0040.0000.0000.0000.000
117A350GLU-1-0.899-0.95027.4900.0750.0750.0000.0000.0000.000
118A351ILE00.008-0.00628.2020.0080.0080.0000.0000.0000.000
119A352VAL0-0.0190.00422.0940.0000.0000.0000.0000.0000.000
120A353SER0-0.059-0.03922.4270.0170.0170.0000.0000.0000.000
121A354ALA00.0360.03724.549-0.002-0.0020.0000.0000.0000.000
122A355LYS10.8750.92019.242-0.222-0.2220.0000.0000.0000.000
123A356LEU00.0320.01726.053-0.009-0.0090.0000.0000.0000.000
124A357LEU0-0.040-0.02226.3460.0180.0180.0000.0000.0000.000
125A358ALA00.0430.01325.960-0.008-0.0080.0000.0000.0000.000
126A359PRO0-0.057-0.02227.940-0.007-0.0070.0000.0000.0000.000
127A360GLN0-0.001-0.01530.835-0.003-0.0030.0000.0000.0000.000
128A361ASP-1-0.921-0.94930.3700.1090.1090.0000.0000.0000.000
129A362ILE00.0140.01731.722-0.004-0.0040.0000.0000.0000.000
130A363PRO00.0130.01830.7550.0110.0110.0000.0000.0000.000
131A364VAL0-0.009-0.00727.177-0.003-0.0030.0000.0000.0000.000
132A365LEU0-0.008-0.00128.7470.0040.0040.0000.0000.0000.000
133A366VAL0-0.033-0.01523.843-0.001-0.0010.0000.0000.0000.000
134A367VAL0-0.003-0.00126.913-0.002-0.0020.0000.0000.0000.000
135A368GLY00.0200.00726.4660.0070.0070.0000.0000.0000.000
136A369CYS0-0.059-0.01727.502-0.007-0.0070.0000.0000.0000.000
137A370ARG10.9450.96924.032-0.083-0.0830.0000.0000.0000.000
138A371ALA00.0440.01330.617-0.003-0.0030.0000.0000.0000.000
139A372GLN0-0.0240.01333.932-0.001-0.0010.0000.0000.0000.000
140A373GLU-1-0.698-0.79234.5410.0600.0600.0000.0000.0000.000
141A374ILE00.0090.01237.899-0.001-0.0010.0000.0000.0000.000
142A375ASN0-0.005-0.00936.5930.0020.0020.0000.0000.0000.000
143A376LEU00.0420.02039.964-0.002-0.0020.0000.0000.0000.000
144A377TYR00.0200.00238.0960.0020.0020.0000.0000.0000.000
145A378ARG10.8550.91044.531-0.032-0.0320.0000.0000.0000.000
146A379LYS10.8430.91248.258-0.028-0.0280.0000.0000.0000.000
147A380LYS10.8020.87950.406-0.027-0.0270.0000.0000.0000.000
148A381LYS10.9090.95852.819-0.022-0.0220.0000.0000.0000.000
149A382THR00.0270.01055.272-0.001-0.0010.0000.0000.0000.000
150A383GLY00.0070.02252.984-0.001-0.0010.0000.0000.0000.000
151A384GLU-1-0.865-0.94651.2050.0230.0230.0000.0000.0000.000
152A385ILE0-0.0060.00646.9010.0010.0010.0000.0000.0000.000
153A386ALA0-0.029-0.01946.1510.0010.0010.0000.0000.0000.000
154A387ALA0-0.065-0.03644.066-0.001-0.0010.0000.0000.0000.000
155A388GLY00.0010.00343.1860.0000.0000.0000.0000.0000.000
156A389ASP-1-0.923-0.95744.2090.0230.0230.0000.0000.0000.000
157A390GLU-1-0.872-0.91440.3050.0260.0260.0000.0000.0000.000
158A391ALA0-0.035-0.02441.0670.0020.0020.0000.0000.0000.000
159A392ASN0-0.089-0.05937.1140.0000.0000.0000.0000.0000.000
160A393ILE0-0.031-0.00937.7470.0020.0020.0000.0000.0000.000
161A394LEU00.0020.00832.7810.0010.0010.0000.0000.0000.000
162A395MET0-0.032-0.03128.758-0.001-0.0010.0000.0000.0000.000
163A396SER00.001-0.00330.0360.0050.0050.0000.0000.0000.000
164A397SER00.006-0.00225.986-0.001-0.0010.0000.0000.0000.000
165A398TYR0-0.044-0.06127.9600.0030.0030.0000.0000.0000.000
166A399ALA0-0.011-0.00325.3470.0040.0040.0000.0000.0000.000
167A400MET0-0.0160.01127.376-0.002-0.0020.0000.0000.0000.000
168A401VAL0-0.0100.00026.9010.0070.0070.0000.0000.0000.000
169A402PHE00.0550.02129.398-0.005-0.0050.0000.0000.0000.000
170A403THR0-0.029-0.04131.7150.0050.0050.0000.0000.0000.000
171A404ARG10.8130.89234.337-0.059-0.0590.0000.0000.0000.000
172A405ASP-1-0.842-0.90837.9100.0650.0650.0000.0000.0000.000
173A406PRO0-0.020-0.03639.700-0.002-0.0020.0000.0000.0000.000
174A407GLU-1-0.958-0.95642.7040.0470.0470.0000.0000.0000.000
175A408GLN0-0.018-0.02742.7270.0020.0020.0000.0000.0000.000
176A409ILE00.0230.01343.1520.0010.0010.0000.0000.0000.000
177A410ASP-1-0.932-0.96145.7810.0410.0410.0000.0000.0000.000
178A411ASP-1-0.849-0.93246.6010.0450.0450.0000.0000.0000.000
179A412ASP-1-0.919-0.94948.7260.0360.0360.0000.0000.0000.000
180A413GLU-1-0.956-0.96346.4830.0450.0450.0000.0000.0000.000
181A414THR0-0.035-0.04542.0180.0010.0010.0000.0000.0000.000
182A415GLU-1-0.824-0.88942.4560.0510.0510.0000.0000.0000.000
183A416GLY00.0850.04842.6900.0020.0020.0000.0000.0000.000
184A417TRP0-0.072-0.03734.9850.0070.0070.0000.0000.0000.000
185A418LYS10.8400.92537.380-0.062-0.0620.0000.0000.0000.000
186A419ILE0-0.010-0.00232.7370.0050.0050.0000.0000.0000.000
187A420LEU00.0080.01330.766-0.002-0.0020.0000.0000.0000.000
188A421GLU-1-0.892-0.97929.2030.1210.1210.0000.0000.0000.000
189A422PHE00.0520.03429.1710.0090.0090.0000.0000.0000.000
190A423VAL0-0.025-0.00925.3600.0000.0000.0000.0000.0000.000
191A424ARG10.8570.91928.850-0.069-0.0690.0000.0000.0000.000
192A425GLY0-0.039-0.01426.051-0.005-0.0050.0000.0000.0000.000