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: JQV39

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2121746.48744
FMO2-HF: Nuclear repulsion 2045155.916268
FMO2-HF: Total energy -76590.571172
FMO2-MP2: Total energy -76816.372553


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.
-13.192-7.9790.91-1.906-4.2170.008
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 : 0.071 / q_NPA : 0.036
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].
3A236GLN0-0.001-0.0232.665-5.964-2.8020.877-1.113-2.9260.006
4A237SER00.0190.0063.097-2.993-1.3860.032-0.667-0.9720.002
5A238LEU0-0.046-0.0174.030-1.112-0.6680.001-0.126-0.3190.000
6A239LYS10.9750.9816.646-2.047-2.0470.0000.0000.0000.000
7A240ASN00.0440.0257.3920.3050.3050.0000.0000.0000.000
8A241LYS11.0611.0347.055-1.750-1.7500.0000.0000.0000.000
9A242LEU00.0340.01810.773-0.137-0.1370.0000.0000.0000.000
10A243TRP0-0.095-0.06512.159-0.165-0.1650.0000.0000.0000.000
11A244ASP-1-0.954-0.97612.4690.6580.6580.0000.0000.0000.000
12A245GLU-1-0.910-0.95414.3450.4390.4390.0000.0000.0000.000
13A246SER0-0.113-0.03816.207-0.059-0.0590.0000.0000.0000.000
14A247GLU-1-0.874-0.97019.1380.2660.2660.0000.0000.0000.000
15A248ASN0-0.0020.00018.591-0.059-0.0590.0000.0000.0000.000
16A249PRO00.0490.00220.5330.0220.0220.0000.0000.0000.000
17A250LEU00.0390.00919.4940.0050.0050.0000.0000.0000.000
18A251ILE0-0.028-0.01515.896-0.004-0.0040.0000.0000.0000.000
19A252VAL0-0.0020.04218.8410.0370.0370.0000.0000.0000.000
20A253VAL0-0.006-0.00220.9850.0010.0010.0000.0000.0000.000
21A254MET0-0.048-0.03118.758-0.006-0.0060.0000.0000.0000.000
22A255ARG10.9440.97816.945-0.484-0.4840.0000.0000.0000.000
23A256LYS10.8140.90220.065-0.207-0.2070.0000.0000.0000.000
24A257ILE0-0.0470.00023.196-0.015-0.0150.0000.0000.0000.000
25A258THR0-0.057-0.01719.094-0.010-0.0100.0000.0000.0000.000
26A259ASN0-0.079-0.04117.8160.0550.0550.0000.0000.0000.000
27A260LYS10.9460.99221.352-0.282-0.2820.0000.0000.0000.000
28A261VAL00.0350.01024.437-0.003-0.0030.0000.0000.0000.000
29A262GLY00.0330.01025.7660.0050.0050.0000.0000.0000.000
30A263GLY0-0.0130.00123.568-0.017-0.0170.0000.0000.0000.000
31A264PHE00.012-0.00921.5140.0200.0200.0000.0000.0000.000
32A265PHE00.002-0.01320.782-0.014-0.0140.0000.0000.0000.000
33A266ALA00.0290.00621.9350.0060.0060.0000.0000.0000.000
34A267GLU-1-0.955-0.96420.2160.0750.0750.0000.0000.0000.000
35A268THR0-0.054-0.01822.552-0.018-0.0180.0000.0000.0000.000
36A269GLU-1-0.814-0.90224.1200.0080.0080.0000.0000.0000.000
37A270SER0-0.020-0.00124.999-0.005-0.0050.0000.0000.0000.000
38A271SER00.0410.00527.1710.0020.0020.0000.0000.0000.000
39A272ARG10.9631.00029.624-0.044-0.0440.0000.0000.0000.000
40A273VAL0-0.0250.00227.7990.0000.0000.0000.0000.0000.000
41A274TYR0-0.012-0.01328.7470.0020.0020.0000.0000.0000.000
42A275SER0-0.081-0.06633.058-0.002-0.0020.0000.0000.0000.000
43A276GLN00.0460.02433.6430.0020.0020.0000.0000.0000.000
44A277PHE00.014-0.00931.852-0.001-0.0010.0000.0000.0000.000
45A278LYS10.8300.91636.829-0.039-0.0390.0000.0000.0000.000
46A279LEU0-0.057-0.02839.001-0.003-0.0030.0000.0000.0000.000
47A280MET0-0.0290.02337.154-0.001-0.0010.0000.0000.0000.000
48A281ASP-1-0.776-0.90141.0930.0440.0440.0000.0000.0000.000
49A282PRO00.0210.00941.5290.0000.0000.0000.0000.0000.000
50A283THR0-0.035-0.00542.392-0.002-0.0020.0000.0000.0000.000
51A284PHE0-0.0160.01934.3730.0000.0000.0000.0000.0000.000
52A285SER0-0.003-0.03237.328-0.003-0.0030.0000.0000.0000.000
53A286ASN00.0840.02631.0790.0070.0070.0000.0000.0000.000
54A287GLU-1-0.953-0.96234.6790.0400.0400.0000.0000.0000.000
55A288SER00.0190.00336.9830.0030.0030.0000.0000.0000.000
56A289PHE0-0.0080.00033.5550.0010.0010.0000.0000.0000.000
57A290THR00.0750.02133.0270.0050.0050.0000.0000.0000.000
58A291ARG10.8640.95335.176-0.037-0.0370.0000.0000.0000.000
59A292HIS00.1030.05038.5300.0010.0010.0000.0000.0000.000
60A293LEU0-0.0330.00032.6760.0040.0040.0000.0000.0000.000
61A294ARG10.9730.97235.569-0.053-0.0530.0000.0000.0000.000
62A295GLU-1-0.965-1.01337.1630.0440.0440.0000.0000.0000.000
63A296TYR0-0.0020.00240.298-0.001-0.0010.0000.0000.0000.000
64A297ILE00.0490.03137.4610.0030.0030.0000.0000.0000.000
65A298VAL0-0.057-0.03234.0520.0040.0040.0000.0000.0000.000
66A299PRO0-0.041-0.02636.6340.0040.0040.0000.0000.0000.000
67A300GLU-1-0.852-0.91039.2220.0700.0700.0000.0000.0000.000
68A301ILE00.034-0.00434.7970.0020.0020.0000.0000.0000.000
69A302LEU0-0.029-0.02633.6660.0040.0040.0000.0000.0000.000
70A303GLU-1-0.976-0.98337.6380.0680.0680.0000.0000.0000.000
71A304ALA00.0210.00041.0040.0000.0000.0000.0000.0000.000
72A305TYR0-0.039-0.01132.9180.0060.0060.0000.0000.0000.000
73A306VAL0-0.0670.00037.606-0.001-0.0010.0000.0000.0000.000
74A307LYS10.9180.94439.613-0.077-0.0770.0000.0000.0000.000
75A308GLY0-0.0230.01542.3150.0030.0030.0000.0000.0000.000
76A309ASP-1-0.919-0.96343.3700.0660.0660.0000.0000.0000.000
77A310VAL00.000-0.01043.3940.0010.0010.0000.0000.0000.000
78A311LYS10.9410.95544.205-0.057-0.0570.0000.0000.0000.000
79A312VAL00.0770.06042.757-0.001-0.0010.0000.0000.0000.000
80A313LEU00.0760.03738.3400.0010.0010.0000.0000.0000.000
81A314LYS10.8500.91340.795-0.072-0.0720.0000.0000.0000.000
82A315LYS10.8560.95143.106-0.066-0.0660.0000.0000.0000.000
83A316TRP00.0630.02638.4310.0030.0030.0000.0000.0000.000
84A317PHE0-0.087-0.05434.9840.0070.0070.0000.0000.0000.000
85A318SER00.013-0.02935.159-0.004-0.0040.0000.0000.0000.000
86A319GLU-1-0.881-0.96637.4340.0960.0960.0000.0000.0000.000
87A320ALA0-0.016-0.00932.9980.0010.0010.0000.0000.0000.000
88A321PRO0-0.0440.00532.8670.0040.0040.0000.0000.0000.000
89A322PHE00.0600.05134.258-0.001-0.0010.0000.0000.0000.000
90A323ASN0-0.019-0.00237.468-0.005-0.0050.0000.0000.0000.000
91A324VAL00.0150.00432.1640.0000.0000.0000.0000.0000.000
92A325TYR00.0400.02635.5610.0000.0000.0000.0000.0000.000
93A326ALA0-0.034-0.04437.096-0.002-0.0020.0000.0000.0000.000
94A327ALA0-0.0140.00436.708-0.005-0.0050.0000.0000.0000.000
95A328GLN00.010-0.02333.278-0.001-0.0010.0000.0000.0000.000
96A329GLN00.0120.03438.280-0.003-0.0030.0000.0000.0000.000
97A330LYS10.9050.93441.524-0.094-0.0940.0000.0000.0000.000
98A331ILE00.0620.05837.595-0.003-0.0030.0000.0000.0000.000
99A332PHE0-0.039-0.01437.240-0.002-0.0020.0000.0000.0000.000
100A333LYS10.8150.91442.337-0.084-0.0840.0000.0000.0000.000
101A334GLU-1-0.902-0.94143.2110.0920.0920.0000.0000.0000.000
102A335GLN0-0.039-0.00940.587-0.001-0.0010.0000.0000.0000.000
103A336ASP-1-0.962-0.98045.9330.0660.0660.0000.0000.0000.000
104A337VAL00.003-0.01144.120-0.003-0.0030.0000.0000.0000.000
105A338TYR0-0.087-0.05545.1330.0020.0020.0000.0000.0000.000
106A339ALA00.0400.01341.314-0.001-0.0010.0000.0000.0000.000
107A340ASP-1-0.873-0.91043.3990.0670.0670.0000.0000.0000.000
108A341GLY00.1090.01741.3820.0020.0020.0000.0000.0000.000
109A342ARG10.8460.90641.565-0.067-0.0670.0000.0000.0000.000
110A343ILE00.0380.02937.2930.0020.0020.0000.0000.0000.000
111A344LEU0-0.010-0.02538.895-0.005-0.0050.0000.0000.0000.000
112A345ASP-1-0.951-0.97236.1150.0720.0720.0000.0000.0000.000
113A346ILE0-0.056-0.02434.8540.0000.0000.0000.0000.0000.000
114A347ARG11.0261.03532.055-0.064-0.0640.0000.0000.0000.000
115A348GLY0-0.017-0.01130.0560.0090.0090.0000.0000.0000.000
116A349VAL0-0.025-0.02430.403-0.006-0.0060.0000.0000.0000.000
117A350GLU-1-0.900-0.94427.3190.0840.0840.0000.0000.0000.000
118A351ILE0-0.028-0.00828.0730.0120.0120.0000.0000.0000.000
119A352VAL00.0070.00721.958-0.006-0.0060.0000.0000.0000.000
120A353SER0-0.099-0.05722.4250.0110.0110.0000.0000.0000.000
121A354ALA00.0780.03824.296-0.001-0.0010.0000.0000.0000.000
122A355LYS10.9260.95519.583-0.216-0.2160.0000.0000.0000.000
123A356LEU00.0480.04825.526-0.001-0.0010.0000.0000.0000.000
124A357LEU0-0.027-0.01525.6900.0130.0130.0000.0000.0000.000
125A358ALA00.0330.01225.777-0.010-0.0100.0000.0000.0000.000
126A359PRO0-0.070-0.02427.461-0.013-0.0130.0000.0000.0000.000
127A360GLN00.010-0.01530.4290.0020.0020.0000.0000.0000.000
128A361ASP-1-0.911-0.96030.2120.0860.0860.0000.0000.0000.000
129A362ILE0-0.0030.01631.088-0.007-0.0070.0000.0000.0000.000
130A363PRO0-0.027-0.02130.3670.0120.0120.0000.0000.0000.000
131A364VAL00.000-0.00527.3060.0000.0000.0000.0000.0000.000
132A365LEU0-0.012-0.00828.3740.0000.0000.0000.0000.0000.000
133A366VAL0-0.052-0.01824.3040.0050.0050.0000.0000.0000.000
134A367VAL00.0090.01026.513-0.003-0.0030.0000.0000.0000.000
135A368GLY00.0100.00526.4160.0140.0140.0000.0000.0000.000
136A369CYS0-0.077-0.02227.473-0.012-0.0120.0000.0000.0000.000
137A370ARG10.9560.96923.879-0.127-0.1270.0000.0000.0000.000
138A371ALA00.0450.01330.402-0.009-0.0090.0000.0000.0000.000
139A372GLN0-0.0170.00333.8270.0020.0020.0000.0000.0000.000
140A373GLU-1-0.748-0.83134.5740.1070.1070.0000.0000.0000.000
141A374ILE00.0040.01537.3190.0020.0020.0000.0000.0000.000
142A375ASN0-0.014-0.02436.739-0.002-0.0020.0000.0000.0000.000
143A376LEU00.0140.00039.275-0.002-0.0020.0000.0000.0000.000
144A377TYR00.0230.00936.9580.0030.0030.0000.0000.0000.000
145A378ARG10.9570.98143.904-0.065-0.0650.0000.0000.0000.000
146A379LYS10.9350.99147.520-0.069-0.0690.0000.0000.0000.000
147A380LYS10.9500.97449.661-0.059-0.0590.0000.0000.0000.000
148A381LYS10.8970.94552.000-0.053-0.0530.0000.0000.0000.000
149A382THR00.0280.00654.888-0.001-0.0010.0000.0000.0000.000
150A383GLY0-0.0270.00452.970-0.002-0.0020.0000.0000.0000.000
151A384GLU-1-0.876-0.94851.2340.0550.0550.0000.0000.0000.000
152A385ILE0-0.0200.00446.7730.0010.0010.0000.0000.0000.000
153A386ALA0-0.010-0.02445.5580.0030.0030.0000.0000.0000.000
154A387ALA0-0.077-0.02543.058-0.002-0.0020.0000.0000.0000.000
155A388GLY00.0100.00443.178-0.001-0.0010.0000.0000.0000.000
156A389ASP-1-0.890-0.95344.2220.0600.0600.0000.0000.0000.000
157A390GLU-1-0.965-0.98040.5260.0730.0730.0000.0000.0000.000
158A391ALA0-0.0250.00440.2830.0050.0050.0000.0000.0000.000
159A392ASN00.003-0.00835.940-0.006-0.0060.0000.0000.0000.000
160A393ILE0-0.021-0.01937.7630.0030.0030.0000.0000.0000.000
161A394LEU0-0.038-0.01332.1430.0020.0020.0000.0000.0000.000
162A395MET00.0350.00629.123-0.003-0.0030.0000.0000.0000.000
163A396SER0-0.0040.01129.6730.0100.0100.0000.0000.0000.000
164A397SER00.009-0.00125.925-0.010-0.0100.0000.0000.0000.000
165A398TYR0-0.018-0.03427.3890.0150.0150.0000.0000.0000.000
166A399ALA0-0.026-0.00124.934-0.001-0.0010.0000.0000.0000.000
167A400MET00.0100.02526.8820.0030.0030.0000.0000.0000.000
168A401VAL0-0.009-0.01026.3880.0030.0030.0000.0000.0000.000
169A402PHE00.007-0.00329.124-0.003-0.0030.0000.0000.0000.000
170A403THR00.010-0.00431.4600.0030.0030.0000.0000.0000.000
171A404ARG10.8660.93533.992-0.062-0.0620.0000.0000.0000.000
172A405ASP-1-0.819-0.90737.4660.0740.0740.0000.0000.0000.000
173A406PRO0-0.038-0.05339.764-0.003-0.0030.0000.0000.0000.000
174A407GLU-1-0.987-0.96442.5890.0570.0570.0000.0000.0000.000
175A408GLN0-0.051-0.03643.2040.0030.0030.0000.0000.0000.000
176A409ILE00.0050.00442.9180.0040.0040.0000.0000.0000.000
177A410ASP-1-0.937-0.96845.7180.0430.0430.0000.0000.0000.000
178A411ASP-1-0.863-0.94846.4270.0590.0590.0000.0000.0000.000
179A412ASP-1-0.912-0.94548.2140.0440.0440.0000.0000.0000.000
180A413GLU-1-0.976-0.99946.3200.0640.0640.0000.0000.0000.000
181A414THR0-0.126-0.04341.3240.0020.0020.0000.0000.0000.000
182A415GLU-1-0.924-0.96942.6760.0530.0530.0000.0000.0000.000
183A416GLY00.0500.01841.6510.0000.0000.0000.0000.0000.000
184A417TRP0-0.086-0.04034.8090.0080.0080.0000.0000.0000.000
185A418LYS10.9580.99136.824-0.080-0.0800.0000.0000.0000.000
186A419ILE00.0050.00332.5500.0050.0050.0000.0000.0000.000
187A420LEU00.0190.03630.3820.0020.0020.0000.0000.0000.000
188A421GLU-1-0.955-1.02528.5970.1950.1950.0000.0000.0000.000
189A422PHE00.0360.02429.3420.0070.0070.0000.0000.0000.000
190A423VAL0-0.036-0.01425.1820.0050.0050.0000.0000.0000.000
191A424ARG10.8510.90728.160-0.135-0.1350.0000.0000.0000.000
192A425GLY00.0060.01326.1640.0080.0080.0000.0000.0000.000