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: 3JMQL

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 OptHSide
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 -2118917.209798
FMO2-HF: Nuclear repulsion 2042323.489369
FMO2-HF: Total energy -76593.720429
FMO2-MP2: Total energy -76819.152117


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.
-7.755-2.7821.272-1.939-4.3070.001
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 : 0.076 / q_NPA : 0.033
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].
3A236GLN00.009-0.0182.224-3.595-0.8731.189-1.089-2.822-0.001
4A237SER0-0.013-0.0172.870-1.3720.5010.084-0.762-1.1950.002
5A238LEU0-0.003-0.0084.310-0.0890.289-0.001-0.088-0.2900.000
6A239LYS10.9690.9856.654-1.536-1.5360.0000.0000.0000.000
7A240ASN0-0.026-0.0087.751-0.160-0.1600.0000.0000.0000.000
8A241LYS11.0301.0226.980-1.117-1.1170.0000.0000.0000.000
9A242LEU00.0340.02310.775-0.055-0.0550.0000.0000.0000.000
10A243TRP0-0.030-0.03712.349-0.080-0.0800.0000.0000.0000.000
11A244ASP-1-0.914-0.94712.3420.1130.1130.0000.0000.0000.000
12A245GLU-1-0.914-0.96014.4890.2270.2270.0000.0000.0000.000
13A246SER0-0.101-0.03216.208-0.038-0.0380.0000.0000.0000.000
14A247GLU-1-0.883-0.97519.2100.0950.0950.0000.0000.0000.000
15A248ASN0-0.006-0.00517.643-0.032-0.0320.0000.0000.0000.000
16A249PRO00.0390.00320.5930.0190.0190.0000.0000.0000.000
17A250LEU00.0350.00719.8770.0080.0080.0000.0000.0000.000
18A251ILE0-0.026-0.02015.4490.0070.0070.0000.0000.0000.000
19A252VAL00.0240.05418.9440.0190.0190.0000.0000.0000.000
20A253VAL0-0.009-0.00920.9910.0010.0010.0000.0000.0000.000
21A254MET0-0.033-0.02119.1180.0120.0120.0000.0000.0000.000
22A255ARG10.8960.96016.595-0.245-0.2450.0000.0000.0000.000
23A256LYS10.7590.89020.065-0.145-0.1450.0000.0000.0000.000
24A257ILE0-0.031-0.00423.572-0.011-0.0110.0000.0000.0000.000
25A258THR0-0.049-0.01618.948-0.004-0.0040.0000.0000.0000.000
26A259ASN0-0.062-0.03617.7170.0220.0220.0000.0000.0000.000
27A260LYS10.9370.98721.292-0.152-0.1520.0000.0000.0000.000
28A261VAL00.021-0.00124.246-0.006-0.0060.0000.0000.0000.000
29A262GLY00.0410.01825.6280.0050.0050.0000.0000.0000.000
30A263GLY0-0.0220.00023.559-0.010-0.0100.0000.0000.0000.000
31A264PHE00.020-0.01321.2120.0210.0210.0000.0000.0000.000
32A265PHE0-0.002-0.00420.145-0.016-0.0160.0000.0000.0000.000
33A266ALA00.0340.00822.0400.0180.0180.0000.0000.0000.000
34A267GLU-1-0.958-0.96319.7080.2220.2220.0000.0000.0000.000
35A268THR0-0.037-0.01122.726-0.015-0.0150.0000.0000.0000.000
36A269GLU-1-0.850-0.91924.1080.1020.1020.0000.0000.0000.000
37A270SER0-0.0070.00625.082-0.012-0.0120.0000.0000.0000.000
38A271SER00.0490.01727.319-0.007-0.0070.0000.0000.0000.000
39A272ARG10.8850.95929.790-0.094-0.0940.0000.0000.0000.000
40A273VAL00.0560.03428.245-0.005-0.0050.0000.0000.0000.000
41A274TYR0-0.023-0.02628.740-0.003-0.0030.0000.0000.0000.000
42A275SER0-0.066-0.06133.204-0.005-0.0050.0000.0000.0000.000
43A276GLN00.0450.02433.577-0.005-0.0050.0000.0000.0000.000
44A277PHE00.0240.00431.934-0.003-0.0030.0000.0000.0000.000
45A278LYS10.8060.89936.979-0.059-0.0590.0000.0000.0000.000
46A279LEU0-0.059-0.02939.159-0.004-0.0040.0000.0000.0000.000
47A280MET0-0.0670.00837.100-0.003-0.0030.0000.0000.0000.000
48A281ASP-1-0.748-0.86341.2340.0500.0500.0000.0000.0000.000
49A282PRO00.0450.01641.6720.0010.0010.0000.0000.0000.000
50A283THR0-0.034-0.01342.5280.0000.0000.0000.0000.0000.000
51A284PHE0-0.0200.00534.3710.0000.0000.0000.0000.0000.000
52A285SER00.013-0.01637.451-0.001-0.0010.0000.0000.0000.000
53A286ASN00.0890.05031.5810.0060.0060.0000.0000.0000.000
54A287GLU-1-0.935-0.95034.8030.0520.0520.0000.0000.0000.000
55A288SER0-0.038-0.01337.1090.0010.0010.0000.0000.0000.000
56A289PHE00.0600.01633.3480.0000.0000.0000.0000.0000.000
57A290THR00.0440.00333.2530.0020.0020.0000.0000.0000.000
58A291ARG10.8220.91235.275-0.041-0.0410.0000.0000.0000.000
59A292HIS00.0310.01138.621-0.001-0.0010.0000.0000.0000.000
60A293LEU0-0.0340.00232.8510.0000.0000.0000.0000.0000.000
61A294ARG10.9290.94935.660-0.051-0.0510.0000.0000.0000.000
62A295GLU-1-0.870-0.94337.2440.0390.0390.0000.0000.0000.000
63A296TYR0-0.081-0.05440.380-0.002-0.0020.0000.0000.0000.000
64A297ILE00.0610.03137.6120.0010.0010.0000.0000.0000.000
65A298VAL0-0.030-0.01933.7950.0010.0010.0000.0000.0000.000
66A299PRO0-0.035-0.01836.7230.0000.0000.0000.0000.0000.000
67A300GLU-1-0.806-0.86139.2990.0470.0470.0000.0000.0000.000
68A301ILE00.010-0.01034.9640.0000.0000.0000.0000.0000.000
69A302LEU0-0.008-0.01133.6530.0000.0000.0000.0000.0000.000
70A303GLU-1-0.873-0.91837.7150.0370.0370.0000.0000.0000.000
71A304ALA00.0140.00841.082-0.002-0.0020.0000.0000.0000.000
72A305TYR0-0.037-0.01332.9510.0020.0020.0000.0000.0000.000
73A306VAL0-0.064-0.02237.307-0.002-0.0020.0000.0000.0000.000
74A307LYS10.8240.89239.622-0.043-0.0430.0000.0000.0000.000
75A308GLY0-0.0220.00842.3210.0020.0020.0000.0000.0000.000
76A309ASP-1-0.932-0.97343.3790.0390.0390.0000.0000.0000.000
77A310VAL0-0.012-0.02143.3980.0020.0020.0000.0000.0000.000
78A311LYS10.9550.96644.209-0.035-0.0350.0000.0000.0000.000
79A312VAL00.0860.06042.5750.0010.0010.0000.0000.0000.000
80A313LEU00.0640.03438.2170.0020.0020.0000.0000.0000.000
81A314LYS10.8410.92640.905-0.050-0.0500.0000.0000.0000.000
82A315LYS10.8220.91143.133-0.048-0.0480.0000.0000.0000.000
83A316TRP00.0240.00838.5960.0040.0040.0000.0000.0000.000
84A317PHE0-0.091-0.06635.1820.0050.0050.0000.0000.0000.000
85A318SER00.0580.02135.350-0.002-0.0020.0000.0000.0000.000
86A319GLU-1-0.896-0.97637.4340.0640.0640.0000.0000.0000.000
87A320ALA0-0.029-0.01333.030-0.001-0.0010.0000.0000.0000.000
88A321PRO0-0.0360.00433.158-0.001-0.0010.0000.0000.0000.000
89A322PHE00.0160.01634.258-0.003-0.0030.0000.0000.0000.000
90A323ASN0-0.015-0.00137.660-0.006-0.0060.0000.0000.0000.000
91A324VAL00.0270.01132.079-0.003-0.0030.0000.0000.0000.000
92A325TYR00.0490.04135.555-0.003-0.0030.0000.0000.0000.000
93A326ALA0-0.037-0.03337.094-0.003-0.0030.0000.0000.0000.000
94A327ALA0-0.0020.00236.698-0.003-0.0030.0000.0000.0000.000
95A328GLN0-0.010-0.02833.524-0.003-0.0030.0000.0000.0000.000
96A329GLN00.0030.01138.272-0.005-0.0050.0000.0000.0000.000
97A330LYS10.9270.95441.519-0.052-0.0520.0000.0000.0000.000
98A331ILE00.0470.04537.273-0.002-0.0020.0000.0000.0000.000
99A332PHE0-0.020-0.01036.856-0.002-0.0020.0000.0000.0000.000
100A333LYS10.7830.88442.330-0.039-0.0390.0000.0000.0000.000
101A334GLU-1-0.874-0.92943.4660.0360.0360.0000.0000.0000.000
102A335GLN0-0.030-0.00240.462-0.001-0.0010.0000.0000.0000.000
103A336ASP-1-0.830-0.90745.9230.0240.0240.0000.0000.0000.000
104A337VAL00.0190.00343.799-0.002-0.0020.0000.0000.0000.000
105A338TYR0-0.038-0.02545.1250.0020.0020.0000.0000.0000.000
106A339ALA00.0490.02141.326-0.001-0.0010.0000.0000.0000.000
107A340ASP-1-0.802-0.84043.4010.0320.0320.0000.0000.0000.000
108A341GLY00.1130.04341.3860.0000.0000.0000.0000.0000.000
109A342ARG10.8290.88741.577-0.032-0.0320.0000.0000.0000.000
110A343ILE00.0090.00938.0020.0000.0000.0000.0000.0000.000
111A344LEU00.004-0.01438.932-0.002-0.0020.0000.0000.0000.000
112A345ASP-1-0.881-0.93635.8980.0430.0430.0000.0000.0000.000
113A346ILE0-0.051-0.02234.8980.0010.0010.0000.0000.0000.000
114A347ARG10.9290.98032.349-0.041-0.0410.0000.0000.0000.000
115A348GLY00.0040.00030.1090.0050.0050.0000.0000.0000.000
116A349VAL0-0.025-0.03330.517-0.002-0.0020.0000.0000.0000.000
117A350GLU-1-0.901-0.93727.6790.0780.0780.0000.0000.0000.000
118A351ILE0-0.004-0.00828.1650.0080.0080.0000.0000.0000.000
119A352VAL0-0.016-0.00222.1810.0000.0000.0000.0000.0000.000
120A353SER0-0.079-0.05022.3900.0180.0180.0000.0000.0000.000
121A354ALA00.0730.03524.424-0.008-0.0080.0000.0000.0000.000
122A355LYS10.9300.95319.280-0.247-0.2470.0000.0000.0000.000
123A356LEU00.0350.03025.685-0.007-0.0070.0000.0000.0000.000
124A357LEU0-0.026-0.01626.1100.0170.0170.0000.0000.0000.000
125A358ALA00.0350.01625.820-0.008-0.0080.0000.0000.0000.000
126A359PRO0-0.067-0.02527.563-0.009-0.0090.0000.0000.0000.000
127A360GLN0-0.005-0.01930.429-0.005-0.0050.0000.0000.0000.000
128A361ASP-1-0.925-0.94930.3840.1230.1230.0000.0000.0000.000
129A362ILE00.0100.01531.251-0.007-0.0070.0000.0000.0000.000
130A363PRO0-0.024-0.01230.5330.0110.0110.0000.0000.0000.000
131A364VAL0-0.007-0.00527.054-0.006-0.0060.0000.0000.0000.000
132A365LEU0-0.0030.00128.5210.0060.0060.0000.0000.0000.000
133A366VAL0-0.059-0.01624.187-0.002-0.0020.0000.0000.0000.000
134A367VAL00.0060.00926.6260.0020.0020.0000.0000.0000.000
135A368GLY00.0280.01226.4970.0060.0060.0000.0000.0000.000
136A369CYS0-0.068-0.02327.557-0.006-0.0060.0000.0000.0000.000
137A370ARG10.9420.97023.870-0.081-0.0810.0000.0000.0000.000
138A371ALA00.027-0.00130.446-0.004-0.0040.0000.0000.0000.000
139A372GLN0-0.0200.00233.869-0.002-0.0020.0000.0000.0000.000
140A373GLU-1-0.668-0.75634.2900.0550.0550.0000.0000.0000.000
141A374ILE00.0170.01437.333-0.001-0.0010.0000.0000.0000.000
142A375ASN0-0.037-0.02336.1020.0010.0010.0000.0000.0000.000
143A376LEU00.0390.01339.283-0.002-0.0020.0000.0000.0000.000
144A377TYR00.009-0.00137.3400.0020.0020.0000.0000.0000.000
145A378ARG10.8970.93943.905-0.028-0.0280.0000.0000.0000.000
146A379LYS10.8640.93947.519-0.024-0.0240.0000.0000.0000.000
147A380LYS10.7980.89049.659-0.023-0.0230.0000.0000.0000.000
148A381LYS10.9230.95551.996-0.020-0.0200.0000.0000.0000.000
149A382THR00.0210.00054.860-0.001-0.0010.0000.0000.0000.000
150A383GLY0-0.0180.00852.973-0.001-0.0010.0000.0000.0000.000
151A384GLU-1-0.868-0.94851.2340.0190.0190.0000.0000.0000.000
152A385ILE0-0.0290.00046.7890.0020.0020.0000.0000.0000.000
153A386ALA0-0.038-0.02945.5800.0010.0010.0000.0000.0000.000
154A387ALA0-0.059-0.01743.075-0.001-0.0010.0000.0000.0000.000
155A388GLY00.0100.00643.178-0.002-0.0020.0000.0000.0000.000
156A389ASP-1-0.921-0.96244.2210.0180.0180.0000.0000.0000.000
157A390GLU-1-0.901-0.94740.0910.0170.0170.0000.0000.0000.000
158A391ALA0-0.0300.00440.2990.0010.0010.0000.0000.0000.000
159A392ASN0-0.054-0.04236.689-0.001-0.0010.0000.0000.0000.000
160A393ILE0-0.014-0.02138.0230.0020.0020.0000.0000.0000.000
161A394LEU0-0.0180.00232.2820.0000.0000.0000.0000.0000.000
162A395MET00.012-0.00929.0660.0010.0010.0000.0000.0000.000
163A396SER0-0.017-0.01029.7160.0030.0030.0000.0000.0000.000
164A397SER0-0.015-0.01426.010-0.001-0.0010.0000.0000.0000.000
165A398TYR0-0.050-0.06427.4470.0060.0060.0000.0000.0000.000
166A399ALA0-0.0040.01125.0030.0040.0040.0000.0000.0000.000
167A400MET0-0.045-0.00126.974-0.002-0.0020.0000.0000.0000.000
168A401VAL0-0.002-0.01126.5630.0070.0070.0000.0000.0000.000
169A402PHE00.0360.00729.252-0.005-0.0050.0000.0000.0000.000
170A403THR0-0.013-0.02431.6030.0060.0060.0000.0000.0000.000
171A404ARG10.8150.90834.138-0.066-0.0660.0000.0000.0000.000
172A405ASP-1-0.806-0.91137.6150.0730.0730.0000.0000.0000.000
173A406PRO0-0.026-0.04339.798-0.003-0.0030.0000.0000.0000.000
174A407GLU-1-0.982-0.95842.7480.0540.0540.0000.0000.0000.000
175A408GLN0-0.043-0.03442.9140.0010.0010.0000.0000.0000.000
176A409ILE00.0280.00842.5190.0020.0020.0000.0000.0000.000
177A410ASP-1-0.932-0.96445.8640.0440.0440.0000.0000.0000.000
178A411ASP-1-0.878-0.94346.5920.0480.0480.0000.0000.0000.000
179A412ASP-1-0.920-0.94948.3290.0380.0380.0000.0000.0000.000
180A413GLU-1-0.929-0.95246.3110.0470.0470.0000.0000.0000.000
181A414THR0-0.061-0.03641.5940.0010.0010.0000.0000.0000.000
182A415GLU-1-0.880-0.93742.8040.0520.0520.0000.0000.0000.000
183A416GLY00.0830.02541.8070.0020.0020.0000.0000.0000.000
184A417TRP0-0.079-0.03934.7040.0070.0070.0000.0000.0000.000
185A418LYS10.8890.95236.953-0.067-0.0670.0000.0000.0000.000
186A419ILE0-0.004-0.00632.7350.0050.0050.0000.0000.0000.000
187A420LEU00.0240.01330.400-0.002-0.0020.0000.0000.0000.000
188A421GLU-1-0.890-0.99228.7490.1270.1270.0000.0000.0000.000
189A422PHE00.0630.05229.4540.0070.0070.0000.0000.0000.000
190A423VAL0-0.022-0.02124.974-0.001-0.0010.0000.0000.0000.000
191A424ARG10.8510.91128.185-0.060-0.0600.0000.0000.0000.000
192A425GLY0-0.0160.00726.159-0.003-0.0030.0000.0000.0000.000