FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2KZZR

Calculation Name: 2YPF-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YPF

Chain ID: A

ChEMBL ID:

UniProt ID: P14727

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 681
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -12815625.728617
FMO2-HF: Nuclear repulsion 12572286.211394
FMO2-HF: Total energy -243339.517223
FMO2-MP2: Total energy -244056.068839


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:184:ACE )


Summations of interaction energy for fragment #1(A:184:ACE )
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.
1.052.310.023-0.649-0.633-0.001
Interaction energy analysis for fragmet #1(A:184:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.005
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].
3A186PHE 0-0.0120.0173.8420.7641.762-0.006-0.454-0.537-0.001
4A187THR 00.0120.0016.029-0.074-0.0740.0000.0000.0000.000
5A188HIS 00.0640.0379.794-0.015-0.0150.0000.0000.0000.000
6A189ALA 00.0250.03311.6190.0250.0250.0000.0000.0000.000
7A190HIS 0-0.091-0.06011.2850.0760.0760.0000.0000.0000.000
8A191ILE 00.010-0.02014.917-0.030-0.0300.0000.0000.0000.000
9A192VAL 00.0100.01016.936-0.011-0.0110.0000.0000.0000.000
10A193ALA 00.0470.01614.796-0.033-0.0330.0000.0000.0000.000
11A194NME 0-0.0280.02614.2670.0150.0150.0000.0000.0000.000
12A194ACE 0-0.007-0.03116.8160.0130.0130.0000.0000.0000.000
13A195LEU 0-0.047-0.03412.547-0.030-0.0300.0000.0000.0000.000
14A196NME 00.0420.03910.832-0.005-0.0050.0000.0000.0000.000
15A196ACE 00.005-0.0117.907-0.035-0.0350.0000.0000.0000.000
16A197SER 0-0.041-0.0318.8390.1050.1050.0000.0000.0000.000
17A198GLN 0-0.024-0.0133.4980.2220.4840.029-0.195-0.0960.000
18A199HIS 0-0.0060.0107.3120.1970.1970.0000.0000.0000.000
19A200PRO 00.0220.0058.3190.0490.0490.0000.0000.0000.000
20A201ALA 00.008-0.02010.7130.0470.0470.0000.0000.0000.000
21A202ALA 00.004-0.01111.0250.0510.0510.0000.0000.0000.000
22A203LEU 00.0560.05914.628-0.027-0.0270.0000.0000.0000.000
23A204ALA 0-0.0230.01416.362-0.006-0.0060.0000.0000.0000.000
24A205THR 0-0.014-0.02519.758-0.015-0.0150.0000.0000.0000.000
25A206VAL 00.0000.00521.9250.0030.0030.0000.0000.0000.000
26A207ALA 0-0.034-0.01825.267-0.002-0.0020.0000.0000.0000.000
27A208VAL 00.0010.00822.201-0.004-0.0040.0000.0000.0000.000
28A209LYS 10.8850.92623.6550.0770.0770.0000.0000.0000.000
29A210TYR 0-0.008-0.01022.578-0.003-0.0030.0000.0000.0000.000
30A211GLN 0-0.042-0.02317.1440.0160.0160.0000.0000.0000.000
31A212ASP -1-0.893-0.93415.084-0.270-0.2700.0000.0000.0000.000
32A213MET 0-0.025-0.00617.8410.0050.0050.0000.0000.0000.000
33A214ILE 00.0260.01116.387-0.014-0.0140.0000.0000.0000.000
34A215ALA 0-0.045-0.03317.8000.0110.0110.0000.0000.0000.000
35A216ALA 0-0.0180.02116.6990.0190.0190.0000.0000.0000.000
36A217LEU 0-0.022-0.01815.789-0.017-0.0170.0000.0000.0000.000
37A218PRO 00.005-0.01515.047-0.005-0.0050.0000.0000.0000.000
38A219GLU -1-0.872-0.93117.8830.0200.0200.0000.0000.0000.000
39A220ALA 0-0.0120.00121.061-0.004-0.0040.0000.0000.0000.000
40A221THR 0-0.084-0.05721.6840.0020.0020.0000.0000.0000.000
41A222HIS 00.0360.01224.747-0.001-0.0010.0000.0000.0000.000
42A223GLU -1-0.857-0.90927.248-0.006-0.0060.0000.0000.0000.000
43A224ALA 0-0.086-0.04930.781-0.003-0.0030.0000.0000.0000.000
44A225ILE 0-0.015-0.00932.6430.0020.0020.0000.0000.0000.000
45A226VAL 00.0030.01231.975-0.001-0.0010.0000.0000.0000.000
46A227ALA 00.0420.02333.3510.0000.0000.0000.0000.0000.000
47A228VAL 00.0950.02728.689-0.001-0.0010.0000.0000.0000.000
48A229ALA 0-0.055-0.02328.474-0.008-0.0080.0000.0000.0000.000
49A230LYS 10.9460.97226.4040.0330.0330.0000.0000.0000.000
50A231GLN 00.011-0.00621.9010.0080.0080.0000.0000.0000.000
51A232TRP 0-0.083-0.03525.704-0.006-0.0060.0000.0000.0000.000
52A233SER 00.0310.00928.167-0.001-0.0010.0000.0000.0000.000
53A234GLY 00.0490.04024.2530.0030.0030.0000.0000.0000.000
54A235ALA 0-0.047-0.02023.499-0.008-0.0080.0000.0000.0000.000
55A236ARG 10.8990.95321.5710.0650.0650.0000.0000.0000.000
56A237ALA 00.001-0.00824.9000.0030.0030.0000.0000.0000.000
57A238LEU 0-0.007-0.02224.706-0.002-0.0020.0000.0000.0000.000
58A239GLU -1-0.865-0.93425.394-0.029-0.0290.0000.0000.0000.000
59A240ALA 00.0950.07827.1100.0010.0010.0000.0000.0000.000
60A241LEU 0-0.033-0.02828.6040.0040.0040.0000.0000.0000.000
61A242LEU 00.003-0.01129.2480.0010.0010.0000.0000.0000.000
62A243THR 0-0.046-0.00332.3240.0010.0010.0000.0000.0000.000
63A244VAL 00.0550.02534.6490.0010.0010.0000.0000.0000.000
64A245ALA 00.0340.00636.018-0.001-0.0010.0000.0000.0000.000
65A246GLY 00.004-0.00337.932-0.001-0.0010.0000.0000.0000.000
66A247GLU -1-0.930-0.97941.064-0.001-0.0010.0000.0000.0000.000
67A248LEU 0-0.0020.00438.267-0.001-0.0010.0000.0000.0000.000
68A249ARG 10.9090.95737.9940.0090.0090.0000.0000.0000.000
69A250GLY 00.0250.03844.0160.0000.0000.0000.0000.0000.000
70A251PRO 00.0050.02046.870-0.001-0.0010.0000.0000.0000.000
71A252PRO 0-0.057-0.04348.1900.0000.0000.0000.0000.0000.000
72A253LEU 0-0.036-0.02644.001-0.001-0.0010.0000.0000.0000.000
73A254GLN 0-0.027-0.02546.8250.0000.0000.0000.0000.0000.000
74A255LEU 0-0.0220.00641.469-0.001-0.0010.0000.0000.0000.000
75A256ASP -1-0.805-0.91843.003-0.019-0.0190.0000.0000.0000.000
76A257THR 0-0.043-0.03337.606-0.001-0.0010.0000.0000.0000.000
77A258GLY 00.010-0.01037.798-0.002-0.0020.0000.0000.0000.000
78A259GLN 00.0240.01838.661-0.002-0.0020.0000.0000.0000.000
79A260LEU 00.0140.00436.864-0.001-0.0010.0000.0000.0000.000
80A261LEU 0-0.0350.00433.466-0.001-0.0010.0000.0000.0000.000
81A262LYS 10.9740.98833.7820.0280.0280.0000.0000.0000.000
82A263ILE 0-0.058-0.03635.596-0.003-0.0030.0000.0000.0000.000
83A264ALA 00.011-0.00131.6850.0010.0010.0000.0000.0000.000
84A265LYS 10.8810.95329.9890.0400.0400.0000.0000.0000.000
85A266ARG 00.1480.06826.225-0.002-0.0020.0000.0000.0000.000
86A267GLY 00.0090.03030.0460.0020.0020.0000.0000.0000.000
87A268GLY 0-0.054-0.04231.4460.0030.0030.0000.0000.0000.000
88A269VAL 00.0980.05529.1560.0020.0020.0000.0000.0000.000
89A270THR 00.0240.01132.2660.0020.0020.0000.0000.0000.000
90A271ALA 0-0.056-0.00634.7890.0020.0020.0000.0000.0000.000
91A272VAL 00.0000.00933.8830.0010.0010.0000.0000.0000.000
92A273GLU -1-0.928-0.97636.078-0.004-0.0040.0000.0000.0000.000
93A274ALA 0-0.053-0.03737.8450.0010.0010.0000.0000.0000.000
94A275VAL 0-0.006-0.00639.5210.0010.0010.0000.0000.0000.000
95A276HIS 0-0.006-0.00239.8480.0000.0000.0000.0000.0000.000
96A277ALA 0-0.015-0.01841.5200.0010.0010.0000.0000.0000.000
97A278TRP 0-0.089-0.04141.5200.0010.0010.0000.0000.0000.000
98A279ARG 10.9791.01444.6710.0040.0040.0000.0000.0000.000
99A280ASN 00.059-0.00147.199-0.001-0.0010.0000.0000.0000.000
100A281ALA 0-0.064-0.01049.5910.0000.0000.0000.0000.0000.000
101A282LEU 00.015-0.00646.509-0.001-0.0010.0000.0000.0000.000
102A283THR 0-0.0330.00547.0450.0000.0000.0000.0000.0000.000
103A284GLY 0-0.027-0.02949.5720.0000.0000.0000.0000.0000.000
104A285ALA 00.000-0.01253.1450.0000.0000.0000.0000.0000.000
105A286PRO 0-0.023-0.00555.4960.0000.0000.0000.0000.0000.000
106A287LEU 00.0060.01952.3740.0000.0000.0000.0000.0000.000
107A288ASN 00.010-0.01051.4600.0000.0000.0000.0000.0000.000
108A289LEU 0-0.054-0.01950.3280.0000.0000.0000.0000.0000.000
109A290THR 00.0750.04851.4570.0000.0000.0000.0000.0000.000
110A291PRO 00.0760.04048.6100.0000.0000.0000.0000.0000.000
111A292GLU -1-0.935-0.98847.009-0.020-0.0200.0000.0000.0000.000
112A293GLN 00.002-0.00846.427-0.001-0.0010.0000.0000.0000.000
113A294VAL 00.0510.04744.602-0.001-0.0010.0000.0000.0000.000
114A295VAL 00.0490.02641.378-0.001-0.0010.0000.0000.0000.000
115A296ALA 0-0.0090.04741.835-0.003-0.0030.0000.0000.0000.000
116A297ILE 0-0.006-0.00842.428-0.002-0.0020.0000.0000.0000.000
117A298ALA 0-0.008-0.01339.957-0.001-0.0010.0000.0000.0000.000
118A299SER 0-0.075-0.09337.727-0.001-0.0010.0000.0000.0000.000
119A300HIS 0-0.078-0.05436.314-0.006-0.0060.0000.0000.0000.000
120A301ASP -1-0.829-0.93031.836-0.051-0.0510.0000.0000.0000.000
121A302GLY 0-0.029-0.01634.0250.0010.0010.0000.0000.0000.000
122A303GLY 00.0400.03536.7400.0020.0020.0000.0000.0000.000
123A304LYS 10.9770.99636.7440.0140.0140.0000.0000.0000.000
124A305GLN 0-0.025-0.02037.5510.0020.0020.0000.0000.0000.000
125A306ALA 00.0250.03340.6820.0010.0010.0000.0000.0000.000
126A307LEU 00.040-0.00741.2910.0010.0010.0000.0000.0000.000
127A308GLU -1-0.898-0.94242.656-0.013-0.0130.0000.0000.0000.000
128A309THR 0-0.064-0.06744.1550.0010.0010.0000.0000.0000.000
129A310VAL 00.0180.02146.6610.0000.0000.0000.0000.0000.000
130A311GLN 0-0.0240.00048.0740.0010.0010.0000.0000.0000.000
131A312ARG 10.8120.88945.9800.0140.0140.0000.0000.0000.000
132A313LEU 0-0.016-0.02149.7120.0010.0010.0000.0000.0000.000
133A314LEU 00.0470.04152.3420.0000.0000.0000.0000.0000.000
134A315PRO 00.0390.01553.8210.0000.0000.0000.0000.0000.000
135A316VAL 00.0080.00555.1410.0000.0000.0000.0000.0000.000
136A317LEU 0-0.001-0.00352.2400.0000.0000.0000.0000.0000.000
137A318CYS 0-0.043-0.01656.5390.0000.0000.0000.0000.0000.000
138A319GLN 0-0.0250.01558.9550.0000.0000.0000.0000.0000.000
139A320ALA 0-0.056-0.02960.2610.0000.0000.0000.0000.0000.000
140A321HIS 0-0.055-0.03858.1970.0000.0000.0000.0000.0000.000
141A322GLY 00.0030.02160.8820.0000.0000.0000.0000.0000.000
142A323LEU 0-0.0040.01155.229-0.001-0.0010.0000.0000.0000.000
143A324THR 00.022-0.00258.0160.0000.0000.0000.0000.0000.000
144A325PRO 00.0820.00555.284-0.001-0.0010.0000.0000.0000.000
145A326GLN 00.003-0.00253.528-0.001-0.0010.0000.0000.0000.000
146A327GLN 00.0850.04052.492-0.001-0.0010.0000.0000.0000.000
147A328VAL 00.0270.03650.857-0.001-0.0010.0000.0000.0000.000
148A329VAL 00.0330.01048.267-0.001-0.0010.0000.0000.0000.000
149A330ALA 0-0.0270.03447.798-0.002-0.0020.0000.0000.0000.000
150A331ILE 00.0100.01947.540-0.001-0.0010.0000.0000.0000.000
151A332ALA 0-0.059-0.04045.503-0.001-0.0010.0000.0000.0000.000
152A333SER 0-0.069-0.08243.783-0.001-0.0010.0000.0000.0000.000
153A334ASN 00.0030.01041.205-0.001-0.0010.0000.0000.0000.000
154A335GLY 00.0560.02637.8650.0010.0010.0000.0000.0000.000
155A336GLY 0-0.005-0.02038.7570.0000.0000.0000.0000.0000.000
156A337GLY 00.0750.04940.3710.0020.0020.0000.0000.0000.000
157A338LYS 10.9400.96841.3280.0190.0190.0000.0000.0000.000
158A339GLN 0-0.019-0.01640.9780.0020.0020.0000.0000.0000.000
159A340ALA 00.0270.03144.0240.0010.0010.0000.0000.0000.000
160A341LEU 00.0340.02746.3340.0010.0010.0000.0000.0000.000
161A342GLU -1-0.850-0.92546.116-0.016-0.0160.0000.0000.0000.000
162A343THR 0-0.065-0.06147.1140.0010.0010.0000.0000.0000.000
163A344VAL 00.0670.02749.8220.0000.0000.0000.0000.0000.000
164A345GLN 0-0.059-0.02851.3960.0020.0020.0000.0000.0000.000
165A346ARG 10.8720.94746.6770.0190.0190.0000.0000.0000.000
166A347LEU 00.0270.00851.4500.0000.0000.0000.0000.0000.000
167A348LEU 00.0010.02055.4180.0000.0000.0000.0000.0000.000
168A349PRO 00.0740.02657.1180.0000.0000.0000.0000.0000.000
169A350VAL 0-0.014-0.00857.8930.0000.0000.0000.0000.0000.000
170A351LEU 00.018-0.00154.1650.0000.0000.0000.0000.0000.000
171A352CYS 0-0.042-0.01458.9470.0000.0000.0000.0000.0000.000
172A353GLN 0-0.035-0.00861.8960.0000.0000.0000.0000.0000.000
173A354ALA 0-0.057-0.01661.4380.0000.0000.0000.0000.0000.000
174A355HIS 0-0.026-0.01958.6650.0000.0000.0000.0000.0000.000
175A356GLY 0-0.0020.01162.0280.0000.0000.0000.0000.0000.000
176A357LEU 0-0.051-0.02557.237-0.001-0.0010.0000.0000.0000.000
177A358THR 00.0370.00560.8310.0000.0000.0000.0000.0000.000
178A359PRO 00.1040.02859.103-0.001-0.0010.0000.0000.0000.000
179A360GLU -1-0.917-0.96157.346-0.018-0.0180.0000.0000.0000.000
180A361GLN 00.0210.02956.141-0.001-0.0010.0000.0000.0000.000
181A362VAL 00.0280.01953.723-0.001-0.0010.0000.0000.0000.000
182A363VAL 0-0.009-0.01452.752-0.001-0.0010.0000.0000.0000.000
183A364ALA 0-0.0150.02251.607-0.001-0.0010.0000.0000.0000.000
184A365ILE 0-0.032-0.01549.844-0.001-0.0010.0000.0000.0000.000
185A366ALA 0-0.044-0.02448.400-0.001-0.0010.0000.0000.0000.000
186A367SER 0-0.054-0.04646.828-0.001-0.0010.0000.0000.0000.000
187A368ASN 0-0.001-0.00344.173-0.002-0.0020.0000.0000.0000.000
188A369ILE 00.0110.01037.5930.0010.0010.0000.0000.0000.000
189A370GLY 0-0.018-0.01841.086-0.001-0.0010.0000.0000.0000.000
190A371GLY 00.0760.05941.9060.0010.0010.0000.0000.0000.000
191A372LYS 10.9080.95742.5730.0260.0260.0000.0000.0000.000
192A373GLN 0-0.017-0.02441.5770.0000.0000.0000.0000.0000.000
193A374ALA 00.0370.04144.9660.0000.0000.0000.0000.0000.000
194A375LEU 00.0350.01147.3570.0010.0010.0000.0000.0000.000
195A376GLU -1-0.947-0.98346.929-0.023-0.0230.0000.0000.0000.000
196A377THR 0-0.025-0.02447.3220.0000.0000.0000.0000.0000.000
197A378VAL 00.0130.00350.0110.0000.0000.0000.0000.0000.000
198A379GLN 00.0120.00353.0580.0020.0020.0000.0000.0000.000
199A380ALA 0-0.039-0.01452.1290.0010.0010.0000.0000.0000.000
200A381LEU 0-0.017-0.02250.3990.0000.0000.0000.0000.0000.000
201A382LEU 00.0290.01154.7260.0000.0000.0000.0000.0000.000
202A383PRO 0-0.0120.00257.1290.0000.0000.0000.0000.0000.000
203A384VAL 00.006-0.00656.7760.0000.0000.0000.0000.0000.000
204A385LEU 0-0.027-0.00953.2680.0000.0000.0000.0000.0000.000
205A386CYS 0-0.0030.00557.7760.0000.0000.0000.0000.0000.000
206A387GLN 0-0.0330.00360.9550.0000.0000.0000.0000.0000.000
207A388ALA 0-0.035-0.02460.2370.0000.0000.0000.0000.0000.000
208A389HIS 0-0.029-0.02255.7210.0000.0000.0000.0000.0000.000
209A390GLY 00.0090.02960.0030.0000.0000.0000.0000.0000.000
210A391LEU 0-0.025-0.00155.8230.0000.0000.0000.0000.0000.000
211A392THR 00.033-0.00260.3600.0010.0010.0000.0000.0000.000
212A393PRO 00.0530.00659.367-0.001-0.0010.0000.0000.0000.000
213A394GLN 0-0.016-0.02858.4060.0000.0000.0000.0000.0000.000
214A395GLN 00.0560.03456.7860.0000.0000.0000.0000.0000.000
215A396VAL 00.0310.04054.193-0.001-0.0010.0000.0000.0000.000
216A397VAL 00.0360.00253.308-0.001-0.0010.0000.0000.0000.000
217A398ALA 00.0100.03952.705-0.001-0.0010.0000.0000.0000.000
218A399ILE 0-0.0050.02049.582-0.001-0.0010.0000.0000.0000.000
219A400ALA 0-0.064-0.03148.946-0.002-0.0020.0000.0000.0000.000
220A401SER 0-0.055-0.06448.7080.0000.0000.0000.0000.0000.000
221A402ASN 0-0.013-0.01045.048-0.001-0.0010.0000.0000.0000.000
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