Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 6Y52Z

Calculation Name: 5I45-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I45

Chain ID: A

ChEMBL ID:

UniProt ID: Q5NFJ9

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2260367.720904
FMO2-HF: Nuclear repulsion 2184516.570103
FMO2-HF: Total energy -75851.150801
FMO2-MP2: Total energy -76075.531941


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:141:GLY)


Summations of interaction energy for fragment #1(A:141:GLY)
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.
-2.7891.9823.376-3.928-4.219-0.017
Interaction energy analysis for fragmet #1(A:141:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / 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].
3A143ASP-1-0.821-0.9183.755-1.2440.507-0.017-0.867-0.8670.004
4A144THR00.030-0.0096.7670.3530.3530.0000.0000.0000.000
5A145GLN0-0.054-0.0118.9380.3790.3790.0000.0000.0000.000
6A146VAL0-0.031-0.00210.3040.1460.1460.0000.0000.0000.000
7A147PHE0-0.024-0.0228.4770.1700.1700.0000.0000.0000.000
8A148TYR00.0220.00910.5320.0080.0080.0000.0000.0000.000
9A149PRO00.001-0.01113.1420.0250.0250.0000.0000.0000.000
10A150ALA00.0040.00616.2450.0050.0050.0000.0000.0000.000
11A151GLU-1-0.929-0.95319.679-0.204-0.2040.0000.0000.0000.000
12A152ASN0-0.006-0.01022.5350.0180.0180.0000.0000.0000.000
13A153ARG10.8710.91417.9160.2870.2870.0000.0000.0000.000
14A154GLN00.0350.00923.0600.0040.0040.0000.0000.0000.000
15A155GLN0-0.065-0.03126.6230.0140.0140.0000.0000.0000.000
16A156GLN00.0170.00321.496-0.030-0.0300.0000.0000.0000.000
17A157TRP00.000-0.00723.870-0.023-0.0230.0000.0000.0000.000
18A158GLN0-0.046-0.02925.5810.0070.0070.0000.0000.0000.000
19A159ASP-1-0.882-0.93526.460-0.220-0.2200.0000.0000.0000.000
20A160LYS10.8520.93221.7120.3760.3760.0000.0000.0000.000
21A161LYS10.8600.93827.4030.1730.1730.0000.0000.0000.000
22A162ILE0-0.0060.00426.1930.0050.0050.0000.0000.0000.000
23A163PRO0-0.0020.00530.7150.0030.0030.0000.0000.0000.000
24A164GLY00.0470.04230.597-0.008-0.0080.0000.0000.0000.000
25A165LYS10.9090.95330.0830.1150.1150.0000.0000.0000.000
26A166TYR00.0030.01925.899-0.004-0.0040.0000.0000.0000.000
27A167GLY00.0570.03423.9470.0090.0090.0000.0000.0000.000
28A168ILE0-0.007-0.01021.562-0.011-0.0110.0000.0000.0000.000
29A169GLY00.0310.01019.8570.0080.0080.0000.0000.0000.000
30A170ILE0-0.045-0.00917.795-0.002-0.0020.0000.0000.0000.000
31A171PHE00.0650.03514.5700.0070.0070.0000.0000.0000.000
32A172GLY0-0.020-0.01015.949-0.013-0.0130.0000.0000.0000.000
33A173ARG10.8720.94516.7720.2890.2890.0000.0000.0000.000
34A174ILE00.0190.02319.5000.0120.0120.0000.0000.0000.000
35A175ARG10.8570.90121.5380.1660.1660.0000.0000.0000.000
36A176LYS10.9660.99522.5900.0860.0860.0000.0000.0000.000
37A177THR0-0.006-0.01020.7480.0000.0000.0000.0000.0000.000
38A178LYS10.9220.96514.2780.3730.3730.0000.0000.0000.000
39A179GLY00.0540.03619.007-0.018-0.0180.0000.0000.0000.000
40A180THR00.016-0.00421.4380.0060.0060.0000.0000.0000.000
41A181GLN00.0170.00123.001-0.002-0.0020.0000.0000.0000.000
42A182GLU-1-0.800-0.88923.672-0.094-0.0940.0000.0000.0000.000
43A183PHE00.0260.01221.5960.0070.0070.0000.0000.0000.000
44A184ILE00.0250.01024.0970.0050.0050.0000.0000.0000.000
45A185GLU-1-0.896-0.96427.310-0.074-0.0740.0000.0000.0000.000
46A186ALA00.0090.00325.7860.0080.0080.0000.0000.0000.000
47A187ALA00.0210.01626.5990.0060.0060.0000.0000.0000.000
48A188ILE0-0.018-0.01328.3120.0060.0060.0000.0000.0000.000
49A189VAL0-0.038-0.02031.0940.0060.0060.0000.0000.0000.000
50A190THR0-0.008-0.02127.8880.0060.0060.0000.0000.0000.000
51A191LEU0-0.019-0.02628.2090.0030.0030.0000.0000.0000.000
52A192LYS10.9100.97531.8500.0760.0760.0000.0000.0000.000
53A193LYS10.8470.92833.2340.0570.0570.0000.0000.0000.000
54A194TYR0-0.043-0.03830.8370.0040.0040.0000.0000.0000.000
55A195PRO00.026-0.00232.399-0.010-0.0100.0000.0000.0000.000
56A196ASP-1-0.916-0.94431.982-0.109-0.1090.0000.0000.0000.000
57A197TRP0-0.009-0.00323.874-0.016-0.0160.0000.0000.0000.000
58A198THR0-0.015-0.03127.5250.0140.0140.0000.0000.0000.000
59A199ALA0-0.034-0.00625.061-0.014-0.0140.0000.0000.0000.000
60A200VAL0-0.003-0.00421.9290.0090.0090.0000.0000.0000.000
61A201VAL0-0.023-0.01522.021-0.018-0.0180.0000.0000.0000.000
62A202ILE00.0080.01118.6680.0150.0150.0000.0000.0000.000
63A203GLY00.0480.00918.965-0.052-0.0520.0000.0000.0000.000
64A204GLU-1-0.861-0.94220.695-0.230-0.2300.0000.0000.0000.000
65A205ALA0-0.0100.00722.572-0.011-0.0110.0000.0000.0000.000
66A206THR00.005-0.01623.1470.0070.0070.0000.0000.0000.000
67A207PRO00.0860.01125.8660.0100.0100.0000.0000.0000.000
68A208ARG10.8910.94625.9390.1340.1340.0000.0000.0000.000
69A209ASP-1-0.780-0.87325.230-0.154-0.1540.0000.0000.0000.000
70A210LEU00.0100.00928.289-0.003-0.0030.0000.0000.0000.000
71A211ASP-1-0.901-0.95030.502-0.108-0.1080.0000.0000.0000.000
72A212PHE00.0010.00124.9500.0030.0030.0000.0000.0000.000
73A213LYS10.8980.94627.0890.1870.1870.0000.0000.0000.000
74A214LYS10.9800.98629.3270.1080.1080.0000.0000.0000.000
75A215GLU-1-0.916-0.95032.404-0.081-0.0810.0000.0000.0000.000
76A216LEU0-0.037-0.02726.6600.0030.0030.0000.0000.0000.000
77A217GLU-1-0.838-0.91830.843-0.154-0.1540.0000.0000.0000.000
78A218GLN0-0.018-0.00432.7130.0080.0080.0000.0000.0000.000
79A219LYS10.9250.96531.6200.0910.0910.0000.0000.0000.000
80A220VAL00.0050.01030.7640.0050.0050.0000.0000.0000.000
81A221LYS10.9620.98933.9460.0960.0960.0000.0000.0000.000
82A222GLN0-0.053-0.03437.2900.0020.0020.0000.0000.0000.000
83A223ALA0-0.053-0.01135.7030.0060.0060.0000.0000.0000.000
84A224GLY0-0.014-0.00737.8220.0020.0020.0000.0000.0000.000
85A225LEU0-0.026-0.01333.1790.0000.0000.0000.0000.0000.000
86A226ASP-1-0.904-0.96033.594-0.119-0.1190.0000.0000.0000.000
87A227LYS10.9200.95934.0860.0940.0940.0000.0000.0000.000
88A228GLN0-0.038-0.02131.5100.0030.0030.0000.0000.0000.000
89A229ILE0-0.0080.00927.813-0.009-0.0090.0000.0000.0000.000
90A230ILE00.0060.01327.7800.0080.0080.0000.0000.0000.000
91A231PHE0-0.014-0.02226.126-0.019-0.0190.0000.0000.0000.000
92A232ILE0-0.021-0.01123.7120.0140.0140.0000.0000.0000.000
93A233GLY00.0030.00925.225-0.003-0.0030.0000.0000.0000.000
94A234PHE0-0.029-0.01821.506-0.024-0.0240.0000.0000.0000.000
95A235ILE0-0.0170.00022.7410.0250.0250.0000.0000.0000.000
96A236ALA0-0.035-0.02221.739-0.032-0.0320.0000.0000.0000.000
97A237ASP-1-0.896-0.94820.660-0.482-0.4820.0000.0000.0000.000
98A238SER0-0.006-0.00517.008-0.058-0.0580.0000.0000.0000.000
99A239ASN00.018-0.00916.476-0.172-0.1720.0000.0000.0000.000
100A240GLU-1-0.803-0.88818.013-0.399-0.3990.0000.0000.0000.000
101A241ILE0-0.0120.01714.0620.0110.0110.0000.0000.0000.000
102A242PRO00.0250.01813.2530.0230.0230.0000.0000.0000.000
103A243SER0-0.065-0.05815.0370.0630.0630.0000.0000.0000.000
104A244TRP00.021-0.00918.2070.0610.0610.0000.0000.0000.000
105A245TYR00.000-0.00411.7160.1070.1070.0000.0000.0000.000
106A246ARG10.8680.94614.7940.7080.7080.0000.0000.0000.000
107A247ALA0-0.0160.00117.9580.0520.0520.0000.0000.0000.000
108A248LEU0-0.0370.00117.9380.0420.0420.0000.0000.0000.000
109A249ASP-1-0.834-0.92318.905-0.221-0.2210.0000.0000.0000.000
110A250ILE0-0.0360.00018.7170.0060.0060.0000.0000.0000.000
111A251VAL00.008-0.00314.468-0.022-0.0220.0000.0000.0000.000
112A252VAL0-0.0010.00416.8690.0370.0370.0000.0000.0000.000
113A253CYS0-0.056-0.01212.133-0.056-0.0560.0000.0000.0000.000
114A254ALA00.0620.02015.4910.0520.0520.0000.0000.0000.000
115A255SER0-0.073-0.04715.3040.0300.0300.0000.0000.0000.000
116A256HIS0-0.029-0.03317.3100.0440.0440.0000.0000.0000.000
117A257LYS10.9130.94717.3000.0020.0020.0000.0000.0000.000
118A258GLU-1-0.927-0.95014.969-0.159-0.1590.0000.0000.0000.000
119A259GLY00.0190.00711.198-0.042-0.0420.0000.0000.0000.000
120A260PHE00.005-0.0026.5870.1070.1070.0000.0000.0000.000
121A261GLY00.0690.0536.1190.0460.0460.0000.0000.0000.000
122A262LEU00.001-0.0023.320-0.0680.1970.008-0.097-0.1760.000
123A263PRO00.0480.0226.204-0.095-0.0950.0000.0000.0000.000
124A264ALA00.0230.0139.1660.1140.1140.0000.0000.0000.000
125A265LEU00.0310.0082.776-0.427-0.0170.219-0.192-0.437-0.001
126A266GLU-1-0.898-0.9476.664-1.894-1.8940.0000.0000.0000.000
127A267ALA00.0150.0118.5770.2320.2320.0000.0000.0000.000
128A268MET0-0.040-0.0048.7900.0980.0980.0000.0000.0000.000
129A269ALA00.0100.0017.4780.1530.1530.0000.0000.0000.000
130A270SER0-0.026-0.0329.5310.0980.0980.0000.0000.0000.000
131A271LYS10.8470.93112.6680.3040.3040.0000.0000.0000.000
132A272CYS0-0.0380.01313.9960.0390.0390.0000.0000.0000.000
133A273ALA00.0060.00614.6540.0090.0090.0000.0000.0000.000
134A274VAL00.010-0.00112.210-0.031-0.0310.0000.0000.0000.000
135A275ILE00.0050.01715.5080.0640.0640.0000.0000.0000.000
136A276ALA00.002-0.00614.217-0.056-0.0560.0000.0000.0000.000
137A277THR00.0030.00716.2060.0370.0370.0000.0000.0000.000
138A278LYS11.0331.00014.963-0.213-0.2130.0000.0000.0000.000
139A279ALA0-0.052-0.02513.4330.0450.0450.0000.0000.0000.000
140A280GLY0-0.048-0.02611.957-0.041-0.0410.0000.0000.0000.000
141A281ALA00.0360.01510.169-0.152-0.1520.0000.0000.0000.000
142A282TRP0-0.0260.0167.3180.1940.1940.0000.0000.0000.000
143A283PRO0-0.031-0.0247.107-0.090-0.0900.0000.0000.0000.000
144A284GLU-1-0.951-1.00610.2300.6890.6890.0000.0000.0000.000
145A285ILE0-0.0280.0056.5730.0230.0230.0000.0000.0000.000
146A286ILE0-0.037-0.02310.055-0.037-0.0370.0000.0000.0000.000
147A287VAL00.0010.00813.1600.0380.0380.0000.0000.0000.000
148A288ASP-1-0.864-0.95916.3280.0190.0190.0000.0000.0000.000
149A289ASP-1-0.864-0.93219.0690.0510.0510.0000.0000.0000.000
150A290GLU-1-0.968-0.95917.1220.2440.2440.0000.0000.0000.000
151A291ASN00.005-0.02413.390-0.047-0.0470.0000.0000.0000.000
152A292GLY00.0180.00714.150-0.054-0.0540.0000.0000.0000.000
153A293TYR0-0.068-0.04216.1580.0220.0220.0000.0000.0000.000
154A294LEU0-0.029-0.01715.312-0.023-0.0230.0000.0000.0000.000
155A295VAL0-0.053-0.02618.855-0.004-0.0040.0000.0000.0000.000
156A296GLU-1-0.891-0.95520.2210.0760.0760.0000.0000.0000.000
157A297PRO0-0.057-0.03920.485-0.027-0.0270.0000.0000.0000.000
158A298LYS10.8670.92222.0570.0390.0390.0000.0000.0000.000
159A299SER00.0300.02224.5600.0080.0080.0000.0000.0000.000
160A300SER00.0380.02425.7680.0010.0010.0000.0000.0000.000
161A301GLN00.0340.01627.166-0.009-0.0090.0000.0000.0000.000
162A302GLN00.0670.03424.9410.0030.0030.0000.0000.0000.000
163A303ILE0-0.012-0.00721.926-0.002-0.0020.0000.0000.0000.000
164A304ALA00.0110.00024.350-0.007-0.0070.0000.0000.0000.000
165A305ASP-1-0.861-0.92427.500-0.032-0.0320.0000.0000.0000.000
166A306LYS10.9140.96222.3460.0020.0020.0000.0000.0000.000
167A307LEU0-0.014-0.00822.697-0.009-0.0090.0000.0000.0000.000
168A308ASP-1-0.827-0.88525.066-0.057-0.0570.0000.0000.0000.000
169A309MET00.0180.01625.5760.0000.0000.0000.0000.0000.000
170A310LEU0-0.017-0.01020.566-0.004-0.0040.0000.0000.0000.000
171A311ILE0-0.034-0.01324.733-0.008-0.0080.0000.0000.0000.000
172A312SER0-0.047-0.04727.2090.0020.0020.0000.0000.0000.000
173A313ASP-1-0.917-0.91827.447-0.025-0.0250.0000.0000.0000.000
174A314SER00.0410.00825.9890.0000.0000.0000.0000.0000.000
175A315LYS10.9310.96125.0510.0270.0270.0000.0000.0000.000
176A316LEU00.0390.03923.3720.0000.0000.0000.0000.0000.000
177A317ARG10.8460.92021.2920.1410.1410.0000.0000.0000.000
178A318TYR0-0.037-0.03320.269-0.008-0.0080.0000.0000.0000.000
179A319LYS10.9230.96819.835-0.054-0.0540.0000.0000.0000.000
180A320ILE00.0120.02717.3690.0040.0040.0000.0000.0000.000
181A321ALA00.007-0.00615.8580.0050.0050.0000.0000.0000.000
182A322GLN0-0.027-0.01214.833-0.061-0.0610.0000.0000.0000.000
183A323ASN00.0210.01314.9870.0140.0140.0000.0000.0000.000
184A324GLY00.0470.01312.0850.0660.0660.0000.0000.0000.000
185A325TYR0-0.022-0.01210.429-0.014-0.0140.0000.0000.0000.000
186A326ASP-1-0.833-0.91810.6230.0070.0070.0000.0000.0000.000
187A327LEU0-0.0180.0128.7030.1190.1190.0000.0000.0000.000
188A328VAL0-0.022-0.0205.7520.2830.2830.0000.0000.0000.000
189A329THR0-0.064-0.0416.1530.1480.1480.0000.0000.0000.000
190A330THR0-0.053-0.0208.6060.0310.0310.0000.0000.0000.000
191A331LYS10.8940.9447.189-1.171-1.1710.0000.0000.0000.000
192A332TYR0-0.005-0.0062.3310.0380.5230.861-0.626-0.720-0.001
193A333LYS10.9841.0132.662-3.094-1.8031.952-1.908-1.335-0.018
194A334ILE0-0.035-0.0152.8130.4160.9220.353-0.219-0.640-0.001
195A335GLN0-0.0090.0004.2910.3830.4460.000-0.019-0.0440.000