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: 7GR1K

Calculation Name: 5E27-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5E27

Chain ID: A

ChEMBL ID:

UniProt ID: P9WG29

Base Structure: X-ray

Registration Date: 2023-06-20

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1894888.095145
FMO2-HF: Nuclear repulsion 1811837.156263
FMO2-HF: Total energy -83050.938882
FMO2-MP2: Total energy -83294.757327


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:137:SER)


Summations of interaction energy for fragment #1(A:137: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.
-15.576-12.9686.229-3.77-5.0650.015
Interaction energy analysis for fragmet #1(A:137:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.024
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].
3A139LYS10.8460.9132.211-14.930-12.8813.935-2.628-3.3560.019
4A140THR0-0.056-0.0376.2150.1790.1790.0000.0000.0000.000
5A141VAL00.0060.0097.0490.0340.0340.0000.0000.0000.000
6A142GLN00.0120.0129.7900.0000.0000.0000.0000.0000.000
7A143LEU00.0080.01213.0550.0110.0110.0000.0000.0000.000
8A144ASN0-0.031-0.02414.6780.0040.0040.0000.0000.0000.000
9A145ASP-1-0.778-0.88317.780-0.024-0.0240.0000.0000.0000.000
10A146GLY00.0240.01319.4900.0020.0020.0000.0000.0000.000
11A147GLY00.0100.00522.1870.0010.0010.0000.0000.0000.000
12A148LEU0-0.039-0.01921.2250.0030.0030.0000.0000.0000.000
13A149VAL0-0.015-0.00818.068-0.004-0.0040.0000.0000.0000.000
14A150ARG10.8750.94214.5110.0500.0500.0000.0000.0000.000
15A151THR00.007-0.00211.362-0.004-0.0040.0000.0000.0000.000
16A152VAL0-0.071-0.0388.3620.0100.0100.0000.0000.0000.000
17A153HIS00.0180.0026.5500.0140.0140.0000.0000.0000.000
18A154LEU0-0.0050.0054.894-0.344-0.236-0.001-0.007-0.0990.000
19A155PRO0-0.0110.0012.331-1.247-0.8072.275-1.199-1.516-0.003
20A156ALA00.0060.0003.4030.2260.2370.0200.064-0.094-0.001
21A157PRO00.0010.0015.5050.5500.5500.0000.0000.0000.000
22A158ASN00.0200.0047.8230.0780.0780.0000.0000.0000.000
23A159VAL00.0590.0339.551-0.055-0.0550.0000.0000.0000.000
24A160ALA00.0310.02411.146-0.039-0.0390.0000.0000.0000.000
25A161GLY00.0170.02210.326-0.025-0.0250.0000.0000.0000.000
26A162LEU00.0130.0006.415-0.038-0.0380.0000.0000.0000.000
27A163LEU00.000-0.0039.188-0.028-0.0280.0000.0000.0000.000
28A164SER0-0.043-0.04112.7840.0030.0030.0000.0000.0000.000
29A165ALA0-0.011-0.0029.1150.0050.0050.0000.0000.0000.000
30A166ALA0-0.048-0.01111.0940.0080.0080.0000.0000.0000.000
31A167GLY00.0280.01312.4560.0280.0280.0000.0000.0000.000
32A168VAL0-0.047-0.01615.0570.0130.0130.0000.0000.0000.000
33A169PRO00.0760.03816.1730.0040.0040.0000.0000.0000.000
34A170LEU0-0.026-0.00217.1620.0070.0070.0000.0000.0000.000
35A171LEU0-0.028-0.02619.019-0.003-0.0030.0000.0000.0000.000
36A172GLN00.006-0.00922.6320.0050.0050.0000.0000.0000.000
37A173SER0-0.0010.00526.1230.0010.0010.0000.0000.0000.000
38A174ASP-1-0.715-0.80221.620-0.017-0.0170.0000.0000.0000.000
39A175HIS0-0.037-0.01121.7550.0000.0000.0000.0000.0000.000
40A176VAL0-0.006-0.01115.978-0.002-0.0020.0000.0000.0000.000
41A177VAL0-0.0100.02418.6670.0030.0030.0000.0000.0000.000
42A178PRO00.0650.01214.018-0.004-0.0040.0000.0000.0000.000
43A179ALA00.0560.02016.464-0.005-0.0050.0000.0000.0000.000
44A180ALA00.0550.01715.6340.0140.0140.0000.0000.0000.000
45A181THR0-0.021-0.01514.3820.0040.0040.0000.0000.0000.000
46A182ALA0-0.027-0.00113.7420.0090.0090.0000.0000.0000.000
47A183PRO00.0410.0049.5550.0150.0150.0000.0000.0000.000
48A184ILE0-0.014-0.0015.479-0.130-0.1300.0000.0000.0000.000
49A185VAL0-0.004-0.0046.8950.3590.3590.0000.0000.0000.000
50A186GLU-1-0.735-0.8556.667-0.385-0.3850.0000.0000.0000.000
51A187GLY00.000-0.0028.7530.0320.0320.0000.0000.0000.000
52A188MET0-0.074-0.0069.6090.0100.0100.0000.0000.0000.000
53A189GLN0-0.004-0.01312.066-0.030-0.0300.0000.0000.0000.000
54A190ILE0-0.007-0.00610.4500.0120.0120.0000.0000.0000.000
55A191GLN0-0.0130.00114.990-0.008-0.0080.0000.0000.0000.000
56A192VAL00.007-0.00516.9070.0020.0020.0000.0000.0000.000
57A193THR0-0.0120.01219.7070.0000.0000.0000.0000.0000.000
58A194ARG10.6940.79517.4770.0250.0250.0000.0000.0000.000
59A195ASN0-0.011-0.02324.2080.0020.0020.0000.0000.0000.000
60A196ARG10.8240.88621.9970.0190.0190.0000.0000.0000.000
61A197ILE00.0280.01828.9030.0020.0020.0000.0000.0000.000
62A198LYS10.8010.89130.3910.0050.0050.0000.0000.0000.000
63A199LYS10.9560.97932.7290.0140.0140.0000.0000.0000.000
64A200VAL00.0320.01635.0430.0000.0000.0000.0000.0000.000
65A201THR0-0.017-0.00737.5470.0000.0000.0000.0000.0000.000
66A202GLU-1-0.842-0.89240.786-0.002-0.0020.0000.0000.0000.000
67A203ARG10.8690.93143.5170.0020.0020.0000.0000.0000.000
68A204LEU00.000-0.00446.7640.0010.0010.0000.0000.0000.000
69A205PRO00.0470.01049.7000.0000.0000.0000.0000.0000.000
70A206LEU0-0.0230.00652.9240.0000.0000.0000.0000.0000.000
71A207PRO00.022-0.00754.9790.0000.0000.0000.0000.0000.000
72A208PRO00.0040.01558.1420.0000.0000.0000.0000.0000.000
73A209ASN0-0.0060.00360.3500.0000.0000.0000.0000.0000.000
74A210ALA00.0280.01162.6390.0000.0000.0000.0000.0000.000
75A211ARG10.8670.93065.6620.0020.0020.0000.0000.0000.000
76A212ARG10.8160.87068.4300.0030.0030.0000.0000.0000.000
77A213VAL0-0.036-0.01571.1260.0000.0000.0000.0000.0000.000
78A214GLU-1-0.859-0.92074.865-0.002-0.0020.0000.0000.0000.000
79A215ASP-1-0.797-0.88777.903-0.001-0.0010.0000.0000.0000.000
80A216PRO00.0380.02780.7130.0000.0000.0000.0000.0000.000
81A217GLU-1-0.864-0.93983.745-0.001-0.0010.0000.0000.0000.000
82A218MET0-0.055-0.01078.2880.0000.0000.0000.0000.0000.000
83A219ASN0-0.007-0.02680.9150.0000.0000.0000.0000.0000.000
84A220MET0-0.021-0.00577.7330.0000.0000.0000.0000.0000.000
85A221SER0-0.083-0.04576.3090.0000.0000.0000.0000.0000.000
86A222ARG10.9070.95275.3400.0010.0010.0000.0000.0000.000
87A223GLU-1-0.766-0.84970.489-0.002-0.0020.0000.0000.0000.000
88A224VAL0-0.050-0.04272.9320.0000.0000.0000.0000.0000.000
89A225VAL0-0.021-0.00467.6140.0000.0000.0000.0000.0000.000
90A226GLU-1-0.899-0.92870.804-0.001-0.0010.0000.0000.0000.000
91A227ASP-1-0.857-0.92769.537-0.001-0.0010.0000.0000.0000.000
92A228PRO0-0.029-0.02265.9680.0000.0000.0000.0000.0000.000
93A229GLY00.0500.03065.1140.0000.0000.0000.0000.0000.000
94A230VAL0-0.085-0.04761.5320.0000.0000.0000.0000.0000.000
95A231PRO0-0.008-0.01358.3950.0000.0000.0000.0000.0000.000
96A232GLY00.0540.04257.1490.0000.0000.0000.0000.0000.000
97A233THR0-0.120-0.06950.8530.0000.0000.0000.0000.0000.000
98A234GLN0-0.001-0.01649.939-0.001-0.0010.0000.0000.0000.000
99A235ASP-1-0.793-0.88144.814-0.003-0.0030.0000.0000.0000.000
100A236VAL00.014-0.00644.973-0.001-0.0010.0000.0000.0000.000
101A237THR0-0.070-0.03939.3700.0000.0000.0000.0000.0000.000
102A238PHE00.0750.02340.2210.0000.0000.0000.0000.0000.000
103A239ALA0-0.033-0.00837.407-0.001-0.0010.0000.0000.0000.000
104A240VAL00.019-0.00535.3000.0010.0010.0000.0000.0000.000
105A241ALA00.0260.02233.723-0.001-0.0010.0000.0000.0000.000
106A242GLU-1-0.820-0.90330.514-0.005-0.0050.0000.0000.0000.000
107A243VAL00.0220.00328.450-0.001-0.0010.0000.0000.0000.000
108A244ASN0-0.016-0.02725.498-0.001-0.0010.0000.0000.0000.000
109A245GLY00.0020.01426.9260.0010.0010.0000.0000.0000.000
110A246VAL0-0.017-0.00228.6330.0010.0010.0000.0000.0000.000
111A247GLU-1-0.805-0.88232.249-0.003-0.0030.0000.0000.0000.000
112A248THR0-0.064-0.03834.0310.0010.0010.0000.0000.0000.000
113A249GLY00.0320.01936.6210.0000.0000.0000.0000.0000.000
114A250ARG10.7240.82737.9370.0020.0020.0000.0000.0000.000
115A251LEU00.0240.01740.3340.0000.0000.0000.0000.0000.000
116A252PRO0-0.0090.01041.895-0.001-0.0010.0000.0000.0000.000
117A253VAL0-0.030-0.03040.1050.0000.0000.0000.0000.0000.000
118A254ALA0-0.011-0.00643.290-0.001-0.0010.0000.0000.0000.000
119A255ASN0-0.022-0.01244.9970.0010.0010.0000.0000.0000.000
120A256VAL0-0.0140.00846.3650.0000.0000.0000.0000.0000.000
121A257VAL00.0320.02248.9340.0000.0000.0000.0000.0000.000
122A258VAL0-0.069-0.03548.5150.0000.0000.0000.0000.0000.000
123A259THR00.002-0.00551.8700.0000.0000.0000.0000.0000.000
124A260PRO00.009-0.00855.3110.0000.0000.0000.0000.0000.000
125A261ALA00.0240.02857.9430.0000.0000.0000.0000.0000.000
126A262HIS0-0.049-0.01759.8030.0000.0000.0000.0000.0000.000
127A263GLU-1-0.846-0.93163.640-0.003-0.0030.0000.0000.0000.000
128A264ALA00.0070.02565.3680.0000.0000.0000.0000.0000.000
129A265VAL0-0.028-0.01266.9180.0000.0000.0000.0000.0000.000
130A266VAL0-0.014-0.01967.7360.0000.0000.0000.0000.0000.000
131A267ARG10.8190.88771.0050.0010.0010.0000.0000.0000.000
132A268VAL0-0.028-0.02772.3400.0000.0000.0000.0000.0000.000
133A269GLY00.0140.00775.4590.0000.0000.0000.0000.0000.000
134A270THR0-0.045-0.05378.1890.0000.0000.0000.0000.0000.000
135A271LYS10.7940.91780.5730.0010.0010.0000.0000.0000.000
136A272PRO00.0030.00683.9530.0000.0000.0000.0000.0000.000
137A273GLY0-0.0080.00685.2350.0000.0000.0000.0000.0000.000
138A274THR0-0.047-0.03282.3910.0000.0000.0000.0000.0000.000
139A275GLU-1-0.768-0.89080.221-0.002-0.0020.0000.0000.0000.000
140A276VAL0-0.0210.00577.6610.0000.0000.0000.0000.0000.000
141A277PRO0-0.0350.00077.5990.0000.0000.0000.0000.0000.000
142A278PRO0-0.011-0.00973.7420.0000.0000.0000.0000.0000.000
143A279VAL00.0290.01474.4610.0000.0000.0000.0000.0000.000
144A280ILE00.0050.00674.0960.0000.0000.0000.0000.0000.000
145A281ASP-1-0.728-0.84675.626-0.002-0.0020.0000.0000.0000.000
146A282GLY00.0030.00474.2020.0000.0000.0000.0000.0000.000
147A283SER00.002-0.00472.3580.0000.0000.0000.0000.0000.000
148A284ILE00.0120.00074.2070.0000.0000.0000.0000.0000.000
149A285TRP00.0160.00377.6140.0000.0000.0000.0000.0000.000
150A286ASP-1-0.756-0.85974.223-0.001-0.0010.0000.0000.0000.000
151A287ALA0-0.0260.00576.7550.0000.0000.0000.0000.0000.000
152A288ILE0-0.025-0.01877.9650.0000.0000.0000.0000.0000.000
153A289ALA00.0690.04178.6670.0000.0000.0000.0000.0000.000
154A290GLY0-0.029-0.02078.1900.0000.0000.0000.0000.0000.000
155A291CYS0-0.104-0.03278.9710.0000.0000.0000.0000.0000.000
156A292GLU-1-0.853-0.95082.1260.0000.0000.0000.0000.0000.000
157A293ALA0-0.0130.01482.1610.0000.0000.0000.0000.0000.000
158A294GLY0-0.0070.00880.0840.0000.0000.0000.0000.0000.000
159A295GLY0-0.030-0.02177.0280.0000.0000.0000.0000.0000.000
160A296ASN0-0.036-0.01877.6250.0000.0000.0000.0000.0000.000
161A297TRP00.056-0.00376.7580.0000.0000.0000.0000.0000.000
162A298ALA00.0290.03580.4410.0000.0000.0000.0000.0000.000
163A299ILE0-0.043-0.01282.3820.0000.0000.0000.0000.0000.000
164A300ASN0-0.039-0.04484.6950.0000.0000.0000.0000.0000.000
165A301THR0-0.005-0.01088.2460.0000.0000.0000.0000.0000.000
166A302GLY0-0.0130.01290.0220.0000.0000.0000.0000.0000.000
167A303ASN0-0.009-0.01591.0170.0000.0000.0000.0000.0000.000
168A304GLY00.0050.00494.5460.0000.0000.0000.0000.0000.000
169A305TYR0-0.092-0.03891.2470.0000.0000.0000.0000.0000.000
170A306TYR0-0.034-0.01888.9930.0000.0000.0000.0000.0000.000
171A307GLY00.0580.03184.7320.0000.0000.0000.0000.0000.000
172A308GLY0-0.053-0.01981.8210.0000.0000.0000.0000.0000.000
173A309VAL0-0.036-0.02982.6840.0000.0000.0000.0000.0000.000
174A310GLN0-0.023-0.00685.1790.0000.0000.0000.0000.0000.000
175A311PHE00.0440.02886.5820.0000.0000.0000.0000.0000.000
176A312ASP-1-0.805-0.86290.209-0.001-0.0010.0000.0000.0000.000
177A313GLN0-0.064-0.06593.3640.0000.0000.0000.0000.0000.000
178A314GLY00.0320.02495.1710.0000.0000.0000.0000.0000.000
179A315THR0-0.067-0.08993.3550.0000.0000.0000.0000.0000.000
180A316TRP0-0.0050.02085.6310.0000.0000.0000.0000.0000.000
181A317GLU-1-0.891-0.93791.961-0.001-0.0010.0000.0000.0000.000
182A318ALA0-0.046-0.02594.6510.0000.0000.0000.0000.0000.000
183A319ASN0-0.076-0.04590.0860.0000.0000.0000.0000.0000.000
184A320GLY00.0170.01390.5660.0000.0000.0000.0000.0000.000
185A321GLY00.0650.00688.2070.0000.0000.0000.0000.0000.000
186A322LEU0-0.045-0.02288.4540.0000.0000.0000.0000.0000.000
187A323ARG10.8090.92284.2190.0020.0020.0000.0000.0000.000
188A324TYR0-0.053-0.04182.3900.0000.0000.0000.0000.0000.000
189A325ALA00.0750.03185.6530.0000.0000.0000.0000.0000.000
190A326PRO00.002-0.00487.6720.0000.0000.0000.0000.0000.000
191A327ARG10.8760.92789.2240.0000.0000.0000.0000.0000.000
192A328ALA00.0420.02986.5600.0000.0000.0000.0000.0000.000
193A329ASP-1-0.784-0.88784.7350.0000.0000.0000.0000.0000.000
194A330LEU0-0.078-0.03384.1680.0000.0000.0000.0000.0000.000
195A331ALA00.0040.01682.7720.0000.0000.0000.0000.0000.000
196A332THR0-0.010-0.03377.2170.0000.0000.0000.0000.0000.000
197A333ARG10.8050.86073.2320.0010.0010.0000.0000.0000.000
198A334GLU-1-0.844-0.92174.589-0.001-0.0010.0000.0000.0000.000
199A335GLU-1-0.746-0.82077.864-0.001-0.0010.0000.0000.0000.000
200A336GLN0-0.028-0.04281.2710.0000.0000.0000.0000.0000.000
201A337ILE0-0.008-0.00477.6270.0000.0000.0000.0000.0000.000
202A338ALA0-0.024-0.00680.9520.0000.0000.0000.0000.0000.000
203A339VAL0-0.0310.00782.5090.0000.0000.0000.0000.0000.000
204A340ALA00.0170.00684.0040.0000.0000.0000.0000.0000.000
205A341GLU-1-0.789-0.90080.241-0.002-0.0020.0000.0000.0000.000
206A342VAL0-0.0130.01285.0040.0000.0000.0000.0000.0000.000
207A343THR0-0.001-0.00688.3480.0000.0000.0000.0000.0000.000
208A344ARG10.7380.85580.0450.0020.0020.0000.0000.0000.000
209A345LEU0-0.031-0.01984.7390.0000.0000.0000.0000.0000.000
210A346ARG10.9070.96988.2250.0010.0010.0000.0000.0000.000
211A347GLN0-0.023-0.01790.6630.0000.0000.0000.0000.0000.000
212A348GLY00.0160.02587.3850.0000.0000.0000.0000.0000.000
213A349TRP00.012-0.02980.1630.0000.0000.0000.0000.0000.000
214A350GLY0-0.0020.00086.6750.0000.0000.0000.0000.0000.000
215A351ALA0-0.022-0.00489.6880.0000.0000.0000.0000.0000.000
216A352TRP00.0250.01486.8520.0000.0000.0000.0000.0000.000
217A353PRO0-0.0020.00487.9010.0000.0000.0000.0000.0000.000
218A354VAL00.024-0.00387.6840.0000.0000.0000.0000.0000.000
219A356ALA00.0290.01883.4980.0000.0000.0000.0000.0000.000
220A357ALA0-0.018-0.00683.8190.0000.0000.0000.0000.0000.000
221A358ARG10.8860.92481.4390.0000.0000.0000.0000.0000.000
222A359ALA0-0.0090.00279.6280.0000.0000.0000.0000.0000.000
223A360GLY0-0.0130.00979.1290.0000.0000.0000.0000.0000.000
224A361ALA0-0.060-0.02480.8300.0000.0000.0000.0000.0000.000
225A362ARG10.8540.91279.4400.0020.0020.0000.0000.0000.000