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: QY8GY

Calculation Name: 1MW7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MW7

Chain ID: A

ChEMBL ID:

UniProt ID: O24970

Base Structure: X-ray

Registration Date: 2023-06-21

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2528475.002939
FMO2-HF: Nuclear repulsion 2441910.786633
FMO2-HF: Total energy -86564.216306
FMO2-MP2: Total energy -86816.219998


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:21:LYS)


Summations of interaction energy for fragment #1(A:21:LYS)
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.
-343.373-344.28731.197-16.404-13.88-0.173
Interaction energy analysis for fragmet #1(A:21:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.896
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].
3A23PHE00.0200.0053.8871.0193.113-0.016-1.082-0.9960.000
4A24PRO00.0310.0092.2390.5921.3901.718-0.896-1.6200.002
5A25LYS10.8550.9443.30565.77266.3970.020-0.113-0.5330.000
6A26LEU00.0500.0226.5122.8212.8210.0000.0000.0000.000
7A27ALA0-0.009-0.0067.8632.0992.0990.0000.0000.0000.000
8A28LYS10.8050.9068.21828.11328.1130.0000.0000.0000.000
9A29ALA00.0680.02610.5951.4481.4480.0000.0000.0000.000
10A30ILE0-0.034-0.01811.9601.3401.3400.0000.0000.0000.000
11A31THR0-0.068-0.04712.6610.9930.9930.0000.0000.0000.000
12A32LEU00.0200.00014.6760.7810.7810.0000.0000.0000.000
13A33ALA00.0290.02116.4680.7560.7560.0000.0000.0000.000
14A34ALA0-0.0120.00118.0810.7430.7430.0000.0000.0000.000
15A35LYS10.8060.90219.05013.49313.4930.0000.0000.0000.000
16A36ASP-1-0.878-0.93020.712-13.476-13.4760.0000.0000.0000.000
17A37GLY00.0250.01622.8730.2530.2530.0000.0000.0000.000
18A38GLY0-0.0220.01123.6840.4180.4180.0000.0000.0000.000
19A39SER0-0.026-0.04922.386-0.492-0.4920.0000.0000.0000.000
20A40GLU-1-0.831-0.88923.438-10.313-10.3130.0000.0000.0000.000
21A41PRO0-0.023-0.01622.238-0.067-0.0670.0000.0000.0000.000
22A42ASP-1-0.865-0.92024.339-9.894-9.8940.0000.0000.0000.000
23A43THR0-0.029-0.03427.6010.0850.0850.0000.0000.0000.000
24A44ASN0-0.049-0.01521.891-0.195-0.1950.0000.0000.0000.000
25A45ALA00.0420.00823.503-0.323-0.3230.0000.0000.0000.000
26A46LYS10.8710.92719.23214.28914.2890.0000.0000.0000.000
27A47LEU0-0.004-0.00418.054-0.809-0.8090.0000.0000.0000.000
28A48ARG10.8560.91818.92410.41510.4150.0000.0000.0000.000
29A49THR00.0170.00918.055-0.216-0.2160.0000.0000.0000.000
30A50ALA0-0.0040.00214.766-0.753-0.7530.0000.0000.0000.000
31A51ILE0-0.031-0.03214.739-0.677-0.6770.0000.0000.0000.000
32A52LEU0-0.0120.00716.466-0.230-0.2300.0000.0000.0000.000
33A53ASN00.0520.01913.230-0.060-0.0600.0000.0000.0000.000
34A54ALA00.003-0.00511.882-0.970-0.9700.0000.0000.0000.000
35A55LYS10.9040.94312.81812.87012.8700.0000.0000.0000.000
36A56ALA00.0370.03914.8330.2060.2060.0000.0000.0000.000
37A57GLN0-0.040-0.0138.808-1.298-1.2980.0000.0000.0000.000
38A58ASN0-0.046-0.02410.537-0.084-0.0840.0000.0000.0000.000
39A59MET0-0.041-0.0018.4550.4010.4010.0000.0000.0000.000
40A60PRO0-0.0040.00011.5501.0031.0030.0000.0000.0000.000
41A61LYS10.8630.90314.39111.67311.6730.0000.0000.0000.000
42A62ASP-1-0.827-0.92016.767-12.259-12.2590.0000.0000.0000.000
43A63ASN0-0.029-0.01410.998-0.076-0.0760.0000.0000.0000.000
44A64ILE00.0570.02613.122-0.259-0.2590.0000.0000.0000.000
45A65ASP-1-0.851-0.88614.699-11.695-11.6950.0000.0000.0000.000
46A66ALA00.0320.00614.2020.2210.2210.0000.0000.0000.000
47A67ALA0-0.038-0.02212.596-0.090-0.0900.0000.0000.0000.000
48A68ILE00.0310.01414.5050.1520.1520.0000.0000.0000.000
49A69LYS10.8340.88718.12511.80811.8080.0000.0000.0000.000
50A70ARG10.8880.97011.53217.38517.3850.0000.0000.0000.000
51A71ALA00.0680.05217.4830.0300.0300.0000.0000.0000.000
52A72SER0-0.023-0.00719.0160.1750.1750.0000.0000.0000.000
53A73SER0-0.040-0.03818.8990.3470.3470.0000.0000.0000.000
54A74LYS10.8550.90520.09112.45112.4510.0000.0000.0000.000
55A75GLU-1-0.837-0.90515.676-14.388-14.3880.0000.0000.0000.000
56A76GLY00.0360.02015.777-0.899-0.8990.0000.0000.0000.000
57A77ASN0-0.101-0.04817.7620.4530.4530.0000.0000.0000.000
58A78LEU00.0230.01912.570-0.109-0.1090.0000.0000.0000.000
59A79SER0-0.017-0.00816.4110.8790.8790.0000.0000.0000.000
60A80GLU-1-0.835-0.92116.380-17.815-17.8150.0000.0000.0000.000
61A81ILE0-0.046-0.01816.3611.0261.0260.0000.0000.0000.000
62A82THR00.0080.01215.612-1.292-1.2920.0000.0000.0000.000
63A83TYR00.014-0.00714.3441.4491.4490.0000.0000.0000.000
64A84GLU-1-0.741-0.87116.172-15.381-15.3810.0000.0000.0000.000
65A85GLY00.012-0.00616.9150.0950.0950.0000.0000.0000.000
66A86LYS10.8660.94717.84413.61113.6110.0000.0000.0000.000
67A87ALA00.0240.00216.804-0.397-0.3970.0000.0000.0000.000
68A88ASN00.005-0.00818.8871.3571.3570.0000.0000.0000.000
69A89PHE00.015-0.00318.537-0.184-0.1840.0000.0000.0000.000
70A90GLY00.0370.04222.2310.2030.2030.0000.0000.0000.000
71A91VAL00.0250.03015.589-0.028-0.0280.0000.0000.0000.000
72A92LEU0-0.062-0.03718.4640.3450.3450.0000.0000.0000.000
73A93ILE00.025-0.00112.889-0.685-0.6850.0000.0000.0000.000
74A94ILE0-0.025-0.00714.7801.1051.1050.0000.0000.0000.000
75A95MET0-0.0140.00210.765-1.963-1.9630.0000.0000.0000.000
76A96GLU-1-0.759-0.84011.474-17.259-17.2590.0000.0000.0000.000
77A97CYS0-0.0190.00411.016-3.058-3.0580.0000.0000.0000.000
78A98MET00.0160.02811.4891.8251.8250.0000.0000.0000.000
79A99THR00.009-0.00411.819-1.036-1.0360.0000.0000.0000.000
80A100ASP-1-0.813-0.86413.249-18.373-18.3730.0000.0000.0000.000
81A101ASN0-0.022-0.02015.8411.1791.1790.0000.0000.0000.000
82A102PRO00.0890.03917.013-0.775-0.7750.0000.0000.0000.000
83A103THR0-0.013-0.00718.172-0.392-0.3920.0000.0000.0000.000
84A104ARG10.7690.83212.65521.42321.4230.0000.0000.0000.000
85A105THR00.002-0.00512.669-0.242-0.2420.0000.0000.0000.000
86A106ILE0-0.005-0.00314.415-0.684-0.6840.0000.0000.0000.000
87A107ALA0-0.015-0.00617.1060.2680.2680.0000.0000.0000.000
88A108ASN0-0.029-0.01711.0212.1322.1320.0000.0000.0000.000
89A109LEU00.0660.04110.883-0.397-0.3970.0000.0000.0000.000
90A110LYS10.9060.96513.45016.36616.3660.0000.0000.0000.000
91A111SER0-0.062-0.03213.8750.4430.4430.0000.0000.0000.000
92A112TYR0-0.036-0.0439.4400.5420.5420.0000.0000.0000.000
93A113PHE00.0770.03113.2030.1600.1600.0000.0000.0000.000
94A114ASN0-0.096-0.05815.9611.4421.4420.0000.0000.0000.000
95A115LYS10.9440.97913.56522.71422.7140.0000.0000.0000.000
96A116THR00.001-0.00715.178-1.004-1.0040.0000.0000.0000.000
97A117GLN00.0060.01617.484-0.134-0.1340.0000.0000.0000.000
98A118GLY00.0190.01819.972-0.384-0.3840.0000.0000.0000.000
99A119ALA00.0020.01017.295-0.131-0.1310.0000.0000.0000.000
100A120SER0-0.073-0.03219.1300.4910.4910.0000.0000.0000.000
101A121ILE00.0140.01516.285-0.249-0.2490.0000.0000.0000.000
102A122VAL0-0.062-0.02918.6990.8770.8770.0000.0000.0000.000
103A123PRO0-0.013-0.00521.239-0.400-0.4000.0000.0000.0000.000
104A124ASN0-0.032-0.03019.6660.1750.1750.0000.0000.0000.000
105A125GLY00.0460.03023.1370.6240.6240.0000.0000.0000.000
106A126SER0-0.067-0.04623.1950.4890.4890.0000.0000.0000.000
107A127LEU0-0.044-0.03019.0420.1660.1660.0000.0000.0000.000
108A128GLU-1-0.903-0.94823.170-11.617-11.6170.0000.0000.0000.000
109A129PHE0-0.031-0.02025.5610.2080.2080.0000.0000.0000.000
110A130MET0-0.0140.00823.0870.2780.2780.0000.0000.0000.000
111A131PHE0-0.030-0.01517.512-0.546-0.5460.0000.0000.0000.000
112A132ASN0-0.0060.01122.3800.9470.9470.0000.0000.0000.000
113A133ARG10.7570.85116.72116.50316.5030.0000.0000.0000.000
114A134LYS10.8110.86821.00612.75012.7500.0000.0000.0000.000
115A135SER0-0.058-0.04920.530-0.949-0.9490.0000.0000.0000.000
116A136VAL0-0.042-0.02017.6030.2680.2680.0000.0000.0000.000
117A137PHE00.0020.00018.711-0.767-0.7670.0000.0000.0000.000
118A138GLU-1-0.793-0.86614.934-19.914-19.9140.0000.0000.0000.000
119A139CYS0-0.032-0.02219.0810.2090.2090.0000.0000.0000.000
120A140LEU00.0220.02319.052-0.093-0.0930.0000.0000.0000.000
121A141LYS10.8800.94321.56711.21011.2100.0000.0000.0000.000
122A142ASN0-0.017-0.03523.2900.7790.7790.0000.0000.0000.000
123A143GLU-1-0.878-0.93923.931-10.625-10.6250.0000.0000.0000.000
124A144VAL0-0.001-0.00526.0850.3370.3370.0000.0000.0000.000
125A145GLU-1-0.858-0.92728.602-9.817-9.8170.0000.0000.0000.000
126A146ASN0-0.130-0.06028.2000.6780.6780.0000.0000.0000.000
127A147LEU0-0.083-0.03928.9600.3320.3320.0000.0000.0000.000
128A148LYS10.8700.93632.7408.1158.1150.0000.0000.0000.000
129A149LEU0-0.0310.00231.1940.3050.3050.0000.0000.0000.000
130A150SER0-0.032-0.04032.710-0.263-0.2630.0000.0000.0000.000
131A151LEU00.0270.00428.384-0.151-0.1510.0000.0000.0000.000
132A152GLU-1-0.840-0.93331.424-9.068-9.0680.0000.0000.0000.000
133A153ASP-1-0.875-0.90734.521-8.287-8.2870.0000.0000.0000.000
134A154LEU0-0.040-0.02126.867-0.011-0.0110.0000.0000.0000.000
135A155GLU-1-0.915-0.96430.897-9.947-9.9470.0000.0000.0000.000
136A156PHE0-0.020-0.01431.8540.1020.1020.0000.0000.0000.000
137A157ALA0-0.031-0.02333.6960.0880.0880.0000.0000.0000.000
138A158LEU0-0.012-0.01327.995-0.087-0.0870.0000.0000.0000.000
139A159ILE0-0.0030.01331.801-0.173-0.1730.0000.0000.0000.000
140A160ASP-1-0.946-0.96933.863-8.325-8.3250.0000.0000.0000.000
141A161TYR0-0.114-0.06230.9960.1400.1400.0000.0000.0000.000
142A162GLY0-0.010-0.01030.559-0.323-0.3230.0000.0000.0000.000
143A163LEU0-0.032-0.00328.043-0.436-0.4360.0000.0000.0000.000
144A164GLU-1-0.865-0.93027.087-11.267-11.2670.0000.0000.0000.000
145A165GLU-1-0.879-0.93123.899-13.004-13.0040.0000.0000.0000.000
146A166LEU00.0220.00025.839-0.334-0.3340.0000.0000.0000.000
147A167GLU-1-0.840-0.89520.747-14.574-14.5740.0000.0000.0000.000
148A168GLU-1-0.881-0.95923.364-11.399-11.3990.0000.0000.0000.000
149A169VAL0-0.030-0.02417.309-0.307-0.3070.0000.0000.0000.000
150A170GLU-1-0.913-0.97320.240-12.852-12.8520.0000.0000.0000.000
151A171ASP-1-0.875-0.91519.612-13.922-13.9220.0000.0000.0000.000
152A172LYS10.8170.90614.57118.79018.7900.0000.0000.0000.000
153A173ILE00.0470.03220.9770.1670.1670.0000.0000.0000.000
154A174ILE0-0.053-0.03417.428-0.779-0.7790.0000.0000.0000.000
155A175ILE00.0380.02121.2990.5520.5520.0000.0000.0000.000
156A176ARG10.7540.85018.33814.38114.3810.0000.0000.0000.000
157A177GLY00.1180.06023.6950.6650.6650.0000.0000.0000.000
158A178ASP-1-0.758-0.86624.733-12.173-12.1730.0000.0000.0000.000
159A179TYR0-0.0190.01222.878-0.361-0.3610.0000.0000.0000.000
160A180ASN0-0.077-0.05725.0410.0550.0550.0000.0000.0000.000
161A181SER0-0.027-0.00727.3790.3700.3700.0000.0000.0000.000
162A182PHE0-0.0040.02020.5760.1110.1110.0000.0000.0000.000
163A183LYS10.7960.86625.5999.6419.6410.0000.0000.0000.000
164A184LEU0-0.0100.01827.7340.0720.0720.0000.0000.0000.000
165A185LEU00.0920.03925.1730.1230.1230.0000.0000.0000.000
166A186ASN0-0.072-0.04823.237-0.467-0.4670.0000.0000.0000.000
167A187GLU-1-0.787-0.87926.124-9.299-9.2990.0000.0000.0000.000
168A188GLY00.0650.05129.4850.3680.3680.0000.0000.0000.000
169A189PHE00.026-0.00524.2290.1760.1760.0000.0000.0000.000
170A190GLU-1-0.944-0.96027.223-10.604-10.6040.0000.0000.0000.000
171A191SER0-0.091-0.05629.4150.4300.4300.0000.0000.0000.000
172A192LEU00.002-0.00430.2190.3260.3260.0000.0000.0000.000
173A193LYS10.7910.89729.9488.8878.8870.0000.0000.0000.000
174A194LEU00.0370.03925.918-0.004-0.0040.0000.0000.0000.000
175A195PRO0-0.024-0.02523.280-0.333-0.3330.0000.0000.0000.000
176A196ILE00.0010.02919.386-0.256-0.2560.0000.0000.0000.000
177A197LEU0-0.028-0.01615.918-0.072-0.0720.0000.0000.0000.000
178A198LYS10.8250.89012.04721.13821.1380.0000.0000.0000.000
179A199ALA00.0370.03416.5100.6700.6700.0000.0000.0000.000
180A200SER0-0.054-0.03315.305-1.281-1.2810.0000.0000.0000.000
181A201LEU00.0350.02417.2460.8010.8010.0000.0000.0000.000
182A202GLN00.0270.02314.790-0.967-0.9670.0000.0000.0000.000
183A203ARG10.8350.89716.44918.59818.5980.0000.0000.0000.000
184A204ILE00.0580.03017.319-1.042-1.0420.0000.0000.0000.000
185A205ALA00.0210.01019.6790.7780.7780.0000.0000.0000.000
186A206THR0-0.027-0.02521.3670.1880.1880.0000.0000.0000.000
187A207THR0-0.080-0.04824.0670.6990.6990.0000.0000.0000.000
188A208PRO00.0150.02020.808-0.273-0.2730.0000.0000.0000.000
189A209ILE0-0.066-0.02420.1550.8080.8080.0000.0000.0000.000
190A210GLU-1-0.897-0.92820.139-13.674-13.6740.0000.0000.0000.000
191A211LEU0-0.060-0.04316.9580.2770.2770.0000.0000.0000.000
192A212ASN0-0.010-0.00220.502-0.635-0.6350.0000.0000.0000.000
193A213ASP-1-0.830-0.93318.728-15.664-15.6640.0000.0000.0000.000
194A214GLU-1-0.917-0.95317.979-14.194-14.1940.0000.0000.0000.000
195A215GLN0-0.014-0.01918.501-0.760-0.7600.0000.0000.0000.000
196A216MET00.0220.04214.028-1.141-1.1410.0000.0000.0000.000
197A217GLU-1-0.817-0.88813.938-20.535-20.5350.0000.0000.0000.000
198A218LEU0-0.091-0.06213.924-1.219-1.2190.0000.0000.0000.000
199A219THR0-0.043-0.03813.176-0.460-0.4600.0000.0000.0000.000
200A220GLU-1-0.861-0.9489.885-26.768-26.7680.0000.0000.0000.000
201A221LYS10.8200.9158.96018.97018.9700.0000.0000.0000.000
202A222LEU0-0.083-0.03610.492-0.624-0.6240.0000.0000.0000.000
203A223LEU00.017-0.0058.218-2.024-2.0240.0000.0000.0000.000
204A224ASP-1-0.844-0.9164.549-52.263-52.216-0.001-0.002-0.0440.000
205A225ARG10.7270.8414.43416.77216.860-0.001-0.009-0.0780.000
206A226ILE0-0.026-0.0096.768-0.425-0.4250.0000.0000.0000.000
207A227GLU-1-0.816-0.9192.913-56.052-54.7110.070-0.667-0.744-0.004
208A228ASP-1-0.895-0.9301.638-165.420-170.35029.278-14.875-9.474-0.170
209A229ASP-1-0.792-0.8513.008-20.518-21.6100.1301.246-0.284-0.001
210A230ASP-1-0.872-0.9514.651-41.292-41.177-0.001-0.006-0.1070.000
211A231ASP-1-0.855-0.8806.732-20.316-20.3160.0000.0000.0000.000
212A232VAL00.002-0.0026.7593.3603.3600.0000.0000.0000.000
213A233VAL0-0.052-0.0417.100-4.591-4.5910.0000.0000.0000.000
214A234ALA00.0060.0128.798-0.141-0.1410.0000.0000.0000.000
215A235LEU00.0050.0077.2121.9171.9170.0000.0000.0000.000
216A236TYR00.0110.0089.8950.1550.1550.0000.0000.0000.000
217A237THR00.009-0.00912.4440.5340.5340.0000.0000.0000.000
218A238ASN00.0230.01015.225-0.515-0.5150.0000.0000.0000.000
219A239ILE00.004-0.00113.6500.8460.8460.0000.0000.0000.000
220A240GLU-1-0.940-0.96916.581-16.143-16.1430.0000.0000.0000.000