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: Z625N

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2526980.280068
FMO2-HF: Nuclear repulsion 2440419.096401
FMO2-HF: Total energy -86561.183667
FMO2-MP2: Total energy -86813.378459


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.
-229.947-224.9460.505-2.322-3.1820.004
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 : 1.031 / q_NPA : 1.007
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].
3A23PHE00.0320.0083.8260.8203.789-0.025-1.503-1.441-0.002
4A24PRO00.0320.0052.870-0.1401.2300.518-0.705-1.1820.006
5A25LYS10.9400.9733.13246.41746.9210.014-0.107-0.4110.000
6A26LEU00.0140.0206.5192.2732.2730.0000.0000.0000.000
7A27ALA0-0.025-0.0148.0842.0632.0630.0000.0000.0000.000
8A28LYS10.8980.9647.51924.24424.2440.0000.0000.0000.000
9A29ALA00.0550.02910.7181.1981.1980.0000.0000.0000.000
10A30ILE0-0.042-0.02112.7401.2201.2200.0000.0000.0000.000
11A31THR0-0.045-0.02613.1890.9840.9840.0000.0000.0000.000
12A32LEU00.0170.00514.8100.6740.6740.0000.0000.0000.000
13A33ALA00.0240.01816.6610.6620.6620.0000.0000.0000.000
14A34ALA0-0.0120.00618.3390.6550.6550.0000.0000.0000.000
15A35LYS10.8870.94619.36112.08812.0880.0000.0000.0000.000
16A36ASP-1-1.011-0.99321.045-12.271-12.2710.0000.0000.0000.000
17A37GLY00.0470.01123.312-0.032-0.0320.0000.0000.0000.000
18A38GLY0-0.0210.01023.8530.3590.3590.0000.0000.0000.000
19A39SER0-0.024-0.02722.635-0.434-0.4340.0000.0000.0000.000
20A40GLU-1-0.844-0.92523.643-9.877-9.8770.0000.0000.0000.000
21A41PRO0-0.008-0.01722.429-0.032-0.0320.0000.0000.0000.000
22A42ASP-1-0.919-0.95724.590-9.806-9.8060.0000.0000.0000.000
23A43THR0-0.034-0.01827.5890.1600.1600.0000.0000.0000.000
24A44ASN0-0.0400.01122.224-0.120-0.1200.0000.0000.0000.000
25A45ALA00.015-0.01723.787-0.339-0.3390.0000.0000.0000.000
26A46LYS11.0241.00220.13013.14013.1400.0000.0000.0000.000
27A47LEU00.0260.02618.535-0.797-0.7970.0000.0000.0000.000
28A48ARG10.9000.94919.20510.60210.6020.0000.0000.0000.000
29A49THR00.0220.02017.928-0.338-0.3380.0000.0000.0000.000
30A50ALA0-0.007-0.00115.137-0.804-0.8040.0000.0000.0000.000
31A51ILE0-0.043-0.03115.125-0.834-0.8340.0000.0000.0000.000
32A52LEU0-0.011-0.00316.437-0.383-0.3830.0000.0000.0000.000
33A53ASN00.0250.00812.953-0.339-0.3390.0000.0000.0000.000
34A54ALA00.001-0.00911.656-1.115-1.1150.0000.0000.0000.000
35A55LYS10.8660.92812.30613.16713.1670.0000.0000.0000.000
36A56ALA00.0040.01314.392-0.074-0.0740.0000.0000.0000.000
37A57GLN00.1700.1178.221-2.435-2.4350.0000.0000.0000.000
38A58ASN0-0.171-0.0839.8450.0380.0380.0000.0000.0000.000
39A59MET0-0.081-0.0358.7520.6670.6670.0000.0000.0000.000
40A60PRO00.0080.01011.1651.2471.2470.0000.0000.0000.000
41A61LYS11.0140.99714.13711.92611.9260.0000.0000.0000.000
42A62ASP-1-0.882-0.95316.957-12.710-12.7100.0000.0000.0000.000
43A63ASN0-0.043-0.01911.789-0.387-0.3870.0000.0000.0000.000
44A64ILE00.0780.03413.9610.1400.1400.0000.0000.0000.000
45A65ASP-1-0.900-0.93515.197-11.706-11.7060.0000.0000.0000.000
46A66ALA00.013-0.00514.4250.3890.3890.0000.0000.0000.000
47A67ALA0-0.067-0.03712.9230.0200.0200.0000.0000.0000.000
48A68ILE00.0120.01014.7540.2280.2280.0000.0000.0000.000
49A69LYS10.8340.89918.27611.96911.9690.0000.0000.0000.000
50A70ARG10.9420.99411.93016.39416.3940.0000.0000.0000.000
51A71ALA00.0750.04417.6790.1320.1320.0000.0000.0000.000
52A72SER0-0.042-0.01619.3470.4060.4060.0000.0000.0000.000
53A73SER0-0.015-0.01518.9470.3150.3150.0000.0000.0000.000
54A74LYS10.8890.94320.19410.70710.7070.0000.0000.0000.000
55A75GLU-1-0.874-0.94615.562-13.687-13.6870.0000.0000.0000.000
56A76GLY0-0.0110.00315.876-0.732-0.7320.0000.0000.0000.000
57A77ASN0-0.083-0.04618.0180.4240.4240.0000.0000.0000.000
58A78LEU00.0120.00612.627-0.172-0.1720.0000.0000.0000.000
59A79SER0-0.021-0.00816.0860.6790.6790.0000.0000.0000.000
60A80GLU-1-0.895-0.95215.852-17.112-17.1120.0000.0000.0000.000
61A81ILE0-0.057-0.02716.3830.9850.9850.0000.0000.0000.000
62A82THR0-0.012-0.00716.635-0.983-0.9830.0000.0000.0000.000
63A83TYR00.0080.00416.2401.0021.0020.0000.0000.0000.000
64A84GLU-1-0.729-0.86518.519-14.117-14.1170.0000.0000.0000.000
65A85GLY00.008-0.00319.1070.3500.3500.0000.0000.0000.000
66A86LYS10.9380.99419.95412.21212.2120.0000.0000.0000.000
67A87ALA00.0350.00518.427-0.254-0.2540.0000.0000.0000.000
68A88ASN00.009-0.00220.4330.7970.7970.0000.0000.0000.000
69A89PHE00.0190.00419.890-0.175-0.1750.0000.0000.0000.000
70A90GLY00.0170.02722.891-0.007-0.0070.0000.0000.0000.000
71A91VAL00.0520.04816.974-0.063-0.0630.0000.0000.0000.000
72A92LEU0-0.075-0.04019.6200.4800.4800.0000.0000.0000.000
73A93ILE00.016-0.00814.437-0.706-0.7060.0000.0000.0000.000
74A94ILE00.0040.00016.2091.0081.0080.0000.0000.0000.000
75A95MET0-0.041-0.01613.296-1.370-1.3700.0000.0000.0000.000
76A96GLU-1-0.830-0.89113.849-17.128-17.1280.0000.0000.0000.000
77A97CYS0-0.020-0.00512.080-2.175-2.1750.0000.0000.0000.000
78A98MET00.0200.02411.3331.2931.2930.0000.0000.0000.000
79A99THR0-0.025-0.01511.358-0.985-0.9850.0000.0000.0000.000
80A100ASP-1-0.842-0.91113.553-15.534-15.5340.0000.0000.0000.000
81A101ASN0-0.002-0.03315.6701.0621.0620.0000.0000.0000.000
82A102PRO00.0640.03316.783-0.488-0.4880.0000.0000.0000.000
83A103THR0-0.0100.00118.364-0.177-0.1770.0000.0000.0000.000
84A104ARG10.8180.91112.50317.93117.9310.0000.0000.0000.000
85A105THR00.0270.01713.485-0.022-0.0220.0000.0000.0000.000
86A106ILE0-0.014-0.00115.392-0.430-0.4300.0000.0000.0000.000
87A107ALA0-0.019-0.01218.5290.1200.1200.0000.0000.0000.000
88A108ASN00.0410.02113.2270.8770.8770.0000.0000.0000.000
89A109LEU00.0550.04313.504-0.316-0.3160.0000.0000.0000.000
90A110LYS10.8910.95316.31013.96513.9650.0000.0000.0000.000
91A111SER0-0.047-0.01516.7180.4080.4080.0000.0000.0000.000
92A112TYR0-0.039-0.03911.4940.3110.3110.0000.0000.0000.000
93A113PHE00.0910.03015.4470.1520.1520.0000.0000.0000.000
94A114ASN0-0.057-0.03318.2761.2891.2890.0000.0000.0000.000
95A115LYS10.8670.93714.70120.59520.5950.0000.0000.0000.000
96A116THR0-0.078-0.02717.308-0.385-0.3850.0000.0000.0000.000
97A117GLN00.027-0.00319.3870.0520.0520.0000.0000.0000.000
98A118GLY00.0090.00722.177-0.220-0.2200.0000.0000.0000.000
99A119ALA0-0.0070.01719.008-0.005-0.0050.0000.0000.0000.000
100A120SER0-0.091-0.04121.0690.4590.4590.0000.0000.0000.000
101A121ILE00.0340.01620.106-0.156-0.1560.0000.0000.0000.000
102A122VAL0-0.064-0.04521.4940.7130.7130.0000.0000.0000.000
103A123PRO0-0.025-0.00923.757-0.338-0.3380.0000.0000.0000.000
104A124ASN00.027-0.00622.258-0.228-0.2280.0000.0000.0000.000
105A125GLY00.0190.01225.3650.5180.5180.0000.0000.0000.000
106A126SER0-0.067-0.04325.4730.4290.4290.0000.0000.0000.000
107A127LEU0-0.079-0.04920.8150.1870.1870.0000.0000.0000.000
108A128GLU-1-0.927-0.95725.072-10.771-10.7710.0000.0000.0000.000
109A129PHE0-0.051-0.03627.4420.2320.2320.0000.0000.0000.000
110A130MET0-0.0140.00624.6430.2560.2560.0000.0000.0000.000
111A131PHE0-0.034-0.01018.667-0.427-0.4270.0000.0000.0000.000
112A132ASN00.0250.02222.9650.8130.8130.0000.0000.0000.000
113A133ARG10.8990.95819.60614.26814.2680.0000.0000.0000.000
114A134LYS10.9250.93421.34613.02713.0270.0000.0000.0000.000
115A135SER0-0.084-0.04020.663-0.916-0.9160.0000.0000.0000.000
116A136VAL0-0.012-0.00717.2660.3240.3240.0000.0000.0000.000
117A137PHE0-0.009-0.02318.449-0.741-0.7410.0000.0000.0000.000
118A138GLU-1-0.910-0.94614.027-21.452-21.4520.0000.0000.0000.000
119A139CYS0-0.026-0.01818.3180.2980.2980.0000.0000.0000.000
120A140LEU00.0820.04617.792-0.361-0.3610.0000.0000.0000.000
121A141LYS10.9270.96621.00512.23112.2310.0000.0000.0000.000
122A142ASN00.030-0.00223.2760.4190.4190.0000.0000.0000.000
123A143GLU-1-0.918-0.96722.656-11.896-11.8960.0000.0000.0000.000
124A144VAL0-0.017-0.02025.1730.4770.4770.0000.0000.0000.000
125A145GLU-1-0.921-0.97027.616-10.649-10.6490.0000.0000.0000.000
126A146ASN0-0.0190.01827.9350.5920.5920.0000.0000.0000.000
127A147LEU0-0.128-0.04728.4230.4040.4040.0000.0000.0000.000
128A148LYS10.8630.91932.0688.6588.6580.0000.0000.0000.000
129A149LEU0-0.0030.01730.1700.3130.3130.0000.0000.0000.000
130A150SER0-0.018-0.00931.509-0.342-0.3420.0000.0000.0000.000
131A151LEU00.0290.00027.017-0.092-0.0920.0000.0000.0000.000
132A152GLU-1-0.869-0.94330.488-9.399-9.3990.0000.0000.0000.000
133A153ASP-1-0.895-0.94633.697-8.577-8.5770.0000.0000.0000.000
134A154LEU0-0.057-0.03126.3240.0100.0100.0000.0000.0000.000
135A155GLU-1-0.910-0.95930.428-10.408-10.4080.0000.0000.0000.000
136A156PHE0-0.042-0.02931.3160.1590.1590.0000.0000.0000.000
137A157ALA0-0.024-0.01132.8020.1300.1300.0000.0000.0000.000
138A158LEU00.003-0.01427.3110.0520.0520.0000.0000.0000.000
139A159ILE0-0.0120.02031.135-0.169-0.1690.0000.0000.0000.000
140A160ASP-1-0.936-0.95533.159-8.439-8.4390.0000.0000.0000.000
141A161TYR0-0.131-0.08730.6840.1020.1020.0000.0000.0000.000
142A162GLY00.002-0.02429.713-0.349-0.3490.0000.0000.0000.000
143A163LEU0-0.0490.00327.541-0.333-0.3330.0000.0000.0000.000
144A164GLU-1-0.915-0.96227.169-11.197-11.1970.0000.0000.0000.000
145A165GLU-1-0.925-0.97924.456-12.956-12.9560.0000.0000.0000.000
146A166LEU00.0160.00825.054-0.453-0.4530.0000.0000.0000.000
147A167GLU-1-0.861-0.92520.331-15.215-15.2150.0000.0000.0000.000
148A168GLU-1-0.905-0.97722.576-12.370-12.3700.0000.0000.0000.000
149A169VAL0-0.049-0.03016.141-0.383-0.3830.0000.0000.0000.000
150A170GLU-1-0.922-0.98018.793-14.483-14.4830.0000.0000.0000.000
151A171ASP-1-0.911-0.93918.691-16.405-16.4050.0000.0000.0000.000
152A172LYS10.8910.95813.66221.31121.3110.0000.0000.0000.000
153A173ILE0-0.006-0.00120.0060.1980.1980.0000.0000.0000.000
154A174ILE0-0.027-0.01216.961-0.573-0.5730.0000.0000.0000.000
155A175ILE00.0420.02420.5110.5240.5240.0000.0000.0000.000
156A176ARG10.8300.91918.04115.14715.1470.0000.0000.0000.000
157A177GLY00.1320.06623.2800.6510.6510.0000.0000.0000.000
158A178ASP-1-0.860-0.91724.598-11.886-11.8860.0000.0000.0000.000
159A179TYR00.0030.00722.933-0.432-0.4320.0000.0000.0000.000
160A180ASN0-0.035-0.03425.158-0.248-0.2480.0000.0000.0000.000
161A181SER0-0.0130.00027.6150.3930.3930.0000.0000.0000.000
162A182PHE00.0000.02020.2850.0510.0510.0000.0000.0000.000
163A183LYS10.9470.95725.4069.9309.9300.0000.0000.0000.000
164A184LEU0-0.0060.02427.5160.0270.0270.0000.0000.0000.000
165A185LEU00.1070.05125.0120.0700.0700.0000.0000.0000.000
166A186ASN0-0.053-0.03322.726-0.339-0.3390.0000.0000.0000.000
167A187GLU-1-0.937-0.96526.141-9.185-9.1850.0000.0000.0000.000
168A188GLY00.0550.03329.6310.2300.2300.0000.0000.0000.000
169A189PHE00.017-0.01323.8960.1340.1340.0000.0000.0000.000
170A190GLU-1-0.982-0.98426.568-10.940-10.9400.0000.0000.0000.000
171A191SER0-0.100-0.04828.9000.4080.4080.0000.0000.0000.000
172A192LEU0-0.038-0.02229.8720.3010.3010.0000.0000.0000.000
173A193LYS10.8510.93029.2819.1449.1440.0000.0000.0000.000
174A194LEU00.0230.02225.053-0.044-0.0440.0000.0000.0000.000
175A195PRO0-0.026-0.01822.619-0.306-0.3060.0000.0000.0000.000
176A196ILE0-0.0180.00718.788-0.225-0.2250.0000.0000.0000.000
177A197LEU0-0.033-0.00914.724-0.184-0.1840.0000.0000.0000.000
178A198LYS10.9570.95610.43924.49124.4910.0000.0000.0000.000
179A199ALA00.0340.04515.8430.6010.6010.0000.0000.0000.000
180A200SER0-0.085-0.04715.160-1.142-1.1420.0000.0000.0000.000
181A201LEU00.0090.00717.2290.7950.7950.0000.0000.0000.000
182A202GLN00.0070.00413.997-0.300-0.3000.0000.0000.0000.000
183A203ARG10.8090.89517.17817.62617.6260.0000.0000.0000.000
184A204ILE00.0560.02017.874-0.889-0.8890.0000.0000.0000.000
185A205ALA00.0040.00919.8420.7790.7790.0000.0000.0000.000
186A206THR0-0.028-0.02221.7670.0590.0590.0000.0000.0000.000
187A207THR0-0.042-0.02225.0220.4990.4990.0000.0000.0000.000
188A208PRO00.0020.00720.979-0.080-0.0800.0000.0000.0000.000
189A209ILE0-0.055-0.01120.3960.7390.7390.0000.0000.0000.000
190A210GLU-1-0.890-0.93920.393-13.853-13.8530.0000.0000.0000.000
191A211LEU0-0.060-0.03317.3340.5620.5620.0000.0000.0000.000
192A212ASN0-0.0020.01520.304-0.632-0.6320.0000.0000.0000.000
193A213ASP-1-0.832-0.94618.881-16.493-16.4930.0000.0000.0000.000
194A214GLU-1-0.962-0.96818.643-13.704-13.7040.0000.0000.0000.000
195A215GLN0-0.020-0.03719.642-0.748-0.7480.0000.0000.0000.000
196A216MET00.0440.02814.256-0.836-0.8360.0000.0000.0000.000
197A217GLU-1-0.888-0.93114.865-19.292-19.2920.0000.0000.0000.000
198A218LEU0-0.099-0.05615.267-0.835-0.8350.0000.0000.0000.000
199A219THR0-0.067-0.04214.3390.0380.0380.0000.0000.0000.000
200A220GLU-1-0.859-0.94610.085-26.936-26.9360.0000.0000.0000.000
201A221LYS10.9140.97510.61818.66818.6680.0000.0000.0000.000
202A222LEU0-0.100-0.06311.531-1.130-1.1300.0000.0000.0000.000
203A223LEU00.024-0.0019.941-0.325-0.3250.0000.0000.0000.000
204A224ASP-1-0.837-0.9106.758-42.781-42.7810.0000.0000.0000.000
205A225ARG10.7640.8796.87020.40220.4020.0000.0000.0000.000
206A226ILE0-0.024-0.0089.2640.2330.2330.0000.0000.0000.000
207A227GLU-1-0.916-0.9544.598-41.362-41.286-0.001-0.005-0.0700.000
208A228ASP-1-1.031-1.0185.049-50.516-50.5160.0000.0000.0000.000
209A229ASP-1-0.778-0.8576.088-22.699-22.6990.0000.0000.0000.000
210A230ASP-1-0.946-0.9875.042-34.023-33.941-0.001-0.002-0.0780.000
211A231ASP-1-0.906-0.9726.257-19.740-19.7400.0000.0000.0000.000
212A232VAL00.022-0.0078.8022.2352.2350.0000.0000.0000.000
213A233VAL0-0.077-0.0447.947-3.761-3.7610.0000.0000.0000.000
214A234ALA00.0110.0029.372-0.998-0.9980.0000.0000.0000.000
215A235LEU00.0100.0168.8282.4422.4420.0000.0000.0000.000
216A236TYR00.0160.02211.482-0.643-0.6430.0000.0000.0000.000
217A237THR00.0490.01513.1521.2051.2050.0000.0000.0000.000
218A238ASN00.010-0.01815.862-0.504-0.5040.0000.0000.0000.000
219A239ILE0-0.008-0.00614.8070.8940.8940.0000.0000.0000.000
220A240GLU-1-0.961-0.96716.978-16.796-16.7960.0000.0000.0000.000