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: N1M8Q

Calculation Name: 4UV2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UV2

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEA2

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2626913.380801
FMO2-HF: Nuclear repulsion 2536681.982478
FMO2-HF: Total energy -90231.398323
FMO2-MP2: Total energy -90495.851992


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:18:ALA)


Summations of interaction energy for fragment #1(A:18:ALA)
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.
-21.13-16.4483.867-3.255-5.2940.009
Interaction energy analysis for fragmet #1(A:18:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.025
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].
3A20SER00.0320.0093.470-1.6930.3230.012-0.950-1.0780.000
4A21TYR0-0.011-0.0112.977-0.1470.7150.148-0.280-0.729-0.002
5A22LYS10.8850.9532.615-14.814-14.0962.662-1.463-1.9170.015
6A23ASP-1-0.734-0.8236.587-0.045-0.0450.0000.0000.0000.000
7A24LEU00.0110.0107.5820.1610.1610.0000.0000.0000.000
8A25THR0-0.011-0.0267.8520.2610.2610.0000.0000.0000.000
9A26HIS0-0.125-0.0659.6960.2100.2100.0000.0000.0000.000
10A27LEU0-0.0110.01412.2650.0530.0530.0000.0000.0000.000
11A28PRO00.0110.02814.5350.0220.0220.0000.0000.0000.000
12A29ALA00.0330.00918.366-0.031-0.0310.0000.0000.0000.000
13A30PRO00.0270.02019.5720.0140.0140.0000.0000.0000.000
14A31THR0-0.047-0.04422.5500.0070.0070.0000.0000.0000.000
15A32GLY00.0080.00525.0930.0100.0100.0000.0000.0000.000
16A33LYS10.8480.92018.6150.1850.1850.0000.0000.0000.000
17A34ILE00.0120.01620.9780.0120.0120.0000.0000.0000.000
18A35PHE0-0.012-0.01522.140-0.021-0.0210.0000.0000.0000.000
19A36VAL00.0230.01320.2560.0050.0050.0000.0000.0000.000
20A37SER0-0.062-0.01422.760-0.006-0.0060.0000.0000.0000.000
21A38VAL00.004-0.00218.533-0.003-0.0030.0000.0000.0000.000
22A39TYR0-0.006-0.01421.8360.0200.0200.0000.0000.0000.000
23A40ASN0-0.031-0.03620.700-0.027-0.0270.0000.0000.0000.000
24A41ILE0-0.0080.01314.8010.0020.0020.0000.0000.0000.000
25A42GLN00.0100.01218.834-0.014-0.0140.0000.0000.0000.000
26A43ASP-1-0.773-0.85819.584-0.323-0.3230.0000.0000.0000.000
27A44GLU-1-0.860-0.90620.475-0.212-0.2120.0000.0000.0000.000
28A45THR0-0.056-0.03318.6630.0220.0220.0000.0000.0000.000
29A46GLY00.0040.00722.0440.0190.0190.0000.0000.0000.000
30A47GLN0-0.044-0.01921.1830.0230.0230.0000.0000.0000.000
31A48PHE00.003-0.00922.411-0.019-0.0190.0000.0000.0000.000
32A49LYS10.8810.94816.4110.3020.3020.0000.0000.0000.000
33A50PRO00.0250.02122.7920.0090.0090.0000.0000.0000.000
34A51TYR00.0350.02725.685-0.001-0.0010.0000.0000.0000.000
35A52PRO0-0.027-0.02326.2660.0020.0020.0000.0000.0000.000
36A53ALA0-0.026-0.01024.0530.0000.0000.0000.0000.0000.000
37A54SER00.0150.00626.0470.0080.0080.0000.0000.0000.000
38A55ASN00.0590.01826.499-0.010-0.0100.0000.0000.0000.000
39A56PHE00.0070.01327.144-0.004-0.0040.0000.0000.0000.000
40A57SER0-0.052-0.03922.404-0.014-0.0140.0000.0000.0000.000
41A58THR00.0190.01819.7040.0040.0040.0000.0000.0000.000
42A59ALA0-0.054-0.03219.454-0.015-0.0150.0000.0000.0000.000
43A60VAL00.0470.03114.290-0.030-0.0300.0000.0000.0000.000
44A61PRO00.007-0.00112.4030.0330.0330.0000.0000.0000.000
45A62GLN0-0.032-0.02615.547-0.012-0.0120.0000.0000.0000.000
46A63SER0-0.007-0.02114.2370.0110.0110.0000.0000.0000.000
47A64ALA00.0670.03113.580-0.041-0.0410.0000.0000.0000.000
48A65THR00.0630.03014.331-0.043-0.0430.0000.0000.0000.000
49A66ALA00.0260.02015.0020.0030.0030.0000.0000.0000.000
50A67MET0-0.0230.01010.191-0.063-0.0630.0000.0000.0000.000
51A68LEU00.0520.03411.344-0.070-0.0700.0000.0000.0000.000
52A69VAL00.006-0.00413.7220.0110.0110.0000.0000.0000.000
53A70THR0-0.034-0.03010.1220.0560.0560.0000.0000.0000.000
54A71ALA00.0330.0149.6820.0200.0200.0000.0000.0000.000
55A72LEU00.0220.00710.8840.0570.0570.0000.0000.0000.000
56A73LYS10.9170.96714.1860.3840.3840.0000.0000.0000.000
57A74ASP-1-0.832-0.9059.837-0.609-0.6090.0000.0000.0000.000
58A75SER0-0.034-0.01911.6280.0550.0550.0000.0000.0000.000
59A76ARG10.8620.91912.7020.1950.1950.0000.0000.0000.000
60A77TRP00.0150.01015.8380.0460.0460.0000.0000.0000.000
61A78PHE0-0.0090.00516.3620.0290.0290.0000.0000.0000.000
62A79ILE0-0.054-0.02918.996-0.001-0.0010.0000.0000.0000.000
63A80PRO00.0080.01617.4510.0160.0160.0000.0000.0000.000
64A81LEU0-0.084-0.04120.5180.0160.0160.0000.0000.0000.000
65A82GLU-1-0.806-0.91822.698-0.243-0.2430.0000.0000.0000.000
66A83ARG10.8500.90924.2120.1880.1880.0000.0000.0000.000
67A84GLN00.0650.05121.763-0.004-0.0040.0000.0000.0000.000
68A85GLY00.0220.01225.3940.0100.0100.0000.0000.0000.000
69A86LEU0-0.023-0.01427.3450.0120.0120.0000.0000.0000.000
70A87GLN0-0.002-0.01129.7610.0110.0110.0000.0000.0000.000
71A88ASN00.0360.01728.7810.0160.0160.0000.0000.0000.000
72A89LEU00.0380.02728.2060.0090.0090.0000.0000.0000.000
73A90LEU0-0.019-0.02731.4670.0090.0090.0000.0000.0000.000
74A91ASN00.0170.01734.5490.0120.0120.0000.0000.0000.000
75A92GLU-1-0.826-0.91332.489-0.095-0.0950.0000.0000.0000.000
76A93ARG10.8370.91132.7160.1100.1100.0000.0000.0000.000
77A94LYS10.8450.94036.9530.0940.0940.0000.0000.0000.000
78A95ILE00.0560.03437.2440.0050.0050.0000.0000.0000.000
79A96ILE00.0250.00135.0030.0040.0040.0000.0000.0000.000
80A97ARG10.8690.93039.4180.0800.0800.0000.0000.0000.000
81A98ALA00.0840.05342.5960.0030.0030.0000.0000.0000.000
82A99ALA0-0.036-0.01642.1280.0030.0030.0000.0000.0000.000
83A100GLN0-0.071-0.05540.3650.0040.0040.0000.0000.0000.000
84A101GLU-1-0.932-0.96945.276-0.053-0.0530.0000.0000.0000.000
85A102ASN0-0.015-0.00347.7130.0040.0040.0000.0000.0000.000
86A103GLY0-0.0110.00549.0970.0020.0020.0000.0000.0000.000
87A104THR0-0.050-0.04049.7650.0000.0000.0000.0000.0000.000
88A105VAL0-0.0250.00943.4390.0000.0000.0000.0000.0000.000
89A106ALA00.0320.01344.6570.0020.0020.0000.0000.0000.000
90A107ILE00.0310.00244.027-0.003-0.0030.0000.0000.0000.000
91A108ASN0-0.015-0.01841.773-0.001-0.0010.0000.0000.0000.000
92A109ASN0-0.0050.00139.633-0.001-0.0010.0000.0000.0000.000
93A110ARG10.9260.99039.9580.0440.0440.0000.0000.0000.000
94A111ILE00.013-0.00435.505-0.002-0.0020.0000.0000.0000.000
95A112PRO00.0020.00336.5910.0000.0000.0000.0000.0000.000
96A113LEU0-0.019-0.01335.677-0.005-0.0050.0000.0000.0000.000
97A114GLN00.0400.03433.2010.0010.0010.0000.0000.0000.000
98A115SER00.0370.01035.898-0.002-0.0020.0000.0000.0000.000
99A116LEU0-0.033-0.01430.833-0.003-0.0030.0000.0000.0000.000
100A117THR00.0170.02128.0740.0020.0020.0000.0000.0000.000
101A118ALA00.0100.00529.774-0.008-0.0080.0000.0000.0000.000
102A119ALA00.0280.00726.824-0.001-0.0010.0000.0000.0000.000
103A120ASN0-0.005-0.00228.7910.0060.0060.0000.0000.0000.000
104A121ILE00.0090.01723.4050.0010.0010.0000.0000.0000.000
105A122MET0-0.026-0.00924.780-0.002-0.0020.0000.0000.0000.000
106A123VAL0-0.006-0.00718.7980.0000.0000.0000.0000.0000.000
107A124GLU-1-0.816-0.89220.952-0.216-0.2160.0000.0000.0000.000
108A125GLY00.021-0.00918.569-0.018-0.0180.0000.0000.0000.000
109A126SER0-0.040-0.03118.9140.0140.0140.0000.0000.0000.000
110A127ILE0-0.030-0.01715.494-0.025-0.0250.0000.0000.0000.000
111A128ILE00.0370.01417.8050.0250.0250.0000.0000.0000.000
112A129GLY00.002-0.00318.1500.0310.0310.0000.0000.0000.000
113A130TYR0-0.081-0.07314.698-0.046-0.0460.0000.0000.0000.000
114A131GLU-1-0.875-0.90617.017-0.152-0.1520.0000.0000.0000.000
115A132SER0-0.016-0.03516.145-0.015-0.0150.0000.0000.0000.000
116A133ASN0-0.031-0.01218.2470.0130.0130.0000.0000.0000.000
117A134VAL00.0220.02818.918-0.003-0.0030.0000.0000.0000.000
118A135LYS10.8710.93020.2100.0090.0090.0000.0000.0000.000
119A136SER00.0850.06520.9920.0040.0040.0000.0000.0000.000
120A137GLY00.0670.04022.823-0.003-0.0030.0000.0000.0000.000
121A138GLY0-0.042-0.01322.285-0.011-0.0110.0000.0000.0000.000
122A139VAL00.026-0.00617.7910.0150.0150.0000.0000.0000.000
123A140GLY00.0780.03716.5790.0230.0230.0000.0000.0000.000
124A141ALA00.0020.01117.0620.0320.0320.0000.0000.0000.000
125A142ARG10.9440.97519.440-0.112-0.1120.0000.0000.0000.000
126A143TYR0-0.018-0.01414.6000.0100.0100.0000.0000.0000.000
127A144PHE0-0.0070.00411.5920.0600.0600.0000.0000.0000.000
128A145GLY0-0.0050.02515.7390.0370.0370.0000.0000.0000.000
129A146ILE0-0.038-0.01117.617-0.001-0.0010.0000.0000.0000.000
130A147GLY00.0300.01420.737-0.008-0.0080.0000.0000.0000.000
131A148ALA0-0.046-0.04723.205-0.005-0.0050.0000.0000.0000.000
132A149ASP-1-0.891-0.94625.4670.0160.0160.0000.0000.0000.000
133A150THR0-0.010-0.00721.351-0.004-0.0040.0000.0000.0000.000
134A151GLN0-0.014-0.02921.591-0.005-0.0050.0000.0000.0000.000
135A152TYR0-0.061-0.04316.3070.0120.0120.0000.0000.0000.000
136A153GLN0-0.040-0.03614.2630.0240.0240.0000.0000.0000.000
137A154LEU0-0.026-0.01114.8600.0160.0160.0000.0000.0000.000
138A155ASP-1-0.738-0.83712.023-0.333-0.3330.0000.0000.0000.000
139A156GLN0-0.037-0.01812.341-0.053-0.0530.0000.0000.0000.000
140A157ILE0-0.017-0.00911.4140.0190.0190.0000.0000.0000.000
141A158ALA00.0030.00912.985-0.037-0.0370.0000.0000.0000.000
142A159VAL0-0.024-0.02412.7810.0050.0050.0000.0000.0000.000
143A160ASN0-0.0160.00015.6960.0260.0260.0000.0000.0000.000
144A161LEU0-0.029-0.01213.719-0.019-0.0190.0000.0000.0000.000
145A162ARG10.7840.85818.1840.2620.2620.0000.0000.0000.000
146A163VAL0-0.003-0.01020.985-0.013-0.0130.0000.0000.0000.000
147A164VAL00.0110.00323.5210.0140.0140.0000.0000.0000.000
148A165ASN00.045-0.00127.232-0.006-0.0060.0000.0000.0000.000
149A166VAL0-0.009-0.00829.0510.0060.0060.0000.0000.0000.000
150A167SER0-0.051-0.02631.6260.0080.0080.0000.0000.0000.000
151A168THR0-0.069-0.06633.8330.0040.0040.0000.0000.0000.000
152A169GLY00.0060.01232.3550.0030.0030.0000.0000.0000.000
153A170GLU-1-0.875-0.88831.734-0.107-0.1070.0000.0000.0000.000
154A171ILE0-0.016-0.01925.678-0.007-0.0070.0000.0000.0000.000
155A172LEU0-0.0140.00626.2220.0040.0040.0000.0000.0000.000
156A173SER0-0.039-0.05321.497-0.005-0.0050.0000.0000.0000.000
157A174SER00.0290.00621.790-0.012-0.0120.0000.0000.0000.000
158A175VAL00.0100.02916.5170.0110.0110.0000.0000.0000.000
159A176ASN0-0.026-0.01617.524-0.016-0.0160.0000.0000.0000.000
160A177THR0-0.037-0.01112.2350.0270.0270.0000.0000.0000.000
161A178SER00.017-0.01213.306-0.002-0.0020.0000.0000.0000.000
162A179LYS10.8330.9216.7580.7040.7040.0000.0000.0000.000
163A180THR00.0860.03410.5800.0060.0060.0000.0000.0000.000
164A181ILE0-0.016-0.0016.1400.0500.0500.0000.0000.0000.000
165A182LEU0-0.0260.01410.4460.0120.0120.0000.0000.0000.000
166A183SER0-0.022-0.03310.5190.0380.0380.0000.0000.0000.000
167A184TYR00.0650.02612.2180.0150.0150.0000.0000.0000.000
168A185GLU-1-0.836-0.90913.474-0.020-0.0200.0000.0000.0000.000
169A186VAL0-0.079-0.04213.2410.0230.0230.0000.0000.0000.000
170A187GLN0-0.039-0.02715.2670.0160.0160.0000.0000.0000.000
171A188ALA00.0270.02015.525-0.018-0.0180.0000.0000.0000.000
172A189GLY00.0090.01314.5240.0110.0110.0000.0000.0000.000
173A190VAL0-0.055-0.03110.450-0.019-0.0190.0000.0000.0000.000
174A191PHE00.0390.0169.8570.0230.0230.0000.0000.0000.000
175A192ARG10.8660.9279.211-0.374-0.3740.0000.0000.0000.000
176A193PHE0-0.034-0.0302.874-0.583-0.1700.089-0.121-0.381-0.001
177A194ILE0-0.018-0.0108.5000.2550.2550.0000.0000.0000.000
178A195ASP-1-0.786-0.8727.190-0.585-0.5850.0000.0000.0000.000
179A196TYR0-0.064-0.0419.1500.1160.1160.0000.0000.0000.000
180A204VAL00.0070.0038.662-0.105-0.1050.0000.0000.0000.000
181A205GLY0-0.052-0.0235.7170.3870.3870.0000.0000.0000.000
182A206TYR00.005-0.0135.794-0.606-0.6060.0000.0000.0000.000
183A207THR0-0.023-0.0114.774-0.0930.025-0.001-0.005-0.1130.000
184A208SER00.0540.0266.2900.1220.1220.0000.0000.0000.000
185A209ASN0-0.0060.0076.3060.2720.2720.0000.0000.0000.000
186A210GLU-1-0.848-0.9378.692-0.372-0.3720.0000.0000.0000.000
187A211PRO00.0150.0088.761-0.186-0.1860.0000.0000.0000.000
188A212VAL00.0540.0408.984-0.135-0.1350.0000.0000.0000.000
189A213MET00.0020.0028.663-0.028-0.0280.0000.0000.0000.000
190A214LEU0-0.011-0.0062.428-0.704-0.5360.953-0.307-0.815-0.002
191A215CYS0-0.054-0.0285.598-0.293-0.2930.0000.0000.0000.000
192A216LEU00.0400.0267.976-0.031-0.0310.0000.0000.0000.000
193A217MET0-0.015-0.0195.619-0.112-0.1120.0000.0000.0000.000
194A218SER0-0.008-0.0063.8480.1880.2820.000-0.017-0.0770.000
195A219ALA00.0410.0295.3120.2340.223-0.0010.0000.0130.000
196A220ILE00.0130.0099.0050.1420.1420.0000.0000.0000.000
197A221GLU-1-0.844-0.9103.998-3.892-3.5880.005-0.112-0.197-0.001
198A222THR0-0.034-0.0447.5150.2010.2010.0000.0000.0000.000
199A223GLY00.0360.0279.4320.1370.1370.0000.0000.0000.000
200A224VAL0-0.002-0.01011.5720.1000.1000.0000.0000.0000.000
201A225ILE0-0.026-0.0068.8980.0940.0940.0000.0000.0000.000
202A226PHE00.006-0.00912.9730.0700.0700.0000.0000.0000.000
203A227LEU00.0060.00415.2610.0520.0520.0000.0000.0000.000
204A228ILE0-0.0080.00514.5110.0390.0390.0000.0000.0000.000
205A229ASN00.0240.00115.8920.0710.0710.0000.0000.0000.000
206A230ASP-1-0.764-0.83419.006-0.160-0.1600.0000.0000.0000.000
207A231GLY00.0200.00020.8740.0190.0190.0000.0000.0000.000
208A232ILE0-0.046-0.02719.9670.0200.0200.0000.0000.0000.000
209A233ASP-1-0.828-0.88723.187-0.093-0.0930.0000.0000.0000.000
210A234ARG10.7940.89123.9980.1700.1700.0000.0000.0000.000
211A235GLY0-0.0200.00126.7320.0070.0070.0000.0000.0000.000
212A236LEU0-0.056-0.02525.0260.0030.0030.0000.0000.0000.000
213A237TRP0-0.060-0.03220.209-0.006-0.0060.0000.0000.0000.000
214A238ASP-1-0.862-0.92525.119-0.080-0.0800.0000.0000.0000.000
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