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: 142GZ

Calculation Name: 3VJP-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VJP

Chain ID: A

ChEMBL ID:

UniProt ID: P40131

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1897309.51719
FMO2-HF: Nuclear repulsion 1822469.284497
FMO2-HF: Total energy -74840.232693
FMO2-MP2: Total energy -75058.264628


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:1:GLN )


Summations of interaction energy for fragment #1(A:1:GLN )
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.
-16.566-11.8821.297-2.303-3.6790.014
Interaction energy analysis for fragmet #1(A:1:GLN )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / 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].
3A3ILE 00.0420.0093.5261.4833.4830.078-0.661-1.4170.004
4A4ASN 00.0660.0262.370-6.817-4.6301.202-1.517-1.8730.010
5A5ALA 00.0600.0513.344-2.329-1.9440.017-0.118-0.2850.000
6A6GLN 00.0400.0155.0320.2550.3670.000-0.007-0.1040.000
7A7LEU 0-0.035-0.0207.299-0.305-0.3050.0000.0000.0000.000
8A8THR 0-0.014-0.0206.362-0.284-0.2840.0000.0000.0000.000
9A9THR 00.0310.0698.655-0.240-0.2400.0000.0000.0000.000
10A10TRP 0-0.003-0.00410.816-0.015-0.0150.0000.0000.0000.000
11A11PHE 0-0.016-0.04011.715-0.081-0.0810.0000.0000.0000.000
12A12SER 0-0.016-0.05811.746-0.060-0.0600.0000.0000.0000.000
13A13GLN 0-0.017-0.00314.391-0.034-0.0340.0000.0000.0000.000
14A14ARG 10.9100.95916.492-0.347-0.3470.0000.0000.0000.000
15A15LEU 0-0.099-0.04215.983-0.008-0.0080.0000.0000.0000.000
16A16ALA 00.1150.06718.9860.0030.0030.0000.0000.0000.000
17A17GLY 0-0.025-0.01020.658-0.007-0.0070.0000.0000.0000.000
18A18PHE 0-0.086-0.04021.3890.0030.0030.0000.0000.0000.000
19A19SER 0-0.059-0.07918.1690.0340.0340.0000.0000.0000.000
20A20ASP -1-0.926-0.95518.5960.2370.2370.0000.0000.0000.000
21A21GLU -1-0.960-0.97114.6280.5080.5080.0000.0000.0000.000
22A22VAL 0-0.018-0.01612.3950.0810.0810.0000.0000.0000.000
23A23VAL 00.0430.0258.2140.0610.0610.0000.0000.0000.000
24A24VAL 0-0.058-0.0258.709-0.052-0.0520.0000.0000.0000.000
25A25THR 0-0.019-0.0016.8081.1861.1860.0000.0000.0000.000
26A26LEU 00.012-0.0086.628-1.172-1.1720.0000.0000.0000.000
27A27ARG 10.9030.9458.355-1.576-1.5760.0000.0000.0000.000
28A28SER 00.0010.00211.088-0.161-0.1610.0000.0000.0000.000
29A29SER 00.0110.00610.8840.3160.3160.0000.0000.0000.000
30A30PRO 00.0410.0007.970-0.237-0.2370.0000.0000.0000.000
31A31ASN 00.0330.02710.004-0.163-0.1630.0000.0000.0000.000
32A32LEU 0-0.029-0.00412.988-0.182-0.1820.0000.0000.0000.000
33A33LEU 0-0.044-0.0218.3910.0530.0530.0000.0000.0000.000
34A34PRO 0-0.006-0.02712.752-0.112-0.1120.0000.0000.0000.000
35A35SER 00.0380.00612.009-0.045-0.0450.0000.0000.0000.000
36A59CYS 0-0.0480.02112.089-0.171-0.1710.0000.0000.0000.000
37A37GLU -1-0.823-0.9077.680-3.606-3.6060.0000.0000.0000.000
38A38GLN 0-0.049-0.0289.029-0.435-0.4350.0000.0000.0000.000
39A39PRO 0-0.004-0.00910.9050.1280.1280.0000.0000.0000.000
40A40ALA 00.0000.01714.0850.0590.0590.0000.0000.0000.000
41A41PHE 00.0300.01010.3450.1130.1130.0000.0000.0000.000
42A42SER 0-0.013-0.00716.231-0.076-0.0760.0000.0000.0000.000
43A43MET 00.0130.00718.0920.1090.1090.0000.0000.0000.000
44A44THR 0-0.043-0.01420.163-0.064-0.0640.0000.0000.0000.000
45A45GLY 0-0.005-0.00722.045-0.001-0.0010.0000.0000.0000.000
46A46SER 0-0.038-0.01623.887-0.008-0.0080.0000.0000.0000.000
47A47ALA 00.0210.02223.131-0.008-0.0080.0000.0000.0000.000
48A48LYS 10.8790.93220.585-0.726-0.7260.0000.0000.0000.000
49A49LEU 00.0040.01920.0310.0040.0040.0000.0000.0000.000
50A50TRP 00.0720.03417.0740.0720.0720.0000.0000.0000.000
51A51GLY 00.0110.00516.958-0.061-0.0610.0000.0000.0000.000
52A52ASN 0-0.034-0.00615.8820.2080.2080.0000.0000.0000.000
53A53VAL 00.0040.02115.625-0.127-0.1270.0000.0000.0000.000
54A54ASN 00.0430.01116.0700.2140.2140.0000.0000.0000.000
55A55VAL 00.010-0.00113.041-0.106-0.1060.0000.0000.0000.000
56A56VAL 0-0.045-0.03416.2490.0270.0270.0000.0000.0000.000
57A57ALA 00.0430.04313.911-0.048-0.0480.0000.0000.0000.000
58A58ARG 10.9320.94815.857-0.153-0.1530.0000.0000.0000.000
59A60ALA 00.0140.03118.2350.0010.0010.0000.0000.0000.000
60A61ASN 00.000-0.02021.5920.0470.0470.0000.0000.0000.000
61A62GLU -1-0.914-0.94516.9510.0460.0460.0000.0000.0000.000
62A63LYS 10.9270.96119.517-0.218-0.2180.0000.0000.0000.000
63A64ARG 10.9310.97216.132-0.259-0.2590.0000.0000.0000.000
64A65TYR 0-0.009-0.01617.129-0.006-0.0060.0000.0000.0000.000
65A66LEU 00.0340.02611.2410.0320.0320.0000.0000.0000.000
66A67GLN 00.0040.00513.888-0.061-0.0610.0000.0000.0000.000
67A68VAL 00.0200.00310.7120.3270.3270.0000.0000.0000.000
68A69ASN 0-0.082-0.07211.359-0.243-0.2430.0000.0000.0000.000
69A70VAL 0-0.0090.00811.4240.2390.2390.0000.0000.0000.000
70A71GLN 00.008-0.01012.537-0.279-0.2790.0000.0000.0000.000
71A72ALA 00.0390.03214.257-0.032-0.0320.0000.0000.0000.000
72A73THR 00.0400.01216.715-0.017-0.0170.0000.0000.0000.000
73A74GLY 00.0550.04819.271-0.038-0.0380.0000.0000.0000.000
74A75ASN 0-0.031-0.01822.4200.0120.0120.0000.0000.0000.000
75A76TYR 00.0040.00426.2000.0140.0140.0000.0000.0000.000
76A77VAL 00.0150.00928.328-0.017-0.0170.0000.0000.0000.000
77A78ALA 0-0.023-0.00931.7790.0130.0130.0000.0000.0000.000
78A79VAL 0-0.008-0.00633.483-0.017-0.0170.0000.0000.0000.000
79A80ALA 0-0.012-0.00636.9280.0060.0060.0000.0000.0000.000
80A81ALA 00.008-0.00338.578-0.005-0.0050.0000.0000.0000.000
81A82PRO 00.0030.00841.8500.0060.0060.0000.0000.0000.000
82A83ILE 0-0.049-0.01840.677-0.009-0.0090.0000.0000.0000.000
83A84ALA 00.0320.02644.4410.0060.0060.0000.0000.0000.000
84A85ARG 10.9360.96046.428-0.142-0.1420.0000.0000.0000.000
85A86GLY 0-0.028-0.00746.635-0.006-0.0060.0000.0000.0000.000
86A87GLY 00.0070.02646.435-0.007-0.0070.0000.0000.0000.000
87A88LYS 10.9600.98044.750-0.095-0.0950.0000.0000.0000.000
88A89LEU 00.0130.02138.1400.0000.0000.0000.0000.0000.000
89A90THR 0-0.075-0.04942.050-0.006-0.0060.0000.0000.0000.000
90A91PRO 00.0680.00140.5000.0060.0060.0000.0000.0000.000
91A92ALA 00.0140.03141.2660.0020.0020.0000.0000.0000.000
92A93ASN 00.006-0.00342.0450.0060.0060.0000.0000.0000.000
93A94VAL 0-0.0060.00936.9330.0130.0130.0000.0000.0000.000
94A95THR 00.0300.01134.318-0.010-0.0100.0000.0000.0000.000
95A96LEU 00.0000.01130.0730.0150.0150.0000.0000.0000.000
96A97LYS 10.9430.97428.584-0.259-0.2590.0000.0000.0000.000
97A98ARG 11.0181.00522.928-0.235-0.2350.0000.0000.0000.000
98A99GLY 0-0.038-0.02724.074-0.008-0.0080.0000.0000.0000.000
99A100ARG 10.8660.88116.726-0.852-0.8520.0000.0000.0000.000
100A101LEU 00.0400.02020.330-0.005-0.0050.0000.0000.0000.000
101A102ASP -1-0.813-0.86417.5300.8730.8730.0000.0000.0000.000
102A103GLN 0-0.075-0.03719.016-0.019-0.0190.0000.0000.0000.000
103A104LEU 0-0.0270.01422.431-0.053-0.0530.0000.0000.0000.000
104A105PRO 00.0150.02525.3340.0250.0250.0000.0000.0000.000
105A106PRO 00.0270.03926.920-0.008-0.0080.0000.0000.0000.000
106A107ARG 10.9300.95727.896-0.312-0.3120.0000.0000.0000.000
107A108THR 00.020-0.03227.695-0.032-0.0320.0000.0000.0000.000
108A109VAL 0-0.040-0.02928.8430.0060.0060.0000.0000.0000.000
109A110LEU 00.0090.00224.9040.0060.0060.0000.0000.0000.000
110A111ASP -1-0.790-0.89428.5920.1480.1480.0000.0000.0000.000
111A112ILE 00.0350.00630.891-0.001-0.0010.0000.0000.0000.000
112A113ARG 10.8840.94731.058-0.135-0.1350.0000.0000.0000.000
113A114GLN 00.003-0.00930.9260.0030.0030.0000.0000.0000.000
114A115ILE 0-0.041-0.01635.314-0.001-0.0010.0000.0000.0000.000
115A116GLN 00.0380.03537.822-0.006-0.0060.0000.0000.0000.000
116A117ASP -1-0.954-1.01040.6570.1020.1020.0000.0000.0000.000
117A118ALA 00.0270.02840.0820.0020.0020.0000.0000.0000.000
118A119VAL 00.000-0.01042.129-0.004-0.0040.0000.0000.0000.000
119A120SER 00.0370.00442.0920.0120.0120.0000.0000.0000.000
120A121LEU 0-0.029-0.01440.876-0.009-0.0090.0000.0000.0000.000
121A122ARG 10.8890.93639.676-0.211-0.2110.0000.0000.0000.000
122A123ASP -1-0.846-0.91843.5100.1430.1430.0000.0000.0000.000
123A124LEU 0-0.056-0.03638.2960.0120.0120.0000.0000.0000.000
124A125ALA 00.0540.03339.770-0.012-0.0120.0000.0000.0000.000
125A126PRO 00.014-0.01238.5290.0090.0090.0000.0000.0000.000
126A127GLY 0-0.013-0.00134.4850.0060.0060.0000.0000.0000.000
127A128GLN 0-0.011-0.00433.1240.0110.0110.0000.0000.0000.000
128A129PRO 00.0280.01229.993-0.011-0.0110.0000.0000.0000.000
129A130VAL 00.0380.02332.157-0.003-0.0030.0000.0000.0000.000
130A131GLN 00.0130.01531.5320.0110.0110.0000.0000.0000.000
131A132LEU 00.004-0.01731.875-0.015-0.0150.0000.0000.0000.000
132A133THR 0-0.040-0.01534.434-0.009-0.0090.0000.0000.0000.000
133A134MET 0-0.052-0.01635.340-0.011-0.0110.0000.0000.0000.000
134A135ILE 0-0.0060.01237.023-0.011-0.0110.0000.0000.0000.000
135A136ARG 10.9720.98340.145-0.124-0.1240.0000.0000.0000.000
136A137GLN 0-0.061-0.03536.8080.0000.0000.0000.0000.0000.000
137A138ALA 00.0350.03841.644-0.002-0.0020.0000.0000.0000.000
138A139TRP 0-0.049-0.04443.094-0.001-0.0010.0000.0000.0000.000
139A140ARG 10.8870.96541.039-0.088-0.0880.0000.0000.0000.000
140A141VAL 00.0380.02543.257-0.008-0.0080.0000.0000.0000.000
141A142LYS 10.9610.96745.354-0.069-0.0690.0000.0000.0000.000
142A143ALA 0-0.0050.00448.610-0.004-0.0040.0000.0000.0000.000
143A144GLY 0-0.016-0.00850.101-0.002-0.0020.0000.0000.0000.000
144A145GLN 00.0110.00248.743-0.002-0.0020.0000.0000.0000.000
145A146ARG 10.9130.96349.590-0.040-0.0400.0000.0000.0000.000
146A147VAL 0-0.003-0.00244.5680.0020.0020.0000.0000.0000.000
147A148GLN 00.0260.00642.326-0.009-0.0090.0000.0000.0000.000
148A149VAL 0-0.041-0.03140.4540.0080.0080.0000.0000.0000.000
149A150ILE 00.0290.01636.446-0.007-0.0070.0000.0000.0000.000
150A151ALA 0-0.003-0.00436.1860.0120.0120.0000.0000.0000.000
151A152ASN 0-0.0170.00232.106-0.023-0.0230.0000.0000.0000.000
152A153GLY 00.0190.00032.3080.0150.0150.0000.0000.0000.000
153A154GLU -1-0.968-0.98828.564-0.055-0.0550.0000.0000.0000.000
154A155GLY 00.0130.01431.059-0.008-0.0080.0000.0000.0000.000
155A156PHE 0-0.047-0.02632.974-0.002-0.0020.0000.0000.0000.000
156A157SER 00.0180.01534.6230.0100.0100.0000.0000.0000.000
157A158VAL 0-0.013-0.00936.816-0.005-0.0050.0000.0000.0000.000
158A159ASN 00.0510.02339.5260.0120.0120.0000.0000.0000.000
159A160ALA 0-0.028-0.01642.166-0.004-0.0040.0000.0000.0000.000
160A161GLU -1-0.852-0.92244.7490.0420.0420.0000.0000.0000.000
161A162GLY 00.0490.01747.102-0.001-0.0010.0000.0000.0000.000
162A163GLN 0-0.082-0.02747.978-0.001-0.0010.0000.0000.0000.000
163A164ALA 00.0450.03946.5990.0040.0040.0000.0000.0000.000
164A165MET 0-0.049-0.04046.869-0.003-0.0030.0000.0000.0000.000
165A166ASN 0-0.021-0.01342.950-0.002-0.0020.0000.0000.0000.000
166A167ASN 00.0150.01246.251-0.006-0.0060.0000.0000.0000.000
167A168ALA 00.0140.01540.9960.0060.0060.0000.0000.0000.000
168A169ALA 0-0.0140.00139.795-0.007-0.0070.0000.0000.0000.000
169A170VAL 00.0640.02235.6990.0020.0020.0000.0000.0000.000
170A171ALA 0-0.062-0.04632.9470.0120.0120.0000.0000.0000.000
171A172GLN 0-0.0250.00334.5130.0050.0050.0000.0000.0000.000
172A173ASN 0-0.029-0.02436.909-0.010-0.0100.0000.0000.0000.000
173A174ALA 00.0100.00638.242-0.003-0.0030.0000.0000.0000.000
174A175ARG 10.9440.96341.117-0.108-0.1080.0000.0000.0000.000
175A176VAL 00.0310.01343.011-0.003-0.0030.0000.0000.0000.000
176A177ARG 10.9480.97245.372-0.060-0.0600.0000.0000.0000.000
177A178MET 00.0250.01144.715-0.001-0.0010.0000.0000.0000.000
178A179THR 00.0670.03148.0340.0000.0000.0000.0000.0000.000
179A180SER 0-0.032-0.01348.5540.0000.0000.0000.0000.0000.000
180A181GLY 00.0110.00751.017-0.001-0.0010.0000.0000.0000.000
181A182GLN 0-0.028-0.00143.1010.0000.0000.0000.0000.0000.000
182A183ILE 0-0.028-0.02544.7720.0020.0020.0000.0000.0000.000
183A184VAL 00.0110.01340.0480.0030.0030.0000.0000.0000.000
184A185SER 0-0.054-0.02538.5490.0060.0060.0000.0000.0000.000
185A186GLY 00.0920.04236.569-0.001-0.0010.0000.0000.0000.000
186A187THR 0-0.049-0.01633.2520.0090.0090.0000.0000.0000.000
187A188VAL 00.0000.01636.136-0.010-0.0100.0000.0000.0000.000
188A189ASP -1-0.740-0.87635.3030.1020.1020.0000.0000.0000.000
189A190SER 0-0.003-0.02436.188-0.002-0.0020.0000.0000.0000.000
190A191ASP -1-0.898-0.93938.0320.0660.0660.0000.0000.0000.000
191A192GLY 0-0.103-0.05540.162-0.006-0.0060.0000.0000.0000.000
192A193ASN 0-0.0030.01239.447-0.006-0.0060.0000.0000.0000.000
193A194ILE 0-0.025-0.01939.1170.0110.0110.0000.0000.0000.000
194A195LEU 00.0010.00733.372-0.007-0.0070.0000.0000.0000.000
195A196ILE 0-0.002-0.02035.1950.0130.0130.0000.0000.0000.000
196A197ASN 0-0.015-0.01127.629-0.025-0.0250.0000.0000.0000.000
197A198LEU 0-0.0050.00028.8610.0100.0100.0000.0000.0000.000
198A199NME 0-0.0200.00233.091-0.010-0.0100.0000.0000.0000.000