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

tag_button

FMODB ID: 14ZYZ

Calculation Name: 3VJP-A-Xray372

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: 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1895958.940744
FMO2-HF: Nuclear repulsion 1821136.221913
FMO2-HF: Total energy -74822.718831
FMO2-MP2: Total energy -75040.583164


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.
-9.311-5.2521.088-2.02-3.1290.011
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 : 0.009 / q_NPA : -0.006
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].
3A3ILE00.0290.0143.3931.4993.4370.067-0.687-1.3180.004
4A4ASN00.0460.0122.370-3.975-2.2071.019-1.182-1.6060.007
5A5ALA00.0530.0493.745-1.256-0.9030.002-0.151-0.2050.000
6A6GLN00.0070.0025.4970.8650.8650.0000.0000.0000.000
7A7LEU0-0.014-0.0097.587-0.045-0.0450.0000.0000.0000.000
8A8THR00.016-0.0056.834-0.142-0.1420.0000.0000.0000.000
9A9THR0-0.0060.0109.245-0.114-0.1140.0000.0000.0000.000
10A10TRP00.0260.00711.4180.0660.0660.0000.0000.0000.000
11A11PHE0-0.002-0.03212.106-0.002-0.0020.0000.0000.0000.000
12A12SER00.007-0.01112.488-0.014-0.0140.0000.0000.0000.000
13A13GLN0-0.027-0.01414.9940.0000.0000.0000.0000.0000.000
14A14ARG10.8780.93616.992-0.102-0.1020.0000.0000.0000.000
15A15LEU0-0.060-0.02216.1940.0190.0190.0000.0000.0000.000
16A16ALA00.0760.04719.3670.0090.0090.0000.0000.0000.000
17A17GLY0-0.027-0.00120.761-0.001-0.0010.0000.0000.0000.000
18A18PHE0-0.059-0.03321.9320.0070.0070.0000.0000.0000.000
19A19SER0-0.031-0.05718.3670.0310.0310.0000.0000.0000.000
20A20ASP-1-0.809-0.86319.0040.1010.1010.0000.0000.0000.000
21A21GLU-1-0.867-0.89715.3550.3220.3220.0000.0000.0000.000
22A22VAL0-0.010-0.01212.5620.0680.0680.0000.0000.0000.000
23A23VAL00.0170.0138.127-0.025-0.0250.0000.0000.0000.000
24A24VAL0-0.058-0.0328.335-0.042-0.0420.0000.0000.0000.000
25A25THR0-0.0030.0036.5671.1091.1090.0000.0000.0000.000
26A26LEU00.0030.0006.441-1.099-1.0990.0000.0000.0000.000
27A27ARG10.8840.9278.155-1.283-1.2830.0000.0000.0000.000
28A28SER0-0.0020.01310.880-0.202-0.2020.0000.0000.0000.000
29A29SER00.0100.00510.8260.2460.2460.0000.0000.0000.000
30A30PRO00.0640.0237.715-0.191-0.1910.0000.0000.0000.000
31A31ASN00.0100.0009.728-0.189-0.1890.0000.0000.0000.000
32A32LEU0-0.0120.00112.321-0.135-0.1350.0000.0000.0000.000
33A33LEU00.0030.0087.6490.0430.0430.0000.0000.0000.000
34A34PRO0-0.040-0.02712.259-0.067-0.0670.0000.0000.0000.000
35A35SER00.010-0.02312.181-0.098-0.0980.0000.0000.0000.000
36A36CYS0-0.052-0.01612.645-0.116-0.1160.0000.0000.0000.000
37A37GLU-1-0.863-0.9258.605-2.864-2.8640.0000.0000.0000.000
38A38GLN0-0.017-0.0088.932-0.329-0.3290.0000.0000.0000.000
39A39PRO0-0.0190.00111.0870.1730.1730.0000.0000.0000.000
40A40ALA00.0150.00714.0870.0400.0400.0000.0000.0000.000
41A41PHE00.0160.00310.2090.1580.1580.0000.0000.0000.000
42A42SER00.004-0.00716.177-0.060-0.0600.0000.0000.0000.000
43A43MET0-0.0040.00818.6040.0780.0780.0000.0000.0000.000
44A44THR0-0.0100.00020.122-0.035-0.0350.0000.0000.0000.000
45A45GLY0-0.001-0.00721.7590.0050.0050.0000.0000.0000.000
46A46SER0-0.034-0.02523.716-0.007-0.0070.0000.0000.0000.000
47A47ALA00.0040.01923.7020.0010.0010.0000.0000.0000.000
48A48LYS10.8240.90220.290-0.538-0.5380.0000.0000.0000.000
49A49LEU00.0340.02420.391-0.004-0.0040.0000.0000.0000.000
50A50TRP00.0570.02417.2500.0340.0340.0000.0000.0000.000
51A51GLY00.0340.01716.940-0.046-0.0460.0000.0000.0000.000
52A52ASN0-0.0070.00015.8550.1990.1990.0000.0000.0000.000
53A53VAL0-0.0100.01415.651-0.139-0.1390.0000.0000.0000.000
54A54ASN00.0400.01715.9500.1600.1600.0000.0000.0000.000
55A55VAL00.0050.00213.191-0.072-0.0720.0000.0000.0000.000
56A56VAL0-0.031-0.02116.2230.0360.0360.0000.0000.0000.000
57A57ALA00.0140.03214.037-0.054-0.0540.0000.0000.0000.000
58A58ARG10.9540.96115.9930.0310.0310.0000.0000.0000.000
59A60ALA00.0260.01117.7580.0150.0150.0000.0000.0000.000
60A61ASN00.0050.00721.4800.0500.0500.0000.0000.0000.000
61A62GLU-1-0.782-0.83916.717-0.093-0.0930.0000.0000.0000.000
62A63LYS10.9050.93919.310-0.133-0.1330.0000.0000.0000.000
63A64ARG10.8190.89715.503-0.080-0.0800.0000.0000.0000.000
64A65TYR00.0250.00817.606-0.040-0.0400.0000.0000.0000.000
65A66LEU00.0330.03411.0350.0220.0220.0000.0000.0000.000
66A67GLN00.004-0.00913.949-0.026-0.0260.0000.0000.0000.000
67A68VAL00.0270.00810.5300.2840.2840.0000.0000.0000.000
68A69ASN0-0.072-0.05311.250-0.207-0.2070.0000.0000.0000.000
69A70VAL00.0190.02311.1960.2300.2300.0000.0000.0000.000
70A71GLN00.0010.00712.432-0.240-0.2400.0000.0000.0000.000
71A72ALA00.0480.01513.923-0.008-0.0080.0000.0000.0000.000
72A73THR0-0.054-0.04216.659-0.001-0.0010.0000.0000.0000.000
73A74GLY00.0480.03819.425-0.028-0.0280.0000.0000.0000.000
74A75ASN0-0.046-0.01622.5070.0150.0150.0000.0000.0000.000
75A76TYR00.0150.00426.2620.0100.0100.0000.0000.0000.000
76A77VAL00.0020.00028.270-0.012-0.0120.0000.0000.0000.000
77A78ALA0-0.014-0.00231.8040.0140.0140.0000.0000.0000.000
78A79VAL00.0030.00233.597-0.013-0.0130.0000.0000.0000.000
79A80ALA0-0.029-0.01636.9400.0050.0050.0000.0000.0000.000
80A81ALA00.0060.00038.844-0.002-0.0020.0000.0000.0000.000
81A82PRO0-0.005-0.01242.0870.0030.0030.0000.0000.0000.000
82A83ILE0-0.0400.00140.656-0.006-0.0060.0000.0000.0000.000
83A84ALA00.0310.02544.4760.0050.0050.0000.0000.0000.000
84A85ARG10.8570.88546.419-0.105-0.1050.0000.0000.0000.000
85A86GLY0-0.023-0.00146.897-0.004-0.0040.0000.0000.0000.000
86A87GLY0-0.0100.00346.836-0.004-0.0040.0000.0000.0000.000
87A88LYS10.8890.93045.085-0.057-0.0570.0000.0000.0000.000
88A89LEU00.0010.01538.3670.0020.0020.0000.0000.0000.000
89A90THR0-0.027-0.02442.092-0.007-0.0070.0000.0000.0000.000
90A91PRO00.0440.00840.4410.0050.0050.0000.0000.0000.000
91A92ALA00.0170.02341.5160.0000.0000.0000.0000.0000.000
92A93ASN0-0.005-0.01142.0740.0020.0020.0000.0000.0000.000
93A94VAL0-0.0060.00337.0450.0090.0090.0000.0000.0000.000
94A95THR00.0140.01034.433-0.010-0.0100.0000.0000.0000.000
95A96LEU00.0020.00530.1930.0100.0100.0000.0000.0000.000
96A97LYS10.9100.95927.933-0.197-0.1970.0000.0000.0000.000
97A98ARG10.8930.90721.225-0.147-0.1470.0000.0000.0000.000
98A99GLY0-0.037-0.02924.075-0.003-0.0030.0000.0000.0000.000
99A100ARG10.8700.90015.103-0.680-0.6800.0000.0000.0000.000
100A101LEU00.0500.01520.2150.0020.0020.0000.0000.0000.000
101A102ASP-1-0.835-0.88417.7080.6360.6360.0000.0000.0000.000
102A103GLN0-0.062-0.03918.9720.0060.0060.0000.0000.0000.000
103A104LEU0-0.0370.01222.495-0.036-0.0360.0000.0000.0000.000
104A105PRO00.0090.02225.3600.0200.0200.0000.0000.0000.000
105A106PRO00.0310.00327.200-0.013-0.0130.0000.0000.0000.000
106A107ARG10.9390.96328.071-0.222-0.2220.0000.0000.0000.000
107A108THR00.0280.01027.778-0.024-0.0240.0000.0000.0000.000
108A109VAL0-0.053-0.02329.0220.0020.0020.0000.0000.0000.000
109A110LEU0-0.003-0.00425.1650.0080.0080.0000.0000.0000.000
110A111ASP-1-0.774-0.86228.8070.0710.0710.0000.0000.0000.000
111A112ILE00.0680.01431.2020.0020.0020.0000.0000.0000.000
112A113ARG10.8660.91031.690-0.060-0.0600.0000.0000.0000.000
113A114GLN00.0230.00530.8250.0010.0010.0000.0000.0000.000
114A115ILE0-0.011-0.01135.3910.0030.0030.0000.0000.0000.000
115A116GLN00.0140.01138.046-0.008-0.0080.0000.0000.0000.000
116A117ASP-1-0.897-0.94540.6840.0610.0610.0000.0000.0000.000
117A118ALA0-0.0020.01640.2530.0010.0010.0000.0000.0000.000
118A119VAL0-0.002-0.00642.288-0.002-0.0020.0000.0000.0000.000
119A120SER00.033-0.00442.2630.0080.0080.0000.0000.0000.000
120A121LEU0-0.058-0.03341.161-0.007-0.0070.0000.0000.0000.000
121A122ARG10.9060.94539.188-0.157-0.1570.0000.0000.0000.000
122A123ASP-1-0.746-0.82543.8740.1030.1030.0000.0000.0000.000
123A124LEU0-0.051-0.02738.3900.0090.0090.0000.0000.0000.000
124A125ALA00.0410.01839.505-0.009-0.0090.0000.0000.0000.000
125A126PRO00.024-0.00938.2040.0070.0070.0000.0000.0000.000
126A127GLY00.0070.01434.3390.0060.0060.0000.0000.0000.000
127A128GLN0-0.0040.00432.9570.0070.0070.0000.0000.0000.000
128A129PRO00.015-0.00229.877-0.010-0.0100.0000.0000.0000.000
129A130VAL00.0260.02232.071-0.003-0.0030.0000.0000.0000.000
130A131GLN00.002-0.01631.5310.0060.0060.0000.0000.0000.000
131A132LEU00.0250.00032.405-0.010-0.0100.0000.0000.0000.000
132A133THR0-0.045-0.02234.310-0.009-0.0090.0000.0000.0000.000
133A134MET0-0.076-0.02535.181-0.004-0.0040.0000.0000.0000.000
134A135ILE00.0200.02236.946-0.007-0.0070.0000.0000.0000.000
135A136ARG10.9520.97940.377-0.085-0.0850.0000.0000.0000.000
136A137GLN0-0.023-0.02036.9360.0000.0000.0000.0000.0000.000
137A138ALA00.0470.03841.541-0.001-0.0010.0000.0000.0000.000
138A139TRP0-0.027-0.03643.214-0.001-0.0010.0000.0000.0000.000
139A140ARG10.8350.92441.041-0.045-0.0450.0000.0000.0000.000
140A141VAL00.0500.04143.307-0.006-0.0060.0000.0000.0000.000
141A142LYS10.9330.95845.526-0.037-0.0370.0000.0000.0000.000
142A143ALA00.0410.01648.578-0.003-0.0030.0000.0000.0000.000
143A144GLY0-0.020-0.00650.178-0.001-0.0010.0000.0000.0000.000
144A145GLN00.0260.01248.888-0.001-0.0010.0000.0000.0000.000
145A146ARG10.8630.91549.917-0.011-0.0110.0000.0000.0000.000
146A147VAL0-0.006-0.00745.0510.0010.0010.0000.0000.0000.000
147A148GLN00.0370.03142.620-0.006-0.0060.0000.0000.0000.000
148A149VAL0-0.029-0.02240.9880.0060.0060.0000.0000.0000.000
149A150ILE00.0190.00637.437-0.006-0.0060.0000.0000.0000.000
150A151ALA0-0.0010.00736.5490.0070.0070.0000.0000.0000.000
151A152ASN00.0010.01432.678-0.017-0.0170.0000.0000.0000.000
152A153GLY00.0470.01132.1720.0130.0130.0000.0000.0000.000
153A154GLU-1-0.968-0.98028.827-0.120-0.1200.0000.0000.0000.000
154A155GLY00.0210.01631.235-0.003-0.0030.0000.0000.0000.000
155A156PHE0-0.039-0.01533.0590.0020.0020.0000.0000.0000.000
156A157SER0-0.012-0.02734.7460.0070.0070.0000.0000.0000.000
157A158VAL0-0.0040.00637.151-0.003-0.0030.0000.0000.0000.000
158A159ASN0-0.015-0.01340.0320.0090.0090.0000.0000.0000.000
159A160ALA00.0070.00042.353-0.003-0.0030.0000.0000.0000.000
160A161GLU-1-0.751-0.84145.1630.0110.0110.0000.0000.0000.000
161A162GLY00.0450.01347.630-0.001-0.0010.0000.0000.0000.000
162A163GLN0-0.087-0.03948.3810.0000.0000.0000.0000.0000.000
163A164ALA00.0430.03046.7670.0020.0020.0000.0000.0000.000
164A165MET0-0.051-0.03546.925-0.001-0.0010.0000.0000.0000.000
165A166ASN0-0.043-0.02842.912-0.001-0.0010.0000.0000.0000.000
166A167ASN00.0080.01046.451-0.006-0.0060.0000.0000.0000.000
167A168ALA0-0.0040.01341.1480.0050.0050.0000.0000.0000.000
168A169ALA0-0.032-0.00739.872-0.005-0.0050.0000.0000.0000.000
169A170VAL00.0200.01535.8930.0010.0010.0000.0000.0000.000
170A171ALA0-0.025-0.02133.0590.0100.0100.0000.0000.0000.000
171A172GLN0-0.045-0.00434.6560.0030.0030.0000.0000.0000.000
172A173ASN0-0.060-0.03937.273-0.006-0.0060.0000.0000.0000.000
173A174ALA00.0390.01938.5130.0000.0000.0000.0000.0000.000
174A175ARG10.9480.96941.377-0.065-0.0650.0000.0000.0000.000
175A176VAL00.0110.00343.238-0.001-0.0010.0000.0000.0000.000
176A177ARG10.9500.98445.790-0.026-0.0260.0000.0000.0000.000
177A178MET00.0210.01144.5520.0000.0000.0000.0000.0000.000
178A179THR00.022-0.02548.2860.0000.0000.0000.0000.0000.000
179A180SER0-0.023-0.00448.4930.0010.0010.0000.0000.0000.000
180A181GLY0-0.0030.00351.4870.0000.0000.0000.0000.0000.000
181A182GLN0-0.012-0.00343.7230.0010.0010.0000.0000.0000.000
182A183ILE0-0.024-0.01645.3340.0010.0010.0000.0000.0000.000
183A184VAL00.0040.01040.5680.0000.0000.0000.0000.0000.000
184A185SER0-0.055-0.03139.1200.0060.0060.0000.0000.0000.000
185A186GLY00.0920.04536.850-0.003-0.0030.0000.0000.0000.000
186A187THR0-0.037-0.01132.9670.0080.0080.0000.0000.0000.000
187A188VAL00.0140.01336.209-0.008-0.0080.0000.0000.0000.000
188A189ASP-1-0.722-0.84636.1640.0390.0390.0000.0000.0000.000
189A190SER0-0.040-0.06836.7700.0040.0040.0000.0000.0000.000
190A191ASP-1-0.884-0.90638.3860.0230.0230.0000.0000.0000.000
191A192GLY0-0.023-0.01940.720-0.002-0.0020.0000.0000.0000.000
192A193ASN0-0.040-0.01539.376-0.005-0.0050.0000.0000.0000.000
193A194ILE0-0.038-0.02639.5070.0080.0080.0000.0000.0000.000
194A195LEU00.0060.01233.852-0.006-0.0060.0000.0000.0000.000
195A196ILE00.002-0.01035.1400.0110.0110.0000.0000.0000.000
196A197ASN0-0.0060.01028.164-0.020-0.0200.0000.0000.0000.000
197A198LEU0-0.048-0.03129.5350.0050.0050.0000.0000.0000.000