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: P5JVZ

Calculation Name: 3VVV-A-Xray21

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VVV

Chain ID: A

ChEMBL ID:

UniProt ID: Q13137

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 226
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1295011.264792
FMO2-HF: Nuclear repulsion 1239059.547324
FMO2-HF: Total energy -55951.717468
FMO2-MP2: Total energy -56113.266107


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:19:GLY)


Summations of interaction energy for fragment #1(A:19:GLY)
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.
0.9762.9220.036-1.048-0.9340.002
Interaction energy analysis for fragmet #1(A:19:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.029
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].
3A21SER00.0260.0163.815-1.1150.263-0.005-0.750-0.6230.004
4A22GLN00.0250.0215.8540.6730.6730.0000.0000.0000.000
5A23VAL00.0170.0288.2770.4150.4150.0000.0000.0000.000
6A24ILE0-0.012-0.00310.526-0.264-0.2640.0000.0000.0000.000
7A25PHE0-0.004-0.01012.5260.1270.1270.0000.0000.0000.000
8A26ASN0-0.064-0.04215.8300.0140.0140.0000.0000.0000.000
9A27SER00.0580.00719.0490.0300.0300.0000.0000.0000.000
10A28VAL0-0.0310.01617.9320.0200.0200.0000.0000.0000.000
11A29GLU-1-0.808-0.86921.172-0.273-0.2730.0000.0000.0000.000
12A30LYS10.9610.96222.2290.3220.3220.0000.0000.0000.000
13A31PHE0-0.0360.00324.2610.0010.0010.0000.0000.0000.000
14A32TYR00.0520.03622.0560.0020.0020.0000.0000.0000.000
15A33ILE00.0510.01428.1030.0080.0080.0000.0000.0000.000
16A34PRO00.0260.03031.468-0.002-0.0020.0000.0000.0000.000
17A35GLY00.0380.02632.4300.0090.0090.0000.0000.0000.000
18A36GLY0-0.0310.00032.3810.0090.0090.0000.0000.0000.000
19A37ASP-1-0.747-0.86329.984-0.176-0.1760.0000.0000.0000.000
20A38VAL00.0170.01224.134-0.002-0.0020.0000.0000.0000.000
21A39THR00.0140.03924.6700.0050.0050.0000.0000.0000.000
22A40CYS0-0.0570.00518.975-0.032-0.0320.0000.0000.0000.000
23A41HIS00.0690.02720.834-0.006-0.0060.0000.0000.0000.000
24A42TYR0-0.055-0.06415.751-0.073-0.0730.0000.0000.0000.000
25A43THR0-0.0320.00016.0100.0630.0630.0000.0000.0000.000
26A44PHE00.0180.01013.638-0.127-0.1270.0000.0000.0000.000
27A45THR00.012-0.0069.9590.0750.0750.0000.0000.0000.000
28A46GLN00.012-0.01912.5400.0410.0410.0000.0000.0000.000
29A47HIS00.0290.02510.8530.0840.0840.0000.0000.0000.000
30A48PHE0-0.0390.0099.7460.0430.0430.0000.0000.0000.000
31A49ILE00.0100.02711.8160.0450.0450.0000.0000.0000.000
32A50PRO00.0420.05014.1520.0130.0130.0000.0000.0000.000
33A51ARG10.7290.86412.2210.1290.1290.0000.0000.0000.000
34A52ARG10.9070.93817.6130.0820.0820.0000.0000.0000.000
35A53LYS10.9770.99519.3540.0570.0570.0000.0000.0000.000
36A54ASP-1-0.674-0.80414.582-0.346-0.3460.0000.0000.0000.000
37A55TRP0-0.059-0.03515.4390.0060.0060.0000.0000.0000.000
38A56ILE00.0080.01115.206-0.091-0.0910.0000.0000.0000.000
39A57GLY00.0100.00515.9620.0700.0700.0000.0000.0000.000
40A58ILE0-0.0100.00717.069-0.068-0.0680.0000.0000.0000.000
41A59PHE0-0.022-0.00415.1940.0450.0450.0000.0000.0000.000
42A60ARG10.9850.99918.2370.1800.1800.0000.0000.0000.000
43A61VAL0-0.006-0.01616.613-0.029-0.0290.0000.0000.0000.000
44A62GLY00.0090.00415.9730.0550.0550.0000.0000.0000.000
45A63TRP0-0.078-0.01310.7340.0790.0790.0000.0000.0000.000
46A64LYS10.9420.96014.7880.0520.0520.0000.0000.0000.000
47A65THR00.0050.02614.2060.0300.0300.0000.0000.0000.000
48A66THR00.039-0.01412.329-0.007-0.0070.0000.0000.0000.000
49A67ARG10.8800.92315.0800.0410.0410.0000.0000.0000.000
50A68GLU-1-0.813-0.90217.987-0.168-0.1680.0000.0000.0000.000
51A69TYR0-0.051-0.00518.241-0.011-0.0110.0000.0000.0000.000
52A70TYR00.0030.02819.6360.0320.0320.0000.0000.0000.000
53A71THR00.002-0.00421.8210.0360.0360.0000.0000.0000.000
54A72PHE0-0.024-0.01919.848-0.038-0.0380.0000.0000.0000.000
55A73MET0-0.0240.02720.4620.0430.0430.0000.0000.0000.000
56A74TRP00.0020.00319.927-0.036-0.0360.0000.0000.0000.000
57A75VAL0-0.0100.00717.485-0.008-0.0080.0000.0000.0000.000
58A76THR00.026-0.00619.6790.0410.0410.0000.0000.0000.000
59A77LEU0-0.059-0.00221.679-0.003-0.0030.0000.0000.0000.000
60A78PRO00.0280.00024.5220.0060.0060.0000.0000.0000.000
61A79ILE00.0210.00919.145-0.016-0.0160.0000.0000.0000.000
62A80ASP-1-0.881-0.92823.071-0.169-0.1690.0000.0000.0000.000
63A81LEU0-0.002-0.01822.322-0.010-0.0100.0000.0000.0000.000
64A82ASN0-0.012-0.00622.236-0.003-0.0030.0000.0000.0000.000
65A83ASN00.000-0.02920.747-0.017-0.0170.0000.0000.0000.000
66A84LYS10.9270.98817.4180.1930.1930.0000.0000.0000.000
67A85SER00.0070.02416.066-0.008-0.0080.0000.0000.0000.000
68A86ALA0-0.0110.00317.544-0.033-0.0330.0000.0000.0000.000
69A87LYS10.8460.90120.2000.2750.2750.0000.0000.0000.000
70A88GLN00.0450.02720.579-0.060-0.0600.0000.0000.0000.000
71A89GLN00.0150.04519.1250.0530.0530.0000.0000.0000.000
72A90GLU-1-0.838-0.91921.462-0.288-0.2880.0000.0000.0000.000
73A91VAL0-0.0400.00620.4410.0230.0230.0000.0000.0000.000
74A92GLN00.0390.03223.320-0.010-0.0100.0000.0000.0000.000
75A93PHE0-0.012-0.01220.0620.0090.0090.0000.0000.0000.000
76A94LYS10.8250.89426.0060.1620.1620.0000.0000.0000.000
77A95ALA00.0810.02929.215-0.003-0.0030.0000.0000.0000.000
78A96TYR0-0.0230.00631.0370.0000.0000.0000.0000.0000.000
79A97TYR0-0.024-0.01427.1370.0080.0080.0000.0000.0000.000
80A98LEU0-0.0060.01525.498-0.012-0.0120.0000.0000.0000.000
81A99PRO0-0.0110.00124.5070.0180.0180.0000.0000.0000.000
82A100LYS10.8620.93027.7210.1550.1550.0000.0000.0000.000
83A101ASP-1-0.744-0.81327.636-0.182-0.1820.0000.0000.0000.000
84A102ASP-1-0.745-0.86329.177-0.170-0.1700.0000.0000.0000.000
85A103GLU-1-0.834-0.85224.492-0.197-0.1970.0000.0000.0000.000
86A104TYR00.0020.01921.047-0.006-0.0060.0000.0000.0000.000
87A105TYR0-0.034-0.04619.962-0.001-0.0010.0000.0000.0000.000
88A106GLN00.0280.02512.879-0.010-0.0100.0000.0000.0000.000
89A107PHE00.0530.02016.0770.0390.0390.0000.0000.0000.000
90A108CYS0-0.047-0.02311.739-0.160-0.1600.0000.0000.0000.000
91A109TYR0-0.014-0.03111.1910.1350.1350.0000.0000.0000.000
92A110VAL00.0010.00310.491-0.213-0.2130.0000.0000.0000.000
93A111ASP-1-0.697-0.8289.941-0.195-0.1950.0000.0000.0000.000
94A112GLU-1-0.719-0.83512.518-0.023-0.0230.0000.0000.0000.000
95A113ASP-1-0.796-0.86611.6030.1790.1790.0000.0000.0000.000
96A114GLY0-0.0240.00512.4770.0870.0870.0000.0000.0000.000
97A115VAL0-0.0190.0016.1260.0060.0060.0000.0000.0000.000
98A116VAL00.0530.0187.288-0.110-0.1100.0000.0000.0000.000
99A117ARG10.8050.8935.1980.0040.0040.0000.0000.0000.000
100A118GLY00.0420.0107.479-0.329-0.3290.0000.0000.0000.000
101A119ALA00.0270.0149.1730.2170.2170.0000.0000.0000.000
102A120SER0-0.013-0.00111.234-0.085-0.0850.0000.0000.0000.000
103A121ILE0-0.0020.01414.509-0.035-0.0350.0000.0000.0000.000
104A122PRO00.0090.01516.6110.0150.0150.0000.0000.0000.000
105A123PHE00.0050.01418.8650.0140.0140.0000.0000.0000.000
106A124GLN00.012-0.00222.419-0.005-0.0050.0000.0000.0000.000
107A125PHE00.0090.00123.822-0.011-0.0110.0000.0000.0000.000
108A126ARG10.8110.87827.7850.2330.2330.0000.0000.0000.000
109A127PRO00.0180.00831.290-0.009-0.0090.0000.0000.0000.000
110A128GLU-1-0.901-0.93332.503-0.186-0.1860.0000.0000.0000.000
111A129ASN0-0.039-0.02531.4060.0090.0090.0000.0000.0000.000
112A130GLU-1-0.886-0.96434.437-0.134-0.1340.0000.0000.0000.000
113A131GLU-1-0.994-0.98831.642-0.148-0.1480.0000.0000.0000.000
114A132ASP-1-0.803-0.86029.657-0.228-0.2280.0000.0000.0000.000
115A0NME0-0.051-0.01629.9280.0070.0070.0000.0000.0000.000
116A201HOH0-0.020-0.01919.908-0.014-0.0140.0000.0000.0000.000
117A202HOH0-0.005-0.00720.201-0.019-0.0190.0000.0000.0000.000
118A203HOH00.0190.01615.077-0.006-0.0060.0000.0000.0000.000
119A204HOH00.0320.02324.725-0.003-0.0030.0000.0000.0000.000
120A205HOH0-0.029-0.03117.3680.0180.0180.0000.0000.0000.000
121A206HOH0-0.060-0.04323.3060.0110.0110.0000.0000.0000.000
122A208HOH0-0.008-0.00721.044-0.012-0.0120.0000.0000.0000.000
123A209HOH00.0130.00026.023-0.003-0.0030.0000.0000.0000.000
124A210HOH0-0.013-0.00713.3350.0150.0150.0000.0000.0000.000
125A211HOH00.0110.00216.1330.0210.0210.0000.0000.0000.000
126A212HOH00.0210.01324.5030.0020.0020.0000.0000.0000.000
127A213HOH0-0.022-0.01826.395-0.004-0.0040.0000.0000.0000.000
128A214HOH0-0.005-0.01226.5770.0050.0050.0000.0000.0000.000
129A217HOH0-0.013-0.01613.5220.0430.0430.0000.0000.0000.000
130A218HOH0-0.014-0.01133.687-0.003-0.0030.0000.0000.0000.000
131A219HOH0-0.013-0.01823.494-0.015-0.0150.0000.0000.0000.000
132A220HOH0-0.014-0.02326.9730.0050.0050.0000.0000.0000.000
133A221HOH0-0.053-0.04123.2170.0040.0040.0000.0000.0000.000
134A222HOH00.0340.01524.842-0.002-0.0020.0000.0000.0000.000
135A223HOH00.002-0.00112.734-0.022-0.0220.0000.0000.0000.000
136A224HOH00.007-0.00623.397-0.011-0.0110.0000.0000.0000.000
137A225HOH00.0040.00321.5300.0030.0030.0000.0000.0000.000
138A226HOH0-0.002-0.00219.580-0.012-0.0120.0000.0000.0000.000
139A227HOH0-0.023-0.03210.472-0.126-0.1260.0000.0000.0000.000
140A228HOH0-0.056-0.03517.5420.0080.0080.0000.0000.0000.000
141A231HOH0-0.008-0.01110.386-0.032-0.0320.0000.0000.0000.000
142A233HOH00.010-0.00313.7560.0360.0360.0000.0000.0000.000
143A236HOH00.0330.03312.787-0.037-0.0370.0000.0000.0000.000
144A237HOH0-0.017-0.00933.221-0.001-0.0010.0000.0000.0000.000
145A238HOH00.0120.00027.3940.0050.0050.0000.0000.0000.000
146A239HOH0-0.049-0.03525.012-0.005-0.0050.0000.0000.0000.000
147A241HOH00.0130.02012.230-0.016-0.0160.0000.0000.0000.000
148A242HOH0-0.026-0.01330.9080.0030.0030.0000.0000.0000.000
149A243HOH00.0310.01529.367-0.004-0.0040.0000.0000.0000.000
150A244HOH0-0.028-0.03010.4170.0210.0210.0000.0000.0000.000
151A245HOH0-0.002-0.00317.6790.0080.0080.0000.0000.0000.000
152A246HOH0-0.019-0.01912.8480.0310.0310.0000.0000.0000.000
153A247HOH0-0.012-0.01818.5300.0040.0040.0000.0000.0000.000
154A248HOH00.0330.02227.0130.0000.0000.0000.0000.0000.000
155A249HOH00.0210.0186.3520.0010.0010.0000.0000.0000.000
156A251HOH0-0.026-0.02230.0480.0030.0030.0000.0000.0000.000
157A252HOH0-0.009-0.0078.4080.0990.0990.0000.0000.0000.000
158A253HOH0-0.034-0.02829.1570.0030.0030.0000.0000.0000.000
159A254HOH00.0240.02225.473-0.005-0.0050.0000.0000.0000.000
160A255HOH0-0.001-0.00124.269-0.011-0.0110.0000.0000.0000.000
161A256HOH00.0180.02021.0440.0050.0050.0000.0000.0000.000
162A257HOH0-0.097-0.07529.0130.0040.0040.0000.0000.0000.000
163A258HOH0-0.051-0.03719.045-0.006-0.0060.0000.0000.0000.000
164A260HOH0-0.033-0.01616.295-0.008-0.0080.0000.0000.0000.000
165A263HOH00.001-0.01019.1060.0070.0070.0000.0000.0000.000
166A264HOH0-0.030-0.02830.7750.0030.0030.0000.0000.0000.000
167A266HOH0-0.030-0.01522.5020.0060.0060.0000.0000.0000.000
168A267HOH0-0.043-0.02132.2820.0040.0040.0000.0000.0000.000
169A268HOH0-0.056-0.03627.727-0.003-0.0030.0000.0000.0000.000
170A270HOH0-0.048-0.03320.7220.0000.0000.0000.0000.0000.000
171A271HOH0-0.021-0.01525.191-0.002-0.0020.0000.0000.0000.000
172A272HOH00.0150.0109.5830.0900.0900.0000.0000.0000.000
173A273HOH0-0.005-0.0123.7651.0831.1570.000-0.018-0.0560.000
174A275HOH00.002-0.00920.679-0.004-0.0040.0000.0000.0000.000
175A276HOH0-0.047-0.03425.958-0.005-0.0050.0000.0000.0000.000
176A277HOH0-0.040-0.01911.972-0.004-0.0040.0000.0000.0000.000
177A278HOH0-0.014-0.0163.3930.1290.5460.041-0.251-0.207-0.002
178A279HOH00.001-0.00327.653-0.007-0.0070.0000.0000.0000.000
179A280HOH0-0.024-0.02630.9590.0030.0030.0000.0000.0000.000
180A281HOH0-0.014-0.02631.1970.0050.0050.0000.0000.0000.000
181A282HOH0-0.027-0.02526.1240.0050.0050.0000.0000.0000.000
182A283HOH0-0.038-0.02425.7110.0060.0060.0000.0000.0000.000
183A284HOH0-0.022-0.02033.3170.0030.0030.0000.0000.0000.000
184A285HOH0-0.040-0.02533.070-0.001-0.0010.0000.0000.0000.000
185A286HOH00.0080.01226.573-0.010-0.0100.0000.0000.0000.000
186A288HOH0-0.016-0.0147.1600.1130.1130.0000.0000.0000.000
187A291HOH0-0.0060.00028.590-0.001-0.0010.0000.0000.0000.000
188A292HOH00.0330.02213.773-0.014-0.0140.0000.0000.0000.000
189A294HOH0-0.023-0.0029.7640.0370.0370.0000.0000.0000.000
190A296HOH00.0050.00313.7070.0240.0240.0000.0000.0000.000
191A297HOH0-0.035-0.02412.1580.0790.0790.0000.0000.0000.000
192A299HOH0-0.029-0.02635.6870.0010.0010.0000.0000.0000.000
193A300HOH0-0.021-0.01827.6030.0050.0050.0000.0000.0000.000
194A301HOH0-0.037-0.0238.0440.2130.2130.0000.0000.0000.000
195A303HOH00.0050.00830.9510.0010.0010.0000.0000.0000.000
196A304HOH0-0.086-0.06427.3590.0020.0020.0000.0000.0000.000
197A305HOH00.0150.00331.8790.0050.0050.0000.0000.0000.000
198A308HOH0-0.050-0.03621.085-0.020-0.0200.0000.0000.0000.000
199A319HOH0-0.018-0.02433.4320.0000.0000.0000.0000.0000.000
200A320HOH0-0.019-0.02529.6700.0010.0010.0000.0000.0000.000
201A321HOH00.0190.01617.404-0.014-0.0140.0000.0000.0000.000
202A322HOH0-0.040-0.02811.282-0.015-0.0150.0000.0000.0000.000
203A323HOH0-0.001-0.01633.3560.0030.0030.0000.0000.0000.000
204A324HOH00.0290.01725.125-0.010-0.0100.0000.0000.0000.000
205A325HOH0-0.032-0.02528.5780.0000.0000.0000.0000.0000.000
206A328HOH00.0300.02333.844-0.004-0.0040.0000.0000.0000.000
207A329HOH00.0290.0186.769-0.294-0.2940.0000.0000.0000.000
208A331HOH0-0.032-0.02418.8370.0120.0120.0000.0000.0000.000
209A332HOH0-0.017-0.01525.0240.0060.0060.0000.0000.0000.000
210A333HOH0-0.008-0.01528.438-0.002-0.0020.0000.0000.0000.000
211A336HOH00.0350.02420.465-0.008-0.0080.0000.0000.0000.000
212A337HOH0-0.052-0.04614.9420.0040.0040.0000.0000.0000.000
213A344HOH0-0.059-0.04714.5790.0190.0190.0000.0000.0000.000
214A345HOH0-0.047-0.02635.5150.0030.0030.0000.0000.0000.000
215A346HOH0-0.038-0.02430.9970.0010.0010.0000.0000.0000.000
216A347HOH0-0.076-0.06717.5690.0050.0050.0000.0000.0000.000
217A349HOH00.011-0.02127.775-0.003-0.0030.0000.0000.0000.000
218A352HOH0-0.041-0.03029.577-0.002-0.0020.0000.0000.0000.000
219A354HOH0-0.045-0.03015.1160.0270.0270.0000.0000.0000.000
220A355HOH00.0320.02029.918-0.006-0.0060.0000.0000.0000.000
221A356HOH0-0.015-0.01516.038-0.009-0.0090.0000.0000.0000.000
222A357HOH0-0.009-0.01618.269-0.004-0.0040.0000.0000.0000.000
223A359HOH0-0.032-0.02820.5480.0120.0120.0000.0000.0000.000
224A360HOH00.0080.01035.706-0.001-0.0010.0000.0000.0000.000
225A361HOH0-0.027-0.0233.6490.6400.7170.000-0.029-0.0480.000
226A373HOH0-0.051-0.03629.785-0.002-0.0020.0000.0000.0000.000