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: 52J4Z

Calculation Name: 1VZV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VZV

Chain ID: A

ChEMBL ID:

UniProt ID: P09286

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptHSide
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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2488812.451432
FMO2-HF: Nuclear repulsion 2406532.431234
FMO2-HF: Total energy -82280.020198
FMO2-MP2: Total energy -82521.094643


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:11:GLU)


Summations of interaction energy for fragment #1(A:11:GLU)
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.
-106.081-100.58410.342-6.628-9.2130.058
Interaction energy analysis for fragmet #1(A:11:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.911 / q_NPA : -0.968
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].
3A13LEU00.0340.0263.833-1.5681.021-0.028-1.325-1.2360.006
4A14TYR0-0.011-0.0046.330-0.908-0.9080.0000.0000.0000.000
5A15VAL00.0110.0099.878-0.058-0.0580.0000.0000.0000.000
6A16ALA00.015-0.00613.279-0.364-0.3640.0000.0000.0000.000
7A17GLY00.0490.01816.4710.0230.0230.0000.0000.0000.000
8A18TYR0-0.075-0.04220.0830.0450.0450.0000.0000.0000.000
9A19LEU0-0.062-0.02221.285-0.011-0.0110.0000.0000.0000.000
10A20ALA0-0.004-0.02124.439-0.183-0.1830.0000.0000.0000.000
11A21LEU0-0.037-0.00327.9620.0140.0140.0000.0000.0000.000
12A22TYR00.008-0.01730.309-0.139-0.1390.0000.0000.0000.000
13A23SER0-0.0270.01133.361-0.152-0.1520.0000.0000.0000.000
14A24LYS10.8970.90432.810-9.093-9.0930.0000.0000.0000.000
15A25ASP-1-0.902-0.96631.1849.3359.3350.0000.0000.0000.000
16A26GLU-1-0.858-0.91333.1197.9487.9480.0000.0000.0000.000
17A27GLY00.0550.02636.3340.1010.1010.0000.0000.0000.000
18A28GLU-1-0.926-0.96236.9077.9177.9170.0000.0000.0000.000
19A29LEU0-0.099-0.05431.2790.2200.2200.0000.0000.0000.000
20A30ASN0-0.045-0.00932.7250.2210.2210.0000.0000.0000.000
21A31ILE0-0.0060.00729.8130.0150.0150.0000.0000.0000.000
22A32THR00.037-0.00333.116-0.065-0.0650.0000.0000.0000.000
23A33PRO00.0780.03133.7760.1030.1030.0000.0000.0000.000
24A34GLU-1-0.845-0.89534.5707.8407.8400.0000.0000.0000.000
25A35ILE0-0.0140.01132.4310.0490.0490.0000.0000.0000.000
26A36VAL00.0270.00628.6480.2210.2210.0000.0000.0000.000
27A37ARG10.8800.88830.607-8.526-8.5260.0000.0000.0000.000
28A38SER0-0.023-0.03132.4170.0510.0510.0000.0000.0000.000
29A39ALA0-0.039-0.01028.9980.0730.0730.0000.0000.0000.000
30A40LEU0-0.089-0.05225.3150.4390.4390.0000.0000.0000.000
31A41PRO00.0480.00225.676-0.218-0.2180.0000.0000.0000.000
32A42PRO0-0.0010.01223.677-0.233-0.2330.0000.0000.0000.000
33A43THR0-0.023-0.00525.4990.3190.3190.0000.0000.0000.000
34A44SER0-0.017-0.00324.6700.3590.3590.0000.0000.0000.000
35A45LYS10.9010.93817.338-15.130-15.1300.0000.0000.0000.000
36A46ILE00.0270.02520.1690.1640.1640.0000.0000.0000.000
37A47PRO0-0.0140.00017.4870.7500.7500.0000.0000.0000.000
38A48ILE00.0320.01114.019-0.700-0.7000.0000.0000.0000.000
39A49ASN0-0.0290.00015.8460.8200.8200.0000.0000.0000.000
40A50ILE00.0530.01714.395-0.068-0.0680.0000.0000.0000.000
41A51ASP-1-0.819-0.91518.76611.94011.9400.0000.0000.0000.000
42A52HIS0-0.033-0.02121.931-0.652-0.6520.0000.0000.0000.000
43A53ARG10.8410.90521.244-12.704-12.7040.0000.0000.0000.000
44A54LYS10.9870.99220.859-10.320-10.3200.0000.0000.0000.000
45A55ASP-1-0.781-0.84421.22912.98912.9890.0000.0000.0000.000
46A56CYS0-0.038-0.02817.0790.5540.5540.0000.0000.0000.000
47A57VAL00.0020.01315.2560.0840.0840.0000.0000.0000.000
48A58VAL0-0.003-0.02611.7000.3370.3370.0000.0000.0000.000
49A59GLY00.0670.01610.8992.0472.0470.0000.0000.0000.000
50A60GLU-1-0.848-0.89012.33415.67115.6710.0000.0000.0000.000
51A61VAL00.0340.01814.1240.8480.8480.0000.0000.0000.000
52A62ILE0-0.058-0.02512.085-0.612-0.6120.0000.0000.0000.000
53A63ALA00.0090.01015.980-0.534-0.5340.0000.0000.0000.000
54A64ILE0-0.006-0.00819.0010.3340.3340.0000.0000.0000.000
55A65ILE0-0.0080.00821.895-0.350-0.3500.0000.0000.0000.000
56A66GLU-1-0.782-0.86324.5429.2319.2310.0000.0000.0000.000
57A67ASP-1-0.802-0.89826.27010.47410.4740.0000.0000.0000.000
58A68ILE0-0.017-0.01428.266-0.239-0.2390.0000.0000.0000.000
59A69ARG10.8510.92428.901-10.385-10.3850.0000.0000.0000.000
60A70GLY00.0520.02728.819-0.129-0.1290.0000.0000.0000.000
61A71PRO0-0.032-0.00125.4950.2130.2130.0000.0000.0000.000
62A72PHE00.0200.01718.7940.1610.1610.0000.0000.0000.000
63A73PHE0-0.042-0.03316.106-0.075-0.0750.0000.0000.0000.000
64A74LEU00.0630.04112.8790.3210.3210.0000.0000.0000.000
65A75GLY0-0.018-0.02613.838-0.745-0.7450.0000.0000.0000.000
66A76ILE0-0.0250.0157.1760.9650.9650.0000.0000.0000.000
67A77VAL00.0160.0088.876-1.586-1.5860.0000.0000.0000.000
68A78ARG10.9000.9582.564-51.327-50.2042.289-1.488-1.9240.022
69A79CYS0-0.043-0.0156.733-2.368-2.3680.0000.0000.0000.000
70A80PRO00.0000.0006.1070.7660.7660.0000.0000.0000.000
71A81GLN00.0580.0157.1720.5560.5560.0000.0000.0000.000
72A82LEU0-0.021-0.0249.535-0.774-0.7740.0000.0000.0000.000
73A83HIS00.0110.0014.1361.5521.781-0.001-0.024-0.2050.000
74A84ALA0-0.0070.0158.790-0.414-0.4140.0000.0000.0000.000
75A85VAL00.0670.02010.764-1.179-1.1790.0000.0000.0000.000
76A86LEU0-0.030-0.00312.172-1.238-1.2380.0000.0000.0000.000
77A87PHE0-0.029-0.0346.806-0.469-0.4690.0000.0000.0000.000
78A88GLU-1-0.990-0.97112.75716.64216.6420.0000.0000.0000.000
79A89ALA0-0.019-0.01515.580-0.941-0.9410.0000.0000.0000.000
80A90ALA0-0.068-0.01815.670-1.018-1.0180.0000.0000.0000.000
81A91HIS00.0620.02717.6520.1490.1490.0000.0000.0000.000
82A92SER00.010-0.01318.6130.4780.4780.0000.0000.0000.000
83A93ASN0-0.051-0.02819.297-0.218-0.2180.0000.0000.0000.000
84A94PHE0-0.0130.01815.983-0.532-0.5320.0000.0000.0000.000
85A95PHE0-0.014-0.01212.7011.4321.4320.0000.0000.0000.000
86A96GLY00.0370.02417.114-0.537-0.5370.0000.0000.0000.000
87A97ASN00.053-0.00317.3241.5611.5610.0000.0000.0000.000
88A98ARG10.8360.90417.102-16.481-16.4810.0000.0000.0000.000
89A99ASP-1-0.757-0.86513.99318.99318.9930.0000.0000.0000.000
90A100SER0-0.0040.00413.1812.1082.1080.0000.0000.0000.000
91A101VAL0-0.055-0.03313.0661.5991.5990.0000.0000.0000.000
92A102LEU0-0.013-0.00412.556-1.134-1.1340.0000.0000.0000.000
93A103SER0-0.0080.0019.4990.3640.3640.0000.0000.0000.000
94A104PRO0-0.045-0.0304.663-1.181-1.116-0.001-0.006-0.0570.000
95A105LEU00.0580.0492.211-5.238-3.7468.084-3.777-5.8010.030
96A106GLU-1-0.838-0.9334.91826.45726.456-0.001-0.0080.0100.000
97A107ARG10.9120.9577.872-32.022-32.0220.0000.0000.0000.000
98A108ALA0-0.022-0.0026.081-2.895-2.8950.0000.0000.0000.000
99A109LEU00.006-0.0047.296-3.268-3.2680.0000.0000.0000.000
100A110TYR00.0010.0168.840-2.804-2.8040.0000.0000.0000.000
101A111LEU00.0180.01811.556-2.160-2.1600.0000.0000.0000.000
102A112VAL0-0.018-0.0169.643-1.629-1.6290.0000.0000.0000.000
103A113THR0-0.031-0.01612.153-1.424-1.4240.0000.0000.0000.000
104A114ASN0-0.066-0.04614.293-2.058-2.0580.0000.0000.0000.000
105A115TYR0-0.036-0.02216.120-1.042-1.0420.0000.0000.0000.000
106A116LEU0-0.074-0.03214.920-0.982-0.9820.0000.0000.0000.000
107A117PRO00.0560.04816.8850.3170.3170.0000.0000.0000.000
108A118SER0-0.013-0.00818.709-0.342-0.3420.0000.0000.0000.000
109A119VAL0-0.027-0.01318.2160.4710.4710.0000.0000.0000.000
110A120SER0-0.059-0.04120.841-0.762-0.7620.0000.0000.0000.000
111A121LEU00.0320.02823.2750.2970.2970.0000.0000.0000.000
112A122SER00.011-0.00624.705-0.503-0.5030.0000.0000.0000.000
113A123SER00.003-0.00426.9200.1230.1230.0000.0000.0000.000
114A124LYS10.9250.96528.973-9.038-9.0380.0000.0000.0000.000
115A125ARG10.7980.90331.030-8.595-8.5950.0000.0000.0000.000
116A126LEU0-0.0310.02729.6790.0620.0620.0000.0000.0000.000
117A137PHE00.0470.00125.1170.1110.1110.0000.0000.0000.000
118A138THR00.016-0.01025.349-0.398-0.3980.0000.0000.0000.000
119A139HIS0-0.029-0.00321.3650.3540.3540.0000.0000.0000.000
120A140VAL00.0290.03418.390-0.586-0.5860.0000.0000.0000.000
121A141ALA0-0.020-0.00919.3790.5510.5510.0000.0000.0000.000
122A142LEU00.0350.03814.232-0.136-0.1360.0000.0000.0000.000
123A143CYS0-0.048-0.03618.669-0.532-0.5320.0000.0000.0000.000
124A144VAL00.0720.05320.5120.2660.2660.0000.0000.0000.000
125A145VAL00.0190.00222.5180.1320.1320.0000.0000.0000.000
126A146GLY00.0570.03124.941-0.145-0.1450.0000.0000.0000.000
127A147ARG10.9470.96526.251-9.625-9.6250.0000.0000.0000.000
128A148ARG10.8080.90427.754-10.326-10.3260.0000.0000.0000.000
129A149VAL00.0680.02428.3170.3460.3460.0000.0000.0000.000
130A150GLY00.0290.01726.991-0.044-0.0440.0000.0000.0000.000
131A151THR0-0.111-0.04623.8770.3410.3410.0000.0000.0000.000
132A152VAL00.0270.01820.6450.2620.2620.0000.0000.0000.000
133A153VAL0-0.086-0.04316.578-0.113-0.1130.0000.0000.0000.000
134A154ASN0-0.017-0.00914.8440.0270.0270.0000.0000.0000.000
135A155TYR0-0.017-0.04310.5590.2360.2360.0000.0000.0000.000
136A156ASP-1-0.821-0.9109.72924.85424.8540.0000.0000.0000.000
137A157CYS0-0.041-0.0395.4522.1382.1380.0000.0000.0000.000
138A158THR00.026-0.0016.5661.8241.8240.0000.0000.0000.000
139A159PRO0-0.0100.0119.002-1.295-1.2950.0000.0000.0000.000
140A160GLU-1-0.846-0.92611.83220.69220.6920.0000.0000.0000.000
141A161SER00.0400.01211.688-1.421-1.4210.0000.0000.0000.000
142A162SER0-0.076-0.03311.721-0.392-0.3920.0000.0000.0000.000
143A163ILE00.008-0.01513.922-1.095-1.0950.0000.0000.0000.000
144A164GLU-1-0.927-0.94016.40315.10015.1000.0000.0000.0000.000
145A165PRO00.0070.00317.265-1.036-1.0360.0000.0000.0000.000
146A166PHE0-0.048-0.02518.098-0.754-0.7540.0000.0000.0000.000
147A167ARG10.8760.91922.551-11.739-11.7390.0000.0000.0000.000
148A168VAL0-0.0050.01025.703-0.312-0.3120.0000.0000.0000.000
149A169LEU0-0.0320.00921.503-0.263-0.2630.0000.0000.0000.000
150A170SER00.1110.05025.2760.3160.3160.0000.0000.0000.000
151A171MET00.0630.02321.7760.4160.4160.0000.0000.0000.000
152A172GLU-1-0.931-0.96224.44010.02310.0230.0000.0000.0000.000
153A173SER00.011-0.00524.3750.0660.0660.0000.0000.0000.000
154A174LYS10.8140.90620.551-12.891-12.8910.0000.0000.0000.000
155A175ALA00.0110.00420.1660.5800.5800.0000.0000.0000.000
156A176ARG10.9780.99321.059-11.055-11.0550.0000.0000.0000.000
157A177LEU0-0.030-0.01418.1120.2030.2030.0000.0000.0000.000
158A178LEU00.0520.01115.6670.5180.5180.0000.0000.0000.000
159A179SER00.0020.01616.9510.3850.3850.0000.0000.0000.000
160A180LEU0-0.039-0.01418.8050.1080.1080.0000.0000.0000.000
161A181VAL0-0.041-0.02812.5850.3620.3620.0000.0000.0000.000
162A182LYS10.9120.95214.901-16.148-16.1480.0000.0000.0000.000
163A183ASP-1-0.932-0.94416.24313.53413.5340.0000.0000.0000.000
164A184TYR0-0.071-0.07511.5190.7560.7560.0000.0000.0000.000
165A185ALA00.0500.04314.1261.1741.1740.0000.0000.0000.000
166A186GLY00.0340.01112.905-0.662-0.6620.0000.0000.0000.000
167A187LEU0-0.005-0.0048.9150.9880.9880.0000.0000.0000.000
168A188ASN0-0.038-0.0357.3262.1372.1370.0000.0000.0000.000
169A189LYS10.8770.9347.609-15.749-15.7490.0000.0000.0000.000
170A190VAL00.0180.0165.5211.7301.7300.0000.0000.0000.000
171A191TRP0-0.015-0.0128.259-1.880-1.8800.0000.0000.0000.000
172A192LYS10.9801.00110.168-21.412-21.4120.0000.0000.0000.000
173A193VAL00.0070.00712.251-1.382-1.3820.0000.0000.0000.000
174A194SER00.010-0.01714.3970.4990.4990.0000.0000.0000.000
175A195GLU-1-0.753-0.89713.56520.54320.5430.0000.0000.0000.000
176A196ASP-1-0.821-0.88716.64212.84512.8450.0000.0000.0000.000
177A197LYS10.7950.86918.777-14.501-14.5010.0000.0000.0000.000
178A198LEU0-0.0290.00013.155-0.386-0.3860.0000.0000.0000.000
179A199ALA00.0630.02317.734-0.100-0.1000.0000.0000.0000.000
180A200LYS10.8380.91619.366-13.262-13.2620.0000.0000.0000.000
181A201VAL0-0.027-0.01519.475-0.477-0.4770.0000.0000.0000.000
182A202LEU00.027-0.00115.059-0.312-0.3120.0000.0000.0000.000
183A203LEU00.0240.04619.719-0.187-0.1870.0000.0000.0000.000
184A204SER0-0.055-0.04422.933-0.674-0.6740.0000.0000.0000.000
185A205THR00.0030.00721.037-0.262-0.2620.0000.0000.0000.000
186A206ALA00.0170.02023.417-0.286-0.2860.0000.0000.0000.000
187A207VAL00.0840.02124.954-0.430-0.4300.0000.0000.0000.000
188A208ASN0-0.051-0.01827.340-0.742-0.7420.0000.0000.0000.000
189A209ASN0-0.060-0.04925.526-0.153-0.1530.0000.0000.0000.000
190A210MET0-0.0210.00928.3630.0370.0370.0000.0000.0000.000
191A211LEU00.0140.00829.948-0.107-0.1070.0000.0000.0000.000
192A212LEU0-0.0240.00927.615-0.262-0.2620.0000.0000.0000.000
193A213ARG10.9290.94831.085-8.445-8.4450.0000.0000.0000.000
194A214ASP-1-0.836-0.91231.4559.1069.1060.0000.0000.0000.000
195A215ARG10.8620.93724.991-11.051-11.0510.0000.0000.0000.000
196A216TRP00.0560.00820.2130.0740.0740.0000.0000.0000.000
197A217ASP-1-0.825-0.90726.55610.13310.1330.0000.0000.0000.000
198A218VAL0-0.068-0.02327.768-0.082-0.0820.0000.0000.0000.000
199A219VAL00.029-0.00122.2370.0090.0090.0000.0000.0000.000
200A220ALA0-0.0040.01524.9170.2580.2580.0000.0000.0000.000
201A221LYS10.8820.91226.856-9.607-9.6070.0000.0000.0000.000
202A222ARG10.8820.95625.647-10.705-10.7050.0000.0000.0000.000
203A223ARG10.9801.00321.613-12.783-12.7830.0000.0000.0000.000
204A224ARG10.9320.95724.635-10.008-10.0080.0000.0000.0000.000
205A225GLU-1-0.783-0.86727.6529.3369.3360.0000.0000.0000.000
206A226ALA00.0050.00923.736-0.161-0.1610.0000.0000.0000.000
207A227GLY00.0340.01425.2450.1070.1070.0000.0000.0000.000
208A228ILE0-0.0230.02619.8540.0860.0860.0000.0000.0000.000
209A229MET0-0.056-0.05223.122-0.233-0.2330.0000.0000.0000.000
210A230GLY0-0.013-0.01321.881-0.115-0.1150.0000.0000.0000.000
211A231HIS00.0740.04722.5030.2750.2750.0000.0000.0000.000