FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YZVJ2

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2488066.806469
FMO2-HF: Nuclear repulsion 2405785.134246
FMO2-HF: Total energy -82281.672223
FMO2-MP2: Total energy -82522.535317


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.
-121.991-118.70214.686-8.225-9.750.08
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 : -0.891 / q_NPA : -0.943
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].
3A13LEU00.0310.0263.8520.2232.239-0.022-1.005-0.9900.004
4A14TYR0-0.002-0.0026.529-1.305-1.3050.0000.0000.0000.000
5A15VAL00.002-0.0049.806-0.007-0.0070.0000.0000.0000.000
6A16ALA00.0240.01513.350-0.596-0.5960.0000.0000.0000.000
7A17GLY00.0600.01316.7740.0360.0360.0000.0000.0000.000
8A18TYR0-0.066-0.04420.503-0.017-0.0170.0000.0000.0000.000
9A19LEU0-0.056-0.02321.4620.0250.0250.0000.0000.0000.000
10A20ALA0-0.013-0.02024.796-0.248-0.2480.0000.0000.0000.000
11A21LEU0-0.0320.00028.2230.1840.1840.0000.0000.0000.000
12A22TYR00.000-0.03430.611-0.135-0.1350.0000.0000.0000.000
13A23SER0-0.0140.01933.715-0.161-0.1610.0000.0000.0000.000
14A24LYS10.8590.88633.278-9.169-9.1690.0000.0000.0000.000
15A25ASP-1-0.900-0.97031.6079.4029.4020.0000.0000.0000.000
16A26GLU-1-0.881-0.92833.4658.0898.0890.0000.0000.0000.000
17A27GLY00.0570.02636.6730.0850.0850.0000.0000.0000.000
18A28GLU-1-0.919-0.95437.2707.8707.8700.0000.0000.0000.000
19A29LEU0-0.125-0.06831.3640.2430.2430.0000.0000.0000.000
20A30ASN0-0.043-0.01233.2320.1520.1520.0000.0000.0000.000
21A31ILE0-0.0210.00630.126-0.010-0.0100.0000.0000.0000.000
22A32THR00.0410.00333.381-0.050-0.0500.0000.0000.0000.000
23A33PRO00.0570.01833.9170.1310.1310.0000.0000.0000.000
24A34GLU-1-0.838-0.87234.8457.9317.9310.0000.0000.0000.000
25A35ILE00.0230.02232.1030.0850.0850.0000.0000.0000.000
26A36VAL00.023-0.01028.6700.1920.1920.0000.0000.0000.000
27A37ARG10.8360.87230.581-8.520-8.5200.0000.0000.0000.000
28A38SER00.010-0.00932.833-0.094-0.0940.0000.0000.0000.000
29A39ALA0-0.050-0.02428.7150.0330.0330.0000.0000.0000.000
30A40LEU0-0.076-0.02125.3580.4170.4170.0000.0000.0000.000
31A41PRO00.026-0.00325.683-0.246-0.2460.0000.0000.0000.000
32A42PRO00.0080.00823.527-0.237-0.2370.0000.0000.0000.000
33A43THR0-0.0020.00325.4230.3380.3380.0000.0000.0000.000
34A44SER0-0.0100.00124.7640.1490.1490.0000.0000.0000.000
35A45LYS10.8620.92917.681-14.878-14.8780.0000.0000.0000.000
36A46ILE00.0040.01020.3640.2400.2400.0000.0000.0000.000
37A47PRO00.0080.01317.7500.7090.7090.0000.0000.0000.000
38A48ILE00.0090.00014.285-0.627-0.6270.0000.0000.0000.000
39A49ASN0-0.022-0.01116.2830.7300.7300.0000.0000.0000.000
40A50ILE00.0740.03914.8100.2380.2380.0000.0000.0000.000
41A51ASP-1-0.789-0.88519.05011.79411.7940.0000.0000.0000.000
42A52HIS0-0.040-0.01522.452-0.674-0.6740.0000.0000.0000.000
43A53ARG10.8490.90721.924-12.570-12.5700.0000.0000.0000.000
44A54LYS10.9850.97421.813-10.273-10.2730.0000.0000.0000.000
45A55ASP-1-0.780-0.83321.93212.90612.9060.0000.0000.0000.000
46A56CYS0-0.013-0.00417.5830.4270.4270.0000.0000.0000.000
47A57VAL0-0.019-0.00516.0180.4180.4180.0000.0000.0000.000
48A58VAL0-0.004-0.01912.4480.3520.3520.0000.0000.0000.000
49A59GLY00.0660.02011.5152.0252.0250.0000.0000.0000.000
50A60GLU-1-0.825-0.87312.94315.90115.9010.0000.0000.0000.000
51A61VAL00.0520.01914.3920.9300.9300.0000.0000.0000.000
52A62ILE0-0.034-0.00111.992-0.809-0.8090.0000.0000.0000.000
53A63ALA00.0070.00415.918-0.676-0.6760.0000.0000.0000.000
54A64ILE0-0.012-0.01918.8310.2430.2430.0000.0000.0000.000
55A65ILE0-0.0150.00321.915-0.274-0.2740.0000.0000.0000.000
56A66GLU-1-0.755-0.83924.6549.2379.2370.0000.0000.0000.000
57A67ASP-1-0.762-0.86126.36910.53110.5310.0000.0000.0000.000
58A68ILE0-0.021-0.01128.279-0.236-0.2360.0000.0000.0000.000
59A69ARG10.8390.91428.203-10.624-10.6240.0000.0000.0000.000
60A70GLY00.0270.01729.326-0.126-0.1260.0000.0000.0000.000
61A71PRO0-0.051-0.00526.0300.2110.2110.0000.0000.0000.000
62A72PHE00.0260.00919.2360.1450.1450.0000.0000.0000.000
63A73PHE0-0.047-0.03016.101-0.095-0.0950.0000.0000.0000.000
64A74LEU00.0410.02613.1980.2610.2610.0000.0000.0000.000
65A75GLY0-0.052-0.02614.053-0.665-0.6650.0000.0000.0000.000
66A76ILE0-0.0240.0057.2730.8850.8850.0000.0000.0000.000
67A77VAL00.016-0.0058.981-1.683-1.6830.0000.0000.0000.000
68A78ARG10.8390.9272.007-57.605-60.86710.081-3.618-3.2000.044
69A79CYS0-0.056-0.0277.049-2.066-2.0660.0000.0000.0000.000
70A80PRO00.0300.0205.9670.4020.4020.0000.0000.0000.000
71A81GLN0-0.014-0.0247.2600.4080.4080.0000.0000.0000.000
72A82LEU00.003-0.0119.957-0.916-0.9160.0000.0000.0000.000
73A83HIS00.011-0.0014.5401.6871.821-0.001-0.006-0.1260.000
74A84ALA00.0030.0219.269-0.730-0.7300.0000.0000.0000.000
75A85VAL00.0290.00711.168-1.051-1.0510.0000.0000.0000.000
76A86LEU0-0.031-0.01212.178-1.092-1.0920.0000.0000.0000.000
77A87PHE0-0.016-0.0257.018-0.107-0.1070.0000.0000.0000.000
78A88GLU-1-0.974-0.97612.93516.23816.2380.0000.0000.0000.000
79A89ALA0-0.035-0.01715.932-1.017-1.0170.0000.0000.0000.000
80A90ALA0-0.049-0.00815.600-0.857-0.8570.0000.0000.0000.000
81A91HIS00.0420.01517.5250.0390.0390.0000.0000.0000.000
82A92SER00.016-0.00518.5810.4360.4360.0000.0000.0000.000
83A93ASN0-0.064-0.02919.556-0.322-0.3220.0000.0000.0000.000
84A94PHE0-0.0170.00816.110-0.619-0.6190.0000.0000.0000.000
85A95PHE0-0.005-0.00313.0411.6061.6060.0000.0000.0000.000
86A96GLY00.0430.01917.237-0.814-0.8140.0000.0000.0000.000
87A97ASN00.032-0.00717.3341.6641.6640.0000.0000.0000.000
88A98ARG10.8500.90717.209-16.686-16.6860.0000.0000.0000.000
89A99ASP-1-0.730-0.84214.01018.98418.9840.0000.0000.0000.000
90A100SER0-0.045-0.01313.1232.3772.3770.0000.0000.0000.000
91A101VAL0-0.046-0.02013.0871.5711.5710.0000.0000.0000.000
92A102LEU0-0.008-0.00112.435-0.998-0.9980.0000.0000.0000.000
93A103SER00.015-0.0059.2810.8630.8630.0000.0000.0000.000
94A104PRO0-0.0090.0014.2940.2790.432-0.001-0.031-0.1220.000
95A105LEU00.0200.0052.265-14.773-10.6124.629-3.519-5.2710.032
96A106GLU-1-0.833-0.9174.56824.66324.7500.000-0.046-0.0410.000
97A107ARG10.8590.9347.856-32.896-32.8960.0000.0000.0000.000
98A108ALA00.0280.0146.488-3.407-3.4070.0000.0000.0000.000
99A109LEU0-0.0140.0017.612-3.071-3.0710.0000.0000.0000.000
100A110TYR00.0200.0219.101-3.159-3.1590.0000.0000.0000.000
101A111LEU00.0210.01511.796-2.144-2.1440.0000.0000.0000.000
102A112VAL00.000-0.00710.224-1.847-1.8470.0000.0000.0000.000
103A113THR0-0.043-0.03212.400-1.619-1.6190.0000.0000.0000.000
104A114ASN0-0.076-0.04514.626-2.273-2.2730.0000.0000.0000.000
105A115TYR0-0.047-0.03416.237-1.039-1.0390.0000.0000.0000.000
106A116LEU0-0.072-0.03115.198-0.962-0.9620.0000.0000.0000.000
107A117PRO00.0430.04517.2200.3990.3990.0000.0000.0000.000
108A118SER0-0.023-0.01418.897-0.466-0.4660.0000.0000.0000.000
109A119VAL0-0.0160.00018.5580.4240.4240.0000.0000.0000.000
110A120SER0-0.020-0.03221.175-0.806-0.8060.0000.0000.0000.000
111A121LEU00.0200.00823.7130.2650.2650.0000.0000.0000.000
112A122SER0-0.007-0.01324.776-0.478-0.4780.0000.0000.0000.000
113A123SER0-0.004-0.00427.0570.1000.1000.0000.0000.0000.000
114A124LYS10.9130.95529.152-9.008-9.0080.0000.0000.0000.000
115A125ARG10.8100.91031.883-8.617-8.6170.0000.0000.0000.000
116A126LEU00.0030.01529.6750.2240.2240.0000.0000.0000.000
117A137PHE00.0680.01825.0860.1580.1580.0000.0000.0000.000
118A138THR0-0.043-0.03125.660-0.463-0.4630.0000.0000.0000.000
119A139HIS0-0.007-0.00521.7410.3400.3400.0000.0000.0000.000
120A140VAL00.0220.03619.218-0.535-0.5350.0000.0000.0000.000
121A141ALA0-0.0100.01319.8780.5220.5220.0000.0000.0000.000
122A142LEU00.0180.00814.053-0.317-0.3170.0000.0000.0000.000
123A143CYS0-0.050-0.03318.569-0.559-0.5590.0000.0000.0000.000
124A144VAL00.0750.04420.5850.3310.3310.0000.0000.0000.000
125A145VAL00.012-0.00722.6410.0770.0770.0000.0000.0000.000
126A146GLY00.0650.04425.079-0.152-0.1520.0000.0000.0000.000
127A147ARG10.9360.96326.007-9.628-9.6280.0000.0000.0000.000
128A148ARG10.8620.93228.113-10.294-10.2940.0000.0000.0000.000
129A149VAL00.0420.01928.3180.3990.3990.0000.0000.0000.000
130A150GLY00.009-0.00627.1560.0080.0080.0000.0000.0000.000
131A151THR0-0.048-0.03724.0370.3860.3860.0000.0000.0000.000
132A152VAL0-0.0120.00920.9520.3640.3640.0000.0000.0000.000
133A153VAL0-0.053-0.02216.876-0.244-0.2440.0000.0000.0000.000
134A154ASN0-0.041-0.02315.2040.0000.0000.0000.0000.0000.000
135A155TYR0-0.011-0.03210.9220.1970.1970.0000.0000.0000.000
136A156ASP-1-0.829-0.91010.15425.97025.9700.0000.0000.0000.000
137A157CYS0-0.023-0.0195.8202.3442.3440.0000.0000.0000.000
138A158THR0-0.050-0.0496.1052.0702.0700.0000.0000.0000.000
139A159PRO0-0.0060.0028.850-1.326-1.3260.0000.0000.0000.000
140A160GLU-1-0.804-0.89611.81321.38021.3800.0000.0000.0000.000
141A161SER00.0300.01711.731-1.625-1.6250.0000.0000.0000.000
142A162SER0-0.027-0.01811.792-0.629-0.6290.0000.0000.0000.000
143A163ILE00.007-0.00513.955-1.109-1.1090.0000.0000.0000.000
144A164GLU-1-0.930-0.94016.84915.26315.2630.0000.0000.0000.000
145A165PRO00.006-0.00417.672-1.084-1.0840.0000.0000.0000.000
146A166PHE0-0.044-0.02018.216-0.795-0.7950.0000.0000.0000.000
147A167ARG10.8550.90922.641-11.838-11.8380.0000.0000.0000.000
148A168VAL0-0.015-0.00725.908-0.379-0.3790.0000.0000.0000.000
149A169LEU0-0.0050.02921.796-0.289-0.2890.0000.0000.0000.000
150A170SER00.037-0.00425.4630.3650.3650.0000.0000.0000.000
151A171MET00.0600.01521.4550.4120.4120.0000.0000.0000.000
152A172GLU-1-0.844-0.89324.18610.33410.3340.0000.0000.0000.000
153A173SER00.002-0.01124.7500.1780.1780.0000.0000.0000.000
154A174LYS10.8020.89020.449-13.182-13.1820.0000.0000.0000.000
155A175ALA00.0280.01520.0240.6460.6460.0000.0000.0000.000
156A176ARG10.9510.97821.160-11.169-11.1690.0000.0000.0000.000
157A177LEU0-0.018-0.01518.1970.2010.2010.0000.0000.0000.000
158A178LEU00.0350.00615.7780.5520.5520.0000.0000.0000.000
159A179SER0-0.0050.00617.0590.3640.3640.0000.0000.0000.000
160A180LEU0-0.023-0.00618.9220.0910.0910.0000.0000.0000.000
161A181VAL0-0.032-0.02212.2740.4330.4330.0000.0000.0000.000
162A182LYS10.8980.95114.380-15.676-15.6760.0000.0000.0000.000
163A183ASP-1-0.888-0.94116.21713.46113.4610.0000.0000.0000.000
164A184TYR0-0.089-0.06811.1800.4050.4050.0000.0000.0000.000
165A185ALA00.0050.00113.8921.3491.3490.0000.0000.0000.000
166A186GLY00.0160.00112.855-0.815-0.8150.0000.0000.0000.000
167A187LEU00.0120.0148.6170.9100.9100.0000.0000.0000.000
168A188ASN00.0110.0006.7853.2723.2720.0000.0000.0000.000
169A189LYS10.8400.9177.537-16.673-16.6730.0000.0000.0000.000
170A190VAL00.0160.0085.9921.3171.3170.0000.0000.0000.000
171A191TRP00.0170.0188.593-1.794-1.7940.0000.0000.0000.000
172A192LYS10.9190.95010.511-21.328-21.3280.0000.0000.0000.000
173A193VAL00.0150.00513.084-1.279-1.2790.0000.0000.0000.000
174A194SER00.0260.00215.0770.6670.6670.0000.0000.0000.000
175A195GLU-1-0.703-0.85413.09120.10220.1020.0000.0000.0000.000
176A196ASP-1-0.813-0.87416.78712.49612.4960.0000.0000.0000.000
177A197LYS10.8240.88219.175-14.425-14.4250.0000.0000.0000.000
178A198LEU0-0.028-0.00213.752-0.393-0.3930.0000.0000.0000.000
179A199ALA00.0550.03018.256-0.050-0.0500.0000.0000.0000.000
180A200LYS10.8350.89619.740-13.016-13.0160.0000.0000.0000.000
181A201VAL0-0.027-0.01019.881-0.526-0.5260.0000.0000.0000.000
182A202LEU00.0420.01515.450-0.322-0.3220.0000.0000.0000.000
183A203LEU00.0280.03219.956-0.306-0.3060.0000.0000.0000.000
184A204SER0-0.059-0.04723.418-0.647-0.6470.0000.0000.0000.000
185A205THR0-0.051-0.02920.679-0.186-0.1860.0000.0000.0000.000
186A206ALA00.0330.02323.162-0.344-0.3440.0000.0000.0000.000
187A207VAL00.035-0.00124.736-0.425-0.4250.0000.0000.0000.000
188A208ASN0-0.035-0.01627.254-0.720-0.7200.0000.0000.0000.000
189A209ASN0-0.041-0.02725.723-0.256-0.2560.0000.0000.0000.000
190A210MET00.0040.01728.2150.0160.0160.0000.0000.0000.000
191A211LEU00.0120.00029.825-0.119-0.1190.0000.0000.0000.000
192A212LEU0-0.0430.00427.816-0.276-0.2760.0000.0000.0000.000
193A213ARG10.9420.96031.022-8.449-8.4490.0000.0000.0000.000
194A214ASP-1-0.840-0.92231.8659.1789.1780.0000.0000.0000.000
195A215ARG10.8450.92425.363-11.084-11.0840.0000.0000.0000.000
196A216TRP00.0630.02020.7660.1870.1870.0000.0000.0000.000
197A217ASP-1-0.815-0.90426.89810.26810.2680.0000.0000.0000.000
198A218VAL0-0.055-0.02327.961-0.109-0.1090.0000.0000.0000.000
199A219VAL00.0410.02222.5080.0180.0180.0000.0000.0000.000
200A220ALA00.0080.00525.3820.2020.2020.0000.0000.0000.000
201A221LYS10.8710.91727.010-9.740-9.7400.0000.0000.0000.000
202A222ARG10.8740.94526.088-10.818-10.8180.0000.0000.0000.000
203A223ARG10.9170.96622.057-13.063-13.0630.0000.0000.0000.000
204A224ARG10.8950.94924.984-10.124-10.1240.0000.0000.0000.000
205A225GLU-1-0.747-0.85328.1749.4229.4220.0000.0000.0000.000
206A226ALA00.0180.01623.708-0.140-0.1400.0000.0000.0000.000
207A227GLY00.0270.00725.0360.1950.1950.0000.0000.0000.000
208A228ILE00.0020.03320.0850.0210.0210.0000.0000.0000.000
209A229MET0-0.047-0.04123.3310.0590.0590.0000.0000.0000.000
210A230GLY00.0360.03422.275-0.253-0.2530.0000.0000.0000.000
211A231HIS00.0500.03123.3560.1050.1050.0000.0000.0000.000