FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 1VM9Z

Calculation Name: 1AST-A-Xray549

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1AST

Chain ID: A

ChEMBL ID:

UniProt ID: P07584

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2332856.029749
FMO2-HF: Nuclear repulsion 2252088.030439
FMO2-HF: Total energy -80767.999309
FMO2-MP2: Total energy -80999.57127


3D Structure Molmil
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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-329.154-314.3684.087-8.025-10.85-0.073
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.849 / q_NPA : 0.929
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].
3A3ILE00.0750.0353.8841.1332.600-0.014-0.723-0.730-0.002
94A95MET00.0080.0184.7951.0991.131-0.001-0.001-0.0300.000
99A100PHE0-0.049-0.0112.663-5.103-4.3240.080-0.236-0.623-0.001
100A101TYR00.0340.0273.26011.40412.3620.013-0.307-0.6640.000
101A102HIS00.005-0.0083.986-1.142-0.8330.001-0.119-0.192-0.001
102A103GLU-1-0.814-0.9192.546-109.466-104.4300.876-3.172-2.741-0.039
103A104HIS00.0340.0134.4010.2480.333-0.001-0.002-0.0810.000
105A106ARG10.7370.8492.24351.94552.6291.554-0.579-1.659-0.002
106A107MET0-0.022-0.0104.4448.5348.604-0.001-0.011-0.0580.000
130A131ASP-1-0.796-0.8673.809-51.133-50.9610.001-0.061-0.1120.000
133A134SER0-0.021-0.0212.868-4.662-3.9310.214-0.350-0.595-0.002
134A135ARG10.7840.8603.66635.23235.5560.004-0.092-0.2350.000
135A136TYR00.0350.0062.703-15.419-13.0191.145-1.554-1.992-0.018
136A137VAL0-0.011-0.0133.8295.7015.8060.001-0.029-0.0780.000
146A147MET0-0.0120.0094.3263.9374.003-0.001-0.006-0.0580.000
188A189GLN0-0.018-0.0022.918-13.372-11.8040.216-0.783-1.002-0.008
4A4LEU0-0.032-0.0056.9111.4581.4580.0000.0000.0000.000
5A5GLY00.0340.0218.5711.2101.2100.0000.0000.0000.000
6A6ASP-1-0.805-0.89611.456-24.846-24.8460.0000.0000.0000.000
7A7GLU-1-0.900-0.96013.689-19.169-19.1690.0000.0000.0000.000
8A8TYR0-0.053-0.00712.1711.2261.2260.0000.0000.0000.000
9A9LEU00.0140.03210.641-1.460-1.4600.0000.0000.0000.000
10A10TRP0-0.047-0.03213.8352.7662.7660.0000.0000.0000.000
11A11SER0-0.023-0.02016.6670.1400.1400.0000.0000.0000.000
12A12GLY00.011-0.00419.2280.4290.4290.0000.0000.0000.000
13A13GLY00.0060.00216.4100.0930.0930.0000.0000.0000.000
14A14VAL0-0.056-0.02517.429-0.145-0.1450.0000.0000.0000.000
15A15ILE00.0120.00014.614-0.247-0.2470.0000.0000.0000.000
16A16PRO00.0030.00119.2060.4410.4410.0000.0000.0000.000
17A17TYR0-0.020-0.00120.747-0.552-0.5520.0000.0000.0000.000
18A18THR0-0.020-0.01222.5710.8540.8540.0000.0000.0000.000
19A19PHE00.0420.01023.064-0.493-0.4930.0000.0000.0000.000
20A20ALA00.0200.01225.8440.5520.5520.0000.0000.0000.000
21A21GLY0-0.037-0.03027.553-0.137-0.1370.0000.0000.0000.000
22A22VAL0-0.0260.01724.8410.1190.1190.0000.0000.0000.000
23A23SER0-0.015-0.02228.0090.4290.4290.0000.0000.0000.000
24A24GLY00.0590.01328.756-0.291-0.2910.0000.0000.0000.000
25A25ALA0-0.0080.00829.381-0.123-0.1230.0000.0000.0000.000
26A26ASP-1-0.766-0.88025.050-12.071-12.0710.0000.0000.0000.000
27A27GLN0-0.047-0.03124.417-0.506-0.5060.0000.0000.0000.000
28A28SER0-0.021-0.01124.953-0.252-0.2520.0000.0000.0000.000
29A29ALA0-0.0110.01022.887-0.256-0.2560.0000.0000.0000.000
30A30ILE00.005-0.01019.755-0.632-0.6320.0000.0000.0000.000
31A31LEU00.000-0.00520.305-0.615-0.6150.0000.0000.0000.000
32A32SER0-0.020-0.01521.836-0.093-0.0930.0000.0000.0000.000
33A33GLY0-0.003-0.00817.962-0.365-0.3650.0000.0000.0000.000
34A34MET0-0.034-0.01316.864-0.703-0.7030.0000.0000.0000.000
35A35GLN0-0.032-0.01418.257-0.203-0.2030.0000.0000.0000.000
36A36GLU-1-0.697-0.80315.578-19.011-19.0110.0000.0000.0000.000
37A37LEU00.010-0.00811.703-0.871-0.8710.0000.0000.0000.000
38A38GLU-1-0.875-0.92015.451-15.272-15.2720.0000.0000.0000.000
39A39GLU-1-0.952-0.96918.569-13.974-13.9740.0000.0000.0000.000
40A40LYS10.7700.88214.41420.02820.0280.0000.0000.0000.000
41A41THR0-0.038-0.03512.097-1.238-1.2380.0000.0000.0000.000
42A42CYS0-0.059-0.03015.3281.5051.5050.0000.0000.0000.000
43A43ILE00.0200.02813.0450.7290.7290.0000.0000.0000.000
44A44ARG10.7990.90616.41516.45316.4530.0000.0000.0000.000
45A45PHE00.0400.01314.949-0.277-0.2770.0000.0000.0000.000
46A46VAL00.0070.00020.7370.7250.7250.0000.0000.0000.000
47A47PRO0-0.018-0.01724.170-0.193-0.1930.0000.0000.0000.000
48A48ARG10.8570.93625.08811.61211.6120.0000.0000.0000.000
49A49THR0-0.084-0.04626.8780.5150.5150.0000.0000.0000.000
50A50THR0-0.069-0.05529.5180.2640.2640.0000.0000.0000.000
51A51GLU-1-0.776-0.87125.306-11.782-11.7820.0000.0000.0000.000
52A52SER0-0.019-0.02925.0170.2280.2280.0000.0000.0000.000
53A53ASP-1-0.798-0.86721.031-14.565-14.5650.0000.0000.0000.000
54A54TYR0-0.046-0.03421.3960.1740.1740.0000.0000.0000.000
55A55VAL00.0380.02317.115-0.124-0.1240.0000.0000.0000.000
56A56GLU-1-0.925-0.96120.183-11.737-11.7370.0000.0000.0000.000
57A57ILE00.0260.01419.540-0.408-0.4080.0000.0000.0000.000
58A58PHE00.0040.00321.4530.9370.9370.0000.0000.0000.000
59A59THR00.0290.00922.770-0.376-0.3760.0000.0000.0000.000
60A60SER0-0.023-0.01324.9480.0090.0090.0000.0000.0000.000
61A61GLY00.0430.02923.8420.3140.3140.0000.0000.0000.000
62A62SER0-0.051-0.02523.4140.2270.2270.0000.0000.0000.000
63A63GLY00.0600.02319.934-0.494-0.4940.0000.0000.0000.000
64A64CYS0-0.092-0.02016.1750.1270.1270.0000.0000.0000.000
65A65TRP00.0190.00514.401-0.784-0.7840.0000.0000.0000.000
66A66SER00.012-0.00912.6051.7921.7920.0000.0000.0000.000
67A67TYR0-0.0170.00312.987-1.047-1.0470.0000.0000.0000.000
68A68VAL0-0.027-0.0037.916-0.452-0.4520.0000.0000.0000.000
69A69GLY00.0340.02410.8270.6900.6900.0000.0000.0000.000
70A70ARG10.7560.87512.07118.90418.9040.0000.0000.0000.000
71A71ILE0-0.015-0.02415.3810.0970.0970.0000.0000.0000.000
72A72SER0-0.078-0.02417.4691.2411.2410.0000.0000.0000.000
73A73GLY0-0.011-0.01020.8620.0820.0820.0000.0000.0000.000
74A74ALA00.0060.00522.088-0.492-0.4920.0000.0000.0000.000
75A75GLN0-0.002-0.00715.2590.4190.4190.0000.0000.0000.000
76A76GLN0-0.056-0.04319.849-0.427-0.4270.0000.0000.0000.000
77A77VAL00.011-0.00315.828-1.007-1.0070.0000.0000.0000.000
78A78SER0-0.043-0.00918.3091.3431.3430.0000.0000.0000.000
79A79LEU00.028-0.01916.745-0.914-0.9140.0000.0000.0000.000
80A80GLN0-0.0050.01020.3470.3810.3810.0000.0000.0000.000
81A81ALA00.0360.00023.397-0.163-0.1630.0000.0000.0000.000
82A82ASN0-0.071-0.03825.424-0.045-0.0450.0000.0000.0000.000
83A83GLY00.0390.00423.3980.1730.1730.0000.0000.0000.000
84A85VAL0-0.0270.01119.399-0.794-0.7940.0000.0000.0000.000
85A86TYR0-0.006-0.00919.0830.6460.6460.0000.0000.0000.000
86A87HIS0-0.022-0.02417.873-0.439-0.4390.0000.0000.0000.000
87A88GLY00.0740.03214.738-0.650-0.6500.0000.0000.0000.000
88A89THR00.022-0.00513.452-1.842-1.8420.0000.0000.0000.000
89A90ILE0-0.0160.00214.448-0.796-0.7960.0000.0000.0000.000
90A91ILE00.0160.00611.302-0.669-0.6690.0000.0000.0000.000
91A92HIS0-0.035-0.0278.737-4.361-4.3610.0000.0000.0000.000
92A93GLU-1-0.846-0.92310.045-26.557-26.5570.0000.0000.0000.000
93A94LEU0-0.011-0.00112.303-0.441-0.4410.0000.0000.0000.000
95A96HIS10.8170.8977.04033.29133.2910.0000.0000.0000.000
96A97ALA00.0540.0289.147-0.651-0.6510.0000.0000.0000.000
97A98ILE0-0.0120.0079.4630.5940.5940.0000.0000.0000.000
98A99GLY00.0130.0198.6981.4381.4380.0000.0000.0000.000
104A105THR0-0.032-0.0525.0065.5455.5450.0000.0000.0000.000
107A108ASP-1-0.795-0.8686.077-37.420-37.4200.0000.0000.0000.000
108A109ARG10.8210.8927.56229.38529.3850.0000.0000.0000.000
109A110ASP-1-0.838-0.9038.973-21.437-21.4370.0000.0000.0000.000
110A111ASN0-0.068-0.03111.1862.7422.7420.0000.0000.0000.000
111A112TYR0-0.062-0.0169.1981.8611.8610.0000.0000.0000.000
112A113VAL00.0070.00310.8881.4231.4230.0000.0000.0000.000
113A114THR00.0040.01113.6010.3820.3820.0000.0000.0000.000
114A115ILE00.0080.00812.058-0.184-0.1840.0000.0000.0000.000
115A116ASN0-0.027-0.00616.0991.0641.0640.0000.0000.0000.000
116A117TYR00.0560.00514.1950.3690.3690.0000.0000.0000.000
117A118GLN0-0.045-0.02019.868-0.037-0.0370.0000.0000.0000.000
118A119ASN0-0.053-0.04221.5791.0721.0720.0000.0000.0000.000
119A120VAL0-0.0170.00317.574-0.096-0.0960.0000.0000.0000.000
120A121ASP-1-0.828-0.88620.571-12.710-12.7100.0000.0000.0000.000
121A122PRO0-0.011-0.02820.927-0.586-0.5860.0000.0000.0000.000
122A123SER0-0.101-0.06721.949-0.327-0.3270.0000.0000.0000.000
123A124MET00.0150.00817.435-0.086-0.0860.0000.0000.0000.000
124A125THR0-0.038-0.01016.529-1.313-1.3130.0000.0000.0000.000
125A126SER00.021-0.00615.058-0.424-0.4240.0000.0000.0000.000
126A127ASN0-0.110-0.04812.517-0.597-0.5970.0000.0000.0000.000
127A128PHE00.003-0.00511.123-2.014-2.0140.0000.0000.0000.000
128A129ASP-1-0.843-0.90011.497-20.850-20.8500.0000.0000.0000.000
129A130ILE0-0.017-0.0067.041-2.482-2.4820.0000.0000.0000.000
131A132THR0-0.063-0.0495.400-1.841-1.8410.0000.0000.0000.000
132A133TYR0-0.065-0.0347.9191.8911.8910.0000.0000.0000.000
137A138GLY00.0180.0056.0500.8700.8700.0000.0000.0000.000
138A139GLU-1-0.857-0.9126.166-26.118-26.1180.0000.0000.0000.000
139A140ASP-1-0.916-0.9456.132-34.996-34.9960.0000.0000.0000.000
140A141TYR0-0.061-0.0445.906-2.488-2.4880.0000.0000.0000.000
141A142GLN0-0.048-0.0206.4587.2057.2050.0000.0000.0000.000
142A143TYR0-0.027-0.0538.229-1.985-1.9850.0000.0000.0000.000
143A144TYR0-0.042-0.02310.7700.7880.7880.0000.0000.0000.000
144A145SER0-0.012-0.0206.294-0.425-0.4250.0000.0000.0000.000
145A146ILE0-0.034-0.0277.8911.5791.5790.0000.0000.0000.000
147A148HIS0-0.0170.0046.680-3.507-3.5070.0000.0000.0000.000
148A149TYR0-0.026-0.0118.8361.9701.9700.0000.0000.0000.000
149A150GLY00.0660.03611.899-0.105-0.1050.0000.0000.0000.000
150A151LYS10.8680.93415.39914.60314.6030.0000.0000.0000.000
151A152TYR0-0.0020.01517.5250.3860.3860.0000.0000.0000.000
152A153SER00.0080.00014.6510.3480.3480.0000.0000.0000.000
153A154PHE00.0240.01013.1270.0510.0510.0000.0000.0000.000
154A155SER0-0.006-0.00918.5140.6760.6760.0000.0000.0000.000
155A156ILE0-0.022-0.01121.3040.4110.4110.0000.0000.0000.000
156A157GLN0-0.031-0.02524.4460.5940.5940.0000.0000.0000.000
157A158TRP00.0700.03219.5420.3730.3730.0000.0000.0000.000
158A159GLY0-0.017-0.00323.3440.5450.5450.0000.0000.0000.000
159A160VAL0-0.092-0.03925.2120.3870.3870.0000.0000.0000.000
160A161LEU0-0.022-0.00824.458-0.059-0.0590.0000.0000.0000.000
161A162GLU-1-0.841-0.90320.179-15.056-15.0560.0000.0000.0000.000
162A163THR0-0.029-0.03417.3800.4070.4070.0000.0000.0000.000
163A164ILE0-0.0150.00511.984-0.680-0.6800.0000.0000.0000.000
164A165VAL00.0270.01115.8330.7240.7240.0000.0000.0000.000
165A166PRO0-0.0110.00315.118-0.944-0.9440.0000.0000.0000.000
166A167LEU0-0.009-0.00815.4051.3421.3420.0000.0000.0000.000
167A168GLN0-0.031-0.00514.5741.0221.0220.0000.0000.0000.000
168A169ASN0-0.025-0.03317.9970.2060.2060.0000.0000.0000.000
169A170GLY00.0140.00419.832-0.360-0.3600.0000.0000.0000.000
170A171ILE0-0.049-0.00814.788-0.185-0.1850.0000.0000.0000.000
171A172ASP-1-0.890-0.95218.025-14.745-14.7450.0000.0000.0000.000
172A173LEU0-0.029-0.00713.030-0.618-0.6180.0000.0000.0000.000
173A174THR00.0410.03415.8510.1140.1140.0000.0000.0000.000
174A175ASP-1-0.765-0.87114.485-21.122-21.1220.0000.0000.0000.000
175A176PRO00.013-0.00611.4310.5250.5250.0000.0000.0000.000
176A177TYR0-0.075-0.04513.7870.5820.5820.0000.0000.0000.000
177A178ASP-1-0.866-0.93117.307-15.589-15.5890.0000.0000.0000.000
178A179LYS10.7700.89712.38522.83322.8330.0000.0000.0000.000
179A180ALA0-0.004-0.01016.2150.1800.1800.0000.0000.0000.000
180A181HIS10.7900.86116.17917.15417.1540.0000.0000.0000.000
181A182MET00.0100.0359.9560.0410.0410.0000.0000.0000.000
182A183LEU00.001-0.0059.7192.4172.4170.0000.0000.0000.000
183A184GLN0-0.029-0.02811.454-0.084-0.0840.0000.0000.0000.000
184A185THR00.0860.0368.5460.9310.9310.0000.0000.0000.000
185A186ASP-1-0.778-0.8606.905-40.525-40.5250.0000.0000.0000.000
186A187ALA00.0370.0137.975-1.324-1.3240.0000.0000.0000.000
187A188ASN0-0.047-0.02310.0021.7711.7710.0000.0000.0000.000
189A190ILE00.0140.0046.9190.1000.1000.0000.0000.0000.000
190A191ASN00.030-0.0108.9972.0222.0220.0000.0000.0000.000
191A192ASN0-0.045-0.0358.4913.2503.2500.0000.0000.0000.000
192A193LEU0-0.084-0.0316.7180.2730.2730.0000.0000.0000.000
193A194TYR0-0.002-0.0299.1752.5012.5010.0000.0000.0000.000
194A195THR0-0.0160.01512.7391.0261.0260.0000.0000.0000.000
195A196ASN0-0.023-0.02814.9641.5621.5620.0000.0000.0000.000
196A197GLU-1-0.843-0.89315.935-15.767-15.7670.0000.0000.0000.000
197A199SER0-0.064-0.01918.4701.0271.0270.0000.0000.0000.000
198A200LEU-1-0.930-0.95317.016-16.177-16.1770.0000.0000.0000.000