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: G4671

Calculation Name: 3H0N-A-Xray549

Preferred Name:

Target Type:

Ligand Name: acetate ion | glycerol | nickel (ii) ion | zinc ion

Ligand 3-letter code: ACT | GOL | NI | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3H0N

Chain ID: A

ChEMBL ID:

UniProt ID: Q28PN4

Base Structure: X-ray

Registration Date: 2025-10-12

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 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1882500.376298
FMO2-HF: Nuclear repulsion 1810280.457016
FMO2-HF: Total energy -72219.919282
FMO2-MP2: Total energy -72428.116876


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-34.935-24.53111.768-6.142-16.029-0.059
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.813 / q_NPA : 0.914
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].
3A3LEU00.0440.0212.836-1.7241.2190.748-1.045-2.646-0.010
4A4ASP-1-0.821-0.9023.899-25.905-25.6530.005-0.032-0.225-0.001
5A5SER0-0.102-0.0474.1532.4862.598-0.001-0.011-0.1000.000
8A8ARG10.7720.8732.52744.04545.8414.586-1.447-4.935-0.013
11A11LEU0-0.076-0.0242.749-0.3690.1561.316-0.372-1.468-0.004
135A135GLU-1-0.793-0.8842.752-54.443-52.1091.638-1.772-2.200-0.022
140A140ASN0-0.050-0.0303.4870.8741.2840.030-0.134-0.306-0.001
157A157PHE00.0930.0422.613-3.429-2.6843.242-0.872-3.116-0.009
159A159THR00.0260.0153.059-2.173-1.1390.204-0.306-0.9320.002
160A160SER0-0.077-0.0423.826-9.926-9.6730.000-0.151-0.101-0.001
6A6TYR00.0480.0196.8000.5110.5110.0000.0000.0000.000
7A7GLU-1-0.812-0.9136.134-28.139-28.1390.0000.0000.0000.000
9A9THR00.0690.0225.9680.4850.4850.0000.0000.0000.000
10A10GLY00.0650.0409.2951.0051.0050.0000.0000.0000.000
12A12ARG10.7700.8586.90026.60926.6090.0000.0000.0000.000
13A13VAL00.0940.0498.2980.9260.9260.0000.0000.0000.000
14A14SER00.026-0.0119.5971.7031.7030.0000.0000.0000.000
15A15LEU0-0.073-0.0366.7710.7120.7120.0000.0000.0000.000
16A16ASP-1-0.915-0.95611.127-19.744-19.7440.0000.0000.0000.000
17A17LEU00.0120.00713.5151.0181.0180.0000.0000.0000.000
18A18VAL0-0.033-0.00114.1260.9280.9280.0000.0000.0000.000
19A19ASN0-0.025-0.02613.1231.5811.5810.0000.0000.0000.000
20A20ILE0-0.0140.00916.6960.6310.6310.0000.0000.0000.000
21A21ALA00.0640.03919.4110.5900.5900.0000.0000.0000.000
22A22THR0-0.011-0.00518.3950.6860.6860.0000.0000.0000.000
23A23PRO00.0060.00621.138-0.162-0.1620.0000.0000.0000.000
24A24GLY00.0410.02722.639-0.410-0.4100.0000.0000.0000.000
25A25SER0-0.100-0.04822.6950.4480.4480.0000.0000.0000.000
26A26ARG11.0201.01119.65012.91512.9150.0000.0000.0000.000
27A27ARG10.9100.90116.74416.17716.1770.0000.0000.0000.000
28A28GLY0-0.0140.00422.5370.2350.2350.0000.0000.0000.000
29A29THR0-0.049-0.02425.5140.6300.6300.0000.0000.0000.000
30A30PRO0-0.014-0.01925.854-0.388-0.3880.0000.0000.0000.000
31A31HIS0-0.044-0.03622.1070.1460.1460.0000.0000.0000.000
32A32THR00.017-0.00325.686-0.075-0.0750.0000.0000.0000.000
33A33GLY0-0.0020.01623.7530.0850.0850.0000.0000.0000.000
34A34GLY0-0.034-0.01624.3300.4250.4250.0000.0000.0000.000
35A35CYS0-0.064-0.03922.541-0.345-0.3450.0000.0000.0000.000
36A36VAL00.0120.01024.9660.4370.4370.0000.0000.0000.000
37A37ILE00.0580.02925.014-0.492-0.4920.0000.0000.0000.000
38A38GLU-1-0.891-0.95824.890-10.542-10.5420.0000.0000.0000.000
39A39ASP-1-0.865-0.92921.488-12.440-12.4400.0000.0000.0000.000
40A40LEU0-0.040-0.02220.416-0.764-0.7640.0000.0000.0000.000
41A41HIS00.0380.01120.557-0.781-0.7810.0000.0000.0000.000
42A42ASP-1-0.873-0.92218.132-15.899-15.8990.0000.0000.0000.000
43A43LEU0-0.059-0.02114.963-0.908-0.9080.0000.0000.0000.000
44A44LEU0-0.016-0.01615.633-1.009-1.0090.0000.0000.0000.000
45A45LYS10.8020.89514.95617.02117.0210.0000.0000.0000.000
46A46ASP-1-0.868-0.92612.431-20.020-20.0200.0000.0000.0000.000
47A47ASP-1-0.843-0.89515.882-14.046-14.0460.0000.0000.0000.000
48A48PRO0-0.003-0.01318.5170.5920.5920.0000.0000.0000.000
49A49ALA0-0.0130.00521.7750.6020.6020.0000.0000.0000.000
50A50SER00.020-0.02420.5760.4690.4690.0000.0000.0000.000
51A51VAL0-0.017-0.00120.9890.4370.4370.0000.0000.0000.000
52A52ALA0-0.053-0.02723.6260.4370.4370.0000.0000.0000.000
53A53GLN0-0.072-0.04025.9310.5750.5750.0000.0000.0000.000
54A54LEU0-0.0320.00122.2940.0750.0750.0000.0000.0000.000
55A55GLY00.0320.01126.4810.3240.3240.0000.0000.0000.000
56A56ASP-1-0.892-0.95928.035-9.600-9.6000.0000.0000.0000.000
57A57ASP-1-0.935-0.96429.659-9.672-9.6720.0000.0000.0000.000
58A58HIS00.007-0.00824.684-0.495-0.4950.0000.0000.0000.000
59A59VAL00.0000.01224.967-0.430-0.4300.0000.0000.0000.000
60A60GLU-1-0.948-0.97225.283-9.541-9.5410.0000.0000.0000.000
61A61GLY00.0180.00424.902-0.176-0.1760.0000.0000.0000.000
62A62PHE00.030-0.00118.615-0.504-0.5040.0000.0000.0000.000
63A63VAL00.013-0.00120.790-0.481-0.4810.0000.0000.0000.000
64A64GLU-1-0.896-0.93822.480-10.998-10.9980.0000.0000.0000.000
65A65LEU0-0.020-0.00916.896-0.301-0.3010.0000.0000.0000.000
66A66ALA00.0190.01217.660-0.635-0.6350.0000.0000.0000.000
67A67ARG10.9040.94518.15510.28310.2830.0000.0000.0000.000
68A68LEU0-0.0310.00119.001-0.233-0.2330.0000.0000.0000.000
69A69LEU00.0150.00213.105-0.400-0.4000.0000.0000.0000.000
70A70HIS00.0440.02014.237-1.209-1.2090.0000.0000.0000.000
71A71THR0-0.050-0.03416.105-0.079-0.0790.0000.0000.0000.000
72A72ALA0-0.028-0.01313.590-0.016-0.0160.0000.0000.0000.000
73A73ILE00.001-0.01010.238-0.717-0.7170.0000.0000.0000.000
74A74ASP-1-0.892-0.92912.626-14.465-14.4650.0000.0000.0000.000
75A75ALA00.0320.01915.771-0.087-0.0870.0000.0000.0000.000
76A76LEU0-0.052-0.0349.392-0.018-0.0180.0000.0000.0000.000
77A77SER0-0.063-0.03012.872-0.132-0.1320.0000.0000.0000.000
78A78ASN0-0.058-0.03313.7490.4060.4060.0000.0000.0000.000
79A79GLY0-0.027-0.01115.1410.6260.6260.0000.0000.0000.000
80A80GLN0-0.0190.00116.1260.3830.3830.0000.0000.0000.000
81A81VAL00.013-0.01713.490-0.008-0.0080.0000.0000.0000.000
82A82ALA00.0170.01615.684-0.068-0.0680.0000.0000.0000.000
83A83THR00.0280.02318.7700.3010.3010.0000.0000.0000.000
84A84ALA00.0450.03013.6970.1880.1880.0000.0000.0000.000
85A85ALA00.0140.00415.318-0.065-0.0650.0000.0000.0000.000
86A86THR0-0.061-0.03716.1370.3910.3910.0000.0000.0000.000
87A87ALA00.0030.00217.4930.3420.3420.0000.0000.0000.000
88A88LEU00.0030.00212.0220.2570.2570.0000.0000.0000.000
89A89ASN00.019-0.00616.103-0.176-0.1760.0000.0000.0000.000
90A90HIS0-0.054-0.02218.5500.4390.4390.0000.0000.0000.000
91A91LEU0-0.011-0.00716.5460.3790.3790.0000.0000.0000.000
92A92LEU00.001-0.01614.5130.2540.2540.0000.0000.0000.000
93A93ARG10.9030.96618.84311.81611.8160.0000.0000.0000.000
94A94LYS10.8950.96622.31511.01611.0160.0000.0000.0000.000
95A95HIS00.0250.01820.5400.5230.5230.0000.0000.0000.000
96A96PRO00.0270.00621.868-0.208-0.2080.0000.0000.0000.000
97A97ALA00.0590.01917.703-0.393-0.3930.0000.0000.0000.000
98A98THR0-0.059-0.02618.293-0.523-0.5230.0000.0000.0000.000
99A99PRO0-0.017-0.01216.7660.0340.0340.0000.0000.0000.000
100A100GLU-1-0.827-0.89918.778-11.352-11.3520.0000.0000.0000.000
101A101LEU0-0.065-0.03118.295-0.807-0.8070.0000.0000.0000.000
102A102ALA00.0380.01919.7680.6780.6780.0000.0000.0000.000
103A103GLN0-0.072-0.04619.974-0.298-0.2980.0000.0000.0000.000
104A104ASP-1-0.757-0.86117.164-16.217-16.2170.0000.0000.0000.000
105A105PRO0-0.015-0.02620.8040.3210.3210.0000.0000.0000.000
106A106ASP-1-0.884-0.90519.175-14.972-14.9720.0000.0000.0000.000
107A107GLY0-0.0050.00322.6260.1640.1640.0000.0000.0000.000
108A108THR0-0.080-0.05815.943-0.262-0.2620.0000.0000.0000.000
109A109TRP0-0.032-0.00918.7950.1610.1610.0000.0000.0000.000
110A110ARG10.8360.90212.91117.97517.9750.0000.0000.0000.000
111A111LEU0-0.0060.00013.9430.8540.8540.0000.0000.0000.000
112A112HIS00.0810.06114.479-1.341-1.3410.0000.0000.0000.000
113A113HIS0-0.009-0.01210.9221.5501.5500.0000.0000.0000.000
114A114HIS10.8370.89315.68014.32314.3230.0000.0000.0000.000
115A115PRO00.0160.03719.274-0.248-0.2480.0000.0000.0000.000
116A116LEU0-0.032-0.03821.056-0.238-0.2380.0000.0000.0000.000
117A117ASP-1-0.936-0.95523.999-10.464-10.4640.0000.0000.0000.000
118A118ALA0-0.065-0.02422.6620.2260.2260.0000.0000.0000.000
119A119GLU-1-0.854-0.92824.727-10.040-10.0400.0000.0000.0000.000
120A120LEU00.0060.02122.403-0.501-0.5010.0000.0000.0000.000
121A121VAL00.0410.01421.649-0.540-0.5400.0000.0000.0000.000
122A122PRO0-0.009-0.00720.841-0.560-0.5600.0000.0000.0000.000
123A123MET00.0270.02919.081-0.483-0.4830.0000.0000.0000.000
124A124TRP00.029-0.01513.686-1.371-1.3710.0000.0000.0000.000
125A125THR0-0.031-0.02515.950-0.793-0.7930.0000.0000.0000.000
126A126ALA0-0.023-0.00416.002-0.630-0.6300.0000.0000.0000.000
127A127ILE00.0040.00612.647-1.005-1.0050.0000.0000.0000.000
128A128CYS0-0.054-0.02311.593-1.632-1.6320.0000.0000.0000.000
129A129ALA0-0.012-0.01011.164-1.066-1.0660.0000.0000.0000.000
130A130GLU-1-0.769-0.84710.093-23.970-23.9700.0000.0000.0000.000
131A131GLY00.0340.0208.031-1.211-1.2110.0000.0000.0000.000
132A132LEU0-0.037-0.0236.871-2.636-2.6360.0000.0000.0000.000
133A133ALA00.0110.0068.555-0.552-0.5520.0000.0000.0000.000
134A134ARG10.7200.8155.56828.18328.1830.0000.0000.0000.000
136A136ILE0-0.037-0.0085.6950.2120.2120.0000.0000.0000.000
137A137GLY00.0120.0149.2980.5180.5180.0000.0000.0000.000
138A138HIS0-0.063-0.0455.424-2.696-2.6960.0000.0000.0000.000
139A139GLN0-0.050-0.0267.407-1.001-1.0010.0000.0000.0000.000
141A141VAL00.0390.0216.585-0.342-0.3420.0000.0000.0000.000
142A142ARG10.9750.9729.24318.45918.4590.0000.0000.0000.000
143A143ARG10.8090.9114.80540.64140.6410.0000.0000.0000.000
144A144PHE00.0270.0206.151-1.448-1.4480.0000.0000.0000.000
145A145GLY00.0190.0159.1451.2231.2230.0000.0000.0000.000
146A146ILE00.0530.02912.408-0.259-0.2590.0000.0000.0000.000
147A147CYS0-0.130-0.01515.644-0.336-0.3360.0000.0000.0000.000
148A148ASN00.0860.04217.3110.8240.8240.0000.0000.0000.000
149A149ALA0-0.037-0.03020.0590.5950.5950.0000.0000.0000.000
150A150HIS00.0450.01422.162-0.097-0.0970.0000.0000.0000.000
151A151ARG10.9290.96325.0419.7759.7750.0000.0000.0000.000
152A152CYS0-0.051-0.01319.435-0.218-0.2180.0000.0000.0000.000
153A153ASP-1-0.726-0.83519.539-13.212-13.2120.0000.0000.0000.000
154A154ARG10.7490.84916.32713.53713.5370.0000.0000.0000.000
155A155VAL00.0550.03112.082-0.439-0.4390.0000.0000.0000.000
156A156TYR0-0.077-0.05910.023-0.400-0.4000.0000.0000.0000.000
158A158ASP-1-0.807-0.8926.963-33.640-33.6400.0000.0000.0000.000
161A161ARG10.9820.9736.37326.90426.9040.0000.0000.0000.000
162A162ASN0-0.039-0.0177.2452.3162.3160.0000.0000.0000.000
163A163GLY00.0240.0299.3741.1631.1630.0000.0000.0000.000
164A164THR00.001-0.00710.4551.4231.4230.0000.0000.0000.000
165A165ARG10.8740.9417.08133.53533.5350.0000.0000.0000.000
166A166GLN00.0310.03112.6060.5700.5700.0000.0000.0000.000
167A167TYR00.026-0.00714.6141.0201.0200.0000.0000.0000.000
168A168CYS00.007-0.01413.209-1.111-1.1110.0000.0000.0000.000
169A169SER00.041-0.00113.302-0.452-0.4520.0000.0000.0000.000
170A170LEU00.0420.01915.0920.6180.6180.0000.0000.0000.000
171A171ALA00.0080.00116.5840.8570.8570.0000.0000.0000.000
172A172CYS-1-0.758-0.76518.069-14.378-14.3780.0000.0000.0000.000
173A173GLN00.0040.01215.955-0.321-0.3210.0000.0000.0000.000
174A174ASN0-0.005-0.02218.8770.3380.3380.0000.0000.0000.000
175A175ARG10.8210.85221.16413.96713.9670.0000.0000.0000.000
176A176VAL00.0420.02521.9410.5530.5530.0000.0000.0000.000
177A177LYS10.8870.94820.37514.98914.9890.0000.0000.0000.000
178A178ALA0-0.027-0.02024.3420.3770.3770.0000.0000.0000.000
179A179ALA0-0.038-0.00626.8910.4580.4580.0000.0000.0000.000
180A180ALA00.0350.00926.4540.3870.3870.0000.0000.0000.000
181A181PHE00.0120.01028.5740.2640.2640.0000.0000.0000.000
182A182ARG10.7990.88629.47010.54310.5430.0000.0000.0000.000
183A183GLU-1-0.878-0.93129.364-10.296-10.2960.0000.0000.0000.000
184A184ARG0-0.0160.01632.541-0.296-0.2960.0000.0000.0000.000