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: RMLV8

Calculation Name: 4HNZ-A-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4HNZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q383Q5

Base Structure: X-ray

Registration Date: 2025-10-04

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 OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1732061.138073
FMO2-HF: Nuclear repulsion 1666130.552699
FMO2-HF: Total energy -65930.585374
FMO2-MP2: Total energy -66123.938396


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:THR)


Summations of interaction energy for fragment #1(A:1:THR)
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.
-252.473-243.57238.307-21.139-26.069-0.193
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.712 / q_NPA : 0.854
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].
3A3ILE0-0.0030.0102.4753.6635.6450.676-0.650-2.008-0.005
4A4LEU0-0.007-0.0034.6540.7790.785-0.001-0.004-0.0010.000
17A17ASP-1-0.767-0.8622.160-77.080-75.4156.183-4.000-3.848-0.045
18A18ARG10.8400.8914.69424.39824.522-0.001-0.007-0.1170.000
19A19GLN0-0.062-0.0204.3976.6306.701-0.001-0.009-0.0610.000
20A20VAL0-0.005-0.0044.268-4.961-4.720-0.001-0.015-0.2250.000
21A21THR00.0340.0134.2483.7913.852-0.001-0.001-0.0590.000
34A34LYS10.7890.8951.98851.85551.2067.134-2.548-3.9370.029
47A47ALA0-0.010-0.0072.334-8.147-7.0721.426-0.866-1.635-0.003
48A48GLY00.0710.0263.1436.0835.5730.0450.681-0.215-0.001
49A49SER0-0.068-0.0605.160-1.702-1.626-0.0010.000-0.0750.000
123A123ILE0-0.0030.0204.1260.5750.729-0.001-0.016-0.1370.000
124A124GLY00.005-0.0072.991-7.111-6.5420.124-0.295-0.398-0.001
125A125SER0-0.038-0.0432.138-7.727-6.8093.643-2.024-2.538-0.026
126A126GLY00.0510.0283.47410.42810.8410.001-0.135-0.2780.000
127A127GLY00.0050.0085.1117.4227.523-0.001-0.007-0.0930.000
160A160ASP-1-0.732-0.8291.849-117.709-118.4058.471-4.546-3.229-0.062
161A161VAL00.0420.0214.863-4.050-3.997-0.001-0.003-0.0490.000
162A162PHE0-0.062-0.0302.8413.8735.0540.397-0.664-0.915-0.003
163A163SER0-0.074-0.0661.965-37.177-35.31210.200-5.963-6.102-0.075
164A164ASN00.0000.0043.6076.3186.5190.016-0.067-0.149-0.001
5A5SER0-0.048-0.0248.3561.3651.3650.0000.0000.0000.000
6A6VAL00.021-0.00211.654-0.061-0.0610.0000.0000.0000.000
7A7ARG10.8750.93215.15015.23215.2320.0000.0000.0000.000
8A8LYS10.8090.90218.61813.40413.4040.0000.0000.0000.000
9A9GLY0-0.020-0.00621.6890.1390.1390.0000.0000.0000.000
10A10ASP-1-0.901-0.96023.588-11.194-11.1940.0000.0000.0000.000
11A11THR0-0.030-0.01319.850-0.111-0.1110.0000.0000.0000.000
12A12VAL0-0.058-0.03615.931-0.441-0.4410.0000.0000.0000.000
13A13VAL0-0.0090.00013.979-0.019-0.0190.0000.0000.0000.000
14A14LEU00.0020.0028.902-0.886-0.8860.0000.0000.0000.000
15A15LEU00.009-0.0039.2390.6820.6820.0000.0000.0000.000
16A16GLY00.0320.0025.241-2.462-2.4620.0000.0000.0000.000
22A22LEU00.000-0.0056.8090.5730.5730.0000.0000.0000.000
23A23GLY0-0.009-0.02010.0620.3450.3450.0000.0000.0000.000
24A24GLU-1-0.918-0.9558.308-27.642-27.6420.0000.0000.0000.000
25A25ARG10.9030.9539.39821.37821.3780.0000.0000.0000.000
26A26ILE0-0.0060.00710.5680.8920.8920.0000.0000.0000.000
27A27VAL00.0250.0197.882-2.023-2.0230.0000.0000.0000.000
28A28ALA0-0.0090.0029.9742.2922.2920.0000.0000.0000.000
29A29LYS10.8770.92310.11122.97122.9710.0000.0000.0000.000
30A30SER00.0440.0329.089-2.520-2.5200.0000.0000.0000.000
31A31SER00.0460.02510.144-0.379-0.3790.0000.0000.0000.000
32A32ALA0-0.040-0.0227.9782.3952.3950.0000.0000.0000.000
33A33CYS00.0460.0507.656-2.636-2.6360.0000.0000.0000.000
35A35LEU00.0240.0186.395-0.706-0.7060.0000.0000.0000.000
36A36ARG10.8320.8879.24222.83622.8360.0000.0000.0000.000
37A37ARG10.8400.91412.67114.35514.3550.0000.0000.0000.000
38A38ILE0-0.009-0.00115.2390.2420.2420.0000.0000.0000.000
39A39ASN0-0.006-0.00417.9930.4740.4740.0000.0000.0000.000
40A40ASP-1-0.907-0.95320.277-12.089-12.0890.0000.0000.0000.000
41A41ASP-1-0.899-0.93021.920-11.814-11.8140.0000.0000.0000.000
42A42VAL0-0.053-0.03016.819-0.449-0.4490.0000.0000.0000.000
43A43VAL0-0.0050.00113.904-0.190-0.1900.0000.0000.0000.000
44A44ILE0-0.001-0.00910.467-0.157-0.1570.0000.0000.0000.000
45A45GLY00.0160.0067.697-0.176-0.1760.0000.0000.0000.000
46A46PHE0-0.025-0.0155.1880.7080.7080.0000.0000.0000.000
50A50THR00.022-0.0097.817-0.185-0.1850.0000.0000.0000.000
51A51ALA00.0250.0219.8361.0231.0230.0000.0000.0000.000
52A52ASP-1-0.799-0.8519.875-21.084-21.0840.0000.0000.0000.000
53A53ALA00.0590.0227.8920.7670.7670.0000.0000.0000.000
54A54ILE0-0.030-0.01510.0110.7980.7980.0000.0000.0000.000
55A55SER0-0.011-0.01613.1621.1771.1770.0000.0000.0000.000
56A56LEU0-0.027-0.01711.6020.9200.9200.0000.0000.0000.000
57A57MET0-0.050-0.01410.3850.2300.2300.0000.0000.0000.000
58A58GLU-1-0.860-0.92914.393-13.811-13.8110.0000.0000.0000.000
59A59LYS10.8200.91017.27813.81013.8100.0000.0000.0000.000
60A60LEU00.0150.00014.7410.5380.5380.0000.0000.0000.000
61A61GLU-1-0.890-0.94817.332-14.211-14.2110.0000.0000.0000.000
62A62ASN0-0.040-0.01719.9150.8360.8360.0000.0000.0000.000
63A63LYS10.8370.92720.61312.25012.2500.0000.0000.0000.000
64A64ILE00.010-0.00418.3880.3180.3180.0000.0000.0000.000
65A65GLY0-0.015-0.00322.6190.4030.4030.0000.0000.0000.000
66A66GLU-1-0.933-0.96425.324-10.360-10.3600.0000.0000.0000.000
67A67PHE0-0.072-0.04724.8480.4590.4590.0000.0000.0000.000
68A68PRO00.0210.00825.648-0.263-0.2630.0000.0000.0000.000
69A69ASN00.0020.00325.7730.0210.0210.0000.0000.0000.000
70A70GLN0-0.0090.00525.0520.0250.0250.0000.0000.0000.000
71A71LEU00.0620.04817.464-0.136-0.1360.0000.0000.0000.000
72A72THR00.003-0.04420.134-0.579-0.5790.0000.0000.0000.000
73A73ARG10.8480.92921.18510.16410.1640.0000.0000.0000.000
74A74ALA00.0370.01720.709-0.035-0.0350.0000.0000.0000.000
75A75ALA00.0340.01617.100-0.332-0.3320.0000.0000.0000.000
76A76VAL00.0070.00318.440-0.334-0.3340.0000.0000.0000.000
77A77GLU-1-0.843-0.91320.992-11.288-11.2880.0000.0000.0000.000
78A78LEU00.0130.01814.5320.1270.1270.0000.0000.0000.000
79A79ALA00.0160.01217.518-0.204-0.2040.0000.0000.0000.000
80A80LYS10.7760.86418.42511.40411.4040.0000.0000.0000.000
81A81GLU-1-0.833-0.89620.577-12.538-12.5380.0000.0000.0000.000
82A82TRP00.013-0.00510.7290.2450.2450.0000.0000.0000.000
83A83ARG10.8700.93517.61015.88115.8810.0000.0000.0000.000
84A84THR0-0.085-0.05720.2790.5040.5040.0000.0000.0000.000
85A85ASP-1-0.789-0.88821.362-12.325-12.3250.0000.0000.0000.000
86A86ARG10.8970.93221.57210.70210.7020.0000.0000.0000.000
87A87ALA0-0.038-0.01620.802-0.212-0.2120.0000.0000.0000.000
88A88LEU00.0480.02417.017-0.711-0.7110.0000.0000.0000.000
89A89ARG10.8860.94116.46813.39213.3920.0000.0000.0000.000
90A90ARG10.8040.90517.25713.56613.5660.0000.0000.0000.000
91A91LEU0-0.0130.02213.025-0.239-0.2390.0000.0000.0000.000
92A92GLU-1-0.955-0.9699.675-24.253-24.2530.0000.0000.0000.000
93A93ALA0-0.015-0.0267.663-2.191-2.1910.0000.0000.0000.000
94A94SER0-0.072-0.0466.7081.0651.0650.0000.0000.0000.000
95A95LEU0-0.011-0.0076.597-2.851-2.8510.0000.0000.0000.000
96A96ILE00.0110.0097.3910.4470.4470.0000.0000.0000.000
97A97VAL00.0120.0069.825-0.132-0.1320.0000.0000.0000.000
98A98CYS0-0.029-0.00512.883-0.184-0.1840.0000.0000.0000.000
99A99SER00.0880.05215.5270.0800.0800.0000.0000.0000.000
100A100ALA00.0920.04218.829-0.528-0.5280.0000.0000.0000.000
101A101GLU-1-0.915-0.95521.286-12.053-12.0530.0000.0000.0000.000
102A102GLU-1-0.820-0.89119.633-13.000-13.0000.0000.0000.0000.000
103A103THR0-0.007-0.02413.541-0.102-0.1020.0000.0000.0000.000
104A104LEU0-0.034-0.00914.4840.3850.3850.0000.0000.0000.000
105A105GLU-1-0.901-0.94810.209-25.850-25.8500.0000.0000.0000.000
106A106ILE0-0.012-0.00510.9911.6191.6190.0000.0000.0000.000
107A107ASP-1-0.751-0.86510.738-23.195-23.1950.0000.0000.0000.000
108A108GLY00.0880.05411.8911.5621.5620.0000.0000.0000.000
109A109GLN0-0.096-0.05312.2001.9991.9990.0000.0000.0000.000
110A110GLY0-0.041-0.03215.7611.2691.2690.0000.0000.0000.000
111A111ASN0-0.122-0.05914.5561.8901.8900.0000.0000.0000.000
112A112VAL00.003-0.01515.336-0.614-0.6140.0000.0000.0000.000
113A113ILE0-0.033-0.00613.5480.9190.9190.0000.0000.0000.000
114A114THR00.0360.02815.174-0.511-0.5110.0000.0000.0000.000
115A115PRO0-0.049-0.01416.124-0.386-0.3860.0000.0000.0000.000
116A116GLU-1-0.902-0.94617.172-14.215-14.2150.0000.0000.0000.000
117A117ALA0-0.020-0.02620.261-0.023-0.0230.0000.0000.0000.000
118A118ASP-1-0.810-0.89518.129-16.610-16.6100.0000.0000.0000.000
119A119GLY00.0420.02218.397-0.271-0.2710.0000.0000.0000.000
120A120ILE0-0.067-0.03213.250-0.916-0.9160.0000.0000.0000.000
121A121VAL0-0.007-0.00710.3820.0230.0230.0000.0000.0000.000
122A122ALA0-0.019-0.0217.901-0.828-0.8280.0000.0000.0000.000
128A128THR00.011-0.0126.9164.3644.3640.0000.0000.0000.000
129A129PHE00.0150.0107.0993.8053.8050.0000.0000.0000.000
130A130ALA00.0280.0228.5212.8772.8770.0000.0000.0000.000
131A131LYS10.9720.98310.44925.83725.8370.0000.0000.0000.000
132A132ALA0-0.021-0.01112.4142.0482.0480.0000.0000.0000.000
133A133ALA0-0.018-0.01213.2411.6231.6230.0000.0000.0000.000
134A134ALA00.021-0.00313.7711.2581.2580.0000.0000.0000.000
135A135ARG10.8390.89615.63518.65818.6580.0000.0000.0000.000
136A136ALA0-0.034-0.00118.1570.9910.9910.0000.0000.0000.000
137A137LEU0-0.051-0.03517.9870.7290.7290.0000.0000.0000.000
138A138ILE0-0.0030.01018.6810.3900.3900.0000.0000.0000.000
139A139ASP-1-0.897-0.94920.951-12.446-12.4460.0000.0000.0000.000
140A140VAL0-0.0310.00623.7540.5240.5240.0000.0000.0000.000
141A141ASP-1-0.868-0.93725.486-10.808-10.8080.0000.0000.0000.000
142A142GLY0-0.020-0.02326.969-0.222-0.2220.0000.0000.0000.000
143A143TYR0-0.040-0.02820.426-0.656-0.6560.0000.0000.0000.000
144A144ASP-1-0.773-0.87421.021-13.991-13.9910.0000.0000.0000.000
145A145ALA00.0780.02817.938-0.627-0.6270.0000.0000.0000.000
146A146GLU-1-0.756-0.85316.197-17.592-17.5920.0000.0000.0000.000
147A147LYS10.8150.90416.57912.28412.2840.0000.0000.0000.000
148A148ILE0-0.027-0.00715.866-0.559-0.5590.0000.0000.0000.000
149A149ALA00.0350.02212.695-1.118-1.1180.0000.0000.0000.000
150A150ARG10.8460.88812.73316.45416.4540.0000.0000.0000.000
151A151LYS10.8810.95613.63015.57215.5720.0000.0000.0000.000
152A152ALA00.0200.00612.828-0.395-0.3950.0000.0000.0000.000
153A153MET00.0060.0046.056-2.695-2.6950.0000.0000.0000.000
154A154ARG10.8640.9649.46919.13519.1350.0000.0000.0000.000
155A155ILE00.0190.00910.900-0.934-0.9340.0000.0000.0000.000
156A156ALA0-0.014-0.0037.395-0.299-0.2990.0000.0000.0000.000
157A157THR0-0.066-0.0645.418-3.559-3.5590.0000.0000.0000.000
158A158ASP-1-0.885-0.9397.048-25.106-25.1060.0000.0000.0000.000
159A159ILE0-0.076-0.0268.5172.0882.0880.0000.0000.0000.000
165A165GLU-1-0.803-0.9127.036-27.774-27.7740.0000.0000.0000.000
166A166HIS0-0.125-0.0499.0692.8652.8650.0000.0000.0000.000
167A167TRP0-0.004-0.0337.355-0.914-0.9140.0000.0000.0000.000
168A168ASP-1-0.828-0.8738.449-21.711-21.7110.0000.0000.0000.000
169A169VAL0-0.018-0.0389.777-1.660-1.6600.0000.0000.0000.000
170A170GLU-1-0.842-0.90712.397-15.962-15.9620.0000.0000.0000.000
171A171VAL0-0.013-0.00914.311-0.603-0.6030.0000.0000.0000.000
172A172LEU0-0.038-0.01417.4490.4180.4180.0000.0000.0000.000
173A173GLU-1-0.830-0.89520.104-12.981-12.9810.0000.0000.0000.000
174A174HIS0-0.034-0.00323.4620.4820.4820.0000.0000.0000.000