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: VVJ71

Calculation Name: 1MNG-A-Xray547

Preferred Name:

Target Type:

Ligand Name: azide ion | manganese (ii) ion

Ligand 3-letter code: AZI | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MNG

Chain ID: A

ChEMBL ID:

UniProt ID: P61503

Base Structure: X-ray

Registration Date: 2025-10-03

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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2419489.924587
FMO2-HF: Nuclear repulsion 2339967.074394
FMO2-HF: Total energy -79522.850193
FMO2-MP2: Total energy -79760.396552


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:PRO)


Summations of interaction energy for fragment #1(A:1:PRO)
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.
-183.454-179.26727.137-14.77-16.555-0.164
Interaction energy analysis for fragmet #1(A:1:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.756 / q_NPA : 0.858
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].
3A3PRO0-0.033-0.0213.262-1.2790.5900.039-0.858-1.050-0.003
4A4PHE0-0.004-0.0052.663-8.096-6.9981.447-0.856-1.689-0.008
5A5LYS00.0630.0355.2896.1166.215-0.001-0.006-0.0910.000
52A52GLY00.0250.0122.555-12.154-11.4222.190-0.996-1.927-0.013
53A53VAL0-0.042-0.0152.727-3.369-2.4340.962-0.494-1.403-0.006
54A54GLU-1-0.755-0.8741.805-142.791-143.45222.499-11.556-10.282-0.134
55A55VAL00.0210.0133.71410.06710.1820.001-0.004-0.1130.000
6A6LEU0-0.026-0.0207.899-1.237-1.2370.0000.0000.0000.000
7A7PRO0-0.030-0.0019.4230.3090.3090.0000.0000.0000.000
8A8ASP-1-0.869-0.93911.208-19.321-19.3210.0000.0000.0000.000
9A9LEU0-0.049-0.02114.780-0.396-0.3960.0000.0000.0000.000
10A10GLY00.0080.00517.4320.1460.1460.0000.0000.0000.000
11A11TYR0-0.038-0.04018.7190.9260.9260.0000.0000.0000.000
12A12PRO00.0320.00722.069-0.304-0.3040.0000.0000.0000.000
13A13TYR00.0240.00420.3870.2870.2870.0000.0000.0000.000
14A14GLU-1-0.908-0.96524.987-10.186-10.1860.0000.0000.0000.000
15A15ALA0-0.047-0.01625.7340.3430.3430.0000.0000.0000.000
16A16LEU00.0050.00023.5550.1050.1050.0000.0000.0000.000
17A17GLU-1-0.804-0.88928.063-9.644-9.6440.0000.0000.0000.000
18A18PRO0-0.074-0.03531.5440.0340.0340.0000.0000.0000.000
19A19HIS00.0200.00030.2500.2200.2200.0000.0000.0000.000
20A20ILE00.0200.00725.4740.0350.0350.0000.0000.0000.000
21A21ASP-1-0.799-0.86529.113-10.631-10.6310.0000.0000.0000.000
22A22ALA00.0630.01727.640-0.430-0.4300.0000.0000.0000.000
23A23LYS10.9480.98426.6779.6809.6800.0000.0000.0000.000
24A24THR0-0.058-0.06325.353-0.397-0.3970.0000.0000.0000.000
25A25MET0-0.0220.00421.729-0.589-0.5890.0000.0000.0000.000
26A26GLU-1-0.944-0.96121.953-12.807-12.8070.0000.0000.0000.000
27A27ILE0-0.075-0.04521.795-0.610-0.6100.0000.0000.0000.000
28A28HIS0-0.027-0.01319.931-0.246-0.2460.0000.0000.0000.000
29A29HIS00.0290.00014.9910.0650.0650.0000.0000.0000.000
30A30GLN00.0410.01017.183-1.003-1.0030.0000.0000.0000.000
31A31LYS10.8660.94118.68813.63113.6310.0000.0000.0000.000
32A32HIS00.0090.00118.629-0.555-0.5550.0000.0000.0000.000
33A33HIS00.0070.01610.7131.1131.1130.0000.0000.0000.000
34A34GLY00.0810.04113.687-1.543-1.5430.0000.0000.0000.000
35A35ALA0-0.0090.00614.386-0.887-0.8870.0000.0000.0000.000
36A36TYR0-0.036-0.01013.478-0.094-0.0940.0000.0000.0000.000
37A37VAL00.0360.0188.912-1.140-1.1400.0000.0000.0000.000
38A38THR0-0.032-0.02310.610-1.605-1.6050.0000.0000.0000.000
39A39ASN0-0.040-0.03313.020-0.038-0.0380.0000.0000.0000.000
40A40LEU0-0.045-0.0096.5930.6340.6340.0000.0000.0000.000
41A41ASN00.030-0.0017.771-4.957-4.9570.0000.0000.0000.000
42A42ALA00.0630.0369.8750.3610.3610.0000.0000.0000.000
43A43ALA0-0.056-0.01911.4591.4721.4720.0000.0000.0000.000
44A44LEU00.0470.0025.8470.7410.7410.0000.0000.0000.000
45A45GLU-1-0.941-0.9419.891-20.520-20.5200.0000.0000.0000.000
46A46LYS10.8730.92911.25419.23519.2350.0000.0000.0000.000
47A47TYR0-0.062-0.06311.3231.4501.4500.0000.0000.0000.000
48A48PRO00.0690.0188.998-2.093-2.0930.0000.0000.0000.000
49A49TYR0-0.026-0.0088.213-2.511-2.5110.0000.0000.0000.000
50A50LEU00.004-0.0027.242-0.678-0.6780.0000.0000.0000.000
51A51HIS0-0.069-0.0304.858-6.246-6.2460.0000.0000.0000.000
56A56GLU-1-0.828-0.9346.044-34.738-34.7380.0000.0000.0000.000
57A57VAL0-0.077-0.0277.0874.1484.1480.0000.0000.0000.000
58A58LEU00.0290.0115.3633.7823.7820.0000.0000.0000.000
59A59LEU0-0.017-0.0188.7173.1193.1190.0000.0000.0000.000
60A60ARG10.9080.95710.49227.10827.1080.0000.0000.0000.000
61A61HIS0-0.045-0.02511.4042.6192.6190.0000.0000.0000.000
62A62LEU00.0120.01312.5680.4600.4600.0000.0000.0000.000
63A63ALA0-0.010-0.00714.4620.2680.2680.0000.0000.0000.000
64A64ALA0-0.023-0.00915.0190.8310.8310.0000.0000.0000.000
65A65LEU0-0.0300.00110.489-0.648-0.6480.0000.0000.0000.000
66A66PRO00.0120.01413.4101.2791.2790.0000.0000.0000.000
67A67GLN00.0570.01516.369-0.590-0.5900.0000.0000.0000.000
68A68ASP-1-0.883-0.91217.727-16.773-16.7730.0000.0000.0000.000
69A69ILE0-0.027-0.01711.691-0.260-0.2600.0000.0000.0000.000
70A70GLN0-0.0300.00214.468-0.505-0.5050.0000.0000.0000.000
71A71THR00.030-0.00515.141-0.767-0.7670.0000.0000.0000.000
72A72ALA0-0.0060.01414.761-0.033-0.0330.0000.0000.0000.000
73A73VAL00.0580.0189.388-0.784-0.7840.0000.0000.0000.000
74A74ARG10.8360.88211.77014.45214.4520.0000.0000.0000.000
75A75ASN0-0.018-0.01614.255-0.392-0.3920.0000.0000.0000.000
76A76ASN0-0.041-0.03412.8110.9240.9240.0000.0000.0000.000
77A77GLY00.0640.0369.580-1.427-1.4270.0000.0000.0000.000
78A78GLY00.0370.01910.327-1.166-1.1660.0000.0000.0000.000
79A79GLY0-0.014-0.00413.2310.1960.1960.0000.0000.0000.000
80A80HIS00.0380.0295.9404.4754.4750.0000.0000.0000.000
81A81LEU00.0270.0319.2960.2390.2390.0000.0000.0000.000
82A82ASN00.017-0.01211.1440.2560.2560.0000.0000.0000.000
83A83HIS0-0.001-0.01714.2822.0092.0090.0000.0000.0000.000
84A84SER0-0.031-0.02110.3660.2250.2250.0000.0000.0000.000
85A85LEU0-0.042-0.01512.5040.5920.5920.0000.0000.0000.000
86A86PHE00.0050.00314.8491.1521.1520.0000.0000.0000.000
87A87TRP00.003-0.01514.3331.3271.3270.0000.0000.0000.000
88A88ARG10.8930.95613.33021.49721.4970.0000.0000.0000.000
89A89LEU00.0180.01917.1480.9320.9320.0000.0000.0000.000
90A90LEU0-0.010-0.00320.1300.9090.9090.0000.0000.0000.000
91A91THR0-0.043-0.02019.5970.2570.2570.0000.0000.0000.000
92A92PRO00.0220.00422.0230.4290.4290.0000.0000.0000.000
93A93GLY0-0.024-0.01325.163-0.270-0.2700.0000.0000.0000.000
94A94GLY00.0160.02925.8930.1910.1910.0000.0000.0000.000
95A95ALA0-0.017-0.02026.8530.3870.3870.0000.0000.0000.000
96A96LYS10.8370.89627.86410.89110.8910.0000.0000.0000.000
97A97GLU-1-0.937-0.96330.640-8.934-8.9340.0000.0000.0000.000
98A98PRO0-0.030-0.01828.335-0.230-0.2300.0000.0000.0000.000
99A99VAL00.0350.01426.9320.4370.4370.0000.0000.0000.000
100A100GLY0-0.008-0.00527.981-0.282-0.2820.0000.0000.0000.000
101A101GLU-1-0.858-0.93425.928-10.352-10.3520.0000.0000.0000.000
102A102LEU0-0.009-0.00523.5460.2130.2130.0000.0000.0000.000
103A103LYS10.8490.91426.7389.4379.4370.0000.0000.0000.000
104A104LYS10.8760.93130.29610.42010.4200.0000.0000.0000.000
105A105ALA00.0430.02827.9760.2340.2340.0000.0000.0000.000
106A106ILE0-0.016-0.01727.3430.1410.1410.0000.0000.0000.000
107A107ASP-1-0.853-0.92831.094-8.940-8.9400.0000.0000.0000.000
108A108GLU-1-0.985-0.98633.263-9.165-9.1650.0000.0000.0000.000
109A109GLN0-0.048-0.02429.2140.0230.0230.0000.0000.0000.000
110A110PHE0-0.062-0.04328.836-0.026-0.0260.0000.0000.0000.000
111A111GLY00.0380.03734.5050.2060.2060.0000.0000.0000.000
112A112GLY00.0200.01734.8660.2030.2030.0000.0000.0000.000
113A113PHE0-0.034-0.03530.396-0.139-0.1390.0000.0000.0000.000
114A114GLN00.0170.01633.662-0.206-0.2060.0000.0000.0000.000
115A115ALA00.0780.03435.914-0.047-0.0470.0000.0000.0000.000
116A116LEU0-0.022-0.00328.149-0.127-0.1270.0000.0000.0000.000
117A117LYS10.9550.99031.4268.9938.9930.0000.0000.0000.000
118A118GLU-1-0.907-0.92932.874-8.333-8.3330.0000.0000.0000.000
119A119LYS10.9550.97731.5949.3199.3190.0000.0000.0000.000
120A120LEU00.007-0.00426.082-0.155-0.1550.0000.0000.0000.000
121A121THR0-0.011-0.01929.938-0.215-0.2150.0000.0000.0000.000
122A122GLN0-0.028-0.02332.4430.0680.0680.0000.0000.0000.000
123A123ALA0-0.017-0.00228.4630.0280.0280.0000.0000.0000.000
124A124ALA00.010-0.00128.488-0.240-0.2400.0000.0000.0000.000
125A125MET0-0.032-0.01529.528-0.096-0.0960.0000.0000.0000.000
126A126GLY00.0030.00732.8000.1230.1230.0000.0000.0000.000
127A127ARG10.8490.93526.18711.75211.7520.0000.0000.0000.000
128A128PHE00.0120.01129.700-0.091-0.0910.0000.0000.0000.000
129A129GLY00.0070.00829.666-0.258-0.2580.0000.0000.0000.000
130A130SER00.0310.00924.5170.1060.1060.0000.0000.0000.000
131A131GLY00.005-0.00722.9660.0090.0090.0000.0000.0000.000
132A132TRP0-0.0130.00318.409-0.067-0.0670.0000.0000.0000.000
133A133ALA0-0.007-0.00222.8980.3140.3140.0000.0000.0000.000
134A134TRP0-0.021-0.02516.777-0.693-0.6930.0000.0000.0000.000
135A135LEU0-0.0070.01123.0330.6950.6950.0000.0000.0000.000
136A136VAL00.003-0.00920.483-0.755-0.7550.0000.0000.0000.000
137A137LYS10.8330.90520.88715.17915.1790.0000.0000.0000.000
138A138ASP-1-0.733-0.84921.030-12.801-12.8010.0000.0000.0000.000
139A139PRO00.024-0.00520.5400.1470.1470.0000.0000.0000.000
140A140PHE0-0.046-0.01222.8460.2760.2760.0000.0000.0000.000
141A141GLY00.0020.01225.1590.4900.4900.0000.0000.0000.000
142A142LYS10.8720.93826.45010.48810.4880.0000.0000.0000.000
143A143LEU00.0230.01224.840-0.616-0.6160.0000.0000.0000.000
144A144HIS10.7910.87025.17612.25412.2540.0000.0000.0000.000
145A145VAL00.0190.01925.590-0.405-0.4050.0000.0000.0000.000
146A146LEU0-0.0220.00122.5500.3820.3820.0000.0000.0000.000
147A147SER00.0410.01324.746-0.234-0.2340.0000.0000.0000.000
148A148THR0-0.0070.00820.0300.4560.4560.0000.0000.0000.000
149A149PRO00.0150.01022.4350.2230.2230.0000.0000.0000.000
150A150ASN00.015-0.01621.278-0.484-0.4840.0000.0000.0000.000
151A151GLN00.0440.03516.340-0.444-0.4440.0000.0000.0000.000
152A152ASP-1-0.739-0.81416.410-16.879-16.8790.0000.0000.0000.000
153A153ASN00.0450.01514.2680.5250.5250.0000.0000.0000.000
154A154PRO00.0290.01216.361-0.159-0.1590.0000.0000.0000.000
155A155VAL00.0100.01212.0990.3330.3330.0000.0000.0000.000
156A156MET0-0.116-0.04214.912-0.226-0.2260.0000.0000.0000.000
157A157GLU-1-0.962-0.97616.347-13.178-13.1780.0000.0000.0000.000
158A158GLY0-0.034-0.01017.5770.6400.6400.0000.0000.0000.000
159A159PHE0-0.048-0.02118.5380.3060.3060.0000.0000.0000.000
160A160THR00.0190.00115.891-1.650-1.6500.0000.0000.0000.000
161A161PRO0-0.040-0.02815.1991.1481.1480.0000.0000.0000.000
162A162ILE0-0.052-0.01317.323-0.533-0.5330.0000.0000.0000.000
163A163VAL00.0460.00519.968-0.104-0.1040.0000.0000.0000.000
164A164GLY00.0190.00719.6110.1440.1440.0000.0000.0000.000
165A165ILE0-0.022-0.01620.6130.0060.0060.0000.0000.0000.000
166A166ASP-1-0.774-0.88321.162-14.354-14.3540.0000.0000.0000.000
167A167VAL00.0080.00122.7940.6410.6410.0000.0000.0000.000
168A168TRP0-0.040-0.03921.1420.5960.5960.0000.0000.0000.000
169A169GLU-1-0.888-0.94325.603-10.075-10.0750.0000.0000.0000.000
170A170HIS10.8110.91621.03814.45414.4540.0000.0000.0000.000
171A171ALA00.0080.01423.950-0.149-0.1490.0000.0000.0000.000
172A172TYR00.0170.02225.4640.1130.1130.0000.0000.0000.000
173A173TYR0-0.004-0.00229.2810.4490.4490.0000.0000.0000.000
174A174LEU0-0.031-0.02129.0530.4000.4000.0000.0000.0000.000
175A175LYS10.8930.97232.0249.6759.6750.0000.0000.0000.000
176A176TYR0-0.046-0.05831.3170.4000.4000.0000.0000.0000.000
177A177GLN0-0.036-0.00334.3060.3900.3900.0000.0000.0000.000
178A178ASN00.0530.00733.861-0.242-0.2420.0000.0000.0000.000
179A179ARG10.8070.91135.7358.3518.3510.0000.0000.0000.000
180A180ARG10.8530.89929.68910.63410.6340.0000.0000.0000.000
181A181ALA00.0520.01132.636-0.200-0.2000.0000.0000.0000.000
182A182ASP-1-0.832-0.90234.832-8.456-8.4560.0000.0000.0000.000
183A183TYR0-0.022-0.02725.304-0.047-0.0470.0000.0000.0000.000
184A184LEU0-0.014-0.01228.919-0.265-0.2650.0000.0000.0000.000
185A185GLN0-0.040-0.02431.351-0.208-0.2080.0000.0000.0000.000
186A186ALA00.0070.01331.7150.0380.0380.0000.0000.0000.000
187A187ILE00.0150.00225.473-0.190-0.1900.0000.0000.0000.000
188A188TRP0-0.017-0.01728.300-0.425-0.4250.0000.0000.0000.000
189A189ASN0-0.031-0.00530.6120.1220.1220.0000.0000.0000.000
190A190VAL0-0.025-0.00626.356-0.006-0.0060.0000.0000.0000.000
191A191LEU0-0.0070.00523.618-0.377-0.3770.0000.0000.0000.000
192A192ASN0-0.0130.01222.7050.5230.5230.0000.0000.0000.000
193A193TRP00.007-0.01623.286-0.721-0.7210.0000.0000.0000.000
194A194ASP-1-0.824-0.90724.049-12.071-12.0710.0000.0000.0000.000
195A195VAL0-0.0030.00517.883-0.449-0.4490.0000.0000.0000.000
196A196ALA00.0350.02019.328-0.681-0.6810.0000.0000.0000.000
197A197GLU-1-0.753-0.85821.239-12.651-12.6510.0000.0000.0000.000
198A198GLU-1-0.861-0.92416.995-18.143-18.1430.0000.0000.0000.000
199A199PHE0-0.065-0.04015.139-0.789-0.7890.0000.0000.0000.000
200A200PHE00.0250.01017.825-0.408-0.4080.0000.0000.0000.000
201A201LYS10.8530.91220.68413.35813.3580.0000.0000.0000.000
202A202LYS10.8560.94312.99620.04920.0490.0000.0000.0000.000
203A203ALA-1-0.842-0.89215.755-16.608-16.6080.0000.0000.0000.000