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: 2MNJR

Calculation Name: 1WPN-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | manganese (ii) ion

Ligand 3-letter code: SO4 | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1WPN

Chain ID: A

ChEMBL ID:

UniProt ID: P37487

Base Structure: X-ray

Registration Date: 2025-10-05

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 187
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2072215.342035
FMO2-HF: Nuclear repulsion 1999263.432737
FMO2-HF: Total energy -72951.909297
FMO2-MP2: Total energy -73164.256039


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:2:GLU)


Summations of interaction energy for fragment #1(A:2: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.
-27.534-27.65714.611-7.208-7.2810.046
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.071 / q_NPA : -0.038
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].
3A4ILE00.0380.0192.5234.4217.2831.081-1.667-2.277-0.017
4A5LEU0-0.011-0.0065.066-1.659-1.577-0.001-0.006-0.0750.000
32A33ASN0-0.035-0.0253.8384.3754.7890.000-0.080-0.3340.000
67A68VAL0-0.062-0.0324.4120.2910.462-0.001-0.026-0.1440.000
68A69ASN00.006-0.0051.737-26.390-30.32313.532-5.390-4.2090.063
69A70GLY0-0.0130.0044.380-4.552-4.2710.000-0.039-0.2420.000
5A6ILE00.0080.0038.6250.5760.5760.0000.0000.0000.000
6A7PHE00.0270.00711.278-0.165-0.1650.0000.0000.0000.000
7A8GLY00.0580.03015.0080.1130.1130.0000.0000.0000.000
8A9HIS10.7750.88118.435-0.146-0.1460.0000.0000.0000.000
9A10GLN0-0.035-0.04221.073-0.222-0.2220.0000.0000.0000.000
10A11ASN0-0.080-0.04322.859-0.078-0.0780.0000.0000.0000.000
11A12PRO00.0030.01722.374-0.024-0.0240.0000.0000.0000.000
12A13ASP-1-0.786-0.89524.4390.0290.0290.0000.0000.0000.000
13A14THR00.046-0.01624.628-0.052-0.0520.0000.0000.0000.000
14A15ASP-1-0.654-0.80123.819-0.473-0.4730.0000.0000.0000.000
15A16THR0-0.056-0.03420.674-0.060-0.0600.0000.0000.0000.000
16A17ILE0-0.044-0.01519.768-0.024-0.0240.0000.0000.0000.000
17A18CYS0-0.052-0.02219.958-0.191-0.1910.0000.0000.0000.000
18A19SER00.013-0.03919.919-0.282-0.2820.0000.0000.0000.000
19A20ALA0-0.0080.01115.905-0.200-0.2000.0000.0000.0000.000
20A21ILE0-0.012-0.01515.643-0.405-0.4050.0000.0000.0000.000
21A22ALA00.0060.00316.618-0.402-0.4020.0000.0000.0000.000
22A23TYR0-0.018-0.04013.177-0.508-0.5080.0000.0000.0000.000
23A24ALA00.0080.00811.995-0.621-0.6210.0000.0000.0000.000
24A25ASP-1-0.796-0.85612.171-4.025-4.0250.0000.0000.0000.000
25A26LEU0-0.021-0.00413.838-0.548-0.5480.0000.0000.0000.000
26A27LYS10.8360.8948.9493.2843.2840.0000.0000.0000.000
27A28ASN0-0.009-0.0119.358-2.715-2.7150.0000.0000.0000.000
28A29LYS10.7670.85510.6672.7482.7480.0000.0000.0000.000
29A30LEU0-0.039-0.00811.3090.3350.3350.0000.0000.0000.000
30A31GLY0-0.037-0.0069.060-0.320-0.3200.0000.0000.0000.000
31A32PHE0-0.052-0.0225.131-3.801-3.8010.0000.0000.0000.000
33A34ALA00.0400.0155.847-0.762-0.7620.0000.0000.0000.000
34A35GLU-1-0.774-0.8428.557-1.103-1.1030.0000.0000.0000.000
35A36PRO0-0.0040.02110.9600.6050.6050.0000.0000.0000.000
36A37VAL0-0.030-0.02212.2240.0560.0560.0000.0000.0000.000
37A38ARG10.8580.90814.8890.1360.1360.0000.0000.0000.000
38A39LEU00.0590.03416.1560.1040.1040.0000.0000.0000.000
39A40GLY00.0310.01019.6370.0600.0600.0000.0000.0000.000
40A41GLN0-0.054-0.01622.821-0.060-0.0600.0000.0000.0000.000
41A42VAL00.0360.01723.8750.0220.0220.0000.0000.0000.000
42A43ASN00.0010.01526.362-0.015-0.0150.0000.0000.0000.000
43A44GLY00.0680.02129.725-0.055-0.0550.0000.0000.0000.000
44A45GLU-1-0.757-0.81430.785-0.250-0.2500.0000.0000.0000.000
45A46THR0-0.010-0.05025.286-0.041-0.0410.0000.0000.0000.000
46A47GLN0-0.071-0.04127.698-0.048-0.0480.0000.0000.0000.000
47A48TYR00.0100.01029.137-0.063-0.0630.0000.0000.0000.000
48A49ALA00.0140.00228.103-0.055-0.0550.0000.0000.0000.000
49A50LEU0-0.048-0.02223.105-0.093-0.0930.0000.0000.0000.000
50A51ASP-1-0.843-0.91626.911-0.612-0.6120.0000.0000.0000.000
51A52TYR0-0.083-0.03329.904-0.030-0.0300.0000.0000.0000.000
52A53PHE0-0.051-0.01526.896-0.046-0.0460.0000.0000.0000.000
53A54LYS10.9060.95326.5690.7220.7220.0000.0000.0000.000
54A55GLN0-0.029-0.00721.678-0.257-0.2570.0000.0000.0000.000
55A56GLU-1-0.917-0.95720.993-1.182-1.1820.0000.0000.0000.000
56A57SER0-0.019-0.01521.2980.0060.0060.0000.0000.0000.000
57A58PRO00.0170.00817.075-0.028-0.0280.0000.0000.0000.000
58A59ARG10.7430.81011.147-0.008-0.0080.0000.0000.0000.000
59A60LEU0-0.064-0.02316.7720.1070.1070.0000.0000.0000.000
60A61VAL0-0.011-0.01013.3630.0150.0150.0000.0000.0000.000
61A62GLU-1-0.892-0.94716.6041.3281.3280.0000.0000.0000.000
62A63THR0-0.054-0.05313.986-0.203-0.2030.0000.0000.0000.000
63A64ALA00.007-0.0119.624-0.446-0.4460.0000.0000.0000.000
64A65ALA00.0680.0308.8001.2911.2910.0000.0000.0000.000
65A66ASN0-0.064-0.0149.0880.9240.9240.0000.0000.0000.000
66A67GLU-1-0.873-0.9008.1750.6340.6340.0000.0000.0000.000
70A71VAL0-0.012-0.0135.833-2.727-2.7270.0000.0000.0000.000
71A72ILE0-0.048-0.0218.573-0.202-0.2020.0000.0000.0000.000
72A73LEU00.0030.01611.352-0.192-0.1920.0000.0000.0000.000
73A74VAL00.015-0.00614.957-0.312-0.3120.0000.0000.0000.000
74A75ASP-1-0.770-0.87517.6470.2850.2850.0000.0000.0000.000
75A76HIS0-0.057-0.01517.1230.2990.2990.0000.0000.0000.000
76A77ASN00.004-0.02219.4880.1260.1260.0000.0000.0000.000
77A78GLU-1-0.806-0.85820.4781.0271.0270.0000.0000.0000.000
78A79ARG10.9290.94320.355-2.164-2.1640.0000.0000.0000.000
79A80GLN0-0.046-0.03721.3090.1500.1500.0000.0000.0000.000
80A81GLN0-0.045-0.02322.511-0.140-0.1400.0000.0000.0000.000
81A82SER00.0490.01317.2980.0080.0080.0000.0000.0000.000
82A83ILE0-0.0110.01713.490-0.197-0.1970.0000.0000.0000.000
83A84LYS10.8380.91217.253-1.696-1.6960.0000.0000.0000.000
84A85ASP-1-0.716-0.85113.0034.2554.2550.0000.0000.0000.000
85A86ILE0-0.026-0.01213.6830.6480.6480.0000.0000.0000.000
86A87GLU-1-0.854-0.91613.9463.1263.1260.0000.0000.0000.000
87A88GLU-1-1.002-0.99412.4754.6254.6250.0000.0000.0000.000
88A89VAL0-0.040-0.0088.4001.5181.5180.0000.0000.0000.000
89A90GLN0-0.011-0.0056.340-3.077-3.0770.0000.0000.0000.000
90A91VAL00.0180.0038.7690.2750.2750.0000.0000.0000.000
91A92LEU0-0.0100.0025.299-0.220-0.2200.0000.0000.0000.000
92A93GLU-1-0.794-0.8719.826-3.032-3.0320.0000.0000.0000.000
93A94VAL0-0.0090.00512.8760.2650.2650.0000.0000.0000.000
94A95ILE00.0090.01615.628-0.176-0.1760.0000.0000.0000.000
95A96ASP-1-0.745-0.87418.3830.4510.4510.0000.0000.0000.000
96A97HIS10.8060.90921.793-0.016-0.0160.0000.0000.0000.000
97A98HIS10.7990.90824.163-0.286-0.2860.0000.0000.0000.000
98A99ARG10.8610.91226.392-0.700-0.7000.0000.0000.0000.000
99A100ILE00.0320.03022.8950.0240.0240.0000.0000.0000.000
100A101ALA0-0.048-0.02824.774-0.052-0.0520.0000.0000.0000.000
101A102ASN0-0.073-0.04824.2230.0850.0850.0000.0000.0000.000
102A103PHE00.0580.02516.0540.0880.0880.0000.0000.0000.000
103A104GLU-1-0.961-0.98019.3661.6351.6350.0000.0000.0000.000
104A105THR0-0.021-0.02414.7410.1410.1410.0000.0000.0000.000
105A106ALA0-0.0220.00214.638-0.274-0.2740.0000.0000.0000.000
106A107GLU-1-0.899-0.94511.4773.9093.9090.0000.0000.0000.000
107A108PRO0-0.052-0.02914.278-0.291-0.2910.0000.0000.0000.000
108A109LEU00.0190.02212.9810.3780.3780.0000.0000.0000.000
109A110TYR0-0.018-0.00713.410-0.460-0.4600.0000.0000.0000.000
110A111TYR00.0190.00315.174-0.042-0.0420.0000.0000.0000.000
111A112ARG10.6950.81118.1020.6140.6140.0000.0000.0000.000
112A113ALA00.0320.01320.238-0.004-0.0040.0000.0000.0000.000
113A114GLU-1-0.771-0.87123.336-0.490-0.4900.0000.0000.0000.000
114A115PRO0-0.044-0.01626.3940.0210.0210.0000.0000.0000.000
115A116VAL0-0.061-0.03227.130-0.035-0.0350.0000.0000.0000.000
116A117GLY00.0630.01429.4820.0550.0550.0000.0000.0000.000
117A118CYS0-0.119-0.03327.0260.0030.0030.0000.0000.0000.000
118A119THR0-0.020-0.02920.6980.0060.0060.0000.0000.0000.000
119A120ALA00.0490.02222.964-0.127-0.1270.0000.0000.0000.000
120A121THR0-0.043-0.05424.014-0.140-0.1400.0000.0000.0000.000
121A122ILE0-0.039-0.00721.334-0.059-0.0590.0000.0000.0000.000
122A123LEU00.0070.00717.881-0.136-0.1360.0000.0000.0000.000
123A124ASN0-0.018-0.02320.989-0.275-0.2750.0000.0000.0000.000
124A125LYS10.7730.88223.3800.4560.4560.0000.0000.0000.000
125A126MET00.0210.02016.170-0.031-0.0310.0000.0000.0000.000
126A127TYR0-0.005-0.04017.980-0.178-0.1780.0000.0000.0000.000
127A128LYS10.8180.89620.1810.8310.8310.0000.0000.0000.000
128A129GLU-1-0.832-0.89020.401-1.101-1.1010.0000.0000.0000.000
129A130ASN0-0.066-0.03715.974-0.280-0.2800.0000.0000.0000.000
130A131ASN0-0.069-0.02918.836-0.077-0.0770.0000.0000.0000.000
131A132VAL00.0020.01016.405-0.088-0.0880.0000.0000.0000.000
132A133LYS10.8940.94619.8171.9551.9550.0000.0000.0000.000
133A134ILE00.0510.03121.031-0.173-0.1730.0000.0000.0000.000
134A135GLU-1-0.924-0.96220.234-2.290-2.2900.0000.0000.0000.000
135A136LYS10.9520.99323.6641.0311.0310.0000.0000.0000.000
136A137GLU-1-0.880-0.94824.195-1.288-1.2880.0000.0000.0000.000
137A138ILE00.0070.00519.6650.1100.1100.0000.0000.0000.000
138A139ALA00.0550.01022.9380.0980.0980.0000.0000.0000.000
139A140GLY00.0520.01625.6870.1110.1110.0000.0000.0000.000
140A141LEU0-0.0230.00622.1610.1170.1170.0000.0000.0000.000
141A142MET0-0.034-0.01922.4200.0480.0480.0000.0000.0000.000
142A143LEU0-0.007-0.00225.2510.1050.1050.0000.0000.0000.000
143A144SER00.001-0.02527.8130.1010.1010.0000.0000.0000.000
144A145ALA0-0.0140.00025.3350.0850.0850.0000.0000.0000.000
145A146ILE00.0290.01027.4260.0840.0840.0000.0000.0000.000
146A147ILE0-0.0200.00630.0070.0670.0670.0000.0000.0000.000
147A148SER0-0.027-0.02929.5540.0630.0630.0000.0000.0000.000
148A149ASP-1-0.765-0.88227.785-0.068-0.0680.0000.0000.0000.000
149A150SER0-0.098-0.07531.1490.0450.0450.0000.0000.0000.000
150A151LEU0-0.026-0.01834.3060.0210.0210.0000.0000.0000.000
151A152LEU0-0.061-0.02335.7370.0110.0110.0000.0000.0000.000
152A153PHE00.005-0.02234.4260.0080.0080.0000.0000.0000.000
153A154LYS10.9150.97438.2470.1640.1640.0000.0000.0000.000
154A155SER0-0.0120.01634.5470.0410.0410.0000.0000.0000.000
155A156PRO0-0.023-0.02137.551-0.019-0.0190.0000.0000.0000.000
156A157THR0-0.039-0.02332.8260.0050.0050.0000.0000.0000.000
157A158CYS0-0.0240.00533.665-0.036-0.0360.0000.0000.0000.000
158A159THR0-0.029-0.03532.6730.0030.0030.0000.0000.0000.000
159A160ASP-1-0.859-0.94334.862-0.277-0.2770.0000.0000.0000.000
160A161GLN00.0000.00230.384-0.092-0.0920.0000.0000.0000.000
161A162ASP-1-0.704-0.79930.193-0.349-0.3490.0000.0000.0000.000
162A163VAL00.0280.01531.871-0.042-0.0420.0000.0000.0000.000
163A164ALA0-0.038-0.01833.083-0.031-0.0310.0000.0000.0000.000
164A165ALA0-0.0030.00028.384-0.048-0.0480.0000.0000.0000.000
165A166ALA00.0520.02230.238-0.060-0.0600.0000.0000.0000.000
166A167LYS10.9550.97431.9730.4640.4640.0000.0000.0000.000
167A168GLU-1-0.832-0.88929.474-0.844-0.8440.0000.0000.0000.000
168A169LEU0-0.022-0.01225.749-0.063-0.0630.0000.0000.0000.000
169A170ALA00.0050.00929.491-0.040-0.0400.0000.0000.0000.000
170A171GLU-1-0.963-0.96932.641-0.708-0.7080.0000.0000.0000.000
171A172ILE0-0.058-0.03526.713-0.036-0.0360.0000.0000.0000.000
172A173ALA00.005-0.00129.381-0.064-0.0640.0000.0000.0000.000
173A174GLY0-0.083-0.03430.3720.0030.0030.0000.0000.0000.000
174A175VAL0-0.058-0.03633.2020.0330.0330.0000.0000.0000.000
175A176ASP-1-0.798-0.90335.791-0.437-0.4370.0000.0000.0000.000
176A177ALA00.015-0.00935.658-0.003-0.0030.0000.0000.0000.000
177A178GLU-1-0.885-0.95336.590-0.284-0.2840.0000.0000.0000.000
178A179GLU-1-1.001-0.99539.744-0.403-0.4030.0000.0000.0000.000
179A180TYR0-0.012-0.01930.8110.0120.0120.0000.0000.0000.000
180A181GLY00.0410.01335.6900.0140.0140.0000.0000.0000.000
181A182LEU0-0.026-0.01936.7340.0370.0370.0000.0000.0000.000
182A183ASN0-0.122-0.06238.2890.0500.0500.0000.0000.0000.000
183A184MET0-0.0080.01831.824-0.005-0.0050.0000.0000.0000.000
184A185LEU0-0.005-0.01234.4960.0290.0290.0000.0000.0000.000
185A186LYS10.8710.94836.5390.2590.2590.0000.0000.0000.000
186A187ALA0-0.042-0.01934.8250.0130.0130.0000.0000.0000.000
187A188GLY-1-0.954-0.95934.599-0.050-0.0500.0000.0000.0000.000