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: RQV58

Calculation Name: 1JR9-A-Xray547

Preferred Name:

Target Type:

Ligand Name: manganese (ii) ion

Ligand 3-letter code: MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JR9

Chain ID: A

ChEMBL ID:

UniProt ID: Q7SIC3

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 201
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2314216.660698
FMO2-HF: Nuclear repulsion 2235525.679935
FMO2-HF: Total energy -78690.980763
FMO2-MP2: Total energy -78923.379575


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:LYS)


Summations of interaction energy for fragment #1(A:2:LYS)
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.
-477.713-471.9134.005-22.043-17.766-0.286
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.582 / q_NPA : 1.773
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].
3A4GLU-1-0.790-0.8841.752-157.194-152.69612.407-10.184-6.722-0.128
4A5LEU0-0.0070.0015.0044.0274.093-0.001-0.007-0.0580.000
39A40ASN0-0.073-0.0633.647-14.190-13.7890.007-0.205-0.203-0.001
49A50LYS10.8750.9353.78464.62565.7880.004-0.567-0.600-0.002
50A51ASN0-0.025-0.0221.779-49.759-51.13912.742-6.397-4.964-0.083
51A52LYS10.9240.9852.37241.34943.3002.191-1.912-2.231-0.034
52A53SER0-0.033-0.0381.988-38.669-39.6536.656-2.768-2.904-0.038
53A54LEU00.016-0.0034.5082.8422.930-0.001-0.003-0.0840.000
5A6PRO0-0.0140.0068.722-0.572-0.5720.0000.0000.0000.000
6A7GLU-1-0.909-0.96410.181-33.791-33.7910.0000.0000.0000.000
7A8LEU0-0.0140.00312.888-0.108-0.1080.0000.0000.0000.000
8A9PRO0-0.027-0.01016.3350.9160.9160.0000.0000.0000.000
9A10TYR0-0.031-0.04318.3621.7241.7240.0000.0000.0000.000
10A11ALA00.0260.02220.444-0.919-0.9190.0000.0000.0000.000
11A12TYR0-0.009-0.03316.6500.5960.5960.0000.0000.0000.000
12A13ASP-1-0.890-0.96922.779-21.615-21.6150.0000.0000.0000.000
13A14ALA0-0.0180.00124.7690.8520.8520.0000.0000.0000.000
14A15LEU00.0570.01023.7080.1250.1250.0000.0000.0000.000
15A16GLU-1-0.783-0.87627.651-19.229-19.2290.0000.0000.0000.000
16A17PRO0-0.058-0.01830.0600.3670.3670.0000.0000.0000.000
17A18THR0-0.0050.00329.9180.6590.6590.0000.0000.0000.000
18A19ILE00.008-0.00425.5190.1540.1540.0000.0000.0000.000
19A20ASP-1-0.761-0.84128.024-21.458-21.4580.0000.0000.0000.000
20A21LYS10.8980.91725.52919.09919.0990.0000.0000.0000.000
21A22GLU-1-0.997-0.98224.500-21.284-21.2840.0000.0000.0000.000
22A23THR0-0.017-0.04324.402-1.054-1.0540.0000.0000.0000.000
23A24MET0-0.0240.00820.742-1.257-1.2570.0000.0000.0000.000
24A25ASN00.010-0.00120.283-2.481-2.4810.0000.0000.0000.000
25A26ILE0-0.042-0.00119.592-1.647-1.6470.0000.0000.0000.000
26A27HIS00.022-0.00119.264-1.825-1.8250.0000.0000.0000.000
27A28HIS00.0680.04813.4860.1120.1120.0000.0000.0000.000
28A29THR00.002-0.02215.180-1.879-1.8790.0000.0000.0000.000
29A30LYS10.8490.92416.34530.13330.1330.0000.0000.0000.000
30A31HIS00.0210.02315.962-1.821-1.8210.0000.0000.0000.000
31A32HIS00.0540.04011.3591.0301.0300.0000.0000.0000.000
32A33ASN00.0560.02911.246-4.950-4.9500.0000.0000.0000.000
33A34THR0-0.063-0.03511.188-2.574-2.5740.0000.0000.0000.000
34A35TYR0-0.031-0.00512.522-0.663-0.6630.0000.0000.0000.000
35A36VAL00.0580.0286.334-2.700-2.7000.0000.0000.0000.000
36A37THR0-0.051-0.0317.840-5.481-5.4810.0000.0000.0000.000
37A38LYS10.8880.9359.60634.60234.6020.0000.0000.0000.000
38A39LEU00.0070.0236.8450.8230.8230.0000.0000.0000.000
40A41GLY0-0.008-0.0026.5120.7300.7300.0000.0000.0000.000
41A42ALA0-0.024-0.0069.9523.4473.4470.0000.0000.0000.000
42A43LEU00.003-0.0124.8211.4081.4080.0000.0000.0000.000
43A44GLU-1-0.850-0.8968.102-65.054-65.0540.0000.0000.0000.000
44A45GLY0-0.020-0.0119.5264.0284.0280.0000.0000.0000.000
45A46HIS0-0.033-0.0149.4004.6424.6420.0000.0000.0000.000
46A47GLU-1-0.911-0.9557.610-55.048-55.0480.0000.0000.0000.000
47A48ASP-1-0.865-0.9356.153-59.027-59.0270.0000.0000.0000.000
48A49LEU0-0.038-0.0206.396-5.493-5.4930.0000.0000.0000.000
54A55ASN00.0380.0176.3947.2807.2800.0000.0000.0000.000
55A56ASP-1-0.822-0.8737.075-56.853-56.8530.0000.0000.0000.000
56A57LEU0-0.059-0.0275.5144.3164.3160.0000.0000.0000.000
57A58ILE0-0.018-0.0048.0063.8033.8030.0000.0000.0000.000
58A59SER0-0.004-0.01911.0524.1324.1320.0000.0000.0000.000
59A60ASN0-0.038-0.01811.6794.1964.1960.0000.0000.0000.000
60A61LEU0-0.007-0.00912.297-1.466-1.4660.0000.0000.0000.000
61A62ASP-1-0.863-0.93713.846-29.682-29.6820.0000.0000.0000.000
62A63ALA0-0.095-0.05411.7730.4300.4300.0000.0000.0000.000
63A64VAL0-0.0190.00110.333-2.390-2.3900.0000.0000.0000.000
64A65PRO00.0790.03712.9382.3602.3600.0000.0000.0000.000
65A66GLU-1-0.812-0.91516.145-30.300-30.3000.0000.0000.0000.000
66A67ASN0-0.074-0.03918.3431.0631.0630.0000.0000.0000.000
67A68ILE0-0.0010.00111.736-0.097-0.0970.0000.0000.0000.000
68A69ARG10.8650.95414.69429.96329.9630.0000.0000.0000.000
69A70THR00.020-0.00715.398-1.012-1.0120.0000.0000.0000.000
70A71ALA0-0.029-0.00314.424-0.213-0.2130.0000.0000.0000.000
71A72VAL00.0620.0229.673-1.945-1.9450.0000.0000.0000.000
72A73ARG10.8810.93212.19128.08728.0870.0000.0000.0000.000
73A74ASN0-0.011-0.01414.736-0.431-0.4310.0000.0000.0000.000
74A75ASN0-0.071-0.04912.3351.7311.7310.0000.0000.0000.000
75A76GLY00.0580.01910.202-2.301-2.3010.0000.0000.0000.000
76A77GLY00.0700.04110.930-1.189-1.1890.0000.0000.0000.000
77A78GLY0-0.012-0.00314.2460.4290.4290.0000.0000.0000.000
78A79HIS00.0290.0146.8024.9934.9930.0000.0000.0000.000
79A80ALA00.0180.02211.615-0.456-0.4560.0000.0000.0000.000
80A81ASN00.003-0.00512.5220.7410.7410.0000.0000.0000.000
81A82HIS0-0.039-0.02814.9190.0490.0490.0000.0000.0000.000
82A83SER0-0.059-0.04911.358-0.122-0.1220.0000.0000.0000.000
83A84LEU0-0.040-0.00113.6190.5420.5420.0000.0000.0000.000
84A85PHE00.015-0.00316.1441.6401.6400.0000.0000.0000.000
85A86TRP0-0.012-0.02414.4512.3812.3810.0000.0000.0000.000
86A87LYS10.9080.94914.84538.36038.3600.0000.0000.0000.000
87A88LEU0-0.0280.00719.3891.3171.3170.0000.0000.0000.000
88A89MET0-0.040-0.00921.8641.7311.7310.0000.0000.0000.000
89A90SER0-0.010-0.01023.148-0.931-0.9310.0000.0000.0000.000
90A91PRO0-0.0070.01125.1460.6400.6400.0000.0000.0000.000
91A92ASN0-0.056-0.03526.7531.1701.1700.0000.0000.0000.000
92A93GLY00.013-0.00228.779-0.579-0.5790.0000.0000.0000.000
93A94GLY00.0250.04229.7040.6380.6380.0000.0000.0000.000
94A95GLY0-0.035-0.01831.5040.1730.1730.0000.0000.0000.000
95A96LYS10.9330.95733.98516.10916.1090.0000.0000.0000.000
96A97PRO00.0210.01831.615-0.206-0.2060.0000.0000.0000.000
97A98THR00.000-0.00430.2060.8360.8360.0000.0000.0000.000
98A99GLY00.0320.01430.881-0.579-0.5790.0000.0000.0000.000
99A100GLU-1-0.869-0.94329.161-20.507-20.5070.0000.0000.0000.000
100A101VAL0-0.0050.00827.2260.1780.1780.0000.0000.0000.000
101A102ALA0-0.014-0.01230.4480.2640.2640.0000.0000.0000.000
102A103ASP-1-0.908-0.94833.927-17.116-17.1160.0000.0000.0000.000
103A104LYS10.8490.92430.59719.22419.2240.0000.0000.0000.000
104A105ILE0-0.006-0.00330.7760.1320.1320.0000.0000.0000.000
105A106ASN0-0.011-0.01434.2810.3360.3360.0000.0000.0000.000
106A107ASP-1-0.877-0.93635.893-16.818-16.8180.0000.0000.0000.000
107A108LYS10.8230.92232.53618.90018.9000.0000.0000.0000.000
108A109TYR00.009-0.00832.774-0.022-0.0220.0000.0000.0000.000
109A110GLY0-0.0060.01238.3470.3850.3850.0000.0000.0000.000
110A111SER0-0.062-0.05639.9030.1260.1260.0000.0000.0000.000
111A112PHE00.0650.03133.108-0.287-0.2870.0000.0000.0000.000
112A113GLU-1-0.866-0.92936.847-16.218-16.2180.0000.0000.0000.000
113A114LYS10.8270.90939.08314.98614.9860.0000.0000.0000.000
114A115PHE00.0330.01429.961-0.251-0.2510.0000.0000.0000.000
115A116GLN0-0.020-0.01634.478-0.224-0.2240.0000.0000.0000.000
116A117GLU-1-0.871-0.91135.502-15.407-15.4070.0000.0000.0000.000
117A118GLU-1-0.904-0.95434.961-17.106-17.1060.0000.0000.0000.000
118A119PHE0-0.017-0.01026.841-0.380-0.3800.0000.0000.0000.000
119A120ALA0-0.001-0.01432.200-0.488-0.4880.0000.0000.0000.000
120A121ALA00.0100.01134.411-0.076-0.0760.0000.0000.0000.000
121A122ALA0-0.007-0.00230.671-0.073-0.0730.0000.0000.0000.000
122A123ALA0-0.011-0.01530.190-0.481-0.4810.0000.0000.0000.000
123A124ALA0-0.039-0.02331.159-0.191-0.1910.0000.0000.0000.000
124A125GLY0-0.0030.00334.3410.0840.0840.0000.0000.0000.000
125A126ARG10.8460.92827.46522.18222.1820.0000.0000.0000.000
126A127PHE00.0110.00931.031-0.163-0.1630.0000.0000.0000.000
127A128GLY0-0.0020.00430.411-0.533-0.5330.0000.0000.0000.000
128A129SER00.012-0.00425.0870.2760.2760.0000.0000.0000.000
129A130GLY00.014-0.00324.1290.1600.1600.0000.0000.0000.000
130A131TRP0-0.024-0.00519.324-0.153-0.1530.0000.0000.0000.000
131A132ALA0-0.0010.00724.3980.5320.5320.0000.0000.0000.000
132A133TRP0-0.019-0.04118.778-1.116-1.1160.0000.0000.0000.000
133A134LEU00.0090.01525.0701.0761.0760.0000.0000.0000.000
134A135VAL0-0.025-0.02522.973-1.197-1.1970.0000.0000.0000.000
135A136VAL00.0360.01122.9941.1351.1350.0000.0000.0000.000
136A137ASN0-0.041-0.01323.181-1.303-1.3030.0000.0000.0000.000
137A138ASN00.0370.00124.5150.7050.7050.0000.0000.0000.000
138A139GLY00.0620.03426.181-0.377-0.3770.0000.0000.0000.000
139A140GLU-1-1.015-0.99028.790-18.911-18.9110.0000.0000.0000.000
140A141ILE00.0340.00427.367-0.806-0.8060.0000.0000.0000.000
141A142GLU-1-0.835-0.90027.116-20.945-20.9450.0000.0000.0000.000
142A143ILE00.0070.01428.047-0.776-0.7760.0000.0000.0000.000
143A144MET0-0.035-0.00223.8490.3520.3520.0000.0000.0000.000
144A145SER00.0330.00726.183-0.436-0.4360.0000.0000.0000.000
145A146THR0-0.0070.01421.2410.7830.7830.0000.0000.0000.000
146A147PRO00.0010.00023.5170.3570.3570.0000.0000.0000.000
147A148ILE00.008-0.01921.044-1.285-1.2850.0000.0000.0000.000
148A149GLN00.0430.02117.237-0.349-0.3490.0000.0000.0000.000
149A150ASP-1-0.808-0.87317.615-31.428-31.4280.0000.0000.0000.000
150A151ASN00.018-0.00215.7881.0591.0590.0000.0000.0000.000
151A152PRO00.0660.03417.906-0.230-0.2300.0000.0000.0000.000
152A153LEU00.0250.01914.1080.6400.6400.0000.0000.0000.000
153A154MET0-0.084-0.01615.183-0.856-0.8560.0000.0000.0000.000
154A155GLU-1-0.954-0.97717.044-24.682-24.6820.0000.0000.0000.000
155A156GLY0-0.027-0.01218.5831.1951.1950.0000.0000.0000.000
156A157LYS10.8090.89719.56423.67923.6790.0000.0000.0000.000
157A158LYS10.9680.98015.93632.59032.5900.0000.0000.0000.000
158A159PRO0-0.037-0.00817.7831.3701.3700.0000.0000.0000.000
159A160ILE00.0150.01419.854-0.917-0.9170.0000.0000.0000.000
160A161LEU00.0230.00922.2240.2930.2930.0000.0000.0000.000
161A162GLY00.004-0.00321.9070.0240.0240.0000.0000.0000.000
162A163LEU0-0.040-0.01022.943-0.011-0.0110.0000.0000.0000.000
163A164ASP-1-0.773-0.89121.585-28.033-28.0330.0000.0000.0000.000
164A165VAL00.0400.01023.8811.0491.0490.0000.0000.0000.000
165A166TRP0-0.049-0.03221.5690.9700.9700.0000.0000.0000.000
166A167GLU-1-0.888-0.94126.297-19.975-19.9750.0000.0000.0000.000
167A168HIS10.7900.90121.52628.03728.0370.0000.0000.0000.000
168A169ALA0-0.0180.00024.175-0.613-0.6130.0000.0000.0000.000
169A170TYR00.0280.03025.4060.2050.2050.0000.0000.0000.000
170A171TYR0-0.005-0.01629.1440.8310.8310.0000.0000.0000.000
171A172LEU0-0.019-0.00727.5690.6170.6170.0000.0000.0000.000
172A173LYS10.8800.97131.24919.06819.0680.0000.0000.0000.000
173A174TYR0-0.055-0.05031.2190.7960.7960.0000.0000.0000.000
174A175GLN0-0.013-0.00133.9560.2640.2640.0000.0000.0000.000
175A176ASN00.019-0.00833.999-0.424-0.4240.0000.0000.0000.000
176A177LYS10.8510.93536.26016.38216.3820.0000.0000.0000.000
177A178ARG10.8740.91530.99320.32320.3230.0000.0000.0000.000
178A179PRO00.0470.01034.056-0.322-0.3220.0000.0000.0000.000
179A180ASP-1-0.821-0.88036.259-16.432-16.4320.0000.0000.0000.000
180A181TYR0-0.025-0.01926.476-0.049-0.0490.0000.0000.0000.000
181A182ILE0-0.036-0.01531.368-0.429-0.4290.0000.0000.0000.000
182A183SER0-0.044-0.03032.613-0.029-0.0290.0000.0000.0000.000
183A184ALA0-0.027-0.01432.8620.0510.0510.0000.0000.0000.000
184A185PHE00.0520.01225.297-0.124-0.1240.0000.0000.0000.000
185A186TRP00.0510.02030.034-0.650-0.6500.0000.0000.0000.000
186A187ASN0-0.086-0.04432.2660.3850.3850.0000.0000.0000.000
187A188VAL00.0090.00227.2620.0560.0560.0000.0000.0000.000
188A189VAL0-0.0050.01526.715-0.811-0.8110.0000.0000.0000.000
189A190ASN00.0050.00723.4201.3591.3590.0000.0000.0000.000
190A191TRP00.046-0.00425.432-0.986-0.9860.0000.0000.0000.000
191A192ASP-1-0.892-0.93626.308-21.948-21.9480.0000.0000.0000.000
192A193GLU-1-0.845-0.89818.672-33.085-33.0850.0000.0000.0000.000
193A194VAL0-0.025-0.01522.294-0.675-0.6750.0000.0000.0000.000
194A195ALA0-0.007-0.00524.223-0.138-0.1380.0000.0000.0000.000
195A196ALA0-0.019-0.00821.283-0.080-0.0800.0000.0000.0000.000
196A197GLN0-0.062-0.05818.563-0.592-0.5920.0000.0000.0000.000
197A198TYR0-0.013-0.00520.777-0.232-0.2320.0000.0000.0000.000
198A199SER00.0220.00023.520-0.061-0.0610.0000.0000.0000.000
199A200GLN0-0.064-0.02616.704-1.479-1.4790.0000.0000.0000.000
200A201ALA0-0.128-0.05319.480-1.148-1.1480.0000.0000.0000.000
201A202ALA-1-0.923-0.94620.811-25.601-25.6010.0000.0000.0000.000