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: G75R1

Calculation Name: 3J7Q-Q-Other547

Preferred Name:

Target Type:

Ligand Name: magnesium ion | zinc ion

Ligand 3-letter code: MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3J7Q

Chain ID: Q

ChEMBL ID:

UniProt ID: Q29195

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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 -1822165.262867
FMO2-HF: Nuclear repulsion 1748040.364845
FMO2-HF: Total energy -74124.898022
FMO2-MP2: Total energy -74343.153498


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:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
235.682237.5290.031-0.832-1.045-0.004
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.849 / q_NPA : 0.917
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].
3A4ASP-1-0.897-0.9273.375-64.050-62.2030.031-0.832-1.045-0.004
4A5ILE0-0.018-0.0025.6377.4227.4220.0000.0000.0000.000
5A6ARG10.9620.9798.34719.86619.8660.0000.0000.0000.000
6A7HIS00.0650.0377.6803.9833.9830.0000.0000.0000.000
7A8ASN0-0.024-0.01911.9751.4911.4910.0000.0000.0000.000
8A9LYS10.8930.92815.19719.64419.6440.0000.0000.0000.000
9A10ASP-1-0.809-0.87514.153-20.439-20.4390.0000.0000.0000.000
10A11ARG10.9760.98116.48915.97415.9740.0000.0000.0000.000
11A12LYS10.9350.95918.84315.70715.7070.0000.0000.0000.000
12A13VAL00.0140.01322.1050.3000.3000.0000.0000.0000.000
13A14ARG10.9260.96124.55413.02213.0220.0000.0000.0000.000
14A15ARG10.8640.91327.6939.1359.1350.0000.0000.0000.000
15A16LYS10.9840.98025.35412.07512.0750.0000.0000.0000.000
16A17GLU-1-0.799-0.88630.724-9.481-9.4810.0000.0000.0000.000
17A18PRO0-0.004-0.00633.915-0.127-0.1270.0000.0000.0000.000
18A19LYS10.9250.96132.4359.4739.4730.0000.0000.0000.000
19A20SER0-0.051-0.03136.540-0.038-0.0380.0000.0000.0000.000
20A21GLN00.0950.03538.397-0.269-0.2690.0000.0000.0000.000
21A22ASP-1-0.799-0.87541.463-7.357-7.3570.0000.0000.0000.000
22A23ILE00.0940.03243.838-0.117-0.1170.0000.0000.0000.000
23A24TYR00.0700.04045.169-0.100-0.1000.0000.0000.0000.000
24A25LEU0-0.047-0.01341.288-0.042-0.0420.0000.0000.0000.000
25A26ARG10.8080.86635.8168.4528.4520.0000.0000.0000.000
26A27LEU00.0370.03341.397-0.167-0.1670.0000.0000.0000.000
27A28LEU00.0330.01343.248-0.056-0.0560.0000.0000.0000.000
28A29VAL0-0.050-0.03737.391-0.142-0.1420.0000.0000.0000.000
29A30LYS10.9610.98239.1087.5487.5480.0000.0000.0000.000
30A31LEU00.0430.03640.431-0.107-0.1070.0000.0000.0000.000
31A32TYR0-0.020-0.04839.846-0.110-0.1100.0000.0000.0000.000
32A33ARG10.8790.94434.2669.0099.0090.0000.0000.0000.000
33A34PHE00.0410.03337.151-0.229-0.2290.0000.0000.0000.000
34A35LEU00.0320.01039.613-0.082-0.0820.0000.0000.0000.000
35A36ALA0-0.043-0.04136.742-0.036-0.0360.0000.0000.0000.000
36A37ARG10.8880.94134.8018.8458.8450.0000.0000.0000.000
37A38ARG10.9410.99935.9467.9677.9670.0000.0000.0000.000
38A39THR00.0460.03038.9360.0720.0720.0000.0000.0000.000
39A40ASN00.0480.02038.620-0.097-0.0970.0000.0000.0000.000
40A41SER0-0.014-0.00339.704-0.005-0.0050.0000.0000.0000.000
41A42THR00.0700.02536.6090.0030.0030.0000.0000.0000.000
42A43PHE00.0370.01838.936-0.137-0.1370.0000.0000.0000.000
43A44ASN00.0670.04039.9520.0150.0150.0000.0000.0000.000
44A45GLN00.0670.03134.466-0.073-0.0730.0000.0000.0000.000
45A46VAL0-0.059-0.03036.440-0.192-0.1920.0000.0000.0000.000
46A47VAL00.003-0.00238.287-0.041-0.0410.0000.0000.0000.000
47A48LEU00.0080.01435.164-0.056-0.0560.0000.0000.0000.000
48A49LYS10.9340.96432.4149.2349.2340.0000.0000.0000.000
49A50ARG10.8760.91635.6067.6477.6470.0000.0000.0000.000
50A51LEU00.0280.01938.6740.0380.0380.0000.0000.0000.000
51A52PHE00.0320.03932.5140.0660.0660.0000.0000.0000.000
52A53MET0-0.080-0.01635.948-0.156-0.1560.0000.0000.0000.000
53A54SER00.0310.02737.5490.0880.0880.0000.0000.0000.000
54A55ARG11.0481.01439.1276.9336.9330.0000.0000.0000.000
55A56THR00.0370.01439.2530.0870.0870.0000.0000.0000.000
56A57ASN00.0240.01236.1540.1740.1740.0000.0000.0000.000
57A58ARG10.8960.96940.2277.5237.5230.0000.0000.0000.000
58A59PRO0-0.0110.01342.9580.1240.1240.0000.0000.0000.000
59A60PRO00.0160.00845.916-0.016-0.0160.0000.0000.0000.000
60A61LEU00.014-0.00949.446-0.039-0.0390.0000.0000.0000.000
61A62SER0-0.056-0.02251.2820.0340.0340.0000.0000.0000.000
62A63LEU00.0670.02454.919-0.062-0.0620.0000.0000.0000.000
63A64SER00.040-0.01057.522-0.014-0.0140.0000.0000.0000.000
64A65ARG10.8760.94149.6616.3706.3700.0000.0000.0000.000
65A66MET00.0130.00954.240-0.098-0.0980.0000.0000.0000.000
66A67ILE00.0500.03555.150-0.011-0.0110.0000.0000.0000.000
67A68ARG10.9580.97855.7285.5985.5980.0000.0000.0000.000
68A69LYS10.8920.93851.0416.1546.1540.0000.0000.0000.000
69A70MET0-0.018-0.00354.488-0.134-0.1340.0000.0000.0000.000
70A71LYS10.9820.99556.8475.1855.1850.0000.0000.0000.000
71A72LEU0-0.0100.01954.2610.0410.0410.0000.0000.0000.000
72A73PRO00.1110.05557.4510.0040.0040.0000.0000.0000.000
73A74GLY00.0710.03556.825-0.115-0.1150.0000.0000.0000.000
74A75ARG10.7830.88250.1496.1336.1330.0000.0000.0000.000
75A76GLU-1-0.865-0.93056.420-5.213-5.2130.0000.0000.0000.000
76A77GLY00.0310.01758.430-0.049-0.0490.0000.0000.0000.000
77A78LYS10.8650.95252.6356.0256.0250.0000.0000.0000.000
78A79THR0-0.0150.00251.9630.0570.0570.0000.0000.0000.000
79A80ALA00.0300.00051.954-0.132-0.1320.0000.0000.0000.000
80A81VAL0-0.004-0.00346.7020.0040.0040.0000.0000.0000.000
81A82VAL0-0.015-0.01747.504-0.152-0.1520.0000.0000.0000.000
82A83VAL00.0200.00941.9760.0220.0220.0000.0000.0000.000
83A84GLY0-0.016-0.03044.187-0.185-0.1850.0000.0000.0000.000
84A85THR0-0.069-0.03246.7710.0770.0770.0000.0000.0000.000
85A86ILE00.0640.04450.461-0.036-0.0360.0000.0000.0000.000
86A87THR0-0.044-0.03453.1800.0670.0670.0000.0000.0000.000
87A88ASP-1-0.751-0.89355.629-5.280-5.2800.0000.0000.0000.000
88A89ASP-1-0.814-0.85558.327-5.626-5.6260.0000.0000.0000.000
89A90VAL00.0640.02660.3610.0550.0550.0000.0000.0000.000
90A91ARG10.8970.94657.4395.5625.5620.0000.0000.0000.000
91A92VAL0-0.042-0.03061.626-0.085-0.0850.0000.0000.0000.000
92A93GLN00.0410.03064.406-0.082-0.0820.0000.0000.0000.000
93A94GLU-1-0.808-0.89667.403-4.736-4.7360.0000.0000.0000.000
94A95VAL0-0.123-0.07163.182-0.113-0.1130.0000.0000.0000.000
95A96PRO00.0300.00262.0850.0460.0460.0000.0000.0000.000
96A97LYS10.9670.99463.3944.9824.9820.0000.0000.0000.000
97A98LEU0-0.041-0.02857.958-0.076-0.0760.0000.0000.0000.000
98A99LYS10.9200.94255.7215.7945.7940.0000.0000.0000.000
99A100VAL0-0.038-0.01953.814-0.099-0.0990.0000.0000.0000.000
100A101CYS00.0300.04150.3150.0430.0430.0000.0000.0000.000
101A102ALA0-0.041-0.03049.862-0.107-0.1070.0000.0000.0000.000
102A103LEU0-0.0090.00444.366-0.002-0.0020.0000.0000.0000.000
103A104ARG10.9550.96749.0506.2856.2850.0000.0000.0000.000
104A105VAL00.0310.01552.137-0.063-0.0630.0000.0000.0000.000
105A106SER0-0.021-0.01455.3620.0810.0810.0000.0000.0000.000
106A107SER00.0750.02857.4710.0110.0110.0000.0000.0000.000
107A108ARG11.0201.02560.9285.1195.1190.0000.0000.0000.000
108A109ALA00.0500.03258.5040.0500.0500.0000.0000.0000.000
109A110ARG10.9360.96756.9235.5555.5550.0000.0000.0000.000
110A111SER0-0.023-0.02361.1250.0610.0610.0000.0000.0000.000
111A112ARG10.8510.91962.6825.1565.1560.0000.0000.0000.000
112A113ILE00.000-0.01558.2910.0270.0270.0000.0000.0000.000
113A114LEU0-0.019-0.01662.0440.0070.0070.0000.0000.0000.000
114A115LYS11.0021.01064.7664.7034.7030.0000.0000.0000.000
115A116ALA00.0020.01564.8900.0600.0600.0000.0000.0000.000
116A117GLY00.0890.05867.0350.0100.0100.0000.0000.0000.000
117A118GLY0-0.031-0.01762.636-0.036-0.0360.0000.0000.0000.000
118A119LYS10.9180.95958.6025.3335.3330.0000.0000.0000.000
119A120ILE0-0.050-0.02856.751-0.087-0.0870.0000.0000.0000.000
120A121LEU00.0470.02453.8040.0610.0610.0000.0000.0000.000
121A122THR0-0.022-0.03651.394-0.045-0.0450.0000.0000.0000.000
122A123PHE0-0.033-0.03845.089-0.041-0.0410.0000.0000.0000.000
123A124ASP-1-0.790-0.85647.618-6.459-6.4590.0000.0000.0000.000
124A125GLN00.0850.03249.3430.0080.0080.0000.0000.0000.000
125A126LEU0-0.016-0.01347.3230.0280.0280.0000.0000.0000.000
126A127ALA0-0.052-0.03046.989-0.039-0.0390.0000.0000.0000.000
127A128LEU00.0270.01448.720-0.040-0.0400.0000.0000.0000.000
128A129ASP-1-0.857-0.89652.186-5.817-5.8170.0000.0000.0000.000
129A130SER00.0200.00349.5920.0460.0460.0000.0000.0000.000
130A131PRO00.0300.02446.768-0.174-0.1740.0000.0000.0000.000
131A132LYS10.9180.95943.2967.1547.1540.0000.0000.0000.000
132A133GLY00.004-0.00145.410-0.124-0.1240.0000.0000.0000.000
133A134CYS0-0.0030.00346.961-0.008-0.0080.0000.0000.0000.000
134A135GLY00.1020.05649.6990.0920.0920.0000.0000.0000.000
135A136THR0-0.079-0.04348.1190.0400.0400.0000.0000.0000.000
136A137VAL00.0420.01549.116-0.021-0.0210.0000.0000.0000.000
137A138LEU0-0.031-0.00242.539-0.009-0.0090.0000.0000.0000.000
138A139LEU00.0020.00646.6150.0200.0200.0000.0000.0000.000
139A140SER0-0.011-0.02444.273-0.211-0.2110.0000.0000.0000.000
140A141GLY00.0260.03346.3310.1190.1190.0000.0000.0000.000
141A142PRO0-0.032-0.02345.817-0.176-0.1760.0000.0000.0000.000
142A143ARG10.9060.94037.2228.3708.3700.0000.0000.0000.000
143A144LYS10.9630.98138.6338.1198.1190.0000.0000.0000.000
144A145GLY00.0090.01844.0030.0960.0960.0000.0000.0000.000
145A146ARG10.8650.92740.4367.7677.7670.0000.0000.0000.000
146A147GLU-1-0.843-0.92845.812-6.404-6.4040.0000.0000.0000.000
147A148VAL00.0350.01241.671-0.003-0.0030.0000.0000.0000.000
148A149TYR0-0.001-0.01638.142-0.097-0.0970.0000.0000.0000.000
149A150ARG10.9600.98643.4926.4336.4330.0000.0000.0000.000
150A151HIS0-0.043-0.01643.6500.1450.1450.0000.0000.0000.000
151A152PHE0-0.037-0.02137.311-0.164-0.1640.0000.0000.0000.000
152A153GLY0-0.012-0.00939.0300.1780.1780.0000.0000.0000.000
153A154LYS10.9570.99238.3167.3127.3120.0000.0000.0000.000
154A155ALA00.0930.03739.544-0.115-0.1150.0000.0000.0000.000
155A156PRO0-0.056-0.00542.2160.1050.1050.0000.0000.0000.000
156A157GLY00.0320.01045.583-0.033-0.0330.0000.0000.0000.000
157A158THR0-0.013-0.01141.331-0.041-0.0410.0000.0000.0000.000
158A159PRO00.012-0.00843.8450.1060.1060.0000.0000.0000.000
159A160HIS00.0690.03145.598-0.065-0.0650.0000.0000.0000.000
160A161SER0-0.028-0.01844.041-0.194-0.1940.0000.0000.0000.000
161A162HIS00.0150.02246.117-0.038-0.0380.0000.0000.0000.000
162A163THR0-0.0170.00943.2640.0290.0290.0000.0000.0000.000
163A164LYS10.8340.90846.3896.5156.5150.0000.0000.0000.000
164A165PRO00.0620.04346.555-0.167-0.1670.0000.0000.0000.000
165A166TYR0-0.004-0.01841.9820.0620.0620.0000.0000.0000.000
166A167VAL0-0.0160.00348.1030.0290.0290.0000.0000.0000.000
167A168ARG10.9940.99851.7345.8085.8080.0000.0000.0000.000
168A169SER00.0790.01853.2880.0890.0890.0000.0000.0000.000
169A170LYS10.9080.98056.0445.5945.5940.0000.0000.0000.000
170A171GLY00.1110.04057.3850.0880.0880.0000.0000.0000.000
171A172ARG11.0001.00359.7524.8144.8140.0000.0000.0000.000
172A173LYS10.9950.98260.7295.0665.0660.0000.0000.0000.000
173A174PHE0-0.0090.01155.602-0.050-0.0500.0000.0000.0000.000
174A175GLU-1-0.845-0.93750.795-6.355-6.3550.0000.0000.0000.000
175A176ARG10.8030.89054.8715.5325.5320.0000.0000.0000.000
176A177ALA00.0340.01055.9790.1080.1080.0000.0000.0000.000
177A178ARG11.0481.03150.7596.0946.0940.0000.0000.0000.000
178A179GLY00.0610.04051.699-0.091-0.0910.0000.0000.0000.000
179A180ARG10.8420.91650.1746.1736.1730.0000.0000.0000.000
180A181ARG10.9380.94954.9065.4255.4250.0000.0000.0000.000
181A182ALA00.0940.05357.523-0.011-0.0110.0000.0000.0000.000
182A183SER00.0450.03558.512-0.034-0.0340.0000.0000.0000.000
183A184ARG10.9030.94558.9195.1825.1820.0000.0000.0000.000
184A185GLY00.0350.02356.234-0.100-0.1000.0000.0000.0000.000
185A186TYR00.0560.04148.6670.0030.0030.0000.0000.0000.000
186A187LYS10.7820.88853.1415.9835.9830.0000.0000.0000.000
187A188ASN-1-0.823-0.88848.699-6.259-6.2590.0000.0000.0000.000