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: 2GL3R

Calculation Name: 3J7Q-I-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: I

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 213
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2357695.370195
FMO2-HF: Nuclear repulsion 2270423.318657
FMO2-HF: Total energy -87272.051538
FMO2-MP2: Total energy -87519.830331


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.
291.079291.673-0.006-0.293-0.2950
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 : 0.898 / q_NPA : 0.941
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].
3A4ARG10.9750.9913.84435.65836.252-0.006-0.293-0.2950.000
4A5PRO00.0440.0076.8221.7761.7760.0000.0000.0000.000
5A6ALA00.0310.0019.2860.6900.6900.0000.0000.0000.000
6A7ARG11.0111.00711.90723.84723.8470.0000.0000.0000.000
7A8CYS00.0040.00411.0720.8890.8890.0000.0000.0000.000
8A9TYR0-0.065-0.0379.870-0.526-0.5260.0000.0000.0000.000
9A10ARG10.8600.96013.93115.68515.6850.0000.0000.0000.000
10A11TYR00.0730.03616.8560.5050.5050.0000.0000.0000.000
11A12CYS0-0.070-0.02219.310-0.905-0.9050.0000.0000.0000.000
12A13LYS11.0121.01818.78817.06317.0630.0000.0000.0000.000
13A14ASN0-0.035-0.00919.2250.1130.1130.0000.0000.0000.000
14A15LYS11.0821.02921.85411.54111.5410.0000.0000.0000.000
15A16PRO0-0.0150.00021.578-0.707-0.7070.0000.0000.0000.000
16A17TYR00.0460.01217.5710.1200.1200.0000.0000.0000.000
17A18PRO00.0880.04719.247-0.908-0.9080.0000.0000.0000.000
18A19LYS10.9790.98417.47815.95415.9540.0000.0000.0000.000
19A20SER0-0.036-0.01619.9390.7770.7770.0000.0000.0000.000
20A21ARG10.9550.97322.68410.20710.2070.0000.0000.0000.000
21A22PHE00.0610.02623.627-0.097-0.0970.0000.0000.0000.000
22A23CYS0-0.075-0.01018.165-0.734-0.7340.0000.0000.0000.000
23A24ARG11.0330.99718.36713.57113.5710.0000.0000.0000.000
24A25GLY00.0370.02515.676-0.377-0.3770.0000.0000.0000.000
25A26VAL0-0.048-0.03113.500-1.398-1.3980.0000.0000.0000.000
26A27PRO00.0100.0199.0251.1331.1330.0000.0000.0000.000
27A28ASP-1-0.824-0.91811.527-16.954-16.9540.0000.0000.0000.000
28A29ALA0-0.0080.00012.707-1.222-1.2220.0000.0000.0000.000
29A30LYS10.8630.92710.32223.91223.9120.0000.0000.0000.000
30A31ILE0-0.031-0.00713.1780.7520.7520.0000.0000.0000.000
31A32ARG10.8680.91615.33417.64717.6470.0000.0000.0000.000
32A33ILE00.0110.01719.3460.6580.6580.0000.0000.0000.000
33A34PHE00.0640.01619.948-0.350-0.3500.0000.0000.0000.000
34A35ASP-1-0.819-0.91024.388-10.501-10.5010.0000.0000.0000.000
35A36LEU0-0.066-0.01523.538-0.140-0.1400.0000.0000.0000.000
36A37GLY00.1110.07128.1050.1760.1760.0000.0000.0000.000
37A38ARG10.8440.90031.1147.9627.9620.0000.0000.0000.000
38A39LYS10.8580.92128.30610.87910.8790.0000.0000.0000.000
39A40LYS10.9360.94933.6118.5448.5440.0000.0000.0000.000
40A41ALA0-0.0170.01237.0410.2110.2110.0000.0000.0000.000
41A42LYS10.9590.97839.0937.2387.2380.0000.0000.0000.000
42A43VAL00.0020.00340.356-0.231-0.2310.0000.0000.0000.000
43A44ASP-1-0.819-0.91442.234-6.974-6.9740.0000.0000.0000.000
44A45GLU-1-0.802-0.86741.297-7.615-7.6150.0000.0000.0000.000
45A46PHE0-0.125-0.06636.236-0.109-0.1090.0000.0000.0000.000
46A47PRO00.1020.05040.032-0.150-0.1500.0000.0000.0000.000
47A48LEU00.0010.01337.283-0.038-0.0380.0000.0000.0000.000
48A49GLY00.0260.00935.880-0.269-0.2690.0000.0000.0000.000
49A50GLY00.0260.01934.0970.1290.1290.0000.0000.0000.000
50A51HIS0-0.016-0.03031.097-0.597-0.5970.0000.0000.0000.000
51A52MET0-0.0060.01123.624-0.139-0.1390.0000.0000.0000.000
52A53VAL0-0.013-0.01528.239-0.175-0.1750.0000.0000.0000.000
53A54SER00.0230.01025.457-0.080-0.0800.0000.0000.0000.000
54A55ASP-1-0.793-0.88927.044-9.652-9.6520.0000.0000.0000.000
55A56GLU-1-0.834-0.90324.455-12.543-12.5430.0000.0000.0000.000
56A57TYR0-0.007-0.00825.184-0.298-0.2980.0000.0000.0000.000
57A58GLU-1-0.804-0.91220.676-14.663-14.6630.0000.0000.0000.000
58A59GLN0-0.004-0.02116.6440.7510.7510.0000.0000.0000.000
59A60LEU00.0350.03116.877-0.629-0.6290.0000.0000.0000.000
60A61SER0-0.024-0.01611.821-0.806-0.8060.0000.0000.0000.000
61A62SER00.0700.01611.7440.4080.4080.0000.0000.0000.000
62A63GLU-1-0.861-0.9367.917-33.256-33.2560.0000.0000.0000.000
63A64ALA0-0.0040.01112.3970.4640.4640.0000.0000.0000.000
64A65LEU00.0300.01614.7280.9430.9430.0000.0000.0000.000
65A66GLU-1-0.779-0.86814.640-17.783-17.7830.0000.0000.0000.000
66A67ALA00.0220.00714.6690.8580.8580.0000.0000.0000.000
67A68ALA00.0430.02316.7150.8210.8210.0000.0000.0000.000
68A69ARG10.8600.91618.36016.04516.0450.0000.0000.0000.000
69A70ILE0-0.028-0.01916.9900.6860.6860.0000.0000.0000.000
70A71CYS0-0.075-0.02420.5440.4760.4760.0000.0000.0000.000
71A72ALA00.1020.05222.2820.5210.5210.0000.0000.0000.000
72A73ASN0-0.017-0.03124.2520.7910.7910.0000.0000.0000.000
73A74LYS10.8380.92622.28513.17013.1700.0000.0000.0000.000
74A75TYR00.0350.02826.0720.1370.1370.0000.0000.0000.000
75A76MET00.0350.04828.4560.3720.3720.0000.0000.0000.000
76A77VAL0-0.019-0.00928.869-0.321-0.3210.0000.0000.0000.000
77A78LYS10.9280.97029.34910.10410.1040.0000.0000.0000.000
78A79SER0-0.004-0.02932.4410.1940.1940.0000.0000.0000.000
79A80CYS00.0150.02534.4700.0960.0960.0000.0000.0000.000
80A81GLY00.0550.04635.5800.1530.1530.0000.0000.0000.000
81A82ARG10.8850.92129.6589.5889.5880.0000.0000.0000.000
82A83ASP-1-0.905-0.95833.279-8.604-8.6040.0000.0000.0000.000
83A84GLY00.1040.05335.9600.1570.1570.0000.0000.0000.000
84A85PHE0-0.012-0.02429.2790.0010.0010.0000.0000.0000.000
85A86HIS0-0.0300.00330.7500.1580.1580.0000.0000.0000.000
86A87MET0-0.0110.00224.8120.0090.0090.0000.0000.0000.000
87A88ARG10.8890.93627.84310.07310.0730.0000.0000.0000.000
88A89VAL0-0.016-0.01021.412-0.085-0.0850.0000.0000.0000.000
89A90ARG10.9090.94224.87310.19310.1930.0000.0000.0000.000
90A91LEU00.0230.02021.6090.0470.0470.0000.0000.0000.000
91A92HIS00.0180.01120.826-0.166-0.1660.0000.0000.0000.000
92A93PRO0-0.075-0.02315.8850.0420.0420.0000.0000.0000.000
93A94PHE00.007-0.00818.056-0.205-0.2050.0000.0000.0000.000
94A95HIS0-0.028-0.00817.7070.5800.5800.0000.0000.0000.000
95A96VAL0-0.006-0.01114.037-1.141-1.1410.0000.0000.0000.000
96A97ILE0-0.0330.00111.2220.4080.4080.0000.0000.0000.000
97A98ARG10.9510.96612.26016.83016.8300.0000.0000.0000.000
98A99ILE0-0.0040.0056.111-1.514-1.5140.0000.0000.0000.000
99A100ASN00.0590.04010.2900.7440.7440.0000.0000.0000.000
100A101LYS10.8940.9539.82817.36417.3640.0000.0000.0000.000
101A102MET0-0.037-0.0695.797-0.670-0.6700.0000.0000.0000.000
102A103LEU00.0390.06310.1410.4250.4250.0000.0000.0000.000
103A104SER0-0.031-0.0189.949-0.927-0.9270.0000.0000.0000.000
104A105CYS00.0110.00711.1111.1531.1530.0000.0000.0000.000
105A106ALA00.0400.02113.124-0.011-0.0110.0000.0000.0000.000
106A107GLY00.0040.01016.4560.8660.8660.0000.0000.0000.000
107A108ALA00.0420.01819.0780.4400.4400.0000.0000.0000.000
108A109ASP-1-0.838-0.89417.698-17.459-17.4590.0000.0000.0000.000
109A110ARG10.9300.97219.04214.22414.2240.0000.0000.0000.000
110A111LEU0-0.043-0.02117.5140.8530.8530.0000.0000.0000.000
111A112GLN00.0230.00420.320-0.269-0.2690.0000.0000.0000.000
112A113THR0-0.016-0.04116.5100.0710.0710.0000.0000.0000.000
113A114GLY00.0840.05419.1890.9270.9270.0000.0000.0000.000
114A115MET0-0.022-0.02418.241-1.141-1.1410.0000.0000.0000.000
115A116ARG10.9300.97220.14612.69412.6940.0000.0000.0000.000
116A117GLY00.0410.01219.525-0.553-0.5530.0000.0000.0000.000
117A118ALA00.0050.00317.223-1.052-1.0520.0000.0000.0000.000
118A119PHE0-0.037-0.01316.384-1.184-1.1840.0000.0000.0000.000
119A120GLY0-0.008-0.00413.599-0.553-0.5530.0000.0000.0000.000
120A121LYS10.9710.98310.98422.17222.1720.0000.0000.0000.000
121A122PRO00.021-0.00112.217-0.968-0.9680.0000.0000.0000.000
122A123GLN0-0.007-0.0036.690-5.137-5.1370.0000.0000.0000.000
123A124GLY00.0400.0117.941-2.921-2.9210.0000.0000.0000.000
124A125THR0-0.0050.00410.4561.7801.7800.0000.0000.0000.000
125A126VAL0-0.004-0.00913.591-1.000-1.0000.0000.0000.0000.000
126A127ALA00.0200.02816.0180.8550.8550.0000.0000.0000.000
127A128ARG10.8160.89019.58914.45014.4500.0000.0000.0000.000
128A129VAL00.0290.01721.2160.3020.3020.0000.0000.0000.000
129A130HIS0-0.034-0.02924.0450.1660.1660.0000.0000.0000.000
130A131ILE00.0680.04027.599-0.077-0.0770.0000.0000.0000.000
131A132GLY00.0200.00829.8230.2650.2650.0000.0000.0000.000
132A133GLN00.0040.01026.439-0.019-0.0190.0000.0000.0000.000
133A134VAL0-0.022-0.01028.434-0.259-0.2590.0000.0000.0000.000
134A135ILE0-0.0170.00422.447-0.267-0.2670.0000.0000.0000.000
135A136MET0-0.042-0.02823.633-0.451-0.4510.0000.0000.0000.000
136A137SER0-0.0100.00226.6580.3000.3000.0000.0000.0000.000
137A138ILE0-0.031-0.02128.023-0.225-0.2250.0000.0000.0000.000
138A139ARG10.8210.93031.6418.7668.7660.0000.0000.0000.000
139A140THR00.0600.01735.018-0.227-0.2270.0000.0000.0000.000
140A141LYS10.9410.95837.3087.4767.4760.0000.0000.0000.000
141A142LEU00.0420.02040.247-0.173-0.1730.0000.0000.0000.000
142A143GLN00.0430.02642.0540.0360.0360.0000.0000.0000.000
143A144ASN0-0.001-0.00136.938-0.247-0.2470.0000.0000.0000.000
144A145GLU-1-0.814-0.90736.818-8.173-8.1730.0000.0000.0000.000
145A146GLU-1-0.804-0.91335.922-8.244-8.2440.0000.0000.0000.000
146A147HIS0-0.062-0.04033.849-0.174-0.1740.0000.0000.0000.000
147A148VAL00.006-0.00331.873-0.447-0.4470.0000.0000.0000.000
148A149ILE00.0190.01231.029-0.484-0.4840.0000.0000.0000.000
149A150GLU-1-0.731-0.83930.458-10.521-10.5210.0000.0000.0000.000
150A151ALA0-0.025-0.01027.959-0.483-0.4830.0000.0000.0000.000
151A152LEU0-0.022-0.01926.371-0.674-0.6740.0000.0000.0000.000
152A153ARG10.8730.91126.13710.08310.0830.0000.0000.0000.000
153A154ARG10.8500.91124.46710.44410.4440.0000.0000.0000.000
154A155ALA0-0.010-0.00922.085-0.662-0.6620.0000.0000.0000.000
155A156LYS10.9420.97521.27810.48210.4820.0000.0000.0000.000
156A157PHE00.0030.01821.054-0.443-0.4430.0000.0000.0000.000
157A158LYS10.8470.92816.74115.46515.4650.0000.0000.0000.000
158A159PHE0-0.038-0.03316.538-1.160-1.1600.0000.0000.0000.000
159A160PRO0-0.038-0.00916.3050.1150.1150.0000.0000.0000.000
160A161GLY00.0430.01918.7590.2400.2400.0000.0000.0000.000
161A162ARG10.9070.94522.20110.73210.7320.0000.0000.0000.000
162A163GLN0-0.011-0.01722.209-0.009-0.0090.0000.0000.0000.000
163A164LYS10.8660.91727.07210.04910.0490.0000.0000.0000.000
164A165ILE0-0.038-0.01928.378-0.358-0.3580.0000.0000.0000.000
165A166HIS00.0160.01031.5550.1760.1760.0000.0000.0000.000
166A167ILE00.0380.03034.540-0.262-0.2620.0000.0000.0000.000
167A168SER0-0.050-0.02336.8770.1650.1650.0000.0000.0000.000
168A169LYS11.0331.01838.4537.4357.4350.0000.0000.0000.000
169A170LYS10.8430.93439.4297.6987.6980.0000.0000.0000.000
170A171TRP00.1080.07840.828-0.203-0.2030.0000.0000.0000.000
171A172GLY00.0280.02538.479-0.107-0.1070.0000.0000.0000.000
172A173PHE0-0.103-0.07531.907-0.247-0.2470.0000.0000.0000.000
173A174THR0-0.031-0.00336.793-0.072-0.0720.0000.0000.0000.000
174A175LYS10.9450.96539.2397.6397.6390.0000.0000.0000.000
175A176PHE00.0500.01641.1460.0500.0500.0000.0000.0000.000
176A177ASN0-0.006-0.01543.980-0.279-0.2790.0000.0000.0000.000
177A178ALA00.032-0.00843.7260.1040.1040.0000.0000.0000.000
178A179ASP-1-0.905-0.95245.732-6.401-6.4010.0000.0000.0000.000
179A180GLU-1-0.851-0.91348.805-5.937-5.9370.0000.0000.0000.000
180A181PHE0-0.049-0.04344.7480.0330.0330.0000.0000.0000.000
181A182GLU-1-0.840-0.92948.823-6.441-6.4410.0000.0000.0000.000
182A183ASN00.0850.04551.4670.1030.1030.0000.0000.0000.000
183A184MET0-0.068-0.02549.9940.0290.0290.0000.0000.0000.000
184A185VAL00.0330.02448.7550.0210.0210.0000.0000.0000.000
185A186ALA00.0310.01351.9020.0780.0780.0000.0000.0000.000
186A187LYS10.8380.90254.7245.9175.9170.0000.0000.0000.000
187A188LYS10.8210.92252.8715.6615.6610.0000.0000.0000.000
188A189CYS00.0370.03852.0220.0500.0500.0000.0000.0000.000
189A190LEU0-0.067-0.04146.360-0.164-0.1640.0000.0000.0000.000
190A191ILE00.0520.02247.9820.1010.1010.0000.0000.0000.000
191A192PRO00.006-0.00145.261-0.183-0.1830.0000.0000.0000.000
192A193ASP-1-0.880-0.92341.681-7.427-7.4270.0000.0000.0000.000
193A194GLY00.0130.00239.992-0.231-0.2310.0000.0000.0000.000
194A195CYS0-0.047-0.02836.232-0.037-0.0370.0000.0000.0000.000
195A196GLY0-0.020-0.00438.534-0.068-0.0680.0000.0000.0000.000
196A197VAL0-0.005-0.00840.0040.1110.1110.0000.0000.0000.000
197A198LYS10.8880.94343.2737.0447.0440.0000.0000.0000.000
198A199TYR0-0.004-0.00645.4700.0510.0510.0000.0000.0000.000
199A200VAL0-0.029-0.01647.633-0.060-0.0600.0000.0000.0000.000
200A201PRO00.0170.01950.1060.0760.0760.0000.0000.0000.000
201A202ASN00.0140.00253.077-0.045-0.0450.0000.0000.0000.000
202A203HIS00.000-0.00751.8590.1120.1120.0000.0000.0000.000
203A204GLY0-0.0210.00355.2740.0330.0330.0000.0000.0000.000
204A205PRO00.0550.02855.5290.0830.0830.0000.0000.0000.000
205A206LEU00.0800.02758.287-0.067-0.0670.0000.0000.0000.000
206A207ASP-1-0.840-0.91359.692-5.188-5.1880.0000.0000.0000.000
207A208LYS10.8290.92052.4185.8345.8340.0000.0000.0000.000
208A209TRP00.0150.00956.091-0.063-0.0630.0000.0000.0000.000
209A210ARG10.9620.95457.9934.9454.9450.0000.0000.0000.000
210A211VAL0-0.0190.00454.9260.0090.0090.0000.0000.0000.000
211A212LEU0-0.089-0.03853.587-0.072-0.0720.0000.0000.0000.000
212A213HIS0-0.041-0.02457.1890.0110.0110.0000.0000.0000.000
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