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: 4YQVN

Calculation Name: 2G7F-A-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion | chloride ion

Ligand 3-letter code: MG | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2G7F

Chain ID: A

ChEMBL ID:

UniProt ID: Q2XSK9

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 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2625381.678608
FMO2-HF: Nuclear repulsion 2538339.13806
FMO2-HF: Total energy -87042.540548
FMO2-MP2: Total energy -87290.127399


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:23:SER)


Summations of interaction energy for fragment #1(A:23:SER)
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.
49.32554.50617.484-11.646-11.022-0.077
Interaction energy analysis for fragmet #1(A:23:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.838 / q_NPA : 0.892
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].
3A25SER0-0.035-0.0152.6905.9919.2120.774-1.689-2.3070.009
4A26HIS00.0720.0401.854-23.559-26.64315.591-6.754-5.753-0.045
5A27ALA00.0920.0654.0976.3866.6240.001-0.071-0.1690.000
79A103THR0-0.015-0.0334.429-2.376-2.313-0.001-0.008-0.0540.000
86A110ASN0-0.086-0.0752.386-31.297-26.9411.122-2.973-2.505-0.040
87A111GLN0-0.0100.0153.966-9.401-9.243-0.001-0.109-0.048-0.001
89A113GLU-1-0.873-0.9244.741-47.144-47.002-0.001-0.009-0.1320.000
90A114ALA0-0.048-0.0403.786-0.145-0.058-0.001-0.033-0.0540.000
6A28LYS10.9130.9796.46337.77037.7700.0000.0000.0000.000
7A29ASN0-0.034-0.0215.7116.1066.1060.0000.0000.0000.000
8A30GLU-1-0.789-0.8767.864-25.371-25.3710.0000.0000.0000.000
9A31ALA00.0270.02210.3402.6332.6330.0000.0000.0000.000
10A32VAL0-0.022-0.02411.9482.0092.0090.0000.0000.0000.000
11A33LYS10.7700.87210.45926.37126.3710.0000.0000.0000.000
12A34ILE00.0160.02013.9151.3391.3390.0000.0000.0000.000
13A35TYR00.031-0.01216.3031.0121.0120.0000.0000.0000.000
14A36ARG10.9330.99115.62917.51517.5150.0000.0000.0000.000
15A37ASP-1-0.802-0.87419.982-13.341-13.3410.0000.0000.0000.000
16A38HIS10.8710.94121.80513.59413.5940.0000.0000.0000.000
17A39PRO00.0270.02221.940-0.664-0.6640.0000.0000.0000.000
18A40VAL00.0240.00922.7850.5120.5120.0000.0000.0000.000
19A41SER0-0.085-0.04821.991-0.605-0.6050.0000.0000.0000.000
20A42PHE0-0.022-0.02620.6420.4200.4200.0000.0000.0000.000
21A43TYR0-0.020-0.05719.9690.5940.5940.0000.0000.0000.000
22A44CYS0-0.068-0.02825.0960.0950.0950.0000.0000.0000.000
23A45GLY00.0360.02926.4010.4120.4120.0000.0000.0000.000
24A46CYS0-0.109-0.01326.5700.2000.2000.0000.0000.0000.000
25A47GLU-1-0.849-0.92425.655-11.101-11.1010.0000.0000.0000.000
26A48ILE0-0.077-0.03619.987-0.380-0.3800.0000.0000.0000.000
27A49ARG10.9740.98323.10011.70611.7060.0000.0000.0000.000
28A50TRP0-0.002-0.01316.227-0.863-0.8630.0000.0000.0000.000
29A51GLN00.0460.02118.6470.9820.9820.0000.0000.0000.000
30A52GLY00.0080.00716.708-0.442-0.4420.0000.0000.0000.000
31A53LYS10.9230.9578.48224.38524.3850.0000.0000.0000.000
32A54LYS10.8750.94113.23813.59613.5960.0000.0000.0000.000
33A55GLY00.0800.03615.9020.4630.4630.0000.0000.0000.000
34A56ILE0-0.043-0.04218.659-0.275-0.2750.0000.0000.0000.000
35A57PRO0-0.0290.00321.7700.0970.0970.0000.0000.0000.000
36A58ASP-1-0.819-0.89324.240-9.952-9.9520.0000.0000.0000.000
37A59LEU0-0.037-0.04126.155-0.035-0.0350.0000.0000.0000.000
38A60GLU-1-0.908-0.93829.462-8.556-8.5560.0000.0000.0000.000
39A61SER00.006-0.01029.5960.0450.0450.0000.0000.0000.000
40A63GLY00.0850.04432.0060.0380.0380.0000.0000.0000.000
41A64TYR0-0.060-0.07827.097-0.147-0.1470.0000.0000.0000.000
42A65GLN0-0.034-0.01431.2100.0540.0540.0000.0000.0000.000
43A66VAL0-0.017-0.02128.547-0.294-0.2940.0000.0000.0000.000
44A67ARG10.8980.95528.09410.91410.9140.0000.0000.0000.000
45A68LYS10.9140.94228.81810.54210.5420.0000.0000.0000.000
46A69ASN0-0.055-0.03123.653-0.104-0.1040.0000.0000.0000.000
47A70GLU-1-0.787-0.89625.655-10.405-10.4050.0000.0000.0000.000
48A71ASN0-0.0010.00321.457-0.516-0.5160.0000.0000.0000.000
49A72ARG10.7980.86617.64715.56015.5600.0000.0000.0000.000
50A73ALA00.0500.03221.927-0.451-0.4510.0000.0000.0000.000
51A74SER0-0.021-0.00822.837-0.129-0.1290.0000.0000.0000.000
52A75ARG10.7860.86517.59215.72215.7220.0000.0000.0000.000
53A76ILE00.0250.04416.5790.1320.1320.0000.0000.0000.000
54A77GLU-1-0.811-0.84615.096-17.905-17.9050.0000.0000.0000.000
55A78TRP0-0.022-0.02211.7130.0090.0090.0000.0000.0000.000
56A79GLU-1-0.765-0.83313.188-18.801-18.8010.0000.0000.0000.000
57A80HIS0-0.058-0.0408.6050.6760.6760.0000.0000.0000.000
58A81VAL00.0520.02713.7631.1001.1000.0000.0000.0000.000
59A82VAL00.0520.03215.3921.2461.2460.0000.0000.0000.000
60A83PRO00.0160.00014.230-1.811-1.8110.0000.0000.0000.000
61A84ALA00.0370.00110.7740.0610.0610.0000.0000.0000.000
62A85TRP0-0.001-0.00212.243-0.425-0.4250.0000.0000.0000.000
63A86GLN0-0.0130.00015.3420.9030.9030.0000.0000.0000.000
64A87PHE00.0360.0198.9400.5200.5200.0000.0000.0000.000
65A88GLY00.0120.01012.527-0.732-0.7320.0000.0000.0000.000
66A89HIS0-0.097-0.06813.1540.9340.9340.0000.0000.0000.000
67A90GLN00.0440.01916.6240.6620.6620.0000.0000.0000.000
68A91LEU00.0260.03611.6330.3340.3340.0000.0000.0000.000
69A92GLN00.0530.01315.5450.2120.2120.0000.0000.0000.000
70A93CYS0-0.0070.0339.172-0.262-0.2620.0000.0000.0000.000
71A94TRP00.0350.01811.401-0.597-0.5970.0000.0000.0000.000
72A95GLN00.002-0.01014.9781.1651.1650.0000.0000.0000.000
73A96GLN00.0190.02217.5010.8040.8040.0000.0000.0000.000
74A97GLY00.0040.00416.2560.3230.3230.0000.0000.0000.000
75A98GLY0-0.025-0.00814.743-0.785-0.7850.0000.0000.0000.000
76A99ARG10.8500.9098.29530.11630.1160.0000.0000.0000.000
77A100LYS10.9620.9969.55618.12018.1200.0000.0000.0000.000
78A101ASN0-0.0060.00310.239-1.483-1.4830.0000.0000.0000.000
80A104ARG10.8570.9355.85918.50718.5070.0000.0000.0000.000
81A105THR0-0.011-0.0278.6281.3861.3860.0000.0000.0000.000
82A106SER00.0460.0378.3311.0991.0990.0000.0000.0000.000
83A107PRO00.0290.0066.249-5.686-5.6860.0000.0000.0000.000
84A108GLU-1-0.835-0.9146.769-26.958-26.9580.0000.0000.0000.000
85A109PHE00.007-0.0066.363-0.090-0.0900.0000.0000.0000.000
88A112MET00.0280.0246.5371.7291.7290.0000.0000.0000.000
91A115ASP-1-0.717-0.7955.893-22.277-22.2770.0000.0000.0000.000
92A116LEU00.029-0.0029.4582.0432.0430.0000.0000.0000.000
93A117HIS10.7980.92311.57221.76021.7600.0000.0000.0000.000
94A118ASN00.0370.00811.8123.1503.1500.0000.0000.0000.000
95A119LEU0-0.057-0.0038.7060.2020.2020.0000.0000.0000.000
96A120THR0-0.0190.00113.3790.8320.8320.0000.0000.0000.000
97A121PRO00.0000.01516.201-0.703-0.7030.0000.0000.0000.000
98A122ALA00.0380.02117.9001.1181.1180.0000.0000.0000.000
99A123ILE00.0750.03919.318-0.541-0.5410.0000.0000.0000.000
100A124GLY00.012-0.00919.252-0.176-0.1760.0000.0000.0000.000
101A125GLU-1-0.754-0.84520.083-11.504-11.5040.0000.0000.0000.000
102A126VAL00.0460.02123.1180.0260.0260.0000.0000.0000.000
103A127ASN0-0.029-0.02315.418-0.048-0.0480.0000.0000.0000.000
104A128GLY0-0.043-0.03719.714-0.245-0.2450.0000.0000.0000.000
105A129ASN0-0.042-0.00120.5620.7780.7780.0000.0000.0000.000
106A130ARG10.8810.94818.11516.49416.4940.0000.0000.0000.000
107A131SER0-0.023-0.00519.598-0.016-0.0160.0000.0000.0000.000
108A132ASN0-0.023-0.02817.969-0.255-0.2550.0000.0000.0000.000
109A133PHE00.0050.01419.4280.1970.1970.0000.0000.0000.000
110A134SER00.0080.01221.998-0.493-0.4930.0000.0000.0000.000
111A135PHE00.0120.00320.8130.2940.2940.0000.0000.0000.000
112A136SER00.005-0.00425.7960.3020.3020.0000.0000.0000.000
113A137GLN00.0480.00429.550-0.364-0.3640.0000.0000.0000.000
114A138TRP0-0.005-0.01230.3090.0120.0120.0000.0000.0000.000
115A139ASN00.0270.00235.899-0.102-0.1020.0000.0000.0000.000
116A140GLY00.0120.01539.0970.0260.0260.0000.0000.0000.000
117A141ILE0-0.042-0.02236.855-0.245-0.2450.0000.0000.0000.000
118A142ASP-1-0.841-0.91335.948-8.636-8.6360.0000.0000.0000.000
119A143GLY00.0160.00733.204-0.324-0.3240.0000.0000.0000.000
120A144VAL0-0.112-0.05329.9790.2230.2230.0000.0000.0000.000
121A145THR00.0520.02031.873-0.265-0.2650.0000.0000.0000.000
122A146TYR0-0.017-0.04527.466-0.186-0.1860.0000.0000.0000.000
123A147GLY00.0340.01931.863-0.123-0.1230.0000.0000.0000.000
124A148GLN00.0110.01834.7620.1920.1920.0000.0000.0000.000
125A150GLU-1-0.734-0.84531.753-10.099-10.0990.0000.0000.0000.000
126A151MET0-0.059-0.01824.398-0.107-0.1070.0000.0000.0000.000
127A152GLN00.0240.00929.8470.3060.3060.0000.0000.0000.000
128A153VAL0-0.026-0.01326.424-0.405-0.4050.0000.0000.0000.000
129A154ASN00.0180.01829.2990.0950.0950.0000.0000.0000.000
130A155PHE0-0.056-0.05526.192-0.248-0.2480.0000.0000.0000.000
131A156LYS10.9090.96629.7128.4028.4020.0000.0000.0000.000
132A157GLU-1-0.853-0.92831.390-9.234-9.2340.0000.0000.0000.000
133A158ARG10.8290.92622.66312.45512.4550.0000.0000.0000.000
134A159THR00.0370.02726.216-0.583-0.5830.0000.0000.0000.000
135A160ALA00.010-0.01125.2370.1360.1360.0000.0000.0000.000
136A161MET00.0280.05927.333-0.063-0.0630.0000.0000.0000.000
137A162PRO0-0.011-0.00225.4600.0210.0210.0000.0000.0000.000
138A163PRO00.0290.00227.2440.3060.3060.0000.0000.0000.000
139A164GLU-1-0.828-0.90428.630-9.634-9.6340.0000.0000.0000.000
140A165ARG10.7650.84027.35610.53710.5370.0000.0000.0000.000
141A166ALA00.0010.00924.123-0.350-0.3500.0000.0000.0000.000
142A167ARG10.8380.93324.9819.7239.7230.0000.0000.0000.000
143A168GLY00.0750.04826.261-0.219-0.2190.0000.0000.0000.000
144A169ALA00.0440.02422.319-0.325-0.3250.0000.0000.0000.000
145A170ILE0-0.060-0.02321.418-0.875-0.8750.0000.0000.0000.000
146A171ALA00.0190.00421.836-0.550-0.5500.0000.0000.0000.000
147A172ARG10.7660.85423.01511.73611.7360.0000.0000.0000.000
148A173THR0-0.040-0.01216.948-0.844-0.8440.0000.0000.0000.000
149A174TYR0-0.028-0.03818.548-0.936-0.9360.0000.0000.0000.000
150A175LEU0-0.031-0.00720.429-0.233-0.2330.0000.0000.0000.000
151A176TYR00.000-0.01613.4010.1720.1720.0000.0000.0000.000
152A177MET0-0.039-0.01912.091-0.715-0.7150.0000.0000.0000.000
153A178SER0-0.092-0.05417.009-0.108-0.1080.0000.0000.0000.000
154A179GLU-1-0.807-0.87020.052-13.380-13.3800.0000.0000.0000.000
155A180GLN0-0.024-0.00814.6180.7720.7720.0000.0000.0000.000
156A181TYR0-0.038-0.06811.389-1.575-1.5750.0000.0000.0000.000
157A182GLY00.0230.03216.0890.0010.0010.0000.0000.0000.000
158A183LEU0-0.045-0.01215.0470.5280.5280.0000.0000.0000.000
159A184ARG10.9730.98419.29913.24613.2460.0000.0000.0000.000
160A185LEU00.0320.02821.2770.0510.0510.0000.0000.0000.000
161A186SER00.0200.00624.3140.4280.4280.0000.0000.0000.000
162A187LYS10.9870.99027.6788.8008.8000.0000.0000.0000.000
163A188ALA00.0230.01130.4440.0670.0670.0000.0000.0000.000
164A189GLN0-0.008-0.00924.649-0.452-0.4520.0000.0000.0000.000
165A190ASN00.0600.02527.237-0.385-0.3850.0000.0000.0000.000
166A191GLN00.006-0.01028.0750.1460.1460.0000.0000.0000.000
167A192LEU0-0.0110.01727.2500.2050.2050.0000.0000.0000.000
168A193MET0-0.0040.01123.5020.0550.0550.0000.0000.0000.000
169A194GLN0-0.010-0.01227.5850.1500.1500.0000.0000.0000.000
170A195ALA0-0.0070.00430.2790.1650.1650.0000.0000.0000.000
171A196TRP0-0.019-0.05225.920-0.103-0.1030.0000.0000.0000.000
172A197ASN00.0370.02327.758-0.254-0.2540.0000.0000.0000.000
173A198ASN0-0.011-0.00329.289-0.077-0.0770.0000.0000.0000.000
174A199GLN0-0.0100.01033.0500.2900.2900.0000.0000.0000.000
175A200TYR0-0.082-0.06130.0340.0870.0870.0000.0000.0000.000
176A201PRO00.1020.05329.714-0.503-0.5030.0000.0000.0000.000
177A202VAL0-0.038-0.00626.095-0.275-0.2750.0000.0000.0000.000
178A203SER0-0.020-0.02126.2600.2690.2690.0000.0000.0000.000
179A204GLU-1-0.861-0.94327.077-10.806-10.8060.0000.0000.0000.000
180A205TRP0-0.024-0.02319.701-0.390-0.3900.0000.0000.0000.000
181A206GLU-1-0.776-0.86522.470-13.492-13.4920.0000.0000.0000.000
182A207CYS0-0.0240.01222.342-0.572-0.5720.0000.0000.0000.000
183A208VAL00.0230.01022.970-0.444-0.4440.0000.0000.0000.000
184A209ARG10.8100.88915.89117.85117.8510.0000.0000.0000.000
185A210ASP-1-0.745-0.85718.509-17.129-17.1290.0000.0000.0000.000
186A211GLN00.0620.03719.119-0.971-0.9710.0000.0000.0000.000
187A212LYS10.7430.85618.01014.58014.5800.0000.0000.0000.000
188A213ILE0-0.037-0.02813.399-0.930-0.9300.0000.0000.0000.000
189A214GLU-1-0.822-0.87914.930-16.123-16.1230.0000.0000.0000.000
190A215LYS10.9240.96516.82914.02714.0270.0000.0000.0000.000
191A216VAL0-0.052-0.02511.533-0.239-0.2390.0000.0000.0000.000
192A217GLN0-0.076-0.05010.221-3.513-3.5130.0000.0000.0000.000
193A218GLY00.0210.02112.271-0.641-0.6410.0000.0000.0000.000
194A219ASN00.0230.00014.3220.0030.0030.0000.0000.0000.000
195A220SER0-0.012-0.01616.646-0.412-0.4120.0000.0000.0000.000
196A221ASN0-0.063-0.05318.4140.0920.0920.0000.0000.0000.000
197A222ARG10.8260.85719.88213.04313.0430.0000.0000.0000.000
198A223PHE00.0260.01321.8630.6030.6030.0000.0000.0000.000
199A224VAL0-0.070-0.03521.7440.3800.3800.0000.0000.0000.000
200A225ARG10.8300.87521.46414.41414.4140.0000.0000.0000.000
201A226GLU-1-0.851-0.91225.441-11.392-11.3920.0000.0000.0000.000
202A227GLN0-0.048-0.03427.8340.6440.6440.0000.0000.0000.000
203A229PRO0-0.0030.01129.1420.1310.1310.0000.0000.0000.000
204A230ASN-1-0.962-0.98627.620-11.165-11.1650.0000.0000.0000.000