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

tag_button

FMODB ID: NL83Q

Calculation Name: 2I3D-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: 2I3D

Chain ID: A

ChEMBL ID:

UniProt ID: A9CIK7

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 218
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2695470.902052
FMO2-HF: Nuclear repulsion 2610190.462272
FMO2-HF: Total energy -85280.439781
FMO2-MP2: Total energy -85529.015649


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:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-18.874-11.5584.779-5.64-6.452-0.05
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.885 / q_NPA : 0.928
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].
3A4VAL0-0.0090.0143.708-3.537-1.740-0.007-0.861-0.9290.000
15A16ARG10.6940.8443.24237.32737.7890.016-0.125-0.3530.000
16A17TYR00.051-0.0053.1304.1455.0540.025-0.279-0.654-0.001
17A18GLN0-0.037-0.0292.168-32.011-27.9664.747-4.354-4.437-0.049
18A19PRO0-0.0030.0234.7155.4875.531-0.001-0.017-0.0250.000
49A50PHE0-0.029-0.0154.770-0.584-0.525-0.001-0.004-0.0540.000
4A5ILE0-0.009-0.0136.0763.7363.7360.0000.0000.0000.000
5A6PHE00.0000.0209.795-0.341-0.3410.0000.0000.0000.000
6A7ASN0-0.008-0.01512.4150.5250.5250.0000.0000.0000.000
7A8GLY00.0860.03616.178-0.259-0.2590.0000.0000.0000.000
8A9PRO0-0.051-0.03018.3930.3350.3350.0000.0000.0000.000
9A10ALA00.0060.01520.7710.5910.5910.0000.0000.0000.000
10A11GLY0-0.0030.01120.0110.1500.1500.0000.0000.0000.000
11A12ARG10.9300.95714.48817.75817.7580.0000.0000.0000.000
12A13LEU00.0270.02813.7480.9210.9210.0000.0000.0000.000
13A14GLU-1-0.794-0.8909.858-28.941-28.9410.0000.0000.0000.000
14A15GLY00.0520.0108.2132.4282.4280.0000.0000.0000.000
19A20SER00.002-0.0057.558-0.065-0.0650.0000.0000.0000.000
20A21LYS10.8950.93210.85624.01224.0120.0000.0000.0000.000
21A22GLU-1-0.853-0.91512.454-15.693-15.6930.0000.0000.0000.000
22A23LYS10.9210.94815.17216.19616.1960.0000.0000.0000.000
23A24SER0-0.066-0.06317.3960.7720.7720.0000.0000.0000.000
24A25ALA00.0160.02614.3900.6630.6630.0000.0000.0000.000
25A26PRO00.0470.05515.834-0.473-0.4730.0000.0000.0000.000
26A27ILE0-0.001-0.01112.451-1.696-1.6960.0000.0000.0000.000
27A28ALA00.0060.00412.3931.4231.4230.0000.0000.0000.000
28A29ILE0-0.011-0.00411.731-2.309-2.3090.0000.0000.0000.000
29A30ILE0-0.031-0.02111.4771.3001.3000.0000.0000.0000.000
30A31LEU0-0.020-0.00513.571-0.870-0.8700.0000.0000.0000.000
31A32HIS00.003-0.00314.2800.0050.0050.0000.0000.0000.000
32A33PRO00.0060.00017.0750.5460.5460.0000.0000.0000.000
33A34HIS00.1220.08019.963-0.666-0.6660.0000.0000.0000.000
34A35PRO00.0340.01321.0670.0090.0090.0000.0000.0000.000
35A36GLN0-0.046-0.01722.0840.0050.0050.0000.0000.0000.000
36A37PHE0-0.034-0.02823.2680.4110.4110.0000.0000.0000.000
37A38GLY00.0250.02020.931-0.271-0.2710.0000.0000.0000.000
38A39GLY0-0.037-0.00318.611-0.814-0.8140.0000.0000.0000.000
39A40THR00.002-0.00313.938-0.685-0.6850.0000.0000.0000.000
40A41MET0-0.0100.0018.209-0.449-0.4490.0000.0000.0000.000
41A42ASN0-0.006-0.0068.826-3.489-3.4890.0000.0000.0000.000
42A43ASN00.0180.01111.6380.8450.8450.0000.0000.0000.000
43A44GLN00.0470.01614.074-1.152-1.1520.0000.0000.0000.000
44A45ILE00.0500.02914.910-0.689-0.6890.0000.0000.0000.000
45A46VAL00.0140.01312.125-0.218-0.2180.0000.0000.0000.000
46A47TYR0-0.035-0.0167.403-2.577-2.5770.0000.0000.0000.000
47A48GLN00.0270.00011.089-1.467-1.4670.0000.0000.0000.000
48A49LEU00.0420.02213.748-0.046-0.0460.0000.0000.0000.000
50A51TYR00.000-0.0128.857-0.186-0.1860.0000.0000.0000.000
51A52LEU00.0290.02910.530-0.045-0.0450.0000.0000.0000.000
52A53PHE00.0380.00812.3030.2650.2650.0000.0000.0000.000
53A54GLN0-0.011-0.0045.906-0.510-0.5100.0000.0000.0000.000
54A55LYS10.8720.92610.16319.56319.5630.0000.0000.0000.000
55A56ARG10.6830.80612.97416.56316.5630.0000.0000.0000.000
56A57GLY00.0040.01212.9450.7390.7390.0000.0000.0000.000
57A58PHE00.0610.03612.7150.0510.0510.0000.0000.0000.000
58A59THR0-0.0160.0039.131-2.883-2.8830.0000.0000.0000.000
59A60THR0-0.028-0.0088.1472.5782.5780.0000.0000.0000.000
60A61LEU0-0.044-0.0216.969-5.973-5.9730.0000.0000.0000.000
61A62ARG10.8630.9485.75536.69236.6920.0000.0000.0000.000
62A63PHE00.001-0.0228.695-3.719-3.7190.0000.0000.0000.000
63A64ASN00.0300.01711.0741.7331.7330.0000.0000.0000.000
64A65PHE00.0360.03013.434-0.198-0.1980.0000.0000.0000.000
65A66ARG10.8690.92317.02213.54013.5400.0000.0000.0000.000
66A67SER0-0.076-0.03319.3720.6560.6560.0000.0000.0000.000
67A68ILE0-0.0340.00315.3190.0460.0460.0000.0000.0000.000
68A69GLY0-0.006-0.00914.291-1.378-1.3780.0000.0000.0000.000
69A70ARG10.8370.88810.63326.08926.0890.0000.0000.0000.000
70A71SER0-0.054-0.03014.493-0.545-0.5450.0000.0000.0000.000
71A72GLN0-0.023-0.00416.0530.4970.4970.0000.0000.0000.000
72A73GLY00.0400.01819.645-0.071-0.0710.0000.0000.0000.000
73A74GLU-1-0.939-0.97022.936-11.290-11.2900.0000.0000.0000.000
74A75PHE0-0.014-0.01620.127-0.299-0.2990.0000.0000.0000.000
75A76ASP-1-0.786-0.90524.115-11.524-11.5240.0000.0000.0000.000
76A77HIS0-0.021-0.02226.408-0.147-0.1470.0000.0000.0000.000
77A78GLY00.0550.00724.9870.0690.0690.0000.0000.0000.000
78A79ALA0-0.0290.00424.861-0.332-0.3320.0000.0000.0000.000
79A80GLY0-0.003-0.01124.125-0.205-0.2050.0000.0000.0000.000
80A81GLU-1-0.767-0.88920.562-13.864-13.8640.0000.0000.0000.000
81A82LEU00.003-0.00119.979-0.810-0.8100.0000.0000.0000.000
82A83SER0-0.052-0.03421.291-0.164-0.1640.0000.0000.0000.000
83A84ASP-1-0.802-0.87917.328-16.210-16.2100.0000.0000.0000.000
84A85ALA0-0.004-0.01716.452-1.126-1.1260.0000.0000.0000.000
85A86ALA0-0.023-0.00416.952-0.544-0.5440.0000.0000.0000.000
86A87SER00.026-0.00217.147-0.215-0.2150.0000.0000.0000.000
87A88ALA0-0.031-0.01112.789-0.984-0.9840.0000.0000.0000.000
88A89LEU0-0.018-0.00612.992-1.589-1.5890.0000.0000.0000.000
89A90ASP-1-0.807-0.88515.094-16.034-16.0340.0000.0000.0000.000
90A91TRP0-0.011-0.0056.466-1.090-1.0900.0000.0000.0000.000
91A92VAL00.0030.0019.573-1.108-1.1080.0000.0000.0000.000
92A93GLN0-0.004-0.03211.8120.0460.0460.0000.0000.0000.000
93A94SER0-0.100-0.05813.7640.4170.4170.0000.0000.0000.000
94A95LEU0-0.032-0.0118.946-0.036-0.0360.0000.0000.0000.000
95A96HIS0-0.035-0.0059.818-2.859-2.8590.0000.0000.0000.000
96A97PRO00.0580.03414.2280.6160.6160.0000.0000.0000.000
97A98ASP-1-0.910-0.95017.962-14.445-14.4450.0000.0000.0000.000
98A99SER0-0.092-0.05015.6850.4770.4770.0000.0000.0000.000
99A100LYS10.9270.95817.83314.36414.3640.0000.0000.0000.000
100A101SER0-0.0290.00219.5610.3290.3290.0000.0000.0000.000
101A102CYS0-0.067-0.02117.039-1.377-1.3770.0000.0000.0000.000
102A103TRP00.0570.02516.9500.7830.7830.0000.0000.0000.000
103A104VAL0-0.0100.00416.575-1.107-1.1070.0000.0000.0000.000
104A105ALA00.0110.00615.8150.8450.8450.0000.0000.0000.000
105A106GLY00.0250.01516.827-0.976-0.9760.0000.0000.0000.000
106A107TYR0-0.045-0.05318.3580.5010.5010.0000.0000.0000.000
107A108SER0-0.034-0.02920.477-0.063-0.0630.0000.0000.0000.000
108A109PHE00.0070.00621.2150.1440.1440.0000.0000.0000.000
109A110GLY00.0670.02819.6260.0850.0850.0000.0000.0000.000
110A111ALA0-0.030-0.00520.553-0.248-0.2480.0000.0000.0000.000
111A112TRP00.000-0.00922.929-0.014-0.0140.0000.0000.0000.000
112A113ILE0-0.059-0.00720.4790.1580.1580.0000.0000.0000.000
113A114GLY00.0430.00520.658-0.099-0.0990.0000.0000.0000.000
114A115MET00.0100.01921.4190.1860.1860.0000.0000.0000.000
115A116GLN0-0.001-0.00325.0090.5380.5380.0000.0000.0000.000
116A117LEU0-0.046-0.02518.2910.1870.1870.0000.0000.0000.000
117A118LEU0-0.006-0.00722.8090.1100.1100.0000.0000.0000.000
118A119MET0-0.0320.00024.1510.2060.2060.0000.0000.0000.000
119A120ARG10.8920.95224.36412.55912.5590.0000.0000.0000.000
120A121ARG10.7350.85819.52714.74014.7400.0000.0000.0000.000
121A122PRO00.0430.01323.794-0.236-0.2360.0000.0000.0000.000
122A123GLU-1-0.740-0.84219.954-14.079-14.0790.0000.0000.0000.000
123A124ILE0-0.052-0.03119.794-0.558-0.5580.0000.0000.0000.000
124A125GLU-1-0.810-0.88322.005-12.617-12.6170.0000.0000.0000.000
125A126GLY00.0030.00922.2320.5250.5250.0000.0000.0000.000
126A127PHE0-0.018-0.00721.284-0.621-0.6210.0000.0000.0000.000
127A128MET0-0.0190.00419.2580.1650.1650.0000.0000.0000.000
128A129SER0-0.013-0.02821.143-0.670-0.6700.0000.0000.0000.000
129A130ILE00.0180.01419.7980.5690.5690.0000.0000.0000.000
130A131ALA00.003-0.01623.284-0.160-0.1600.0000.0000.0000.000
131A132PRO00.0030.00626.139-0.076-0.0760.0000.0000.0000.000
132A133GLN00.0470.02126.466-0.129-0.1290.0000.0000.0000.000
133A134PRO00.0170.01429.8230.0310.0310.0000.0000.0000.000
134A135ASN0-0.011-0.00932.826-0.013-0.0130.0000.0000.0000.000
135A136THR0-0.088-0.03630.3750.1070.1070.0000.0000.0000.000
136A137TYR0-0.010-0.01127.545-0.111-0.1110.0000.0000.0000.000
137A138ASP-1-0.775-0.86231.428-8.854-8.8540.0000.0000.0000.000
138A139PHE00.015-0.00927.570-0.392-0.3920.0000.0000.0000.000
139A140SER0-0.088-0.06032.4340.0130.0130.0000.0000.0000.000
140A141PHE0-0.021-0.00828.0440.1260.1260.0000.0000.0000.000
141A142LEU00.0100.00628.609-0.107-0.1070.0000.0000.0000.000
142A143ALA0-0.052-0.01532.6640.2320.2320.0000.0000.0000.000
143A144PRO0-0.022-0.00834.4810.1510.1510.0000.0000.0000.000
144A145CYS00.012-0.01529.374-0.362-0.3620.0000.0000.0000.000
145A146PRO0-0.027-0.00827.6490.2300.2300.0000.0000.0000.000
146A147SER00.023-0.00925.6540.1880.1880.0000.0000.0000.000
147A148SER00.0420.02228.0970.3140.3140.0000.0000.0000.000
148A149GLY00.020-0.00325.418-0.548-0.5480.0000.0000.0000.000
149A150LEU0-0.0400.00522.9850.4800.4800.0000.0000.0000.000
150A151ILE0-0.010-0.00725.152-0.363-0.3630.0000.0000.0000.000
151A152ILE00.0340.01823.6720.2770.2770.0000.0000.0000.000
152A153ASN00.0210.01126.154-0.430-0.4300.0000.0000.0000.000
153A154GLY00.0340.02228.5990.0200.0200.0000.0000.0000.000
154A155ASP-1-0.774-0.89330.644-8.820-8.8200.0000.0000.0000.000
155A156ALA0-0.027-0.00432.9640.2640.2640.0000.0000.0000.000
156A157ASP-1-0.790-0.88629.251-10.490-10.4900.0000.0000.0000.000
157A158LYS10.9330.95532.0928.5158.5150.0000.0000.0000.000
158A159VAL0-0.041-0.00528.8160.1380.1380.0000.0000.0000.000
159A160ALA0-0.018-0.01229.8650.0760.0760.0000.0000.0000.000
160A161PRO00.0030.01231.842-0.082-0.0820.0000.0000.0000.000
161A162GLU-1-0.830-0.92734.867-8.470-8.4700.0000.0000.0000.000
162A163LYS10.9080.96635.9287.3907.3900.0000.0000.0000.000
163A164ASP-1-0.854-0.93535.156-8.268-8.2680.0000.0000.0000.000
164A165VAL0-0.002-0.00230.843-0.099-0.0990.0000.0000.0000.000
165A166ASN00.0290.00333.607-0.279-0.2790.0000.0000.0000.000
166A167GLY00.0070.01236.2560.0890.0890.0000.0000.0000.000
167A168LEU0-0.030-0.01230.2880.0620.0620.0000.0000.0000.000
168A169VAL00.005-0.00732.035-0.023-0.0230.0000.0000.0000.000
169A170GLU-1-0.913-0.96334.373-7.922-7.9220.0000.0000.0000.000
170A171LYS10.9460.98036.7278.2058.2050.0000.0000.0000.000
171A172LEU0-0.009-0.01031.0290.0580.0580.0000.0000.0000.000
172A173LYS10.9570.98334.6958.6338.6330.0000.0000.0000.000
173A174THR0-0.124-0.05836.9630.1620.1620.0000.0000.0000.000
174A175GLN0-0.050-0.01234.517-0.018-0.0180.0000.0000.0000.000
175A176LYS10.9670.96736.4897.1497.1490.0000.0000.0000.000
176A177GLY00.0520.03336.023-0.009-0.0090.0000.0000.0000.000
177A178ILE0-0.0260.00331.272-0.265-0.2650.0000.0000.0000.000
178A179LEU00.0030.00231.3600.3060.3060.0000.0000.0000.000
179A180ILE0-0.011-0.00930.315-0.407-0.4070.0000.0000.0000.000
180A181THR00.0080.00828.3940.3280.3280.0000.0000.0000.000
181A182HIS0-0.064-0.04629.125-0.163-0.1630.0000.0000.0000.000
182A183ARG10.8300.90228.34010.14810.1480.0000.0000.0000.000
183A184THR00.0180.01429.553-0.368-0.3680.0000.0000.0000.000
184A185LEU0-0.018-0.01026.0040.1170.1170.0000.0000.0000.000
185A186PRO00.003-0.00230.6680.0600.0600.0000.0000.0000.000
186A187GLY0-0.010-0.01632.286-0.144-0.1440.0000.0000.0000.000
187A188ALA0-0.0270.00828.289-0.218-0.2180.0000.0000.0000.000
188A189ASN00.019-0.01927.802-0.078-0.0780.0000.0000.0000.000
189A190HIS10.8070.88525.79910.96610.9660.0000.0000.0000.000
190A191PHE0-0.027-0.00923.750-0.402-0.4020.0000.0000.0000.000
191A192PHE00.0260.01823.289-0.444-0.4440.0000.0000.0000.000
192A193ASN0-0.0030.00624.7030.0680.0680.0000.0000.0000.000
193A194GLY00.0150.00925.5960.3530.3530.0000.0000.0000.000
194A195LYS10.8530.92425.65110.32210.3220.0000.0000.0000.000
195A196VAL0-0.001-0.00119.281-0.159-0.1590.0000.0000.0000.000
196A197ASP-1-0.873-0.93121.067-13.978-13.9780.0000.0000.0000.000
197A198GLU-1-0.840-0.92022.642-11.050-11.0500.0000.0000.0000.000
198A199LEU0-0.024-0.01721.1050.0000.0000.0000.0000.0000.000
199A200MET0-0.027-0.01716.431-0.335-0.3350.0000.0000.0000.000
200A201GLY00.0620.03720.444-0.319-0.3190.0000.0000.0000.000
201A202GLU-1-0.809-0.89222.878-10.442-10.4420.0000.0000.0000.000
202A203CYS0-0.086-0.05219.6800.0350.0350.0000.0000.0000.000
203A204GLU-1-0.866-0.92219.178-15.360-15.3600.0000.0000.0000.000
204A205ASP-1-0.870-0.93120.735-11.560-11.5600.0000.0000.0000.000
205A206TYR0-0.050-0.02322.8100.1440.1440.0000.0000.0000.000
206A207LEU0-0.020-0.01016.9760.0820.0820.0000.0000.0000.000
207A208ASP-1-0.743-0.84221.007-14.052-14.0520.0000.0000.0000.000
208A209ARG10.8370.90222.93810.41710.4170.0000.0000.0000.000
209A210ARG10.7970.89023.66712.25912.2590.0000.0000.0000.000
210A211LEU0-0.061-0.02819.097-0.021-0.0210.0000.0000.0000.000
211A212ASN0-0.109-0.05523.7230.0990.0990.0000.0000.0000.000
212A213GLY00.0070.01126.9140.3990.3990.0000.0000.0000.000
213A214GLU-1-0.797-0.87328.792-9.765-9.7650.0000.0000.0000.000
214A215LEU0-0.069-0.06027.414-0.282-0.2820.0000.0000.0000.000
215A216VAL00.0120.00228.779-0.315-0.3150.0000.0000.0000.000
216A217PRO0-0.066-0.02231.4270.1860.1860.0000.0000.0000.000
217A218GLU-1-0.934-0.97534.514-8.680-8.6800.0000.0000.0000.000
218A219PRO-1-0.988-0.97734.504-8.112-8.1120.0000.0000.0000.000