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: LGJM9

Calculation Name: 2X3Y-A-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2X3Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q93UJ2

Base Structure: X-ray

Registration Date: 2025-10-04

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 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2026005.540683
FMO2-HF: Nuclear repulsion 1949827.935809
FMO2-HF: Total energy -76177.604875
FMO2-MP2: Total energy -76396.555229


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:-6:GLU)


Summations of interaction energy for fragment #1(A:-6:GLU)
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.
-13.369-10.383.22-2.109-4.099-0.002
Interaction energy analysis for fragmet #1(A:-6:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.013
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].
3A-4LEU00.0730.0273.584-4.948-3.0310.010-0.989-0.9380.002
5A-2PHE00.0760.0302.128-2.745-2.1243.206-1.005-2.822-0.004
6A-1GLN00.0000.0083.524-0.650-0.2790.005-0.114-0.2620.000
7A0SER0-0.088-0.0435.3861.0111.091-0.001-0.001-0.0770.000
4A-3TYR0-0.0070.0125.189-0.949-0.9490.0000.0000.0000.000
8A1MET0-0.042-0.0217.5250.4050.4050.0000.0000.0000.000
9A2GLU-1-0.834-0.9076.077-8.820-8.8200.0000.0000.0000.000
10A3ASN00.0190.0008.4330.3850.3850.0000.0000.0000.000
11A4ARG10.8810.95511.7780.9170.9170.0000.0000.0000.000
12A5GLU-1-0.877-0.9467.5180.3110.3110.0000.0000.0000.000
13A6LEU00.0350.01611.6200.2460.2460.0000.0000.0000.000
14A7THR0-0.009-0.00613.2120.1850.1850.0000.0000.0000.000
15A8TYR0-0.011-0.00314.2910.1150.1150.0000.0000.0000.000
16A9ILE00.0110.01211.4000.1030.1030.0000.0000.0000.000
17A10THR0-0.018-0.03115.9200.0940.0940.0000.0000.0000.000
18A11ASN0-0.007-0.00218.7080.0580.0580.0000.0000.0000.000
19A12SER0-0.023-0.01518.5410.1020.1020.0000.0000.0000.000
20A13ILE0-0.0050.00518.0310.0690.0690.0000.0000.0000.000
21A14ALA00.0200.01021.8900.0240.0240.0000.0000.0000.000
22A15GLU-1-0.791-0.88224.246-0.023-0.0230.0000.0000.0000.000
23A16ALA00.0140.00424.4900.0330.0330.0000.0000.0000.000
24A17GLN0-0.011-0.00426.077-0.012-0.0120.0000.0000.0000.000
25A18ARG10.7630.85227.9830.0510.0510.0000.0000.0000.000
26A19VAL0-0.025-0.00629.4150.0150.0150.0000.0000.0000.000
27A20MET0-0.008-0.00728.5840.0150.0150.0000.0000.0000.000
28A21ALA0-0.008-0.00532.1200.0030.0030.0000.0000.0000.000
29A22ALA0-0.021-0.01233.9910.0030.0030.0000.0000.0000.000
30A23MET0-0.041-0.02632.7110.0210.0210.0000.0000.0000.000
31A24LEU0-0.037-0.00736.4020.0060.0060.0000.0000.0000.000
32A25ALA00.0200.01338.199-0.006-0.0060.0000.0000.0000.000
33A26ASP-1-0.842-0.91140.1070.0190.0190.0000.0000.0000.000
34A27GLU-1-0.875-0.95141.935-0.032-0.0320.0000.0000.0000.000
35A28ARG10.8800.94743.634-0.022-0.0220.0000.0000.0000.000
36A29LEU0-0.0150.01238.0160.0140.0140.0000.0000.0000.000
37A30LEU00.0180.00840.0330.0150.0150.0000.0000.0000.000
38A31ALA0-0.006-0.01143.2720.0090.0090.0000.0000.0000.000
39A32THR0-0.087-0.05944.1540.0070.0070.0000.0000.0000.000
40A33VAL00.015-0.00140.3410.0130.0130.0000.0000.0000.000
41A34ARG10.8260.89743.297-0.055-0.0550.0000.0000.0000.000
42A35LYS10.9870.99746.536-0.056-0.0560.0000.0000.0000.000
43A36VAL00.0090.01142.5560.0080.0080.0000.0000.0000.000
44A37ALA00.0400.02444.5460.0110.0110.0000.0000.0000.000
45A38ASP-1-0.792-0.87946.0280.0770.0770.0000.0000.0000.000
46A39ALA0-0.017-0.00348.2120.0020.0020.0000.0000.0000.000
47A40CYS0-0.060-0.03145.5020.0110.0110.0000.0000.0000.000
48A41ILE0-0.0040.00048.0770.0030.0030.0000.0000.0000.000
49A42ALA0-0.022-0.01150.3970.0000.0000.0000.0000.0000.000
50A43SER0-0.027-0.02750.3560.0030.0030.0000.0000.0000.000
51A44ILE0-0.010-0.00747.0620.0030.0030.0000.0000.0000.000
52A45ALA0-0.034-0.01451.7320.0000.0000.0000.0000.0000.000
53A46GLN0-0.064-0.02955.010-0.002-0.0020.0000.0000.0000.000
54A47GLY0-0.034-0.00954.8040.0010.0010.0000.0000.0000.000
55A48GLY0-0.0040.01952.8920.0090.0090.0000.0000.0000.000
56A49LYS10.7570.83947.939-0.218-0.2180.0000.0000.0000.000
57A50VAL00.0230.00743.352-0.002-0.0020.0000.0000.0000.000
58A51LEU0-0.0050.00043.9820.0180.0180.0000.0000.0000.000
59A52LEU0-0.0020.00538.579-0.009-0.0090.0000.0000.0000.000
60A53ALA00.0040.00038.7800.0230.0230.0000.0000.0000.000
61A54GLY00.0770.02635.324-0.021-0.0210.0000.0000.0000.000
62A55ASN0-0.014-0.01133.6480.0360.0360.0000.0000.0000.000
63A56GLY00.0290.01229.413-0.008-0.0080.0000.0000.0000.000
64A57GLY00.0400.02227.5800.0120.0120.0000.0000.0000.000
65A58SER00.0510.01328.210-0.016-0.0160.0000.0000.0000.000
66A59ALA0-0.041-0.00931.462-0.033-0.0330.0000.0000.0000.000
67A60ALA00.0190.01228.789-0.009-0.0090.0000.0000.0000.000
68A61ASP-1-0.885-0.95529.6480.4200.4200.0000.0000.0000.000
69A62ALA0-0.001-0.00332.063-0.030-0.0300.0000.0000.0000.000
70A63GLN00.020-0.00832.439-0.008-0.0080.0000.0000.0000.000
71A64HIS0-0.063-0.01428.646-0.038-0.0380.0000.0000.0000.000
72A65ILE00.0240.01233.309-0.020-0.0200.0000.0000.0000.000
73A66ALA00.0220.01536.463-0.019-0.0190.0000.0000.0000.000
74A67GLY00.0120.01336.121-0.012-0.0120.0000.0000.0000.000
75A68GLU-1-0.838-0.91233.9330.2430.2430.0000.0000.0000.000
76A69PHE00.0350.00637.727-0.025-0.0250.0000.0000.0000.000
77A70VAL0-0.0120.00940.746-0.015-0.0150.0000.0000.0000.000
78A71SER0-0.057-0.02138.414-0.013-0.0130.0000.0000.0000.000
79A72ARG10.8500.91937.717-0.182-0.1820.0000.0000.0000.000
80A73PHE0-0.018-0.01034.8340.0140.0140.0000.0000.0000.000
81A74ALA0-0.060-0.03237.5560.0000.0000.0000.0000.0000.000
82A75PHE0-0.062-0.04039.405-0.010-0.0100.0000.0000.0000.000
83A76ASP-1-0.862-0.91941.9900.1810.1810.0000.0000.0000.000
84A77ARG10.7160.83741.639-0.199-0.1990.0000.0000.0000.000
85A78PRO0-0.010-0.00445.6990.0140.0140.0000.0000.0000.000
86A79GLY00.0540.04644.745-0.001-0.0010.0000.0000.0000.000
87A80LEU0-0.034-0.01843.997-0.010-0.0100.0000.0000.0000.000
88A81PRO00.009-0.00945.1640.0180.0180.0000.0000.0000.000
89A82ALA00.0060.01642.219-0.006-0.0060.0000.0000.0000.000
90A83VAL0-0.003-0.00742.2350.0130.0130.0000.0000.0000.000
91A84ALA00.0180.02437.536-0.007-0.0070.0000.0000.0000.000
92A85LEU0-0.021-0.01039.6650.0180.0180.0000.0000.0000.000
93A86THR0-0.043-0.03335.140-0.001-0.0010.0000.0000.0000.000
94A87THR0-0.011-0.00135.7250.0310.0310.0000.0000.0000.000
95A88ASP-1-0.806-0.88737.0510.4830.4830.0000.0000.0000.000
96A89THR00.037-0.00534.700-0.018-0.0180.0000.0000.0000.000
97A90SER00.0100.02937.9820.0110.0110.0000.0000.0000.000
98A91ILE0-0.012-0.00541.439-0.014-0.0140.0000.0000.0000.000
99A92LEU0-0.037-0.02336.609-0.008-0.0080.0000.0000.0000.000
100A93THR0-0.052-0.05338.031-0.008-0.0080.0000.0000.0000.000
101A94ALA00.0230.02540.590-0.007-0.0070.0000.0000.0000.000
102A95ILE0-0.029-0.00943.600-0.017-0.0170.0000.0000.0000.000
103A96GLY0-0.015-0.01341.466-0.011-0.0110.0000.0000.0000.000
104A97ASN0-0.050-0.03142.4550.0060.0060.0000.0000.0000.000
105A98ASP-1-0.928-0.95744.6800.3680.3680.0000.0000.0000.000
106A99TYR0-0.063-0.04746.824-0.028-0.0280.0000.0000.0000.000
107A100GLY00.0440.04144.507-0.013-0.0130.0000.0000.0000.000
108A101TYR00.007-0.02335.7130.0010.0010.0000.0000.0000.000
109A102GLU-1-0.970-0.99341.5300.3010.3010.0000.0000.0000.000
110A103LYS10.9620.96943.479-0.300-0.3000.0000.0000.0000.000
111A104LEU0-0.0290.01438.181-0.010-0.0100.0000.0000.0000.000
112A105PHE00.0130.00837.207-0.004-0.0040.0000.0000.0000.000
113A106SER00.0470.02543.359-0.008-0.0080.0000.0000.0000.000
114A107ARG10.9460.98346.708-0.309-0.3090.0000.0000.0000.000
115A108GLN0-0.016-0.02641.419-0.010-0.0100.0000.0000.0000.000
116A109VAL00.0190.00945.976-0.010-0.0100.0000.0000.0000.000
117A110GLN00.0060.00348.474-0.004-0.0040.0000.0000.0000.000
118A111ALA0-0.064-0.02850.199-0.012-0.0120.0000.0000.0000.000
119A112LEU0-0.008-0.00146.671-0.006-0.0060.0000.0000.0000.000
120A113GLY0-0.0160.00350.602-0.006-0.0060.0000.0000.0000.000
121A114ASN0-0.028-0.03551.5450.0000.0000.0000.0000.0000.000
122A115GLU-1-0.904-0.95253.9480.1390.1390.0000.0000.0000.000
123A116GLY00.0170.00954.912-0.003-0.0030.0000.0000.0000.000
124A117ASP-1-0.758-0.83049.9070.2010.2010.0000.0000.0000.000
125A118VAL0-0.016-0.01645.871-0.008-0.0080.0000.0000.0000.000
126A119LEU0-0.032-0.00543.5140.0160.0160.0000.0000.0000.000
127A120ILE00.0190.00939.768-0.011-0.0110.0000.0000.0000.000
128A121GLY0-0.008-0.00540.2480.0240.0240.0000.0000.0000.000
129A122TYR00.021-0.00734.790-0.013-0.0130.0000.0000.0000.000
130A123SER00.010-0.00735.5260.0370.0370.0000.0000.0000.000
131A124THR00.0080.01530.451-0.033-0.0330.0000.0000.0000.000
132A125SER00.0110.00133.673-0.034-0.0340.0000.0000.0000.000
133A126GLY00.0220.00835.261-0.014-0.0140.0000.0000.0000.000
134A127LYS10.9290.95137.988-0.258-0.2580.0000.0000.0000.000
135A128SER0-0.013-0.00636.5720.0200.0200.0000.0000.0000.000
136A129PRO00.0590.02438.679-0.010-0.0100.0000.0000.0000.000
137A130ASN00.0640.03137.935-0.027-0.0270.0000.0000.0000.000
138A131ILE0-0.0500.00238.375-0.006-0.0060.0000.0000.0000.000
139A132LEU0-0.017-0.00341.740-0.016-0.0160.0000.0000.0000.000
140A133ALA0-0.006-0.00944.517-0.015-0.0150.0000.0000.0000.000
141A134ALA0-0.005-0.00344.118-0.009-0.0090.0000.0000.0000.000
142A135PHE00.0240.00942.376-0.008-0.0080.0000.0000.0000.000
143A136ARG10.8590.92046.959-0.242-0.2420.0000.0000.0000.000
144A137GLU-1-0.906-0.96149.3580.2230.2230.0000.0000.0000.000
145A138ALA00.038-0.00248.563-0.008-0.0080.0000.0000.0000.000
146A139LYS10.8390.90650.629-0.159-0.1590.0000.0000.0000.000
147A140ALA0-0.045-0.02252.952-0.009-0.0090.0000.0000.0000.000
148A141LYS10.7930.91252.525-0.217-0.2170.0000.0000.0000.000
149A142GLY00.0280.03255.462-0.003-0.0030.0000.0000.0000.000
150A143MET0-0.062-0.00948.6330.0030.0030.0000.0000.0000.000
151A144THR00.0010.00449.117-0.006-0.0060.0000.0000.0000.000
152A145CYS0-0.060-0.01347.3210.0160.0160.0000.0000.0000.000
153A146VAL00.0280.00342.487-0.013-0.0130.0000.0000.0000.000
154A147GLY00.0500.00341.6970.0200.0200.0000.0000.0000.000
155A148PHE0-0.0050.00335.986-0.017-0.0170.0000.0000.0000.000
156A149THR0-0.014-0.03336.2490.0250.0250.0000.0000.0000.000
157A150GLY00.0870.04634.622-0.011-0.0110.0000.0000.0000.000
158A151ASN0-0.002-0.01034.9450.0110.0110.0000.0000.0000.000
159A152ARG10.9090.94734.731-0.182-0.1820.0000.0000.0000.000
160A153GLY00.0650.03639.195-0.008-0.0080.0000.0000.0000.000
161A154GLY0-0.037-0.01941.2590.0180.0180.0000.0000.0000.000
162A155GLU-1-0.762-0.87843.2590.2110.2110.0000.0000.0000.000
163A156MET0-0.0370.01239.6190.0000.0000.0000.0000.0000.000
164A157ARG10.7960.89142.866-0.123-0.1230.0000.0000.0000.000
165A158GLU-1-0.942-0.96046.4190.1420.1420.0000.0000.0000.000
166A159LEU0-0.055-0.02746.218-0.001-0.0010.0000.0000.0000.000
167A160CYS0-0.079-0.02344.9540.0040.0040.0000.0000.0000.000
168A161ASP-1-0.796-0.88347.6430.1370.1370.0000.0000.0000.000
169A162LEU0-0.053-0.02246.168-0.014-0.0140.0000.0000.0000.000
170A163LEU0-0.025-0.00941.7700.0180.0180.0000.0000.0000.000
171A164LEU0-0.0020.00739.141-0.018-0.0180.0000.0000.0000.000
172A165GLU-1-0.851-0.92038.2730.1330.1330.0000.0000.0000.000
173A166VAL00.0290.01631.929-0.023-0.0230.0000.0000.0000.000
174A167PRO00.0150.02334.2240.0110.0110.0000.0000.0000.000
175A168SER00.011-0.02029.259-0.018-0.0180.0000.0000.0000.000
176A169ALA0-0.021-0.00831.4560.0140.0140.0000.0000.0000.000
177A170ASP-1-0.869-0.93725.0020.3420.3420.0000.0000.0000.000
178A171THR00.0540.01526.386-0.009-0.0090.0000.0000.0000.000
179A172PRO0-0.033-0.01323.0010.0080.0080.0000.0000.0000.000
180A173LYS10.8270.90322.504-0.188-0.1880.0000.0000.0000.000
181A174ILE0-0.043-0.00927.186-0.027-0.0270.0000.0000.0000.000
182A175GLN00.0340.01226.0540.0060.0060.0000.0000.0000.000
183A176GLU-1-0.811-0.89623.6920.2200.2200.0000.0000.0000.000
184A177GLY00.0200.00827.956-0.027-0.0270.0000.0000.0000.000
185A178HIS0-0.043-0.04131.5230.0090.0090.0000.0000.0000.000
186A179LEU00.0350.02927.929-0.011-0.0110.0000.0000.0000.000
187A180VAL0-0.023-0.00730.216-0.015-0.0150.0000.0000.0000.000
188A181LEU00.001-0.01432.799-0.012-0.0120.0000.0000.0000.000
189A182GLY00.0220.01235.197-0.007-0.0070.0000.0000.0000.000
190A183HIS10.8450.90230.461-0.243-0.2430.0000.0000.0000.000
191A184ILE0-0.0110.00935.974-0.011-0.0110.0000.0000.0000.000
192A185VAL0-0.009-0.00838.627-0.009-0.0090.0000.0000.0000.000
193A186CYS0-0.0190.00138.503-0.003-0.0030.0000.0000.0000.000
194A187GLY00.0460.01839.726-0.004-0.0040.0000.0000.0000.000
195A188LEU0-0.059-0.03441.174-0.011-0.0110.0000.0000.0000.000
196A189VAL0-0.023-0.01043.860-0.006-0.0060.0000.0000.0000.000
197A190GLU-1-0.704-0.83841.6030.1460.1460.0000.0000.0000.000
198A191HIS0-0.040-0.01944.901-0.003-0.0030.0000.0000.0000.000
199A192SER0-0.030-0.01846.581-0.007-0.0070.0000.0000.0000.000
200A193ILE0-0.023-0.01148.379-0.002-0.0020.0000.0000.0000.000
201A194PHE0-0.066-0.04947.0650.0030.0030.0000.0000.0000.000
202A195GLY-1-0.923-0.93848.6540.0530.0530.0000.0000.0000.000