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: 645YZ

Calculation Name: 2WRS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: citrate anion | citric acid | zinc ion

Ligand 3-letter code: FLC | CIT | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2WRS

Chain ID: A

ChEMBL ID:

UniProt ID: Q70E11

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 230
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2738331.354379
FMO2-HF: Nuclear repulsion 2654043.855348
FMO2-HF: Total energy -84287.499031
FMO2-MP2: Total energy -84539.532878


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:32:GLU)


Summations of interaction energy for fragment #1(A:32: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.
-26.919-31.22117.264-6.905-6.0570.066
Interaction energy analysis for fragmet #1(A:32:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.028
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].
3A34PRO0-0.0100.0083.753-6.280-4.8890.012-0.535-0.8680.001
16A47TYR0-0.031-0.0481.690-23.380-29.07317.252-6.370-5.1890.065
4A35THR00.0380.0105.6710.9290.9290.0000.0000.0000.000
5A36VAL00.026-0.0047.9530.6800.6800.0000.0000.0000.000
6A37ASN0-0.059-0.02410.084-0.205-0.2050.0000.0000.0000.000
7A38GLU-1-0.885-0.9325.653-7.829-7.8290.0000.0000.0000.000
8A39ILE0-0.0100.0029.5240.4120.4120.0000.0000.0000.000
9A40PRO00.0110.03112.473-0.042-0.0420.0000.0000.0000.000
10A41VAL00.0280.00916.1890.1420.1420.0000.0000.0000.000
11A42GLY0-0.089-0.05418.6270.0630.0630.0000.0000.0000.000
12A43GLU-1-0.947-0.96114.801-0.108-0.1080.0000.0000.0000.000
13A44VAL0-0.032-0.02614.147-0.145-0.1450.0000.0000.0000.000
14A45ARG10.8480.9285.5312.8122.8120.0000.0000.0000.000
15A46LEU00.0200.01410.391-0.242-0.2420.0000.0000.0000.000
17A48GLN0-0.029-0.0126.370-1.624-1.6240.0000.0000.0000.000
18A49ILE0-0.044-0.0226.8732.0862.0860.0000.0000.0000.000
19A50ALA00.0350.0109.2870.0030.0030.0000.0000.0000.000
20A51ASP-1-0.886-0.93411.8103.6623.6620.0000.0000.0000.000
21A52GLY0-0.072-0.03214.075-0.422-0.4220.0000.0000.0000.000
22A53VAL0-0.017-0.00813.384-0.460-0.4600.0000.0000.0000.000
23A54TRP00.0470.01210.0720.5420.5420.0000.0000.0000.000
24A55SER00.0160.0039.966-0.264-0.2640.0000.0000.0000.000
25A56HIS0-0.062-0.02211.1940.4470.4470.0000.0000.0000.000
26A57ILE0-0.009-0.0068.968-0.312-0.3120.0000.0000.0000.000
27A58ALA00.0470.02912.3740.0560.0560.0000.0000.0000.000
28A59THR0-0.017-0.02413.520-0.200-0.2000.0000.0000.0000.000
29A60GLN00.0000.00216.1370.1470.1470.0000.0000.0000.000
30A61SER0-0.021-0.01119.770-0.161-0.1610.0000.0000.0000.000
31A62PHE0-0.024-0.02022.0770.0920.0920.0000.0000.0000.000
32A63ASP-1-0.897-0.95123.251-0.740-0.7400.0000.0000.0000.000
33A64GLY0-0.028-0.00425.501-0.038-0.0380.0000.0000.0000.000
34A65ALA0-0.0280.00120.458-0.042-0.0420.0000.0000.0000.000
35A66VAL0-0.003-0.01016.7310.0930.0930.0000.0000.0000.000
36A67TYR00.0010.00216.766-0.236-0.2360.0000.0000.0000.000
37A68PRO00.0260.01612.2870.1410.1410.0000.0000.0000.000
38A69SER0-0.039-0.02114.2670.0770.0770.0000.0000.0000.000
39A70ASN0-0.008-0.00711.520-0.049-0.0490.0000.0000.0000.000
40A71GLY00.0580.03614.660-0.097-0.0970.0000.0000.0000.000
41A72LEU0-0.047-0.01913.8970.2360.2360.0000.0000.0000.000
42A73ILE00.0160.00714.092-0.211-0.2110.0000.0000.0000.000
43A74VAL0-0.002-0.00515.6010.3190.3190.0000.0000.0000.000
44A75ARG10.9390.96618.032-1.803-1.8030.0000.0000.0000.000
45A76ASP-1-0.839-0.90719.7770.8520.8520.0000.0000.0000.000
46A77GLY0-0.039-0.02423.051-0.088-0.0880.0000.0000.0000.000
47A78ASP-1-0.941-0.96623.5931.0281.0280.0000.0000.0000.000
48A79GLU-1-0.834-0.88124.2570.7920.7920.0000.0000.0000.000
49A80LEU0-0.030-0.01818.2410.1650.1650.0000.0000.0000.000
50A81LEU0-0.018-0.00521.225-0.148-0.1480.0000.0000.0000.000
51A82LEU0-0.007-0.00618.8270.1590.1590.0000.0000.0000.000
52A83ILE0-0.039-0.02819.217-0.117-0.1170.0000.0000.0000.000
53A84ASP-1-0.670-0.80419.3920.2350.2350.0000.0000.0000.000
54A85THR0-0.035-0.01220.6610.1030.1030.0000.0000.0000.000
55A86ALA00.0190.01018.297-0.036-0.0360.0000.0000.0000.000
56A87TRP0-0.0100.00618.710-0.168-0.1680.0000.0000.0000.000
57A88GLY00.0730.03721.595-0.075-0.0750.0000.0000.0000.000
58A89ALA00.0310.01023.6610.0470.0470.0000.0000.0000.000
59A90LYS10.9200.94622.4740.2530.2530.0000.0000.0000.000
60A91ASN00.0290.01019.1620.0450.0450.0000.0000.0000.000
61A92THR00.0150.00019.9830.1190.1190.0000.0000.0000.000
62A93ALA00.0060.00322.1930.0900.0900.0000.0000.0000.000
63A94ALA0-0.0080.00318.4890.0850.0850.0000.0000.0000.000
64A95LEU00.006-0.00216.6210.1260.1260.0000.0000.0000.000
65A96LEU00.0040.00718.2020.1810.1810.0000.0000.0000.000
66A97ALA00.0050.00520.4770.0930.0930.0000.0000.0000.000
67A98GLU-1-0.807-0.87613.9361.4861.4860.0000.0000.0000.000
68A99ILE00.019-0.00915.8710.2770.2770.0000.0000.0000.000
69A100GLU-1-0.943-0.96317.1471.1821.1820.0000.0000.0000.000
70A101LYS10.7900.87414.677-1.182-1.1820.0000.0000.0000.000
71A102GLN0-0.119-0.07310.8630.6850.6850.0000.0000.0000.000
72A103ILE0-0.056-0.02313.9780.2650.2650.0000.0000.0000.000
73A104GLY00.0200.02616.683-0.053-0.0530.0000.0000.0000.000
74A105LEU0-0.046-0.01420.036-0.073-0.0730.0000.0000.0000.000
75A106PRO00.0070.01421.661-0.001-0.0010.0000.0000.0000.000
76A107VAL00.012-0.00120.8520.0370.0370.0000.0000.0000.000
77A108THR0-0.039-0.04123.557-0.075-0.0750.0000.0000.0000.000
78A109ARG10.7980.88125.505-0.775-0.7750.0000.0000.0000.000
79A110ALA00.0420.02324.2780.0800.0800.0000.0000.0000.000
80A111VAL0-0.028-0.01524.234-0.069-0.0690.0000.0000.0000.000
81A112SER0-0.011-0.01324.0300.0380.0380.0000.0000.0000.000
82A113THR0-0.057-0.06222.339-0.041-0.0410.0000.0000.0000.000
83A114HIS00.0180.00623.644-0.029-0.0290.0000.0000.0000.000
84A115PHE0-0.005-0.00727.2370.0180.0180.0000.0000.0000.000
85A116HIS00.0490.03825.779-0.016-0.0160.0000.0000.0000.000
86A117ASP-1-0.777-0.91626.220-0.082-0.0820.0000.0000.0000.000
87A118ASP-1-0.880-0.95920.926-0.316-0.3160.0000.0000.0000.000
88A119ARG10.7250.85218.3000.1660.1660.0000.0000.0000.000
89A120VAL00.0330.02423.8980.0940.0940.0000.0000.0000.000
90A121GLY00.0720.05226.0740.0270.0270.0000.0000.0000.000
91A122GLY0-0.059-0.04324.9230.0070.0070.0000.0000.0000.000
92A123VAL00.0310.01626.6520.0750.0750.0000.0000.0000.000
93A124ASP-1-0.849-0.91128.7490.1660.1660.0000.0000.0000.000
94A125VAL0-0.084-0.04125.8820.0140.0140.0000.0000.0000.000
95A126LEU00.0070.00123.4820.0420.0420.0000.0000.0000.000
96A127ARG10.8370.90427.499-0.179-0.1790.0000.0000.0000.000
97A128ALA0-0.053-0.02530.9040.0070.0070.0000.0000.0000.000
98A129ALA0-0.049-0.01827.1040.0050.0050.0000.0000.0000.000
99A130GLY0-0.013-0.00128.8650.0460.0460.0000.0000.0000.000
100A131VAL0-0.032-0.00425.4570.0180.0180.0000.0000.0000.000
101A132ALA0-0.014-0.00728.641-0.060-0.0600.0000.0000.0000.000
102A133THR00.0370.02127.9710.0280.0280.0000.0000.0000.000
103A134TYR0-0.014-0.01728.833-0.026-0.0260.0000.0000.0000.000
104A135ALA00.0650.02428.8740.0030.0030.0000.0000.0000.000
105A136SER00.0650.03630.626-0.006-0.0060.0000.0000.0000.000
106A137PRO00.017-0.01132.807-0.021-0.0210.0000.0000.0000.000
107A138SER0-0.053-0.02333.889-0.022-0.0220.0000.0000.0000.000
108A139THR00.0460.00229.444-0.005-0.0050.0000.0000.0000.000
109A140ARG10.8090.91232.602-0.190-0.1900.0000.0000.0000.000
110A141ARG10.9630.98734.984-0.076-0.0760.0000.0000.0000.000
111A142LEU00.0000.00932.975-0.011-0.0110.0000.0000.0000.000
112A143ALA00.0060.01132.217-0.019-0.0190.0000.0000.0000.000
113A144GLU-1-0.978-0.99633.9040.0410.0410.0000.0000.0000.000
114A145ALA0-0.075-0.04137.587-0.009-0.0090.0000.0000.0000.000
115A146GLU-1-0.942-0.96632.572-0.174-0.1740.0000.0000.0000.000
116A147GLY0-0.050-0.01335.892-0.015-0.0150.0000.0000.0000.000
117A148ASN0-0.036-0.01630.636-0.015-0.0150.0000.0000.0000.000
118A149GLU-1-0.814-0.90329.3270.0970.0970.0000.0000.0000.000
119A150ILE00.0420.01631.6670.0100.0100.0000.0000.0000.000
120A151PRO0-0.041-0.02129.9030.0260.0260.0000.0000.0000.000
121A152THR0-0.0110.00232.270-0.029-0.0290.0000.0000.0000.000
122A153HIS0-0.013-0.00732.651-0.036-0.0360.0000.0000.0000.000
123A154SER00.018-0.00633.576-0.006-0.0060.0000.0000.0000.000
124A155LEU0-0.049-0.00729.0840.0230.0230.0000.0000.0000.000
125A156GLU-1-0.898-0.96433.5480.1790.1790.0000.0000.0000.000
126A157GLY0-0.028-0.01734.5550.0230.0230.0000.0000.0000.000
127A158LEU0-0.002-0.00529.9680.0140.0140.0000.0000.0000.000
128A159SER0-0.028-0.01133.610-0.016-0.0160.0000.0000.0000.000
129A160SER0-0.078-0.04436.143-0.030-0.0300.0000.0000.0000.000
130A161SER00.0180.00333.1910.0210.0210.0000.0000.0000.000
131A162GLY0-0.032-0.02431.775-0.007-0.0070.0000.0000.0000.000
132A163ASP-1-0.856-0.88932.5720.2030.2030.0000.0000.0000.000
133A164ALA0-0.012-0.02329.3900.0060.0060.0000.0000.0000.000
134A165VAL0-0.0120.00729.709-0.006-0.0060.0000.0000.0000.000
135A166ARG10.9010.95726.427-0.745-0.7450.0000.0000.0000.000
136A167PHE0-0.008-0.00926.215-0.053-0.0530.0000.0000.0000.000
137A168GLY00.0690.03425.9720.0520.0520.0000.0000.0000.000
138A169PRO0-0.063-0.02321.713-0.052-0.0520.0000.0000.0000.000
139A170VAL00.0110.00920.8020.0550.0550.0000.0000.0000.000
140A171GLU-1-0.908-0.93323.3600.4320.4320.0000.0000.0000.000
141A172LEU0-0.0070.00224.1130.0220.0220.0000.0000.0000.000
142A173PHE00.0420.00625.862-0.033-0.0330.0000.0000.0000.000
143A174TYR00.000-0.01227.246-0.019-0.0190.0000.0000.0000.000
144A175PRO0-0.0200.00326.013-0.007-0.0070.0000.0000.0000.000
145A176GLY00.0710.02028.994-0.032-0.0320.0000.0000.0000.000
146A177ALA0-0.0290.00829.9270.0010.0010.0000.0000.0000.000
147A178ALA00.002-0.02425.891-0.006-0.0060.0000.0000.0000.000
148A179HIS0-0.0180.00624.195-0.067-0.0670.0000.0000.0000.000
149A180SER0-0.011-0.02826.322-0.016-0.0160.0000.0000.0000.000
150A181THR00.0490.00229.2260.0200.0200.0000.0000.0000.000
151A182ASP-1-0.764-0.84730.1620.0090.0090.0000.0000.0000.000
152A183ASN0-0.0310.00225.512-0.013-0.0130.0000.0000.0000.000
153A184LEU00.0100.00226.0430.0060.0060.0000.0000.0000.000
154A185VAL0-0.054-0.01722.031-0.037-0.0370.0000.0000.0000.000
155A186VAL0-0.004-0.01320.4740.0240.0240.0000.0000.0000.000
156A187TYR0-0.021-0.02419.1840.0920.0920.0000.0000.0000.000
157A188VAL00.0400.01417.095-0.031-0.0310.0000.0000.0000.000
158A189PRO0-0.001-0.00419.3070.0920.0920.0000.0000.0000.000
159A190SER0-0.056-0.03219.367-0.056-0.0560.0000.0000.0000.000
160A191ALA0-0.012-0.01215.2960.1440.1440.0000.0000.0000.000
161A192ASN0-0.0140.00615.7610.2490.2490.0000.0000.0000.000
162A193VAL00.0410.02913.428-0.095-0.0950.0000.0000.0000.000
163A194LEU0-0.022-0.01015.823-0.126-0.1260.0000.0000.0000.000
164A195TYR0-0.022-0.04115.435-0.089-0.0890.0000.0000.0000.000
165A196GLY00.0360.00017.431-0.038-0.0380.0000.0000.0000.000
166A197GLY00.0740.03818.864-0.070-0.0700.0000.0000.0000.000
167A198CYS0-0.093-0.04719.102-0.144-0.1440.0000.0000.0000.000
168A199ALA0-0.0030.01420.968-0.070-0.0700.0000.0000.0000.000
169A200VAL0-0.038-0.00916.812-0.008-0.0080.0000.0000.0000.000
170A201HIS00.0210.01317.055-0.112-0.1120.0000.0000.0000.000
171A202GLU-1-0.818-0.88711.354-3.074-3.0740.0000.0000.0000.000
172A203LEU00.021-0.00811.9020.0300.0300.0000.0000.0000.000
173A204SER0-0.079-0.04912.0170.2050.2050.0000.0000.0000.000
174A205ARG10.8800.94814.0361.2091.2090.0000.0000.0000.000
175A206THR00.0110.00016.9020.1280.1280.0000.0000.0000.000
176A207SER0-0.013-0.00420.1730.0690.0690.0000.0000.0000.000
177A208ALA00.0440.01421.453-0.034-0.0340.0000.0000.0000.000
178A209GLY0-0.016-0.00922.303-0.077-0.0770.0000.0000.0000.000
179A210ASN00.0300.01423.0260.0040.0040.0000.0000.0000.000
180A211VAL00.002-0.01625.9830.0140.0140.0000.0000.0000.000
181A212ALA0-0.036-0.00428.7140.0290.0290.0000.0000.0000.000
182A213ASP-1-0.818-0.90430.191-0.206-0.2060.0000.0000.0000.000
183A214ALA0-0.044-0.01128.3490.0280.0280.0000.0000.0000.000
184A215ASP-1-0.830-0.90830.219-0.166-0.1660.0000.0000.0000.000
185A216LEU00.007-0.00928.795-0.006-0.0060.0000.0000.0000.000
186A217ALA0-0.078-0.03431.246-0.017-0.0170.0000.0000.0000.000
187A218GLU-1-0.802-0.88932.230-0.081-0.0810.0000.0000.0000.000
188A219TRP0-0.0040.00722.856-0.004-0.0040.0000.0000.0000.000
189A220PRO0-0.031-0.03527.3790.0090.0090.0000.0000.0000.000
190A221THR00.0370.02728.3610.0090.0090.0000.0000.0000.000
191A222SER0-0.008-0.02628.3700.0460.0460.0000.0000.0000.000
192A223VAL0-0.0080.00323.3470.0450.0450.0000.0000.0000.000
193A224GLU-1-0.969-0.98825.500-0.108-0.1080.0000.0000.0000.000
194A225ARG10.7210.83927.9520.0530.0530.0000.0000.0000.000
195A226ILE00.0070.00622.4040.0510.0510.0000.0000.0000.000
196A227GLN0-0.010-0.01022.9430.0980.0980.0000.0000.0000.000
197A228LYS10.9170.94625.082-0.051-0.0510.0000.0000.0000.000
198A229HIS10.8360.94126.832-0.328-0.3280.0000.0000.0000.000
199A230TYR0-0.029-0.04122.0510.0290.0290.0000.0000.0000.000
200A231PRO0-0.009-0.00922.2950.0020.0020.0000.0000.0000.000
201A232GLU-1-0.869-0.92821.9520.6050.6050.0000.0000.0000.000
202A233ALA0-0.0050.01118.0830.1380.1380.0000.0000.0000.000
203A234GLU-1-0.970-0.97814.8681.3831.3830.0000.0000.0000.000
204A235VAL0-0.037-0.01310.4770.0110.0110.0000.0000.0000.000
205A236VAL0-0.031-0.01113.300-0.013-0.0130.0000.0000.0000.000
206A237ILE00.020-0.00211.370-0.186-0.1860.0000.0000.0000.000
207A238PRO00.0010.02412.0920.1160.1160.0000.0000.0000.000
208A239GLY00.0450.03014.5240.0270.0270.0000.0000.0000.000
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