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: 5YMMZ

Calculation Name: 7C2D-A-Xray547

Preferred Name:

Target Type:

Ligand Name: acetate ion | cadmium ion

Ligand 3-letter code: ACT | CD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7C2D

Chain ID: A

ChEMBL ID:

UniProt ID: A0A4P1

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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1791885.956022
FMO2-HF: Nuclear repulsion 1721237.258223
FMO2-HF: Total energy -70648.697799
FMO2-MP2: Total energy -70857.725179


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:0:SER)


Summations of interaction energy for fragment #1(A:0: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.
-41.348-38.010.629-1.665-2.302-0.011
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.911
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].
3A2GLY00.0360.0243.325-4.550-2.4550.040-0.990-1.145-0.005
39A38GLY0-0.0050.0044.6820.3980.437-0.0010.000-0.0370.000
40A39ILE0-0.069-0.0333.964-7.218-7.016-0.001-0.072-0.1290.000
41A40ASN0-0.0050.0022.7232.2453.2470.591-0.603-0.991-0.006
4A3GLU-1-0.897-0.9405.255-33.842-33.8420.0000.0000.0000.000
5A4SER0-0.077-0.0416.826-2.355-2.3550.0000.0000.0000.000
6A5ARG10.8540.8977.79828.48628.4860.0000.0000.0000.000
7A6VAL00.0160.01810.1580.4660.4660.0000.0000.0000.000
8A7ILE0-0.015-0.00612.3930.9420.9420.0000.0000.0000.000
9A8LEU0-0.018-0.00215.9170.2000.2000.0000.0000.0000.000
10A9ALA00.0050.00719.4010.0810.0810.0000.0000.0000.000
11A10PHE00.0060.00021.0250.3450.3450.0000.0000.0000.000
12A11GLY00.0540.01124.7040.1310.1310.0000.0000.0000.000
13A12ASP-1-0.831-0.88827.200-9.839-9.8390.0000.0000.0000.000
14A13ALA00.0390.00428.014-0.361-0.3610.0000.0000.0000.000
15A14LEU0-0.0030.00926.778-0.227-0.2270.0000.0000.0000.000
16A15PHE0-0.039-0.01722.830-0.558-0.5580.0000.0000.0000.000
17A16ALA00.0040.00923.712-0.475-0.4750.0000.0000.0000.000
18A17GLY0-0.024-0.01325.649-0.323-0.3230.0000.0000.0000.000
19A18TYR0-0.052-0.02026.3630.1340.1340.0000.0000.0000.000
20A19GLY00.0260.01830.1920.0220.0220.0000.0000.0000.000
21A20LEU0-0.0420.00025.403-0.021-0.0210.0000.0000.0000.000
22A21ASP-1-0.834-0.91326.294-11.017-11.0170.0000.0000.0000.000
23A22LYS10.8960.93421.97013.26013.2600.0000.0000.0000.000
24A23GLY0-0.016-0.01020.189-0.401-0.4010.0000.0000.0000.000
25A24GLU-1-0.918-0.96719.844-12.922-12.9220.0000.0000.0000.000
26A25SER00.0150.01921.718-0.151-0.1510.0000.0000.0000.000
27A26TYR00.0640.02619.422-0.727-0.7270.0000.0000.0000.000
28A27PRO00.0100.00017.967-0.767-0.7670.0000.0000.0000.000
29A28ALA00.0550.04216.158-1.128-1.1280.0000.0000.0000.000
30A29LYS10.9370.97315.39713.49613.4960.0000.0000.0000.000
31A30LEU00.0140.01414.485-0.834-0.8340.0000.0000.0000.000
32A31GLU-1-0.870-0.94111.326-23.483-23.4830.0000.0000.0000.000
33A32THR0-0.085-0.05010.489-2.653-2.6530.0000.0000.0000.000
34A33ALA0-0.0020.00010.830-1.550-1.5500.0000.0000.0000.000
35A34LEU00.000-0.0069.379-0.626-0.6260.0000.0000.0000.000
36A35ARG10.9801.0036.16826.58826.5880.0000.0000.0000.000
37A36SER0-0.039-0.0206.488-2.688-2.6880.0000.0000.0000.000
38A37HIS0-0.050-0.0208.6821.2061.2060.0000.0000.0000.000
42A41ALA00.010-0.0015.7641.1411.1410.0000.0000.0000.000
43A42ARG10.8790.9179.54618.87518.8750.0000.0000.0000.000
44A43ILE0-0.043-0.02812.2141.0591.0590.0000.0000.0000.000
45A44ILE0-0.019-0.00415.4880.5880.5880.0000.0000.0000.000
46A45ASN0-0.003-0.01918.6230.7230.7230.0000.0000.0000.000
47A46ALA00.0200.01421.2550.3510.3510.0000.0000.0000.000
48A47GLY00.0370.01924.5110.4690.4690.0000.0000.0000.000
49A48VAL0-0.021-0.01126.3150.0230.0230.0000.0000.0000.000
50A49SER00.024-0.01030.0040.0960.0960.0000.0000.0000.000
51A50GLY00.0090.01532.4520.1900.1900.0000.0000.0000.000
52A51ASP-1-0.806-0.88332.044-9.297-9.2970.0000.0000.0000.000
53A52THR00.005-0.00133.973-0.104-0.1040.0000.0000.0000.000
54A53THR0-0.007-0.04133.949-0.135-0.1350.0000.0000.0000.000
55A54ALA00.0130.01034.907-0.139-0.1390.0000.0000.0000.000
56A55ALA0-0.0070.00735.324-0.011-0.0110.0000.0000.0000.000
57A56GLY00.0720.02331.804-0.166-0.1660.0000.0000.0000.000
58A57LEU0-0.019-0.01432.165-0.229-0.2290.0000.0000.0000.000
59A58GLN0-0.052-0.01234.3090.1220.1220.0000.0000.0000.000
60A59ARG10.7690.85627.55210.50510.5050.0000.0000.0000.000
61A60ILE0-0.0070.00526.907-0.291-0.2910.0000.0000.0000.000
62A61LYS10.8590.91228.3839.2619.2610.0000.0000.0000.000
63A62PHE00.0540.03129.060-0.261-0.2610.0000.0000.0000.000
64A63VAL0-0.0020.00524.897-0.310-0.3100.0000.0000.0000.000
65A64LEU0-0.008-0.00823.582-0.623-0.6230.0000.0000.0000.000
66A65ASP-1-0.807-0.87524.747-10.732-10.7320.0000.0000.0000.000
67A66SER0-0.064-0.03125.6360.0410.0410.0000.0000.0000.000
68A67GLN0-0.073-0.03820.295-0.869-0.8690.0000.0000.0000.000
69A68PRO0-0.0250.00318.4530.2600.2600.0000.0000.0000.000
70A69ASP-1-0.800-0.87715.498-19.156-19.1560.0000.0000.0000.000
71A70LYS10.8650.91717.89513.89313.8930.0000.0000.0000.000
72A71PRO0-0.017-0.01717.368-0.762-0.7620.0000.0000.0000.000
73A72GLU-1-0.776-0.86812.445-22.398-22.3980.0000.0000.0000.000
74A73LEU0-0.041-0.01916.0020.1890.1890.0000.0000.0000.000
75A74ALA0-0.0060.00217.988-0.270-0.2700.0000.0000.0000.000
76A75ILE0-0.004-0.00317.2560.3580.3580.0000.0000.0000.000
77A76VAL00.001-0.00121.5730.1660.1660.0000.0000.0000.000
78A77GLU0-0.024-0.05325.3920.0770.0770.0000.0000.0000.000
79A78LEU00.0170.02127.2800.1000.1000.0000.0000.0000.000
80A79GLY00.0690.04230.9620.0510.0510.0000.0000.0000.000
81A80GLY00.0280.02533.0910.2350.2350.0000.0000.0000.000
82A81ASN0-0.020-0.03933.7520.4030.4030.0000.0000.0000.000
83A82ASP-1-0.768-0.86036.554-8.197-8.1970.0000.0000.0000.000
84A83LEU0-0.0140.01436.1250.2690.2690.0000.0000.0000.000
85A84LEU0-0.030-0.01436.8450.2280.2280.0000.0000.0000.000
86A85ARG10.8770.94138.3178.0248.0240.0000.0000.0000.000
87A86GLY00.0200.02342.6840.1600.1600.0000.0000.0000.000
88A87LEU0-0.033-0.01240.4430.1290.1290.0000.0000.0000.000
89A88SER00.0300.02642.865-0.090-0.0900.0000.0000.0000.000
90A89PRO00.0290.01140.758-0.168-0.1680.0000.0000.0000.000
91A90ALA00.0130.00540.388-0.191-0.1910.0000.0000.0000.000
92A91GLU-1-0.868-0.93641.238-7.059-7.0590.0000.0000.0000.000
93A92ALA00.0100.01237.305-0.187-0.1870.0000.0000.0000.000
94A93ARG10.9280.97636.6287.2457.2450.0000.0000.0000.000
95A94GLN0-0.024-0.00736.980-0.097-0.0970.0000.0000.0000.000
96A95ASN00.005-0.01236.460-0.075-0.0750.0000.0000.0000.000
97A96LEU00.015-0.00431.146-0.245-0.2450.0000.0000.0000.000
98A97SER0-0.038-0.02932.522-0.260-0.2600.0000.0000.0000.000
99A98GLY00.0380.03033.659-0.149-0.1490.0000.0000.0000.000
100A99ILE0-0.050-0.02828.830-0.225-0.2250.0000.0000.0000.000
101A100LEU0-0.015-0.00927.746-0.405-0.4050.0000.0000.0000.000
102A101GLU-1-0.901-0.94229.457-8.862-8.8620.0000.0000.0000.000
103A102GLU-1-0.748-0.83829.176-10.235-10.2350.0000.0000.0000.000
104A103LEU0-0.024-0.01524.154-0.334-0.3340.0000.0000.0000.000
105A104GLN00.0490.02526.180-0.139-0.1390.0000.0000.0000.000
106A105ARG10.8400.90028.0729.7269.7260.0000.0000.0000.000
107A106ARG10.7080.82725.25611.05811.0580.0000.0000.0000.000
108A107LYS10.9200.96424.30510.51610.5160.0000.0000.0000.000
109A108ILE0-0.029-0.00620.614-0.567-0.5670.0000.0000.0000.000
110A109PRO00.0030.00518.7920.4980.4980.0000.0000.0000.000
111A110ILE00.0460.02621.298-0.309-0.3090.0000.0000.0000.000
112A111LEU0-0.037-0.01319.086-0.066-0.0660.0000.0000.0000.000
113A112LEU00.0100.01222.464-0.040-0.0400.0000.0000.0000.000
114A113MET0-0.024-0.01421.371-0.047-0.0470.0000.0000.0000.000
115A114GLY00.0140.01326.4050.3260.3260.0000.0000.0000.000
116A115MET0-0.0310.00029.759-0.186-0.1860.0000.0000.0000.000
117A116ARG10.8780.92832.1419.0959.0950.0000.0000.0000.000
118A117ALA0-0.0080.00635.329-0.004-0.0040.0000.0000.0000.000
119A118PRO00.0140.01538.6540.0680.0680.0000.0000.0000.000
120A119PRO00.047-0.00640.6730.1370.1370.0000.0000.0000.000
121A120ASN0-0.032-0.00744.1190.2110.2110.0000.0000.0000.000
122A121LEU00.0100.01741.7610.1200.1200.0000.0000.0000.000
123A122GLY00.0180.01745.7110.1110.1110.0000.0000.0000.000
124A123ALA00.031-0.00245.582-0.098-0.0980.0000.0000.0000.000
125A124LYS10.8930.95045.9346.0306.0300.0000.0000.0000.000
126A125TYR00.0410.00741.055-0.104-0.1040.0000.0000.0000.000
127A126GLN0-0.020-0.03139.9270.0580.0580.0000.0000.0000.000
128A127ARG10.9200.95740.7676.4566.4560.0000.0000.0000.000
129A128GLU-1-0.916-0.95641.385-7.076-7.0760.0000.0000.0000.000
130A129PHE00.007-0.00535.498-0.137-0.1370.0000.0000.0000.000
131A130ASP-1-0.754-0.88536.460-8.345-8.3450.0000.0000.0000.000
132A131GLY0-0.020-0.00536.024-0.222-0.2220.0000.0000.0000.000
133A132ILE0-0.043-0.02835.057-0.050-0.0500.0000.0000.0000.000
134A133TYR00.022-0.01330.605-0.079-0.0790.0000.0000.0000.000
135A134PRO00.011-0.00731.907-0.233-0.2330.0000.0000.0000.000
136A135TYR00.0110.01533.305-0.093-0.0930.0000.0000.0000.000
137A136LEU0-0.033-0.02231.903-0.016-0.0160.0000.0000.0000.000
138A137ALA0-0.026-0.01328.988-0.184-0.1840.0000.0000.0000.000
139A138GLU-1-0.928-0.95929.998-9.326-9.3260.0000.0000.0000.000
140A139LYS10.8890.95732.4378.2918.2910.0000.0000.0000.000
141A140TYR0-0.039-0.03129.7670.2250.2250.0000.0000.0000.000
142A141ASP-1-0.916-0.94127.723-10.463-10.4630.0000.0000.0000.000
143A142ALA0-0.050-0.01125.430-0.548-0.5480.0000.0000.0000.000
144A143LYS10.9350.95920.12313.45313.4530.0000.0000.0000.000
145A144LEU00.0140.00324.3690.0070.0070.0000.0000.0000.000
146A145VAL00.0080.01422.647-0.118-0.1180.0000.0000.0000.000
147A146PRO00.023-0.00225.5270.2720.2720.0000.0000.0000.000
148A147PHE00.0260.00528.4780.3850.3850.0000.0000.0000.000
149A148PHE0-0.002-0.00922.782-0.181-0.1810.0000.0000.0000.000
150A149LEU0-0.002-0.00626.442-0.287-0.2870.0000.0000.0000.000
151A150GLU-1-0.910-0.94828.504-9.730-9.7300.0000.0000.0000.000
152A151ALA0-0.027-0.02425.9480.1730.1730.0000.0000.0000.000
153A152VAL0-0.023-0.02027.589-0.073-0.0730.0000.0000.0000.000
154A153ALA0-0.0270.00830.2320.2640.2640.0000.0000.0000.000
155A154ASP-1-0.925-0.95833.454-8.328-8.3280.0000.0000.0000.000
156A155ARG10.7800.85329.8709.7679.7670.0000.0000.0000.000
157A156PRO00.0510.02033.198-0.176-0.1760.0000.0000.0000.000
158A157ASP-1-0.832-0.88733.403-9.235-9.2350.0000.0000.0000.000
159A158LEU0-0.048-0.02328.069-0.254-0.2540.0000.0000.0000.000
160A159ILE0-0.061-0.01630.367-0.275-0.2750.0000.0000.0000.000
161A160GLN0-0.013-0.01430.3170.2540.2540.0000.0000.0000.000
162A161LYS10.9500.96734.2207.7367.7360.0000.0000.0000.000
163A162ASP-1-0.821-0.91135.530-8.589-8.5890.0000.0000.0000.000
164A163HIS0-0.065-0.03838.0990.4160.4160.0000.0000.0000.000
165A164VAL0-0.038-0.02441.168-0.017-0.0170.0000.0000.0000.000
166A165HIS00.0160.01342.9150.2840.2840.0000.0000.0000.000
167A166PRO0-0.021-0.00446.278-0.028-0.0280.0000.0000.0000.000
168A167THR00.0420.02048.2760.0610.0610.0000.0000.0000.000
169A168ALA00.0440.01150.3800.0630.0630.0000.0000.0000.000
170A169ARG10.9220.95253.6035.4935.4930.0000.0000.0000.000
171A170GLY00.0510.02351.9740.0510.0510.0000.0000.0000.000
172A171VAL0-0.005-0.00853.0370.0280.0280.0000.0000.0000.000
173A172GLU-1-0.863-0.92255.191-5.292-5.2920.0000.0000.0000.000
174A173GLU-1-0.935-0.94354.820-5.471-5.4710.0000.0000.0000.000
175A174LEU00.014-0.00351.9630.0510.0510.0000.0000.0000.000
176A175VAL00.0050.02356.5030.0630.0630.0000.0000.0000.000
177A176SER0-0.034-0.01359.9060.1300.1300.0000.0000.0000.000
178A177ALA0-0.033-0.00658.0460.0700.0700.0000.0000.0000.000
179A178THR0-0.054-0.05157.6840.0600.0600.0000.0000.0000.000
180A179SER00.013-0.01160.8540.0670.0670.0000.0000.0000.000
181A180ASN00.0180.00064.1840.1040.1040.0000.0000.0000.000
182A181ALA0-0.046-0.00662.4570.0660.0660.0000.0000.0000.000
183A182VAL00.0310.00862.4840.0460.0460.0000.0000.0000.000
184A183ALA00.001-0.00865.0620.0480.0480.0000.0000.0000.000
185A184LYS10.8570.92066.8584.8244.8240.0000.0000.0000.000
186A185ALA0-0.027-0.00165.6840.0310.0310.0000.0000.0000.000
187A186LEU0-0.045-0.01367.710-0.003-0.0030.0000.0000.0000.000
188A187PRO0-0.051-0.03069.7830.0320.0320.0000.0000.0000.000
189A188ALA-1-0.920-0.94673.372-4.167-4.1670.0000.0000.0000.000