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: Y9GJ2

Calculation Name: 1RZ3-A-Xray547

Preferred Name:

Target Type:

Ligand Name: acetate ion | calcium ion

Ligand 3-letter code: ACT | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RZ3

Chain ID: A

ChEMBL ID:

UniProt ID: P84134

Base Structure: X-ray

Registration Date: 2025-10-03

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 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2228459.791118
FMO2-HF: Nuclear repulsion 2150778.749952
FMO2-HF: Total energy -77681.041166
FMO2-MP2: Total energy -77907.897074


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-115.695-111.71614.74-9.087-9.632-0.106
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.703 / q_NPA : 0.853
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].
3A3LEU00.0790.0341.7803.7675.1133.818-2.019-3.145-0.020
4A4ARG10.9150.9612.34656.17257.9690.454-0.631-1.620-0.003
5A5ASP-1-0.763-0.8841.893-116.135-115.47910.469-6.413-4.712-0.083
6A6ARG10.8210.8864.74342.02442.204-0.001-0.024-0.1550.000
7A7ILE0-0.0010.0047.1074.7654.7650.0000.0000.0000.000
8A8ASP-1-0.863-0.9366.391-37.236-37.2360.0000.0000.0000.000
9A9PHE0-0.019-0.0188.7204.0064.0060.0000.0000.0000.000
10A10LEU00.0220.02010.7582.7622.7620.0000.0000.0000.000
11A11CYS00.0110.00912.0112.3782.3780.0000.0000.0000.000
12A12LYS10.8800.95112.91122.19922.1990.0000.0000.0000.000
13A13THR0-0.070-0.04914.6211.5261.5260.0000.0000.0000.000
14A14ILE00.0290.00216.4091.1041.1040.0000.0000.0000.000
15A15LEU0-0.019-0.01416.1360.9190.9190.0000.0000.0000.000
16A16ALA0-0.041-0.00619.3870.5570.5570.0000.0000.0000.000
17A17ILE0-0.0170.01220.8550.7300.7300.0000.0000.0000.000
18A18LYS10.8780.92923.43810.62210.6220.0000.0000.0000.000
19A19THR00.0610.04025.4150.1810.1810.0000.0000.0000.000
20A20ALA0-0.055-0.04327.9210.3510.3510.0000.0000.0000.000
21A21GLY00.0090.02131.5850.1620.1620.0000.0000.0000.000
22A22ARG10.8250.89029.0879.4809.4800.0000.0000.0000.000
23A23LEU00.0140.00622.9870.2270.2270.0000.0000.0000.000
24A24VAL0-0.058-0.03325.951-0.232-0.2320.0000.0000.0000.000
25A25LEU00.0160.00419.993-0.078-0.0780.0000.0000.0000.000
26A26GLY00.013-0.00422.2530.1810.1810.0000.0000.0000.000
27A27ILE0-0.020-0.01616.042-0.629-0.6290.0000.0000.0000.000
28A28ASP-1-0.703-0.83719.044-12.247-12.2470.0000.0000.0000.000
29A29GLY00.0830.04217.810-0.819-0.8190.0000.0000.0000.000
30A30LEU00.0470.04018.5760.5100.5100.0000.0000.0000.000
31A31SER0-0.041-0.01718.474-0.668-0.6680.0000.0000.0000.000
32A32ARG10.8700.92016.03312.40912.4090.0000.0000.0000.000
33A33SER00.0810.04213.901-0.693-0.6930.0000.0000.0000.000
34A34GLY00.0110.00411.610-0.981-0.9810.0000.0000.0000.000
35A35LYS10.8660.95412.66313.50513.5050.0000.0000.0000.000
36A36THR0-0.033-0.02615.097-0.450-0.4500.0000.0000.0000.000
37A37THR0-0.039-0.02210.5030.5760.5760.0000.0000.0000.000
38A38LEU00.0450.04010.549-0.756-0.7560.0000.0000.0000.000
39A39ALA00.0540.01612.570-0.309-0.3090.0000.0000.0000.000
40A40ASN0-0.023-0.01115.5060.8090.8090.0000.0000.0000.000
41A41GLN0-0.002-0.0058.679-0.398-0.3980.0000.0000.0000.000
42A42LEU00.0310.03512.793-0.339-0.3390.0000.0000.0000.000
43A43SER0-0.003-0.02713.9660.6730.6730.0000.0000.0000.000
44A44GLN0-0.022-0.00514.6021.4231.4230.0000.0000.0000.000
45A45THR00.022-0.00611.028-0.188-0.1880.0000.0000.0000.000
46A46LEU00.024-0.00213.7480.4540.4540.0000.0000.0000.000
47A47ARG10.8560.94416.95216.12716.1270.0000.0000.0000.000
48A48GLU-1-0.979-0.98813.889-20.948-20.9480.0000.0000.0000.000
49A49GLN0-0.123-0.05714.1650.2540.2540.0000.0000.0000.000
50A50GLY0-0.015-0.00618.0380.6860.6860.0000.0000.0000.000
51A51ILE0-0.041-0.01920.1740.7190.7190.0000.0000.0000.000
52A52SER00.002-0.00621.642-0.458-0.4580.0000.0000.0000.000
53A53VAL0-0.029-0.00919.6590.2810.2810.0000.0000.0000.000
54A54CYS0-0.0040.01322.8600.0600.0600.0000.0000.0000.000
55A55VAL0-0.023-0.02120.598-0.318-0.3180.0000.0000.0000.000
56A56PHE0-0.023-0.01423.6840.5210.5210.0000.0000.0000.000
57A57HIS10.8650.91619.65513.42713.4270.0000.0000.0000.000
58A58MET00.0180.01223.6180.5250.5250.0000.0000.0000.000
59A59ASP-1-0.879-0.93022.515-11.486-11.4860.0000.0000.0000.000
60A60ASP-1-0.891-0.94625.548-11.276-11.2760.0000.0000.0000.000
61A61HIS10.7670.86927.59310.59110.5910.0000.0000.0000.000
62A62ILE00.0270.04428.0670.1360.1360.0000.0000.0000.000
63A63VAL00.0060.00331.1140.1530.1530.0000.0000.0000.000
64A64GLU-1-0.813-0.90033.751-7.550-7.5500.0000.0000.0000.000
65A65ARG10.8370.89932.3558.5378.5370.0000.0000.0000.000
66A66ALA00.003-0.00435.9910.0310.0310.0000.0000.0000.000
67A67LYS10.8580.92437.9737.4907.4900.0000.0000.0000.000
68A68ARG10.8420.91730.0929.0769.0760.0000.0000.0000.000
69A69TYR0-0.0030.00929.752-0.295-0.2950.0000.0000.0000.000
70A70HIS0-0.026-0.01236.3690.1970.1970.0000.0000.0000.000
71A71THR0-0.023-0.03038.4380.2000.2000.0000.0000.0000.000
72A72GLY0-0.0140.00140.8640.1300.1300.0000.0000.0000.000
73A73ASN0-0.036-0.01838.5490.1120.1120.0000.0000.0000.000
74A74GLU-1-0.817-0.91035.986-7.828-7.8280.0000.0000.0000.000
75A75GLU-1-0.794-0.89432.336-8.677-8.6770.0000.0000.0000.000
76A76TRP00.0250.02331.055-0.250-0.2500.0000.0000.0000.000
77A77PHE00.0180.02132.028-0.181-0.1810.0000.0000.0000.000
78A78GLU-1-0.789-0.86433.828-8.022-8.0220.0000.0000.0000.000
79A79TYR0-0.021-0.02024.064-0.164-0.1640.0000.0000.0000.000
80A80TYR00.0340.01728.586-0.275-0.2750.0000.0000.0000.000
81A81TYR0-0.027-0.03731.087-0.099-0.0990.0000.0000.0000.000
82A82LEU0-0.0340.00534.3900.1410.1410.0000.0000.0000.000
83A83GLN0-0.0020.00827.6610.2840.2840.0000.0000.0000.000
84A84TRP00.005-0.02125.889-0.062-0.0620.0000.0000.0000.000
85A85ASP-1-0.836-0.90732.546-7.750-7.7500.0000.0000.0000.000
86A86VAL00.0390.00633.097-0.104-0.1040.0000.0000.0000.000
87A87GLU-1-0.877-0.91034.969-7.396-7.3960.0000.0000.0000.000
88A88TRP00.0220.00235.109-0.092-0.0920.0000.0000.0000.000
89A89LEU0-0.004-0.01031.195-0.061-0.0610.0000.0000.0000.000
90A90THR0-0.013-0.01934.422-0.220-0.2200.0000.0000.0000.000
91A91HIS0-0.099-0.06435.9140.1390.1390.0000.0000.0000.000
92A92GLN0-0.017-0.01037.2130.0050.0050.0000.0000.0000.000
93A93LEU0-0.018-0.00429.196-0.092-0.0920.0000.0000.0000.000
94A94PHE00.010-0.01127.9560.0020.0020.0000.0000.0000.000
95A95ARG10.9200.96932.9017.7727.7720.0000.0000.0000.000
96A96GLN0-0.031-0.00135.4260.1070.1070.0000.0000.0000.000
97A97LEU00.0030.00829.0650.0210.0210.0000.0000.0000.000
98A98LYS10.8500.91330.12210.30910.3090.0000.0000.0000.000
99A99ALA0-0.0010.00533.6770.0090.0090.0000.0000.0000.000
100A100SER0-0.0040.01536.3880.2510.2510.0000.0000.0000.000
101A101HIS00.0370.02835.593-0.354-0.3540.0000.0000.0000.000
102A102GLN00.0390.02535.025-0.259-0.2590.0000.0000.0000.000
103A103LEU00.0220.02032.3250.2250.2250.0000.0000.0000.000
104A104THR0-0.050-0.03534.993-0.131-0.1310.0000.0000.0000.000
105A105LEU00.0060.00931.7420.1890.1890.0000.0000.0000.000
106A106PRO0-0.022-0.00434.9910.0210.0210.0000.0000.0000.000
107A107PHE00.004-0.00828.103-0.190-0.1900.0000.0000.0000.000
108A108TYR0-0.053-0.05629.6370.2140.2140.0000.0000.0000.000
109A109ASP-1-0.827-0.88329.905-9.566-9.5660.0000.0000.0000.000
110A110HIS00.040-0.00526.7330.3700.3700.0000.0000.0000.000
111A111GLU-1-0.975-0.96629.132-9.643-9.6430.0000.0000.0000.000
112A112THR0-0.062-0.06531.4490.3280.3280.0000.0000.0000.000
113A113ASP-1-0.815-0.86733.753-7.932-7.9320.0000.0000.0000.000
114A114THR0-0.014-0.00334.9100.2270.2270.0000.0000.0000.000
115A115HIS0-0.025-0.02434.071-0.078-0.0780.0000.0000.0000.000
116A116SER0-0.020-0.00334.0830.2050.2050.0000.0000.0000.000
117A117LYS10.9570.97335.5047.3037.3030.0000.0000.0000.000
118A118ARG10.9300.96732.4609.0059.0050.0000.0000.0000.000
119A119THR0-0.0010.00534.9760.0550.0550.0000.0000.0000.000
120A120VAL00.0270.03129.210-0.140-0.1400.0000.0000.0000.000
121A121TYR0-0.018-0.02131.8000.3070.3070.0000.0000.0000.000
122A122LEU0-0.012-0.00130.523-0.337-0.3370.0000.0000.0000.000
123A123SER0-0.032-0.03831.263-0.265-0.2650.0000.0000.0000.000
124A124ASP-1-0.899-0.94031.680-9.967-9.9670.0000.0000.0000.000
125A125SER0-0.035-0.02227.174-0.337-0.3370.0000.0000.0000.000
126A126ASP-1-0.821-0.90424.873-11.846-11.8460.0000.0000.0000.000
127A127MET0-0.021-0.00821.320-0.232-0.2320.0000.0000.0000.000
128A128ILE0-0.044-0.01925.0180.0610.0610.0000.0000.0000.000
129A129MET00.0000.01817.667-0.247-0.2470.0000.0000.0000.000
130A130ILE0-0.019-0.01722.8260.3830.3830.0000.0000.0000.000
131A131GLU-1-0.750-0.83518.792-14.971-14.9710.0000.0000.0000.000
132A132GLY00.033-0.01820.7370.6210.6210.0000.0000.0000.000
133A133VAL00.0020.01521.241-0.430-0.4300.0000.0000.0000.000
134A134PHE0-0.018-0.01922.8900.4410.4410.0000.0000.0000.000
135A135LEU0-0.0020.00622.3570.4820.4820.0000.0000.0000.000
136A136GLN0-0.055-0.03723.0770.4860.4860.0000.0000.0000.000
137A137ARG10.8490.94927.1819.9079.9070.0000.0000.0000.000
138A138LYS10.8530.89230.3518.3948.3940.0000.0000.0000.000
139A139GLU-1-0.855-0.91933.490-8.608-8.6080.0000.0000.0000.000
140A140TRP0-0.046-0.03227.9090.0320.0320.0000.0000.0000.000
141A141ARG10.8210.89028.8779.6039.6030.0000.0000.0000.000
142A142PRO0-0.041-0.02230.351-0.201-0.2010.0000.0000.0000.000
143A143PHE0-0.031-0.01231.4100.2030.2030.0000.0000.0000.000
144A144PHE0-0.0150.00224.883-0.179-0.1790.0000.0000.0000.000
145A145ASP-1-0.805-0.87926.637-10.715-10.7150.0000.0000.0000.000
146A146PHE00.007-0.00118.626-0.243-0.2430.0000.0000.0000.000
147A147VAL0-0.051-0.02621.663-0.044-0.0440.0000.0000.0000.000
148A148VAL00.0090.01015.125-0.247-0.2470.0000.0000.0000.000
149A149TYR0-0.025-0.01618.2820.7740.7740.0000.0000.0000.000
150A150LEU0-0.078-0.04211.597-0.780-0.7800.0000.0000.0000.000
151A151ASP-1-0.869-0.95414.547-14.535-14.5350.0000.0000.0000.000
152A152CYS0-0.106-0.05813.031-1.697-1.6970.0000.0000.0000.000
153A153PRO-1-0.926-0.94012.633-14.265-14.2650.0000.0000.0000.000
154A168ASN00.0340.00426.9280.2550.2550.0000.0000.0000.000
155A169ILE00.0600.02326.301-0.085-0.0850.0000.0000.0000.000
156A170GLN00.0260.01228.320-0.110-0.1100.0000.0000.0000.000
157A171LYS10.8540.90630.5278.5258.5250.0000.0000.0000.000
158A172PHE00.0040.00721.6410.0610.0610.0000.0000.0000.000
159A173ILE00.0420.01127.157-0.125-0.1250.0000.0000.0000.000
160A174ASN0-0.008-0.01228.7360.0040.0040.0000.0000.0000.000
161A175ARG10.7640.86928.6069.0719.0710.0000.0000.0000.000
162A176TYR0-0.005-0.01123.9290.0670.0670.0000.0000.0000.000
163A177TRP00.0300.02122.524-0.048-0.0480.0000.0000.0000.000
164A178LYS10.9030.94326.0688.2668.2660.0000.0000.0000.000
165A179ALA0-0.022-0.00327.7990.1890.1890.0000.0000.0000.000
166A180GLU-1-0.894-0.95822.077-12.174-12.1740.0000.0000.0000.000
167A181ASP-1-0.812-0.89925.414-10.320-10.3200.0000.0000.0000.000
168A182TYR00.0250.02427.3980.0940.0940.0000.0000.0000.000
169A183TYR0-0.037-0.03923.4510.2870.2870.0000.0000.0000.000
170A184LEU0-0.007-0.01822.164-0.033-0.0330.0000.0000.0000.000
171A185GLU-1-0.976-0.97926.330-8.821-8.8210.0000.0000.0000.000
172A186THR0-0.076-0.06129.9590.1400.1400.0000.0000.0000.000
173A187GLU-1-0.804-0.88628.843-9.164-9.1640.0000.0000.0000.000
174A188GLU-1-0.879-0.91827.144-10.137-10.1370.0000.0000.0000.000
175A189PRO00.0050.00922.951-0.223-0.2230.0000.0000.0000.000
176A190ILE00.0430.01320.255-0.265-0.2650.0000.0000.0000.000
177A191LYS10.8210.90922.42510.24210.2420.0000.0000.0000.000
178A192ARG10.8250.91125.30510.28910.2890.0000.0000.0000.000
179A193ALA0-0.0010.02020.6810.1200.1200.0000.0000.0000.000
180A194ASP-1-0.842-0.90821.971-12.901-12.9010.0000.0000.0000.000
181A195VAL0-0.069-0.04415.750-0.529-0.5290.0000.0000.0000.000
182A196VAL00.0290.02616.0520.2000.2000.0000.0000.0000.000
183A197PHE0-0.094-0.0598.442-1.448-1.4480.0000.0000.0000.000
184A198ASP-2-1.761-1.8649.824-45.522-45.5220.0000.0000.0000.000