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: 8QNYY

Calculation Name: 2CZQ-A-Xray547

Preferred Name:

Target Type:

Ligand Name: citric acid

Ligand 3-letter code: CIT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CZQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q874E9

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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2134707.545363
FMO2-HF: Nuclear repulsion 2060399.505478
FMO2-HF: Total energy -74308.039885
FMO2-MP2: Total energy -74522.835612


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-51.418-46.82310.682-8.635-6.643-0.094
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.907
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].
3A3SER00.0190.0063.8402.0773.474-0.005-0.643-0.749-0.001
37A37ALA0-0.0220.0023.534-14.343-12.9800.008-0.742-0.629-0.005
38A38LEU0-0.052-0.0171.781-49.786-49.09610.675-6.746-4.619-0.088
39A39SER00.0340.0043.42216.84817.9620.005-0.498-0.6220.000
40A40GLY00.0510.0144.9452.5092.540-0.001-0.006-0.0240.000
4A4SER00.011-0.0086.0531.5421.5420.0000.0000.0000.000
5A5ALA00.0060.0098.8652.3542.3540.0000.0000.0000.000
6A6CYS0-0.081-0.0389.3094.0634.0630.0000.0000.0000.000
7A7PRO00.0260.0168.579-3.447-3.4470.0000.0000.0000.000
8A8GLN00.0120.0129.610-0.308-0.3080.0000.0000.0000.000
9A9TYR0-0.052-0.0266.8443.9233.9230.0000.0000.0000.000
10A10VAL0-0.056-0.02512.408-0.102-0.1020.0000.0000.0000.000
11A11LEU00.0120.01611.1060.3300.3300.0000.0000.0000.000
12A12ILE0-0.024-0.00715.1270.5550.5550.0000.0000.0000.000
13A13ASN0-0.016-0.01118.5330.7690.7690.0000.0000.0000.000
14A14THR00.0230.02520.4010.3680.3680.0000.0000.0000.000
15A15ARG10.8220.90124.19611.13911.1390.0000.0000.0000.000
16A16GLY00.0640.04125.6670.3070.3070.0000.0000.0000.000
17A17THR00.003-0.00628.765-0.002-0.0020.0000.0000.0000.000
18A18GLY0-0.0160.00732.3470.0190.0190.0000.0000.0000.000
19A19GLU-1-0.733-0.81925.854-12.600-12.6000.0000.0000.0000.000
20A20PRO00.0270.01328.1170.1070.1070.0000.0000.0000.000
21A21GLN0-0.007-0.01625.713-0.050-0.0500.0000.0000.0000.000
22A22GLY00.006-0.00523.737-0.033-0.0330.0000.0000.0000.000
23A23GLN0-0.0080.00416.418-0.553-0.5530.0000.0000.0000.000
24A24SER0-0.029-0.04221.2940.3090.3090.0000.0000.0000.000
25A25ALA0-0.048-0.04821.163-0.783-0.7830.0000.0000.0000.000
26A26GLY00.0370.02121.624-0.402-0.4020.0000.0000.0000.000
27A27PHE00.0400.00217.428-0.289-0.2890.0000.0000.0000.000
28A28ARG10.9080.96516.49813.41213.4120.0000.0000.0000.000
29A29THR00.0050.01415.844-0.930-0.9300.0000.0000.0000.000
30A30MET00.0080.04313.655-1.733-1.7330.0000.0000.0000.000
31A31ASN00.0230.00311.852-3.050-3.0500.0000.0000.0000.000
32A32SER0-0.050-0.01010.895-2.297-2.2970.0000.0000.0000.000
33A33GLN00.0380.0139.350-1.852-1.8520.0000.0000.0000.000
34A34ILE0-0.022-0.0137.445-4.863-4.8630.0000.0000.0000.000
35A35THR0-0.058-0.0466.317-5.518-5.5180.0000.0000.0000.000
36A36ALA0-0.0120.0125.854-4.645-4.6450.0000.0000.0000.000
41A41GLY00.0140.0128.0793.4043.4040.0000.0000.0000.000
42A42THR0-0.059-0.0349.7881.5151.5150.0000.0000.0000.000
43A43ILE00.0170.01213.0770.1790.1790.0000.0000.0000.000
44A44TYR0-0.063-0.06515.3630.6650.6650.0000.0000.0000.000
45A45ASN00.0270.01118.876-0.434-0.4340.0000.0000.0000.000
46A46THR0-0.006-0.00921.9050.2680.2680.0000.0000.0000.000
47A47VAL0-0.040-0.00624.6530.2750.2750.0000.0000.0000.000
48A48TYR0-0.050-0.04027.9060.4210.4210.0000.0000.0000.000
49A49THR00.043-0.00930.910-0.256-0.2560.0000.0000.0000.000
50A50ALA0-0.0170.01430.407-0.046-0.0460.0000.0000.0000.000
51A51ASP-1-0.752-0.83032.545-8.555-8.5550.0000.0000.0000.000
52A52PHE00.038-0.00436.188-0.126-0.1260.0000.0000.0000.000
53A53SER0-0.056-0.03638.3230.0680.0680.0000.0000.0000.000
54A54GLN0-0.035-0.02834.957-0.149-0.1490.0000.0000.0000.000
55A55ASN00.0170.02436.173-0.114-0.1140.0000.0000.0000.000
56A56SER00.007-0.00631.871-0.116-0.1160.0000.0000.0000.000
57A57ALA00.0310.01532.338-0.324-0.3240.0000.0000.0000.000
58A58ALA00.0200.00633.035-0.168-0.1680.0000.0000.0000.000
59A59GLY00.0290.01229.010-0.269-0.2690.0000.0000.0000.000
60A60THR0-0.023-0.02228.045-0.348-0.3480.0000.0000.0000.000
61A61ALA00.0130.00628.882-0.283-0.2830.0000.0000.0000.000
62A62ASP-1-0.743-0.83626.126-12.498-12.4980.0000.0000.0000.000
63A63ILE00.0090.00323.404-0.583-0.5830.0000.0000.0000.000
64A64ILE00.0070.00724.430-0.528-0.5280.0000.0000.0000.000
65A65ARG10.8550.93224.77512.07012.0700.0000.0000.0000.000
66A66ARG10.8840.95917.93416.33316.3330.0000.0000.0000.000
67A67ILE00.0190.01421.405-0.610-0.6100.0000.0000.0000.000
68A68ASN00.0250.00122.620-0.623-0.6230.0000.0000.0000.000
69A69SER0-0.039-0.03724.0700.1660.1660.0000.0000.0000.000
70A70GLY0-0.037-0.01420.387-0.152-0.1520.0000.0000.0000.000
71A71LEU0-0.047-0.02420.494-0.329-0.3290.0000.0000.0000.000
72A72ALA0-0.022-0.00622.5200.1220.1220.0000.0000.0000.000
73A73ALA0-0.0230.00321.1990.2370.2370.0000.0000.0000.000
74A74ASN00.016-0.01615.7970.3320.3320.0000.0000.0000.000
75A75PRO00.0170.01219.824-0.417-0.4170.0000.0000.0000.000
76A76ASN0-0.047-0.02816.5380.4480.4480.0000.0000.0000.000
77A77VAL0-0.064-0.00414.950-1.318-1.3180.0000.0000.0000.000
78A79TYR00.0270.00014.904-0.565-0.5650.0000.0000.0000.000
79A80ILE0-0.0070.00213.1650.1810.1810.0000.0000.0000.000
80A81LEU0-0.028-0.00816.2370.0940.0940.0000.0000.0000.000
81A82GLN00.026-0.00315.2540.1150.1150.0000.0000.0000.000
82A83GLY00.0550.02720.2760.3460.3460.0000.0000.0000.000
83A84TYR0-0.049-0.04123.906-0.026-0.0260.0000.0000.0000.000
84A85SER0-0.010-0.00525.8110.3580.3580.0000.0000.0000.000
85A86GLN0-0.001-0.02429.652-0.015-0.0150.0000.0000.0000.000
86A87GLY00.0640.02027.0070.0730.0730.0000.0000.0000.000
87A88ALA0-0.089-0.01826.382-0.425-0.4250.0000.0000.0000.000
88A89ALA00.0800.04227.380-0.105-0.1050.0000.0000.0000.000
89A90ALA00.0160.01528.4000.0030.0030.0000.0000.0000.000
90A91THR0-0.007-0.02523.489-0.248-0.2480.0000.0000.0000.000
91A92VAL0-0.042-0.01326.774-0.131-0.1310.0000.0000.0000.000
92A93VAL00.0320.01429.0450.0840.0840.0000.0000.0000.000
93A94ALA00.0000.00026.8520.1370.1370.0000.0000.0000.000
94A95LEU0-0.033-0.02924.401-0.033-0.0330.0000.0000.0000.000
95A96GLN0-0.078-0.04427.9190.2640.2640.0000.0000.0000.000
96A97GLN0-0.019-0.01231.3270.0330.0330.0000.0000.0000.000
97A98LEU0-0.038-0.01525.1850.0180.0180.0000.0000.0000.000
98A99GLY00.0190.03329.1870.0060.0060.0000.0000.0000.000
99A100THR0-0.044-0.04227.722-0.334-0.3340.0000.0000.0000.000
100A101SER00.0030.00627.328-0.003-0.0030.0000.0000.0000.000
101A102GLY00.0690.03527.5570.0650.0650.0000.0000.0000.000
102A103ALA00.007-0.00524.361-0.415-0.4150.0000.0000.0000.000
103A104ALA00.0750.03422.872-0.639-0.6390.0000.0000.0000.000
104A105PHE00.0140.01622.408-0.748-0.7480.0000.0000.0000.000
105A106ASN00.002-0.01621.568-0.397-0.3970.0000.0000.0000.000
106A107ALA00.0180.03318.569-0.870-0.8700.0000.0000.0000.000
107A108VAL0-0.014-0.00617.405-1.249-1.2490.0000.0000.0000.000
108A109LYS10.8880.94313.86419.23019.2300.0000.0000.0000.000
109A110GLY00.010-0.00716.6220.1290.1290.0000.0000.0000.000
110A111VAL0-0.034-0.00717.688-0.232-0.2320.0000.0000.0000.000
111A112PHE00.0040.00518.178-0.055-0.0550.0000.0000.0000.000
112A113LEU0-0.019-0.00720.2700.0310.0310.0000.0000.0000.000
113A114ILE00.0220.02322.432-0.144-0.1440.0000.0000.0000.000
114A115GLY00.0570.02025.2520.2050.2050.0000.0000.0000.000
115A116ASN0-0.037-0.04428.0850.3950.3950.0000.0000.0000.000
116A117PRO00.0350.02229.8420.2400.2400.0000.0000.0000.000
117A118ASP-1-0.776-0.89731.724-9.224-9.2240.0000.0000.0000.000
118A119HIS0-0.051-0.01729.370-0.346-0.3460.0000.0000.0000.000
119A120LYS10.9630.98231.8289.1859.1850.0000.0000.0000.000
120A121SER0-0.0090.00432.898-0.251-0.2510.0000.0000.0000.000
121A122GLY00.009-0.00534.0870.1480.1480.0000.0000.0000.000
122A123LEU0-0.041-0.01129.536-0.065-0.0650.0000.0000.0000.000
123A124THR0-0.002-0.02327.486-0.153-0.1530.0000.0000.0000.000
124A125CYS0-0.0180.00524.608-0.196-0.1960.0000.0000.0000.000
125A126ASN0-0.035-0.00624.845-0.700-0.7000.0000.0000.0000.000
126A127VAL0-0.011-0.00123.0360.1000.1000.0000.0000.0000.000
127A128ASP-1-0.740-0.83726.511-11.100-11.1000.0000.0000.0000.000
128A129SER00.012-0.03024.707-0.381-0.3810.0000.0000.0000.000
129A130ASN0-0.093-0.04023.547-0.707-0.7070.0000.0000.0000.000
130A131GLY00.0000.00022.847-0.329-0.3290.0000.0000.0000.000
131A132GLY0-0.0200.01123.6280.1550.1550.0000.0000.0000.000
132A133THR00.005-0.02027.343-0.105-0.1050.0000.0000.0000.000
133A134THR0-0.056-0.04330.0670.3450.3450.0000.0000.0000.000
134A135THR00.003-0.01129.8010.3370.3370.0000.0000.0000.000
135A136ARG10.8580.92826.20611.17011.1700.0000.0000.0000.000
136A137ASN0-0.009-0.01331.649-0.145-0.1450.0000.0000.0000.000
137A138VAL0-0.0030.02033.7530.3340.3340.0000.0000.0000.000
138A139ASN00.0140.00534.957-0.362-0.3620.0000.0000.0000.000
139A140GLY00.0840.06234.9040.0870.0870.0000.0000.0000.000
140A141LEU0-0.060-0.02835.7830.2190.2190.0000.0000.0000.000
141A142SER0-0.042-0.02035.9570.2590.2590.0000.0000.0000.000
142A143VAL0-0.0020.01334.8470.1200.1200.0000.0000.0000.000
143A144ALA0-0.059-0.02836.8250.0400.0400.0000.0000.0000.000
144A145TYR0-0.033-0.01539.0620.1870.1870.0000.0000.0000.000
145A146GLN0-0.054-0.02934.8090.1020.1020.0000.0000.0000.000
146A147GLY00.0230.03435.779-0.206-0.2060.0000.0000.0000.000
147A148SER0-0.011-0.02532.585-0.088-0.0880.0000.0000.0000.000
148A149VAL00.0350.01426.677-0.034-0.0340.0000.0000.0000.000
149A150PRO00.0220.02228.6890.2080.2080.0000.0000.0000.000
150A151SER00.0390.00828.910-0.427-0.4270.0000.0000.0000.000
151A152GLY00.006-0.00228.184-0.245-0.2450.0000.0000.0000.000
152A153TRP00.0520.00521.937-0.752-0.7520.0000.0000.0000.000
153A154VAL0-0.0070.01923.901-0.605-0.6050.0000.0000.0000.000
154A155SER0-0.0100.00323.057-0.425-0.4250.0000.0000.0000.000
155A156LYS10.7770.89819.19313.64513.6450.0000.0000.0000.000
156A157THR00.010-0.01720.046-0.546-0.5460.0000.0000.0000.000
157A158LEU0-0.0200.00218.6770.0660.0660.0000.0000.0000.000
158A159ASP-1-0.847-0.92922.093-11.625-11.6250.0000.0000.0000.000
159A160VAL00.0100.00621.7610.2690.2690.0000.0000.0000.000
160A161CYS0-0.050-0.00725.1200.2140.2140.0000.0000.0000.000
161A162ALA00.0600.02728.3390.0710.0710.0000.0000.0000.000
162A163TYR00.012-0.01529.6170.3960.3960.0000.0000.0000.000
163A164GLY00.0450.01532.9100.0480.0480.0000.0000.0000.000
164A165ASP-1-0.739-0.83430.939-9.999-9.9990.0000.0000.0000.000
165A166GLY00.0320.00733.8760.0030.0030.0000.0000.0000.000
166A167VAL0-0.038-0.01633.1640.2170.2170.0000.0000.0000.000
167A169ASP-1-0.669-0.85533.424-8.869-8.8690.0000.0000.0000.000
168A170THR0-0.063-0.05035.6250.2180.2180.0000.0000.0000.000
169A171ALA0-0.049-0.00638.4730.2300.2300.0000.0000.0000.000
170A172HIS10.8080.87336.1888.7638.7630.0000.0000.0000.000
171A173GLY00.0210.02337.439-0.001-0.0010.0000.0000.0000.000
172A174PHE0-0.056-0.02838.3910.1910.1910.0000.0000.0000.000
173A175GLY00.0260.01739.442-0.008-0.0080.0000.0000.0000.000
174A176ILE00.0010.00634.479-0.223-0.2230.0000.0000.0000.000
175A177ASN00.019-0.00535.210-0.041-0.0410.0000.0000.0000.000
176A178ALA00.0440.00333.794-0.255-0.2550.0000.0000.0000.000
177A179GLN00.0170.01931.761-0.300-0.3000.0000.0000.0000.000
178A180HIS0-0.0140.01230.365-0.461-0.4610.0000.0000.0000.000
179A181LEU0-0.0070.00329.596-0.336-0.3360.0000.0000.0000.000
180A182SER0-0.020-0.00928.035-0.400-0.4000.0000.0000.0000.000
181A183TYR0-0.006-0.04223.734-0.504-0.5040.0000.0000.0000.000
182A184PRO0-0.018-0.00122.286-0.718-0.7180.0000.0000.0000.000
183A185SER0-0.048-0.02721.715-0.427-0.4270.0000.0000.0000.000
184A186ASP-1-0.815-0.88123.391-12.976-12.9760.0000.0000.0000.000
185A187GLN00.0390.00120.382-0.347-0.3470.0000.0000.0000.000
186A188GLY00.0170.03819.585-0.939-0.9390.0000.0000.0000.000
187A189VAL00.017-0.00219.908-0.766-0.7660.0000.0000.0000.000
188A190GLN0-0.026-0.03317.096-1.812-1.8120.0000.0000.0000.000
189A191THR0-0.005-0.01815.122-1.713-1.7130.0000.0000.0000.000
190A192MET0-0.0290.00114.961-1.205-1.2050.0000.0000.0000.000
191A193GLY00.0450.00515.809-0.555-0.5550.0000.0000.0000.000
192A194TYR0-0.010-0.0188.0000.3340.3340.0000.0000.0000.000
193A195LYS10.8860.92911.18220.17820.1780.0000.0000.0000.000
194A196PHE0-0.0130.00711.711-1.028-1.0280.0000.0000.0000.000
195A197ALA00.0280.00912.128-0.187-0.1870.0000.0000.0000.000
196A198VAL00.0150.0046.004-1.224-1.2240.0000.0000.0000.000
197A199ASN0-0.065-0.0518.325-1.437-1.4370.0000.0000.0000.000
198A200LYS10.8660.94810.45817.76017.7600.0000.0000.0000.000
199A201LEU0-0.016-0.0088.8051.1671.1670.0000.0000.0000.000
200A202GLY00.0010.0178.896-1.682-1.6820.0000.0000.0000.000
201A203GLY0-0.018-0.0075.233-2.728-2.7280.0000.0000.0000.000
202A204SER0-0.056-0.0375.0874.3754.3750.0000.0000.0000.000
203A205ALA-1-0.816-0.8666.250-29.076-29.0760.0000.0000.0000.000