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: M8VYZ

Calculation Name: 3F7C-A-Xray547

Preferred Name:

Target Type:

Ligand Name: citric acid

Ligand 3-letter code: CIT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3F7C

Chain ID: A

ChEMBL ID:

UniProt ID: A1TZ69

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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2102615.891086
FMO2-HF: Nuclear repulsion 2023117.487487
FMO2-HF: Total energy -79498.403599
FMO2-MP2: Total energy -79726.54657


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:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
-178.452-173.9558.591-6.553-6.534-0.057
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.895 / q_NPA : 0.939
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].
3A2ASN00.1080.0493.8558.5459.513-0.011-0.395-0.561-0.001
166A165MET0-0.053-0.0275.773-5.957-5.935-0.001-0.006-0.0140.000
169A168TYR00.0030.0072.273-13.960-10.9132.377-2.688-2.737-0.034
170A169TYR00.012-0.0012.521-11.200-10.7953.581-2.131-1.856-0.014
182A181LEU0-0.024-0.0084.475-10.003-9.850-0.001-0.014-0.1370.000
184A183ALA00.0260.0084.2370.8890.943-0.001-0.015-0.0380.000
185A184GLY0-0.073-0.0482.263-14.269-13.9822.626-1.893-1.020-0.005
186A185ALA0-0.037-0.0183.1262.4021.9890.0230.599-0.210-0.003
188A187ASN0-0.079-0.0364.324-3.073-3.073-0.001-0.0080.0100.000
189A188ASP-1-0.898-0.9485.375-44.634-44.660-0.001-0.0020.0290.000
4A3ALA00.0250.0106.7170.8500.8500.0000.0000.0000.000
5A4ASN00.0330.01810.1461.6941.6940.0000.0000.0000.000
6A5GLN0-0.006-0.0036.443-4.602-4.6020.0000.0000.0000.000
7A6PHE00.0310.0228.649-2.937-2.9370.0000.0000.0000.000
8A7LEU00.1030.04310.218-0.684-0.6840.0000.0000.0000.000
9A8LYS10.8770.9546.57040.68040.6800.0000.0000.0000.000
10A9ALA0-0.006-0.0096.933-0.278-0.2780.0000.0000.0000.000
11A10VAL00.0160.0208.6960.9430.9430.0000.0000.0000.000
12A11SER0-0.029-0.02612.0441.0921.0920.0000.0000.0000.000
13A12GLN0-0.022-0.0066.651-0.147-0.1470.0000.0000.0000.000
14A13LEU0-0.051-0.00811.393-0.325-0.3250.0000.0000.0000.000
15A14GLN00.0270.00713.4011.2071.2070.0000.0000.0000.000
16A15GLY00.0140.00815.961-0.596-0.5960.0000.0000.0000.000
17A16TRP00.0800.01914.407-0.646-0.6460.0000.0000.0000.000
18A17ARG10.8580.92911.17424.75424.7540.0000.0000.0000.000
19A18GLU-1-0.786-0.88015.322-17.355-17.3550.0000.0000.0000.000
20A19CYS-1-0.789-0.85317.023-14.371-14.3710.0000.0000.0000.000
21A20ALA0-0.013-0.01516.7620.3980.3980.0000.0000.0000.000
22A21PHE0-0.025-0.01015.053-0.059-0.0590.0000.0000.0000.000
23A22LEU0-0.008-0.00917.1040.5010.5010.0000.0000.0000.000
24A23LEU00.0170.00820.5400.5830.5830.0000.0000.0000.000
25A24ALA0-0.0050.00518.2430.5060.5060.0000.0000.0000.000
26A25LEU0-0.021-0.00618.3350.4020.4020.0000.0000.0000.000
27A26ALA00.0280.02421.4510.5780.5780.0000.0000.0000.000
28A27GLU-1-0.788-0.86823.343-10.871-10.8710.0000.0000.0000.000
29A28ARG10.8950.95220.53814.41214.4120.0000.0000.0000.000
30A29SER00.0430.01724.2590.3150.3150.0000.0000.0000.000
31A30PHE0-0.0040.00627.0540.5420.5420.0000.0000.0000.000
32A31PRO0-0.024-0.03028.6520.4240.4240.0000.0000.0000.000
33A32ASN00.0430.03128.7410.4660.4660.0000.0000.0000.000
34A33TYR0-0.011-0.02132.2140.3860.3860.0000.0000.0000.000
35A34ALA0-0.057-0.02733.8470.3160.3160.0000.0000.0000.000
36A35LEU00.0120.00635.3940.2740.2740.0000.0000.0000.000
37A36PHE00.0270.02036.6090.2370.2370.0000.0000.0000.000
38A37ALA0-0.014-0.01438.1520.2440.2440.0000.0000.0000.000
39A38ASP-1-0.985-0.99439.937-7.177-7.1770.0000.0000.0000.000
40A39ALA00.0020.00641.2280.2220.2220.0000.0000.0000.000
41A40VAL0-0.045-0.01142.2500.1950.1950.0000.0000.0000.000
42A41GLY0-0.0160.00144.5820.1470.1470.0000.0000.0000.000
43A42LEU0-0.0070.01441.2940.1290.1290.0000.0000.0000.000
44A43LYS10.9010.93443.1776.7256.7250.0000.0000.0000.000
45A44THR00.006-0.01639.4190.0940.0940.0000.0000.0000.000
46A45GLY00.0860.05237.161-0.156-0.1560.0000.0000.0000.000
47A46GLY00.0190.00336.465-0.215-0.2150.0000.0000.0000.000
48A47LYS10.8850.93837.3827.2207.2200.0000.0000.0000.000
49A48MET00.0170.03333.092-0.154-0.1540.0000.0000.0000.000
50A49ARG10.7150.82628.15510.18610.1860.0000.0000.0000.000
51A50GLN00.001-0.01032.556-0.136-0.1360.0000.0000.0000.000
52A51LEU0-0.035-0.00732.547-0.071-0.0710.0000.0000.0000.000
53A52LEU00.0370.02226.347-0.214-0.2140.0000.0000.0000.000
54A53ASP-1-0.844-0.91228.420-10.319-10.3190.0000.0000.0000.000
55A54LEU0-0.031-0.01429.472-0.197-0.1970.0000.0000.0000.000
56A55ALA00.024-0.00427.317-0.192-0.1920.0000.0000.0000.000
57A56TRP0-0.041-0.03520.486-0.740-0.7400.0000.0000.0000.000
58A57ASP-1-0.849-0.91425.387-10.598-10.5980.0000.0000.0000.000
59A58MET0-0.086-0.03627.3960.0180.0180.0000.0000.0000.000
60A59LEU0-0.0070.01120.617-0.218-0.2180.0000.0000.0000.000
61A60GLN0-0.082-0.03923.148-0.604-0.6040.0000.0000.0000.000
62A61LYS10.8410.91525.61510.44010.4400.0000.0000.0000.000
63A62ASP-1-0.879-0.91828.671-10.830-10.8300.0000.0000.0000.000
64A63VAL0-0.041-0.04130.1320.2500.2500.0000.0000.0000.000
65A64ALA0-0.0060.00932.535-0.080-0.0800.0000.0000.0000.000
66A65ASP-1-0.829-0.91832.104-9.917-9.9170.0000.0000.0000.000
67A66ALA0-0.043-0.03533.9770.0430.0430.0000.0000.0000.000
68A67ALA0-0.001-0.00135.7220.2060.2060.0000.0000.0000.000
69A68ILE00.0210.01430.8010.0870.0870.0000.0000.0000.000
70A69PRO00.0240.00434.0190.0050.0050.0000.0000.0000.000
71A70GLN0-0.030-0.00336.5630.0800.0800.0000.0000.0000.000
72A71LEU0-0.017-0.00732.6790.1290.1290.0000.0000.0000.000
73A72LEU00.0230.01431.0540.0020.0020.0000.0000.0000.000
74A73SER0-0.0060.00634.9570.1120.1120.0000.0000.0000.000
75A74LYS10.9260.95837.2628.1978.1970.0000.0000.0000.000
76A75LEU00.0160.00831.6180.1260.1260.0000.0000.0000.000
77A76GLU-1-0.847-0.92735.824-8.619-8.6190.0000.0000.0000.000
78A77THR0-0.115-0.06137.9210.2070.2070.0000.0000.0000.000
79A78LEU0-0.104-0.05336.8610.1950.1950.0000.0000.0000.000
80A79CYS0-0.0020.02735.999-0.154-0.1540.0000.0000.0000.000
81A80PRO0-0.0240.00036.2640.2030.2030.0000.0000.0000.000
82A81ASN00.0270.00838.307-0.335-0.3350.0000.0000.0000.000
83A82VAL00.016-0.01636.3850.0850.0850.0000.0000.0000.000
84A83ASP-1-0.923-0.95139.727-7.591-7.5910.0000.0000.0000.000
85A84GLU-1-0.997-1.00043.132-6.858-6.8580.0000.0000.0000.000
86A85TYR0-0.035-0.03942.0740.0920.0920.0000.0000.0000.000
87A86ASP-1-0.889-0.93542.825-6.894-6.8940.0000.0000.0000.000
88A87ALA0-0.059-0.02241.970-0.068-0.0680.0000.0000.0000.000
89A88TYR00.1020.02932.474-0.040-0.0400.0000.0000.0000.000
90A89GLY00.007-0.00636.252-0.217-0.2170.0000.0000.0000.000
91A90VAL00.0150.01336.064-0.215-0.2150.0000.0000.0000.000
92A91TYR00.0350.02433.997-0.135-0.1350.0000.0000.0000.000
93A92PRO00.0120.01631.062-0.235-0.2350.0000.0000.0000.000
94A93ALA0-0.033-0.01631.100-0.272-0.2720.0000.0000.0000.000
95A94PHE00.0650.03232.924-0.120-0.1200.0000.0000.0000.000
96A95ASP-1-0.763-0.86528.210-10.703-10.7030.0000.0000.0000.000
97A96PHE0-0.035-0.03128.027-0.334-0.3340.0000.0000.0000.000
98A97CYS0-0.062-0.02528.925-0.099-0.0990.0000.0000.0000.000
99A98GLN00.0500.02228.761-0.186-0.1860.0000.0000.0000.000
100A99LEU0-0.025-0.01122.952-0.383-0.3830.0000.0000.0000.000
101A100LEU0-0.030-0.01725.457-0.358-0.3580.0000.0000.0000.000
102A101GLU-1-0.880-0.95727.807-10.343-10.3430.0000.0000.0000.000
103A102GLN0-0.020-0.00724.277-0.432-0.4320.0000.0000.0000.000
104A103ALA00.0230.01624.008-0.309-0.3090.0000.0000.0000.000
105A104LEU0-0.022-0.01724.963-0.008-0.0080.0000.0000.0000.000
106A105LEU0-0.029-0.02827.7330.0690.0690.0000.0000.0000.000
107A106ASN0-0.062-0.06220.6550.1860.1860.0000.0000.0000.000
108A107ARG10.8410.90724.97811.48511.4850.0000.0000.0000.000
109A108LEU0-0.012-0.00326.8050.1980.1980.0000.0000.0000.000
110A109ASN0-0.053-0.03426.845-0.074-0.0740.0000.0000.0000.000
111A110PRO00.0660.05122.443-0.251-0.2510.0000.0000.0000.000
112A111ASN0-0.028-0.01621.688-1.004-1.0040.0000.0000.0000.000
113A112LYS10.8940.96422.56311.65011.6500.0000.0000.0000.000
114A113HIS00.0440.04615.7380.0410.0410.0000.0000.0000.000
115A114ARG10.8130.87819.75113.50713.5070.0000.0000.0000.000
116A115ALA0-0.013-0.00516.0640.1810.1810.0000.0000.0000.000
117A116THR0-0.017-0.04216.812-0.464-0.4640.0000.0000.0000.000
118A117GLU-1-0.883-0.95517.954-13.978-13.9780.0000.0000.0000.000
119A118ALA0-0.0020.00920.0920.4940.4940.0000.0000.0000.000
120A119SER0-0.033-0.03317.1060.0900.0900.0000.0000.0000.000
121A120GLN0-0.0210.00119.1410.2620.2620.0000.0000.0000.000
122A121LEU0-0.0080.00421.7980.3260.3260.0000.0000.0000.000
123A122ALA00.0290.01021.2160.3500.3500.0000.0000.0000.000
124A123THR0-0.024-0.03520.4060.0460.0460.0000.0000.0000.000
125A124ARG10.8970.95722.75311.79711.7970.0000.0000.0000.000
126A125THR0-0.006-0.02026.3180.2260.2260.0000.0000.0000.000
127A126VAL0-0.054-0.02424.2900.4140.4140.0000.0000.0000.000
128A127MET0-0.055-0.02823.2610.2730.2730.0000.0000.0000.000
129A128ASP-1-0.800-0.90727.828-10.259-10.2590.0000.0000.0000.000
130A129PHE0-0.034-0.00930.3330.4160.4160.0000.0000.0000.000
131A130VAL0-0.0080.01328.7500.2800.2800.0000.0000.0000.000
132A131GLU-1-0.930-0.98031.684-9.314-9.3140.0000.0000.0000.000
133A132MET0-0.095-0.02633.6340.3770.3770.0000.0000.0000.000
134A133SER0-0.062-0.05934.0280.2250.2250.0000.0000.0000.000
135A134GLU-1-0.904-0.95132.946-9.502-9.5020.0000.0000.0000.000
136A135GLY00.011-0.00435.6440.0770.0770.0000.0000.0000.000
137A136GLU-1-0.961-0.97336.281-7.257-7.2570.0000.0000.0000.000
138A137GLY0-0.057-0.03240.0560.0720.0720.0000.0000.0000.000
139A138MET0-0.074-0.01035.769-0.058-0.0580.0000.0000.0000.000
140A139ASP-1-0.890-0.94137.533-8.080-8.0800.0000.0000.0000.000
141A140GLU-1-0.939-0.97332.978-9.767-9.7670.0000.0000.0000.000
142A141ASN0-0.024-0.03232.455-0.302-0.3020.0000.0000.0000.000
143A142GLU-1-0.912-0.95232.471-8.605-8.6050.0000.0000.0000.000
144A143LEU00.0850.04931.343-0.232-0.2320.0000.0000.0000.000
145A144VAL0-0.008-0.00427.203-0.375-0.3750.0000.0000.0000.000
146A145ARG10.8400.91827.9489.0539.0530.0000.0000.0000.000
147A146VAL00.0220.01829.068-0.251-0.2510.0000.0000.0000.000
148A147PHE0-0.007-0.03125.955-0.404-0.4040.0000.0000.0000.000
149A148GLU-1-0.976-0.97521.784-14.822-14.8220.0000.0000.0000.000
150A149HIS0-0.043-0.03023.767-0.428-0.4280.0000.0000.0000.000
151A150HIS00.0130.00026.313-0.384-0.3840.0000.0000.0000.000
152A151PRO0-0.037-0.02225.004-0.563-0.5630.0000.0000.0000.000
153A152LEU00.0550.03123.923-0.573-0.5730.0000.0000.0000.000
154A153LEU00.0360.02722.997-0.503-0.5030.0000.0000.0000.000
155A154LYS10.8010.90620.22011.75111.7510.0000.0000.0000.000
156A155ASP-1-0.901-0.96119.056-14.283-14.2830.0000.0000.0000.000
157A156ASP-1-0.876-0.92719.361-15.473-15.4730.0000.0000.0000.000
158A157LYS10.9830.99516.02516.43616.4360.0000.0000.0000.000
159A158LEU0-0.046-0.02114.288-1.746-1.7460.0000.0000.0000.000
160A159PHE00.0140.01614.402-1.258-1.2580.0000.0000.0000.000
161A160GLN00.0560.03615.197-1.628-1.6280.0000.0000.0000.000
162A161ARG10.8520.9086.80232.23132.2310.0000.0000.0000.000
163A162ASP-1-0.908-0.95810.176-23.789-23.7890.0000.0000.0000.000
164A163THR0-0.054-0.03611.137-1.155-1.1550.0000.0000.0000.000
165A164VAL00.0080.0038.804-1.113-1.1130.0000.0000.0000.000
167A166ALA00.0030.0087.091-2.933-2.9330.0000.0000.0000.000
168A167LEU0-0.0080.0009.792-0.422-0.4220.0000.0000.0000.000
171A170TYR0-0.0100.0186.8121.7011.7010.0000.0000.0000.000
172A171ARG10.7660.8616.89336.08736.0870.0000.0000.0000.000
173A172THR00.0090.01712.6660.9050.9050.0000.0000.0000.000
174A173PRO00.0780.03816.098-0.103-0.1030.0000.0000.0000.000
175A174LYS10.9840.96414.97015.10715.1070.0000.0000.0000.000
176A175GLU-1-0.929-0.95713.961-18.714-18.7140.0000.0000.0000.000
177A176ALA00.0550.02511.986-1.419-1.4190.0000.0000.0000.000
178A177PHE0-0.0080.0049.666-2.567-2.5670.0000.0000.0000.000
179A178LEU0-0.001-0.0139.226-2.527-2.5270.0000.0000.0000.000
180A179ALA0-0.0050.0039.449-1.573-1.5730.0000.0000.0000.000
181A180GLU-1-0.821-0.9025.393-49.982-49.9820.0000.0000.0000.000
183A182ARG10.9300.9706.17822.27522.2750.0000.0000.0000.000
187A186ALA0-0.031-0.0166.2723.3123.3120.0000.0000.0000.000
190A189GLY0-0.0080.0037.3353.9323.9320.0000.0000.0000.000
191A190VAL0-0.055-0.0179.0123.2053.2050.0000.0000.0000.000
192A191SER0-0.014-0.0139.474-2.437-2.4370.0000.0000.0000.000
193A192ASN00.006-0.01911.045-0.532-0.5320.0000.0000.0000.000
194A193LEU0-0.036-0.01711.8780.8590.8590.0000.0000.0000.000
195A194GLY0-0.013-0.00113.1341.1541.1540.0000.0000.0000.000
196A195ILE0-0.0160.00614.1350.1440.1440.0000.0000.0000.000
197A196SER00.0660.03213.197-1.222-1.2220.0000.0000.0000.000
198A197LEU0-0.094-0.05114.8931.3741.3740.0000.0000.0000.000
199A198GLU-2-1.898-1.93115.937-35.036-35.0360.0000.0000.0000.000