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: G7JM1

Calculation Name: 1E5K-A-Xray549

Preferred Name:

Target Type:

Ligand Name: citric acid | lithium ion

Ligand 3-letter code: CIT | LI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1E5K

Chain ID: A

ChEMBL ID:

UniProt ID: P32173

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2057605.564406
FMO2-HF: Nuclear repulsion 1983690.338274
FMO2-HF: Total energy -73915.226132
FMO2-MP2: Total energy -74128.445297


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:4:MET)


Summations of interaction energy for fragment #1(A:4: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.
-104.764-100.680.806-2.61-2.281-0.025
Interaction energy analysis for fragmet #1(A:4:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.912
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].
3A6THR00.004-0.0072.454-21.566-17.6450.808-2.604-2.126-0.025
4A7ILE0-0.003-0.0025.1422.5602.678-0.001-0.006-0.1110.000
90A93GLU-1-0.936-0.9805.381-29.861-29.816-0.0010.000-0.0440.000
5A8THR00.0040.0166.625-4.580-4.5800.0000.0000.0000.000
6A9GLY00.0240.0108.1443.1543.1540.0000.0000.0000.000
7A10VAL0-0.016-0.01611.614-0.296-0.2960.0000.0000.0000.000
8A11VAL00.0240.02114.2321.0741.0740.0000.0000.0000.000
9A12LEU0-0.028-0.02117.7130.0520.0520.0000.0000.0000.000
10A13ALA00.005-0.01820.2090.7020.7020.0000.0000.0000.000
11A14GLY0-0.0210.00922.7930.6410.6410.0000.0000.0000.000
12A15GLY00.0940.03924.300-0.289-0.2890.0000.0000.0000.000
13A16LYS10.7050.84526.32311.15711.1570.0000.0000.0000.000
14A17ALA00.0690.02429.7490.2400.2400.0000.0000.0000.000
15A18ARG10.9400.96331.8109.0699.0690.0000.0000.0000.000
16A19ARG10.9560.97334.7617.8367.8360.0000.0000.0000.000
17A20MET00.0500.03135.0820.1680.1680.0000.0000.0000.000
18A21GLY00.0060.00132.787-0.140-0.1400.0000.0000.0000.000
19A22GLY0-0.0170.01633.6980.0400.0400.0000.0000.0000.000
20A23VAL00.0500.01833.151-0.127-0.1270.0000.0000.0000.000
21A24ASP-1-0.800-0.88128.037-11.431-11.4310.0000.0000.0000.000
22A25LYS10.8640.92628.93410.61410.6140.0000.0000.0000.000
23A26GLY00.0730.03625.554-0.035-0.0350.0000.0000.0000.000
24A27LEU0-0.009-0.00725.815-0.195-0.1950.0000.0000.0000.000
25A28LEU0-0.044-0.00828.0340.2880.2880.0000.0000.0000.000
26A29GLU-1-0.923-0.96129.372-10.344-10.3440.0000.0000.0000.000
27A30LEU0-0.0060.01028.5610.2990.2990.0000.0000.0000.000
28A31ASN0-0.035-0.02630.088-0.173-0.1730.0000.0000.0000.000
29A32GLY0-0.0140.00631.240-0.144-0.1440.0000.0000.0000.000
30A33LYS10.8710.92823.48212.78112.7810.0000.0000.0000.000
31A34PRO00.0330.01825.1570.0800.0800.0000.0000.0000.000
32A35LEU0-0.0020.00225.310-0.483-0.4830.0000.0000.0000.000
33A36TRP00.035-0.00417.952-0.658-0.6580.0000.0000.0000.000
34A37GLN00.0030.00918.910-0.678-0.6780.0000.0000.0000.000
35A38HIS0-0.015-0.01021.068-0.802-0.8020.0000.0000.0000.000
36A39VAL0-0.043-0.01318.921-0.506-0.5060.0000.0000.0000.000
37A40ALA00.0270.00616.928-0.983-0.9830.0000.0000.0000.000
38A41ASP-1-0.777-0.87316.518-16.236-16.2360.0000.0000.0000.000
39A42ALA00.0060.02118.031-0.621-0.6210.0000.0000.0000.000
40A43LEU0-0.029-0.01013.925-0.799-0.7990.0000.0000.0000.000
41A44MET00.001-0.00513.254-1.675-1.6750.0000.0000.0000.000
42A45THR0-0.089-0.04114.031-0.247-0.2470.0000.0000.0000.000
43A46GLN0-0.085-0.04914.265-0.026-0.0260.0000.0000.0000.000
44A47LEU0-0.057-0.0269.285-1.725-1.7250.0000.0000.0000.000
45A48SER00.001-0.0086.7820.1470.1470.0000.0000.0000.000
46A49HIS0-0.079-0.0395.4110.8020.8020.0000.0000.0000.000
47A50VAL00.0030.0027.8340.3480.3480.0000.0000.0000.000
48A51VAL0-0.0190.00310.3090.4120.4120.0000.0000.0000.000
49A52VAL0-0.0010.00413.0750.7130.7130.0000.0000.0000.000
50A53ASN0-0.065-0.04016.7580.3270.3270.0000.0000.0000.000
51A54ALA00.0250.00618.6780.5870.5870.0000.0000.0000.000
52A55ASN0-0.029-0.02722.077-0.068-0.0680.0000.0000.0000.000
53A56ARG10.8300.90724.91510.70010.7000.0000.0000.0000.000
54A57HIS0-0.058-0.04626.0470.0250.0250.0000.0000.0000.000
55A58GLN00.0350.01423.2550.2750.2750.0000.0000.0000.000
56A59GLU-1-0.849-0.91823.202-13.153-13.1530.0000.0000.0000.000
57A60ILE0-0.031-0.02724.456-0.127-0.1270.0000.0000.0000.000
58A61TYR0-0.070-0.05120.947-0.262-0.2620.0000.0000.0000.000
59A62GLN0-0.038-0.03719.770-0.959-0.9590.0000.0000.0000.000
60A63ALA0-0.0260.00220.496-0.409-0.4090.0000.0000.0000.000
61A64SER0-0.063-0.03119.9160.0500.0500.0000.0000.0000.000
62A65GLY0-0.017-0.00717.460-0.498-0.4980.0000.0000.0000.000
63A66LEU0-0.039-0.01613.479-1.283-1.2830.0000.0000.0000.000
64A67LYS10.8220.89810.98626.20726.2070.0000.0000.0000.000
65A68VAL00.0380.01814.605-0.297-0.2970.0000.0000.0000.000
66A69ILE0-0.064-0.02712.674-0.405-0.4050.0000.0000.0000.000
67A70GLU-1-0.834-0.90617.353-12.840-12.8400.0000.0000.0000.000
68A71ASP-1-0.821-0.92519.971-14.524-14.5240.0000.0000.0000.000
69A72SER0-0.023-0.00821.6610.4240.4240.0000.0000.0000.000
70A73LEU00.014-0.01623.0390.4070.4070.0000.0000.0000.000
71A74ALA0-0.026-0.00525.9850.4470.4470.0000.0000.0000.000
72A75ASP-1-0.806-0.87727.087-10.273-10.2730.0000.0000.0000.000
73A76TYR00.0670.03324.4640.5180.5180.0000.0000.0000.000
74A77PRO0-0.038-0.03427.6280.0240.0240.0000.0000.0000.000
75A78GLY00.003-0.00527.398-0.169-0.1690.0000.0000.0000.000
76A79PRO00.011-0.01223.494-0.213-0.2130.0000.0000.0000.000
77A80LEU00.0380.02322.018-0.584-0.5840.0000.0000.0000.000
78A81ALA00.0220.03121.632-0.577-0.5770.0000.0000.0000.000
79A82GLY00.0870.06920.584-0.473-0.4730.0000.0000.0000.000
80A83MET0-0.071-0.03717.626-0.678-0.6780.0000.0000.0000.000
81A84LEU00.0240.01216.764-1.181-1.1810.0000.0000.0000.000
82A85SER0-0.026-0.01517.326-0.582-0.5820.0000.0000.0000.000
83A86VAL00.0380.02212.867-0.540-0.5400.0000.0000.0000.000
84A87MET0-0.069-0.01512.765-1.079-1.0790.0000.0000.0000.000
85A88GLN00.0100.00412.944-1.215-1.2150.0000.0000.0000.000
86A89GLN0-0.089-0.04113.7060.3280.3280.0000.0000.0000.000
87A90GLU-1-0.775-0.8647.988-34.495-34.4950.0000.0000.0000.000
88A91ALA00.0080.0235.9991.1101.1100.0000.0000.0000.000
89A92GLY00.003-0.0044.839-4.387-4.3870.0000.0000.0000.000
91A94TRP0-0.022-0.0117.3296.1406.1400.0000.0000.0000.000
92A95PHE00.0360.0278.451-3.362-3.3620.0000.0000.0000.000
93A96LEU00.0110.00511.2151.6131.6130.0000.0000.0000.000
94A97PHE00.0060.00013.630-0.144-0.1440.0000.0000.0000.000
95A98CYS00.0530.02816.5640.6680.6680.0000.0000.0000.000
96A99PRO0-0.0460.00119.422-0.242-0.2420.0000.0000.0000.000
97A100CYS0-0.005-0.00822.3250.0770.0770.0000.0000.0000.000
98A101ASP-1-0.783-0.88823.271-11.372-11.3720.0000.0000.0000.000
99A102THR00.0320.02123.2540.4570.4570.0000.0000.0000.000
100A103PRO0-0.021-0.01024.005-0.624-0.6240.0000.0000.0000.000
101A104TYR00.0180.01025.114-0.124-0.1240.0000.0000.0000.000
102A105ILE00.0050.01718.8190.0440.0440.0000.0000.0000.000
103A106PRO00.0050.01021.947-0.156-0.1560.0000.0000.0000.000
104A107PRO00.0360.01019.124-0.764-0.7640.0000.0000.0000.000
105A108ASP-1-0.839-0.90118.246-15.249-15.2490.0000.0000.0000.000
106A109LEU00.0030.01617.913-0.085-0.0850.0000.0000.0000.000
107A110ALA00.0600.01313.2080.0260.0260.0000.0000.0000.000
108A111ALA0-0.020-0.00615.295-0.376-0.3760.0000.0000.0000.000
109A112ARG10.8700.92116.65113.07513.0750.0000.0000.0000.000
110A113LEU00.0070.00417.0190.5500.5500.0000.0000.0000.000
111A114ASN00.015-0.00713.9300.0750.0750.0000.0000.0000.000
112A115HIS0-0.0270.00016.1640.5700.5700.0000.0000.0000.000
113A116GLN0-0.028-0.02819.2211.1681.1680.0000.0000.0000.000
114A117ARG10.9020.96814.89320.19020.1900.0000.0000.0000.000
115A118LYS10.8840.93519.40213.30613.3060.0000.0000.0000.000
116A119ASP-1-0.855-0.92719.104-14.968-14.9680.0000.0000.0000.000
117A120ALA0-0.0270.00819.107-0.454-0.4540.0000.0000.0000.000
118A121PRO00.0130.01416.737-1.101-1.1010.0000.0000.0000.000
119A122VAL00.020-0.01416.390-1.030-1.0300.0000.0000.0000.000
120A123VAL0-0.054-0.01317.9910.8300.8300.0000.0000.0000.000
121A124TRP0-0.076-0.03619.185-0.916-0.9160.0000.0000.0000.000
122A125VAL00.0380.02321.6020.3720.3720.0000.0000.0000.000
123A126HIS0-0.008-0.00123.9220.1150.1150.0000.0000.0000.000
124A127ASP-1-0.759-0.87327.700-10.535-10.5350.0000.0000.0000.000
125A128GLY00.005-0.00529.7120.2010.2010.0000.0000.0000.000
126A129GLU-1-0.988-0.97932.856-8.257-8.2570.0000.0000.0000.000
127A130ARG10.8200.89128.72010.80010.8000.0000.0000.0000.000
128A131ASP-1-0.833-0.90427.780-11.293-11.2930.0000.0000.0000.000
129A132HIS0-0.027-0.02925.049-0.056-0.0560.0000.0000.0000.000
130A133PRO0-0.012-0.01523.771-0.597-0.5970.0000.0000.0000.000
131A134THR0-0.034-0.03521.778-0.386-0.3860.0000.0000.0000.000
132A135ILE00.0150.01920.184-0.622-0.6220.0000.0000.0000.000
133A136ALA0-0.010-0.01018.6300.4280.4280.0000.0000.0000.000
134A137LEU0-0.0170.01412.086-1.022-1.0220.0000.0000.0000.000
135A138VAL0-0.004-0.01713.9081.3381.3380.0000.0000.0000.000
136A139ASN00.0450.02311.843-0.929-0.9290.0000.0000.0000.000
137A140ARG10.7990.8529.14328.90828.9080.0000.0000.0000.000
138A141ALA00.000-0.00412.4931.1481.1480.0000.0000.0000.000
139A142ILE0-0.021-0.00615.8191.3501.3500.0000.0000.0000.000
140A143GLU-1-0.818-0.89614.381-20.197-20.1970.0000.0000.0000.000
141A144PRO0-0.014-0.01717.1160.9020.9020.0000.0000.0000.000
142A145LEU00.0560.03920.2880.6700.6700.0000.0000.0000.000
143A146LEU0-0.022-0.01518.7930.7390.7390.0000.0000.0000.000
144A147LEU00.002-0.00321.1240.5250.5250.0000.0000.0000.000
145A148GLU-1-0.961-0.97522.848-11.176-11.1760.0000.0000.0000.000
146A149TYR0-0.010-0.03125.2020.7000.7000.0000.0000.0000.000
147A150LEU0-0.044-0.02923.1480.4910.4910.0000.0000.0000.000
148A151GLN0-0.033-0.01626.0300.3820.3820.0000.0000.0000.000
149A152ALA0-0.028-0.00228.6860.4140.4140.0000.0000.0000.000
150A153GLY0-0.0050.00930.2890.3700.3700.0000.0000.0000.000
151A154GLU-1-0.895-0.92229.497-9.389-9.3890.0000.0000.0000.000
152A155ARG10.9910.97328.8579.2489.2480.0000.0000.0000.000
153A156ARG10.7890.89528.8269.2979.2970.0000.0000.0000.000
154A157VAL00.1070.05124.142-0.016-0.0160.0000.0000.0000.000
155A158MET00.0540.02626.080-0.304-0.3040.0000.0000.0000.000
156A159VAL0-0.080-0.03328.2460.1180.1180.0000.0000.0000.000
157A160PHE00.0450.02720.6980.0010.0010.0000.0000.0000.000
158A161MET00.0270.01320.262-0.314-0.3140.0000.0000.0000.000
159A162ARG10.9310.96824.11110.14010.1400.0000.0000.0000.000
160A163LEU0-0.028-0.00526.3780.0770.0770.0000.0000.0000.000
161A164ALA0-0.005-0.00321.138-0.029-0.0290.0000.0000.0000.000
162A165GLY0-0.0080.00122.153-0.498-0.4980.0000.0000.0000.000
163A166GLY0-0.0050.00222.180-0.321-0.3210.0000.0000.0000.000
164A167HIS10.7410.84322.29114.30914.3090.0000.0000.0000.000
165A168ALA00.0600.04323.337-0.551-0.5510.0000.0000.0000.000
166A169VAL0-0.040-0.02021.5950.0400.0400.0000.0000.0000.000
167A170ASP-1-0.805-0.86924.762-10.779-10.7790.0000.0000.0000.000
168A171PHE00.020-0.00220.706-0.510-0.5100.0000.0000.0000.000
169A172SER00.0450.02427.0330.1750.1750.0000.0000.0000.000
170A173ASP-1-0.875-0.91428.255-11.247-11.2470.0000.0000.0000.000
171A174HIS10.7380.81824.00912.94712.9470.0000.0000.0000.000
172A175LYS10.8540.91029.0119.6579.6570.0000.0000.0000.000
173A176ASP-1-0.860-0.93130.809-9.718-9.7180.0000.0000.0000.000
174A177ALA0-0.027-0.01425.852-0.096-0.0960.0000.0000.0000.000
175A178PHE0-0.025-0.02322.774-0.598-0.5980.0000.0000.0000.000
176A179VAL00.0160.02327.6310.1360.1360.0000.0000.0000.000
177A180ASN0-0.102-0.07928.527-0.219-0.2190.0000.0000.0000.000
178A181VAL00.0120.01929.5560.3710.3710.0000.0000.0000.000
179A182ASN0-0.065-0.05231.228-0.318-0.3180.0000.0000.0000.000
180A183THR00.001-0.01333.365-0.040-0.0400.0000.0000.0000.000
181A184PRO00.033-0.00635.426-0.065-0.0650.0000.0000.0000.000
182A185GLU-1-0.950-0.95836.639-7.584-7.5840.0000.0000.0000.000
183A186GLU-1-0.853-0.91934.965-9.068-9.0680.0000.0000.0000.000
184A187LEU0-0.019-0.01332.115-0.055-0.0550.0000.0000.0000.000
185A188ALA0-0.0040.00035.270-0.002-0.0020.0000.0000.0000.000
186A189ARG10.9000.94438.6758.1158.1150.0000.0000.0000.000
187A190TRP0-0.086-0.03630.9430.1060.1060.0000.0000.0000.000
188A191GLN-1-0.841-0.90834.081-9.100-9.1000.0000.0000.0000.000