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: 4G76N

Calculation Name: 1VMA-A-Xray549

Preferred Name:

Target Type:

Ligand Name: citric acid

Ligand 3-letter code: CIT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VMA

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WZ40

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 294
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -4046994.322366
FMO2-HF: Nuclear repulsion 3936269.395859
FMO2-HF: Total energy -110724.926506
FMO2-MP2: Total energy -111053.393216


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.
-98.522-86.5159.605-8.345-13.267-0.076
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 : 0.809 / q_NPA : 0.905
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].
3A3LEU00.0260.0153.123-6.568-4.0680.065-1.259-1.306-0.004
5A5ASP-1-0.856-0.9262.287-79.408-73.9335.625-5.337-5.762-0.059
6A6PHE0-0.048-0.0262.7700.4653.0511.428-1.381-2.633-0.010
7A7LEU00.0580.0293.7203.9483.5300.0280.632-0.242-0.001
9A9LYS10.7790.8642.25732.45933.1872.288-0.595-2.422-0.002
10A10GLY0-0.011-0.0224.4282.5162.602-0.001-0.029-0.0560.000
272A272VAL0-0.043-0.0095.2801.4251.505-0.001-0.008-0.0710.000
280A280ARG10.8180.9082.57453.50354.4730.173-0.368-0.7750.000
4A4PHE00.1230.0495.814-0.234-0.2340.0000.0000.0000.000
8A8LYS10.9760.9955.25933.51333.5130.0000.0000.0000.000
11A11LEU00.0280.0127.8771.8691.8690.0000.0000.0000.000
12A12GLN0-0.042-0.0207.2791.3931.3930.0000.0000.0000.000
13A13LYS10.9090.9539.32021.06421.0640.0000.0000.0000.000
14A14THR00.0300.03412.2091.3691.3690.0000.0000.0000.000
15A15LYS10.8050.91411.10519.91219.9120.0000.0000.0000.000
16A16GLU-1-0.877-0.92911.482-17.743-17.7430.0000.0000.0000.000
17A17THR0-0.091-0.04415.0920.8980.8980.0000.0000.0000.000
18A18PHE00.0160.00317.3040.6720.6720.0000.0000.0000.000
19A19PHE00.0590.01216.3450.2540.2540.0000.0000.0000.000
20A20GLY00.0330.02417.2860.0700.0700.0000.0000.0000.000
21A21ARG10.8450.91718.27512.16612.1660.0000.0000.0000.000
22A22VAL00.0560.03420.9560.3590.3590.0000.0000.0000.000
23A23VAL00.0250.01518.1800.4180.4180.0000.0000.0000.000
24A24LYS10.8980.93821.54011.40711.4070.0000.0000.0000.000
25A25LEU0-0.0320.00023.7680.2730.2730.0000.0000.0000.000
26A26LEU00.0400.01724.8460.3480.3480.0000.0000.0000.000
27A27LYS10.8380.91322.50712.84912.8490.0000.0000.0000.000
28A28GLY0-0.053-0.02725.8280.2790.2790.0000.0000.0000.000
29A29LYS10.8480.93028.9709.9779.9770.0000.0000.0000.000
30A30LYS10.9510.97631.0718.4938.4930.0000.0000.0000.000
31A31LEU00.0430.01930.826-0.040-0.0400.0000.0000.0000.000
32A32ASP-1-0.869-0.89533.798-8.192-8.1920.0000.0000.0000.000
33A33ASP-1-0.817-0.92235.230-7.731-7.7310.0000.0000.0000.000
34A34GLU-1-0.925-0.94634.057-8.213-8.2130.0000.0000.0000.000
35A35THR0-0.070-0.06630.396-0.318-0.3180.0000.0000.0000.000
36A36ARG10.7600.87130.8277.6787.6780.0000.0000.0000.000
37A37GLU-1-0.829-0.91031.786-8.000-8.0000.0000.0000.0000.000
38A38GLU-1-0.946-0.98129.102-9.673-9.6730.0000.0000.0000.000
39A39LEU0-0.059-0.03625.532-0.442-0.4420.0000.0000.0000.000
40A40GLU-1-0.912-0.95427.267-8.989-8.9890.0000.0000.0000.000
41A41GLU-1-0.950-0.97328.396-9.449-9.4490.0000.0000.0000.000
42A42LEU0-0.059-0.04223.406-0.435-0.4350.0000.0000.0000.000
43A43LEU0-0.015-0.01122.850-0.577-0.5770.0000.0000.0000.000
44A44ILE0-0.018-0.00224.317-0.263-0.2630.0000.0000.0000.000
45A45GLN0-0.024-0.01124.0080.0180.0180.0000.0000.0000.000
46A46ALA0-0.045-0.01719.963-0.356-0.3560.0000.0000.0000.000
47A47ASP-1-0.858-0.95320.529-12.317-12.3170.0000.0000.0000.000
48A48VAL0-0.024-0.00321.737-0.243-0.2430.0000.0000.0000.000
49A49GLY00.0230.01123.6480.1090.1090.0000.0000.0000.000
50A50VAL00.0170.00327.038-0.008-0.0080.0000.0000.0000.000
51A51GLU-1-0.843-0.90430.616-9.364-9.3640.0000.0000.0000.000
52A52THR0-0.019-0.02525.3470.1340.1340.0000.0000.0000.000
53A53THR0-0.016-0.00727.377-0.284-0.2840.0000.0000.0000.000
54A54GLU-1-0.847-0.92028.549-8.520-8.5200.0000.0000.0000.000
55A55TYR0-0.010-0.01028.1840.0850.0850.0000.0000.0000.000
56A56ILE0-0.041-0.03524.909-0.149-0.1490.0000.0000.0000.000
57A57LEU0-0.0030.00929.191-0.086-0.0860.0000.0000.0000.000
58A58GLU-1-0.874-0.93931.968-8.373-8.3730.0000.0000.0000.000
59A59ARG10.7390.83530.0919.7609.7600.0000.0000.0000.000
60A60LEU0-0.062-0.03827.906-0.158-0.1580.0000.0000.0000.000
61A61GLU-1-0.899-0.95932.041-8.267-8.2670.0000.0000.0000.000
62A62GLU-1-0.970-0.96434.800-8.415-8.4150.0000.0000.0000.000
63A63LYS10.7700.88328.95410.32110.3210.0000.0000.0000.000
64A64ASP-1-0.910-0.94934.870-8.299-8.2990.0000.0000.0000.000
65A65GLY0-0.036-0.02232.8570.0630.0630.0000.0000.0000.000
66A66ASP-1-0.861-0.93126.977-11.189-11.1890.0000.0000.0000.000
67A67ALA00.0940.04328.914-0.174-0.1740.0000.0000.0000.000
68A68LEU0-0.023-0.00121.167-0.240-0.2400.0000.0000.0000.000
69A69GLU-1-0.860-0.91923.343-13.762-13.7620.0000.0000.0000.000
70A70SER00.000-0.00425.249-0.074-0.0740.0000.0000.0000.000
71A71LEU00.0320.01622.9090.0130.0130.0000.0000.0000.000
72A72LYS10.8050.87019.44614.06014.0600.0000.0000.0000.000
73A73GLU-1-0.862-0.91722.212-11.180-11.1800.0000.0000.0000.000
74A74ILE00.0130.02424.772-0.122-0.1220.0000.0000.0000.000
75A75ILE0-0.014-0.02219.755-0.114-0.1140.0000.0000.0000.000
76A76LEU0-0.013-0.00219.105-0.333-0.3330.0000.0000.0000.000
77A77GLU-1-0.848-0.91721.602-10.564-10.5640.0000.0000.0000.000
78A78ILE0-0.067-0.03122.8170.1430.1430.0000.0000.0000.000
79A79LEU0-0.046-0.03117.571-0.222-0.2220.0000.0000.0000.000
80A80ASN0-0.0280.01420.610-0.772-0.7720.0000.0000.0000.000
81A81PHE0-0.009-0.00618.7710.6090.6090.0000.0000.0000.000
82A82ASP-1-0.847-0.93421.532-13.660-13.6600.0000.0000.0000.000
83A83THR00.004-0.00616.9270.3510.3510.0000.0000.0000.000
84A84LYS10.8660.94318.83912.41912.4190.0000.0000.0000.000
85A85LEU00.0110.00718.7590.4710.4710.0000.0000.0000.000
86A86ASN0-0.030-0.02422.027-0.025-0.0250.0000.0000.0000.000
87A87VAL0-0.045-0.02423.2580.3170.3170.0000.0000.0000.000
88A88PRO0-0.0230.00026.2220.2130.2130.0000.0000.0000.000
89A89PRO0-0.018-0.01829.308-0.237-0.2370.0000.0000.0000.000
90A90GLU-1-0.900-0.95031.649-9.155-9.1550.0000.0000.0000.000
91A91PRO0-0.0540.00629.095-0.164-0.1640.0000.0000.0000.000
92A92PRO0-0.043-0.03029.2280.3650.3650.0000.0000.0000.000
93A93PHE00.020-0.01122.1270.2330.2330.0000.0000.0000.000
94A94VAL0-0.052-0.03326.598-0.208-0.2080.0000.0000.0000.000
95A95ILE00.0320.01921.4480.0490.0490.0000.0000.0000.000
96A96MET0-0.077-0.03025.4410.2750.2750.0000.0000.0000.000
97A97VAL00.0330.02021.451-0.202-0.2020.0000.0000.0000.000
98A98VAL0-0.0160.00424.3940.4090.4090.0000.0000.0000.000
99A99GLY00.1100.05024.389-0.530-0.5300.0000.0000.0000.000
100A100VAL0-0.031-0.01125.2120.3290.3290.0000.0000.0000.000
101A101ASN00.010-0.00124.602-0.639-0.6390.0000.0000.0000.000
102A102GLY00.0020.00222.6630.0960.0960.0000.0000.0000.000
103A103THR00.0170.00720.246-0.626-0.6260.0000.0000.0000.000
104A104GLY00.0310.02017.924-0.766-0.7660.0000.0000.0000.000
105A105LYS10.8380.94218.54410.67710.6770.0000.0000.0000.000
106A106THR00.0300.00520.245-0.416-0.4160.0000.0000.0000.000
107A107THR0-0.029-0.01414.9660.0680.0680.0000.0000.0000.000
108A108SER00.000-0.00615.897-1.124-1.1240.0000.0000.0000.000
109A109CYS0-0.037-0.01316.978-0.225-0.2250.0000.0000.0000.000
110A110GLY00.0440.01617.884-0.017-0.0170.0000.0000.0000.000
111A111LYS10.8130.91610.07323.86723.8670.0000.0000.0000.000
112A112LEU00.0030.00814.223-0.733-0.7330.0000.0000.0000.000
113A113ALA00.0060.00016.4380.0550.0550.0000.0000.0000.000
114A114LYS10.8070.88510.48924.40624.4060.0000.0000.0000.000
115A115MET0-0.0100.00613.080-0.729-0.7290.0000.0000.0000.000
116A116PHE00.025-0.00314.3150.2940.2940.0000.0000.0000.000
117A117VAL0-0.0020.00417.4530.5350.5350.0000.0000.0000.000
118A118ASP-1-0.851-0.89611.979-23.420-23.4200.0000.0000.0000.000
119A119GLU-1-0.987-0.99015.166-18.288-18.2880.0000.0000.0000.000
120A120GLY0-0.032-0.01117.2300.9170.9170.0000.0000.0000.000
121A121LYS10.8580.93820.02014.22814.2280.0000.0000.0000.000
122A122SER0-0.005-0.03721.698-0.105-0.1050.0000.0000.0000.000
123A123VAL00.0380.00820.7210.2750.2750.0000.0000.0000.000
124A124VAL0-0.069-0.03824.1860.3750.3750.0000.0000.0000.000
125A125LEU00.0210.02221.267-0.203-0.2030.0000.0000.0000.000
126A126ALA00.010-0.01025.3990.4170.4170.0000.0000.0000.000
127A127ALA00.017-0.00427.849-0.207-0.2070.0000.0000.0000.000
128A128ALA00.008-0.00229.2060.3790.3790.0000.0000.0000.000
129A129ASP-1-0.804-0.88128.283-10.194-10.1940.0000.0000.0000.000
130A130THR0-0.011-0.02730.469-0.095-0.0950.0000.0000.0000.000
131A131PHE0-0.027-0.00133.6300.1300.1300.0000.0000.0000.000
132A132ARG10.8100.88425.78310.84610.8460.0000.0000.0000.000
133A133ALA00.0880.04230.448-0.299-0.2990.0000.0000.0000.000
134A134ALA00.001-0.00127.751-0.213-0.2130.0000.0000.0000.000
135A135ALA0-0.010-0.00225.946-0.440-0.4400.0000.0000.0000.000
136A136ILE00.0040.00426.170-0.368-0.3680.0000.0000.0000.000
137A137GLU-1-0.823-0.89927.637-10.397-10.3970.0000.0000.0000.000
138A138GLN0-0.014-0.00622.037-0.786-0.7860.0000.0000.0000.000
139A139LEU0-0.0090.00022.506-0.636-0.6360.0000.0000.0000.000
140A140LYS10.8490.92023.6479.7039.7030.0000.0000.0000.000
141A141ILE00.0260.01920.887-0.347-0.3470.0000.0000.0000.000
142A142TRP0-0.014-0.02513.864-0.951-0.9510.0000.0000.0000.000
143A143GLY00.0210.00219.904-0.560-0.5600.0000.0000.0000.000
144A144GLU-1-0.936-0.97422.215-11.826-11.8260.0000.0000.0000.000
145A145ARG10.8190.92114.08118.52118.5210.0000.0000.0000.000
146A146VAL0-0.052-0.01916.346-1.068-1.0680.0000.0000.0000.000
147A147GLY00.0290.03218.588-0.211-0.2110.0000.0000.0000.000
148A148ALA0-0.043-0.01721.4720.2620.2620.0000.0000.0000.000
149A149THR0-0.037-0.02223.1730.2990.2990.0000.0000.0000.000
150A150VAL00.0350.02025.232-0.092-0.0920.0000.0000.0000.000
151A151ILE0-0.037-0.00527.7920.3750.3750.0000.0000.0000.000
152A152SER00.003-0.03130.513-0.269-0.2690.0000.0000.0000.000
153A153HIS0-0.064-0.02532.5600.2160.2160.0000.0000.0000.000
154A154SER00.0090.00534.736-0.196-0.1960.0000.0000.0000.000
155A155GLU-1-0.886-0.96735.120-8.336-8.3360.0000.0000.0000.000
156A156GLY00.0260.02236.3990.2280.2280.0000.0000.0000.000
157A157ALA0-0.0170.00836.8580.1880.1880.0000.0000.0000.000
158A158ASP-1-0.768-0.87537.823-7.922-7.9220.0000.0000.0000.000
159A159PRO00.0360.01833.785-0.063-0.0630.0000.0000.0000.000
160A160ALA0-0.039-0.03534.485-0.186-0.1860.0000.0000.0000.000
161A161ALA0-0.0010.00436.7950.0130.0130.0000.0000.0000.000
162A162VAL00.0410.03031.866-0.047-0.0470.0000.0000.0000.000
163A163ALA00.0130.00532.212-0.204-0.2040.0000.0000.0000.000
164A164PHE0-0.060-0.02933.230-0.051-0.0510.0000.0000.0000.000
165A165ASP-1-0.824-0.91035.635-8.266-8.2660.0000.0000.0000.000
166A166ALA0-0.027-0.01330.331-0.071-0.0710.0000.0000.0000.000
167A167VAL00.0190.00631.275-0.159-0.1590.0000.0000.0000.000
168A168ALA0-0.015-0.00733.1770.0570.0570.0000.0000.0000.000
169A169HIS0-0.019-0.01331.8690.2860.2860.0000.0000.0000.000
170A170ALA00.005-0.00530.547-0.015-0.0150.0000.0000.0000.000
171A171LEU00.0250.02032.232-0.019-0.0190.0000.0000.0000.000
172A172ALA0-0.030-0.01434.9720.0930.0930.0000.0000.0000.000
173A173ARG10.8310.90933.1618.6608.6600.0000.0000.0000.000
174A174ASN0-0.0170.00732.309-0.049-0.0490.0000.0000.0000.000
175A175LYS10.8840.95026.79611.11211.1120.0000.0000.0000.000
176A176ASP-1-0.767-0.86124.873-11.970-11.9700.0000.0000.0000.000
177A177VAL0-0.0060.00422.3590.0740.0740.0000.0000.0000.000
178A178VAL0-0.045-0.02725.5300.1860.1860.0000.0000.0000.000
179A179ILE00.0170.01720.339-0.129-0.1290.0000.0000.0000.000
180A180ILE0-0.028-0.01924.6060.2180.2180.0000.0000.0000.000
181A181ASP-1-0.732-0.85724.258-12.533-12.5330.0000.0000.0000.000
182A182THR0-0.043-0.04125.8160.5790.5790.0000.0000.0000.000
183A183ALA00.0700.04227.982-0.246-0.2460.0000.0000.0000.000
184A184GLY00.0330.00528.124-0.126-0.1260.0000.0000.0000.000
185A185ARG10.9020.94729.1808.1278.1270.0000.0000.0000.000
186A186LEU00.0660.02729.7110.2050.2050.0000.0000.0000.000
187A187HIS0-0.052-0.02532.5280.2060.2060.0000.0000.0000.000
188A188THR0-0.0010.00535.8300.2350.2350.0000.0000.0000.000
189A189LYS10.9290.95435.8188.1248.1240.0000.0000.0000.000
190A190LYS10.9930.99737.0716.8476.8470.0000.0000.0000.000
191A191ASN00.0130.01037.5830.1570.1570.0000.0000.0000.000
192A192LEU00.0250.01631.101-0.009-0.0090.0000.0000.0000.000
193A193MET00.0070.01835.125-0.186-0.1860.0000.0000.0000.000
194A194GLU-1-0.850-0.94636.528-7.538-7.5380.0000.0000.0000.000
195A195GLU-1-0.942-0.97634.102-8.831-8.8310.0000.0000.0000.000
196A196LEU00.0240.00630.704-0.069-0.0690.0000.0000.0000.000
197A197ARG10.8640.91234.0877.9197.9190.0000.0000.0000.000
198A198LYS10.7380.87036.8737.9027.9020.0000.0000.0000.000
199A199VAL00.002-0.01031.5760.0810.0810.0000.0000.0000.000
200A200HIS00.0320.00231.4460.1800.1800.0000.0000.0000.000
201A201ARG10.9550.98334.1397.6947.6940.0000.0000.0000.000
202A202VAL0-0.082-0.03136.0070.1970.1970.0000.0000.0000.000
203A203VAL00.0530.02032.7060.1610.1610.0000.0000.0000.000
204A204LYS10.8700.95134.7938.9048.9040.0000.0000.0000.000
205A205LYS10.8990.96238.0477.6047.6040.0000.0000.0000.000
206A206LYS10.8040.90136.7337.9597.9590.0000.0000.0000.000
207A207ILE00.0910.04233.2090.0750.0750.0000.0000.0000.000
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