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

tag_button

FMODB ID: QLJVY

Calculation Name: 3JCU-S-Other547

Preferred Name:

Target Type:

Ligand Name: chlorophyll a | chlorophyll b | pheophytin a | protoporphyrin ix containing fe | digalactosyl diacyl glycerol (dgdg) | 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone | (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol | (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol | (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | ca-mn4-o5 cluster | bicarbonate ion | fe (ii) ion

Ligand 3-letter code: CLA | CHL | PHO | HEM | DGD | PL9 | XAT | NEX | LUT | SQD | BCR | LMG | LHG | OEX | BCT | FE2

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JCU

Chain ID: S

ChEMBL ID:

UniProt ID: P12333

Base Structure: ElectronMicroscopy

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 214
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2084769.206257
FMO2-HF: Nuclear repulsion 2003831.456595
FMO2-HF: Total energy -80937.749662
FMO2-MP2: Total energy -81176.409223


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:23:LEU)


Summations of interaction energy for fragment #1(A:23:LEU)
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.
-144.368-140.99314.274-3.004-14.645-0.14
Interaction energy analysis for fragmet #1(A:23:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.808 / q_NPA : 0.949
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].
3A25LYS10.9920.9782.57646.88241.1040.4337.228-1.883-0.016
4A26TRP0-0.071-0.0462.085-0.1340.6973.919-2.232-2.517-0.022
5A27TYR00.0530.0282.382-8.827-5.1061.333-2.223-2.831-0.025
6A28GLY00.0480.0324.8710.6220.635-0.001-0.002-0.0100.000
158A180ASP-1-0.830-0.9532.519-87.052-82.4134.432-3.981-5.090-0.052
159A181GLN0-0.034-0.0164.449-3.027-2.939-0.001-0.008-0.0790.000
162A184LEU0-0.023-0.0261.788-5.964-6.1664.161-1.784-2.176-0.025
163A185LEU0-0.050-0.0225.2723.6773.685-0.0010.000-0.0070.000
165A187VAL0-0.003-0.0014.5202.1822.237-0.001-0.002-0.0520.000
7A29PRO00.021-0.0047.695-0.190-0.1900.0000.0000.0000.000
8A30ASP-1-0.877-0.9327.377-26.451-26.4510.0000.0000.0000.000
9A31ARG10.7140.8676.29923.44423.4440.0000.0000.0000.000
10A32ARG10.8890.9397.01333.97033.9700.0000.0000.0000.000
11A33ILE00.0860.0459.111-0.796-0.7960.0000.0000.0000.000
12A34PHE0-0.007-0.01412.4510.4100.4100.0000.0000.0000.000
13A35LEU0-0.008-0.01415.2410.8440.8440.0000.0000.0000.000
14A36PRO0-0.077-0.02013.1330.2520.2520.0000.0000.0000.000
15A37ASP-1-0.801-0.90115.041-20.393-20.3930.0000.0000.0000.000
16A38GLY0-0.040-0.01617.5930.4710.4710.0000.0000.0000.000
17A39LEU0-0.058-0.04220.4750.7290.7290.0000.0000.0000.000
18A40LEU0-0.051-0.01516.4880.4090.4090.0000.0000.0000.000
19A41ASP-1-0.934-0.97519.492-15.042-15.0420.0000.0000.0000.000
20A42ARG10.8330.92112.31920.98820.9880.0000.0000.0000.000
21A43ASP-1-0.873-0.92318.228-12.947-12.9470.0000.0000.0000.000
22A44ASP-1-0.923-0.98116.805-17.386-17.3860.0000.0000.0000.000
23A45ILE0-0.046-0.01720.5110.2250.2250.0000.0000.0000.000
24A46PRO0-0.0090.02216.0720.3020.3020.0000.0000.0000.000
25A47GLU-1-0.982-1.00016.524-18.442-18.4420.0000.0000.0000.000
26A48TYR0-0.064-0.05418.6771.0411.0410.0000.0000.0000.000
27A49LEU0-0.0120.02214.873-0.307-0.3070.0000.0000.0000.000
28A50ASN00.0380.02613.476-1.095-1.0950.0000.0000.0000.000
29A51GLY00.013-0.0029.510-0.838-0.8380.0000.0000.0000.000
30A52GLU-1-0.937-0.9767.882-35.968-35.9680.0000.0000.0000.000
31A53VAL0-0.037-0.0118.583-1.577-1.5770.0000.0000.0000.000
32A54PRO0-0.031-0.0206.827-2.770-2.7700.0000.0000.0000.000
33A55GLY00.0260.0006.9372.9442.9440.0000.0000.0000.000
34A56ASP-1-0.776-0.8638.751-20.784-20.7840.0000.0000.0000.000
35A57TYR-1-0.904-0.9439.373-32.556-32.5560.0000.0000.0000.000
36A58GLY00.1070.03411.9691.1211.1210.0000.0000.0000.000
37A59TYR0-0.082-0.04114.8771.4661.4660.0000.0000.0000.000
38A60ASP-1-0.825-0.93316.918-14.504-14.5040.0000.0000.0000.000
39A61PRO0-0.036-0.00919.8760.4050.4050.0000.0000.0000.000
40A62PHE0-0.039-0.02222.6930.6730.6730.0000.0000.0000.000
41A63GLY0-0.0140.01423.4240.5260.5260.0000.0000.0000.000
42A64LEU0-0.112-0.05624.3540.2130.2130.0000.0000.0000.000
43A65GLY00.1500.07621.297-0.093-0.0930.0000.0000.0000.000
44A66LYS10.8870.93922.33410.97510.9750.0000.0000.0000.000
45A67LYS10.9410.98524.39211.01311.0130.0000.0000.0000.000
46A68PRO00.0870.04020.222-0.302-0.3020.0000.0000.0000.000
47A69GLU-1-0.896-0.95620.248-12.573-12.5730.0000.0000.0000.000
48A70ASP-1-0.894-0.94922.664-11.792-11.7920.0000.0000.0000.000
49A71PHE00.0560.03114.6870.0130.0130.0000.0000.0000.000
50A72ALA00.0280.01618.132-0.620-0.6200.0000.0000.0000.000
51A73LYS10.8830.93419.18311.61111.6110.0000.0000.0000.000
52A74TYR00.000-0.01020.6490.2970.2970.0000.0000.0000.000
53A75GLN00.0230.01613.551-1.249-1.2490.0000.0000.0000.000
54A76ALA00.0110.00617.567-0.414-0.4140.0000.0000.0000.000
55A77PHE0-0.034-0.03019.6990.2220.2220.0000.0000.0000.000
56A78GLU-1-0.822-0.87216.388-18.781-18.7810.0000.0000.0000.000
57A79LEU00.010-0.00414.138-0.164-0.1640.0000.0000.0000.000
58A80ILE0-0.018-0.00717.5150.1860.1860.0000.0000.0000.000
59A81HIS00.014-0.00121.1470.2660.2660.0000.0000.0000.000
60A82ALA0-0.0120.00517.0000.2050.2050.0000.0000.0000.000
61A83ARG10.8550.89816.18817.96817.9680.0000.0000.0000.000
62A84TRP00.018-0.00119.9290.4160.4160.0000.0000.0000.000
63A85ALA00.0050.01221.5600.5210.5210.0000.0000.0000.000
64A86MET0-0.023-0.00716.495-0.003-0.0030.0000.0000.0000.000
65A87LEU0-0.022-0.00121.7050.4250.4250.0000.0000.0000.000
66A88GLY00.0140.01324.7690.4980.4980.0000.0000.0000.000
67A89ALA00.0560.00623.6740.4430.4430.0000.0000.0000.000
68A90ALA0-0.017-0.00824.3520.3180.3180.0000.0000.0000.000
69A91GLY0-0.001-0.00426.1730.4150.4150.0000.0000.0000.000
70A92CYS0-0.081-0.05229.0160.5180.5180.0000.0000.0000.000
71A93VAL00.0020.01027.3600.2800.2800.0000.0000.0000.000
72A94ILE0-0.013-0.01128.0300.2800.2800.0000.0000.0000.000
73A95PRO0-0.003-0.00430.5910.2270.2270.0000.0000.0000.000
74A96GLU-1-0.708-0.86233.766-9.002-9.0020.0000.0000.0000.000
75A97ALA0-0.051-0.02731.2650.1420.1420.0000.0000.0000.000
76A98PHE0-0.063-0.03931.7010.0360.0360.0000.0000.0000.000
77A99ASN00.0260.00435.8600.3330.3330.0000.0000.0000.000
78A100LYS10.9200.98134.5569.1669.1660.0000.0000.0000.000
79A101PHE0-0.078-0.04537.2360.1680.1680.0000.0000.0000.000
80A102GLY00.0040.02240.4970.0050.0050.0000.0000.0000.000
81A103ALA0-0.0050.00040.239-0.110-0.1100.0000.0000.0000.000
82A104ASN0-0.100-0.04535.6140.0810.0810.0000.0000.0000.000
83A105CYS00.045-0.00237.664-0.237-0.2370.0000.0000.0000.000
84A106GLY0-0.0030.03440.1340.0900.0900.0000.0000.0000.000
85A107PRO00.036-0.01341.9560.1340.1340.0000.0000.0000.000
86A108GLU-1-0.842-0.93141.623-7.701-7.7010.0000.0000.0000.000
87A109ALA0-0.043-0.02436.668-0.048-0.0480.0000.0000.0000.000
88A110VAL00.0300.02536.490-0.078-0.0780.0000.0000.0000.000
89A111TRP00.0340.01732.7660.2150.2150.0000.0000.0000.000
90A112PHE0-0.011-0.00235.4400.1490.1490.0000.0000.0000.000
91A113LYS10.9250.96237.2707.8957.8950.0000.0000.0000.000
92A114THR00.005-0.00136.2930.1630.1630.0000.0000.0000.000
93A115GLY0-0.0040.00039.6090.0330.0330.0000.0000.0000.000
94A116ALA0-0.019-0.01340.9680.1490.1490.0000.0000.0000.000
95A117LEU0-0.0330.00140.9720.1610.1610.0000.0000.0000.000
96A118LEU0-0.034-0.01641.5360.1350.1350.0000.0000.0000.000
97A119LEU0-0.043-0.00545.7960.0240.0240.0000.0000.0000.000
98A120ASP-1-0.955-0.98047.814-6.299-6.2990.0000.0000.0000.000
99A121GLY0-0.012-0.00249.2070.0820.0820.0000.0000.0000.000
100A122ASN0-0.039-0.02846.733-0.086-0.0860.0000.0000.0000.000
101A123THR00.0640.03140.882-0.036-0.0360.0000.0000.0000.000
102A124LEU0-0.0420.00042.9150.0770.0770.0000.0000.0000.000
103A125ASN00.0060.00237.065-0.120-0.1200.0000.0000.0000.000
104A126TYR00.1170.06839.9960.0640.0640.0000.0000.0000.000
105A127PHE0-0.043-0.03239.4650.0650.0650.0000.0000.0000.000
106A128GLY00.0460.02344.6140.1740.1740.0000.0000.0000.000
107A129LYS10.9010.94145.1616.8466.8460.0000.0000.0000.000
108A130ASN0-0.019-0.01341.820-0.131-0.1310.0000.0000.0000.000
109A131ILE0-0.035-0.01042.2110.1580.1580.0000.0000.0000.000
110A132PRO0-0.048-0.00144.9720.1510.1510.0000.0000.0000.000
111A133ILE0-0.020-0.03142.2390.1100.1100.0000.0000.0000.000
112A134ASN00.1440.06744.464-0.192-0.1920.0000.0000.0000.000
113A135LEU00.0550.00343.512-0.090-0.0900.0000.0000.0000.000
114A136VAL0-0.029-0.00544.286-0.081-0.0810.0000.0000.0000.000
115A137LEU0-0.015-0.01043.3470.0270.0270.0000.0000.0000.000
116A138ALA00.0210.02240.269-0.156-0.1560.0000.0000.0000.000
117A139VAL00.0700.03639.644-0.179-0.1790.0000.0000.0000.000
118A140VAL0-0.024-0.00440.152-0.119-0.1190.0000.0000.0000.000
119A141ALA0-0.001-0.00438.415-0.122-0.1220.0000.0000.0000.000
120A142GLU-1-0.916-0.95735.598-8.838-8.8380.0000.0000.0000.000
121A143VAL0-0.005-0.01435.579-0.242-0.2420.0000.0000.0000.000
122A144VAL0-0.044-0.02237.124-0.105-0.1050.0000.0000.0000.000
123A145LEU0-0.033-0.01834.026-0.141-0.1410.0000.0000.0000.000
124A146LEU00.0030.01229.238-0.297-0.2970.0000.0000.0000.000
125A147GLY00.0360.01131.988-0.223-0.2230.0000.0000.0000.000
126A148GLY00.0130.00333.929-0.057-0.0570.0000.0000.0000.000
127A149ALA0-0.006-0.01129.468-0.137-0.1370.0000.0000.0000.000
128A150GLU-1-0.877-0.92528.033-11.641-11.6410.0000.0000.0000.000
129A151TYR00.0110.00829.930-0.143-0.1430.0000.0000.0000.000
130A152TYR0-0.0250.00529.9210.1260.1260.0000.0000.0000.000
131A153ARG10.8320.90224.54912.00512.0050.0000.0000.0000.000
132A154ILE0-0.044-0.02026.673-0.440-0.4400.0000.0000.0000.000
133A155THR0-0.073-0.04328.9200.2270.2270.0000.0000.0000.000
134A156ASN0-0.038-0.03129.628-0.480-0.4800.0000.0000.0000.000
135A157GLY00.0560.03826.827-0.127-0.1270.0000.0000.0000.000
136A158LEU0-0.104-0.04523.9400.0600.0600.0000.0000.0000.000
137A159ASP-1-0.873-0.93520.015-14.841-14.8410.0000.0000.0000.000
138A160PHE00.004-0.01915.6700.3550.3550.0000.0000.0000.000
139A161GLU-1-0.908-0.95620.076-13.728-13.7280.0000.0000.0000.000
140A162ASP-1-0.898-0.95717.215-17.197-17.1970.0000.0000.0000.000
141A163LYS10.7890.92820.28013.96113.9610.0000.0000.0000.000
142A164LEU00.0110.03415.528-0.470-0.4700.0000.0000.0000.000
143A165HIS0-0.074-0.07113.1500.8180.8180.0000.0000.0000.000
144A166PRO00.0730.04616.669-0.531-0.5310.0000.0000.0000.000
145A167GLY00.0500.01517.535-1.068-1.0680.0000.0000.0000.000
146A168GLY00.0200.00818.8930.8740.8740.0000.0000.0000.000
147A169PRO0-0.015-0.02220.924-0.257-0.2570.0000.0000.0000.000
148A170PHE0-0.031-0.01120.7470.3540.3540.0000.0000.0000.000
149A171ASP-1-0.851-0.92816.053-19.956-19.9560.0000.0000.0000.000
150A172PRO0-0.0280.01019.6060.0680.0680.0000.0000.0000.000
151A173LEU00.057-0.01220.0270.1100.1100.0000.0000.0000.000
152A174GLY0-0.084-0.01816.703-0.059-0.0590.0000.0000.0000.000
153A175LEU0-0.0020.00213.786-1.214-1.2140.0000.0000.0000.000
154A176ALA00.0470.04212.975-1.899-1.8990.0000.0000.0000.000
155A177LYS10.7910.89110.92720.98320.9830.0000.0000.0000.000
156A178ASP-1-0.841-0.9049.135-26.594-26.5940.0000.0000.0000.000
157A179PRO0-0.022-0.0275.2020.5500.5500.0000.0000.0000.000
160A182ALA00.1070.0617.510-0.959-0.9590.0000.0000.0000.000
161A183ALA0-0.0040.0014.8131.0811.0810.0000.0000.0000.000
164A186LYS10.9921.0088.38129.22929.2290.0000.0000.0000.000
166A188LYS10.9210.9517.22737.09037.0900.0000.0000.0000.000
167A189GLU-1-0.823-0.8749.849-18.067-18.0670.0000.0000.0000.000
168A190ILE00.0440.02410.1121.7401.7400.0000.0000.0000.000
169A191LYS10.8280.9238.63331.14731.1470.0000.0000.0000.000
170A192ASN0-0.057-0.04712.4362.4972.4970.0000.0000.0000.000
171A193GLY00.0650.02515.3541.2961.2960.0000.0000.0000.000
172A194ARG10.7990.85712.16723.11423.1140.0000.0000.0000.000
173A195LEU0-0.0020.00716.5050.9910.9910.0000.0000.0000.000
174A196ALA00.0050.01818.2921.0341.0340.0000.0000.0000.000
175A197MET00.003-0.00318.5431.0281.0280.0000.0000.0000.000
176A198PHE0-0.027-0.00120.7130.7440.7440.0000.0000.0000.000
177A199SER0-0.020-0.02721.9850.6960.6960.0000.0000.0000.000
178A200MET0-0.0190.00324.3140.5720.5720.0000.0000.0000.000
179A201PHE00.0040.00725.6360.5620.5620.0000.0000.0000.000
180A202ALA00.0110.00226.5250.5010.5010.0000.0000.0000.000
181A203PHE0-0.014-0.02426.7730.4170.4170.0000.0000.0000.000
182A204PHE0-0.017-0.01228.8300.3850.3850.0000.0000.0000.000
183A205ILE00.0150.01230.7580.3800.3800.0000.0000.0000.000
184A206GLN00.011-0.00330.0780.3240.3240.0000.0000.0000.000
185A207ALA00.0130.04033.9350.2410.2410.0000.0000.0000.000
186A208TYR0-0.078-0.03135.8330.3340.3340.0000.0000.0000.000
187A209VAL0-0.028-0.01336.8500.2200.2200.0000.0000.0000.000
188A210THR00.009-0.02336.0770.2220.2220.0000.0000.0000.000
189A211GLY0-0.0080.00739.1450.2160.2160.0000.0000.0000.000
190A212GLN0-0.049-0.03138.0230.1200.1200.0000.0000.0000.000
191A213GLY00.0150.00835.251-0.178-0.1780.0000.0000.0000.000
192A214PRO0-0.009-0.00330.1570.0570.0570.0000.0000.0000.000
193A215VAL0-0.019-0.01431.290-0.180-0.1800.0000.0000.0000.000
194A216GLU-1-0.890-0.95433.249-8.267-8.2670.0000.0000.0000.000
195A217ASN0-0.037-0.02233.5070.2930.2930.0000.0000.0000.000
196A218LEU0-0.031-0.01329.335-0.007-0.0070.0000.0000.0000.000
197A219SER0-0.037-0.03132.9430.0040.0040.0000.0000.0000.000
198A220ALA00.0020.01136.1840.1640.1640.0000.0000.0000.000
199A221HIS00.0410.01732.1710.2130.2130.0000.0000.0000.000
200A222LEU0-0.071-0.05231.494-0.111-0.1110.0000.0000.0000.000
201A223SER0-0.082-0.02235.4710.1170.1170.0000.0000.0000.000
202A224ASP-1-0.885-0.93039.134-7.515-7.5150.0000.0000.0000.000
203A225PRO00.0020.01534.6410.0140.0140.0000.0000.0000.000
204A226PHE0-0.055-0.04036.211-0.148-0.1480.0000.0000.0000.000
205A227GLY0-0.0110.00239.0510.1340.1340.0000.0000.0000.000
206A228ASN00.003-0.00839.2740.0450.0450.0000.0000.0000.000
207A229ASN00.0350.02035.162-0.190-0.1900.0000.0000.0000.000
208A230LEU00.0310.02033.2360.1910.1910.0000.0000.0000.000
209A231LEU0-0.027-0.02635.8190.1430.1430.0000.0000.0000.000
210A232THR0-0.072-0.03938.9020.2250.2250.0000.0000.0000.000
211A233VAL00.010-0.00238.6200.1420.1420.0000.0000.0000.000
212A234ILE0-0.069-0.02639.4430.0550.0550.0000.0000.0000.000
213A235GLY0-0.033-0.01541.3880.1170.1170.0000.0000.0000.000
214A236GLY-1-0.963-0.96744.811-6.545-6.5450.0000.0000.0000.000