FMO DATABASE

FMODB ID: K8GL3

Calculation Name: 3JCU-j-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: j

ChEMBL ID:

UniProt ID: P12333

Base Structure: ElectronMicroscopy

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	34
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-96206.666928
FMO2-HF: Nuclear repulsion	84479.416951
FMO2-HF: Total energy	-11727.249977
FMO2-MP2: Total energy	-11762.793857

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLY)

Summations of interaction energy for fragment #1(A:6: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.
21.709	23.625	0.005	-0.751	-1.169	-0.003

Interaction energy analysis for fragmet #1(A:6:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.876 / q_NPA : 0.922

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

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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].
3	A	8	ILE	0	0.095	0.058	3.850	7.279	8.496	-0.006	-0.498	-0.713	-0.002
4	A	9	PRO	0	-0.012	-0.005	3.667	-9.381	-8.740	0.012	-0.247	-0.406	-0.001
5	A	10	LEU	0	0.065	0.028	4.779	6.247	6.305	-0.001	-0.006	-0.050	0.000
6	A	11	TRP	0	0.092	0.038	6.615	3.855	3.855	0.000	0.000	0.000	0.000
7	A	12	ILE	0	0.004	0.024	8.361	2.866	2.866	0.000	0.000	0.000	0.000
8	A	13	ILE	0	-0.004	-0.002	6.485	2.322	2.322	0.000	0.000	0.000	0.000
9	A	14	GLY	0	0.017	0.007	10.168	2.178	2.178	0.000	0.000	0.000	0.000
10	A	15	THR	0	-0.019	-0.019	12.416	2.052	2.052	0.000	0.000	0.000	0.000
11	A	16	VAL	0	-0.009	-0.009	13.382	1.388	1.388	0.000	0.000	0.000	0.000
12	A	17	ALA	0	0.013	0.006	14.245	1.241	1.241	0.000	0.000	0.000	0.000
13	A	18	GLY	0	0.029	0.018	16.026	1.092	1.092	0.000	0.000	0.000	0.000
14	A	19	ILE	0	-0.004	-0.008	17.725	0.959	0.959	0.000	0.000	0.000	0.000
15	A	20	LEU	0	-0.012	0.004	18.658	0.789	0.789	0.000	0.000	0.000	0.000
16	A	21	VAL	0	0.003	-0.002	19.846	0.769	0.769	0.000	0.000	0.000	0.000
17	A	22	ILE	0	0.001	-0.002	21.627	0.686	0.686	0.000	0.000	0.000	0.000
18	A	23	GLY	0	0.012	0.007	23.372	0.595	0.595	0.000	0.000	0.000	0.000
19	A	24	LEU	0	-0.039	-0.012	24.351	0.484	0.484	0.000	0.000	0.000	0.000
20	A	25	VAL	0	0.006	-0.001	26.147	0.461	0.461	0.000	0.000	0.000	0.000
21	A	26	GLY	0	0.010	0.010	27.684	0.434	0.434	0.000	0.000	0.000	0.000
22	A	27	ILE	0	-0.023	-0.015	28.612	0.403	0.403	0.000	0.000	0.000	0.000
23	A	28	PHE	0	-0.002	-0.007	28.520	0.314	0.314	0.000	0.000	0.000	0.000
24	A	29	PHE	0	0.001	-0.010	31.889	0.292	0.292	0.000	0.000	0.000	0.000
25	A	30	TYR	0	-0.004	-0.001	33.416	0.292	0.292	0.000	0.000	0.000	0.000
26	A	31	GLY	0	-0.006	-0.005	34.691	0.255	0.255	0.000	0.000	0.000	0.000
27	A	32	SER	0	-0.015	-0.001	36.529	0.177	0.177	0.000	0.000	0.000	0.000
28	A	33	TYR	0	-0.059	-0.029	37.177	0.264	0.264	0.000	0.000	0.000	0.000
29	A	34	SER	0	-0.037	-0.020	38.537	0.118	0.118	0.000	0.000	0.000	0.000
30	A	35	GLY	0	0.019	0.022	40.329	-0.124	-0.124	0.000	0.000	0.000	0.000
31	A	36	LEU	0	-0.021	-0.019	41.901	0.134	0.134	0.000	0.000	0.000	0.000
32	A	37	GLY	0	0.008	0.002	41.790	-0.153	-0.153	0.000	0.000	0.000	0.000
33	A	38	SER	0	-0.065	-0.026	41.921	0.020	0.020	0.000	0.000	0.000	0.000
34	A	39	SER	-1	-0.967	-0.973	43.624	-6.599	-6.599	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLY)