FMO DATABASE

FMODB ID: 3M8JL

Calculation Name: 3JCU-k-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: k

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	37
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-131663.222733
FMO2-HF: Nuclear repulsion	117080.540043
FMO2-HF: Total energy	-14582.68269
FMO2-MP2: Total energy	-14626.204932

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:23:LYS)

Summations of interaction energy for fragment #1(A:23:LYS)

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.
-107.79	-105.664	0.028	-1.201	-0.953	-0.007

Interaction energy analysis for fragmet #1(A:23:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.813 / q_NPA : 1.889

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 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	25	PRO	0	0.019	0.005	3.326	-15.614	-13.488	0.028	-1.201	-0.953	-0.007
4	A	26	GLU	-1	-0.893	-0.943	5.799	-54.446	-54.446	0.000	0.000	0.000	0.000
5	A	27	ALA	0	0.004	0.002	7.232	1.948	1.948	0.000	0.000	0.000	0.000
6	A	28	TYR	0	-0.004	-0.010	7.926	4.295	4.295	0.000	0.000	0.000	0.000
7	A	29	ALA	0	0.008	0.012	6.031	-1.682	-1.682	0.000	0.000	0.000	0.000
8	A	30	PHE	0	0.006	0.017	6.938	-1.518	-1.518	0.000	0.000	0.000	0.000
9	A	31	LEU	0	0.025	0.014	8.648	1.810	1.810	0.000	0.000	0.000	0.000
10	A	32	SER	0	-0.032	-0.047	5.317	-3.026	-3.026	0.000	0.000	0.000	0.000
11	A	33	PRO	0	0.036	0.015	7.187	0.476	0.476	0.000	0.000	0.000	0.000
12	A	34	ILE	0	-0.004	0.001	9.554	3.233	3.233	0.000	0.000	0.000	0.000
13	A	35	VAL	0	-0.036	-0.024	7.256	2.283	2.283	0.000	0.000	0.000	0.000
14	A	36	ASP	-1	-0.901	-0.951	6.816	-70.925	-70.925	0.000	0.000	0.000	0.000
15	A	37	PHE	0	-0.022	-0.012	9.598	3.084	3.084	0.000	0.000	0.000	0.000
16	A	38	MET	0	-0.024	-0.009	12.164	3.490	3.490	0.000	0.000	0.000	0.000
17	A	39	PRO	0	-0.033	-0.020	12.068	2.733	2.733	0.000	0.000	0.000	0.000
18	A	40	VAL	0	0.004	0.011	14.978	1.994	1.994	0.000	0.000	0.000	0.000
19	A	41	ILE	0	0.020	0.018	16.596	2.037	2.037	0.000	0.000	0.000	0.000
20	A	42	PRO	0	-0.001	-0.012	18.708	1.665	1.665	0.000	0.000	0.000	0.000
21	A	43	LEU	0	0.022	0.011	21.091	1.397	1.397	0.000	0.000	0.000	0.000
22	A	44	PHE	0	0.019	0.006	19.473	1.106	1.106	0.000	0.000	0.000	0.000
23	A	45	PHE	0	0.006	0.006	22.142	1.036	1.036	0.000	0.000	0.000	0.000
24	A	46	PHE	0	-0.007	0.005	26.035	0.955	0.955	0.000	0.000	0.000	0.000
25	A	47	LEU	0	0.008	-0.008	25.328	0.836	0.836	0.000	0.000	0.000	0.000
26	A	48	LEU	0	-0.009	-0.003	27.823	0.769	0.769	0.000	0.000	0.000	0.000
27	A	49	ALA	0	0.028	0.023	29.838	0.696	0.696	0.000	0.000	0.000	0.000
28	A	50	PHE	0	0.006	-0.001	31.653	0.754	0.754	0.000	0.000	0.000	0.000
29	A	51	VAL	0	-0.014	0.000	30.752	0.509	0.509	0.000	0.000	0.000	0.000
30	A	52	TRP	0	-0.018	-0.003	33.855	0.498	0.498	0.000	0.000	0.000	0.000
31	A	53	GLN	0	0.001	-0.014	35.661	0.297	0.297	0.000	0.000	0.000	0.000
32	A	54	ALA	0	-0.012	0.000	36.742	0.499	0.499	0.000	0.000	0.000	0.000
33	A	55	ALA	0	-0.041	-0.017	37.271	0.427	0.427	0.000	0.000	0.000	0.000
34	A	56	VAL	0	-0.051	-0.010	39.226	0.429	0.429	0.000	0.000	0.000	0.000
35	A	57	SER	0	-0.104	-0.059	41.846	0.555	0.555	0.000	0.000	0.000	0.000
36	A	58	PHE	0	-0.057	-0.043	37.438	0.157	0.157	0.000	0.000	0.000	0.000
37	A	59	ARG	0	0.089	0.067	42.589	-0.547	-0.547	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:23:LYS)