FMO DATABASE

FMODB ID: 5YJVZ

Calculation Name: 3JCU-m-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: m

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	33
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-104003.210728
FMO2-HF: Nuclear repulsion	91716.544227
FMO2-HF: Total energy	-12286.666501
FMO2-MP2: Total energy	-12323.862636

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:2:GLU)

Summations of interaction energy for fragment #1(A:2:GLU)

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.
4.43	5.694	-0.014	-0.539	-0.712	0.002

Interaction energy analysis for fragmet #1(A:2:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.029

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	4	ASN	0	0.040	0.012	3.882	1.697	2.961	-0.014	-0.539	-0.712	0.002
4	A	5	ILE	0	0.071	0.028	6.076	0.262	0.262	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.026	-0.003	8.729	0.142	0.142	0.000	0.000	0.000	0.000
6	A	7	ALA	0	0.020	0.016	9.398	0.308	0.308	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.006	0.024	6.806	0.344	0.344	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.032	0.018	12.137	0.297	0.297	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.014	0.009	14.457	0.194	0.194	0.000	0.000	0.000	0.000
10	A	11	THR	0	-0.007	-0.017	13.700	0.173	0.173	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.005	-0.004	16.235	0.183	0.183	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.012	-0.008	18.174	0.164	0.164	0.000	0.000	0.000	0.000
13	A	14	PHE	0	-0.012	-0.009	19.096	0.115	0.115	0.000	0.000	0.000	0.000
14	A	15	ILE	0	0.027	0.020	18.771	0.068	0.068	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.004	0.014	22.052	0.110	0.110	0.000	0.000	0.000	0.000
16	A	17	VAL	0	0.006	0.008	23.971	0.087	0.087	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.001	0.003	24.514	0.078	0.078	0.000	0.000	0.000	0.000
18	A	19	THR	0	-0.013	-0.034	25.614	0.059	0.059	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.034	0.021	27.928	0.053	0.053	0.000	0.000	0.000	0.000
20	A	21	PHE	0	-0.019	-0.011	29.857	0.051	0.051	0.000	0.000	0.000	0.000
21	A	22	LEU	0	0.010	-0.003	29.954	0.038	0.038	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.006	0.006	30.419	0.033	0.033	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.015	0.000	33.185	0.036	0.036	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.034	-0.014	35.589	0.033	0.033	0.000	0.000	0.000	0.000
25	A	26	TYR	0	0.003	0.016	36.520	0.019	0.019	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.024	0.004	37.131	0.019	0.019	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.936	0.973	39.552	0.345	0.345	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.052	-0.027	41.126	0.019	0.019	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.049	0.017	41.485	0.013	0.013	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.119	-0.054	43.746	0.014	0.014	0.000	0.000	0.000	0.000
31	A	32	GLN	0	-0.080	-0.039	45.466	0.020	0.020	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.084	-0.048	48.206	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	34	ASP	-2	-1.852	-1.913	46.431	-0.540	-0.540	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLU)