FMO DATABASE

FMODB ID: 9RK82

Calculation Name: 3JCU-f-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: f

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	32
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-102766.057557
FMO2-HF: Nuclear repulsion	90361.734082
FMO2-HF: Total energy	-12404.323476
FMO2-MP2: Total energy	-12441.016662

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:14:PRO)

Summations of interaction energy for fragment #1(A:14:PRO)

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.
42.454	44.344	0.013	-0.655	-1.248	-0.001

Interaction energy analysis for fragmet #1(A:14:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.901 / q_NPA : 0.927

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	16	PHE	0	0.068	0.033	3.600	1.010	2.780	0.014	-0.646	-1.139	-0.001
4	A	17	THR	0	0.010	0.010	5.023	4.138	4.258	-0.001	-0.009	-0.109	0.000
5	A	18	VAL	0	0.097	0.046	8.468	0.410	0.410	0.000	0.000	0.000	0.000
6	A	19	ARG	1	1.005	0.995	11.243	21.998	21.998	0.000	0.000	0.000	0.000
7	A	20	TRP	0	0.008	0.008	5.887	-0.169	-0.169	0.000	0.000	0.000	0.000
8	A	21	LEU	0	0.039	0.018	7.214	1.003	1.003	0.000	0.000	0.000	0.000
9	A	22	ALA	0	-0.005	0.002	9.812	1.318	1.318	0.000	0.000	0.000	0.000
10	A	23	ILE	0	0.002	0.009	11.986	1.151	1.151	0.000	0.000	0.000	0.000
11	A	24	HIS	0	-0.033	-0.034	9.545	1.146	1.146	0.000	0.000	0.000	0.000
12	A	25	GLY	0	0.005	0.004	11.681	0.756	0.756	0.000	0.000	0.000	0.000
13	A	26	LEU	0	0.010	0.017	13.456	1.142	1.142	0.000	0.000	0.000	0.000
14	A	27	ALA	0	0.014	0.010	14.408	0.811	0.811	0.000	0.000	0.000	0.000
15	A	28	VAL	0	0.011	0.008	12.061	0.618	0.618	0.000	0.000	0.000	0.000
16	A	29	PRO	0	0.008	-0.001	15.268	0.753	0.753	0.000	0.000	0.000	0.000
17	A	30	THR	0	-0.008	-0.005	18.383	0.942	0.942	0.000	0.000	0.000	0.000
18	A	31	VAL	0	-0.003	-0.008	17.865	0.673	0.673	0.000	0.000	0.000	0.000
19	A	32	PHE	0	-0.015	0.005	19.081	0.571	0.571	0.000	0.000	0.000	0.000
20	A	33	PHE	0	0.017	0.004	20.819	0.562	0.562	0.000	0.000	0.000	0.000
21	A	34	LEU	0	0.038	0.027	22.752	0.562	0.562	0.000	0.000	0.000	0.000
22	A	35	GLY	0	0.022	0.030	23.556	0.460	0.460	0.000	0.000	0.000	0.000
23	A	36	SER	0	-0.070	-0.044	24.973	0.487	0.487	0.000	0.000	0.000	0.000
24	A	37	ILE	0	0.041	0.001	27.102	0.399	0.399	0.000	0.000	0.000	0.000
25	A	38	SER	0	-0.036	-0.036	27.377	0.407	0.407	0.000	0.000	0.000	0.000
26	A	39	ALA	0	0.020	0.007	29.167	0.342	0.342	0.000	0.000	0.000	0.000
27	A	40	MET	0	-0.030	-0.025	29.708	0.322	0.322	0.000	0.000	0.000	0.000
28	A	41	GLN	0	-0.068	-0.021	32.778	0.471	0.471	0.000	0.000	0.000	0.000
29	A	42	PHE	0	-0.037	-0.019	32.705	0.260	0.260	0.000	0.000	0.000	0.000
30	A	43	ILE	0	-0.069	-0.017	33.409	0.134	0.134	0.000	0.000	0.000	0.000
31	A	44	GLN	0	-0.044	-0.019	37.328	0.187	0.187	0.000	0.000	0.000	0.000
32	A	45	ARG	0	0.044	0.030	41.057	-0.410	-0.410	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:PRO)