FMO DATABASE

FMODB ID: JYJJ9

Calculation Name: 7C9R-4-Other547

Preferred Name:

Target Type:

Ligand Name: bacteriochlorophyll a | cardiolipin | bacteriopheophytin a | protoporphyrin ix containing fe | ubiquinone-8 | menaquinone 8 | (6~{e},8~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{e},24~{e},26~{e})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26-undecaene | (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate | dodecyl-beta-d-maltoside | diacyl glycerol | octadecane | fe (iii) ion

Ligand 3-letter code: BCL | CDL | BPH | HEM | UQ8 | MQ8 | H4X | PGV | LMT | DGA | 8K6 | FE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7C9R

Chain ID: 4

ChEMBL ID:

UniProt ID:

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	44
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-165783.640918
FMO2-HF: Nuclear repulsion	147640.527823
FMO2-HF: Total energy	-18143.113095
FMO2-MP2: Total energy	-18194.820548

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:3:GLU)

Summations of interaction energy for fragment #1(A:3: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.
-5.06	-3.323	-0.02	-0.814	-0.903	0.002

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.091 / q_NPA : -0.055

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	5	PRO	0	0.019	0.022	3.865	-3.066	-1.329	-0.020	-0.814	-0.903	0.002
4	A	6	SER	0	-0.006	-0.013	6.787	0.196	0.196	0.000	0.000	0.000	0.000
5	A	7	THR	0	0.041	0.015	8.981	0.138	0.138	0.000	0.000	0.000	0.000
6	A	8	GLY	0	-0.024	-0.001	11.083	0.397	0.397	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.005	0.015	12.338	0.176	0.176	0.000	0.000	0.000	0.000
8	A	10	THR	0	-0.042	-0.046	14.093	-0.329	-0.329	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.941	-0.988	16.227	-1.936	-1.936	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.064	-0.034	18.021	0.310	0.310	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.731	-0.840	18.296	-2.723	-2.723	0.000	0.000	0.000	0.000
12	A	14	ALA	0	-0.001	0.003	17.712	0.174	0.174	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.932	0.963	19.860	1.588	1.588	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.940	-0.963	22.983	-1.318	-1.318	0.000	0.000	0.000	0.000
15	A	17	PHE	0	0.000	-0.003	22.075	0.131	0.131	0.000	0.000	0.000	0.000
16	A	18	HIS	0	0.011	-0.003	22.925	0.081	0.081	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.017	0.011	24.734	0.122	0.122	0.000	0.000	0.000	0.000
18	A	20	LEU	0	0.036	0.013	27.588	0.104	0.104	0.000	0.000	0.000	0.000
19	A	21	PHE	0	-0.011	0.015	25.906	0.091	0.091	0.000	0.000	0.000	0.000
20	A	22	MET	0	-0.004	-0.004	26.515	0.117	0.117	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.005	0.020	29.869	0.079	0.079	0.000	0.000	0.000	0.000
22	A	24	SER	0	-0.018	-0.026	30.904	0.061	0.061	0.000	0.000	0.000	0.000
23	A	25	MET	0	-0.028	-0.009	29.458	0.053	0.053	0.000	0.000	0.000	0.000
24	A	26	THR	0	-0.026	-0.024	32.353	0.067	0.067	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.006	0.000	35.214	0.043	0.043	0.000	0.000	0.000	0.000
26	A	28	TRP	0	-0.006	-0.002	34.072	0.034	0.034	0.000	0.000	0.000	0.000
27	A	29	PHE	0	0.021	-0.011	31.797	0.035	0.035	0.000	0.000	0.000	0.000
28	A	30	GLY	0	0.032	0.024	37.526	0.032	0.032	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.015	-0.009	39.603	0.026	0.026	0.000	0.000	0.000	0.000
30	A	32	VAL	0	0.017	0.012	37.985	0.026	0.026	0.000	0.000	0.000	0.000
31	A	33	VAL	0	0.008	0.012	40.697	0.029	0.029	0.000	0.000	0.000	0.000
32	A	34	LEU	0	0.006	0.005	43.128	0.019	0.019	0.000	0.000	0.000	0.000
33	A	35	ALA	0	0.019	0.008	44.145	0.016	0.016	0.000	0.000	0.000	0.000
34	A	36	HIS	0	-0.041	-0.019	41.706	0.032	0.032	0.000	0.000	0.000	0.000
35	A	37	ILE	0	0.013	0.009	46.420	0.016	0.016	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.012	-0.014	49.133	0.011	0.011	0.000	0.000	0.000	0.000
37	A	39	SER	0	-0.035	-0.028	48.337	0.011	0.011	0.000	0.000	0.000	0.000
38	A	40	TRP	0	-0.010	-0.006	49.973	0.009	0.009	0.000	0.000	0.000	0.000
39	A	41	MET	0	-0.052	-0.028	51.772	0.008	0.008	0.000	0.000	0.000	0.000
40	A	42	TYR	0	-0.052	-0.007	54.205	0.007	0.007	0.000	0.000	0.000	0.000
41	A	43	ARG	1	0.896	0.937	53.772	0.060	0.060	0.000	0.000	0.000	0.000
42	A	44	PRO	0	0.024	0.031	52.795	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	45	TRP	0	-0.056	-0.042	46.318	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	46	LEU	-1	-0.930	-0.947	47.215	0.017	0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)