FMO DATABASE

FMODB ID: 4G79N

Calculation Name: 1V54-K-Xray549

Preferred Name:

Target Type:

Ligand Name: cardiolipin | heme-a | (7r,17e,20e)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4-phosphahexacosa-17,20-dien-1-aminium 4-oxide | tristearoylglycerol | (1s)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl (5e,8e,11e,14e)-icosa-5,8,11,14-tetraenoate | (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate | decyl-beta-d-maltopyranoside | cholic acid | phosphothreonine | n-acetyl-serine | n-formylmethionine | dinuclear copper ion | copper (ii) ion | zinc ion | unknown atom or ion

Ligand 3-letter code: CDL | HEA | PSC | TGL | PEK | PGV | DMU | CHD | TPO | SAC | FME | CUA | CU | ZN | UNX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1V54

Chain ID: K

ChEMBL ID:

UniProt ID: P00396

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	49
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-170959.526812
FMO2-HF: Nuclear repulsion	151851.956481
FMO2-HF: Total energy	-19107.570331
FMO2-MP2: Total energy	-19162.923508

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(K:6:ALA)

Summations of interaction energy for fragment #1(K:6:ALA)

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.
-17.496	-16.433	-0.01	-0.336	-0.718	-0.001

Interaction energy analysis for fragmet #1(K:6:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.837 / q_NPA : 0.904

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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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	K	8	ASP	-1	-0.811	-0.916	3.843	-34.807	-33.744	-0.010	-0.336	-0.718	-0.001
4	K	9	PHE	0	-0.018	-0.021	6.556	2.725	2.725	0.000	0.000	0.000	0.000
5	K	10	HIS	0	0.012	-0.007	9.943	3.673	3.673	0.000	0.000	0.000	0.000
6	K	11	ASP	-1	-0.827	-0.908	5.777	-47.417	-47.417	0.000	0.000	0.000	0.000
7	K	12	LYS	1	0.826	0.931	5.690	41.450	41.450	0.000	0.000	0.000	0.000
8	K	13	TYR	0	0.010	-0.004	10.578	1.563	1.563	0.000	0.000	0.000	0.000
9	K	14	GLY	0	0.027	0.027	13.110	1.775	1.775	0.000	0.000	0.000	0.000
10	K	15	ASN	0	0.008	-0.002	13.513	2.266	2.266	0.000	0.000	0.000	0.000
11	K	16	ALA	0	0.037	0.021	16.653	1.178	1.178	0.000	0.000	0.000	0.000
12	K	17	VAL	0	0.002	0.015	17.363	1.125	1.125	0.000	0.000	0.000	0.000
13	K	18	LEU	0	0.007	0.013	19.028	0.946	0.946	0.000	0.000	0.000	0.000
14	K	19	ALA	0	0.021	0.012	20.859	0.850	0.850	0.000	0.000	0.000	0.000
15	K	20	SER	0	-0.036	-0.028	21.848	0.823	0.823	0.000	0.000	0.000	0.000
16	K	21	GLY	0	0.048	0.025	23.314	0.634	0.634	0.000	0.000	0.000	0.000
17	K	22	ALA	0	-0.005	-0.005	24.865	0.604	0.604	0.000	0.000	0.000	0.000
18	K	23	THR	0	-0.026	-0.026	26.603	0.627	0.627	0.000	0.000	0.000	0.000
19	K	24	PHE	0	-0.007	-0.006	27.993	0.486	0.486	0.000	0.000	0.000	0.000
20	K	25	CYS	0	-0.030	-0.008	29.092	0.551	0.551	0.000	0.000	0.000	0.000
21	K	26	VAL	0	0.040	0.008	30.859	0.404	0.404	0.000	0.000	0.000	0.000
22	K	27	ALA	0	0.007	0.005	32.563	0.366	0.366	0.000	0.000	0.000	0.000
23	K	28	VAL	0	-0.013	-0.007	33.194	0.364	0.364	0.000	0.000	0.000	0.000
24	K	29	TRP	0	0.028	0.006	33.646	0.434	0.434	0.000	0.000	0.000	0.000
25	K	30	VAL	0	0.005	0.007	36.859	0.290	0.290	0.000	0.000	0.000	0.000
26	K	31	TYR	0	0.007	0.014	38.306	0.294	0.294	0.000	0.000	0.000	0.000
27	K	32	MET	0	-0.027	-0.011	39.406	0.215	0.215	0.000	0.000	0.000	0.000
28	K	33	ALA	0	-0.014	-0.014	40.954	0.214	0.214	0.000	0.000	0.000	0.000
29	K	34	THR	0	-0.054	-0.028	42.589	0.206	0.206	0.000	0.000	0.000	0.000
30	K	35	GLN	0	-0.038	-0.022	42.967	0.240	0.240	0.000	0.000	0.000	0.000
31	K	36	ILE	0	-0.033	-0.012	42.914	0.102	0.102	0.000	0.000	0.000	0.000
32	K	37	GLY	0	-0.012	0.003	46.448	0.073	0.073	0.000	0.000	0.000	0.000
33	K	38	ILE	0	-0.014	-0.004	44.245	0.109	0.109	0.000	0.000	0.000	0.000
34	K	39	GLU	-1	-0.888	-0.933	48.534	-6.139	-6.139	0.000	0.000	0.000	0.000
35	K	40	TRP	0	-0.031	-0.033	42.868	-0.075	-0.075	0.000	0.000	0.000	0.000
36	K	41	ASN	0	-0.076	-0.031	49.712	0.056	0.056	0.000	0.000	0.000	0.000
37	K	42	PRO	0	0.033	0.028	50.600	0.003	0.003	0.000	0.000	0.000	0.000
38	K	43	SER	0	0.043	0.017	52.280	0.179	0.179	0.000	0.000	0.000	0.000
39	K	44	PRO	0	0.057	0.014	54.960	-0.020	-0.020	0.000	0.000	0.000	0.000
40	K	45	VAL	0	-0.003	-0.002	56.895	0.058	0.058	0.000	0.000	0.000	0.000
41	K	46	GLY	0	-0.001	0.002	56.311	-0.105	-0.105	0.000	0.000	0.000	0.000
42	K	47	ARG	1	0.853	0.920	54.786	5.863	5.863	0.000	0.000	0.000	0.000
43	K	48	VAL	0	-0.025	-0.005	57.330	0.010	0.010	0.000	0.000	0.000	0.000
44	K	49	THR	0	0.000	0.008	60.593	0.041	0.041	0.000	0.000	0.000	0.000
45	K	50	PRO	0	-0.032	-0.023	64.101	0.009	0.009	0.000	0.000	0.000	0.000
46	K	51	LYS	1	0.951	0.972	66.627	4.768	4.768	0.000	0.000	0.000	0.000
47	K	52	GLU	-1	-0.911	-0.958	69.322	-4.427	-4.427	0.000	0.000	0.000	0.000
48	K	53	TRP	0	-0.068	-0.040	70.697	-0.024	-0.024	0.000	0.000	0.000	0.000
49	K	54	ARG	0	0.050	0.048	72.729	-0.056	-0.056	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(K:6:ALA)