FMO DATABASE

FMODB ID: Q5QYY

Calculation Name: 1V54-M-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: M

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	43
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-144521.596062
FMO2-HF: Nuclear repulsion	128494.536212
FMO2-HF: Total energy	-16027.05985
FMO2-MP2: Total energy	-16075.416909

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(M:1:ILE)

Summations of interaction energy for fragment #1(M:1:ILE)

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.
46.081	48.691	0.837	-1.417	-2.031	-0.011

Interaction energy analysis for fragmet #1(M:1:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / q_NPA : 0.930

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	M	3	ALA	0	0.033	0.013	2.646	-1.828	0.766	0.838	-1.411	-2.022	-0.011
4	M	4	LYS	1	0.965	0.988	4.936	25.235	25.251	-0.001	-0.006	-0.009	0.000
5	M	5	PRO	0	0.042	0.007	8.744	-0.611	-0.611	0.000	0.000	0.000	0.000
6	M	6	ALA	0	0.009	0.012	11.427	0.286	0.286	0.000	0.000	0.000	0.000
7	M	7	LYS	1	0.977	0.970	12.643	18.777	18.777	0.000	0.000	0.000	0.000
8	M	8	THR	0	0.022	0.018	15.369	0.894	0.894	0.000	0.000	0.000	0.000
9	M	9	PRO	0	-0.034	-0.017	15.642	-0.493	-0.493	0.000	0.000	0.000	0.000
10	M	10	THR	0	0.044	0.041	16.015	0.478	0.478	0.000	0.000	0.000	0.000
11	M	11	SER	0	0.016	0.022	17.529	-0.393	-0.393	0.000	0.000	0.000	0.000
12	M	12	PRO	0	0.064	0.009	19.441	0.124	0.124	0.000	0.000	0.000	0.000
13	M	13	LYS	1	0.971	0.993	20.904	10.994	10.994	0.000	0.000	0.000	0.000
14	M	14	GLU	-1	-0.847	-0.933	21.094	-13.100	-13.100	0.000	0.000	0.000	0.000
15	M	15	GLN	0	-0.047	-0.030	16.005	0.002	0.002	0.000	0.000	0.000	0.000
16	M	16	ALA	0	0.013	0.017	20.412	0.117	0.117	0.000	0.000	0.000	0.000
17	M	17	ILE	0	0.004	0.015	23.690	0.343	0.343	0.000	0.000	0.000	0.000
18	M	18	GLY	0	0.036	0.016	21.753	0.262	0.262	0.000	0.000	0.000	0.000
19	M	19	LEU	0	0.002	0.017	20.504	0.085	0.085	0.000	0.000	0.000	0.000
20	M	20	SER	0	-0.003	-0.014	22.754	0.365	0.365	0.000	0.000	0.000	0.000
21	M	21	VAL	0	-0.006	-0.009	25.546	0.335	0.335	0.000	0.000	0.000	0.000
22	M	22	THR	0	-0.018	-0.015	21.670	0.150	0.150	0.000	0.000	0.000	0.000
23	M	23	PHE	0	0.004	-0.004	22.350	0.219	0.219	0.000	0.000	0.000	0.000
24	M	24	LEU	0	0.013	0.001	26.672	0.313	0.313	0.000	0.000	0.000	0.000
25	M	25	SER	0	-0.055	-0.033	26.693	0.258	0.258	0.000	0.000	0.000	0.000
26	M	26	PHE	0	0.000	0.002	24.109	0.161	0.161	0.000	0.000	0.000	0.000
27	M	27	LEU	0	-0.011	-0.018	29.326	0.308	0.308	0.000	0.000	0.000	0.000
28	M	28	LEU	0	-0.007	0.007	31.862	0.296	0.296	0.000	0.000	0.000	0.000
29	M	29	PRO	0	0.000	0.002	32.631	0.299	0.299	0.000	0.000	0.000	0.000
30	M	30	ALA	0	0.023	0.015	33.520	0.236	0.236	0.000	0.000	0.000	0.000
31	M	31	GLY	0	0.032	0.014	35.449	0.203	0.203	0.000	0.000	0.000	0.000
32	M	32	TRP	0	0.010	0.002	37.311	0.222	0.222	0.000	0.000	0.000	0.000
33	M	33	VAL	0	0.006	0.005	38.751	0.223	0.223	0.000	0.000	0.000	0.000
34	M	34	LEU	0	-0.019	-0.027	37.034	0.163	0.163	0.000	0.000	0.000	0.000
35	M	35	TYR	0	-0.042	-0.005	40.844	0.132	0.132	0.000	0.000	0.000	0.000
36	M	36	HIS	0	-0.057	-0.030	43.135	0.289	0.289	0.000	0.000	0.000	0.000
37	M	37	LEU	0	0.008	0.006	42.447	0.127	0.127	0.000	0.000	0.000	0.000
38	M	38	ASP	-1	-0.865	-0.929	45.441	-6.091	-6.091	0.000	0.000	0.000	0.000
39	M	39	ASN	0	0.028	0.007	48.777	0.060	0.060	0.000	0.000	0.000	0.000
40	M	40	TYR	0	-0.021	0.007	43.254	0.033	0.033	0.000	0.000	0.000	0.000
41	M	41	LYS	1	0.830	0.914	47.420	6.400	6.400	0.000	0.000	0.000	0.000
42	M	42	LYS	1	0.768	0.866	50.315	5.809	5.809	0.000	0.000	0.000	0.000
43	M	43	SER	-1	-0.846	-0.896	52.667	-5.601	-5.601	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(M:1:ILE)