FMO DATABASE

FMODB ID: 5GM2Z

Calculation Name: 1V54-J-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: J

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	58
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-241650.030251
FMO2-HF: Nuclear repulsion	218481.935128
FMO2-HF: Total energy	-23168.095123
FMO2-MP2: Total energy	-23234.576102

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(J:1:PHE)

Summations of interaction energy for fragment #1(J:1:PHE)

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.
51.027	52.703	-0.012	-0.777	-0.887	-0.001

Interaction energy analysis for fragmet #1(J:1:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.854 / q_NPA : 0.916

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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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	J	3	ASN	0	0.013	-0.002	3.831	1.157	2.833	-0.012	-0.777	-0.887	-0.001
4	J	4	ARG	1	0.932	0.978	5.884	39.665	39.665	0.000	0.000	0.000	0.000
5	J	5	VAL	0	0.002	0.009	7.970	2.515	2.515	0.000	0.000	0.000	0.000
6	J	6	ALA	0	0.058	0.029	10.330	1.727	1.727	0.000	0.000	0.000	0.000
7	J	7	GLU	-1	-0.902	-0.957	10.279	-25.695	-25.695	0.000	0.000	0.000	0.000
8	J	8	LYS	1	0.938	0.963	10.670	22.392	22.392	0.000	0.000	0.000	0.000
9	J	9	GLN	0	0.029	0.012	13.514	0.649	0.649	0.000	0.000	0.000	0.000
10	J	10	LYS	1	0.970	0.988	16.247	16.162	16.162	0.000	0.000	0.000	0.000
11	J	11	LEU	0	0.009	0.014	15.567	0.540	0.540	0.000	0.000	0.000	0.000
12	J	12	PHE	0	0.014	-0.014	14.506	0.516	0.516	0.000	0.000	0.000	0.000
13	J	13	GLN	0	-0.045	-0.029	19.201	0.146	0.146	0.000	0.000	0.000	0.000
14	J	14	GLU	-1	-0.894	-0.919	21.248	-12.591	-12.591	0.000	0.000	0.000	0.000
15	J	15	ASP	-1	-0.931	-0.956	23.077	-10.158	-10.158	0.000	0.000	0.000	0.000
16	J	16	ASN	0	0.006	-0.018	22.913	0.471	0.471	0.000	0.000	0.000	0.000
17	J	17	GLY	0	0.011	0.008	27.273	0.193	0.193	0.000	0.000	0.000	0.000
18	J	18	LEU	0	-0.049	-0.009	23.888	0.205	0.205	0.000	0.000	0.000	0.000
19	J	19	PRO	0	0.003	0.005	25.611	-0.200	-0.200	0.000	0.000	0.000	0.000
20	J	20	VAL	0	0.049	-0.001	20.521	-0.292	-0.292	0.000	0.000	0.000	0.000
21	J	21	HIS	0	-0.018	-0.012	21.088	-0.707	-0.707	0.000	0.000	0.000	0.000
22	J	22	LEU	0	-0.052	-0.036	22.511	0.136	0.136	0.000	0.000	0.000	0.000
23	J	23	LYS	1	0.784	0.911	20.603	12.540	12.540	0.000	0.000	0.000	0.000
24	J	24	GLY	0	-0.001	0.004	17.304	-0.511	-0.511	0.000	0.000	0.000	0.000
25	J	25	GLY	0	0.001	0.006	17.749	-0.479	-0.479	0.000	0.000	0.000	0.000
26	J	26	ALA	0	0.030	0.001	20.435	0.215	0.215	0.000	0.000	0.000	0.000
27	J	27	THR	0	-0.004	-0.012	16.358	0.584	0.584	0.000	0.000	0.000	0.000
28	J	28	ASP	-1	-0.791	-0.878	18.406	-14.088	-14.088	0.000	0.000	0.000	0.000
29	J	29	ASN	0	0.006	-0.005	20.717	0.240	0.240	0.000	0.000	0.000	0.000
30	J	30	ILE	0	-0.029	-0.012	22.075	0.540	0.540	0.000	0.000	0.000	0.000
31	J	31	LEU	0	0.042	0.023	18.447	0.375	0.375	0.000	0.000	0.000	0.000
32	J	32	TYR	0	0.037	0.028	22.372	0.326	0.326	0.000	0.000	0.000	0.000
33	J	33	ARG	1	0.956	0.977	25.077	10.220	10.220	0.000	0.000	0.000	0.000
34	J	34	VAL	0	-0.002	0.018	24.646	0.374	0.374	0.000	0.000	0.000	0.000
35	J	35	THR	0	0.004	-0.014	24.089	0.217	0.217	0.000	0.000	0.000	0.000
36	J	36	MET	0	0.035	0.019	26.619	0.336	0.336	0.000	0.000	0.000	0.000
37	J	37	THR	0	-0.035	-0.030	29.846	0.393	0.393	0.000	0.000	0.000	0.000
38	J	38	LEU	0	-0.023	-0.010	26.719	0.272	0.272	0.000	0.000	0.000	0.000
39	J	39	CYS	0	-0.030	-0.009	29.263	0.179	0.179	0.000	0.000	0.000	0.000
40	J	40	LEU	0	0.007	0.012	32.102	0.269	0.269	0.000	0.000	0.000	0.000
41	J	41	GLY	0	0.031	0.016	34.411	0.244	0.244	0.000	0.000	0.000	0.000
42	J	42	GLY	0	0.013	0.003	34.284	0.194	0.194	0.000	0.000	0.000	0.000
43	J	43	THR	0	-0.013	-0.015	35.409	0.186	0.186	0.000	0.000	0.000	0.000
44	J	44	LEU	0	0.007	0.006	37.817	0.211	0.211	0.000	0.000	0.000	0.000
45	J	45	TYR	0	0.014	0.010	37.645	0.154	0.154	0.000	0.000	0.000	0.000
46	J	46	SER	0	-0.028	-0.021	38.690	0.156	0.156	0.000	0.000	0.000	0.000
47	J	47	LEU	0	0.025	0.006	40.626	0.159	0.159	0.000	0.000	0.000	0.000
48	J	48	TYR	0	-0.012	0.004	43.261	0.200	0.200	0.000	0.000	0.000	0.000
49	J	49	CYS	0	-0.058	-0.033	41.798	0.123	0.123	0.000	0.000	0.000	0.000
50	J	50	LEU	0	0.005	0.010	44.484	0.109	0.109	0.000	0.000	0.000	0.000
51	J	51	GLY	0	0.022	0.014	46.400	0.143	0.143	0.000	0.000	0.000	0.000
52	J	52	TRP	0	-0.024	-0.020	47.423	0.094	0.094	0.000	0.000	0.000	0.000
53	J	53	ALA	0	0.001	-0.004	47.500	0.104	0.104	0.000	0.000	0.000	0.000
54	J	54	SER	0	-0.063	-0.032	49.521	0.068	0.068	0.000	0.000	0.000	0.000
55	J	55	PHE	0	-0.044	-0.016	52.126	0.144	0.144	0.000	0.000	0.000	0.000
56	J	56	PRO	0	-0.052	-0.021	54.168	-0.043	-0.043	0.000	0.000	0.000	0.000
57	J	57	HIS	0	-0.032	-0.036	51.843	0.122	0.122	0.000	0.000	0.000	0.000
58	J	58	LYS	0	0.015	0.031	56.150	-0.174	-0.174	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(J:1:PHE)