FMO DATABASE

FMODB ID: Y7LY2

Calculation Name: 1V54-I-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: I

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	72
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-325234.621142
FMO2-HF: Nuclear repulsion	295679.753379
FMO2-HF: Total energy	-29554.867763
FMO2-MP2: Total energy	-29639.818093

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(I:2:THR)

Summations of interaction energy for fragment #1(I:2:THR)

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.
88.231	90.95	0.88	-1.556	-2.043	-0.016

Interaction energy analysis for fragmet #1(I:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.862 / q_NPA : 0.921

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	I	4	LEU	0	0.031	0.013	2.642	-8.140	-5.471	0.881	-1.555	-1.995	-0.016
4	I	5	ALA	0	0.028	0.018	5.387	2.880	2.930	-0.001	-0.001	-0.048	0.000
5	I	6	LYS	1	0.976	0.985	7.413	19.327	19.327	0.000	0.000	0.000	0.000
6	I	7	PRO	0	0.040	0.029	10.986	0.973	0.973	0.000	0.000	0.000	0.000
7	I	8	GLN	0	0.005	-0.018	13.396	0.671	0.671	0.000	0.000	0.000	0.000
8	I	9	MET	0	0.001	-0.005	16.446	-0.291	-0.291	0.000	0.000	0.000	0.000
9	I	10	ARG	1	0.985	0.993	19.123	13.847	13.847	0.000	0.000	0.000	0.000
10	I	11	GLY	0	0.060	0.034	22.615	-0.028	-0.028	0.000	0.000	0.000	0.000
11	I	12	LEU	0	-0.003	0.000	19.929	0.375	0.375	0.000	0.000	0.000	0.000
12	I	13	LEU	0	0.057	0.028	24.105	0.068	0.068	0.000	0.000	0.000	0.000
13	I	14	ALA	0	0.056	0.031	27.663	0.276	0.276	0.000	0.000	0.000	0.000
14	I	15	ARG	1	0.969	0.983	20.128	14.088	14.088	0.000	0.000	0.000	0.000
15	I	16	ARG	1	0.970	0.979	26.213	10.868	10.868	0.000	0.000	0.000	0.000
16	I	17	LEU	0	0.036	0.029	27.650	0.163	0.163	0.000	0.000	0.000	0.000
17	I	18	ARG	1	0.997	0.992	29.138	10.369	10.369	0.000	0.000	0.000	0.000
18	I	19	PHE	0	-0.014	-0.003	26.617	0.179	0.179	0.000	0.000	0.000	0.000
19	I	20	HIS	0	-0.013	-0.022	27.698	0.115	0.115	0.000	0.000	0.000	0.000
20	I	21	ILE	0	0.009	0.020	32.344	0.255	0.255	0.000	0.000	0.000	0.000
21	I	22	VAL	0	0.003	0.004	32.623	0.247	0.247	0.000	0.000	0.000	0.000
22	I	23	GLY	0	0.022	0.009	33.365	0.170	0.170	0.000	0.000	0.000	0.000
23	I	24	ALA	0	0.025	0.004	34.371	0.203	0.203	0.000	0.000	0.000	0.000
24	I	25	PHE	0	0.016	0.021	37.654	0.256	0.256	0.000	0.000	0.000	0.000
25	I	26	MET	0	0.015	0.002	35.440	0.276	0.276	0.000	0.000	0.000	0.000
26	I	27	VAL	0	0.016	0.009	37.030	0.173	0.173	0.000	0.000	0.000	0.000
27	I	28	SER	0	-0.023	-0.017	39.665	0.250	0.250	0.000	0.000	0.000	0.000
28	I	29	LEU	0	-0.010	-0.003	41.250	0.225	0.225	0.000	0.000	0.000	0.000
29	I	30	GLY	0	0.017	0.027	41.919	0.164	0.164	0.000	0.000	0.000	0.000
30	I	31	PHE	0	0.017	0.003	43.018	0.174	0.174	0.000	0.000	0.000	0.000
31	I	32	ALA	0	0.012	0.001	45.430	0.188	0.188	0.000	0.000	0.000	0.000
32	I	33	THR	0	-0.064	-0.046	45.716	0.215	0.215	0.000	0.000	0.000	0.000
33	I	34	PHE	0	0.038	0.016	46.582	0.135	0.135	0.000	0.000	0.000	0.000
34	I	35	TYR	0	0.037	0.015	48.446	0.177	0.177	0.000	0.000	0.000	0.000
35	I	36	LYS	1	0.914	0.939	49.478	6.430	6.430	0.000	0.000	0.000	0.000
36	I	37	PHE	0	0.018	0.022	50.505	0.082	0.082	0.000	0.000	0.000	0.000
37	I	38	ALA	0	-0.008	-0.002	51.739	0.126	0.126	0.000	0.000	0.000	0.000
38	I	39	VAL	0	-0.048	-0.021	53.662	0.102	0.102	0.000	0.000	0.000	0.000
39	I	40	ALA	0	-0.025	-0.012	55.420	0.121	0.121	0.000	0.000	0.000	0.000
40	I	41	GLU	-1	-0.808	-0.902	56.300	-5.294	-5.294	0.000	0.000	0.000	0.000
41	I	42	LYS	1	0.961	0.996	57.199	5.606	5.606	0.000	0.000	0.000	0.000
42	I	43	ARG	1	0.940	0.973	59.052	5.314	5.314	0.000	0.000	0.000	0.000
43	I	44	LYS	1	0.900	0.936	59.186	5.430	5.430	0.000	0.000	0.000	0.000
44	I	45	LYS	1	0.898	0.934	60.698	5.186	5.186	0.000	0.000	0.000	0.000
45	I	46	ALA	0	-0.005	0.005	63.104	0.070	0.070	0.000	0.000	0.000	0.000
46	I	47	TYR	0	0.018	0.005	64.891	0.043	0.043	0.000	0.000	0.000	0.000
47	I	48	ALA	0	-0.002	-0.005	66.127	0.078	0.078	0.000	0.000	0.000	0.000
48	I	49	ASP	-1	-0.838	-0.902	65.043	-4.848	-4.848	0.000	0.000	0.000	0.000
49	I	50	PHE	0	-0.031	0.002	68.305	0.045	0.045	0.000	0.000	0.000	0.000
50	I	51	TYR	0	0.009	-0.013	70.858	0.039	0.039	0.000	0.000	0.000	0.000
51	I	52	ARG	1	0.826	0.919	66.913	4.713	4.713	0.000	0.000	0.000	0.000
52	I	53	ASN	0	-0.031	-0.022	72.954	0.070	0.070	0.000	0.000	0.000	0.000
53	I	54	TYR	0	-0.064	-0.050	75.310	0.026	0.026	0.000	0.000	0.000	0.000
54	I	55	ASP	-1	-0.845	-0.915	76.962	-3.836	-3.836	0.000	0.000	0.000	0.000
55	I	56	SER	0	0.025	0.000	80.732	0.009	0.009	0.000	0.000	0.000	0.000
56	I	57	MET	0	0.014	0.017	81.930	0.026	0.026	0.000	0.000	0.000	0.000
57	I	58	LYS	1	0.927	0.966	80.312	4.006	4.006	0.000	0.000	0.000	0.000
58	I	59	ASP	-1	-0.821	-0.883	79.450	-4.074	-4.074	0.000	0.000	0.000	0.000
59	I	60	PHE	0	0.021	0.009	81.899	0.014	0.014	0.000	0.000	0.000	0.000
60	I	61	GLU	-1	-0.836	-0.924	84.978	-3.562	-3.562	0.000	0.000	0.000	0.000
61	I	62	GLU	-1	-0.964	-0.988	80.857	-3.952	-3.952	0.000	0.000	0.000	0.000
62	I	63	MET	0	-0.025	-0.015	79.678	0.024	0.024	0.000	0.000	0.000	0.000
63	I	64	ARG	1	0.757	0.853	84.455	3.544	3.544	0.000	0.000	0.000	0.000
64	I	65	LYS	1	0.909	0.960	87.284	3.671	3.671	0.000	0.000	0.000	0.000
65	I	66	ALA	0	-0.024	0.002	84.204	0.014	0.014	0.000	0.000	0.000	0.000
66	I	67	GLY	0	-0.004	0.005	86.187	-0.004	-0.004	0.000	0.000	0.000	0.000
67	I	68	ILE	0	-0.048	-0.032	82.820	0.024	0.024	0.000	0.000	0.000	0.000
68	I	69	PHE	0	-0.018	0.003	84.686	-0.004	-0.004	0.000	0.000	0.000	0.000
69	I	70	GLN	0	-0.013	-0.013	88.687	0.041	0.041	0.000	0.000	0.000	0.000
70	I	71	SER	0	-0.022	-0.017	91.019	0.029	0.029	0.000	0.000	0.000	0.000
71	I	72	ALA	0	0.004	0.006	91.019	0.029	0.029	0.000	0.000	0.000	0.000
72	I	73	LYS	0	0.056	0.055	91.189	0.045	0.045	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(I:2:THR)