FMO DATABASE

FMODB ID: G79N1

Calculation Name: 1V54-F-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: F

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	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-586958.044454
FMO2-HF: Nuclear repulsion	548820.992534
FMO2-HF: Total energy	-38137.051921
FMO2-MP2: Total energy	-38245.76745

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(F:1:ALA)

Summations of interaction energy for fragment #1(F:1: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.
-45.261	-42.928	0.01	-1.377	-0.966	-0.006

Interaction energy analysis for fragmet #1(F:1:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.841 / q_NPA : 0.912

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	F	3	GLY	0	0.016	-0.003	3.223	-12.226	-9.893	0.010	-1.377	-0.966	-0.006
4	F	4	GLY	0	0.018	0.007	6.057	2.747	2.747	0.000	0.000	0.000	0.000
5	F	5	GLY	0	0.001	0.004	9.893	-0.844	-0.844	0.000	0.000	0.000	0.000
6	F	6	VAL	0	-0.024	-0.001	11.962	1.023	1.023	0.000	0.000	0.000	0.000
7	F	7	PRO	0	-0.015	0.011	14.366	-0.269	-0.269	0.000	0.000	0.000	0.000
8	F	8	THR	0	-0.021	-0.042	17.844	0.183	0.183	0.000	0.000	0.000	0.000
9	F	9	ASP	-1	-0.842	-0.927	19.773	-13.672	-13.672	0.000	0.000	0.000	0.000
10	F	10	GLU	-1	-0.852	-0.914	22.883	-11.367	-11.367	0.000	0.000	0.000	0.000
11	F	11	GLU	-1	-0.876	-0.914	19.376	-16.247	-16.247	0.000	0.000	0.000	0.000
12	F	12	GLN	0	-0.035	-0.018	21.290	0.282	0.282	0.000	0.000	0.000	0.000
13	F	13	ALA	0	0.049	0.045	24.594	0.370	0.370	0.000	0.000	0.000	0.000
14	F	14	THR	0	-0.015	-0.021	26.983	0.388	0.388	0.000	0.000	0.000	0.000
15	F	15	GLY	0	0.021	0.006	30.416	0.101	0.101	0.000	0.000	0.000	0.000
16	F	16	LEU	0	0.045	0.014	33.895	-0.118	-0.118	0.000	0.000	0.000	0.000
17	F	17	GLU	-1	-0.899	-0.940	27.444	-11.665	-11.665	0.000	0.000	0.000	0.000
18	F	18	ARG	1	0.816	0.895	26.863	11.450	11.450	0.000	0.000	0.000	0.000
19	F	19	GLU	-1	-0.866	-0.910	31.431	-8.495	-8.495	0.000	0.000	0.000	0.000
20	F	20	VAL	0	-0.003	-0.002	32.743	0.108	0.108	0.000	0.000	0.000	0.000
21	F	21	MET	0	-0.022	0.004	27.082	-0.096	-0.096	0.000	0.000	0.000	0.000
22	F	22	LEU	0	-0.047	-0.035	29.996	-0.039	-0.039	0.000	0.000	0.000	0.000
23	F	23	ALA	0	-0.027	-0.005	32.912	0.180	0.180	0.000	0.000	0.000	0.000
24	F	24	ALA	0	0.055	0.030	32.396	0.133	0.133	0.000	0.000	0.000	0.000
25	F	25	ARG	1	0.806	0.888	26.984	11.622	11.622	0.000	0.000	0.000	0.000
26	F	26	LYS	1	0.908	0.958	32.515	8.694	8.694	0.000	0.000	0.000	0.000
27	F	27	GLY	0	-0.006	0.004	35.460	0.255	0.255	0.000	0.000	0.000	0.000
28	F	28	GLN	0	-0.078	-0.044	37.149	0.179	0.179	0.000	0.000	0.000	0.000
29	F	29	ASP	-1	-0.758	-0.884	37.914	-8.404	-8.404	0.000	0.000	0.000	0.000
30	F	30	PRO	0	-0.030	-0.011	38.894	0.216	0.216	0.000	0.000	0.000	0.000
31	F	31	TYR	0	-0.048	-0.078	38.266	0.245	0.245	0.000	0.000	0.000	0.000
32	F	32	ASN	0	-0.074	-0.017	40.895	0.218	0.218	0.000	0.000	0.000	0.000
33	F	33	ILE	0	0.039	0.015	35.393	0.033	0.033	0.000	0.000	0.000	0.000
34	F	34	LEU	0	-0.051	-0.022	36.518	-0.092	-0.092	0.000	0.000	0.000	0.000
35	F	35	ALA	0	0.009	0.008	40.315	0.192	0.192	0.000	0.000	0.000	0.000
36	F	36	PRO	0	-0.033	-0.012	43.344	-0.063	-0.063	0.000	0.000	0.000	0.000
37	F	37	LYS	1	0.962	0.966	42.664	7.420	7.420	0.000	0.000	0.000	0.000
38	F	38	ALA	0	-0.006	0.009	47.007	0.041	0.041	0.000	0.000	0.000	0.000
39	F	39	THR	0	-0.058	-0.043	50.786	-0.075	-0.075	0.000	0.000	0.000	0.000
40	F	40	SER	0	-0.062	-0.067	53.289	0.055	0.055	0.000	0.000	0.000	0.000
41	F	41	GLY	0	-0.007	0.008	56.335	0.077	0.077	0.000	0.000	0.000	0.000
42	F	42	THR	0	0.018	-0.007	58.081	0.076	0.076	0.000	0.000	0.000	0.000
43	F	43	LYS	1	0.956	0.969	60.972	4.735	4.735	0.000	0.000	0.000	0.000
44	F	44	GLU	-1	-0.891	-0.939	62.022	-5.071	-5.071	0.000	0.000	0.000	0.000
45	F	45	ASP	-1	-0.780	-0.855	55.747	-5.918	-5.918	0.000	0.000	0.000	0.000
46	F	46	PRO	0	-0.026	0.010	57.480	-0.051	-0.051	0.000	0.000	0.000	0.000
47	F	47	ASN	0	0.044	0.011	53.431	-0.194	-0.194	0.000	0.000	0.000	0.000
48	F	48	LEU	0	-0.004	-0.002	52.030	0.063	0.063	0.000	0.000	0.000	0.000
49	F	49	VAL	0	0.004	0.003	51.538	-0.141	-0.141	0.000	0.000	0.000	0.000
50	F	50	PRO	0	0.048	0.024	47.726	0.104	0.104	0.000	0.000	0.000	0.000
51	F	51	SER	0	-0.018	-0.010	50.422	-0.050	-0.050	0.000	0.000	0.000	0.000
52	F	52	ILE	0	0.092	0.055	47.687	0.027	0.027	0.000	0.000	0.000	0.000
53	F	53	THR	0	-0.020	-0.008	51.056	0.132	0.132	0.000	0.000	0.000	0.000
54	F	54	ASN	0	0.011	-0.018	54.719	-0.052	-0.052	0.000	0.000	0.000	0.000
55	F	55	LYS	1	0.937	0.975	56.571	5.722	5.722	0.000	0.000	0.000	0.000
56	F	56	ARG	1	0.837	0.913	47.034	6.628	6.628	0.000	0.000	0.000	0.000
57	F	57	ILE	0	0.010	0.013	53.553	0.110	0.110	0.000	0.000	0.000	0.000
58	F	58	VAL	0	0.001	0.004	53.069	-0.149	-0.149	0.000	0.000	0.000	0.000
59	F	59	GLY	0	0.055	0.010	53.018	0.107	0.107	0.000	0.000	0.000	0.000
60	F	60	CYS	0	-0.047	-0.008	52.943	-0.084	-0.084	0.000	0.000	0.000	0.000
61	F	61	ILE	0	0.053	0.027	49.867	0.109	0.109	0.000	0.000	0.000	0.000
62	F	62	CYS	0	-0.076	-0.054	54.027	0.024	0.024	0.000	0.000	0.000	0.000
63	F	63	GLU	-1	-0.877	-0.933	56.000	-5.355	-5.355	0.000	0.000	0.000	0.000
64	F	64	GLU	-1	-0.932	-0.971	49.200	-6.507	-6.507	0.000	0.000	0.000	0.000
65	F	65	ASP	-1	-0.907	-0.954	50.362	-6.249	-6.249	0.000	0.000	0.000	0.000
66	F	66	ASN	0	-0.096	-0.031	52.503	0.073	0.073	0.000	0.000	0.000	0.000
67	F	67	SER	0	-0.006	-0.009	53.320	-0.062	-0.062	0.000	0.000	0.000	0.000
68	F	68	THR	0	-0.051	-0.023	54.402	0.005	0.005	0.000	0.000	0.000	0.000
69	F	69	VAL	0	-0.008	0.007	52.159	0.021	0.021	0.000	0.000	0.000	0.000
70	F	70	ILE	0	-0.007	-0.009	55.511	0.083	0.083	0.000	0.000	0.000	0.000
71	F	71	TRP	0	0.017	0.015	50.797	-0.077	-0.077	0.000	0.000	0.000	0.000
72	F	72	PHE	0	-0.008	-0.009	57.689	0.135	0.135	0.000	0.000	0.000	0.000
73	F	73	TRP	0	0.012	0.005	55.830	-0.138	-0.138	0.000	0.000	0.000	0.000
74	F	74	LEU	0	0.000	0.018	55.827	0.113	0.113	0.000	0.000	0.000	0.000
75	F	75	HIS	0	0.042	-0.009	58.173	-0.124	-0.124	0.000	0.000	0.000	0.000
76	F	76	LYS	1	0.944	0.976	58.967	5.511	5.511	0.000	0.000	0.000	0.000
77	F	77	GLY	0	0.012	0.005	60.603	0.093	0.093	0.000	0.000	0.000	0.000
78	F	78	GLU	-1	-0.964	-0.978	62.462	-4.909	-4.909	0.000	0.000	0.000	0.000
79	F	79	ALA	0	-0.024	-0.007	61.287	-0.055	-0.055	0.000	0.000	0.000	0.000
80	F	80	GLN	0	0.023	0.013	61.387	0.064	0.064	0.000	0.000	0.000	0.000
81	F	81	ARG	1	0.877	0.926	61.348	4.900	4.900	0.000	0.000	0.000	0.000
82	F	82	CYS	0	-0.052	-0.014	59.277	0.035	0.035	0.000	0.000	0.000	0.000
83	F	83	PRO	0	-0.028	-0.026	61.397	0.061	0.061	0.000	0.000	0.000	0.000
84	F	84	SER	0	-0.021	0.008	61.618	0.083	0.083	0.000	0.000	0.000	0.000
85	F	85	CYS	0	0.061	0.032	58.711	0.053	0.053	0.000	0.000	0.000	0.000
86	F	86	GLY	0	0.024	0.023	62.406	0.019	0.019	0.000	0.000	0.000	0.000
87	F	87	THR	0	0.034	0.020	57.511	0.047	0.047	0.000	0.000	0.000	0.000
88	F	88	HIS	0	-0.046	-0.039	60.101	0.095	0.095	0.000	0.000	0.000	0.000
89	F	89	TYR	0	0.045	0.011	53.774	-0.156	-0.156	0.000	0.000	0.000	0.000
90	F	90	LYS	1	0.927	0.949	56.737	5.558	5.558	0.000	0.000	0.000	0.000
91	F	91	LEU	0	-0.029	0.009	54.854	-0.105	-0.105	0.000	0.000	0.000	0.000
92	F	92	VAL	0	-0.032	-0.020	51.577	0.099	0.099	0.000	0.000	0.000	0.000
93	F	93	PRO	0	-0.066	-0.036	52.447	-0.112	-0.112	0.000	0.000	0.000	0.000
94	F	94	HIS	0	-0.034	-0.027	51.991	0.063	0.063	0.000	0.000	0.000	0.000
95	F	95	GLN	0	0.038	0.015	48.037	-0.043	-0.043	0.000	0.000	0.000	0.000
96	F	96	LEU	0	-0.024	0.014	42.789	-0.003	-0.003	0.000	0.000	0.000	0.000
97	F	97	ALA	0	-0.017	-0.008	43.726	-0.165	-0.165	0.000	0.000	0.000	0.000
98	F	98	HIS	-1	-0.973	-0.980	43.893	-6.979	-6.979	0.000	0.000	0.000	0.000

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