FMO DATABASE

FMODB ID: VZ7R1

Calculation Name: 1V54-H-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: H

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-543330.88512
FMO2-HF: Nuclear repulsion	509690.290058
FMO2-HF: Total energy	-33640.595062
FMO2-MP2: Total energy	-33736.412836

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(H:7:LYS)

Summations of interaction energy for fragment #1(H:7:LYS)

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.
149.356	152.414	0.03	-1.306	-1.782	-0.007

Interaction energy analysis for fragmet #1(H:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.858 / q_NPA : 1.908

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	H	9	LYS	1	0.920	0.966	3.065	85.947	88.794	0.031	-1.285	-1.593	-0.007
4	H	10	ASN	0	0.026	0.018	4.457	6.364	6.575	-0.001	-0.021	-0.189	0.000
5	H	11	TYR	0	-0.037	-0.015	6.613	3.897	3.897	0.000	0.000	0.000	0.000
6	H	12	GLN	0	0.021	0.018	8.900	0.433	0.433	0.000	0.000	0.000	0.000
7	H	13	THR	0	0.031	-0.007	12.506	0.679	0.679	0.000	0.000	0.000	0.000
8	H	14	ALA	0	-0.002	0.010	13.970	-1.688	-1.688	0.000	0.000	0.000	0.000
9	H	15	PRO	0	-0.013	0.000	13.908	1.433	1.433	0.000	0.000	0.000	0.000
10	H	16	PHE	0	0.030	0.010	16.798	0.720	0.720	0.000	0.000	0.000	0.000
11	H	17	ASP	-1	-0.794	-0.879	19.291	-29.858	-29.858	0.000	0.000	0.000	0.000
12	H	18	SER	0	0.009	0.004	20.712	1.178	1.178	0.000	0.000	0.000	0.000
13	H	19	ARG	1	0.857	0.908	18.790	29.950	29.950	0.000	0.000	0.000	0.000
14	H	20	PHE	0	-0.059	-0.036	21.398	0.890	0.890	0.000	0.000	0.000	0.000
15	H	21	PRO	0	0.037	0.030	25.076	-0.359	-0.359	0.000	0.000	0.000	0.000
16	H	22	ASN	0	0.008	0.011	26.814	0.697	0.697	0.000	0.000	0.000	0.000
17	H	23	GLN	0	0.067	0.021	27.940	-0.446	-0.446	0.000	0.000	0.000	0.000
18	H	24	ASN	0	0.009	0.020	29.127	-0.789	-0.789	0.000	0.000	0.000	0.000
19	H	25	GLN	0	0.051	0.010	23.603	-1.186	-1.186	0.000	0.000	0.000	0.000
20	H	26	THR	0	-0.008	-0.005	24.795	-0.934	-0.934	0.000	0.000	0.000	0.000
21	H	27	ARG	1	0.918	0.951	25.332	21.621	21.621	0.000	0.000	0.000	0.000
22	H	28	ASN	0	0.035	0.020	20.152	-1.555	-1.555	0.000	0.000	0.000	0.000
23	H	29	CYS	0	-0.068	-0.002	20.338	0.023	0.023	0.000	0.000	0.000	0.000
24	H	30	TRP	0	0.056	0.017	20.940	-1.121	-1.121	0.000	0.000	0.000	0.000
25	H	31	GLN	0	-0.069	-0.033	20.927	0.857	0.857	0.000	0.000	0.000	0.000
26	H	32	ASN	0	-0.011	-0.017	16.263	-2.604	-2.604	0.000	0.000	0.000	0.000
27	H	33	TYR	0	0.031	-0.016	17.279	-1.669	-1.669	0.000	0.000	0.000	0.000
28	H	34	LEU	0	-0.033	-0.003	19.551	-0.318	-0.318	0.000	0.000	0.000	0.000
29	H	35	ASP	-1	-0.857	-0.934	17.097	-30.136	-30.136	0.000	0.000	0.000	0.000
30	H	36	PHE	0	-0.008	-0.018	12.560	-1.554	-1.554	0.000	0.000	0.000	0.000
31	H	37	HIS	1	0.864	0.938	15.797	29.557	29.557	0.000	0.000	0.000	0.000
32	H	38	ARG	1	0.841	0.927	18.660	26.788	26.788	0.000	0.000	0.000	0.000
33	H	39	CYS	0	-0.027	0.009	8.013	1.364	1.364	0.000	0.000	0.000	0.000
34	H	40	GLU	-1	-0.870	-0.949	15.265	-34.689	-34.689	0.000	0.000	0.000	0.000
35	H	41	LYS	1	0.873	0.946	16.136	24.928	24.928	0.000	0.000	0.000	0.000
36	H	42	ALA	0	-0.018	-0.012	17.397	0.679	0.679	0.000	0.000	0.000	0.000
37	H	43	MET	0	-0.054	-0.024	11.541	1.231	1.231	0.000	0.000	0.000	0.000
38	H	44	THR	0	0.010	-0.010	15.800	-0.242	-0.242	0.000	0.000	0.000	0.000
39	H	45	ALA	0	-0.041	-0.008	17.643	1.048	1.048	0.000	0.000	0.000	0.000
40	H	46	LYS	1	0.897	0.935	18.425	28.636	28.636	0.000	0.000	0.000	0.000
41	H	47	GLY	0	0.034	0.044	17.146	0.183	0.183	0.000	0.000	0.000	0.000
42	H	48	GLY	0	-0.001	-0.010	13.313	-0.882	-0.882	0.000	0.000	0.000	0.000
43	H	49	ASP	-1	-0.832	-0.895	7.590	-65.986	-65.986	0.000	0.000	0.000	0.000
44	H	50	VAL	0	0.039	0.006	10.905	-0.074	-0.074	0.000	0.000	0.000	0.000
45	H	51	SER	0	-0.069	-0.053	5.990	-3.207	-3.207	0.000	0.000	0.000	0.000
46	H	52	VAL	0	0.006	-0.012	6.698	-5.464	-5.464	0.000	0.000	0.000	0.000
47	H	54	GLU	-1	-0.790	-0.868	5.997	-55.410	-55.410	0.000	0.000	0.000	0.000
48	H	55	TRP	0	-0.021	-0.019	8.555	-1.278	-1.278	0.000	0.000	0.000	0.000
49	H	56	TYR	0	0.072	0.041	9.674	1.624	1.624	0.000	0.000	0.000	0.000
50	H	57	ARG	1	0.813	0.881	9.986	51.356	51.356	0.000	0.000	0.000	0.000
51	H	58	ARG	1	0.899	0.963	8.565	53.511	53.511	0.000	0.000	0.000	0.000
52	H	59	VAL	0	0.060	0.047	12.189	2.388	2.388	0.000	0.000	0.000	0.000
53	H	60	TYR	0	0.013	0.006	14.808	2.496	2.496	0.000	0.000	0.000	0.000
54	H	61	LYS	1	0.887	0.934	14.905	34.278	34.278	0.000	0.000	0.000	0.000
55	H	62	SER	0	-0.019	-0.002	14.906	0.292	0.292	0.000	0.000	0.000	0.000
56	H	63	LEU	0	-0.011	0.002	17.469	1.323	1.323	0.000	0.000	0.000	0.000
57	H	65	PRO	0	0.047	0.034	22.371	-0.456	-0.456	0.000	0.000	0.000	0.000
58	H	66	ILE	0	0.058	0.021	22.861	-0.115	-0.115	0.000	0.000	0.000	0.000
59	H	67	SER	0	0.048	0.024	24.786	-0.284	-0.284	0.000	0.000	0.000	0.000
60	H	68	TRP	0	0.000	0.008	25.705	0.124	0.124	0.000	0.000	0.000	0.000
61	H	69	VAL	0	0.003	-0.006	20.873	-0.310	-0.310	0.000	0.000	0.000	0.000
62	H	70	SER	0	-0.010	0.008	23.819	-0.219	-0.219	0.000	0.000	0.000	0.000
63	H	71	THR	0	0.004	-0.002	26.231	0.366	0.366	0.000	0.000	0.000	0.000
64	H	72	TRP	0	-0.040	-0.044	23.269	0.136	0.136	0.000	0.000	0.000	0.000
65	H	73	ASP	-1	-0.809	-0.879	22.014	-27.833	-27.833	0.000	0.000	0.000	0.000
66	H	74	ASP	-1	-0.846	-0.923	25.036	-21.142	-21.142	0.000	0.000	0.000	0.000
67	H	75	ARG	1	0.971	0.979	28.680	18.963	18.963	0.000	0.000	0.000	0.000
68	H	76	ARG	1	0.768	0.860	21.850	26.875	26.875	0.000	0.000	0.000	0.000
69	H	77	ALA	0	-0.033	-0.003	27.433	-0.048	-0.048	0.000	0.000	0.000	0.000
70	H	78	GLU	-1	-0.877	-0.908	28.882	-17.541	-17.541	0.000	0.000	0.000	0.000
71	H	79	GLY	0	-0.008	0.007	30.758	0.481	0.481	0.000	0.000	0.000	0.000
72	H	80	THR	0	-0.051	-0.059	31.900	0.069	0.069	0.000	0.000	0.000	0.000
73	H	81	PHE	0	-0.058	-0.027	25.193	-0.031	-0.031	0.000	0.000	0.000	0.000
74	H	82	PRO	0	0.019	0.013	30.001	-0.149	-0.149	0.000	0.000	0.000	0.000
75	H	83	GLY	0	-0.018	-0.008	27.234	0.121	0.121	0.000	0.000	0.000	0.000
76	H	84	LYS	1	0.949	0.972	27.266	20.915	20.915	0.000	0.000	0.000	0.000
77	H	85	ILE	-1	-0.796	-0.890	21.962	-25.488	-25.488	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:7:LYS)