FMO DATABASE

FMODB ID: N651Q

Calculation Name: 1V54-D-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: D

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	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-967330.408518
FMO2-HF: Nuclear repulsion	908632.576873
FMO2-HF: Total energy	-58697.831645
FMO2-MP2: Total energy	-58870.362776

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(D:4:SER)

Summations of interaction energy for fragment #1(D:4:SER)

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.
-22.508	-16.529	4.451	-5.139	-5.29	-0.05

Interaction energy analysis for fragmet #1(D:4:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.910

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	D	6	VAL	0	0.002	0.011	3.882	-3.106	-2.088	-0.011	-0.423	-0.585	0.000
26	D	29	HIS	0	-0.041	-0.012	3.263	-18.221	-16.027	0.178	-1.074	-1.298	-0.010
27	D	30	VAL	0	-0.061	-0.036	2.131	-40.629	-38.000	4.285	-3.612	-3.300	-0.040
28	D	31	LYS	1	1.003	0.999	4.084	51.861	51.999	-0.001	-0.030	-0.107	0.000
4	D	7	LYS	1	0.813	0.896	6.397	32.619	32.619	0.000	0.000	0.000	0.000
5	D	8	SER	0	0.034	0.010	10.169	-0.318	-0.318	0.000	0.000	0.000	0.000
6	D	9	GLU	-1	-0.808	-0.910	12.556	-23.688	-23.688	0.000	0.000	0.000	0.000
7	D	10	ASP	-1	-0.877	-0.927	9.032	-31.107	-31.107	0.000	0.000	0.000	0.000
8	D	11	TYR	0	-0.036	-0.019	11.799	-0.375	-0.375	0.000	0.000	0.000	0.000
9	D	12	ALA	0	-0.007	0.006	13.637	0.735	0.735	0.000	0.000	0.000	0.000
10	D	13	LEU	0	-0.046	-0.016	10.929	0.756	0.756	0.000	0.000	0.000	0.000
11	D	14	PRO	0	0.017	0.004	11.666	-0.783	-0.783	0.000	0.000	0.000	0.000
12	D	15	SER	0	-0.005	-0.004	8.056	-2.627	-2.627	0.000	0.000	0.000	0.000
13	D	16	TYR	0	-0.091	-0.067	5.361	-0.007	-0.007	0.000	0.000	0.000	0.000
14	D	17	VAL	0	0.012	-0.001	7.377	-0.266	-0.266	0.000	0.000	0.000	0.000
15	D	18	ASP	-1	-0.759	-0.860	9.445	-30.493	-30.493	0.000	0.000	0.000	0.000
16	D	19	ARG	1	0.874	0.904	11.848	18.557	18.557	0.000	0.000	0.000	0.000
17	D	20	ARG	1	0.938	0.972	15.559	13.947	13.947	0.000	0.000	0.000	0.000
18	D	21	ASP	-1	-0.831	-0.905	18.795	-15.318	-15.318	0.000	0.000	0.000	0.000
19	D	22	TYR	0	-0.087	-0.062	13.819	1.036	1.036	0.000	0.000	0.000	0.000
20	D	23	PRO	0	0.012	0.011	14.828	-1.325	-1.325	0.000	0.000	0.000	0.000
21	D	24	LEU	0	-0.044	-0.027	14.107	-0.875	-0.875	0.000	0.000	0.000	0.000
22	D	25	PRO	0	0.002	0.002	9.904	0.624	0.624	0.000	0.000	0.000	0.000
23	D	26	ASP	-1	-0.827	-0.883	11.570	-21.863	-21.863	0.000	0.000	0.000	0.000
24	D	27	VAL	0	-0.051	-0.018	6.907	0.024	0.024	0.000	0.000	0.000	0.000
25	D	28	ALA	0	-0.040	-0.021	7.538	0.170	0.170	0.000	0.000	0.000	0.000
29	D	32	ASN	0	-0.044	-0.018	5.826	6.296	6.296	0.000	0.000	0.000	0.000
30	D	33	LEU	0	0.017	0.018	7.313	-1.601	-1.601	0.000	0.000	0.000	0.000
31	D	34	SER	0	0.056	0.014	9.748	2.324	2.324	0.000	0.000	0.000	0.000
32	D	35	ALA	0	0.037	0.008	11.431	0.542	0.542	0.000	0.000	0.000	0.000
33	D	36	SER	0	0.044	0.020	13.270	0.380	0.380	0.000	0.000	0.000	0.000
34	D	37	GLN	0	0.029	0.008	7.454	-0.499	-0.499	0.000	0.000	0.000	0.000
35	D	38	LYS	1	0.901	0.952	12.598	22.162	22.162	0.000	0.000	0.000	0.000
36	D	39	ALA	0	0.050	0.027	15.105	0.564	0.564	0.000	0.000	0.000	0.000
37	D	40	LEU	0	-0.013	0.007	12.821	0.751	0.751	0.000	0.000	0.000	0.000
38	D	41	LYS	1	0.849	0.892	12.417	22.334	22.334	0.000	0.000	0.000	0.000
39	D	42	GLU	-1	-0.851	-0.895	16.182	-14.780	-14.780	0.000	0.000	0.000	0.000
40	D	43	LYS	1	0.832	0.912	19.514	14.497	14.497	0.000	0.000	0.000	0.000
41	D	44	GLU	-1	-0.845	-0.908	15.644	-19.189	-19.189	0.000	0.000	0.000	0.000
42	D	45	LYS	1	0.806	0.891	18.999	16.060	16.060	0.000	0.000	0.000	0.000
43	D	46	ALA	0	-0.003	0.020	22.122	0.706	0.706	0.000	0.000	0.000	0.000
44	D	47	SER	0	0.034	0.009	23.974	-0.355	-0.355	0.000	0.000	0.000	0.000
45	D	48	TRP	0	0.022	-0.009	20.442	-0.064	-0.064	0.000	0.000	0.000	0.000
46	D	49	SER	0	-0.014	-0.012	23.807	-0.093	-0.093	0.000	0.000	0.000	0.000
47	D	50	SER	0	-0.021	-0.009	25.491	0.205	0.205	0.000	0.000	0.000	0.000
48	D	51	LEU	0	-0.051	-0.009	19.146	-0.223	-0.223	0.000	0.000	0.000	0.000
49	D	52	SER	0	0.013	-0.014	20.351	0.188	0.188	0.000	0.000	0.000	0.000
50	D	53	ILE	0	0.027	-0.004	19.534	-0.510	-0.510	0.000	0.000	0.000	0.000
51	D	54	ASP	-1	-0.844	-0.920	16.811	-16.062	-16.062	0.000	0.000	0.000	0.000
52	D	55	GLU	-1	-0.774	-0.862	15.334	-15.875	-15.875	0.000	0.000	0.000	0.000
53	D	56	LYS	1	0.862	0.929	15.424	12.671	12.671	0.000	0.000	0.000	0.000
54	D	57	VAL	0	-0.002	0.006	13.110	-1.035	-1.035	0.000	0.000	0.000	0.000
55	D	58	GLU	-1	-0.866	-0.932	10.051	-25.971	-25.971	0.000	0.000	0.000	0.000
56	D	59	LEU	0	-0.022	-0.023	10.629	-2.506	-2.506	0.000	0.000	0.000	0.000
57	D	60	TYR	0	-0.006	-0.002	11.381	-1.763	-1.763	0.000	0.000	0.000	0.000
58	D	61	ARG	1	0.797	0.856	8.022	24.292	24.292	0.000	0.000	0.000	0.000
59	D	62	LEU	0	-0.007	0.005	6.817	-5.516	-5.516	0.000	0.000	0.000	0.000
60	D	63	LYS	1	0.913	0.969	6.701	20.924	20.924	0.000	0.000	0.000	0.000
61	D	64	PHE	0	0.023	-0.005	8.114	-1.942	-1.942	0.000	0.000	0.000	0.000
62	D	65	LYS	1	0.890	0.966	4.851	34.349	34.349	0.000	0.000	0.000	0.000
63	D	66	GLU	-1	-0.842	-0.916	7.367	-23.923	-23.923	0.000	0.000	0.000	0.000
64	D	67	SER	0	0.006	-0.013	10.705	0.949	0.949	0.000	0.000	0.000	0.000
65	D	68	PHE	0	0.030	-0.005	14.129	0.346	0.346	0.000	0.000	0.000	0.000
66	D	69	ALA	0	0.004	0.012	17.041	0.643	0.643	0.000	0.000	0.000	0.000
67	D	70	GLU	-1	-0.752	-0.817	12.584	-22.422	-22.422	0.000	0.000	0.000	0.000
68	D	71	MET	0	-0.016	0.001	13.034	0.807	0.807	0.000	0.000	0.000	0.000
69	D	72	ASN	0	-0.055	-0.034	15.202	0.635	0.635	0.000	0.000	0.000	0.000
70	D	73	ARG	1	0.800	0.906	13.118	21.168	21.168	0.000	0.000	0.000	0.000
71	D	74	SER	0	0.023	0.017	19.896	-0.198	-0.198	0.000	0.000	0.000	0.000
72	D	75	THR	0	0.027	0.000	20.116	-0.113	-0.113	0.000	0.000	0.000	0.000
73	D	76	ASN	0	0.020	-0.004	22.873	0.966	0.966	0.000	0.000	0.000	0.000
74	D	77	GLU	-1	-0.904	-0.939	22.904	-13.192	-13.192	0.000	0.000	0.000	0.000
75	D	78	TRP	0	0.070	0.020	25.271	0.435	0.435	0.000	0.000	0.000	0.000
76	D	79	LYS	1	0.886	0.946	28.627	10.852	10.852	0.000	0.000	0.000	0.000
77	D	80	THR	0	0.019	0.011	26.401	0.402	0.402	0.000	0.000	0.000	0.000
78	D	81	VAL	0	0.015	0.014	27.298	0.267	0.267	0.000	0.000	0.000	0.000
79	D	82	VAL	0	0.009	0.003	29.975	0.284	0.284	0.000	0.000	0.000	0.000
80	D	83	GLY	0	0.026	0.014	32.830	0.287	0.287	0.000	0.000	0.000	0.000
81	D	84	ALA	0	0.003	-0.002	31.473	0.252	0.252	0.000	0.000	0.000	0.000
82	D	85	ALA	0	0.006	0.005	33.483	0.227	0.227	0.000	0.000	0.000	0.000
83	D	86	MET	0	-0.011	-0.017	35.438	0.218	0.218	0.000	0.000	0.000	0.000
84	D	87	PHE	0	-0.004	0.018	36.186	0.252	0.252	0.000	0.000	0.000	0.000
85	D	88	PHE	0	0.019	-0.001	33.118	0.186	0.186	0.000	0.000	0.000	0.000
86	D	89	ILE	0	-0.008	0.015	38.509	0.205	0.205	0.000	0.000	0.000	0.000
87	D	90	GLY	0	0.019	0.007	41.176	0.213	0.213	0.000	0.000	0.000	0.000
88	D	91	PHE	0	-0.004	-0.018	40.748	0.178	0.178	0.000	0.000	0.000	0.000
89	D	92	THR	0	-0.012	-0.027	41.774	0.137	0.137	0.000	0.000	0.000	0.000
90	D	93	ALA	0	0.008	0.004	44.210	0.171	0.171	0.000	0.000	0.000	0.000
91	D	94	LEU	0	-0.012	-0.004	44.488	0.174	0.174	0.000	0.000	0.000	0.000
92	D	95	LEU	0	-0.015	0.003	43.901	0.144	0.144	0.000	0.000	0.000	0.000
93	D	96	LEU	0	0.025	0.022	48.169	0.132	0.132	0.000	0.000	0.000	0.000
94	D	97	ILE	0	-0.028	-0.009	49.953	0.161	0.161	0.000	0.000	0.000	0.000
95	D	98	TRP	0	-0.004	-0.002	50.849	0.127	0.127	0.000	0.000	0.000	0.000
96	D	99	GLU	-1	-0.829	-0.917	52.154	-5.987	-5.987	0.000	0.000	0.000	0.000
97	D	100	LYS	1	0.855	0.924	53.949	5.518	5.518	0.000	0.000	0.000	0.000
98	D	101	HIS	0	-0.044	-0.007	55.963	0.152	0.152	0.000	0.000	0.000	0.000
99	D	102	TYR	0	-0.059	-0.035	54.895	0.123	0.123	0.000	0.000	0.000	0.000
100	D	103	VAL	0	-0.009	0.009	54.626	0.032	0.032	0.000	0.000	0.000	0.000
101	D	104	TYR	0	-0.112	-0.060	54.794	0.161	0.161	0.000	0.000	0.000	0.000
102	D	105	GLY	0	0.044	0.025	59.896	0.021	0.021	0.000	0.000	0.000	0.000
103	D	106	PRO	0	-0.040	-0.025	63.094	-0.059	-0.059	0.000	0.000	0.000	0.000
104	D	107	ILE	0	0.010	0.008	63.330	-0.022	-0.022	0.000	0.000	0.000	0.000
105	D	108	PRO	0	-0.001	-0.014	66.021	0.060	0.060	0.000	0.000	0.000	0.000
106	D	109	HIS	0	0.090	0.044	69.427	-0.061	-0.061	0.000	0.000	0.000	0.000
107	D	110	THR	0	-0.028	-0.017	69.812	0.021	0.021	0.000	0.000	0.000	0.000
108	D	111	PHE	0	-0.058	-0.036	65.623	-0.021	-0.021	0.000	0.000	0.000	0.000
109	D	112	GLU	-1	-0.906	-0.945	69.304	-4.417	-4.417	0.000	0.000	0.000	0.000
110	D	113	GLU	-1	-0.926	-0.962	71.663	-4.448	-4.448	0.000	0.000	0.000	0.000
111	D	114	GLU	-1	-0.806	-0.911	72.665	-4.019	-4.019	0.000	0.000	0.000	0.000
112	D	115	TRP	0	0.008	0.009	73.513	0.072	0.072	0.000	0.000	0.000	0.000
113	D	116	VAL	0	0.019	0.003	69.848	0.024	0.024	0.000	0.000	0.000	0.000
114	D	117	ALA	0	0.032	0.036	73.014	0.004	0.004	0.000	0.000	0.000	0.000
115	D	118	LYS	1	0.836	0.912	75.598	4.051	4.051	0.000	0.000	0.000	0.000
116	D	119	GLN	0	-0.030	-0.009	71.373	0.063	0.063	0.000	0.000	0.000	0.000
117	D	120	THR	0	-0.002	-0.018	73.055	-0.016	-0.016	0.000	0.000	0.000	0.000
118	D	121	LYS	1	0.916	0.944	74.920	3.941	3.941	0.000	0.000	0.000	0.000
119	D	122	ARG	1	0.988	0.991	77.551	4.143	4.143	0.000	0.000	0.000	0.000
120	D	123	MET	0	-0.048	-0.028	70.700	0.013	0.013	0.000	0.000	0.000	0.000
121	D	124	LEU	0	0.024	0.037	74.871	-0.003	-0.003	0.000	0.000	0.000	0.000
122	D	125	ASP	-1	-0.850	-0.898	77.856	-3.914	-3.914	0.000	0.000	0.000	0.000
123	D	126	MET	0	-0.102	-0.053	77.809	0.025	0.025	0.000	0.000	0.000	0.000
124	D	127	LYS	1	0.916	0.979	77.874	3.938	3.938	0.000	0.000	0.000	0.000
125	D	128	VAL	0	0.050	0.021	71.984	-0.031	-0.031	0.000	0.000	0.000	0.000
126	D	129	ALA	0	0.006	0.005	70.550	-0.032	-0.032	0.000	0.000	0.000	0.000
127	D	130	PRO	0	0.038	0.014	72.554	-0.045	-0.045	0.000	0.000	0.000	0.000
128	D	131	ILE	0	0.012	0.011	72.703	0.013	0.013	0.000	0.000	0.000	0.000
129	D	132	GLN	0	0.014	-0.007	67.593	-0.044	-0.044	0.000	0.000	0.000	0.000
130	D	133	GLY	0	-0.004	0.004	67.684	-0.037	-0.037	0.000	0.000	0.000	0.000
131	D	134	PHE	0	0.007	-0.005	68.237	-0.068	-0.068	0.000	0.000	0.000	0.000
132	D	135	SER	0	0.065	0.003	70.800	0.024	0.024	0.000	0.000	0.000	0.000
133	D	136	ALA	0	-0.029	0.011	71.814	0.046	0.046	0.000	0.000	0.000	0.000
134	D	137	LYS	1	0.893	0.941	66.203	4.856	4.856	0.000	0.000	0.000	0.000
135	D	138	TRP	0	0.019	0.027	72.666	-0.028	-0.028	0.000	0.000	0.000	0.000
136	D	139	ASP	-1	-0.860	-0.940	75.966	-4.063	-4.063	0.000	0.000	0.000	0.000
137	D	140	TYR	0	-0.081	-0.084	78.159	0.006	0.006	0.000	0.000	0.000	0.000
138	D	141	ASP	-1	-0.946	-0.947	81.899	-3.811	-3.811	0.000	0.000	0.000	0.000
139	D	142	LYS	0	-0.039	-0.011	79.351	0.033	0.033	0.000	0.000	0.000	0.000
140	D	143	ASN	0	-0.103	-0.042	81.529	0.014	0.014	0.000	0.000	0.000	0.000
141	D	144	GLU	-1	-0.833	-0.923	77.505	-4.142	-4.142	0.000	0.000	0.000	0.000
142	D	145	TRP	0	-0.040	-0.029	72.585	-0.018	-0.018	0.000	0.000	0.000	0.000
143	D	146	LYS	1	0.822	0.899	73.272	4.310	4.310	0.000	0.000	0.000	0.000
144	D	147	LYS	0	-0.056	-0.012	70.710	-0.445	-0.445	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(D:4:SER)