FMO DATABASE

FMODB ID: RL228

Calculation Name: 4LSD-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4LSD

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NAU1

Base Structure: X-ray

Registration Date: 2025-10-05

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

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	-694940.803609
FMO2-HF: Nuclear repulsion	656366.374993
FMO2-HF: Total energy	-38574.428615
FMO2-MP2: Total energy	-38686.793685

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(A:29:MET)

Summations of interaction energy for fragment #1(A:29:MET)

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.
-118.034	-113.371	4.42	-3.544	-5.538	-0.022

Interaction energy analysis for fragmet #1(A:29:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.909

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	A	31	PRO	0	0.028	0.027	3.838	0.087	2.217	-0.023	-0.985	-1.122	-0.004
80	A	108	GLN	0	-0.026	-0.026	2.748	-11.353	-9.434	4.440	-2.250	-4.108	-0.016
81	A	109	GLY	0	-0.016	-0.003	3.693	-14.283	-13.812	0.004	-0.302	-0.173	-0.002
82	A	110	GLN	0	-0.004	0.010	5.326	6.706	6.849	-0.001	-0.007	-0.135	0.000
4	A	32	SER	0	-0.025	-0.041	6.620	-0.155	-0.155	0.000	0.000	0.000	0.000
5	A	33	ALA	0	-0.031	-0.014	9.406	-0.028	-0.028	0.000	0.000	0.000	0.000
6	A	34	PRO	0	-0.059	-0.021	12.576	0.756	0.756	0.000	0.000	0.000	0.000
7	A	35	VAL	0	0.015	0.006	15.446	0.610	0.610	0.000	0.000	0.000	0.000
8	A	36	ASN	0	-0.075	-0.057	18.068	0.367	0.367	0.000	0.000	0.000	0.000
9	A	37	VAL	0	0.008	0.008	19.664	0.371	0.371	0.000	0.000	0.000	0.000
10	A	38	THR	0	-0.016	-0.001	22.311	0.655	0.655	0.000	0.000	0.000	0.000
11	A	39	VAL	0	0.016	0.015	25.936	-0.196	-0.196	0.000	0.000	0.000	0.000
12	A	40	ARG	1	0.915	0.949	26.508	11.655	11.655	0.000	0.000	0.000	0.000
13	A	41	HIS	0	-0.007	-0.018	30.852	0.061	0.061	0.000	0.000	0.000	0.000
14	A	42	LEU	0	-0.031	-0.003	32.831	-0.035	-0.035	0.000	0.000	0.000	0.000
15	A	43	LYS	1	0.912	0.946	34.672	9.101	9.101	0.000	0.000	0.000	0.000
16	A	44	ALA	0	0.038	0.028	36.875	-0.216	-0.216	0.000	0.000	0.000	0.000
17	A	45	ASN	0	0.040	0.009	37.203	-0.192	-0.192	0.000	0.000	0.000	0.000
18	A	46	SER	0	-0.075	-0.039	33.793	-0.151	-0.151	0.000	0.000	0.000	0.000
19	A	47	ALA	0	0.018	0.012	30.411	0.188	0.188	0.000	0.000	0.000	0.000
20	A	48	VAL	0	-0.028	-0.006	27.336	-0.156	-0.156	0.000	0.000	0.000	0.000
21	A	49	VAL	0	0.041	0.030	22.900	0.126	0.126	0.000	0.000	0.000	0.000
22	A	50	SER	0	-0.043	-0.044	23.003	0.177	0.177	0.000	0.000	0.000	0.000
23	A	51	TRP	0	-0.014	0.003	16.550	0.442	0.442	0.000	0.000	0.000	0.000
24	A	52	ASP	-1	-0.788	-0.868	18.346	-14.163	-14.163	0.000	0.000	0.000	0.000
25	A	53	VAL	0	-0.053	-0.047	12.625	-0.863	-0.863	0.000	0.000	0.000	0.000
26	A	54	LEU	0	0.034	0.014	11.730	0.944	0.944	0.000	0.000	0.000	0.000
27	A	55	GLU	-1	-0.775	-0.869	6.901	-32.401	-32.401	0.000	0.000	0.000	0.000
28	A	56	ASP	-1	-0.827	-0.912	10.490	-19.401	-19.401	0.000	0.000	0.000	0.000
29	A	57	GLU	-1	-0.975	-0.976	9.743	-21.968	-21.968	0.000	0.000	0.000	0.000
30	A	58	VAL	0	-0.036	-0.017	5.230	-1.227	-1.227	0.000	0.000	0.000	0.000
31	A	59	VAL	0	-0.050	-0.026	8.375	-2.461	-2.461	0.000	0.000	0.000	0.000
32	A	60	ILE	0	0.005	0.007	10.578	2.012	2.012	0.000	0.000	0.000	0.000
33	A	61	GLY	0	0.026	0.001	12.763	1.494	1.494	0.000	0.000	0.000	0.000
34	A	62	PHE	0	-0.018	-0.009	13.680	-1.224	-1.224	0.000	0.000	0.000	0.000
35	A	63	ALA	0	0.016	0.002	15.066	0.514	0.514	0.000	0.000	0.000	0.000
36	A	64	ILE	0	-0.014	-0.006	16.717	-0.131	-0.131	0.000	0.000	0.000	0.000
37	A	65	SER	0	-0.003	0.002	19.051	0.101	0.101	0.000	0.000	0.000	0.000
38	A	66	GLN	0	0.076	0.045	21.448	0.122	0.122	0.000	0.000	0.000	0.000
39	A	67	GLN	0	-0.007	0.002	25.242	-0.174	-0.174	0.000	0.000	0.000	0.000
40	A	68	LYS	1	0.861	0.918	27.847	8.976	8.976	0.000	0.000	0.000	0.000
41	A	69	LYS	1	0.829	0.891	30.184	9.096	9.096	0.000	0.000	0.000	0.000
42	A	70	ASP	-1	-0.885	-0.939	31.461	-8.960	-8.960	0.000	0.000	0.000	0.000
43	A	71	VAL	0	-0.061	-0.020	28.240	0.077	0.077	0.000	0.000	0.000	0.000
44	A	72	ARG	1	0.910	0.938	31.118	9.463	9.463	0.000	0.000	0.000	0.000
45	A	73	MET	0	-0.018	0.009	28.469	-0.121	-0.121	0.000	0.000	0.000	0.000
46	A	74	LEU	0	0.015	0.005	24.789	-0.075	-0.075	0.000	0.000	0.000	0.000
47	A	75	ARG	1	0.841	0.895	26.042	10.980	10.980	0.000	0.000	0.000	0.000
48	A	76	PHE	0	0.003	-0.004	20.301	-0.220	-0.220	0.000	0.000	0.000	0.000
49	A	77	ILE	0	-0.004	-0.002	21.175	0.558	0.558	0.000	0.000	0.000	0.000
50	A	78	GLN	0	-0.023	-0.021	14.917	-0.740	-0.740	0.000	0.000	0.000	0.000
51	A	79	GLU	-1	-0.887	-0.926	18.218	-13.520	-13.520	0.000	0.000	0.000	0.000
52	A	80	VAL	0	0.002	-0.020	14.171	-1.266	-1.266	0.000	0.000	0.000	0.000
53	A	81	ASN	0	-0.044	-0.015	15.432	0.443	0.443	0.000	0.000	0.000	0.000
54	A	82	THR	0	-0.001	0.006	16.628	1.260	1.260	0.000	0.000	0.000	0.000
55	A	83	THR	0	0.018	0.000	16.683	-0.822	-0.822	0.000	0.000	0.000	0.000
56	A	84	THR	0	-0.037	-0.003	18.480	0.312	0.312	0.000	0.000	0.000	0.000
57	A	85	ARG	1	0.854	0.909	14.675	16.933	16.933	0.000	0.000	0.000	0.000
58	A	86	SER	0	-0.018	-0.010	20.155	0.516	0.516	0.000	0.000	0.000	0.000
59	A	87	CYS	0	-0.018	0.002	22.454	-0.254	-0.254	0.000	0.000	0.000	0.000
60	A	88	ALA	0	-0.007	0.010	24.348	0.291	0.291	0.000	0.000	0.000	0.000
61	A	89	LEU	0	-0.021	-0.008	25.660	-0.329	-0.329	0.000	0.000	0.000	0.000
62	A	90	TRP	0	0.047	0.017	27.025	0.298	0.298	0.000	0.000	0.000	0.000
63	A	91	ASP	-1	-0.914	-0.962	32.295	-9.330	-9.330	0.000	0.000	0.000	0.000
64	A	92	LEU	0	-0.087	-0.031	30.754	-0.227	-0.227	0.000	0.000	0.000	0.000
65	A	93	GLU	-1	-0.773	-0.874	34.684	-8.144	-8.144	0.000	0.000	0.000	0.000
66	A	94	GLU	-1	-0.786	-0.868	37.171	-7.583	-7.583	0.000	0.000	0.000	0.000
67	A	95	ASP	-1	-0.860	-0.933	39.523	-7.730	-7.730	0.000	0.000	0.000	0.000
68	A	96	THR	0	-0.025	-0.019	34.526	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	97	GLU	-1	-0.877	-0.926	33.227	-9.323	-9.323	0.000	0.000	0.000	0.000
70	A	98	TYR	0	-0.003	0.001	29.470	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	99	ILE	0	-0.016	-0.011	24.671	0.022	0.022	0.000	0.000	0.000	0.000
72	A	100	VAL	0	-0.011	-0.010	22.733	-0.055	-0.055	0.000	0.000	0.000	0.000
73	A	101	HIS	0	0.016	0.025	18.511	0.187	0.187	0.000	0.000	0.000	0.000
74	A	102	VAL	0	0.019	0.002	17.019	0.131	0.131	0.000	0.000	0.000	0.000
75	A	103	GLN	0	-0.045	-0.030	11.366	0.494	0.494	0.000	0.000	0.000	0.000
76	A	104	ALA	0	0.073	0.034	10.865	1.201	1.201	0.000	0.000	0.000	0.000
77	A	105	ILE	0	-0.048	-0.025	10.283	-3.020	-3.020	0.000	0.000	0.000	0.000
78	A	106	SER	0	0.017	0.003	6.045	-0.599	-0.599	0.000	0.000	0.000	0.000
79	A	107	ILE	0	0.009	0.000	7.222	-0.908	-0.908	0.000	0.000	0.000	0.000
83	A	111	SER	0	0.021	0.008	6.938	-4.130	-4.130	0.000	0.000	0.000	0.000
84	A	112	PRO	0	-0.008	0.001	8.121	1.625	1.625	0.000	0.000	0.000	0.000
85	A	113	ALA	0	0.001	0.006	10.846	0.252	0.252	0.000	0.000	0.000	0.000
86	A	114	SER	0	0.007	-0.003	14.493	-0.295	-0.295	0.000	0.000	0.000	0.000
87	A	115	GLU	-1	-0.891	-0.948	16.872	-15.250	-15.250	0.000	0.000	0.000	0.000
88	A	116	PRO	0	-0.067	-0.013	19.884	-0.046	-0.046	0.000	0.000	0.000	0.000
89	A	117	VAL	0	0.026	0.003	22.526	0.483	0.483	0.000	0.000	0.000	0.000
90	A	118	LEU	0	-0.033	-0.016	25.049	0.092	0.092	0.000	0.000	0.000	0.000
91	A	119	PHE	0	-0.023	-0.018	28.015	0.144	0.144	0.000	0.000	0.000	0.000
92	A	120	LYS	1	0.891	0.952	31.509	8.023	8.023	0.000	0.000	0.000	0.000
93	A	121	THR	0	-0.037	-0.037	34.426	0.006	0.006	0.000	0.000	0.000	0.000
94	A	122	PRO	0	-0.037	-0.022	36.556	0.169	0.169	0.000	0.000	0.000	0.000
95	A	123	ARG	1	0.918	0.960	40.103	7.100	7.100	0.000	0.000	0.000	0.000
96	A	124	GLU	-1	-0.879	-0.933	43.266	-7.575	-7.575	0.000	0.000	0.000	0.000
97	A	125	ALA	0	-0.109	-0.062	44.625	0.084	0.084	0.000	0.000	0.000	0.000
98	A	126	GLU	-2	-1.903	-1.932	47.846	-12.428	-12.428	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:29:MET)