FMO DATABASE

FMODB ID: LZ4J9

Calculation Name: 4LSD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LSD

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NAU1

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-696045.953631
FMO2-HF: Nuclear repulsion	657472.099372
FMO2-HF: Total energy	-38573.854258
FMO2-MP2: Total energy	-38686.305864

3D Structure

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.
-5.726	0.437	1.059	-3.156	-4.065	-0.005

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 : 0 / q_Mulliken : 0.006 / q_NPA : 0.005

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	0.016	0.019	3.852	-2.352	1.470	-0.027	-2.134	-1.661	0.006
4	A	32	SER	0	-0.026	-0.015	6.957	0.128	0.128	0.000	0.000	0.000	0.000
5	A	33	ALA	0	-0.048	-0.025	9.590	-0.049	-0.049	0.000	0.000	0.000	0.000
6	A	34	PRO	0	-0.047	-0.013	12.570	0.074	0.074	0.000	0.000	0.000	0.000
7	A	35	VAL	0	0.019	0.006	15.665	0.049	0.049	0.000	0.000	0.000	0.000
8	A	36	ASN	0	-0.054	-0.037	18.168	0.011	0.011	0.000	0.000	0.000	0.000
9	A	37	VAL	0	0.020	0.006	19.840	0.000	0.000	0.000	0.000	0.000	0.000
10	A	38	THR	0	-0.056	-0.020	22.531	0.025	0.025	0.000	0.000	0.000	0.000
11	A	39	VAL	0	0.052	0.024	26.273	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	40	ARG	1	0.935	0.963	26.706	0.197	0.197	0.000	0.000	0.000	0.000
13	A	41	HIS	0	-0.035	-0.031	31.373	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	42	LEU	0	0.008	0.012	32.766	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	43	LYS	1	0.886	0.927	35.040	0.148	0.148	0.000	0.000	0.000	0.000
16	A	44	ALA	0	0.056	0.027	37.096	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	45	ASN	0	0.047	0.030	37.556	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	46	SER	0	-0.068	-0.021	34.068	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	47	ALA	0	0.042	0.022	30.818	0.011	0.011	0.000	0.000	0.000	0.000
20	A	48	VAL	0	-0.014	0.010	27.746	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	49	VAL	0	0.014	0.018	23.346	0.014	0.014	0.000	0.000	0.000	0.000
22	A	50	SER	0	-0.032	-0.032	23.446	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	51	TRP	0	-0.004	0.013	16.971	0.023	0.023	0.000	0.000	0.000	0.000
24	A	52	ASP	-1	-0.815	-0.892	18.526	-0.230	-0.230	0.000	0.000	0.000	0.000
25	A	53	VAL	0	-0.028	-0.023	12.917	-0.054	-0.054	0.000	0.000	0.000	0.000
26	A	54	LEU	0	0.008	0.002	11.889	0.067	0.067	0.000	0.000	0.000	0.000
27	A	55	GLU	-1	-0.811	-0.919	7.299	-0.913	-0.913	0.000	0.000	0.000	0.000
28	A	56	ASP	-1	-0.879	-0.956	11.032	-0.465	-0.465	0.000	0.000	0.000	0.000
29	A	57	GLU	-1	-0.990	-0.986	9.893	0.093	0.093	0.000	0.000	0.000	0.000
30	A	58	VAL	0	-0.012	-0.007	5.864	-0.100	-0.100	0.000	0.000	0.000	0.000
31	A	59	VAL	0	-0.059	-0.026	9.011	-0.317	-0.317	0.000	0.000	0.000	0.000
32	A	60	ILE	0	0.003	0.006	10.845	0.183	0.183	0.000	0.000	0.000	0.000
33	A	61	GLY	0	0.011	-0.013	13.195	0.119	0.119	0.000	0.000	0.000	0.000
34	A	62	PHE	0	-0.030	-0.019	14.292	-0.083	-0.083	0.000	0.000	0.000	0.000
35	A	63	ALA	0	0.032	0.016	15.806	0.040	0.040	0.000	0.000	0.000	0.000
36	A	64	ILE	0	-0.003	-0.009	17.455	0.003	0.003	0.000	0.000	0.000	0.000
37	A	65	SER	0	-0.026	-0.006	19.747	0.009	0.009	0.000	0.000	0.000	0.000
38	A	66	GLN	0	0.062	0.016	22.175	0.009	0.009	0.000	0.000	0.000	0.000
39	A	67	GLN	0	0.001	-0.004	24.965	0.022	0.022	0.000	0.000	0.000	0.000
40	A	68	LYS	1	0.954	0.989	28.272	0.148	0.148	0.000	0.000	0.000	0.000
41	A	69	LYS	1	0.978	0.989	30.645	0.117	0.117	0.000	0.000	0.000	0.000
42	A	70	ASP	-1	-0.920	-0.947	31.853	-0.117	-0.117	0.000	0.000	0.000	0.000
43	A	71	VAL	0	-0.054	-0.019	28.482	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	72	ARG	1	0.944	0.948	31.246	0.146	0.146	0.000	0.000	0.000	0.000
45	A	73	MET	0	-0.051	-0.004	29.485	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	74	LEU	0	-0.004	0.000	25.226	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	75	ARG	1	0.873	0.919	26.618	0.232	0.232	0.000	0.000	0.000	0.000
48	A	76	PHE	0	0.001	-0.010	20.846	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	77	ILE	0	-0.007	0.005	22.155	0.019	0.019	0.000	0.000	0.000	0.000
50	A	78	GLN	0	-0.012	-0.005	15.816	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	79	GLU	-1	-0.916	-0.946	18.797	-0.345	-0.345	0.000	0.000	0.000	0.000
52	A	80	VAL	0	0.011	-0.014	15.040	-0.080	-0.080	0.000	0.000	0.000	0.000
53	A	81	ASN	0	-0.057	-0.016	15.993	0.043	0.043	0.000	0.000	0.000	0.000
54	A	82	THR	0	0.019	0.011	17.147	0.090	0.090	0.000	0.000	0.000	0.000
55	A	83	THR	0	0.028	0.009	17.141	-0.049	-0.049	0.000	0.000	0.000	0.000
56	A	84	THR	0	-0.049	-0.014	18.825	0.034	0.034	0.000	0.000	0.000	0.000
57	A	85	ARG	1	0.900	0.953	15.415	0.405	0.405	0.000	0.000	0.000	0.000
58	A	86	SER	0	-0.015	-0.017	20.821	0.033	0.033	0.000	0.000	0.000	0.000
59	A	87	CYS	0	-0.001	0.013	22.971	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	88	ALA	0	-0.029	-0.003	24.918	0.016	0.016	0.000	0.000	0.000	0.000
61	A	89	LEU	0	-0.032	-0.011	26.020	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	90	TRP	0	0.033	-0.001	28.121	0.014	0.014	0.000	0.000	0.000	0.000
63	A	91	ASP	-1	-0.908	-0.955	33.009	-0.169	-0.169	0.000	0.000	0.000	0.000
64	A	92	LEU	0	-0.097	-0.044	31.066	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	93	GLU	-1	-0.886	-0.957	35.038	-0.120	-0.120	0.000	0.000	0.000	0.000
66	A	94	GLU	-1	-0.820	-0.871	37.357	-0.101	-0.101	0.000	0.000	0.000	0.000
67	A	95	ASP	-1	-0.903	-0.956	40.070	-0.094	-0.094	0.000	0.000	0.000	0.000
68	A	96	THR	0	-0.015	-0.035	34.967	0.002	0.002	0.000	0.000	0.000	0.000
69	A	97	GLU	-1	-0.975	-0.993	33.326	-0.121	-0.121	0.000	0.000	0.000	0.000
70	A	98	TYR	0	-0.018	-0.004	29.430	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	99	ILE	0	-0.017	-0.008	24.724	0.008	0.008	0.000	0.000	0.000	0.000
72	A	100	VAL	0	0.002	-0.003	23.042	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	101	HIS	0	0.007	0.015	18.800	0.009	0.009	0.000	0.000	0.000	0.000
74	A	102	VAL	0	0.019	0.002	17.233	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	103	GLN	0	-0.020	-0.004	11.645	0.082	0.082	0.000	0.000	0.000	0.000
76	A	104	ALA	0	0.037	0.011	11.474	0.075	0.075	0.000	0.000	0.000	0.000
77	A	105	ILE	0	-0.043	-0.012	10.710	-0.302	-0.302	0.000	0.000	0.000	0.000
78	A	106	SER	0	0.071	0.032	5.380	0.156	0.156	0.000	0.000	0.000	0.000
79	A	107	ILE	0	0.013	-0.002	7.225	0.044	0.044	0.000	0.000	0.000	0.000
80	A	108	GLN	0	-0.051	-0.032	2.797	-2.194	0.017	1.087	-1.002	-2.295	-0.011
81	A	109	GLY	0	0.033	0.013	4.761	-0.915	-0.785	-0.001	-0.020	-0.109	0.000
82	A	110	GLN	0	-0.034	-0.007	5.907	1.071	1.071	0.000	0.000	0.000	0.000
83	A	111	SER	0	0.059	0.038	7.168	-0.350	-0.350	0.000	0.000	0.000	0.000
84	A	112	PRO	0	-0.032	-0.016	8.568	0.148	0.148	0.000	0.000	0.000	0.000
85	A	113	ALA	0	0.011	0.003	11.320	-0.017	-0.017	0.000	0.000	0.000	0.000
86	A	114	SER	0	0.028	0.016	15.006	0.022	0.022	0.000	0.000	0.000	0.000
87	A	115	GLU	-1	-0.923	-0.966	16.856	-0.209	-0.209	0.000	0.000	0.000	0.000
88	A	116	PRO	0	-0.070	-0.031	19.944	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	117	VAL	0	0.038	0.029	22.617	0.025	0.025	0.000	0.000	0.000	0.000
90	A	118	LEU	0	-0.034	-0.027	25.224	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	119	PHE	0	-0.028	-0.022	27.896	0.008	0.008	0.000	0.000	0.000	0.000
92	A	120	LYS	1	0.952	0.978	31.764	0.097	0.097	0.000	0.000	0.000	0.000
93	A	121	THR	0	-0.071	-0.068	34.814	0.004	0.004	0.000	0.000	0.000	0.000
94	A	122	PRO	0	-0.040	-0.022	36.951	0.006	0.006	0.000	0.000	0.000	0.000
95	A	123	ARG	1	0.953	0.979	40.473	0.082	0.082	0.000	0.000	0.000	0.000
96	A	124	GLU	-1	-0.839	-0.892	43.608	-0.106	-0.106	0.000	0.000	0.000	0.000
97	A	125	ALA	0	-0.109	-0.055	45.018	0.005	0.005	0.000	0.000	0.000	0.000
98	A	126	GLU	-1	-0.983	-0.981	47.833	-0.069	-0.069	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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