FMO DATABASE

FMODB ID: MVY3Z

Calculation Name: 4LSD-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 4LSD

Chain ID: A

ChEMBL ID:
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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	OptAll
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	-696182.600514
FMO2-HF: Nuclear repulsion	657607.767929
FMO2-HF: Total energy	-38574.832585
FMO2-MP2: Total energy	-38687.263038

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.
-8.448	-9.179	12.117	-5.313	-6.073	0.006

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 : 0.007 / q_NPA : 0.021

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	-0.008	-0.003	3.867	-1.266	1.560	-0.019	-1.504	-1.303	0.005
4	A	32	SER	0	0.001	-0.034	7.100	-0.084	-0.084	0.000	0.000	0.000	0.000
5	A	33	ALA	0	-0.033	-0.017	9.590	-0.101	-0.101	0.000	0.000	0.000	0.000
6	A	34	PRO	0	-0.051	-0.020	12.234	0.103	0.103	0.000	0.000	0.000	0.000
7	A	35	VAL	0	0.022	0.010	15.374	0.046	0.046	0.000	0.000	0.000	0.000
8	A	36	ASN	0	-0.060	-0.052	18.082	0.007	0.007	0.000	0.000	0.000	0.000
9	A	37	VAL	0	-0.010	0.005	19.080	0.013	0.013	0.000	0.000	0.000	0.000
10	A	38	THR	0	-0.003	0.005	21.976	0.032	0.032	0.000	0.000	0.000	0.000
11	A	39	VAL	0	-0.011	-0.002	25.700	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	40	ARG	1	0.905	0.947	26.565	0.224	0.224	0.000	0.000	0.000	0.000
13	A	41	HIS	0	0.020	-0.004	31.177	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	42	LEU	0	-0.019	0.005	32.863	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	43	LYS	1	0.860	0.925	34.710	0.159	0.159	0.000	0.000	0.000	0.000
16	A	44	ALA	0	0.033	0.030	36.862	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	45	ASN	0	0.038	-0.005	37.375	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	46	SER	0	-0.038	-0.024	33.943	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	47	ALA	0	0.003	-0.001	30.536	0.009	0.009	0.000	0.000	0.000	0.000
20	A	48	VAL	0	-0.014	0.002	27.766	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	49	VAL	0	0.045	0.032	22.823	0.012	0.012	0.000	0.000	0.000	0.000
22	A	50	SER	0	-0.053	-0.052	23.385	0.014	0.014	0.000	0.000	0.000	0.000
23	A	51	TRP	0	-0.024	0.003	16.884	0.020	0.020	0.000	0.000	0.000	0.000
24	A	52	ASP	-1	-0.785	-0.864	18.721	-0.246	-0.246	0.000	0.000	0.000	0.000
25	A	53	VAL	0	-0.040	-0.039	13.094	-0.084	-0.084	0.000	0.000	0.000	0.000
26	A	54	LEU	0	0.023	0.012	11.625	0.087	0.087	0.000	0.000	0.000	0.000
27	A	55	GLU	-1	-0.787	-0.868	8.076	-0.840	-0.840	0.000	0.000	0.000	0.000
28	A	56	ASP	-1	-0.799	-0.899	10.891	-0.483	-0.483	0.000	0.000	0.000	0.000
29	A	57	GLU	-1	-0.994	-0.987	10.290	0.240	0.240	0.000	0.000	0.000	0.000
30	A	58	VAL	0	-0.035	-0.019	5.716	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	59	VAL	0	-0.048	-0.018	8.983	-0.328	-0.328	0.000	0.000	0.000	0.000
32	A	60	ILE	0	0.007	0.010	10.512	0.192	0.192	0.000	0.000	0.000	0.000
33	A	61	GLY	0	0.026	-0.005	12.866	0.102	0.102	0.000	0.000	0.000	0.000
34	A	62	PHE	0	-0.030	-0.012	13.741	-0.115	-0.115	0.000	0.000	0.000	0.000
35	A	63	ALA	0	0.017	0.002	15.177	0.040	0.040	0.000	0.000	0.000	0.000
36	A	64	ILE	0	-0.003	-0.002	16.847	0.001	0.001	0.000	0.000	0.000	0.000
37	A	65	SER	0	0.000	0.001	18.946	0.005	0.005	0.000	0.000	0.000	0.000
38	A	66	GLN	0	0.038	0.031	21.378	0.004	0.004	0.000	0.000	0.000	0.000
39	A	67	GLN	0	0.012	0.007	23.987	0.022	0.022	0.000	0.000	0.000	0.000
40	A	68	LYS	1	0.848	0.921	27.753	0.159	0.159	0.000	0.000	0.000	0.000
41	A	69	LYS	1	0.847	0.897	30.097	0.139	0.139	0.000	0.000	0.000	0.000
42	A	70	ASP	-1	-0.916	-0.955	31.553	-0.147	-0.147	0.000	0.000	0.000	0.000
43	A	71	VAL	0	-0.049	-0.014	27.973	0.003	0.003	0.000	0.000	0.000	0.000
44	A	72	ARG	1	0.890	0.935	31.063	0.173	0.173	0.000	0.000	0.000	0.000
45	A	73	MET	0	-0.009	0.005	29.180	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	74	LEU	0	-0.007	0.001	24.299	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	75	ARG	1	0.835	0.893	26.054	0.248	0.248	0.000	0.000	0.000	0.000
48	A	76	PHE	0	0.001	-0.007	20.326	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	77	ILE	0	-0.002	-0.002	21.249	0.032	0.032	0.000	0.000	0.000	0.000
50	A	78	GLN	0	-0.023	-0.017	15.207	-0.041	-0.041	0.000	0.000	0.000	0.000
51	A	79	GLU	-1	-0.864	-0.923	18.233	-0.326	-0.326	0.000	0.000	0.000	0.000
52	A	80	VAL	0	0.013	-0.012	13.731	-0.089	-0.089	0.000	0.000	0.000	0.000
53	A	81	ASN	0	-0.065	-0.025	15.273	0.081	0.081	0.000	0.000	0.000	0.000
54	A	82	THR	0	-0.019	0.001	16.675	0.082	0.082	0.000	0.000	0.000	0.000
55	A	83	THR	0	0.024	0.002	16.853	-0.043	-0.043	0.000	0.000	0.000	0.000
56	A	84	THR	0	-0.038	-0.005	18.862	0.028	0.028	0.000	0.000	0.000	0.000
57	A	85	ARG	1	0.827	0.897	14.722	0.413	0.413	0.000	0.000	0.000	0.000
58	A	86	SER	0	-0.038	-0.012	20.555	0.029	0.029	0.000	0.000	0.000	0.000
59	A	87	CYS	0	0.010	0.016	22.697	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	88	ALA	0	0.000	0.010	24.734	0.015	0.015	0.000	0.000	0.000	0.000
61	A	89	LEU	0	-0.025	-0.013	25.626	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	90	TRP	0	0.048	0.012	27.258	0.017	0.017	0.000	0.000	0.000	0.000
63	A	91	ASP	-1	-0.918	-0.960	32.287	-0.181	-0.181	0.000	0.000	0.000	0.000
64	A	92	LEU	0	-0.030	0.006	30.912	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	93	GLU	-1	-0.804	-0.895	34.828	-0.140	-0.140	0.000	0.000	0.000	0.000
66	A	94	GLU	-1	-0.705	-0.809	37.101	-0.112	-0.112	0.000	0.000	0.000	0.000
67	A	95	ASP	-1	-0.831	-0.908	39.499	-0.113	-0.113	0.000	0.000	0.000	0.000
68	A	96	THR	0	-0.019	-0.005	34.392	0.002	0.002	0.000	0.000	0.000	0.000
69	A	97	GLU	-1	-0.845	-0.904	33.048	-0.153	-0.153	0.000	0.000	0.000	0.000
70	A	98	TYR	0	-0.023	-0.014	29.276	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	99	ILE	0	-0.011	-0.007	24.577	0.006	0.006	0.000	0.000	0.000	0.000
72	A	100	VAL	0	-0.017	-0.017	22.668	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	101	HIS	0	0.014	0.023	18.422	0.011	0.011	0.000	0.000	0.000	0.000
74	A	102	VAL	0	0.007	-0.004	17.024	0.004	0.004	0.000	0.000	0.000	0.000
75	A	103	GLN	0	-0.042	-0.027	10.960	0.090	0.090	0.000	0.000	0.000	0.000
76	A	104	ALA	0	0.059	0.030	11.130	0.116	0.116	0.000	0.000	0.000	0.000
77	A	105	ILE	0	-0.049	-0.026	10.263	-0.366	-0.366	0.000	0.000	0.000	0.000
78	A	106	SER	0	0.059	0.023	5.047	0.344	0.344	0.000	0.000	0.000	0.000
79	A	107	ILE	0	0.005	-0.005	7.094	-0.131	-0.131	0.000	0.000	0.000	0.000
80	A	108	GLN	0	-0.044	-0.041	2.387	-4.999	-8.713	12.137	-3.753	-4.670	0.001
81	A	109	GLY	0	0.007	0.008	4.149	-1.710	-1.553	-0.001	-0.056	-0.100	0.000
82	A	110	GLN	0	-0.025	-0.006	5.764	1.044	1.044	0.000	0.000	0.000	0.000
83	A	111	SER	0	0.026	0.017	6.868	-0.508	-0.508	0.000	0.000	0.000	0.000
84	A	112	PRO	0	0.004	0.003	7.829	0.178	0.178	0.000	0.000	0.000	0.000
85	A	113	ALA	0	-0.005	0.004	10.627	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	114	SER	0	-0.003	-0.009	14.275	0.011	0.011	0.000	0.000	0.000	0.000
87	A	115	GLU	-1	-0.879	-0.945	16.476	-0.305	-0.305	0.000	0.000	0.000	0.000
88	A	116	PRO	0	-0.077	-0.011	19.454	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	117	VAL	0	0.019	0.000	22.183	0.030	0.030	0.000	0.000	0.000	0.000
90	A	118	LEU	0	-0.003	-0.008	24.729	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	119	PHE	0	-0.028	-0.014	28.066	0.009	0.009	0.000	0.000	0.000	0.000
92	A	120	LYS	1	0.852	0.914	31.480	0.117	0.117	0.000	0.000	0.000	0.000
93	A	121	THR	0	-0.033	-0.025	34.523	0.002	0.002	0.000	0.000	0.000	0.000
94	A	122	PRO	0	-0.028	-0.020	36.560	0.006	0.006	0.000	0.000	0.000	0.000
95	A	123	ARG	1	0.822	0.882	40.068	0.100	0.100	0.000	0.000	0.000	0.000
96	A	124	GLU	-1	-0.811	-0.905	43.269	-0.113	-0.113	0.000	0.000	0.000	0.000
97	A	125	ALA	0	-0.091	-0.046	44.503	0.004	0.004	0.000	0.000	0.000	0.000
98	A	126	GLU	-1	-1.002	-0.988	47.276	-0.074	-0.074	0.000	0.000	0.000	0.000

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