FMO DATABASE

FMODB ID: QYZ3Y

Calculation Name: 4L1D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L1D

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NY72

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	OptHSide
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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-991856.958685
FMO2-HF: Nuclear repulsion	943642.153193
FMO2-HF: Total energy	-48214.805492
FMO2-MP2: Total energy	-48353.101486

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:1:VAL)

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

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.
-1.863	1.168	0.056	-1.369	-1.719	0

Interaction energy analysis for fragmet #1(A:1:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.009

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].
3	A	3	VAL	0	0.032	0.016	3.200	-2.056	0.902	0.057	-1.365	-1.650
4	A	4	GLU	-1	-0.770	-0.878	5.324	-0.459	-0.386	-0.001	-0.004	-0.069
5	A	5	VAL	0	-0.028	-0.012	8.535	0.099	0.099	0.000	0.000	0.000
6	A	6	PRO	0	0.017	0.009	11.414	0.059	0.059	0.000	0.000	0.000
7	A	7	SER	0	-0.002	0.001	15.052	-0.049	-0.049	0.000	0.000	0.000
8	A	8	GLU	-1	-0.808	-0.881	17.567	-0.494	-0.494	0.000	0.000	0.000
9	A	9	THR	0	-0.011	-0.029	20.351	0.001	0.001	0.000	0.000	0.000
10	A	10	GLU	-1	-0.790	-0.842	23.575	-0.198	-0.198	0.000	0.000	0.000
11	A	11	ALA	0	0.021	0.003	24.828	-0.019	-0.019	0.000	0.000	0.000
12	A	12	VAL	0	0.004	0.008	26.973	0.015	0.015	0.000	0.000	0.000
13	A	13	GLN	0	0.023	-0.012	29.389	-0.002	-0.002	0.000	0.000	0.000
14	A	14	GLY	0	-0.027	-0.018	31.833	0.004	0.004	0.000	0.000	0.000
15	A	15	ASN	0	-0.071	-0.026	26.708	0.001	0.001	0.000	0.000	0.000
16	A	16	PRO	0	-0.013	-0.009	23.866	0.003	0.003	0.000	0.000	0.000
17	A	17	MET	0	0.007	0.025	21.560	-0.011	-0.011	0.000	0.000	0.000
18	A	18	LYS	1	0.854	0.935	13.356	0.669	0.669	0.000	0.000	0.000
19	A	19	LEU	0	-0.005	0.004	19.868	-0.016	-0.016	0.000	0.000	0.000
20	A	20	ARG	1	0.799	0.860	12.770	0.677	0.677	0.000	0.000	0.000
21	A	21	CYS	0	-0.030	-0.012	15.128	0.045	0.045	0.000	0.000	0.000
22	A	22	ILE	0	-0.002	0.006	8.424	-0.011	-0.011	0.000	0.000	0.000
23	A	23	SER	0	-0.039	-0.008	10.952	0.078	0.078	0.000	0.000	0.000
24	A	25	MET	0	0.006	0.000	7.523	0.098	0.098	0.000	0.000	0.000
25	A	26	LYS	1	0.870	0.910	7.651	0.305	0.305	0.000	0.000	0.000
26	A	27	ARG	1	0.887	0.937	5.787	-0.456	-0.456	0.000	0.000	0.000
27	A	28	GLU	-1	-0.903	-0.924	10.108	0.070	0.070	0.000	0.000	0.000
28	A	29	GLU	-1	-0.901	-0.949	13.725	0.236	0.236	0.000	0.000	0.000
29	A	30	VAL	0	-0.070	-0.049	16.268	-0.011	-0.011	0.000	0.000	0.000
30	A	31	GLU	-1	-0.922	-0.964	18.170	0.067	0.067	0.000	0.000	0.000
31	A	32	ALA	0	-0.002	0.006	14.963	-0.021	-0.021	0.000	0.000	0.000
32	A	33	THR	0	-0.049	-0.004	16.865	-0.015	-0.015	0.000	0.000	0.000
33	A	34	THR	0	-0.028	-0.013	16.288	-0.025	-0.025	0.000	0.000	0.000
34	A	35	VAL	0	-0.010	0.008	18.616	0.007	0.007	0.000	0.000	0.000
35	A	36	VAL	0	-0.022	-0.018	17.967	-0.022	-0.022	0.000	0.000	0.000
36	A	37	GLU	-1	-0.809	-0.876	20.674	-0.118	-0.118	0.000	0.000	0.000
37	A	38	TRP	0	0.014	-0.002	18.535	-0.016	-0.016	0.000	0.000	0.000
38	A	39	PHE	0	0.012	-0.011	23.977	0.019	0.019	0.000	0.000	0.000
39	A	40	TYR	0	0.013	-0.008	26.286	-0.013	-0.013	0.000	0.000	0.000
40	A	41	ARG	1	0.858	0.914	28.954	0.153	0.153	0.000	0.000	0.000
41	A	42	PRO	0	0.009	0.024	31.499	-0.008	-0.008	0.000	0.000	0.000
42	A	43	GLU	-1	-0.896	-0.968	34.124	-0.123	-0.123	0.000	0.000	0.000
43	A	44	GLY	0	-0.018	-0.001	35.626	0.006	0.006	0.000	0.000	0.000
44	A	45	GLY	0	-0.024	-0.006	36.155	0.007	0.007	0.000	0.000	0.000
45	A	46	LYS	1	0.911	0.937	34.929	0.081	0.081	0.000	0.000	0.000
46	A	47	ASP	-1	-0.828	-0.890	28.956	-0.144	-0.144	0.000	0.000	0.000
47	A	48	PHE	0	-0.034	-0.006	31.427	0.009	0.009	0.000	0.000	0.000
48	A	49	LEU	0	-0.002	-0.003	26.832	-0.011	-0.011	0.000	0.000	0.000
49	A	50	ILE	0	-0.028	-0.028	26.115	0.005	0.005	0.000	0.000	0.000
50	A	51	TYR	0	0.022	-0.019	21.891	-0.004	-0.004	0.000	0.000	0.000
51	A	52	GLU	-1	-0.802	-0.890	24.546	-0.107	-0.107	0.000	0.000	0.000
52	A	53	TYR	0	-0.062	-0.018	20.034	0.004	0.004	0.000	0.000	0.000
53	A	54	ARG	1	0.858	0.880	22.740	0.094	0.094	0.000	0.000	0.000
54	A	55	ASN	0	-0.012	0.009	23.781	0.009	0.009	0.000	0.000	0.000
55	A	56	GLY	0	0.065	0.034	23.260	0.006	0.006	0.000	0.000	0.000
56	A	57	HIS	0	-0.034	-0.013	19.386	-0.008	-0.008	0.000	0.000	0.000
57	A	58	GLN	0	-0.015	0.003	24.504	0.011	0.011	0.000	0.000	0.000
58	A	59	GLU	-1	-0.906	-0.947	27.813	-0.098	-0.098	0.000	0.000	0.000
59	A	60	VAL	0	-0.051	-0.018	28.399	0.005	0.005	0.000	0.000	0.000
60	A	61	GLU	-1	-0.926	-0.953	31.252	-0.076	-0.076	0.000	0.000	0.000
61	A	62	SER	0	-0.001	-0.020	31.781	-0.005	-0.005	0.000	0.000	0.000
62	A	63	PRO	0	-0.021	-0.010	34.317	0.001	0.001	0.000	0.000	0.000
63	A	64	PHE	0	0.003	-0.004	29.310	-0.001	-0.001	0.000	0.000	0.000
64	A	65	GLN	0	-0.018	0.000	30.619	-0.007	-0.007	0.000	0.000	0.000
65	A	66	GLY	0	0.007	0.008	30.913	0.006	0.006	0.000	0.000	0.000
66	A	67	ARG	1	0.707	0.811	29.554	0.146	0.146	0.000	0.000	0.000
67	A	68	LEU	0	0.009	0.023	25.374	-0.017	-0.017	0.000	0.000	0.000
68	A	69	GLN	0	0.000	-0.003	21.499	-0.007	-0.007	0.000	0.000	0.000
69	A	70	TRP	0	0.043	0.037	15.936	-0.028	-0.028	0.000	0.000	0.000
70	A	71	ASN	0	-0.052	-0.043	16.973	-0.034	-0.034	0.000	0.000	0.000
71	A	72	GLY	0	0.080	0.043	13.913	-0.078	-0.078	0.000	0.000	0.000
72	A	73	SER	0	-0.095	-0.077	10.188	0.020	0.020	0.000	0.000	0.000
73	A	74	LYS	1	0.980	0.961	12.218	0.114	0.114	0.000	0.000	0.000
74	A	75	ASP	-1	-0.806	-0.868	7.810	-0.425	-0.425	0.000	0.000	0.000
75	A	76	LEU	0	0.035	0.035	11.522	0.016	0.016	0.000	0.000	0.000
76	A	77	GLN	0	0.044	0.022	5.758	0.086	0.086	0.000	0.000	0.000
77	A	78	ASP	-1	-0.828	-0.871	10.118	-0.898	-0.898	0.000	0.000	0.000
78	A	79	VAL	0	0.009	-0.002	11.712	0.102	0.102	0.000	0.000	0.000
79	A	80	SER	0	-0.027	-0.050	14.102	0.042	0.042	0.000	0.000	0.000
80	A	81	ILE	0	-0.035	0.004	16.674	0.028	0.028	0.000	0.000	0.000
81	A	82	THR	0	-0.016	-0.020	19.993	-0.036	-0.036	0.000	0.000	0.000
82	A	83	VAL	0	0.022	0.023	21.963	0.023	0.023	0.000	0.000	0.000
83	A	84	LEU	0	-0.004	-0.017	24.899	-0.007	-0.007	0.000	0.000	0.000
84	A	85	ASN	0	-0.024	-0.021	27.420	0.007	0.007	0.000	0.000	0.000
85	A	86	VAL	0	0.042	0.043	27.130	0.009	0.009	0.000	0.000	0.000
86	A	87	THR	0	0.033	0.006	30.345	0.009	0.009	0.000	0.000	0.000
87	A	88	LEU	0	0.042	0.011	32.900	-0.007	-0.007	0.000	0.000	0.000
88	A	89	ASN	0	-0.011	-0.020	34.806	-0.002	-0.002	0.000	0.000	0.000
89	A	90	ASP	-1	-0.749	-0.809	29.924	-0.155	-0.155	0.000	0.000	0.000
90	A	91	SER	0	0.021	0.013	30.298	-0.016	-0.016	0.000	0.000	0.000
91	A	92	GLY	0	0.009	0.020	30.058	0.013	0.013	0.000	0.000	0.000
92	A	93	LEU	0	-0.057	-0.019	25.742	-0.014	-0.014	0.000	0.000	0.000
93	A	94	TYR	0	-0.012	-0.029	23.968	0.008	0.008	0.000	0.000	0.000
94	A	95	THR	0	-0.026	-0.012	22.926	-0.020	-0.020	0.000	0.000	0.000
95	A	97	ASN	0	0.006	0.003	19.462	-0.017	-0.017	0.000	0.000	0.000
96	A	98	VAL	0	0.033	0.019	14.915	0.004	0.004	0.000	0.000	0.000
97	A	99	SER	0	0.003	-0.010	17.817	0.000	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.788	0.865	12.031	0.247	0.247	0.000	0.000	0.000
99	A	101	GLU	-1	-0.922	-0.962	17.788	-0.036	-0.036	0.000	0.000	0.000
100	A	102	PHE	0	0.061	0.037	17.257	0.003	0.003	0.000	0.000	0.000
101	A	110	PHE	0	0.038	0.026	19.168	0.001	0.001	0.000	0.000	0.000
102	A	111	VAL	0	-0.066	-0.045	14.977	-0.009	-0.009	0.000	0.000	0.000
103	A	112	LYS	1	0.875	0.915	18.177	0.142	0.142	0.000	0.000	0.000
104	A	113	THR	0	-0.060	-0.002	14.185	0.010	0.010	0.000	0.000	0.000
105	A	114	THR	0	0.016	-0.003	17.411	0.004	0.004	0.000	0.000	0.000
106	A	115	ARG	1	0.819	0.893	12.534	0.441	0.441	0.000	0.000	0.000
107	A	116	LEU	0	0.019	0.011	18.827	0.018	0.018	0.000	0.000	0.000
108	A	117	ILE	0	0.004	-0.001	19.285	-0.021	-0.021	0.000	0.000	0.000
109	A	118	PRO	0	-0.006	0.001	22.705	0.019	0.019	0.000	0.000	0.000
110	A	119	LEU	0	-0.024	0.005	24.726	-0.007	-0.007	0.000	0.000	0.000
111	A	120	ARG	1	0.899	0.929	26.814	0.211	0.211	0.000	0.000	0.000
112	A	121	VAL	0	-0.027	-0.013	28.954	-0.012	-0.012	0.000	0.000	0.000
113	A	122	HIS	0	-0.061	-0.037	29.446	0.022	0.022	0.000	0.000	0.000
114	A	123	HIS	0	0.043	0.014	32.736	-0.005	-0.005	0.000	0.000	0.000
115	A	124	HIS	0	-0.011	0.006	32.243	-0.003	-0.003	0.000	0.000	0.000

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