FMO DATABASE

FMODB ID: YVMY2

Calculation Name: 1L1S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1L1S

Chain ID: A

ChEMBL ID:

UniProt ID: O27535

Base Structure: X-ray

Registration Date: 2023-09-23

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	111
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-879140.843168
FMO2-HF: Nuclear repulsion	835165.350617
FMO2-HF: Total energy	-43975.492551
FMO2-MP2: Total energy	-44101.673321

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:3:ASP)

Summations of interaction energy for fragment #1(A:3:ASP)

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.
110.128	116.426	2.967	-4.381	-4.884	0.015

Interaction energy analysis for fragmet #1(A:3:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.918 / q_NPA : -0.979

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	5	ARG	1	0.808	0.902	3.889	-40.342	-39.281	-0.001	-0.543	-0.516	0.002
4	A	6	VAL	0	-0.006	0.003	6.299	-1.360	-1.360	0.000	0.000	0.000	0.000
5	A	7	VAL	0	-0.044	-0.015	9.908	-0.799	-0.799	0.000	0.000	0.000	0.000
6	A	8	PHE	0	0.039	0.004	12.208	-0.583	-0.583	0.000	0.000	0.000	0.000
7	A	9	HIS	0	-0.054	-0.021	15.953	0.072	0.072	0.000	0.000	0.000	0.000
8	A	10	ILE	0	0.006	-0.003	19.533	-0.090	-0.090	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.765	-0.868	22.799	12.024	12.024	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.832	-0.882	26.298	10.781	10.781	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.814	-0.927	27.080	10.257	10.257	0.000	0.000	0.000	0.000
12	A	14	ASP	-1	-0.822	-0.871	29.222	10.667	10.667	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.852	-0.931	28.642	10.279	10.279	0.000	0.000	0.000	0.000
14	A	16	SER	0	-0.050	-0.049	27.796	0.294	0.294	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.821	0.889	24.772	-11.209	-11.209	0.000	0.000	0.000	0.000
16	A	18	VAL	0	-0.013	0.001	23.911	0.785	0.785	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.037	0.015	23.191	0.690	0.690	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.047	-0.011	21.737	0.615	0.615	0.000	0.000	0.000	0.000
19	A	21	LEU	0	-0.034	-0.022	18.046	0.923	0.923	0.000	0.000	0.000	0.000
20	A	22	ILE	0	0.012	0.008	18.349	1.094	1.094	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.023	-0.003	18.541	0.594	0.594	0.000	0.000	0.000	0.000
22	A	24	ASN	0	-0.027	-0.032	16.536	0.620	0.620	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.022	-0.004	13.785	1.565	1.565	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.776	0.847	13.400	-13.427	-13.427	0.000	0.000	0.000	0.000
25	A	27	ASN	0	-0.053	-0.020	14.321	1.460	1.460	0.000	0.000	0.000	0.000
26	A	28	LEU	0	0.053	0.019	9.261	0.959	0.959	0.000	0.000	0.000	0.000
27	A	29	MET	0	-0.068	-0.029	9.451	3.278	3.278	0.000	0.000	0.000	0.000
28	A	30	ALA	0	-0.038	-0.017	10.541	-0.433	-0.433	0.000	0.000	0.000	0.000
29	A	31	ASP	-1	-0.986	-0.979	10.583	26.654	26.654	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.046	-0.020	5.253	2.555	2.555	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.964	-0.978	4.286	42.643	42.758	-0.001	-0.021	-0.094	0.000
32	A	34	SER	0	-0.050	-0.027	2.302	-12.623	-9.232	2.595	-2.893	-3.093	0.020
33	A	35	VAL	0	0.033	0.004	2.991	9.577	11.170	0.375	-0.912	-1.056	-0.007
34	A	36	ARG	1	0.834	0.931	4.610	-31.073	-30.935	-0.001	-0.012	-0.125	0.000
35	A	37	ILE	0	0.048	0.014	6.145	0.132	0.132	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.755	-0.863	9.842	19.372	19.372	0.000	0.000	0.000	0.000
37	A	39	VAL	0	-0.005	-0.003	12.751	0.326	0.326	0.000	0.000	0.000	0.000
38	A	40	VAL	0	-0.039	-0.006	16.259	-0.821	-0.821	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.024	0.021	18.855	-0.057	-0.057	0.000	0.000	0.000	0.000
40	A	42	TYR	0	-0.055	-0.073	22.464	-0.131	-0.131	0.000	0.000	0.000	0.000
41	A	43	SER	0	0.009	-0.003	25.635	-0.137	-0.137	0.000	0.000	0.000	0.000
42	A	44	MET	0	0.042	0.014	29.077	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.013	0.030	25.825	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	46	VAL	0	-0.044	-0.027	25.769	0.336	0.336	0.000	0.000	0.000	0.000
45	A	47	ASN	0	-0.030	-0.030	26.934	-0.067	-0.067	0.000	0.000	0.000	0.000
46	A	48	VAL	0	0.004	0.006	23.758	-0.099	-0.099	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.032	-0.006	21.597	0.222	0.222	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.824	0.876	25.234	-9.203	-9.203	0.000	0.000	0.000	0.000
49	A	51	ARG	1	0.769	0.855	28.319	-9.429	-9.429	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.877	-0.925	29.850	9.087	9.087	0.000	0.000	0.000	0.000
51	A	53	SER	0	-0.035	-0.013	27.009	-0.211	-0.211	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.868	-0.915	29.713	9.796	9.796	0.000	0.000	0.000	0.000
53	A	55	TYR	0	-0.012	-0.037	25.219	0.288	0.288	0.000	0.000	0.000	0.000
54	A	56	SER	0	0.004	-0.009	24.982	0.548	0.548	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.012	0.020	25.008	0.282	0.282	0.000	0.000	0.000	0.000
56	A	58	ASP	-1	-0.794	-0.896	21.876	13.243	13.243	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.003	0.007	20.625	0.752	0.752	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.009	-0.003	20.056	0.605	0.605	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.821	-0.877	19.528	15.327	15.327	0.000	0.000	0.000	0.000
60	A	62	LEU	0	0.002	-0.007	15.678	0.837	0.837	0.000	0.000	0.000	0.000
61	A	63	THR	0	-0.027	-0.028	15.601	1.062	1.062	0.000	0.000	0.000	0.000
62	A	64	GLY	0	-0.048	-0.015	16.154	0.472	0.472	0.000	0.000	0.000	0.000
63	A	65	GLN	0	-0.111	-0.070	13.618	1.011	1.011	0.000	0.000	0.000	0.000
64	A	66	GLY	0	-0.020	0.000	11.733	1.660	1.660	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.037	-0.016	11.712	1.031	1.031	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.794	0.877	12.636	-18.089	-18.089	0.000	0.000	0.000	0.000
67	A	69	PHE	0	0.066	0.024	14.490	0.255	0.255	0.000	0.000	0.000	0.000
68	A	70	CYS	0	-0.080	-0.037	16.533	-0.169	-0.169	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.081	0.043	19.419	-0.053	-0.053	0.000	0.000	0.000	0.000
70	A	72	CYM	-1	-0.910	-0.866	23.124	11.306	11.306	0.000	0.000	0.000	0.000
71	A	73	SER	0	0.046	0.013	24.811	-0.411	-0.411	0.000	0.000	0.000	0.000
72	A	74	ASN	0	-0.136	-0.098	27.090	-0.649	-0.649	0.000	0.000	0.000	0.000
73	A	75	THR	0	0.040	-0.021	27.477	-0.292	-0.292	0.000	0.000	0.000	0.000
74	A	76	LEU	0	0.059	0.060	26.729	-0.247	-0.247	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.990	0.999	30.431	-8.658	-8.658	0.000	0.000	0.000	0.000
76	A	78	ALA	0	-0.083	-0.052	32.991	-0.279	-0.279	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.029	-0.020	32.196	-0.203	-0.203	0.000	0.000	0.000	0.000
78	A	80	GLY	0	-0.067	-0.023	34.635	-0.088	-0.088	0.000	0.000	0.000	0.000
79	A	81	MET	0	-0.027	0.014	31.773	-0.020	-0.020	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.874	-0.946	31.872	9.199	9.199	0.000	0.000	0.000	0.000
81	A	83	GLY	0	-0.028	-0.018	28.203	0.232	0.232	0.000	0.000	0.000	0.000
82	A	84	ASP	-1	-0.873	-0.918	28.659	9.419	9.419	0.000	0.000	0.000	0.000
83	A	85	ASP	-1	-0.800	-0.889	31.143	8.785	8.785	0.000	0.000	0.000	0.000
84	A	86	LEU	0	-0.058	-0.015	24.649	0.135	0.135	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.009	0.006	23.783	-0.317	-0.317	0.000	0.000	0.000	0.000
86	A	88	GLU	-1	-0.951	-0.978	24.779	11.062	11.062	0.000	0.000	0.000	0.000
87	A	89	GLY	0	-0.024	-0.022	20.988	0.266	0.266	0.000	0.000	0.000	0.000
88	A	90	VAL	0	-0.036	-0.002	19.517	0.785	0.785	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.775	-0.862	17.870	14.322	14.322	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.020	-0.007	20.578	-0.185	-0.185	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.020	-0.013	18.604	0.325	0.325	0.000	0.000	0.000	0.000
92	A	94	SER	0	0.003	-0.012	21.905	-0.288	-0.288	0.000	0.000	0.000	0.000
93	A	95	SER	0	0.032	-0.004	22.999	-0.374	-0.374	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.046	0.010	21.618	0.557	0.557	0.000	0.000	0.000	0.000
95	A	97	VAL	0	0.049	0.020	20.782	0.665	0.665	0.000	0.000	0.000	0.000
96	A	98	GLY	0	0.006	0.001	21.369	0.413	0.413	0.000	0.000	0.000	0.000
97	A	99	HIS	0	-0.058	-0.039	14.720	-0.190	-0.190	0.000	0.000	0.000	0.000
98	A	100	ILE	0	0.048	0.028	16.808	0.989	0.989	0.000	0.000	0.000	0.000
99	A	101	VAL	0	0.030	0.018	16.790	0.873	0.873	0.000	0.000	0.000	0.000
100	A	102	ARG	1	0.883	0.959	16.801	-13.318	-13.318	0.000	0.000	0.000	0.000
101	A	103	ARG	1	0.877	0.905	11.920	-19.929	-19.929	0.000	0.000	0.000	0.000
102	A	104	GLN	0	0.006	-0.003	12.968	0.721	0.721	0.000	0.000	0.000	0.000
103	A	105	THR	0	-0.066	-0.036	14.738	0.276	0.276	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.871	-0.895	11.545	21.467	21.467	0.000	0.000	0.000	0.000
105	A	107	GLY	0	0.004	0.010	11.008	2.164	2.164	0.000	0.000	0.000	0.000
106	A	108	TRP	0	-0.117	-0.062	9.229	3.914	3.914	0.000	0.000	0.000	0.000
107	A	109	ALA	0	0.022	0.009	9.639	-2.039	-2.039	0.000	0.000	0.000	0.000
108	A	110	TYR	0	-0.043	-0.055	11.505	-0.543	-0.543	0.000	0.000	0.000	0.000
109	A	111	ILE	0	0.011	0.011	13.844	-0.134	-0.134	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.804	0.884	16.632	-12.927	-12.927	0.000	0.000	0.000	0.000
111	A	113	PRO	0	-0.001	0.021	18.951	-1.263	-1.263	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASP)