FMO DATABASE

FMODB ID: 4JK9N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-876603.125255
FMO2-HF: Nuclear repulsion	832628.43979
FMO2-HF: Total energy	-43974.685465
FMO2-MP2: Total energy	-44100.899466

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.
116.347	121.796	5.708	-5.306	-5.852	-0.022

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 : -0.949 / q_NPA : -0.977

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	0.871	0.949	3.719	-39.731	-38.663	-0.012	-0.456	-0.600	0.002
4	A	6	VAL	0	0.005	0.013	6.576	-1.117	-1.117	0.000	0.000	0.000	0.000
5	A	7	VAL	0	-0.015	-0.001	9.980	-0.719	-0.719	0.000	0.000	0.000	0.000
6	A	8	PHE	0	0.005	-0.016	12.226	-0.497	-0.497	0.000	0.000	0.000	0.000
7	A	9	HIS	0	-0.019	0.018	16.141	0.118	0.118	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.007	-0.009	19.764	-0.067	-0.067	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.885	-0.957	22.742	11.634	11.634	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.903	-0.960	26.320	10.604	10.604	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.843	-0.951	27.081	10.099	10.099	0.000	0.000	0.000	0.000
12	A	14	ASP	-1	-0.861	-0.922	29.182	10.459	10.459	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.830	-0.932	28.565	10.185	10.185	0.000	0.000	0.000	0.000
14	A	16	SER	0	-0.068	-0.029	27.558	0.302	0.302	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.894	0.959	24.389	-11.262	-11.262	0.000	0.000	0.000	0.000
16	A	18	VAL	0	0.004	0.014	23.709	0.774	0.774	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.041	0.010	22.920	0.674	0.674	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.049	-0.013	21.293	0.575	0.575	0.000	0.000	0.000	0.000
19	A	21	LEU	0	-0.012	-0.003	17.777	0.885	0.885	0.000	0.000	0.000	0.000
20	A	22	ILE	0	0.022	0.017	17.947	1.077	1.077	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.046	-0.017	17.985	0.951	0.951	0.000	0.000	0.000	0.000
22	A	24	ASN	0	-0.003	-0.026	15.973	0.772	0.772	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.019	-0.003	13.421	1.521	1.521	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.881	0.926	12.995	-13.236	-13.236	0.000	0.000	0.000	0.000
25	A	27	ASN	0	-0.051	-0.013	13.834	2.029	2.029	0.000	0.000	0.000	0.000
26	A	28	LEU	0	0.058	0.021	8.952	1.044	1.044	0.000	0.000	0.000	0.000
27	A	29	MET	0	-0.069	-0.037	9.256	2.717	2.717	0.000	0.000	0.000	0.000
28	A	30	ALA	0	-0.050	-0.016	10.330	-0.081	-0.081	0.000	0.000	0.000	0.000
29	A	31	ASP	-1	-0.981	-0.982	10.408	27.167	27.167	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.045	-0.017	5.415	3.174	3.174	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.980	-0.981	4.095	52.915	53.236	0.000	-0.057	-0.264	0.000
32	A	34	SER	0	-0.024	-0.014	2.402	-12.771	-9.469	2.300	-2.736	-2.866	0.006
33	A	35	VAL	0	0.055	0.005	2.255	7.596	8.176	3.421	-2.029	-1.973	-0.030
34	A	36	ARG	1	0.912	0.971	4.561	-31.556	-31.378	-0.001	-0.028	-0.149	0.000
35	A	37	ILE	0	0.044	0.006	6.551	0.270	0.270	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.778	-0.869	10.170	18.474	18.474	0.000	0.000	0.000	0.000
37	A	39	VAL	0	0.014	0.016	13.251	0.339	0.339	0.000	0.000	0.000	0.000
38	A	40	VAL	0	-0.043	-0.012	16.737	-0.670	-0.670	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.032	0.020	19.315	-0.055	-0.055	0.000	0.000	0.000	0.000
40	A	42	TYR	0	-0.015	-0.037	22.854	-0.130	-0.130	0.000	0.000	0.000	0.000
41	A	43	SER	0	0.017	0.016	25.993	-0.163	-0.163	0.000	0.000	0.000	0.000
42	A	44	MET	0	0.022	-0.001	29.423	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.020	0.032	26.263	0.004	0.004	0.000	0.000	0.000	0.000
44	A	46	VAL	0	-0.045	-0.020	25.839	0.306	0.306	0.000	0.000	0.000	0.000
45	A	47	ASN	0	-0.022	-0.007	27.150	-0.049	-0.049	0.000	0.000	0.000	0.000
46	A	48	VAL	0	0.008	0.003	24.070	-0.122	-0.122	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.059	-0.039	22.112	0.231	0.231	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.948	0.989	25.697	-9.091	-9.091	0.000	0.000	0.000	0.000
49	A	51	ARG	1	0.881	0.926	28.886	-9.285	-9.285	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.966	-0.984	30.331	8.974	8.974	0.000	0.000	0.000	0.000
51	A	53	SER	0	0.036	0.037	28.139	-0.199	-0.199	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.938	-0.962	29.957	9.649	9.649	0.000	0.000	0.000	0.000
53	A	55	TYR	0	0.070	0.014	25.356	0.257	0.257	0.000	0.000	0.000	0.000
54	A	56	SER	0	-0.004	-0.008	25.292	0.522	0.522	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.000	0.006	25.384	0.313	0.313	0.000	0.000	0.000	0.000
56	A	58	ASP	-1	-0.801	-0.904	22.268	12.889	12.889	0.000	0.000	0.000	0.000
57	A	59	VAL	0	-0.035	-0.020	21.097	0.716	0.716	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.043	-0.022	20.606	0.523	0.523	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.915	-0.961	19.577	14.237	14.237	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.018	-0.025	15.798	0.749	0.749	0.000	0.000	0.000	0.000
61	A	63	THR	0	-0.025	-0.005	15.924	1.050	1.050	0.000	0.000	0.000	0.000
62	A	64	GLY	0	-0.039	-0.009	16.378	0.491	0.491	0.000	0.000	0.000	0.000
63	A	65	GLN	0	-0.060	-0.040	14.140	0.488	0.488	0.000	0.000	0.000	0.000
64	A	66	GLY	0	-0.015	0.000	11.849	1.544	1.544	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.056	-0.011	11.904	1.081	1.081	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.821	0.901	13.304	-17.666	-17.666	0.000	0.000	0.000	0.000
67	A	69	PHE	0	0.050	0.016	15.075	0.414	0.414	0.000	0.000	0.000	0.000
68	A	70	CYS	0	-0.068	-0.037	16.979	-0.187	-0.187	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.085	0.041	19.864	-0.082	-0.082	0.000	0.000	0.000	0.000
70	A	72	CYM	-1	-0.869	-0.853	23.595	11.425	11.425	0.000	0.000	0.000	0.000
71	A	73	SER	0	0.037	0.009	25.351	-0.431	-0.431	0.000	0.000	0.000	0.000
72	A	74	ASN	0	-0.059	-0.029	27.601	-0.525	-0.525	0.000	0.000	0.000	0.000
73	A	75	THR	0	0.017	-0.028	27.742	-0.312	-0.312	0.000	0.000	0.000	0.000
74	A	76	LEU	0	0.062	0.038	27.610	-0.294	-0.294	0.000	0.000	0.000	0.000
75	A	77	ARG	1	1.014	1.020	30.954	-8.505	-8.505	0.000	0.000	0.000	0.000
76	A	78	ALA	0	-0.099	-0.049	33.543	-0.258	-0.258	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.054	-0.028	32.871	-0.196	-0.196	0.000	0.000	0.000	0.000
78	A	80	GLY	0	-0.063	-0.022	34.972	-0.070	-0.070	0.000	0.000	0.000	0.000
79	A	81	MET	0	-0.058	-0.027	31.772	0.026	0.026	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.879	-0.953	31.967	8.875	8.875	0.000	0.000	0.000	0.000
81	A	83	GLY	0	-0.028	-0.032	28.820	0.157	0.157	0.000	0.000	0.000	0.000
82	A	84	ASP	-1	-0.910	-0.933	29.340	9.040	9.040	0.000	0.000	0.000	0.000
83	A	85	ASP	-1	-0.886	-0.938	31.788	8.700	8.700	0.000	0.000	0.000	0.000
84	A	86	LEU	0	-0.079	-0.039	25.691	0.134	0.134	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.015	0.000	24.148	-0.237	-0.237	0.000	0.000	0.000	0.000
86	A	88	GLU	-1	-0.967	-0.985	24.988	11.083	11.083	0.000	0.000	0.000	0.000
87	A	89	GLY	0	-0.011	-0.013	21.442	0.238	0.238	0.000	0.000	0.000	0.000
88	A	90	VAL	0	-0.044	-0.003	20.104	0.698	0.698	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.819	-0.890	17.990	14.218	14.218	0.000	0.000	0.000	0.000
90	A	92	VAL	0	0.004	0.000	21.154	-0.059	-0.059	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.039	-0.011	18.988	0.212	0.212	0.000	0.000	0.000	0.000
92	A	94	SER	0	-0.001	-0.024	22.167	-0.321	-0.321	0.000	0.000	0.000	0.000
93	A	95	SER	0	0.002	-0.016	23.387	-0.335	-0.335	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.052	-0.021	22.093	0.542	0.542	0.000	0.000	0.000	0.000
95	A	97	VAL	0	0.035	0.010	21.234	0.611	0.611	0.000	0.000	0.000	0.000
96	A	98	GLY	0	0.004	0.002	21.736	0.410	0.410	0.000	0.000	0.000	0.000
97	A	99	HIS	0	-0.083	-0.053	15.066	-0.157	-0.157	0.000	0.000	0.000	0.000
98	A	100	ILE	0	0.063	0.035	17.245	0.924	0.924	0.000	0.000	0.000	0.000
99	A	101	VAL	0	-0.002	0.005	17.269	0.830	0.830	0.000	0.000	0.000	0.000
100	A	102	ARG	1	0.912	0.969	17.566	-13.147	-13.147	0.000	0.000	0.000	0.000
101	A	103	ARG	1	0.860	0.919	12.270	-19.393	-19.393	0.000	0.000	0.000	0.000
102	A	104	GLN	0	-0.004	-0.004	13.232	0.940	0.940	0.000	0.000	0.000	0.000
103	A	105	THR	0	-0.085	-0.054	14.344	0.471	0.471	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.925	-0.952	12.007	19.758	19.758	0.000	0.000	0.000	0.000
105	A	107	GLY	0	-0.038	-0.035	10.225	2.143	2.143	0.000	0.000	0.000	0.000
106	A	108	TRP	0	-0.065	-0.020	9.214	3.423	3.423	0.000	0.000	0.000	0.000
107	A	109	ALA	0	0.033	0.010	9.676	-1.896	-1.896	0.000	0.000	0.000	0.000
108	A	110	TYR	0	-0.046	-0.068	11.392	-0.583	-0.583	0.000	0.000	0.000	0.000
109	A	111	ILE	0	0.021	0.014	13.406	-0.119	-0.119	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.911	0.970	16.116	-12.971	-12.971	0.000	0.000	0.000	0.000
111	A	113	PRO	0	-0.036	-0.006	18.297	-0.744	-0.744	0.000	0.000	0.000	0.000

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