FMO DATABASE

FMODB ID: 94JL2

Calculation Name: 1S3J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1S3J

Chain ID: A

ChEMBL ID:

UniProt ID: O32181

Base Structure: X-ray

Registration Date: 2023-09-20

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1163415.456782
FMO2-HF: Nuclear repulsion	1106582.948527
FMO2-HF: Total energy	-56832.508255
FMO2-MP2: Total energy	-56995.368683

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:SER)

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

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.
-2.807	0.713	0.533	-1.52	-2.533	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.018

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	ASP	-1	-0.850	-0.931	3.862	0.694	2.385	-0.011	-0.663	-1.017	0.001
4	A	6	GLN	0	-0.062	-0.020	2.474	-2.794	-1.280	0.545	-0.785	-1.274	0.001
5	A	7	LEU	0	0.042	0.022	3.981	0.149	0.464	-0.001	-0.072	-0.242	0.000
6	A	8	MET	0	-0.023	-0.020	5.886	0.410	0.410	0.000	0.000	0.000	0.000
7	A	9	SER	0	-0.003	-0.005	7.703	0.124	0.124	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.853	-0.916	6.928	-1.774	-1.774	0.000	0.000	0.000	0.000
9	A	11	ILE	0	-0.015	0.002	9.676	0.169	0.169	0.000	0.000	0.000	0.000
10	A	12	GLN	0	-0.018	-0.011	11.718	0.049	0.049	0.000	0.000	0.000	0.000
11	A	13	LEU	0	0.020	0.007	11.917	0.051	0.051	0.000	0.000	0.000	0.000
12	A	14	SER	0	-0.026	-0.024	13.209	0.043	0.043	0.000	0.000	0.000	0.000
13	A	15	LEU	0	-0.002	-0.008	15.708	0.046	0.046	0.000	0.000	0.000	0.000
14	A	16	GLN	0	-0.036	-0.009	17.345	0.029	0.029	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.014	0.006	18.481	0.024	0.024	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.007	-0.002	19.137	0.018	0.018	0.000	0.000	0.000	0.000
17	A	19	PHE	0	0.037	0.018	21.579	0.021	0.021	0.000	0.000	0.000	0.000
18	A	20	GLN	0	-0.012	-0.019	22.378	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.866	0.946	23.016	0.188	0.188	0.000	0.000	0.000	0.000
20	A	22	ILE	0	0.037	0.013	24.439	0.011	0.011	0.000	0.000	0.000	0.000
21	A	23	GLN	0	-0.027	-0.011	27.204	0.005	0.005	0.000	0.000	0.000	0.000
22	A	24	PRO	0	0.043	0.014	28.592	0.008	0.008	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.715	-0.805	30.385	-0.086	-0.086	0.000	0.000	0.000	0.000
24	A	26	MET	0	-0.074	-0.038	29.589	0.010	0.010	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.027	0.002	32.467	0.009	0.009	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.859	-0.922	35.136	-0.054	-0.054	0.000	0.000	0.000	0.000
27	A	29	SER	0	-0.038	-0.035	36.311	0.003	0.003	0.000	0.000	0.000	0.000
28	A	30	MET	0	-0.131	-0.031	36.368	0.004	0.004	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.880	-0.943	38.053	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.889	0.955	41.091	0.032	0.032	0.000	0.000	0.000	0.000
31	A	33	GLN	0	0.000	-0.013	41.847	0.002	0.002	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.002	0.018	43.894	0.003	0.003	0.000	0.000	0.000	0.000
33	A	35	VAL	0	-0.054	-0.031	40.575	0.004	0.004	0.000	0.000	0.000	0.000
34	A	36	THR	0	0.066	0.029	39.228	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.064	0.004	34.492	0.002	0.002	0.000	0.000	0.000	0.000
36	A	38	ALA	0	0.022	0.019	36.643	0.003	0.003	0.000	0.000	0.000	0.000
37	A	39	GLN	0	0.024	0.008	38.780	0.002	0.002	0.000	0.000	0.000	0.000
38	A	40	LEU	0	0.047	0.025	35.638	0.001	0.001	0.000	0.000	0.000	0.000
39	A	41	PHE	0	0.039	0.019	33.729	0.000	0.000	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.012	0.005	37.755	0.003	0.003	0.000	0.000	0.000	0.000
41	A	43	LEU	0	0.004	0.003	41.237	0.002	0.002	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.028	0.010	36.832	0.001	0.001	0.000	0.000	0.000	0.000
43	A	45	SER	0	-0.057	-0.029	38.720	0.004	0.004	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.028	-0.008	39.889	0.002	0.002	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.826	0.900	40.403	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.909	0.960	33.560	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	49	HIS	0	-0.030	-0.030	38.618	0.007	0.007	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.014	0.032	43.159	0.001	0.001	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.089	-0.077	46.390	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.017	-0.006	41.523	0.003	0.003	0.000	0.000	0.000	0.000
51	A	53	LYS	1	0.842	0.919	46.212	-0.040	-0.040	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.018	0.001	45.892	0.002	0.002	0.000	0.000	0.000	0.000
53	A	55	SER	0	-0.013	-0.020	45.368	0.000	0.000	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.773	-0.865	43.080	0.043	0.043	0.000	0.000	0.000	0.000
55	A	57	ILE	0	0.020	0.009	41.228	0.002	0.002	0.000	0.000	0.000	0.000
56	A	58	ALA	0	-0.041	-0.032	40.365	0.001	0.001	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.931	-0.966	39.165	0.059	0.059	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.909	0.954	36.887	-0.046	-0.046	0.000	0.000	0.000	0.000
59	A	61	MET	0	-0.065	-0.016	35.849	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.907	-0.934	33.024	0.076	0.076	0.000	0.000	0.000	0.000
61	A	63	VAL	0	-0.053	-0.016	37.359	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.950	0.961	40.476	-0.043	-0.043	0.000	0.000	0.000	0.000
63	A	65	PRO	0	0.091	0.021	44.238	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	66	SER	0	-0.004	0.015	46.571	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	67	ALA	0	0.023	0.016	43.237	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	68	VAL	0	0.062	0.025	42.651	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	69	THR	0	-0.050	-0.030	45.138	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.020	0.022	46.899	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	71	MET	0	-0.059	-0.025	40.758	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	72	ALA	0	0.038	0.009	46.009	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.814	-0.897	48.611	0.010	0.010	0.000	0.000	0.000	0.000
72	A	74	ARG	1	0.894	0.946	46.620	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.011	0.005	44.529	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.765	-0.860	48.768	0.009	0.009	0.000	0.000	0.000	0.000
75	A	77	GLN	0	-0.055	-0.024	52.325	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.777	0.890	46.229	0.003	0.003	0.000	0.000	0.000	0.000
77	A	79	ASN	0	-0.023	-0.015	52.111	0.000	0.000	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.017	0.006	46.599	0.000	0.000	0.000	0.000	0.000	0.000
79	A	81	ILE	0	-0.034	-0.020	47.282	0.001	0.001	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.031	0.026	50.275	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.727	0.830	52.256	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	84	THR	0	0.016	0.006	53.717	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	85	HIS	0	-0.069	-0.045	54.792	0.001	0.001	0.000	0.000	0.000	0.000
84	A	86	ASN	0	0.002	-0.009	52.327	0.000	0.000	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.008	-0.020	55.374	0.000	0.000	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.882	0.944	54.492	-0.030	-0.030	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.778	-0.862	55.944	0.029	0.029	0.000	0.000	0.000	0.000
88	A	90	ARG	1	1.013	1.005	56.763	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	91	ARG	1	0.803	0.879	57.480	-0.031	-0.031	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.023	0.004	52.295	0.000	0.000	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.010	-0.008	52.190	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.812	-0.888	50.272	0.030	0.030	0.000	0.000	0.000	0.000
93	A	95	LEU	0	0.000	-0.009	46.487	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	96	SER	0	0.017	0.021	48.744	0.001	0.001	0.000	0.000	0.000	0.000
95	A	97	LEU	0	0.017	0.004	44.299	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	98	THR	0	0.013	-0.003	48.773	0.001	0.001	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.880	-0.941	49.860	0.002	0.002	0.000	0.000	0.000	0.000
98	A	100	GLU	-1	-0.847	-0.927	49.951	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.016	0.002	47.731	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	102	ASP	-1	-0.890	-0.925	45.572	0.004	0.004	0.000	0.000	0.000	0.000
101	A	103	ILE	0	0.014	0.010	44.895	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.794	0.879	44.895	0.014	0.014	0.000	0.000	0.000	0.000
103	A	105	PHE	0	-0.009	-0.012	37.868	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.836	-0.924	40.394	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.821	-0.889	40.709	-0.022	-0.022	0.000	0.000	0.000	0.000
106	A	108	VAL	0	-0.022	-0.008	37.800	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.033	-0.003	34.584	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	110	ALA	0	-0.007	-0.007	35.906	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	111	GLY	0	0.024	0.014	36.844	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.922	0.940	31.369	0.017	0.017	0.000	0.000	0.000	0.000
111	A	113	LYS	1	0.967	0.984	32.152	0.028	0.028	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.014	-0.009	32.455	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	115	ILE	0	-0.018	-0.014	30.230	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	116	MET	0	-0.002	-0.004	25.688	-0.014	-0.014	0.000	0.000	0.000	0.000
115	A	117	ALA	0	-0.017	-0.011	28.069	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	118	ARG	1	0.838	0.902	29.672	0.088	0.088	0.000	0.000	0.000	0.000
117	A	119	TYR	0	-0.040	-0.036	24.820	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	120	LEU	0	0.018	-0.002	23.783	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	121	SER	0	-0.090	-0.048	25.839	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	122	PHE	0	-0.039	-0.018	24.206	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	123	LEU	0	-0.058	-0.007	20.508	-0.016	-0.016	0.000	0.000	0.000	0.000
122	A	124	THR	0	0.017	-0.024	22.093	0.021	0.021	0.000	0.000	0.000	0.000
123	A	125	GLU	-1	-0.887	-0.959	24.213	-0.085	-0.085	0.000	0.000	0.000	0.000
124	A	126	GLU	-1	-0.927	-0.965	21.540	-0.084	-0.084	0.000	0.000	0.000	0.000
125	A	127	GLU	-1	-0.848	-0.886	18.679	-0.201	-0.201	0.000	0.000	0.000	0.000
126	A	128	MET	0	-0.026	-0.004	20.798	0.013	0.013	0.000	0.000	0.000	0.000
127	A	129	LEU	0	-0.019	-0.011	23.689	0.016	0.016	0.000	0.000	0.000	0.000
128	A	130	GLN	0	-0.040	-0.028	16.902	0.017	0.017	0.000	0.000	0.000	0.000
129	A	131	ALA	0	0.024	0.014	19.772	0.022	0.022	0.000	0.000	0.000	0.000
130	A	132	ALA	0	-0.004	0.015	20.707	0.017	0.017	0.000	0.000	0.000	0.000
131	A	133	HIS	0	-0.002	0.002	19.661	0.009	0.009	0.000	0.000	0.000	0.000
132	A	134	ILE	0	-0.009	-0.008	15.617	0.027	0.027	0.000	0.000	0.000	0.000
133	A	135	THR	0	-0.048	-0.048	19.389	0.021	0.021	0.000	0.000	0.000	0.000
134	A	136	ALA	0	0.012	0.015	21.796	0.011	0.011	0.000	0.000	0.000	0.000
135	A	137	LYS	1	0.969	0.984	17.790	-0.234	-0.234	0.000	0.000	0.000	0.000
136	A	138	LEU	0	-0.032	-0.021	16.967	0.020	0.020	0.000	0.000	0.000	0.000
137	A	139	ALA	0	0.005	0.003	21.086	0.008	0.008	0.000	0.000	0.000	0.000
138	A	140	GLN	0	-0.022	-0.015	24.768	0.002	0.002	0.000	0.000	0.000	0.000
139	A	141	ALA	0	-0.031	-0.022	21.814	0.005	0.005	0.000	0.000	0.000	0.000
140	A	142	ALA	0	-0.025	-0.007	23.449	0.009	0.009	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.995	-0.989	24.851	0.064	0.064	0.000	0.000	0.000	0.000
142	A	144	THR	0	-0.103	-0.047	26.048	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	145	ASP	-1	-0.960	-0.967	26.526	0.152	0.152	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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