FMO DATABASE

FMODB ID: 39YKL

Calculation Name: 1S3J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1160287.681199
FMO2-HF: Nuclear repulsion	1103456.152497
FMO2-HF: Total energy	-56831.528702
FMO2-MP2: Total energy	-56994.358582

3D Structure Molmil

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.
-4.14	-0.092	0.061	-1.658	-2.452	0.003

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 : -0.003 / q_NPA : -0.022

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	-0.838	-0.916	3.771	-0.442	1.794	-0.005	-0.972	-1.259	0.000
4	A	6	GLN	0	-0.071	-0.047	3.178	-3.088	-1.610	0.067	-0.609	-0.937	0.003
5	A	7	LEU	0	0.016	0.013	4.264	-0.426	-0.092	-0.001	-0.077	-0.256	0.000
6	A	8	MET	0	-0.027	-0.019	6.028	-0.081	-0.081	0.000	0.000	0.000	0.000
7	A	9	SER	0	0.003	0.004	7.935	-0.054	-0.054	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.850	-0.905	7.154	-0.068	-0.068	0.000	0.000	0.000	0.000
9	A	11	ILE	0	0.007	0.004	9.859	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	12	GLN	0	-0.024	-0.006	12.093	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	13	LEU	0	0.042	0.018	12.755	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	14	SER	0	-0.060	-0.029	13.691	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	15	LEU	0	-0.012	-0.021	15.800	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	16	GLN	0	-0.026	0.002	17.642	0.001	0.001	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.017	0.008	18.978	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.018	-0.014	19.396	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	19	PHE	0	0.029	0.013	21.990	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	20	GLN	0	0.002	-0.012	22.706	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.932	0.976	23.955	0.002	0.002	0.000	0.000	0.000	0.000
20	A	22	ILE	0	0.007	0.013	24.665	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	23	GLN	0	-0.059	-0.025	27.549	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	24	PRO	0	0.053	0.013	28.950	0.000	0.000	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.716	-0.854	31.218	0.003	0.003	0.000	0.000	0.000	0.000
24	A	26	MET	0	-0.079	-0.038	29.230	0.000	0.000	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.054	-0.034	32.926	0.000	0.000	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.903	-0.937	35.338	0.003	0.003	0.000	0.000	0.000	0.000
27	A	29	SER	0	-0.026	-0.014	36.632	0.000	0.000	0.000	0.000	0.000	0.000
28	A	30	MET	0	-0.041	-0.001	35.857	0.000	0.000	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.912	-0.951	38.852	0.008	0.008	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.914	0.974	41.532	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	33	GLN	0	-0.008	-0.016	41.916	0.000	0.000	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.025	0.017	43.799	0.000	0.000	0.000	0.000	0.000	0.000
33	A	35	VAL	0	-0.058	-0.022	40.092	0.000	0.000	0.000	0.000	0.000	0.000
34	A	36	THR	0	0.033	0.007	39.609	0.000	0.000	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.089	0.012	34.566	0.000	0.000	0.000	0.000	0.000	0.000
36	A	38	ALA	0	0.020	0.017	36.640	0.000	0.000	0.000	0.000	0.000	0.000
37	A	39	GLN	0	0.060	0.021	38.476	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	40	LEU	0	0.031	0.014	35.119	0.000	0.000	0.000	0.000	0.000	0.000
39	A	41	PHE	0	0.030	0.006	33.281	0.000	0.000	0.000	0.000	0.000	0.000
40	A	42	VAL	0	-0.003	0.000	37.242	0.000	0.000	0.000	0.000	0.000	0.000
41	A	43	LEU	0	0.006	0.000	40.766	0.000	0.000	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.036	0.018	36.565	0.000	0.000	0.000	0.000	0.000	0.000
43	A	45	SER	0	-0.048	-0.036	38.084	0.000	0.000	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.041	-0.013	39.265	0.000	0.000	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.865	0.935	40.297	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.896	0.954	33.920	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	49	HIS	0	-0.004	-0.020	37.391	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.015	0.040	42.211	0.000	0.000	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.069	-0.039	45.581	0.000	0.000	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.019	-0.005	41.062	0.000	0.000	0.000	0.000	0.000	0.000
51	A	53	LYS	1	0.975	0.992	45.590	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.013	-0.001	45.396	0.001	0.001	0.000	0.000	0.000	0.000
53	A	55	SER	0	-0.037	-0.040	44.891	0.000	0.000	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.843	-0.904	42.338	0.014	0.014	0.000	0.000	0.000	0.000
55	A	57	ILE	0	0.012	0.009	40.616	0.001	0.001	0.000	0.000	0.000	0.000
56	A	58	ALA	0	-0.041	-0.032	39.864	0.001	0.001	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.943	-0.967	38.738	0.019	0.019	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.931	0.963	36.146	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	61	MET	0	-0.066	-0.025	34.996	0.000	0.000	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.905	-0.925	32.756	0.031	0.031	0.000	0.000	0.000	0.000
61	A	63	VAL	0	-0.065	-0.021	37.122	0.000	0.000	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.947	0.962	40.096	-0.020	-0.020	0.000	0.000	0.000	0.000
63	A	65	PRO	0	0.101	0.026	43.807	0.000	0.000	0.000	0.000	0.000	0.000
64	A	66	SER	0	-0.022	-0.020	46.174	0.000	0.000	0.000	0.000	0.000	0.000
65	A	67	ALA	0	0.037	0.025	42.806	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	68	VAL	0	0.056	0.030	42.514	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	69	THR	0	-0.049	-0.014	44.905	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.044	0.028	46.478	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	71	MET	0	-0.059	-0.031	40.438	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	72	ALA	0	0.028	0.004	45.674	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.832	-0.907	48.202	0.009	0.009	0.000	0.000	0.000	0.000
72	A	74	ARG	1	0.855	0.933	45.975	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.023	0.003	44.078	0.000	0.000	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.855	-0.929	48.453	0.008	0.008	0.000	0.000	0.000	0.000
75	A	77	GLN	0	-0.042	-0.014	52.002	0.000	0.000	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.803	0.906	45.967	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	79	ASN	0	-0.010	0.003	51.831	0.000	0.000	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.028	0.004	46.340	0.000	0.000	0.000	0.000	0.000	0.000
79	A	81	ILE	0	0.001	-0.011	46.693	0.000	0.000	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.039	0.032	49.765	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.817	0.903	51.165	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	84	THR	0	0.033	0.019	53.326	0.000	0.000	0.000	0.000	0.000	0.000
83	A	85	HIS	0	-0.072	-0.032	54.267	0.000	0.000	0.000	0.000	0.000	0.000
84	A	86	ASN	0	-0.006	0.008	51.474	0.000	0.000	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.002	-0.025	54.633	0.000	0.000	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.916	0.966	52.667	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.779	-0.870	54.878	0.010	0.010	0.000	0.000	0.000	0.000
88	A	90	ARG	1	1.014	0.999	56.063	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	91	ARG	1	0.780	0.862	56.936	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.021	0.010	51.342	0.000	0.000	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.013	-0.009	51.401	0.000	0.000	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.815	-0.914	49.664	0.010	0.010	0.000	0.000	0.000	0.000
93	A	95	LEU	0	-0.032	-0.029	45.870	0.000	0.000	0.000	0.000	0.000	0.000
94	A	96	SER	0	0.027	0.001	47.629	0.000	0.000	0.000	0.000	0.000	0.000
95	A	97	LEU	0	-0.010	-0.002	43.860	0.000	0.000	0.000	0.000	0.000	0.000
96	A	98	THR	0	0.008	0.004	48.107	0.000	0.000	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.861	-0.937	49.427	0.005	0.005	0.000	0.000	0.000	0.000
98	A	100	GLU	-1	-0.909	-0.975	49.729	0.005	0.005	0.000	0.000	0.000	0.000
99	A	101	GLY	0	0.006	-0.005	47.308	0.000	0.000	0.000	0.000	0.000	0.000
100	A	102	ASP	-1	-0.898	-0.921	45.214	0.007	0.007	0.000	0.000	0.000	0.000
101	A	103	ILE	0	0.036	0.017	44.664	0.000	0.000	0.000	0.000	0.000	0.000
102	A	104	LYS	1	0.886	0.965	44.420	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	105	PHE	0	-0.013	-0.027	37.178	0.000	0.000	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.903	-0.960	40.113	0.007	0.007	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.940	-0.967	40.576	0.005	0.005	0.000	0.000	0.000	0.000
106	A	108	VAL	0	-0.034	-0.016	37.630	0.000	0.000	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.018	-0.001	34.534	0.000	0.000	0.000	0.000	0.000	0.000
108	A	110	ALA	0	0.000	0.000	35.699	0.000	0.000	0.000	0.000	0.000	0.000
109	A	111	GLY	0	0.028	0.015	36.738	0.000	0.000	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.908	0.928	30.535	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	113	LYS	1	0.944	0.978	32.075	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.019	-0.014	32.185	0.000	0.000	0.000	0.000	0.000	0.000
113	A	115	ILE	0	0.000	0.004	30.236	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	116	MET	0	0.020	0.010	25.709	0.000	0.000	0.000	0.000	0.000	0.000
115	A	117	ALA	0	-0.031	-0.026	28.004	0.000	0.000	0.000	0.000	0.000	0.000
116	A	118	ARG	1	0.857	0.925	30.101	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	119	TYR	0	-0.044	-0.019	25.032	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	120	LEU	0	0.011	-0.014	23.929	0.000	0.000	0.000	0.000	0.000	0.000
119	A	121	SER	0	-0.061	-0.020	25.975	0.000	0.000	0.000	0.000	0.000	0.000
120	A	122	PHE	0	-0.048	-0.013	24.793	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	123	LEU	0	-0.057	-0.011	20.740	0.000	0.000	0.000	0.000	0.000	0.000
122	A	124	THR	0	0.045	0.024	22.145	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	125	GLU	-1	-0.886	-0.964	24.269	0.001	0.001	0.000	0.000	0.000	0.000
124	A	126	GLU	-1	-0.967	-0.984	21.480	0.002	0.002	0.000	0.000	0.000	0.000
125	A	127	GLU	-1	-0.875	-0.936	18.745	0.016	0.016	0.000	0.000	0.000	0.000
126	A	128	MET	0	-0.020	-0.002	20.900	0.002	0.002	0.000	0.000	0.000	0.000
127	A	129	LEU	0	-0.030	-0.015	23.491	0.000	0.000	0.000	0.000	0.000	0.000
128	A	130	GLN	0	-0.007	-0.007	17.456	0.004	0.004	0.000	0.000	0.000	0.000
129	A	131	ALA	0	0.016	0.009	19.511	0.000	0.000	0.000	0.000	0.000	0.000
130	A	132	ALA	0	-0.009	0.016	20.496	0.000	0.000	0.000	0.000	0.000	0.000
131	A	133	HIS	0	0.001	0.002	18.665	0.001	0.001	0.000	0.000	0.000	0.000
132	A	134	ILE	0	-0.002	-0.012	15.187	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	135	THR	0	-0.037	-0.041	18.693	0.001	0.001	0.000	0.000	0.000	0.000
134	A	136	ALA	0	0.016	0.022	21.062	0.001	0.001	0.000	0.000	0.000	0.000
135	A	137	LYS	1	0.973	0.983	16.443	0.008	0.008	0.000	0.000	0.000	0.000
136	A	138	LEU	0	-0.062	-0.037	15.912	0.001	0.001	0.000	0.000	0.000	0.000
137	A	139	ALA	0	0.014	0.007	19.961	0.003	0.003	0.000	0.000	0.000	0.000
138	A	140	GLN	0	-0.033	-0.013	23.614	0.000	0.000	0.000	0.000	0.000	0.000
139	A	141	ALA	0	-0.036	-0.034	20.560	0.001	0.001	0.000	0.000	0.000	0.000
140	A	142	ALA	0	-0.039	-0.013	22.096	0.002	0.002	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.942	-0.967	23.471	0.021	0.021	0.000	0.000	0.000	0.000
142	A	144	THR	0	-0.137	-0.059	24.956	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	145	ASP	-1	-0.951	-0.956	25.396	0.032	0.032	0.000	0.000	0.000	0.000

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