FMO DATABASE

FMODB ID: YZK32

Calculation Name: 3SMD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SMD

Chain ID: A

ChEMBL ID:

UniProt ID: A0REX4

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	136
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1237623.785943
FMO2-HF: Nuclear repulsion	1184141.478612
FMO2-HF: Total energy	-53482.307331
FMO2-MP2: Total energy	-53641.677011

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:LEU)

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

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.
1.202	4.241	0.012	-0.982	-2.066	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.017

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	LEU	0	0.023	-0.020	3.815	-1.763	-0.273	-0.014	-0.723	-0.752	0.004
4	A	6	TYR	0	0.035	0.031	6.628	0.056	0.056	0.000	0.000	0.000	0.000
5	A	7	TYR	0	0.035	-0.021	3.800	-0.449	-0.099	0.002	-0.036	-0.315	0.000
6	A	8	LYS	1	0.916	0.983	3.303	0.315	0.862	0.019	-0.100	-0.465	0.000
7	A	9	LYS	1	0.952	0.978	4.416	0.170	0.289	0.000	-0.016	-0.103	0.000
8	A	10	ILE	0	-0.005	-0.002	7.820	0.046	0.046	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.836	0.891	5.105	0.044	0.044	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.970	-0.992	7.702	-0.338	-0.338	0.000	0.000	0.000	0.000
11	A	13	GLN	0	-0.053	-0.032	9.451	0.018	0.018	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.000	0.016	11.023	0.014	0.014	0.000	0.000	0.000	0.000
13	A	15	GLY	0	0.048	0.043	11.336	0.009	0.009	0.000	0.000	0.000	0.000
14	A	16	HIS	1	0.848	0.894	10.001	0.134	0.134	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.890	-0.952	11.662	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.050	-0.010	10.948	0.000	0.000	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.032	0.034	6.780	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	20	PHE	0	-0.034	-0.015	10.000	0.016	0.016	0.000	0.000	0.000	0.000
19	A	21	MET	0	0.006	-0.007	4.053	-0.087	0.055	-0.001	-0.016	-0.126	0.000
20	A	22	PRO	0	0.026	0.005	9.773	0.003	0.003	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.025	-0.009	9.319	0.173	0.173	0.000	0.000	0.000	0.000
22	A	24	VAL	0	-0.008	0.005	10.975	-0.139	-0.139	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.028	0.007	12.055	0.068	0.068	0.000	0.000	0.000	0.000
24	A	26	ALA	0	0.005	0.000	14.491	-0.039	-0.039	0.000	0.000	0.000	0.000
25	A	27	VAL	0	-0.036	-0.011	17.099	-0.021	-0.021	0.000	0.000	0.000	0.000
26	A	28	ILE	0	0.021	0.001	17.769	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.926	0.961	21.562	-0.135	-0.135	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.037	-0.012	25.011	0.005	0.005	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.929	-0.975	26.850	0.065	0.065	0.000	0.000	0.000	0.000
30	A	32	GLN	0	-0.046	-0.018	29.856	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	33	GLY	0	-0.023	-0.009	29.374	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.915	-0.939	26.447	0.069	0.069	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.036	-0.044	22.575	0.012	0.012	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.023	-0.002	17.999	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	37	PHE	0	-0.012	-0.009	17.528	0.022	0.022	0.000	0.000	0.000	0.000
36	A	38	GLN	0	-0.034	-0.048	10.504	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	39	TYR	0	-0.042	-0.021	15.225	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.059	0.023	10.570	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.035	-0.015	11.808	0.001	0.001	0.000	0.000	0.000	0.000
40	A	42	GLY	0	-0.012	-0.008	10.880	-0.082	-0.082	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.955	-0.972	12.986	-0.082	-0.082	0.000	0.000	0.000	0.000
42	A	44	TYR	0	-0.032	-0.017	14.128	0.011	0.011	0.000	0.000	0.000	0.000
43	A	45	TRP	0	0.008	0.009	15.055	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	46	SER	0	0.000	-0.025	12.410	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.023	-0.001	14.533	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	48	PRO	0	-0.001	0.001	12.659	0.031	0.031	0.000	0.000	0.000	0.000
47	A	49	ALA	0	-0.011	-0.019	10.839	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.083	0.058	7.410	0.105	0.105	0.000	0.000	0.000	0.000
49	A	51	ALA	0	-0.024	-0.013	5.222	-0.410	-0.410	0.000	0.000	0.000	0.000
50	A	52	ILE	0	-0.009	-0.002	7.149	0.121	0.121	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.794	-0.823	6.424	0.722	0.722	0.000	0.000	0.000	0.000
52	A	54	PRO	0	-0.034	-0.026	9.199	-0.090	-0.090	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.023	-0.015	12.340	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.755	-0.841	11.165	0.748	0.748	0.000	0.000	0.000	0.000
55	A	57	THR	0	-0.029	-0.004	14.924	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	58	PRO	0	0.020	-0.017	15.109	0.043	0.043	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.887	-0.955	15.747	0.290	0.290	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.889	-0.951	16.209	0.293	0.293	0.000	0.000	0.000	0.000
59	A	61	ALA	0	0.034	0.030	11.573	0.041	0.041	0.000	0.000	0.000	0.000
60	A	62	VAL	0	-0.028	-0.017	12.497	0.098	0.098	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.039	-0.016	14.559	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	64	ARG	1	0.722	0.832	7.973	-1.441	-1.441	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.794	-0.897	7.487	2.252	2.252	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.004	0.005	10.916	-0.058	-0.058	0.000	0.000	0.000	0.000
65	A	67	TRP	0	-0.047	0.004	12.704	-0.073	-0.073	0.000	0.000	0.000	0.000
66	A	68	GLU	-1	-0.918	-0.967	7.887	1.418	1.418	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.850	-0.906	7.418	0.742	0.742	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.075	-0.069	11.190	-0.148	-0.148	0.000	0.000	0.000	0.000
69	A	71	GLY	0	-0.060	-0.022	14.915	-0.061	-0.061	0.000	0.000	0.000	0.000
70	A	72	LEU	0	-0.035	-0.018	16.679	-0.036	-0.036	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.993	0.998	17.716	-0.134	-0.134	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.001	-0.012	18.212	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	75	GLN	0	-0.028	-0.028	20.693	0.015	0.015	0.000	0.000	0.000	0.000
74	A	76	VAL	0	0.031	0.002	20.147	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.900	0.975	22.741	-0.135	-0.135	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.927	0.944	24.513	-0.130	-0.130	0.000	0.000	0.000	0.000
77	A	79	GLN	0	0.059	0.050	21.439	0.006	0.006	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.805	0.896	22.185	-0.150	-0.150	0.000	0.000	0.000	0.000
79	A	81	GLY	0	-0.002	-0.004	22.653	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.001	0.000	18.327	0.022	0.022	0.000	0.000	0.000	0.000
81	A	83	PHE	0	-0.048	-0.028	17.794	-0.032	-0.032	0.000	0.000	0.000	0.000
82	A	84	GLY	0	0.092	0.038	16.789	0.031	0.031	0.000	0.000	0.000	0.000
83	A	85	GLY	0	0.010	0.023	17.603	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.950	0.950	17.398	-0.044	-0.044	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.901	-0.940	17.670	0.049	0.049	0.000	0.000	0.000	0.000
86	A	88	PHE	0	-0.016	-0.004	14.231	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	89	ARG	1	0.811	0.896	13.221	-0.036	-0.036	0.000	0.000	0.000	0.000
88	A	90	TYR	0	0.013	0.001	7.354	0.013	0.013	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.038	-0.024	10.283	0.016	0.016	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.044	0.025	3.785	-0.604	-0.213	0.006	-0.091	-0.305	0.000
91	A	93	ALA	0	0.048	0.020	9.034	0.031	0.031	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.043	-0.027	7.190	0.025	0.025	0.000	0.000	0.000	0.000
93	A	95	GLY	0	0.005	-0.003	10.576	0.018	0.018	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.854	-0.900	6.535	-0.141	-0.141	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.861	0.940	9.172	0.016	0.016	0.000	0.000	0.000	0.000
96	A	98	VAL	0	0.003	0.005	5.907	0.014	0.014	0.000	0.000	0.000	0.000
97	A	99	GLU	-1	-0.804	-0.891	9.363	0.075	0.075	0.000	0.000	0.000	0.000
98	A	100	TYR	0	-0.005	0.009	6.696	0.048	0.048	0.000	0.000	0.000	0.000
99	A	101	ILE	0	-0.008	0.008	11.806	-0.052	-0.052	0.000	0.000	0.000	0.000
100	A	102	VAL	0	-0.035	-0.019	12.422	0.051	0.051	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.008	0.013	14.679	-0.057	-0.057	0.000	0.000	0.000	0.000
102	A	104	VAL	0	0.003	0.004	16.341	0.038	0.038	0.000	0.000	0.000	0.000
103	A	105	PHE	0	0.039	0.010	17.076	-0.037	-0.037	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.907	-0.951	19.969	0.142	0.142	0.000	0.000	0.000	0.000
105	A	107	CYS	0	-0.048	-0.039	19.492	0.009	0.009	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.826	-0.896	22.020	0.119	0.119	0.000	0.000	0.000	0.000
107	A	109	ILE	0	0.024	-0.001	21.929	0.012	0.012	0.000	0.000	0.000	0.000
108	A	110	THR	0	-0.048	-0.012	23.477	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	111	SER	0	-0.017	-0.020	23.645	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	112	GLY	0	0.015	0.025	21.496	0.018	0.018	0.000	0.000	0.000	0.000
111	A	113	LYS	1	0.946	0.972	20.061	-0.116	-0.116	0.000	0.000	0.000	0.000
112	A	114	LEU	0	0.054	0.027	18.884	0.020	0.020	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.835	0.923	12.169	-0.321	-0.321	0.000	0.000	0.000	0.000
114	A	123	LYS	1	0.922	0.956	15.355	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	124	LEU	0	0.028	0.030	14.664	0.017	0.017	0.000	0.000	0.000	0.000
116	A	125	GLN	0	-0.036	-0.019	17.995	-0.021	-0.021	0.000	0.000	0.000	0.000
117	A	126	TYR	0	0.024	0.008	21.016	0.017	0.017	0.000	0.000	0.000	0.000
118	A	127	PHE	0	0.034	0.018	21.231	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	128	SER	0	0.060	0.032	25.424	0.011	0.011	0.000	0.000	0.000	0.000
120	A	129	PHE	0	-0.004	-0.022	26.835	0.000	0.000	0.000	0.000	0.000	0.000
121	A	130	SER	0	-0.021	-0.026	27.958	0.000	0.000	0.000	0.000	0.000	0.000
122	A	131	GLU	-1	-0.910	-0.933	28.336	0.037	0.037	0.000	0.000	0.000	0.000
123	A	132	LYS	1	0.852	0.960	23.438	-0.076	-0.076	0.000	0.000	0.000	0.000
124	A	133	PRO	0	0.001	0.013	20.544	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	134	PRO	0	-0.025	-0.011	20.382	0.010	0.010	0.000	0.000	0.000	0.000
126	A	135	LEU	0	0.010	-0.003	16.597	0.001	0.001	0.000	0.000	0.000	0.000
127	A	136	ALA	0	0.030	0.022	13.480	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	137	LEU	0	-0.017	-0.004	11.750	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	138	PRO	0	0.039	0.026	15.912	0.002	0.002	0.000	0.000	0.000	0.000
130	A	139	TYR	0	-0.020	-0.016	14.125	0.007	0.007	0.000	0.000	0.000	0.000
131	A	140	PRO	0	-0.010	-0.010	20.109	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	141	ASP	-1	-0.794	-0.916	23.544	0.085	0.085	0.000	0.000	0.000	0.000
133	A	142	LYS	1	0.921	0.959	24.669	-0.114	-0.114	0.000	0.000	0.000	0.000
134	A	143	ILE	0	-0.053	-0.014	20.030	0.002	0.002	0.000	0.000	0.000	0.000
135	A	144	PHE	0	0.023	0.008	20.526	0.008	0.008	0.000	0.000	0.000	0.000
136	A	145	LEU	0	-0.009	0.013	25.308	0.000	0.000	0.000	0.000	0.000	0.000

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