FMO DATABASE

FMODB ID: V51M1

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	OptHSide
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	-1237916.006599
FMO2-HF: Nuclear repulsion	1184433.020991
FMO2-HF: Total energy	-53482.985608
FMO2-MP2: Total energy	-53642.379383

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.
0.236	3.413	0.034	-1.028	-2.181	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 : -0.018 / q_NPA : -0.019

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	0.038	-0.011	3.815	-1.889	-0.373	-0.014	-0.745	-0.756	0.004
4	A	6	TYR	0	0.014	0.022	6.568	0.038	0.038	0.000	0.000	0.000	0.000
5	A	7	TYR	0	0.047	-0.009	3.854	-0.484	-0.110	0.002	-0.040	-0.336	0.000
6	A	8	LYS	1	0.853	0.938	3.044	0.134	0.738	0.041	-0.127	-0.518	0.000
7	A	9	LYS	1	0.893	0.943	4.376	0.191	0.326	0.000	-0.021	-0.113	0.000
8	A	10	ILE	0	-0.007	-0.007	7.794	0.051	0.051	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.841	0.895	4.806	0.141	0.141	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.883	-0.940	7.545	-0.344	-0.344	0.000	0.000	0.000	0.000
11	A	13	GLN	0	-0.036	-0.016	9.485	0.011	0.011	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.006	0.019	10.847	0.017	0.017	0.000	0.000	0.000	0.000
13	A	15	GLY	0	0.041	0.040	11.233	0.010	0.010	0.000	0.000	0.000	0.000
14	A	16	HIS	1	0.852	0.900	9.794	0.159	0.159	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.832	-0.902	11.405	-0.050	-0.050	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.028	0.000	10.812	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.022	0.028	6.453	0.002	0.002	0.000	0.000	0.000	0.000
18	A	20	PHE	0	-0.044	-0.019	9.657	0.014	0.014	0.000	0.000	0.000	0.000
19	A	21	MET	0	0.008	-0.008	3.643	-0.154	0.065	0.003	-0.035	-0.187	0.000
20	A	22	PRO	0	0.030	0.013	9.256	0.010	0.010	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.021	-0.012	8.755	0.170	0.170	0.000	0.000	0.000	0.000
22	A	24	VAL	0	-0.006	0.005	10.613	-0.128	-0.128	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.022	0.006	11.739	0.063	0.063	0.000	0.000	0.000	0.000
24	A	26	ALA	0	0.006	0.003	14.216	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	27	VAL	0	-0.031	-0.011	17.077	-0.021	-0.021	0.000	0.000	0.000	0.000
26	A	28	ILE	0	0.016	-0.001	17.800	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.873	0.927	21.543	-0.127	-0.127	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.041	-0.027	24.994	0.003	0.003	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.928	-0.970	26.835	0.067	0.067	0.000	0.000	0.000	0.000
30	A	32	GLN	0	-0.066	-0.044	29.615	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	33	GLY	0	-0.031	-0.012	29.357	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.891	-0.904	26.348	0.069	0.069	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.043	-0.046	22.583	0.011	0.011	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.030	-0.003	18.009	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	37	PHE	0	0.001	-0.008	17.508	0.019	0.019	0.000	0.000	0.000	0.000
36	A	38	GLN	0	-0.034	-0.050	10.014	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	39	TYR	0	-0.066	-0.045	15.217	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.065	0.029	10.699	0.001	0.001	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.026	-0.016	11.993	0.001	0.001	0.000	0.000	0.000	0.000
40	A	42	GLY	0	-0.006	0.000	11.016	-0.085	-0.085	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.940	-0.956	13.101	-0.104	-0.104	0.000	0.000	0.000	0.000
42	A	44	TYR	0	-0.027	-0.011	14.284	0.009	0.009	0.000	0.000	0.000	0.000
43	A	45	TRP	0	0.008	0.010	15.175	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	46	SER	0	0.006	-0.016	12.300	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.028	0.000	14.528	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	48	PRO	0	-0.005	-0.005	12.636	0.027	0.027	0.000	0.000	0.000	0.000
47	A	49	ALA	0	-0.014	-0.018	10.628	-0.039	-0.039	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.064	0.047	7.135	0.105	0.105	0.000	0.000	0.000	0.000
49	A	51	ALA	0	-0.019	-0.007	5.167	-0.393	-0.393	0.000	0.000	0.000	0.000
50	A	52	ILE	0	-0.011	-0.001	7.129	0.135	0.135	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.790	-0.861	6.634	0.590	0.590	0.000	0.000	0.000	0.000
52	A	54	PRO	0	-0.037	-0.028	9.261	-0.088	-0.088	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.024	-0.014	12.329	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.774	-0.844	11.000	0.765	0.765	0.000	0.000	0.000	0.000
55	A	57	THR	0	-0.056	-0.055	14.900	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	58	PRO	0	0.003	-0.022	15.082	0.044	0.044	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.867	-0.952	15.719	0.282	0.282	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.839	-0.891	16.144	0.290	0.290	0.000	0.000	0.000	0.000
59	A	61	ALA	0	0.031	0.030	11.538	0.041	0.041	0.000	0.000	0.000	0.000
60	A	62	VAL	0	-0.030	-0.017	12.462	0.097	0.097	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.041	-0.019	14.526	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	64	ARG	1	0.697	0.807	7.746	-1.485	-1.485	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.797	-0.894	7.543	2.234	2.234	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.019	-0.007	10.916	-0.056	-0.056	0.000	0.000	0.000	0.000
65	A	67	TRP	0	-0.045	0.004	13.036	-0.070	-0.070	0.000	0.000	0.000	0.000
66	A	68	GLU	-1	-0.872	-0.929	8.669	1.265	1.265	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.830	-0.894	8.190	0.580	0.580	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.089	-0.080	11.179	-0.149	-0.149	0.000	0.000	0.000	0.000
69	A	71	GLY	0	-0.040	-0.012	14.901	-0.061	-0.061	0.000	0.000	0.000	0.000
70	A	72	LEU	0	-0.041	-0.017	16.692	-0.037	-0.037	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.995	0.998	17.716	-0.138	-0.138	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.003	-0.015	18.184	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	75	GLN	0	-0.018	-0.015	20.693	0.015	0.015	0.000	0.000	0.000	0.000
74	A	76	VAL	0	0.033	0.004	20.099	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.807	0.900	22.708	-0.136	-0.136	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.885	0.912	24.478	-0.130	-0.130	0.000	0.000	0.000	0.000
77	A	79	GLN	0	0.051	0.045	21.232	0.005	0.005	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.761	0.866	21.806	-0.143	-0.143	0.000	0.000	0.000	0.000
79	A	81	GLY	0	-0.014	-0.014	22.291	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.007	0.003	17.871	0.020	0.020	0.000	0.000	0.000	0.000
81	A	83	PHE	0	-0.043	-0.025	17.533	-0.029	-0.029	0.000	0.000	0.000	0.000
82	A	84	GLY	0	0.095	0.039	16.485	0.027	0.027	0.000	0.000	0.000	0.000
83	A	85	GLY	0	-0.003	0.018	17.303	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.973	0.965	16.927	-0.024	-0.024	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.899	-0.944	17.180	0.025	0.025	0.000	0.000	0.000	0.000
86	A	88	PHE	0	-0.017	-0.009	13.965	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	89	ARG	1	0.807	0.887	12.678	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	90	TYR	0	0.013	0.001	7.462	-0.022	-0.022	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.049	-0.026	9.923	0.006	0.006	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.036	0.019	3.933	-0.521	-0.192	0.002	-0.060	-0.271	0.000
91	A	93	ALA	0	0.045	0.019	9.060	0.043	0.043	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.049	-0.037	6.912	0.020	0.020	0.000	0.000	0.000	0.000
93	A	95	GLY	0	-0.001	-0.009	10.392	0.022	0.022	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.852	-0.893	6.375	-0.186	-0.186	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.833	0.909	8.994	0.047	0.047	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.007	-0.002	5.695	0.010	0.010	0.000	0.000	0.000	0.000
97	A	99	GLU	-1	-0.800	-0.879	9.192	0.041	0.041	0.000	0.000	0.000	0.000
98	A	100	TYR	0	-0.005	0.009	5.375	-0.043	-0.043	0.000	0.000	0.000	0.000
99	A	101	ILE	0	-0.013	-0.001	11.485	-0.043	-0.043	0.000	0.000	0.000	0.000
100	A	102	VAL	0	-0.026	-0.014	12.023	0.050	0.050	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.002	0.014	14.306	-0.053	-0.053	0.000	0.000	0.000	0.000
102	A	104	VAL	0	0.007	0.005	15.968	0.037	0.037	0.000	0.000	0.000	0.000
103	A	105	PHE	0	0.040	0.015	17.120	-0.034	-0.034	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.792	-0.866	19.854	0.131	0.131	0.000	0.000	0.000	0.000
105	A	107	CYS	0	-0.040	-0.030	19.633	0.009	0.009	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.770	-0.853	21.999	0.115	0.115	0.000	0.000	0.000	0.000
107	A	109	ILE	0	0.029	0.004	21.900	0.013	0.013	0.000	0.000	0.000	0.000
108	A	110	THR	0	-0.054	-0.017	23.458	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	111	SER	0	-0.010	-0.020	23.644	-0.015	-0.015	0.000	0.000	0.000	0.000
110	A	112	GLY	0	0.015	0.029	21.501	0.018	0.018	0.000	0.000	0.000	0.000
111	A	113	LYS	1	0.950	0.971	20.416	-0.123	-0.123	0.000	0.000	0.000	0.000
112	A	114	LEU	0	0.047	0.031	18.619	0.021	0.021	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.823	0.913	11.851	-0.374	-0.374	0.000	0.000	0.000	0.000
114	A	123	LYS	1	0.929	0.964	15.131	-0.029	-0.029	0.000	0.000	0.000	0.000
115	A	124	LEU	0	-0.034	-0.008	14.520	0.015	0.015	0.000	0.000	0.000	0.000
116	A	125	GLN	0	-0.011	-0.007	17.989	-0.021	-0.021	0.000	0.000	0.000	0.000
117	A	126	TYR	0	0.046	0.019	21.006	0.015	0.015	0.000	0.000	0.000	0.000
118	A	127	PHE	0	0.026	0.014	21.364	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	128	SER	0	0.044	-0.005	25.413	0.010	0.010	0.000	0.000	0.000	0.000
120	A	129	PHE	0	0.013	-0.014	27.021	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	130	SER	0	-0.025	-0.021	27.932	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	131	GLU	-1	-0.891	-0.900	28.467	0.036	0.036	0.000	0.000	0.000	0.000
123	A	132	LYS	1	0.761	0.904	23.458	-0.065	-0.065	0.000	0.000	0.000	0.000
124	A	133	PRO	0	0.001	0.014	20.419	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	134	PRO	0	-0.013	-0.006	20.495	0.009	0.009	0.000	0.000	0.000	0.000
126	A	135	LEU	0	-0.003	-0.010	16.696	0.001	0.001	0.000	0.000	0.000	0.000
127	A	136	ALA	0	0.026	0.018	13.284	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	137	LEU	0	-0.016	-0.002	11.487	0.000	0.000	0.000	0.000	0.000	0.000
129	A	138	PRO	0	0.036	0.025	15.560	0.006	0.006	0.000	0.000	0.000	0.000
130	A	139	TYR	0	0.001	-0.008	13.286	0.013	0.013	0.000	0.000	0.000	0.000
131	A	140	PRO	0	0.001	-0.004	19.939	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	141	ASP	-1	-0.729	-0.877	23.360	0.075	0.075	0.000	0.000	0.000	0.000
133	A	142	LYS	1	0.912	0.960	24.550	-0.104	-0.104	0.000	0.000	0.000	0.000
134	A	143	ILE	0	-0.048	-0.008	19.666	0.003	0.003	0.000	0.000	0.000	0.000
135	A	144	PHE	0	0.037	0.016	20.601	0.010	0.010	0.000	0.000	0.000	0.000
136	A	145	LEU	0	0.006	0.022	25.126	0.003	0.003	0.000	0.000	0.000	0.000

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