FMO DATABASE

FMODB ID: LJ2Y9

Calculation Name: 5B3D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5B3D

Chain ID: A

ChEMBL ID:

UniProt ID: P0A1J7

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-734678.707507
FMO2-HF: Nuclear repulsion	688436.097004
FMO2-HF: Total energy	-46242.610502
FMO2-MP2: Total energy	-46378.101303

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:2:THR)

Summations of interaction energy for fragment #1(A:2:THR)

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.
-13.824	-8.249	0.446	-2.575	-3.446	-0.003

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.008

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	4	LEU	0	0.001	-0.010	3.500	-2.674	-0.102	0.018	-1.186	-1.404	0.006
4	A	5	SER	0	0.030	0.005	2.850	-1.182	-0.296	0.310	-0.319	-0.877	-0.001
5	A	6	GLU	-1	-0.837	-0.904	3.085	-10.489	-8.372	0.118	-1.070	-1.165	-0.008
6	A	7	ILE	0	-0.049	-0.025	5.835	0.578	0.578	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.014	-0.001	7.597	0.063	0.063	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.866	-0.925	7.826	-0.129	-0.129	0.000	0.000	0.000	0.000
9	A	10	GLN	0	-0.032	-0.023	9.789	-0.122	-0.122	0.000	0.000	0.000	0.000
10	A	11	MET	0	-0.011	-0.007	12.012	0.089	0.089	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.016	0.010	12.655	0.012	0.012	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.030	-0.009	13.739	0.015	0.015	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.025	0.013	16.276	0.015	0.015	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.016	-0.015	16.619	0.019	0.019	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.027	-0.012	18.085	0.031	0.031	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.895	-0.944	20.376	-0.114	-0.114	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.044	-0.034	21.372	0.007	0.007	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.803	0.889	23.599	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	20	THR	0	0.007	0.010	24.889	0.006	0.006	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.019	-0.012	26.572	0.003	0.003	0.000	0.000	0.000	0.000
21	A	22	MET	0	0.018	0.000	27.440	0.003	0.003	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.799	-0.865	29.394	0.013	0.013	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.019	-0.014	31.399	0.001	0.001	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.954	-0.980	32.136	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.037	0.016	33.920	0.002	0.002	0.000	0.000	0.000	0.000
26	A	27	GLN	0	-0.025	-0.003	35.260	0.001	0.001	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.056	-0.040	37.102	0.001	0.001	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.011	-0.003	36.818	0.000	0.000	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.065	-0.023	39.209	0.004	0.004	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.008	-0.022	41.708	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.002	0.016	45.382	0.002	0.002	0.000	0.000	0.000	0.000
32	A	33	GLN	0	-0.074	-0.035	41.572	0.002	0.002	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.022	0.006	44.398	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	35	ASN	0	-0.030	-0.014	41.372	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.058	0.044	42.038	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	37	SER	0	0.016	0.026	40.848	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	38	GLN	0	0.036	-0.011	42.511	0.003	0.003	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.036	0.030	42.043	0.000	0.000	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.013	0.022	44.398	0.001	0.001	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.894	0.930	44.233	0.015	0.015	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.012	0.013	46.695	0.001	0.001	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.041	-0.034	47.009	0.001	0.001	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.826	-0.929	48.856	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.921	-0.941	51.927	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.911	0.953	51.602	0.007	0.007	0.000	0.000	0.000	0.000
46	A	47	SER	0	-0.034	-0.035	52.990	0.001	0.001	0.000	0.000	0.000	0.000
47	A	48	SER	0	0.000	-0.008	55.394	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	LEU	0	0.004	0.001	57.045	0.000	0.000	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.036	-0.026	56.061	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.016	0.022	59.679	0.000	0.000	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.020	-0.010	61.415	0.000	0.000	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.030	-0.014	62.382	0.000	0.000	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.883	-0.940	63.122	0.000	0.000	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.002	-0.002	65.092	0.000	0.000	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.001	-0.018	67.298	0.000	0.000	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.766	-0.825	67.759	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.068	-0.042	66.813	0.000	0.000	0.000	0.000	0.000	0.000
58	A	59	GLN	0	0.002	-0.002	71.230	0.001	0.001	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.836	0.891	71.802	0.003	0.003	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.846	0.904	69.528	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.042	-0.017	75.322	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.940	-0.958	77.668	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	GLN	0	-0.083	-0.042	77.220	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.046	-0.028	80.911	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.018	0.034	82.848	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	GLN	0	0.002	-0.011	84.713	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.942	0.978	85.347	0.003	0.003	0.000	0.000	0.000	0.000
68	A	69	SER	0	-0.007	-0.023	84.716	0.000	0.000	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.080	-0.001	86.574	0.000	0.000	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.020	-0.029	84.013	0.000	0.000	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.741	-0.891	81.549	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.790	-0.839	77.899	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	74	ILE	0	0.019	-0.002	78.060	0.000	0.000	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.012	-0.014	77.029	0.000	0.000	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.932	-0.957	75.917	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.804	0.852	73.759	0.005	0.005	0.000	0.000	0.000	0.000
77	A	78	TRP	0	-0.031	-0.021	70.712	0.000	0.000	0.000	0.000	0.000	0.000
78	A	79	GLN	0	-0.021	-0.018	71.121	0.000	0.000	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.030	0.017	69.796	0.000	0.000	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.020	-0.009	68.010	0.000	0.000	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.033	-0.021	66.982	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.851	-0.903	66.447	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.924	0.956	63.515	0.010	0.010	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.015	-0.016	62.178	0.000	0.000	0.000	0.000	0.000	0.000
85	A	86	GLN	0	-0.050	-0.017	61.411	0.001	0.001	0.000	0.000	0.000	0.000
86	A	87	HIS	0	0.037	0.021	57.277	0.000	0.000	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.013	-0.016	57.567	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.877	0.939	57.017	0.006	0.006	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.815	-0.897	56.693	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.014	0.000	51.940	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	92	ASN	0	-0.022	-0.016	52.374	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	GLN	0	0.004	0.008	51.917	0.000	0.000	0.000	0.000	0.000	0.000
93	A	94	HIS	0	0.031	0.024	47.873	0.001	0.001	0.000	0.000	0.000	0.000
94	A	95	ASN	0	0.006	-0.021	47.963	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.004	0.013	46.992	0.000	0.000	0.000	0.000	0.000	0.000
96	A	97	TRP	0	0.027	0.011	46.604	0.000	0.000	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.068	-0.029	43.785	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.040	-0.022	42.490	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.881	-0.946	41.837	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	101	GLY	0	0.025	0.021	40.465	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	GLN	0	-0.036	-0.023	38.002	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.001	0.000	36.992	0.001	0.001	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.926	-0.953	36.864	-0.012	-0.012	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.942	0.957	33.686	0.025	0.025	0.000	0.000	0.000	0.000
105	A	106	ASN	0	-0.021	0.000	32.427	0.004	0.004	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.017	-0.001	32.209	0.003	0.003	0.000	0.000	0.000	0.000
107	A	108	GLN	0	-0.055	-0.031	30.941	0.001	0.001	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.007	-0.006	28.300	0.001	0.001	0.000	0.000	0.000	0.000
109	A	110	LEU	0	-0.004	0.001	27.376	0.005	0.005	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.920	-0.977	27.559	0.051	0.051	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.073	-0.028	22.912	0.007	0.007	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.022	-0.007	22.900	0.009	0.009	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.890	0.984	23.896	-0.056	-0.056	0.000	0.000	0.000	0.000
114	A	115	PRO	0	-0.046	-0.025	21.629	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)