FMO DATABASE

FMODB ID: 89V3Y

Calculation Name: 3B79-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B79

Chain ID: A

ChEMBL ID:

UniProt ID: Q87FE3

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1039389.574172
FMO2-HF: Nuclear repulsion	991583.68155
FMO2-HF: Total energy	-47805.892622
FMO2-MP2: Total energy	-47945.65071

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:0:ALA)

Summations of interaction energy for fragment #1(A:0:ALA)

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.
0.668	2.211	-0.004	-0.649	-0.891	0.003

Interaction energy analysis for fragmet #1(A:0:ALA)

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 : 0.004

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

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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	2	LYS	1	0.986	0.978	3.702	0.711	2.254	-0.004	-0.649	-0.891	0.003
4	A	3	ASP	-1	-0.794	-0.886	5.833	0.048	0.048	0.000	0.000	0.000	0.000
5	A	4	PRO	0	0.075	0.038	9.367	0.115	0.115	0.000	0.000	0.000	0.000
6	A	5	LEU	0	0.039	0.022	10.903	0.105	0.105	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.028	-0.011	9.503	0.085	0.085	0.000	0.000	0.000	0.000
8	A	7	ASN	0	-0.012	-0.019	7.540	0.277	0.277	0.000	0.000	0.000	0.000
9	A	8	SER	0	0.007	0.000	9.882	0.103	0.103	0.000	0.000	0.000	0.000
10	A	9	LEU	0	-0.018	-0.008	13.378	0.031	0.031	0.000	0.000	0.000	0.000
11	A	10	ILE	0	-0.036	-0.018	10.318	0.030	0.030	0.000	0.000	0.000	0.000
12	A	11	TYR	0	0.058	0.029	12.586	0.009	0.009	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.045	0.015	13.779	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.024	-0.009	15.957	0.004	0.004	0.000	0.000	0.000	0.000
15	A	14	ARG	1	0.820	0.904	13.153	-0.519	-0.519	0.000	0.000	0.000	0.000
16	A	15	TYR	0	0.016	0.026	16.766	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	16	TYR	0	-0.025	-0.016	19.091	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	17	GLY	0	-0.027	-0.009	20.148	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.083	-0.036	19.797	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	19	ALA	0	-0.007	0.011	17.307	0.044	0.044	0.000	0.000	0.000	0.000
21	A	20	ASN	0	-0.013	-0.029	15.906	-0.044	-0.044	0.000	0.000	0.000	0.000
22	A	21	SER	0	0.078	0.035	12.552	0.065	0.065	0.000	0.000	0.000	0.000
23	A	22	PRO	0	0.065	-0.001	8.626	-0.105	-0.105	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.920	-0.960	11.518	0.195	0.195	0.000	0.000	0.000	0.000
25	A	24	ALA	0	-0.004	0.001	13.145	-0.072	-0.072	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.023	-0.011	14.143	-0.043	-0.043	0.000	0.000	0.000	0.000
27	A	26	VAL	0	0.019	0.003	13.056	-0.044	-0.044	0.000	0.000	0.000	0.000
28	A	27	ASN	0	0.009	0.021	15.971	-0.048	-0.048	0.000	0.000	0.000	0.000
29	A	28	GLY	0	0.029	0.011	18.204	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.072	-0.024	18.282	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	30	PRO	0	-0.019	-0.008	19.027	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.005	-0.004	13.604	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	32	SER	0	-0.034	-0.020	17.204	0.007	0.007	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.925	-0.959	14.625	-0.418	-0.418	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.017	-0.011	12.628	-0.069	-0.069	0.000	0.000	0.000	0.000
36	A	35	LYS	1	0.924	0.972	9.984	0.525	0.525	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.001	-0.015	13.603	0.053	0.053	0.000	0.000	0.000	0.000
38	A	37	THR	0	0.014	0.009	15.747	-0.021	-0.021	0.000	0.000	0.000	0.000
39	A	38	PRO	0	0.076	0.011	18.603	0.020	0.020	0.000	0.000	0.000	0.000
40	A	39	PHE	0	0.021	0.013	21.172	0.016	0.016	0.000	0.000	0.000	0.000
41	A	40	LEU	0	-0.040	-0.029	18.851	0.014	0.014	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.019	0.030	17.310	0.017	0.017	0.000	0.000	0.000	0.000
43	A	42	PRO	0	0.007	0.005	20.102	0.021	0.021	0.000	0.000	0.000	0.000
44	A	43	ARG	1	0.927	0.969	22.699	0.021	0.021	0.000	0.000	0.000	0.000
45	A	44	ALA	0	0.038	0.021	17.340	0.011	0.011	0.000	0.000	0.000	0.000
46	A	45	ALA	0	-0.011	-0.020	19.458	0.028	0.028	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.960	-0.969	20.740	0.096	0.096	0.000	0.000	0.000	0.000
48	A	47	ARG	1	0.885	0.943	19.378	-0.058	-0.058	0.000	0.000	0.000	0.000
49	A	48	ALA	0	-0.027	-0.006	18.479	0.024	0.024	0.000	0.000	0.000	0.000
50	A	49	GLY	0	-0.006	0.010	20.144	0.016	0.016	0.000	0.000	0.000	0.000
51	A	50	LEU	0	-0.072	-0.045	19.444	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	51	VAL	0	0.004	-0.001	23.516	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	52	ALA	0	0.017	0.010	22.022	0.004	0.004	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.912	0.953	24.128	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.915	-0.950	24.775	-0.033	-0.033	0.000	0.000	0.000	0.000
56	A	55	ASN	0	-0.046	-0.026	26.368	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	56	ARG	1	0.977	0.976	27.697	0.026	0.026	0.000	0.000	0.000	0.000
58	A	57	ALA	0	-0.004	0.003	29.218	0.005	0.005	0.000	0.000	0.000	0.000
59	A	58	GLU	-1	-0.894	-0.944	28.989	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	59	LEU	0	0.057	0.026	24.482	0.005	0.005	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.852	-0.942	28.158	0.002	0.002	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.858	0.927	30.882	0.002	0.002	0.000	0.000	0.000	0.000
63	A	62	ILE	0	-0.039	-0.001	25.780	0.003	0.003	0.000	0.000	0.000	0.000
64	A	63	SER	0	-0.005	0.000	29.527	0.003	0.003	0.000	0.000	0.000	0.000
65	A	64	SER	0	0.093	0.022	28.069	0.003	0.003	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.004	-0.002	27.951	0.007	0.007	0.000	0.000	0.000	0.000
67	A	66	ILE	0	-0.085	-0.039	26.477	0.004	0.004	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.083	0.004	23.546	0.003	0.003	0.000	0.000	0.000	0.000
69	A	68	PRO	0	0.002	0.001	19.595	0.005	0.005	0.000	0.000	0.000	0.000
70	A	69	ALA	0	-0.027	-0.006	21.485	0.000	0.000	0.000	0.000	0.000	0.000
71	A	70	ILE	0	-0.014	-0.006	16.915	0.005	0.005	0.000	0.000	0.000	0.000
72	A	71	LEU	0	0.001	-0.001	18.902	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	72	VAL	0	-0.015	-0.014	18.585	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	73	LEU	0	0.010	0.010	16.071	0.015	0.015	0.000	0.000	0.000	0.000
75	A	74	LYS	1	0.859	0.919	19.210	0.070	0.070	0.000	0.000	0.000	0.000
76	A	75	GLY	0	0.005	0.006	18.115	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	76	GLY	0	-0.071	-0.031	16.490	-0.029	-0.029	0.000	0.000	0.000	0.000
78	A	77	ASP	-1	-0.795	-0.893	12.810	-0.269	-0.269	0.000	0.000	0.000	0.000
79	A	78	SER	0	-0.116	-0.068	13.795	0.048	0.048	0.000	0.000	0.000	0.000
80	A	79	CYS	0	0.026	0.030	13.951	-0.021	-0.021	0.000	0.000	0.000	0.000
81	A	80	VAL	0	-0.004	0.006	14.496	0.008	0.008	0.000	0.000	0.000	0.000
82	A	81	LEU	0	0.014	0.017	16.944	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	82	ASN	0	0.018	-0.018	17.359	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	83	SER	0	-0.035	-0.023	21.041	0.000	0.000	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.045	0.016	23.806	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	85	ASN	0	-0.007	0.013	26.555	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	86	MET	0	0.004	-0.013	29.130	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.970	-0.960	31.940	0.013	0.013	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.020	-0.036	28.485	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	89	ARG	1	0.924	0.970	29.668	0.002	0.002	0.000	0.000	0.000	0.000
91	A	90	GLU	-1	-0.857	-0.913	24.427	0.008	0.008	0.000	0.000	0.000	0.000
92	A	91	ALA	0	-0.050	-0.028	22.515	0.004	0.004	0.000	0.000	0.000	0.000
93	A	92	GLU	-1	-0.846	-0.906	19.365	0.086	0.086	0.000	0.000	0.000	0.000
94	A	93	VAL	0	0.036	0.001	16.480	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	94	THR	0	-0.028	-0.017	11.998	0.032	0.032	0.000	0.000	0.000	0.000
96	A	95	THR	0	0.040	0.009	11.768	0.003	0.003	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.020	-0.011	6.349	0.056	0.056	0.000	0.000	0.000	0.000
98	A	97	GLU	-1	-0.916	-0.963	6.962	-0.223	-0.223	0.000	0.000	0.000	0.000
99	A	98	SER	0	-0.024	-0.005	8.405	0.080	0.080	0.000	0.000	0.000	0.000
100	A	99	GLY	0	0.027	0.025	7.243	0.139	0.139	0.000	0.000	0.000	0.000
101	A	100	MET	0	-0.077	-0.052	7.986	-0.044	-0.044	0.000	0.000	0.000	0.000
102	A	101	VAL	0	-0.015	-0.004	10.843	-0.034	-0.034	0.000	0.000	0.000	0.000
103	A	102	PRO	0	-0.049	-0.010	13.259	-0.032	-0.032	0.000	0.000	0.000	0.000
104	A	103	ILE	0	0.002	0.003	14.489	0.006	0.006	0.000	0.000	0.000	0.000
105	A	104	SER	0	-0.009	-0.009	17.287	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	105	ILE	0	-0.058	-0.022	18.147	-0.010	-0.010	0.000	0.000	0.000	0.000
107	A	106	PRO	0	0.129	0.073	21.362	0.007	0.007	0.000	0.000	0.000	0.000
108	A	107	LEU	0	-0.040	-0.034	23.791	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	108	GLU	-1	-0.981	-1.000	25.638	-0.031	-0.031	0.000	0.000	0.000	0.000
110	A	109	ASP	-1	-0.829	-0.917	21.331	-0.053	-0.053	0.000	0.000	0.000	0.000
111	A	110	LEU	0	-0.045	-0.020	20.032	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	111	LEU	0	-0.082	-0.057	22.471	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	112	GLU	-1	-0.913	-0.944	23.847	-0.073	-0.073	0.000	0.000	0.000	0.000
114	A	113	GLN	0	0.017	0.007	19.164	-0.019	-0.019	0.000	0.000	0.000	0.000
115	A	114	TYR	0	-0.032	-0.011	21.456	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	115	THR	0	-0.078	-0.052	22.034	0.003	0.003	0.000	0.000	0.000	0.000
117	A	116	GLY	0	0.003	0.001	24.677	0.002	0.002	0.000	0.000	0.000	0.000
118	A	117	ARG	1	0.868	0.943	23.383	0.070	0.070	0.000	0.000	0.000	0.000
119	A	118	TYR	0	0.063	0.028	22.970	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	119	PHE	0	0.009	-0.001	21.234	0.001	0.001	0.000	0.000	0.000	0.000
121	A	120	LEU	0	0.009	0.009	23.050	0.007	0.007	0.000	0.000	0.000	0.000
122	A	121	VAL	0	0.019	-0.008	20.402	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	122	LYS	1	0.960	0.995	23.700	-0.053	-0.053	0.000	0.000	0.000	0.000
124	A	123	LYS	1	1.002	1.004	25.061	-0.136	-0.136	0.000	0.000	0.000	0.000
125	A	124	GLN	0	-0.032	-0.012	26.064	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)