FMO DATABASE

FMODB ID: JQ9J9

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	OptAll
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	-1041946.060089
FMO2-HF: Nuclear repulsion	994139.309301
FMO2-HF: Total energy	-47806.750789
FMO2-MP2: Total energy	-47946.365667

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.
0.405	1.873	-0.005	-0.706	-0.757	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 : 0.013 / q_NPA : -0.002

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	0.957	0.963	3.803	0.295	1.763	-0.005	-0.706	-0.757	0.003
4	A	3	ASP	-1	-0.744	-0.870	6.089	0.050	0.050	0.000	0.000	0.000	0.000
5	A	4	PRO	0	0.061	0.042	9.545	0.106	0.106	0.000	0.000	0.000	0.000
6	A	5	LEU	0	0.017	0.029	11.218	0.101	0.101	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.024	-0.023	9.849	0.073	0.073	0.000	0.000	0.000	0.000
8	A	7	ASN	0	-0.043	-0.029	7.848	0.267	0.267	0.000	0.000	0.000	0.000
9	A	8	SER	0	0.028	-0.005	10.080	0.091	0.091	0.000	0.000	0.000	0.000
10	A	9	LEU	0	-0.016	-0.011	13.581	0.023	0.023	0.000	0.000	0.000	0.000
11	A	10	ILE	0	-0.036	-0.016	10.511	0.019	0.019	0.000	0.000	0.000	0.000
12	A	11	TYR	0	0.056	0.028	12.799	0.002	0.002	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.026	0.006	14.101	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	13	SER	0	-0.030	-0.003	16.065	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	14	ARG	1	0.834	0.909	13.377	-0.510	-0.510	0.000	0.000	0.000	0.000
16	A	15	TYR	0	0.041	0.030	17.098	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	16	TYR	0	-0.026	-0.015	19.619	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	17	GLY	0	-0.008	-0.007	20.844	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.084	-0.038	20.087	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	19	ALA	0	-0.007	-0.004	17.320	0.040	0.040	0.000	0.000	0.000	0.000
21	A	20	ASN	0	0.005	0.001	16.198	-0.049	-0.049	0.000	0.000	0.000	0.000
22	A	21	SER	0	0.012	-0.021	12.008	0.063	0.063	0.000	0.000	0.000	0.000
23	A	22	PRO	0	0.043	-0.009	8.420	-0.091	-0.091	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.850	-0.901	11.197	0.264	0.264	0.000	0.000	0.000	0.000
25	A	24	ALA	0	0.003	0.003	13.202	-0.065	-0.065	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.017	-0.004	14.433	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	26	VAL	0	0.021	0.004	13.333	-0.040	-0.040	0.000	0.000	0.000	0.000
28	A	27	ASN	0	-0.017	0.010	16.252	-0.047	-0.047	0.000	0.000	0.000	0.000
29	A	28	GLY	0	0.045	0.025	18.487	0.002	0.002	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.045	-0.015	18.606	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	30	PRO	0	-0.023	-0.012	19.130	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.010	-0.010	13.714	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	32	SER	0	-0.034	-0.017	17.111	0.004	0.004	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.847	-0.915	14.010	-0.420	-0.420	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.015	-0.005	12.284	-0.072	-0.072	0.000	0.000	0.000	0.000
36	A	35	LYS	1	0.828	0.914	10.403	0.452	0.452	0.000	0.000	0.000	0.000
37	A	36	LEU	0	0.003	-0.010	13.506	0.046	0.046	0.000	0.000	0.000	0.000
38	A	37	THR	0	0.045	0.013	15.913	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	38	PRO	0	0.072	0.024	18.862	0.020	0.020	0.000	0.000	0.000	0.000
40	A	39	PHE	0	0.013	0.005	21.572	0.015	0.015	0.000	0.000	0.000	0.000
41	A	40	LEU	0	-0.041	-0.010	18.866	0.009	0.009	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.021	0.030	17.069	0.016	0.016	0.000	0.000	0.000	0.000
43	A	42	PRO	0	0.005	-0.004	20.214	0.019	0.019	0.000	0.000	0.000	0.000
44	A	43	ARG	1	0.899	0.940	22.511	0.018	0.018	0.000	0.000	0.000	0.000
45	A	44	ALA	0	0.047	0.033	17.309	0.011	0.011	0.000	0.000	0.000	0.000
46	A	45	ALA	0	-0.012	-0.014	19.246	0.028	0.028	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.876	-0.926	20.975	0.083	0.083	0.000	0.000	0.000	0.000
48	A	47	ARG	1	0.800	0.882	19.581	-0.051	-0.051	0.000	0.000	0.000	0.000
49	A	48	ALA	0	-0.009	0.004	18.524	0.025	0.025	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.017	0.011	20.026	0.018	0.018	0.000	0.000	0.000	0.000
51	A	50	LEU	0	-0.069	-0.037	19.672	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	51	VAL	0	-0.017	-0.013	23.747	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	52	ALA	0	0.016	0.009	22.248	0.005	0.005	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.882	0.929	24.303	-0.023	-0.023	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.832	-0.885	24.765	-0.025	-0.025	0.000	0.000	0.000	0.000
56	A	55	ASN	0	-0.054	-0.028	26.320	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	56	ARG	1	0.974	0.978	27.997	0.015	0.015	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.013	0.013	29.733	0.004	0.004	0.000	0.000	0.000	0.000
59	A	58	GLU	-1	-0.807	-0.878	29.555	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	59	LEU	0	0.065	0.034	24.406	0.004	0.004	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.772	-0.883	28.228	0.013	0.013	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.802	0.884	30.901	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	62	ILE	0	-0.047	-0.004	25.737	0.002	0.002	0.000	0.000	0.000	0.000
64	A	63	SER	0	-0.005	0.001	29.494	0.004	0.004	0.000	0.000	0.000	0.000
65	A	64	SER	0	0.086	0.016	28.232	0.002	0.002	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.027	-0.015	28.384	0.007	0.007	0.000	0.000	0.000	0.000
67	A	66	ILE	0	-0.069	-0.029	27.360	0.002	0.002	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.046	0.016	23.852	0.000	0.000	0.000	0.000	0.000	0.000
69	A	68	PRO	0	-0.020	-0.001	19.705	0.003	0.003	0.000	0.000	0.000	0.000
70	A	69	ALA	0	-0.023	0.000	21.834	0.000	0.000	0.000	0.000	0.000	0.000
71	A	70	ILE	0	-0.024	-0.014	16.882	0.008	0.008	0.000	0.000	0.000	0.000
72	A	71	LEU	0	0.010	0.011	19.384	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	72	VAL	0	-0.011	-0.017	18.882	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	73	LEU	0	0.002	0.019	16.714	0.011	0.011	0.000	0.000	0.000	0.000
75	A	74	LYS	1	0.827	0.905	19.733	0.051	0.051	0.000	0.000	0.000	0.000
76	A	75	GLY	0	-0.023	-0.011	18.231	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	76	GLY	0	-0.061	-0.023	17.124	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	77	ASP	-1	-0.828	-0.913	13.034	-0.188	-0.188	0.000	0.000	0.000	0.000
79	A	78	SER	0	-0.098	-0.059	14.350	0.031	0.031	0.000	0.000	0.000	0.000
80	A	79	CYS	0	0.036	0.026	14.179	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	80	VAL	0	-0.014	0.001	14.608	0.000	0.000	0.000	0.000	0.000	0.000
82	A	81	LEU	0	0.007	0.014	17.148	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	82	ASN	0	0.021	-0.012	17.457	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	83	SER	0	-0.031	-0.024	21.282	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.033	0.009	24.120	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	85	ASN	0	-0.020	0.003	26.875	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	86	MET	0	0.007	-0.014	29.353	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.943	-0.951	32.132	0.020	0.020	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.040	-0.039	28.890	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	89	ARG	1	0.841	0.915	30.149	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	90	GLU	-1	-0.851	-0.911	24.430	0.027	0.027	0.000	0.000	0.000	0.000
92	A	91	ALA	0	-0.036	-0.036	23.133	0.002	0.002	0.000	0.000	0.000	0.000
93	A	92	GLU	-1	-0.858	-0.889	19.841	0.112	0.112	0.000	0.000	0.000	0.000
94	A	93	VAL	0	0.024	-0.010	16.837	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	94	THR	0	0.006	-0.009	12.246	0.032	0.032	0.000	0.000	0.000	0.000
96	A	95	THR	0	-0.012	-0.030	12.062	0.003	0.003	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.011	-0.013	6.530	0.056	0.056	0.000	0.000	0.000	0.000
98	A	97	GLU	-1	-0.871	-0.917	7.122	-0.082	-0.082	0.000	0.000	0.000	0.000
99	A	98	SER	0	-0.024	-0.008	8.682	0.084	0.084	0.000	0.000	0.000	0.000
100	A	99	GLY	0	0.032	0.025	7.642	0.128	0.128	0.000	0.000	0.000	0.000
101	A	100	MET	0	-0.077	-0.042	8.252	-0.049	-0.049	0.000	0.000	0.000	0.000
102	A	101	VAL	0	-0.019	-0.007	11.042	-0.031	-0.031	0.000	0.000	0.000	0.000
103	A	102	PRO	0	-0.065	-0.016	13.435	-0.026	-0.026	0.000	0.000	0.000	0.000
104	A	103	ILE	0	0.026	0.011	14.449	0.008	0.008	0.000	0.000	0.000	0.000
105	A	104	SER	0	-0.019	-0.021	17.591	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	105	ILE	0	-0.055	-0.013	18.699	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	106	PRO	0	0.117	0.064	21.681	0.004	0.004	0.000	0.000	0.000	0.000
108	A	107	LEU	0	-0.048	-0.035	24.271	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	108	GLU	-1	-0.969	-0.995	26.355	-0.012	-0.012	0.000	0.000	0.000	0.000
110	A	109	ASP	-1	-0.850	-0.925	21.755	-0.034	-0.034	0.000	0.000	0.000	0.000
111	A	110	LEU	0	-0.044	-0.027	20.309	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	111	LEU	0	-0.071	-0.051	22.956	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	112	GLU	-1	-0.861	-0.917	24.230	-0.062	-0.062	0.000	0.000	0.000	0.000
114	A	113	GLN	0	0.026	0.010	19.710	-0.017	-0.017	0.000	0.000	0.000	0.000
115	A	114	TYR	0	0.000	-0.003	21.906	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	115	THR	0	-0.077	-0.056	22.549	0.000	0.000	0.000	0.000	0.000	0.000
117	A	116	GLY	0	0.002	-0.004	25.079	0.000	0.000	0.000	0.000	0.000	0.000
118	A	117	ARG	1	0.787	0.876	23.147	0.047	0.047	0.000	0.000	0.000	0.000
119	A	118	TYR	0	0.055	0.033	23.151	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	119	PHE	0	0.010	-0.007	21.455	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	120	LEU	0	0.020	0.019	23.219	0.009	0.009	0.000	0.000	0.000	0.000
122	A	121	VAL	0	0.009	-0.016	20.660	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	122	LYS	1	0.965	0.997	23.897	-0.058	-0.058	0.000	0.000	0.000	0.000
124	A	123	LYS	1	0.959	0.984	24.573	-0.153	-0.153	0.000	0.000	0.000	0.000
125	A	124	GLN	0	-0.048	-0.014	26.107	-0.002	-0.002	0.000	0.000	0.000	0.000

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