FMO DATABASE

FMODB ID: YVZ82

Calculation Name: 3EQZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EQZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q483U6

Base Structure: X-ray

Registration Date: 2023-09-21

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1057580.244489
FMO2-HF: Nuclear repulsion	1008934.311445
FMO2-HF: Total energy	-48645.933044
FMO2-MP2: Total energy	-48786.009305

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:LEU)

Summations of interaction energy for fragment #1(A:2: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.
-20.208	-7.528	11.496	-8.607	-15.569	-0.058

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.026

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	4	ARG	1	0.819	0.896	3.711	-3.257	0.070	-0.025	-1.810	-1.492	0.000
4	A	5	VAL	0	-0.016	0.006	4.848	-0.482	-0.334	-0.001	-0.009	-0.138	0.000
5	A	6	PHE	0	0.004	0.009	7.161	0.164	0.164	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.007	-0.001	10.138	-0.090	-0.090	0.000	0.000	0.000	0.000
7	A	8	VAL	0	0.004	-0.007	12.723	0.056	0.056	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.757	-0.890	15.240	-0.207	-0.207	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.842	-0.928	18.355	-0.094	-0.094	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.797	-0.859	21.721	-0.141	-0.141	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.011	-0.009	21.199	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.059	-0.025	21.956	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.006	-0.032	17.588	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	15	CYS	0	-0.031	0.022	17.343	-0.031	-0.031	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.003	0.000	17.140	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.015	0.014	17.978	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.033	0.005	12.993	-0.037	-0.037	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.837	0.913	13.505	0.150	0.150	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.055	-0.037	14.284	-0.028	-0.028	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.038	-0.016	12.531	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.022	0.009	8.422	-0.073	-0.073	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.862	-0.909	10.310	-0.330	-0.330	0.000	0.000	0.000	0.000
23	A	24	PRO	0	-0.023	-0.019	12.293	0.004	0.004	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.057	-0.023	7.672	0.024	0.024	0.000	0.000	0.000	0.000
25	A	26	PHE	0	-0.020	-0.030	3.067	-0.809	-0.044	0.111	-0.217	-0.659	-0.001
26	A	27	GLY	0	0.040	0.021	8.080	0.122	0.122	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.061	-0.027	7.688	0.053	0.053	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.016	0.009	8.637	-0.086	-0.086	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.842	-0.914	10.748	0.213	0.213	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.025	-0.030	12.895	-0.057	-0.057	0.000	0.000	0.000	0.000
31	A	32	PHE	0	-0.009	-0.008	14.493	0.038	0.038	0.000	0.000	0.000	0.000
32	A	33	GLN	0	-0.001	-0.018	17.626	0.005	0.005	0.000	0.000	0.000	0.000
33	A	34	HIS	0	-0.002	-0.005	20.004	0.011	0.011	0.000	0.000	0.000	0.000
34	A	35	PRO	0	0.057	0.025	18.323	0.018	0.018	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.815	0.866	19.010	0.027	0.027	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.018	0.016	20.251	0.016	0.016	0.000	0.000	0.000	0.000
37	A	38	PHE	0	0.031	0.028	11.041	0.022	0.022	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.000	-0.004	15.639	0.030	0.030	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.099	-0.053	17.433	0.025	0.025	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.039	-0.004	13.537	0.033	0.033	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.023	-0.018	13.877	-0.026	-0.026	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.024	0.007	8.999	0.093	0.093	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.041	-0.039	6.573	0.638	0.638	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.968	0.984	4.794	-0.802	-0.655	-0.001	-0.014	-0.131	0.000
45	A	46	GLN	0	-0.020	-0.006	2.263	-3.147	-1.015	3.109	-2.221	-3.021	-0.006
46	A	47	ASP	-1	-0.730	-0.839	2.436	-1.868	-1.327	2.560	-1.089	-2.012	-0.026
47	A	48	ILE	0	0.000	0.000	2.269	-1.820	-0.974	3.030	-0.813	-3.064	-0.003
48	A	49	ILE	0	-0.004	-0.005	4.376	0.205	0.272	0.000	-0.022	-0.044	0.000
49	A	50	ILE	0	0.005	0.005	8.100	-0.083	-0.083	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.013	-0.004	10.854	0.062	0.062	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.772	-0.885	13.836	-0.194	-0.194	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.014	-0.018	17.464	0.020	0.020	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.072	-0.029	18.281	0.025	0.025	0.000	0.000	0.000	0.000
54	A	55	MET	0	-0.048	0.008	22.352	0.014	0.014	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.010	-0.012	25.198	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.896	-0.962	26.483	-0.058	-0.058	0.000	0.000	0.000	0.000
57	A	58	MET	0	-0.025	-0.018	23.910	0.008	0.008	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.743	-0.838	22.352	-0.033	-0.033	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.009	0.007	18.488	0.007	0.007	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.007	-0.017	18.077	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.812	-0.873	20.090	0.019	0.019	0.000	0.000	0.000	0.000
62	A	63	VAL	0	-0.020	-0.005	14.629	0.016	0.016	0.000	0.000	0.000	0.000
63	A	64	ILE	0	0.002	0.000	15.216	0.016	0.016	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.766	0.850	16.589	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	66	HIS	0	0.065	0.033	16.442	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.010	-0.008	11.391	0.036	0.036	0.000	0.000	0.000	0.000
67	A	68	ALA	0	0.046	0.030	14.598	0.032	0.032	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.895	-0.931	16.292	0.085	0.085	0.000	0.000	0.000	0.000
69	A	70	HIS	0	-0.077	-0.045	16.004	0.025	0.025	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.782	0.887	14.620	-0.058	-0.058	0.000	0.000	0.000	0.000
71	A	72	SER	0	0.032	0.019	10.371	0.087	0.087	0.000	0.000	0.000	0.000
72	A	73	PRO	0	-0.016	-0.014	7.848	-0.057	-0.057	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.025	0.001	5.450	0.066	0.066	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.007	0.001	2.481	-1.922	-0.630	0.615	-0.705	-1.203	-0.005
75	A	76	LEU	0	-0.028	-0.010	4.880	-0.065	-0.034	-0.001	-0.006	-0.023	0.000
76	A	77	ILE	0	-0.007	0.003	6.210	-0.053	-0.053	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.014	0.021	9.819	0.056	0.056	0.000	0.000	0.000	0.000
78	A	79	ILE	0	0.002	-0.005	13.642	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	80	SER	0	0.060	0.013	16.236	0.033	0.033	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.013	0.023	20.079	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	82	TYR	0	-0.038	-0.004	23.256	0.011	0.011	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.779	-0.913	24.153	-0.119	-0.119	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.020	0.002	22.111	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.036	0.027	22.219	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	86	VAL	0	-0.016	-0.014	22.876	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.037	-0.007	16.722	0.002	0.002	0.000	0.000	0.000	0.000
87	A	88	HIS	0	-0.015	-0.016	18.423	0.007	0.007	0.000	0.000	0.000	0.000
88	A	89	SER	0	-0.030	-0.023	19.756	0.006	0.006	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.004	-0.001	18.645	0.009	0.009	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.823	-0.894	14.390	-0.305	-0.305	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.002	-0.009	16.068	0.002	0.002	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.039	-0.025	18.497	0.015	0.015	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.033	0.017	14.120	0.019	0.019	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.013	-0.002	12.244	0.020	0.020	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.056	-0.023	14.959	0.023	0.023	0.000	0.000	0.000	0.000
96	A	97	CYS	0	-0.110	-0.051	16.721	0.024	0.024	0.000	0.000	0.000	0.000
97	A	98	GLY	0	-0.033	-0.014	14.454	0.030	0.030	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.021	-0.003	11.184	0.019	0.019	0.000	0.000	0.000	0.000
99	A	100	ASN	0	-0.007	-0.007	4.687	0.032	0.061	-0.001	-0.002	-0.027	0.000
100	A	101	VAL	0	-0.018	-0.015	7.447	-0.137	-0.137	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.036	-0.020	4.129	-0.170	-0.033	0.000	-0.012	-0.125	0.000
102	A	103	ASN	0	-0.027	-0.023	8.256	0.042	0.042	0.000	0.000	0.000	0.000
103	A	104	THR	0	-0.008	-0.015	10.834	0.029	0.029	0.000	0.000	0.000	0.000
104	A	105	PHE	0	-0.026	-0.012	10.550	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	106	THR	0	0.011	0.004	15.701	0.018	0.018	0.000	0.000	0.000	0.000
106	A	107	LYS	1	0.762	0.854	18.824	0.180	0.180	0.000	0.000	0.000	0.000
107	A	108	PRO	0	-0.036	-0.026	20.848	0.015	0.015	0.000	0.000	0.000	0.000
108	A	109	ILE	0	0.036	0.010	15.479	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	110	ASN	0	-0.016	-0.014	17.822	-0.019	-0.019	0.000	0.000	0.000	0.000
110	A	111	THR	0	0.049	-0.001	16.339	-0.036	-0.036	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.843	-0.874	15.691	-0.349	-0.349	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.045	0.018	13.838	-0.051	-0.051	0.000	0.000	0.000	0.000
113	A	114	LEU	0	0.022	0.023	10.233	-0.080	-0.080	0.000	0.000	0.000	0.000
114	A	115	THR	0	0.003	-0.015	10.772	-0.117	-0.117	0.000	0.000	0.000	0.000
115	A	116	CYS	0	-0.076	-0.036	11.378	-0.085	-0.085	0.000	0.000	0.000	0.000
116	A	117	PHE	0	0.017	0.015	7.219	-0.118	-0.118	0.000	0.000	0.000	0.000
117	A	118	LEU	0	0.046	0.025	6.337	-0.243	-0.243	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.026	-0.029	6.485	-0.316	-0.316	0.000	0.000	0.000	0.000
119	A	120	SER	0	-0.087	-0.048	7.408	-0.114	-0.114	0.000	0.000	0.000	0.000
120	A	121	LEU	0	-0.005	0.014	2.538	-1.087	-0.277	1.080	-0.314	-1.575	0.001
121	A	122	SER	0	-0.023	-0.017	2.685	-4.586	-2.401	1.021	-1.358	-1.848	-0.018
122	A	123	ASN	0	-0.014	-0.008	4.003	-0.446	-0.223	-0.001	-0.015	-0.207	0.000
123	A	124	ARG	1	0.800	0.905	6.903	1.224	1.224	0.000	0.000	0.000	0.000
124	A	125	GLN	0	0.011	0.010	10.111	-0.019	-0.019	0.000	0.000	0.000	0.000

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