FMO DATABASE

FMODB ID: N1LLQ

Calculation Name: 3EQ5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EQ5

Chain ID: A

ChEMBL ID:

UniProt ID: P12757

Base Structure: X-ray

Registration Date: 2023-03-14

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-740159.680295
FMO2-HF: Nuclear repulsion	699240.655131
FMO2-HF: Total energy	-40919.025164
FMO2-MP2: Total energy	-41033.159145

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:135:SER)

Summations of interaction energy for fragment #1(A:135:SER)

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.
-8.987	-3.27	3.065	-4.351	-4.431	-0.031

Interaction energy analysis for fragmet #1(A:135:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / 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	137	PRO	0	-0.001	-0.020	3.093	-1.543	0.962	0.097	-1.336	-1.266	0.001
4	A	138	SER	0	-0.030	-0.025	5.484	0.668	0.668	0.000	0.000	0.000	0.000
5	A	139	ASP	-1	-0.848	-0.906	2.502	-11.029	-7.883	2.969	-3.011	-3.104	-0.032
6	A	140	SER	0	-0.019	-0.045	4.791	0.645	0.711	-0.001	-0.004	-0.061	0.000
7	A	141	SER	0	-0.007	0.003	6.728	-0.205	-0.205	0.000	0.000	0.000	0.000
8	A	142	THR	0	-0.039	-0.024	9.234	-0.089	-0.089	0.000	0.000	0.000	0.000
9	A	143	GLU	-1	-0.826	-0.879	5.358	2.682	2.682	0.000	0.000	0.000	0.000
10	A	144	LEU	0	-0.057	-0.015	9.358	-0.232	-0.232	0.000	0.000	0.000	0.000
11	A	145	THR	0	-0.005	-0.008	10.451	0.067	0.067	0.000	0.000	0.000	0.000
12	A	146	GLN	0	0.040	0.027	12.561	-0.086	-0.086	0.000	0.000	0.000	0.000
13	A	147	THR	0	-0.011	-0.015	14.902	-0.067	-0.067	0.000	0.000	0.000	0.000
14	A	148	VAL	0	0.004	0.026	17.422	0.016	0.016	0.000	0.000	0.000	0.000
15	A	149	LEU	0	-0.029	-0.020	21.053	-0.034	-0.034	0.000	0.000	0.000	0.000
16	A	150	GLU	-1	-0.791	-0.874	23.553	-0.060	-0.060	0.000	0.000	0.000	0.000
17	A	151	GLY	0	0.002	0.012	25.625	0.005	0.005	0.000	0.000	0.000	0.000
18	A	152	GLU	-1	-0.848	-0.889	24.465	0.067	0.067	0.000	0.000	0.000	0.000
19	A	153	SER	0	-0.040	-0.036	19.728	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	154	ILE	0	-0.030	-0.013	19.714	0.022	0.022	0.000	0.000	0.000	0.000
21	A	155	SER	0	0.043	-0.001	17.225	0.013	0.013	0.000	0.000	0.000	0.000
22	A	156	CYS	0	-0.127	-0.060	13.999	-0.073	-0.073	0.000	0.000	0.000	0.000
23	A	157	PHE	0	0.052	0.033	11.763	0.094	0.094	0.000	0.000	0.000	0.000
24	A	158	GLN	0	0.007	0.007	8.754	0.058	0.058	0.000	0.000	0.000	0.000
25	A	159	VAL	0	0.003	-0.030	10.730	0.055	0.055	0.000	0.000	0.000	0.000
26	A	160	GLY	0	-0.002	0.001	13.261	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	161	GLY	0	0.031	0.025	11.541	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	162	GLU	-1	-0.806	-0.870	12.299	-0.402	-0.402	0.000	0.000	0.000	0.000
29	A	163	LYS	1	0.926	0.960	12.115	0.194	0.194	0.000	0.000	0.000	0.000
30	A	164	ARG	1	0.831	0.901	13.956	0.237	0.237	0.000	0.000	0.000	0.000
31	A	165	LEU	0	0.027	0.010	16.004	0.046	0.046	0.000	0.000	0.000	0.000
32	A	166	CYS	0	0.007	-0.001	18.662	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	167	LEU	0	0.035	0.023	20.760	0.001	0.001	0.000	0.000	0.000	0.000
34	A	168	PRO	0	0.003	-0.016	23.603	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	169	GLN	0	0.090	0.057	21.465	0.012	0.012	0.000	0.000	0.000	0.000
36	A	170	VAL	0	0.010	0.006	23.343	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	171	LEU	0	0.000	-0.004	26.068	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	172	ASN	0	-0.089	-0.057	28.882	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	173	SER	0	-0.044	-0.032	27.970	0.003	0.003	0.000	0.000	0.000	0.000
40	A	174	VAL	0	0.006	-0.001	25.749	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	175	LEU	0	-0.009	-0.015	28.877	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	176	ARG	1	0.911	0.961	31.560	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	177	GLU	-1	-0.923	-0.956	33.869	0.006	0.006	0.000	0.000	0.000	0.000
44	A	178	PHE	0	-0.001	0.008	33.663	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	179	THR	0	0.019	0.010	36.376	0.003	0.003	0.000	0.000	0.000	0.000
46	A	180	LEU	0	0.051	0.006	33.095	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	181	GLN	0	0.005	0.016	35.783	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	182	GLN	0	0.032	0.024	37.291	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	183	ILE	0	0.029	0.009	31.294	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	184	ASN	0	-0.001	-0.004	33.011	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	185	THR	0	0.018	0.004	34.198	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	186	VAL	0	0.007	0.004	32.643	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	187	CYS	0	-0.076	-0.053	30.284	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	188	ASP	-1	-0.914	-0.949	31.427	-0.068	-0.068	0.000	0.000	0.000	0.000
55	A	189	GLU	-1	-0.956	-0.971	34.008	-0.078	-0.078	0.000	0.000	0.000	0.000
56	A	190	LEU	0	-0.074	-0.034	30.147	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	191	TYR	0	-0.029	-0.016	30.075	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	192	ILE	0	-0.044	-0.013	25.832	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	193	TYR	0	-0.003	0.005	22.006	0.008	0.008	0.000	0.000	0.000	0.000
60	A	194	CYS	0	-0.068	-0.030	23.306	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	195	SER	0	-0.020	-0.009	20.893	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	196	ARG	1	0.927	0.944	22.181	0.003	0.003	0.000	0.000	0.000	0.000
63	A	197	CYS	0	-0.012	0.016	19.002	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	198	THR	0	0.039	0.018	16.722	0.002	0.002	0.000	0.000	0.000	0.000
65	A	199	SER	0	0.020	-0.019	19.530	0.005	0.005	0.000	0.000	0.000	0.000
66	A	200	ASP	-1	-0.872	-0.913	16.304	0.227	0.227	0.000	0.000	0.000	0.000
67	A	201	GLN	0	0.016	-0.001	13.515	0.019	0.019	0.000	0.000	0.000	0.000
68	A	202	LEU	0	-0.044	-0.014	17.018	0.014	0.014	0.000	0.000	0.000	0.000
69	A	203	HIS	0	0.002	-0.004	19.493	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	204	ILE	0	-0.005	-0.005	13.660	0.004	0.004	0.000	0.000	0.000	0.000
71	A	205	LEU	0	0.021	-0.009	17.644	0.013	0.013	0.000	0.000	0.000	0.000
72	A	206	LYS	1	0.780	0.911	19.469	-0.158	-0.158	0.000	0.000	0.000	0.000
73	A	207	VAL	0	-0.031	-0.023	18.517	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	208	LEU	0	-0.037	-0.007	14.827	0.024	0.024	0.000	0.000	0.000	0.000
75	A	209	GLY	0	-0.011	-0.001	19.445	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	210	ILE	0	-0.034	-0.007	19.323	-0.026	-0.026	0.000	0.000	0.000	0.000
77	A	211	LEU	0	-0.011	-0.016	22.668	-0.033	-0.033	0.000	0.000	0.000	0.000
78	A	212	PRO	0	0.034	0.024	25.092	0.015	0.015	0.000	0.000	0.000	0.000
79	A	213	PHE	0	0.105	0.021	24.222	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	214	ASN	0	-0.026	-0.011	27.827	0.005	0.005	0.000	0.000	0.000	0.000
81	A	215	ALA	0	0.010	0.023	26.667	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	216	PRO	0	0.039	0.019	27.336	0.010	0.010	0.000	0.000	0.000	0.000
83	A	217	SER	0	-0.077	-0.040	25.404	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	218	CYS	0	0.029	0.018	21.863	0.009	0.009	0.000	0.000	0.000	0.000
85	A	219	GLY	0	0.008	0.016	23.200	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	220	LEU	0	-0.018	-0.019	17.178	0.017	0.017	0.000	0.000	0.000	0.000
87	A	221	ILE	0	0.044	0.036	20.838	-0.016	-0.016	0.000	0.000	0.000	0.000
88	A	222	THR	0	0.001	-0.012	18.574	0.014	0.014	0.000	0.000	0.000	0.000
89	A	223	LEU	0	0.029	0.011	16.810	0.020	0.020	0.000	0.000	0.000	0.000
90	A	224	THR	0	0.047	0.020	19.403	0.019	0.019	0.000	0.000	0.000	0.000
91	A	225	ASP	-1	-0.767	-0.887	21.799	-0.145	-0.145	0.000	0.000	0.000	0.000
92	A	226	ALA	0	-0.013	-0.011	22.349	0.018	0.018	0.000	0.000	0.000	0.000
93	A	227	GLN	0	0.038	0.017	21.157	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	228	ARG	1	0.772	0.882	25.091	0.162	0.162	0.000	0.000	0.000	0.000
95	A	229	LEU	0	0.025	0.014	27.296	0.009	0.009	0.000	0.000	0.000	0.000
96	A	230	CYS	0	-0.020	-0.016	26.800	0.013	0.013	0.000	0.000	0.000	0.000
97	A	231	ASN	0	0.001	0.002	28.338	0.014	0.014	0.000	0.000	0.000	0.000
98	A	232	ALA	0	0.003	0.008	31.133	0.006	0.006	0.000	0.000	0.000	0.000
99	A	233	LEU	0	-0.045	-0.007	31.757	0.006	0.006	0.000	0.000	0.000	0.000
100	A	234	LEU	0	-0.017	-0.018	30.689	0.005	0.005	0.000	0.000	0.000	0.000
101	A	235	ARG	1	0.701	0.815	29.210	0.084	0.084	0.000	0.000	0.000	0.000
102	A	236	PRO	0	-0.009	0.013	35.585	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:135:SER)