FMO DATABASE

FMODB ID: R8L78

Calculation Name: 3EPU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EPU

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ZNP3

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	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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1124049.2404
FMO2-HF: Nuclear repulsion	1069477.600313
FMO2-HF: Total energy	-54571.640087
FMO2-MP2: Total energy	-54728.792168

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(B:3:SER)

Summations of interaction energy for fragment #1(B:3: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.
-28.044	-29.655	21.207	-11.645	-7.953	-0.073

Interaction energy analysis for fragmet #1(B:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.025

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	B	5	ALA	0	0.039	0.025	2.765	-1.707	0.777	0.120	-1.259	-1.346	0.003
4	B	6	ASP	-1	-0.739	-0.844	1.644	-29.077	-33.741	21.087	-10.226	-6.198	-0.076
5	B	7	ARG	1	0.945	0.977	3.896	-1.449	-0.942	0.001	-0.156	-0.352	0.000
6	B	8	LEU	0	-0.002	0.001	6.047	0.377	0.377	0.000	0.000	0.000	0.000
7	B	9	LEU	0	0.064	0.026	6.596	0.321	0.321	0.000	0.000	0.000	0.000
8	B	10	ARG	1	0.821	0.896	7.614	1.485	1.485	0.000	0.000	0.000	0.000
9	B	11	GLN	0	-0.007	-0.015	9.693	0.211	0.211	0.000	0.000	0.000	0.000
10	B	12	PHE	0	-0.009	0.000	11.764	0.113	0.113	0.000	0.000	0.000	0.000
11	B	13	SER	0	0.031	-0.002	11.771	0.068	0.068	0.000	0.000	0.000	0.000
12	B	14	LEU	0	-0.011	-0.002	13.202	0.085	0.085	0.000	0.000	0.000	0.000
13	B	15	LYS	1	0.757	0.862	15.922	0.277	0.277	0.000	0.000	0.000	0.000
14	B	16	LEU	0	0.040	0.019	16.329	0.035	0.035	0.000	0.000	0.000	0.000
15	B	17	ASN	0	0.033	0.022	18.184	0.022	0.022	0.000	0.000	0.000	0.000
16	B	18	THR	0	-0.087	-0.046	19.821	0.047	0.047	0.000	0.000	0.000	0.000
17	B	19	ASP	-1	-0.847	-0.882	21.835	-0.192	-0.192	0.000	0.000	0.000	0.000
18	B	20	SER	0	-0.061	-0.036	23.697	0.010	0.010	0.000	0.000	0.000	0.000
19	B	21	ILE	0	-0.052	-0.021	20.939	0.001	0.001	0.000	0.000	0.000	0.000
20	B	22	VAL	0	0.017	0.007	20.783	-0.017	-0.017	0.000	0.000	0.000	0.000
21	B	23	PHE	0	-0.051	-0.031	14.401	-0.019	-0.019	0.000	0.000	0.000	0.000
22	B	24	ASP	-1	-0.879	-0.927	17.441	-0.449	-0.449	0.000	0.000	0.000	0.000
23	B	25	GLU	-1	-0.848	-0.893	11.380	-1.105	-1.105	0.000	0.000	0.000	0.000
24	B	26	ASN	0	0.053	-0.009	12.449	0.084	0.084	0.000	0.000	0.000	0.000
25	B	27	ARG	1	0.844	0.935	3.939	3.486	3.548	-0.001	-0.004	-0.057	0.000
26	B	28	LEU	0	0.015	0.005	10.607	0.217	0.217	0.000	0.000	0.000	0.000
27	B	29	CYS	0	-0.035	-0.018	10.722	-0.204	-0.204	0.000	0.000	0.000	0.000
28	B	30	SER	0	-0.024	0.007	12.697	0.136	0.136	0.000	0.000	0.000	0.000
29	B	31	PHE	0	0.032	0.008	15.458	-0.029	-0.029	0.000	0.000	0.000	0.000
30	B	32	ILE	0	-0.013	-0.003	18.018	0.006	0.006	0.000	0.000	0.000	0.000
31	B	33	ILE	0	0.023	0.025	20.583	0.006	0.006	0.000	0.000	0.000	0.000
32	B	34	ASP	-1	-0.825	-0.916	23.700	-0.126	-0.126	0.000	0.000	0.000	0.000
33	B	35	ASN	0	-0.134	-0.076	25.163	-0.006	-0.006	0.000	0.000	0.000	0.000
34	B	36	ARG	1	0.843	0.904	26.398	0.132	0.132	0.000	0.000	0.000	0.000
35	B	37	TYR	0	0.012	-0.013	25.305	-0.008	-0.008	0.000	0.000	0.000	0.000
36	B	38	ARG	1	0.898	0.953	18.071	0.423	0.423	0.000	0.000	0.000	0.000
37	B	39	ILE	0	0.026	0.013	19.141	0.010	0.010	0.000	0.000	0.000	0.000
38	B	40	LEU	0	-0.049	-0.034	15.912	-0.057	-0.057	0.000	0.000	0.000	0.000
39	B	41	LEU	0	0.041	0.027	14.844	0.035	0.035	0.000	0.000	0.000	0.000
40	B	42	THR	0	-0.003	-0.017	14.598	-0.099	-0.099	0.000	0.000	0.000	0.000
41	B	43	SER	0	-0.018	-0.003	12.450	0.064	0.064	0.000	0.000	0.000	0.000
42	B	44	THR	0	0.069	0.022	13.510	-0.125	-0.125	0.000	0.000	0.000	0.000
43	B	45	ASN	0	0.000	0.001	15.986	0.016	0.016	0.000	0.000	0.000	0.000
44	B	46	SER	0	0.013	-0.003	16.245	-0.014	-0.014	0.000	0.000	0.000	0.000
45	B	47	GLU	-1	-0.964	-0.960	17.175	-0.181	-0.181	0.000	0.000	0.000	0.000
46	B	48	TYR	0	-0.011	-0.011	19.245	0.035	0.035	0.000	0.000	0.000	0.000
47	B	49	ILE	0	-0.040	-0.012	14.652	-0.065	-0.065	0.000	0.000	0.000	0.000
48	B	50	MET	0	-0.057	0.005	18.096	0.063	0.063	0.000	0.000	0.000	0.000
49	B	51	ILE	0	0.018	0.004	18.707	-0.054	-0.054	0.000	0.000	0.000	0.000
50	B	52	TYR	0	0.014	-0.002	19.845	0.046	0.046	0.000	0.000	0.000	0.000
51	B	53	GLY	0	0.072	0.019	22.029	-0.020	-0.020	0.000	0.000	0.000	0.000
52	B	54	PHE	0	-0.071	-0.048	21.461	0.008	0.008	0.000	0.000	0.000	0.000
53	B	55	CYS	0	-0.020	0.008	25.593	0.011	0.011	0.000	0.000	0.000	0.000
54	B	56	GLY	0	0.079	0.033	29.237	0.010	0.010	0.000	0.000	0.000	0.000
55	B	57	LYS	1	0.873	0.925	28.766	0.235	0.235	0.000	0.000	0.000	0.000
56	B	58	PRO	0	-0.017	0.005	32.371	0.010	0.010	0.000	0.000	0.000	0.000
57	B	59	PRO	0	0.012	-0.007	35.674	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	60	ASP	-1	-0.906	-0.936	37.498	-0.162	-0.162	0.000	0.000	0.000	0.000
59	B	61	ASN	0	-0.015	-0.022	39.797	0.010	0.010	0.000	0.000	0.000	0.000
60	B	62	ASN	0	0.023	-0.005	41.775	-0.006	-0.006	0.000	0.000	0.000	0.000
61	B	63	ASN	0	0.002	-0.006	43.004	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	64	LEU	0	0.008	0.014	39.913	0.002	0.002	0.000	0.000	0.000	0.000
63	B	65	ALA	0	0.036	0.017	38.956	-0.002	-0.002	0.000	0.000	0.000	0.000
64	B	66	PHE	0	-0.005	-0.008	39.808	-0.003	-0.003	0.000	0.000	0.000	0.000
65	B	67	GLU	-1	-0.847	-0.917	41.651	-0.095	-0.095	0.000	0.000	0.000	0.000
66	B	68	PHE	0	0.002	-0.007	36.473	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	69	LEU	0	-0.025	-0.019	37.196	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	70	ASN	0	-0.031	-0.021	39.182	0.003	0.003	0.000	0.000	0.000	0.000
69	B	71	ALA	0	0.024	0.017	38.159	0.003	0.003	0.000	0.000	0.000	0.000
70	B	72	ASN	0	-0.050	-0.036	34.609	-0.004	-0.004	0.000	0.000	0.000	0.000
71	B	73	LEU	0	-0.012	0.009	37.500	0.000	0.000	0.000	0.000	0.000	0.000
72	B	74	TRP	0	0.031	0.027	35.695	0.001	0.001	0.000	0.000	0.000	0.000
73	B	75	PHE	0	0.045	0.003	33.753	0.002	0.002	0.000	0.000	0.000	0.000
74	B	76	ALA	0	-0.025	0.003	35.404	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	77	GLU	-1	-0.980	-0.985	36.907	-0.076	-0.076	0.000	0.000	0.000	0.000
76	B	78	ASN	0	-0.107	-0.061	36.843	0.009	0.009	0.000	0.000	0.000	0.000
77	B	79	ASN	0	-0.093	-0.038	33.346	-0.004	-0.004	0.000	0.000	0.000	0.000
78	B	80	GLY	0	0.042	0.029	31.704	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	81	PRO	0	-0.051	-0.034	27.945	-0.005	-0.005	0.000	0.000	0.000	0.000
80	B	82	HIS	0	0.009	0.008	29.186	0.005	0.005	0.000	0.000	0.000	0.000
81	B	83	LEU	0	0.001	0.020	29.753	-0.015	-0.015	0.000	0.000	0.000	0.000
82	B	84	CYS	0	-0.044	-0.027	29.131	0.007	0.007	0.000	0.000	0.000	0.000
83	B	85	TYR	0	0.032	0.003	30.624	-0.006	-0.006	0.000	0.000	0.000	0.000
84	B	86	ASP	-1	-0.754	-0.830	25.546	-0.334	-0.334	0.000	0.000	0.000	0.000
85	B	87	ASN	0	-0.023	-0.034	28.394	0.013	0.013	0.000	0.000	0.000	0.000
86	B	88	ASN	0	-0.097	-0.043	25.491	0.007	0.007	0.000	0.000	0.000	0.000
87	B	89	SER	0	-0.074	-0.062	24.702	0.008	0.008	0.000	0.000	0.000	0.000
88	B	90	GLN	0	-0.006	-0.008	26.764	0.008	0.008	0.000	0.000	0.000	0.000
89	B	91	SER	0	0.002	0.003	27.308	0.015	0.015	0.000	0.000	0.000	0.000
90	B	92	LEU	0	-0.016	0.001	29.460	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	93	LEU	0	-0.047	-0.039	24.386	-0.009	-0.009	0.000	0.000	0.000	0.000
92	B	94	LEU	0	0.019	0.027	27.222	0.015	0.015	0.000	0.000	0.000	0.000
93	B	95	ALA	0	-0.013	-0.014	25.115	-0.021	-0.021	0.000	0.000	0.000	0.000
94	B	96	LEU	0	0.033	0.012	24.345	0.019	0.019	0.000	0.000	0.000	0.000
95	B	97	ASN	0	-0.036	-0.023	23.120	-0.016	-0.016	0.000	0.000	0.000	0.000
96	B	98	PHE	0	0.023	0.011	19.162	0.024	0.024	0.000	0.000	0.000	0.000
97	B	99	SER	0	0.051	0.016	20.918	-0.019	-0.019	0.000	0.000	0.000	0.000
98	B	100	LEU	0	0.020	0.002	16.414	0.008	0.008	0.000	0.000	0.000	0.000
99	B	101	ASN	0	-0.058	-0.012	20.323	0.032	0.032	0.000	0.000	0.000	0.000
100	B	102	GLU	-1	-0.957	-0.976	23.508	-0.044	-0.044	0.000	0.000	0.000	0.000
101	B	103	SER	0	-0.059	-0.021	19.535	-0.006	-0.006	0.000	0.000	0.000	0.000
102	B	104	SER	0	-0.033	-0.061	19.343	0.016	0.016	0.000	0.000	0.000	0.000
103	B	105	VAL	0	0.014	0.001	16.766	-0.034	-0.034	0.000	0.000	0.000	0.000
104	B	106	GLU	-1	-0.782	-0.869	18.610	-0.017	-0.017	0.000	0.000	0.000	0.000
105	B	107	LYS	1	0.874	0.932	22.334	0.098	0.098	0.000	0.000	0.000	0.000
106	B	108	LEU	0	-0.009	-0.018	16.239	-0.017	-0.017	0.000	0.000	0.000	0.000
107	B	109	GLU	-1	-0.926	-0.962	20.159	-0.110	-0.110	0.000	0.000	0.000	0.000
108	B	110	CYS	0	-0.065	-0.029	21.983	0.001	0.001	0.000	0.000	0.000	0.000
109	B	111	GLU	-1	-0.811	-0.905	23.118	-0.140	-0.140	0.000	0.000	0.000	0.000
110	B	112	ILE	0	-0.014	-0.010	18.551	-0.016	-0.016	0.000	0.000	0.000	0.000
111	B	113	GLU	-1	-0.807	-0.884	23.126	-0.114	-0.114	0.000	0.000	0.000	0.000
112	B	114	VAL	0	-0.004	0.006	26.297	0.006	0.006	0.000	0.000	0.000	0.000
113	B	115	VAL	0	-0.012	-0.003	24.570	0.004	0.004	0.000	0.000	0.000	0.000
114	B	116	ILE	0	0.038	0.014	23.464	0.000	0.000	0.000	0.000	0.000	0.000
115	B	117	ARG	1	0.851	0.899	27.474	0.103	0.103	0.000	0.000	0.000	0.000
116	B	118	SER	0	-0.029	-0.006	30.105	0.010	0.010	0.000	0.000	0.000	0.000
117	B	119	MET	0	-0.050	-0.013	26.223	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	120	GLU	-1	-0.789	-0.849	30.890	-0.114	-0.114	0.000	0.000	0.000	0.000
119	B	121	ASN	0	-0.012	-0.018	32.981	0.009	0.009	0.000	0.000	0.000	0.000
120	B	122	LEU	0	0.003	0.005	32.833	0.005	0.005	0.000	0.000	0.000	0.000
121	B	123	TYR	0	-0.024	-0.035	29.824	0.003	0.003	0.000	0.000	0.000	0.000
122	B	124	HIS	0	-0.028	-0.014	35.623	0.010	0.010	0.000	0.000	0.000	0.000
123	B	125	ILE	0	-0.012	0.002	38.430	0.006	0.006	0.000	0.000	0.000	0.000
124	B	126	LEU	0	-0.074	-0.042	35.963	0.003	0.003	0.000	0.000	0.000	0.000
125	B	127	GLN	0	-0.005	0.002	39.339	-0.002	-0.002	0.000	0.000	0.000	0.000
126	B	128	ASP	-1	-0.914	-0.933	40.992	-0.078	-0.078	0.000	0.000	0.000	0.000
127	B	129	LYS	1	0.808	0.908	43.043	0.099	0.099	0.000	0.000	0.000	0.000
128	B	130	GLY	0	-0.035	-0.014	43.517	0.000	0.000	0.000	0.000	0.000	0.000
129	B	131	ILE	0	-0.072	-0.038	39.579	-0.002	-0.002	0.000	0.000	0.000	0.000
130	B	132	THR	0	0.029	0.007	37.001	0.000	0.000	0.000	0.000	0.000	0.000
131	B	133	LEU	0	-0.048	-0.020	32.670	0.001	0.001	0.000	0.000	0.000	0.000
132	B	134	ASP	-1	-0.874	-0.919	31.826	-0.194	-0.194	0.000	0.000	0.000	0.000
133	B	135	THR	0	-0.003	0.007	27.665	-0.011	-0.011	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:3:SER)