FMO DATABASE

FMODB ID: QY2JY

Calculation Name: 3E8P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E8P

Chain ID: A

ChEMBL ID:

UniProt ID: Q8E9M7

Base Structure: X-ray

Registration Date: 2023-09-20

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1399853.290627
FMO2-HF: Nuclear repulsion	1340955.185708
FMO2-HF: Total energy	-58898.104919
FMO2-MP2: Total energy	-59069.923237

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:12:SER)

Summations of interaction energy for fragment #1(A:12: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.
-8.391	-3.268	9.992	-6.041	-9.077	-0.013

Interaction energy analysis for fragmet #1(A:12:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : 0.001

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	14	PRO	0	0.048	-0.006	3.385	-3.006	-0.958	0.031	-1.169	-0.911	0.004
4	A	15	ILE	0	0.019	0.017	5.900	0.595	0.595	0.000	0.000	0.000	0.000
5	A	16	GLN	0	0.026	0.008	2.423	-3.882	-2.090	2.908	-1.989	-2.711	-0.018
6	A	17	ALA	0	0.044	0.016	2.589	-0.723	1.137	0.442	-0.986	-1.317	0.007
7	A	18	GLU	-1	-0.900	-0.932	4.166	-0.257	-0.121	0.002	-0.038	-0.101	0.000
8	A	19	VAL	0	-0.010	-0.015	7.094	0.265	0.265	0.000	0.000	0.000	0.000
9	A	20	LEU	0	0.000	0.019	4.079	-0.021	0.099	0.000	-0.016	-0.104	0.000
10	A	21	LYS	1	0.914	0.953	7.914	0.335	0.335	0.000	0.000	0.000	0.000
11	A	22	ARG	1	0.947	0.977	9.825	0.116	0.116	0.000	0.000	0.000	0.000
12	A	23	VAL	0	-0.029	-0.026	11.037	0.009	0.009	0.000	0.000	0.000	0.000
13	A	24	ALA	0	0.003	-0.008	11.488	0.002	0.002	0.000	0.000	0.000	0.000
14	A	25	GLU	-1	-0.866	-0.927	13.316	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	26	VAL	0	-0.034	-0.019	15.782	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	27	PHE	0	-0.013	-0.025	16.416	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	28	ASP	-1	-0.802	-0.873	17.196	0.100	0.100	0.000	0.000	0.000	0.000
18	A	29	GLN	0	-0.009	0.005	19.143	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	30	HIS	0	-0.126	-0.055	19.778	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	31	VAL	0	0.010	0.015	20.893	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	32	PRO	0	0.012	-0.002	23.610	0.007	0.007	0.000	0.000	0.000	0.000
22	A	33	PHE	0	0.005	-0.009	26.659	0.003	0.003	0.000	0.000	0.000	0.000
23	A	34	HIS	0	0.000	-0.020	20.348	0.000	0.000	0.000	0.000	0.000	0.000
24	A	35	ASN	0	0.031	0.013	24.586	0.011	0.011	0.000	0.000	0.000	0.000
25	A	36	LEU	0	-0.069	-0.013	26.769	0.000	0.000	0.000	0.000	0.000	0.000
26	A	37	LEU	0	-0.036	-0.027	27.352	0.001	0.001	0.000	0.000	0.000	0.000
27	A	38	GLY	0	-0.021	-0.015	26.348	0.001	0.001	0.000	0.000	0.000	0.000
28	A	39	LEU	0	-0.086	-0.036	20.247	0.006	0.006	0.000	0.000	0.000	0.000
29	A	40	ASP	-1	-0.844	-0.914	20.001	0.084	0.084	0.000	0.000	0.000	0.000
30	A	41	ILE	0	-0.055	-0.045	13.888	0.016	0.016	0.000	0.000	0.000	0.000
31	A	42	LYS	1	0.837	0.924	15.611	-0.173	-0.173	0.000	0.000	0.000	0.000
32	A	43	ARG	1	0.856	0.889	11.360	-0.325	-0.325	0.000	0.000	0.000	0.000
33	A	44	TYR	0	-0.050	-0.053	9.962	-0.098	-0.098	0.000	0.000	0.000	0.000
34	A	45	ASP	-1	-0.863	-0.927	5.194	1.327	1.405	-0.001	-0.003	-0.074	0.000
35	A	46	ILE	0	-0.024	-0.034	2.211	-1.982	-2.959	6.611	-1.813	-3.821	-0.006
36	A	47	ASP	-1	-0.969	-0.947	4.469	0.168	0.234	-0.001	-0.027	-0.038	0.000
37	A	48	GLY	0	-0.034	-0.030	7.479	-0.140	-0.140	0.000	0.000	0.000	0.000
38	A	49	VAL	0	-0.051	-0.017	9.586	0.102	0.102	0.000	0.000	0.000	0.000
39	A	50	GLU	-1	-0.799	-0.859	12.299	0.229	0.229	0.000	0.000	0.000	0.000
40	A	51	VAL	0	-0.004	-0.009	15.289	0.003	0.003	0.000	0.000	0.000	0.000
41	A	52	ALA	0	-0.022	-0.012	18.223	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	53	ILE	0	0.043	0.033	21.398	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	54	ASN	0	-0.015	-0.006	24.830	0.002	0.002	0.000	0.000	0.000	0.000
44	A	55	MET	0	-0.012	0.005	27.749	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	56	LYS	1	0.884	0.939	30.587	-0.036	-0.036	0.000	0.000	0.000	0.000
46	A	57	PRO	0	0.039	0.002	33.609	0.000	0.000	0.000	0.000	0.000	0.000
47	A	58	GLU	-1	-0.908	-0.966	34.587	0.027	0.027	0.000	0.000	0.000	0.000
48	A	59	LEU	0	-0.045	-0.005	29.755	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	60	ILE	0	-0.038	-0.011	33.869	0.002	0.002	0.000	0.000	0.000	0.000
50	A	61	GLY	0	-0.014	-0.001	36.645	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	62	ASN	0	-0.050	-0.027	38.047	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	63	ILE	0	0.083	0.026	40.668	0.002	0.002	0.000	0.000	0.000	0.000
53	A	64	HIS	0	0.008	0.015	42.755	0.002	0.002	0.000	0.000	0.000	0.000
54	A	65	GLN	0	-0.003	-0.003	40.529	0.003	0.003	0.000	0.000	0.000	0.000
55	A	66	GLN	0	-0.004	-0.004	38.647	0.004	0.004	0.000	0.000	0.000	0.000
56	A	67	ILE	0	-0.060	-0.017	35.954	0.003	0.003	0.000	0.000	0.000	0.000
57	A	68	LEU	0	0.044	0.011	28.966	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	69	HIS	0	0.038	0.020	33.604	0.001	0.001	0.000	0.000	0.000	0.000
59	A	70	GLY	0	0.040	0.017	32.230	0.003	0.003	0.000	0.000	0.000	0.000
60	A	71	GLY	0	0.036	0.016	31.079	0.002	0.002	0.000	0.000	0.000	0.000
61	A	72	VAL	0	0.030	0.023	27.984	0.000	0.000	0.000	0.000	0.000	0.000
62	A	73	THR	0	0.003	-0.002	27.194	0.005	0.005	0.000	0.000	0.000	0.000
63	A	74	ALA	0	-0.014	-0.005	26.168	0.005	0.005	0.000	0.000	0.000	0.000
64	A	75	THR	0	0.001	-0.008	24.985	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	76	VAL	0	0.021	0.004	21.704	0.001	0.001	0.000	0.000	0.000	0.000
66	A	77	LEU	0	-0.027	-0.010	21.305	0.008	0.008	0.000	0.000	0.000	0.000
67	A	78	ASP	-1	-0.764	-0.861	21.083	0.033	0.033	0.000	0.000	0.000	0.000
68	A	79	VAL	0	0.003	0.013	18.519	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	80	VAL	0	0.000	0.008	16.660	0.007	0.007	0.000	0.000	0.000	0.000
70	A	81	GLY	0	0.032	0.012	16.052	0.012	0.012	0.000	0.000	0.000	0.000
71	A	82	GLY	0	0.025	0.015	16.650	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	83	LEU	0	0.025	0.013	13.106	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	84	THR	0	-0.027	-0.009	11.910	0.019	0.019	0.000	0.000	0.000	0.000
74	A	85	ALA	0	-0.044	-0.031	12.095	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	86	PHE	0	-0.008	-0.013	10.120	-0.042	-0.042	0.000	0.000	0.000	0.000
76	A	87	ALA	0	0.059	0.036	7.777	-0.076	-0.076	0.000	0.000	0.000	0.000
77	A	88	GLY	0	0.019	0.007	7.875	-0.117	-0.117	0.000	0.000	0.000	0.000
78	A	89	LEU	0	-0.075	-0.022	10.229	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	90	VAL	0	0.021	0.008	5.154	-0.076	-0.076	0.000	0.000	0.000	0.000
80	A	91	ALA	0	0.020	0.004	5.603	-0.270	-0.270	0.000	0.000	0.000	0.000
81	A	92	SER	0	-0.120	-0.059	6.593	0.164	0.164	0.000	0.000	0.000	0.000
82	A	93	ARG	1	0.760	0.854	8.372	0.380	0.380	0.000	0.000	0.000	0.000
83	A	94	ASP	-1	-0.834	-0.928	6.086	-0.622	-0.622	0.000	0.000	0.000	0.000
84	A	95	ASP	-1	-0.960	-0.965	8.447	-0.366	-0.366	0.000	0.000	0.000	0.000
85	A	96	TRP	0	-0.047	-0.007	7.901	0.121	0.121	0.000	0.000	0.000	0.000
86	A	97	THR	0	0.029	0.012	10.434	-0.114	-0.114	0.000	0.000	0.000	0.000
87	A	98	ILE	0	0.033	-0.006	10.992	0.019	0.019	0.000	0.000	0.000	0.000
88	A	99	GLU	-1	-0.916	-0.966	12.400	-0.211	-0.211	0.000	0.000	0.000	0.000
89	A	100	GLU	-1	-0.808	-0.883	13.871	-0.299	-0.299	0.000	0.000	0.000	0.000
90	A	101	LEU	0	-0.006	-0.008	8.529	0.034	0.034	0.000	0.000	0.000	0.000
91	A	102	GLN	0	-0.031	-0.015	12.730	0.072	0.072	0.000	0.000	0.000	0.000
92	A	103	GLN	0	-0.006	-0.005	15.019	0.023	0.023	0.000	0.000	0.000	0.000
93	A	104	ARG	1	0.809	0.889	14.089	0.194	0.194	0.000	0.000	0.000	0.000
94	A	105	LEU	0	-0.013	-0.003	13.844	0.026	0.026	0.000	0.000	0.000	0.000
95	A	106	GLN	0	-0.038	-0.018	15.966	0.032	0.032	0.000	0.000	0.000	0.000
96	A	107	THR	0	-0.074	-0.033	18.896	0.013	0.013	0.000	0.000	0.000	0.000
97	A	108	LEU	0	-0.079	-0.015	15.356	0.010	0.010	0.000	0.000	0.000	0.000
98	A	109	GLY	0	0.047	0.024	18.819	0.004	0.004	0.000	0.000	0.000	0.000
99	A	110	THR	0	-0.046	-0.042	21.676	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	111	ILE	0	-0.087	-0.032	23.487	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	112	ASP	-1	-0.886	-0.933	25.577	0.018	0.018	0.000	0.000	0.000	0.000
102	A	113	MET	0	0.024	0.005	24.746	0.005	0.005	0.000	0.000	0.000	0.000
103	A	114	ARG	1	0.760	0.864	26.682	-0.041	-0.041	0.000	0.000	0.000	0.000
104	A	115	VAL	0	0.020	-0.002	26.949	0.005	0.005	0.000	0.000	0.000	0.000
105	A	116	ASP	-1	-0.826	-0.866	28.737	0.041	0.041	0.000	0.000	0.000	0.000
106	A	117	TYR	0	-0.037	-0.045	29.984	0.004	0.004	0.000	0.000	0.000	0.000
107	A	118	LEU	0	-0.032	-0.003	28.641	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	119	ARG	1	0.876	0.927	31.232	-0.064	-0.064	0.000	0.000	0.000	0.000
109	A	120	PRO	0	-0.028	-0.021	33.547	0.001	0.001	0.000	0.000	0.000	0.000
110	A	121	GLY	0	0.092	0.053	32.251	0.003	0.003	0.000	0.000	0.000	0.000
111	A	122	ARG	1	0.896	0.950	33.060	-0.044	-0.044	0.000	0.000	0.000	0.000
112	A	123	GLY	0	0.028	0.008	31.165	0.004	0.004	0.000	0.000	0.000	0.000
113	A	124	GLN	0	-0.090	-0.056	30.756	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	125	ILE	0	0.008	-0.006	24.728	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	126	PHE	0	-0.043	-0.020	25.780	0.002	0.002	0.000	0.000	0.000	0.000
116	A	127	THR	0	0.010	-0.006	19.693	0.006	0.006	0.000	0.000	0.000	0.000
117	A	128	GLY	0	-0.012	-0.005	20.153	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	129	THR	0	-0.019	-0.005	16.120	0.024	0.024	0.000	0.000	0.000	0.000
119	A	130	GLY	0	0.076	0.008	15.578	-0.026	-0.026	0.000	0.000	0.000	0.000
120	A	131	SER	0	-0.033	-0.004	14.253	0.020	0.020	0.000	0.000	0.000	0.000
121	A	132	VAL	0	0.050	0.016	12.869	-0.018	-0.018	0.000	0.000	0.000	0.000
122	A	133	ILE	0	-0.040	-0.018	15.569	0.008	0.008	0.000	0.000	0.000	0.000
123	A	134	ARG	1	0.920	0.956	18.230	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	135	ALA	0	0.074	0.045	14.357	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	136	GLY	0	-0.032	-0.031	16.305	0.005	0.005	0.000	0.000	0.000	0.000
126	A	137	ASN	0	0.054	0.039	16.390	-0.030	-0.030	0.000	0.000	0.000	0.000
127	A	138	ARG	1	0.916	0.962	17.739	0.018	0.018	0.000	0.000	0.000	0.000
128	A	139	VAL	0	0.019	0.016	20.088	0.003	0.003	0.000	0.000	0.000	0.000
129	A	140	SER	0	0.038	0.021	15.690	0.000	0.000	0.000	0.000	0.000	0.000
130	A	141	VAL	0	-0.004	0.011	18.663	0.001	0.001	0.000	0.000	0.000	0.000
131	A	142	CYS	0	-0.029	-0.007	16.603	0.004	0.004	0.000	0.000	0.000	0.000
132	A	143	ARG	1	0.970	0.994	18.665	-0.080	-0.080	0.000	0.000	0.000	0.000
133	A	144	MET	0	-0.032	-0.003	18.846	0.010	0.010	0.000	0.000	0.000	0.000
134	A	145	GLU	-1	-0.850	-0.911	20.512	0.121	0.121	0.000	0.000	0.000	0.000
135	A	146	LEU	0	0.060	0.045	21.489	0.008	0.008	0.000	0.000	0.000	0.000
136	A	147	HIS	0	-0.018	-0.024	20.634	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	148	ASN	0	0.015	-0.006	25.447	0.005	0.005	0.000	0.000	0.000	0.000
138	A	149	GLU	-1	-0.717	-0.846	26.306	0.079	0.079	0.000	0.000	0.000	0.000
139	A	150	GLN	0	-0.088	-0.041	27.390	0.002	0.002	0.000	0.000	0.000	0.000
140	A	151	GLY	0	0.009	0.014	25.876	0.001	0.001	0.000	0.000	0.000	0.000
141	A	152	THR	0	-0.070	-0.027	26.913	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	153	HIS	0	0.055	0.021	23.808	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	154	ILE	0	-0.050	-0.018	27.585	-0.008	-0.008	0.000	0.000	0.000	0.000
144	A	155	ALA	0	-0.014	-0.023	27.442	-0.007	-0.007	0.000	0.000	0.000	0.000
145	A	156	PHE	0	-0.007	0.008	25.054	0.007	0.007	0.000	0.000	0.000	0.000
146	A	157	GLY	0	0.056	0.027	24.092	-0.007	-0.007	0.000	0.000	0.000	0.000
147	A	158	THR	0	-0.067	-0.045	22.920	0.007	0.007	0.000	0.000	0.000	0.000
148	A	159	GLY	0	0.028	0.030	21.922	-0.004	-0.004	0.000	0.000	0.000	0.000
149	A	160	THR	0	-0.056	-0.032	21.414	0.003	0.003	0.000	0.000	0.000	0.000
150	A	161	TYR	0	0.011	-0.028	18.672	0.001	0.001	0.000	0.000	0.000	0.000
151	A	162	MET	0	0.002	0.007	20.435	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	163	VAL	0	0.005	-0.009	15.647	0.000	0.000	0.000	0.000	0.000	0.000
153	A	164	GLY	0	0.012	0.016	16.900	-0.021	-0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:SER)