FMO DATABASE

FMODB ID: R97V8

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	OptH
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	-1399677.06057
FMO2-HF: Nuclear repulsion	1340779.71614
FMO2-HF: Total energy	-58897.34443
FMO2-MP2: Total energy	-59069.277035

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.
-7.091	-4.019	12.034	-6.042	-9.062	-0.012

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 : 0.011 / q_NPA : -0.005

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	0.025	-0.009	3.533	-2.821	-0.870	0.015	-1.103	-0.863	0.003
4	A	15	ILE	0	0.043	0.028	5.746	0.682	0.682	0.000	0.000	0.000	0.000
5	A	16	GLN	0	-0.004	-0.021	2.426	-3.367	-1.445	2.012	-1.570	-2.364	-0.014
6	A	17	ALA	0	0.043	0.012	2.618	-0.924	0.907	0.511	-0.989	-1.352	0.008
7	A	18	GLU	-1	-0.985	-0.986	4.268	-0.344	-0.191	0.002	-0.045	-0.110	0.000
8	A	19	VAL	0	0.005	-0.004	6.853	0.220	0.220	0.000	0.000	0.000	0.000
9	A	20	LEU	0	-0.008	0.014	3.970	-0.036	0.106	0.001	-0.021	-0.121	0.000
10	A	21	LYS	1	0.999	1.006	7.924	-0.017	-0.017	0.000	0.000	0.000	0.000
11	A	22	ARG	1	0.953	0.982	9.810	0.060	0.060	0.000	0.000	0.000	0.000
12	A	23	VAL	0	-0.028	-0.027	10.807	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	24	ALA	0	-0.004	-0.015	11.550	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	25	GLU	-1	-0.886	-0.950	13.319	0.006	0.006	0.000	0.000	0.000	0.000
15	A	26	VAL	0	-0.052	-0.021	15.803	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	27	PHE	0	-0.025	-0.034	16.339	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	28	ASP	-1	-0.822	-0.911	17.327	0.092	0.092	0.000	0.000	0.000	0.000
18	A	29	GLN	0	0.069	0.052	19.179	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	30	HIS	0	-0.114	-0.027	20.074	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	31	VAL	0	0.002	0.016	20.793	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	32	PRO	0	0.008	-0.008	23.602	0.005	0.005	0.000	0.000	0.000	0.000
22	A	33	PHE	0	0.012	-0.005	26.611	0.002	0.002	0.000	0.000	0.000	0.000
23	A	34	HIS	0	-0.002	-0.018	20.397	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	35	ASN	0	0.027	0.007	24.787	0.009	0.009	0.000	0.000	0.000	0.000
25	A	36	LEU	0	-0.067	-0.015	26.810	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	37	LEU	0	-0.034	-0.029	27.367	0.000	0.000	0.000	0.000	0.000	0.000
27	A	38	GLY	0	-0.043	-0.022	26.406	0.000	0.000	0.000	0.000	0.000	0.000
28	A	39	LEU	0	-0.098	-0.036	20.266	0.005	0.005	0.000	0.000	0.000	0.000
29	A	40	ASP	-1	-0.797	-0.895	20.004	0.079	0.079	0.000	0.000	0.000	0.000
30	A	41	ILE	0	-0.075	-0.039	13.927	0.013	0.013	0.000	0.000	0.000	0.000
31	A	42	LYS	1	0.850	0.952	15.683	-0.145	-0.145	0.000	0.000	0.000	0.000
32	A	43	ARG	1	0.813	0.890	11.435	-0.277	-0.277	0.000	0.000	0.000	0.000
33	A	44	TYR	0	-0.035	-0.040	9.933	-0.090	-0.090	0.000	0.000	0.000	0.000
34	A	45	ASP	-1	-0.840	-0.914	5.088	1.112	1.112	0.000	0.000	0.000	0.000
35	A	46	ILE	0	-0.028	-0.040	2.041	-0.881	-3.857	9.494	-2.287	-4.231	-0.009
36	A	47	ASP	-1	-0.976	-0.949	4.481	0.076	0.125	-0.001	-0.027	-0.021	0.000
37	A	48	GLY	0	-0.037	-0.035	7.429	-0.075	-0.075	0.000	0.000	0.000	0.000
38	A	49	VAL	0	-0.048	-0.018	9.566	0.090	0.090	0.000	0.000	0.000	0.000
39	A	50	GLU	-1	-0.795	-0.900	12.278	0.178	0.178	0.000	0.000	0.000	0.000
40	A	51	VAL	0	-0.016	-0.015	15.240	0.007	0.007	0.000	0.000	0.000	0.000
41	A	52	ALA	0	-0.018	-0.010	18.193	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	53	ILE	0	0.036	0.031	21.353	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	54	ASN	0	-0.009	-0.006	24.794	0.003	0.003	0.000	0.000	0.000	0.000
44	A	55	MET	0	-0.013	0.002	27.819	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	56	LYS	1	0.880	0.938	30.518	-0.035	-0.035	0.000	0.000	0.000	0.000
46	A	57	PRO	0	0.033	0.001	33.670	0.000	0.000	0.000	0.000	0.000	0.000
47	A	58	GLU	-1	-0.899	-0.961	34.645	0.024	0.024	0.000	0.000	0.000	0.000
48	A	59	LEU	0	-0.046	-0.007	29.636	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	60	ILE	0	-0.030	-0.008	33.857	0.002	0.002	0.000	0.000	0.000	0.000
50	A	61	GLY	0	-0.026	-0.008	36.627	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	62	ASN	0	-0.049	-0.016	38.040	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	63	ILE	0	0.083	0.025	40.642	0.001	0.001	0.000	0.000	0.000	0.000
53	A	64	HIS	0	-0.026	-0.005	42.730	0.001	0.001	0.000	0.000	0.000	0.000
54	A	65	GLN	0	0.039	0.005	40.519	0.002	0.002	0.000	0.000	0.000	0.000
55	A	66	GLN	0	-0.034	-0.007	38.503	0.003	0.003	0.000	0.000	0.000	0.000
56	A	67	ILE	0	-0.063	-0.021	35.921	0.002	0.002	0.000	0.000	0.000	0.000
57	A	68	LEU	0	0.048	0.010	28.833	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	69	HIS	0	0.046	0.035	33.581	0.001	0.001	0.000	0.000	0.000	0.000
59	A	70	GLY	0	0.036	0.010	32.232	0.002	0.002	0.000	0.000	0.000	0.000
60	A	71	GLY	0	0.022	-0.005	31.094	0.002	0.002	0.000	0.000	0.000	0.000
61	A	72	VAL	0	0.032	0.029	28.078	0.001	0.001	0.000	0.000	0.000	0.000
62	A	73	THR	0	-0.008	-0.007	27.202	0.005	0.005	0.000	0.000	0.000	0.000
63	A	74	ALA	0	-0.018	-0.011	26.178	0.004	0.004	0.000	0.000	0.000	0.000
64	A	75	THR	0	0.008	-0.002	24.992	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	76	VAL	0	0.024	0.006	21.703	0.002	0.002	0.000	0.000	0.000	0.000
66	A	77	LEU	0	-0.027	-0.014	21.322	0.007	0.007	0.000	0.000	0.000	0.000
67	A	78	ASP	-1	-0.791	-0.887	21.115	0.035	0.035	0.000	0.000	0.000	0.000
68	A	79	VAL	0	0.022	0.019	18.431	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	80	VAL	0	0.003	0.012	16.460	0.007	0.007	0.000	0.000	0.000	0.000
70	A	81	GLY	0	0.029	0.010	16.088	0.010	0.010	0.000	0.000	0.000	0.000
71	A	82	GLY	0	0.026	0.015	16.718	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	83	LEU	0	0.027	0.014	13.111	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	84	THR	0	-0.027	-0.015	11.979	0.014	0.014	0.000	0.000	0.000	0.000
74	A	85	ALA	0	-0.041	-0.032	12.167	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	86	PHE	0	-0.019	-0.013	10.376	-0.035	-0.035	0.000	0.000	0.000	0.000
76	A	87	ALA	0	0.058	0.035	7.826	-0.058	-0.058	0.000	0.000	0.000	0.000
77	A	88	GLY	0	0.021	0.007	7.990	-0.097	-0.097	0.000	0.000	0.000	0.000
78	A	89	LEU	0	-0.074	-0.020	10.330	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	90	VAL	0	0.035	0.023	5.062	-0.055	-0.055	0.000	0.000	0.000	0.000
80	A	91	ALA	0	0.009	0.001	5.610	-0.237	-0.237	0.000	0.000	0.000	0.000
81	A	92	SER	0	-0.118	-0.067	6.585	0.167	0.167	0.000	0.000	0.000	0.000
82	A	93	ARG	1	0.878	0.934	8.340	0.275	0.275	0.000	0.000	0.000	0.000
83	A	94	ASP	-1	-0.876	-0.937	6.493	-0.201	-0.201	0.000	0.000	0.000	0.000
84	A	95	ASP	-1	-1.005	-1.010	8.435	-0.324	-0.324	0.000	0.000	0.000	0.000
85	A	96	TRP	0	-0.060	-0.020	7.937	0.094	0.094	0.000	0.000	0.000	0.000
86	A	97	THR	0	0.017	0.006	10.468	-0.115	-0.115	0.000	0.000	0.000	0.000
87	A	98	ILE	0	0.052	-0.002	11.219	0.020	0.020	0.000	0.000	0.000	0.000
88	A	99	GLU	-1	-0.903	-0.959	12.459	-0.170	-0.170	0.000	0.000	0.000	0.000
89	A	100	GLU	-1	-0.876	-0.920	13.745	-0.247	-0.247	0.000	0.000	0.000	0.000
90	A	101	LEU	0	0.002	-0.005	8.391	0.035	0.035	0.000	0.000	0.000	0.000
91	A	102	GLN	0	-0.032	-0.014	12.720	0.042	0.042	0.000	0.000	0.000	0.000
92	A	103	GLN	0	-0.017	-0.013	15.028	0.020	0.020	0.000	0.000	0.000	0.000
93	A	104	ARG	1	0.788	0.867	14.015	0.149	0.149	0.000	0.000	0.000	0.000
94	A	105	LEU	0	-0.010	-0.004	13.826	0.021	0.021	0.000	0.000	0.000	0.000
95	A	106	GLN	0	-0.023	-0.009	15.930	0.028	0.028	0.000	0.000	0.000	0.000
96	A	107	THR	0	-0.084	-0.034	18.849	0.010	0.010	0.000	0.000	0.000	0.000
97	A	108	LEU	0	-0.076	-0.015	15.461	0.008	0.008	0.000	0.000	0.000	0.000
98	A	109	GLY	0	0.044	0.023	18.746	0.003	0.003	0.000	0.000	0.000	0.000
99	A	110	THR	0	-0.045	-0.047	21.621	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	111	ILE	0	-0.082	-0.026	23.539	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	112	ASP	-1	-0.919	-0.962	25.665	0.021	0.021	0.000	0.000	0.000	0.000
102	A	113	MET	0	0.031	0.000	24.680	0.004	0.004	0.000	0.000	0.000	0.000
103	A	114	ARG	1	0.801	0.914	26.734	-0.039	-0.039	0.000	0.000	0.000	0.000
104	A	115	VAL	0	0.017	-0.002	27.118	0.004	0.004	0.000	0.000	0.000	0.000
105	A	116	ASP	-1	-0.865	-0.915	28.751	0.039	0.039	0.000	0.000	0.000	0.000
106	A	117	TYR	0	-0.026	-0.033	29.981	0.003	0.003	0.000	0.000	0.000	0.000
107	A	118	LEU	0	-0.030	-0.002	28.612	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	119	ARG	1	0.887	0.935	31.223	-0.056	-0.056	0.000	0.000	0.000	0.000
109	A	120	PRO	0	-0.030	-0.022	33.516	0.001	0.001	0.000	0.000	0.000	0.000
110	A	121	GLY	0	0.099	0.054	32.208	0.002	0.002	0.000	0.000	0.000	0.000
111	A	122	ARG	1	0.918	0.966	33.025	-0.039	-0.039	0.000	0.000	0.000	0.000
112	A	123	GLY	0	0.021	-0.002	31.101	0.003	0.003	0.000	0.000	0.000	0.000
113	A	124	GLN	0	-0.078	-0.037	30.701	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	125	ILE	0	0.016	0.005	24.697	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	126	PHE	0	-0.053	-0.025	25.727	0.001	0.001	0.000	0.000	0.000	0.000
116	A	127	THR	0	0.029	0.005	19.730	0.005	0.005	0.000	0.000	0.000	0.000
117	A	128	GLY	0	-0.017	-0.007	20.098	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	129	THR	0	-0.011	0.007	16.143	0.019	0.019	0.000	0.000	0.000	0.000
119	A	130	GLY	0	0.068	0.003	15.556	-0.020	-0.020	0.000	0.000	0.000	0.000
120	A	131	SER	0	-0.043	-0.010	14.266	0.014	0.014	0.000	0.000	0.000	0.000
121	A	132	VAL	0	0.060	0.024	12.888	-0.014	-0.014	0.000	0.000	0.000	0.000
122	A	133	ILE	0	-0.046	-0.020	15.617	0.008	0.008	0.000	0.000	0.000	0.000
123	A	134	ARG	1	0.936	0.963	18.302	-0.023	-0.023	0.000	0.000	0.000	0.000
124	A	135	ALA	0	0.077	0.046	14.455	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	136	GLY	0	-0.052	-0.049	16.407	0.005	0.005	0.000	0.000	0.000	0.000
126	A	137	ASN	0	0.066	0.053	16.409	-0.023	-0.023	0.000	0.000	0.000	0.000
127	A	138	ARG	1	0.928	0.986	17.727	0.000	0.000	0.000	0.000	0.000	0.000
128	A	139	VAL	0	0.039	0.019	20.030	0.001	0.001	0.000	0.000	0.000	0.000
129	A	140	SER	0	0.013	0.012	16.400	0.002	0.002	0.000	0.000	0.000	0.000
130	A	141	VAL	0	-0.010	0.007	18.770	0.000	0.000	0.000	0.000	0.000	0.000
131	A	142	CYS	0	-0.039	-0.016	16.792	0.004	0.004	0.000	0.000	0.000	0.000
132	A	143	ARG	1	0.973	0.995	18.691	-0.075	-0.075	0.000	0.000	0.000	0.000
133	A	144	MET	0	-0.033	-0.002	18.858	0.008	0.008	0.000	0.000	0.000	0.000
134	A	145	GLU	-1	-0.825	-0.904	20.492	0.100	0.100	0.000	0.000	0.000	0.000
135	A	146	LEU	0	0.037	0.037	21.461	0.006	0.006	0.000	0.000	0.000	0.000
136	A	147	HIS	0	-0.015	-0.026	20.675	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	148	ASN	0	0.018	0.012	25.389	0.005	0.005	0.000	0.000	0.000	0.000
138	A	149	GLU	-1	-0.735	-0.878	26.218	0.068	0.068	0.000	0.000	0.000	0.000
139	A	150	GLN	0	-0.091	-0.043	27.301	0.001	0.001	0.000	0.000	0.000	0.000
140	A	151	GLY	0	0.011	0.017	25.791	0.000	0.000	0.000	0.000	0.000	0.000
141	A	152	THR	0	-0.080	-0.035	26.824	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	153	HIS	0	0.047	0.015	24.051	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	154	ILE	0	-0.050	-0.016	27.544	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	155	ALA	0	-0.012	-0.026	27.414	-0.006	-0.006	0.000	0.000	0.000	0.000
145	A	156	PHE	0	-0.004	0.013	25.100	0.006	0.006	0.000	0.000	0.000	0.000
146	A	157	GLY	0	0.045	0.018	24.101	-0.006	-0.006	0.000	0.000	0.000	0.000
147	A	158	THR	0	-0.057	-0.035	22.975	0.006	0.006	0.000	0.000	0.000	0.000
148	A	159	GLY	0	0.019	0.023	21.980	-0.004	-0.004	0.000	0.000	0.000	0.000
149	A	160	THR	0	-0.023	0.002	21.489	0.004	0.004	0.000	0.000	0.000	0.000
150	A	161	TYR	0	0.018	-0.003	18.783	0.000	0.000	0.000	0.000	0.000	0.000
151	A	162	MET	0	-0.001	0.007	20.518	-0.003	-0.003	0.000	0.000	0.000	0.000
152	A	163	VAL	0	0.016	-0.003	15.637	0.000	0.000	0.000	0.000	0.000	0.000
153	A	164	GLY	0	0.016	0.017	16.815	-0.017	-0.017	0.000	0.000	0.000	0.000

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