FMO DATABASE

FMODB ID: K94M3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1403421.606453
FMO2-HF: Nuclear repulsion	1344523.244518
FMO2-HF: Total energy	-58898.361934
FMO2-MP2: Total energy	-59070.200691

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.
-9.511	-2.922	6.981	-5.305	-8.267	-0.015

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 : 0.004

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	0.028	-0.011	3.161	-2.401	-0.207	0.110	-1.216	-1.089	0.000
4	A	15	ILE	0	0.004	0.006	5.387	0.826	0.951	-0.001	-0.007	-0.117	0.000
5	A	16	GLN	0	0.021	0.002	2.472	-3.928	-2.231	2.355	-1.673	-2.380	-0.015
6	A	17	ALA	0	0.026	0.012	2.729	-0.906	1.001	0.393	-0.980	-1.321	0.006
7	A	18	GLU	-1	-0.886	-0.928	4.069	-0.234	-0.082	0.004	-0.041	-0.115	0.000
8	A	19	VAL	0	-0.009	-0.011	7.244	0.202	0.202	0.000	0.000	0.000	0.000
9	A	20	LEU	0	0.001	0.021	4.127	-0.057	0.053	0.000	-0.016	-0.093	0.000
10	A	21	LYS	1	0.890	0.935	7.701	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	22	ARG	1	0.947	0.973	9.634	0.038	0.038	0.000	0.000	0.000	0.000
12	A	23	VAL	0	-0.010	-0.006	11.176	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	24	ALA	0	0.022	0.006	11.714	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	25	GLU	-1	-0.880	-0.923	13.411	0.002	0.002	0.000	0.000	0.000	0.000
15	A	26	VAL	0	-0.008	-0.016	15.682	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	27	PHE	0	0.000	-0.022	16.238	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	28	ASP	-1	-0.836	-0.883	17.419	0.122	0.122	0.000	0.000	0.000	0.000
18	A	29	GLN	0	-0.052	-0.034	19.286	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	30	HIS	0	-0.096	-0.051	19.861	-0.020	-0.020	0.000	0.000	0.000	0.000
20	A	31	VAL	0	0.000	0.010	20.775	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	32	PRO	0	0.011	-0.002	23.585	0.007	0.007	0.000	0.000	0.000	0.000
22	A	33	PHE	0	-0.006	-0.003	26.681	0.003	0.003	0.000	0.000	0.000	0.000
23	A	34	HIS	0	0.007	-0.018	20.491	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	35	ASN	0	0.013	0.001	24.751	0.004	0.004	0.000	0.000	0.000	0.000
25	A	36	LEU	0	-0.052	-0.013	26.662	0.001	0.001	0.000	0.000	0.000	0.000
26	A	37	LEU	0	-0.029	-0.028	27.088	0.001	0.001	0.000	0.000	0.000	0.000
27	A	38	GLY	0	-0.008	0.009	26.369	0.001	0.001	0.000	0.000	0.000	0.000
28	A	39	LEU	0	-0.064	-0.034	20.700	0.005	0.005	0.000	0.000	0.000	0.000
29	A	40	ASP	-1	-0.820	-0.906	20.314	0.100	0.100	0.000	0.000	0.000	0.000
30	A	41	ILE	0	-0.047	-0.045	13.979	0.007	0.007	0.000	0.000	0.000	0.000
31	A	42	LYS	1	0.809	0.907	15.375	-0.143	-0.143	0.000	0.000	0.000	0.000
32	A	43	ARG	1	0.858	0.890	11.719	-0.313	-0.313	0.000	0.000	0.000	0.000
33	A	44	TYR	0	-0.058	-0.047	9.934	-0.112	-0.112	0.000	0.000	0.000	0.000
34	A	45	ASP	-1	-0.869	-0.931	5.180	0.998	0.998	0.000	0.000	0.000	0.000
35	A	46	ILE	0	-0.010	-0.026	2.260	-2.332	-1.961	4.121	-1.359	-3.133	-0.006
36	A	47	ASP	-1	-0.959	-0.949	4.717	0.131	0.164	-0.001	-0.013	-0.019	0.000
37	A	48	GLY	0	-0.050	-0.038	7.733	-0.035	-0.035	0.000	0.000	0.000	0.000
38	A	49	VAL	0	-0.045	-0.015	9.599	0.067	0.067	0.000	0.000	0.000	0.000
39	A	50	GLU	-1	-0.801	-0.868	12.375	0.226	0.226	0.000	0.000	0.000	0.000
40	A	51	VAL	0	0.006	0.007	15.197	0.014	0.014	0.000	0.000	0.000	0.000
41	A	52	ALA	0	-0.031	-0.024	18.052	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	53	ILE	0	0.015	0.011	21.433	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	54	ASN	0	-0.026	-0.004	24.759	0.001	0.001	0.000	0.000	0.000	0.000
44	A	55	MET	0	-0.038	-0.002	27.762	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	56	LYS	1	0.852	0.918	30.534	-0.040	-0.040	0.000	0.000	0.000	0.000
46	A	57	PRO	0	0.030	-0.003	33.834	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	58	GLU	-1	-0.862	-0.932	34.374	0.033	0.033	0.000	0.000	0.000	0.000
48	A	59	LEU	0	-0.011	0.014	29.694	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	60	ILE	0	-0.055	-0.012	33.721	0.001	0.001	0.000	0.000	0.000	0.000
50	A	61	GLY	0	-0.009	-0.006	36.492	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	62	ASN	0	-0.044	-0.034	37.712	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	63	ILE	0	0.071	0.031	40.606	0.002	0.002	0.000	0.000	0.000	0.000
53	A	64	HIS	0	0.014	0.024	42.557	0.002	0.002	0.000	0.000	0.000	0.000
54	A	65	GLN	0	-0.010	-0.010	40.555	0.003	0.003	0.000	0.000	0.000	0.000
55	A	66	GLN	0	-0.004	-0.009	38.345	0.004	0.004	0.000	0.000	0.000	0.000
56	A	67	ILE	0	-0.046	-0.005	35.699	0.003	0.003	0.000	0.000	0.000	0.000
57	A	68	LEU	0	0.060	0.024	28.681	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	69	HIS	0	0.024	0.008	33.328	0.000	0.000	0.000	0.000	0.000	0.000
59	A	70	GLY	0	0.043	0.018	31.919	0.002	0.002	0.000	0.000	0.000	0.000
60	A	71	GLY	0	0.027	0.015	31.053	0.001	0.001	0.000	0.000	0.000	0.000
61	A	72	VAL	0	0.032	0.031	28.213	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	73	THR	0	0.011	-0.005	27.157	0.005	0.005	0.000	0.000	0.000	0.000
63	A	74	ALA	0	-0.013	-0.004	26.173	0.003	0.003	0.000	0.000	0.000	0.000
64	A	75	THR	0	0.003	-0.008	24.756	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	76	VAL	0	0.027	0.014	21.480	0.000	0.000	0.000	0.000	0.000	0.000
66	A	77	LEU	0	-0.026	-0.004	21.207	0.004	0.004	0.000	0.000	0.000	0.000
67	A	78	ASP	-1	-0.753	-0.850	21.124	0.007	0.007	0.000	0.000	0.000	0.000
68	A	79	VAL	0	-0.015	0.006	18.455	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	80	VAL	0	0.020	0.013	16.881	0.001	0.001	0.000	0.000	0.000	0.000
70	A	81	GLY	0	0.026	0.013	16.263	0.000	0.000	0.000	0.000	0.000	0.000
71	A	82	GLY	0	0.049	0.021	16.889	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	83	LEU	0	0.012	0.011	13.335	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	84	THR	0	-0.018	-0.011	12.269	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	85	ALA	0	-0.042	-0.033	12.466	-0.030	-0.030	0.000	0.000	0.000	0.000
75	A	86	PHE	0	-0.001	-0.006	10.097	-0.050	-0.050	0.000	0.000	0.000	0.000
76	A	87	ALA	0	0.057	0.037	8.298	-0.081	-0.081	0.000	0.000	0.000	0.000
77	A	88	GLY	0	0.016	0.005	8.154	-0.140	-0.140	0.000	0.000	0.000	0.000
78	A	89	LEU	0	-0.059	-0.021	10.399	-0.031	-0.031	0.000	0.000	0.000	0.000
79	A	90	VAL	0	0.014	0.020	5.136	-0.090	-0.090	0.000	0.000	0.000	0.000
80	A	91	ALA	0	0.025	0.003	5.565	-0.290	-0.290	0.000	0.000	0.000	0.000
81	A	92	SER	0	-0.133	-0.071	6.613	0.167	0.167	0.000	0.000	0.000	0.000
82	A	93	ARG	1	0.749	0.849	8.379	0.503	0.503	0.000	0.000	0.000	0.000
83	A	94	ASP	-1	-0.808	-0.899	5.785	-1.189	-1.189	0.000	0.000	0.000	0.000
84	A	95	ASP	-1	-0.917	-0.948	8.309	-0.478	-0.478	0.000	0.000	0.000	0.000
85	A	96	TRP	0	-0.062	-0.019	7.931	0.179	0.179	0.000	0.000	0.000	0.000
86	A	97	THR	0	0.005	-0.014	10.402	-0.115	-0.115	0.000	0.000	0.000	0.000
87	A	98	ILE	0	0.012	-0.013	11.035	0.009	0.009	0.000	0.000	0.000	0.000
88	A	99	GLU	-1	-0.913	-0.955	12.497	-0.207	-0.207	0.000	0.000	0.000	0.000
89	A	100	GLU	-1	-0.776	-0.850	14.098	-0.370	-0.370	0.000	0.000	0.000	0.000
90	A	101	LEU	0	0.042	0.010	8.449	0.043	0.043	0.000	0.000	0.000	0.000
91	A	102	GLN	0	-0.046	-0.025	12.699	0.091	0.091	0.000	0.000	0.000	0.000
92	A	103	GLN	0	-0.013	-0.006	15.100	0.037	0.037	0.000	0.000	0.000	0.000
93	A	104	ARG	1	0.797	0.879	14.198	0.247	0.247	0.000	0.000	0.000	0.000
94	A	105	LEU	0	0.002	0.006	14.266	0.025	0.025	0.000	0.000	0.000	0.000
95	A	106	GLN	0	-0.046	-0.024	16.181	0.032	0.032	0.000	0.000	0.000	0.000
96	A	107	THR	0	-0.076	-0.038	18.897	0.014	0.014	0.000	0.000	0.000	0.000
97	A	108	LEU	0	-0.068	-0.012	15.235	0.007	0.007	0.000	0.000	0.000	0.000
98	A	109	GLY	0	0.031	0.013	18.802	0.010	0.010	0.000	0.000	0.000	0.000
99	A	110	THR	0	-0.063	-0.054	21.723	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	111	ILE	0	-0.088	-0.033	23.622	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	112	ASP	-1	-0.894	-0.941	25.600	0.000	0.000	0.000	0.000	0.000	0.000
102	A	113	MET	0	0.038	0.015	24.913	0.002	0.002	0.000	0.000	0.000	0.000
103	A	114	ARG	1	0.771	0.877	26.735	-0.025	-0.025	0.000	0.000	0.000	0.000
104	A	115	VAL	0	0.021	-0.005	27.054	0.003	0.003	0.000	0.000	0.000	0.000
105	A	116	ASP	-1	-0.841	-0.881	28.814	0.029	0.029	0.000	0.000	0.000	0.000
106	A	117	TYR	0	-0.016	-0.036	30.056	0.004	0.004	0.000	0.000	0.000	0.000
107	A	118	LEU	0	-0.027	0.000	28.564	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	119	ARG	1	0.866	0.922	31.236	-0.055	-0.055	0.000	0.000	0.000	0.000
109	A	120	PRO	0	-0.028	-0.018	33.786	0.001	0.001	0.000	0.000	0.000	0.000
110	A	121	GLY	0	0.094	0.049	32.296	0.002	0.002	0.000	0.000	0.000	0.000
111	A	122	ARG	1	0.855	0.925	33.039	-0.040	-0.040	0.000	0.000	0.000	0.000
112	A	123	GLY	0	0.018	0.005	31.128	0.003	0.003	0.000	0.000	0.000	0.000
113	A	124	GLN	0	-0.097	-0.063	30.762	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	125	ILE	0	0.005	-0.006	24.708	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	126	PHE	0	-0.018	-0.004	25.845	0.002	0.002	0.000	0.000	0.000	0.000
116	A	127	THR	0	-0.001	-0.014	19.585	0.012	0.012	0.000	0.000	0.000	0.000
117	A	128	GLY	0	-0.003	0.013	20.098	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	129	THR	0	-0.035	-0.016	16.042	0.017	0.017	0.000	0.000	0.000	0.000
119	A	130	GLY	0	0.057	-0.001	15.683	-0.019	-0.019	0.000	0.000	0.000	0.000
120	A	131	SER	0	-0.017	0.004	14.498	0.012	0.012	0.000	0.000	0.000	0.000
121	A	132	VAL	0	0.035	0.010	13.370	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	133	ILE	0	-0.041	-0.020	15.939	0.011	0.011	0.000	0.000	0.000	0.000
123	A	134	ARG	1	0.917	0.958	18.885	0.019	0.019	0.000	0.000	0.000	0.000
124	A	135	ALA	0	0.096	0.054	14.880	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	136	GLY	0	-0.006	-0.026	16.564	0.012	0.012	0.000	0.000	0.000	0.000
126	A	137	ASN	0	0.052	0.023	16.651	-0.023	-0.023	0.000	0.000	0.000	0.000
127	A	138	ARG	1	0.880	0.950	17.660	0.059	0.059	0.000	0.000	0.000	0.000
128	A	139	VAL	0	0.059	0.032	20.235	0.004	0.004	0.000	0.000	0.000	0.000
129	A	140	SER	0	-0.022	0.013	16.997	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	141	VAL	0	-0.013	-0.007	19.105	0.004	0.004	0.000	0.000	0.000	0.000
131	A	142	CYS	0	-0.031	-0.003	16.957	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	143	ARG	1	0.949	0.968	18.863	-0.046	-0.046	0.000	0.000	0.000	0.000
133	A	144	MET	0	-0.017	0.016	18.857	0.004	0.004	0.000	0.000	0.000	0.000
134	A	145	GLU	-1	-0.825	-0.890	20.428	0.105	0.105	0.000	0.000	0.000	0.000
135	A	146	LEU	0	0.047	0.029	21.708	0.004	0.004	0.000	0.000	0.000	0.000
136	A	147	HIS	0	-0.037	-0.036	20.699	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	148	ASN	0	0.025	0.002	25.576	0.006	0.006	0.000	0.000	0.000	0.000
138	A	149	GLU	-1	-0.709	-0.841	26.153	0.079	0.079	0.000	0.000	0.000	0.000
139	A	150	GLN	0	-0.067	-0.031	27.236	0.002	0.002	0.000	0.000	0.000	0.000
140	A	151	GLY	0	0.013	0.020	25.937	0.001	0.001	0.000	0.000	0.000	0.000
141	A	152	THR	0	-0.063	-0.030	26.993	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	153	HIS	0	0.056	0.017	23.533	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	154	ILE	0	-0.043	-0.004	27.813	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	155	ALA	0	-0.029	-0.026	27.595	-0.006	-0.006	0.000	0.000	0.000	0.000
145	A	156	PHE	0	-0.003	0.007	24.982	0.006	0.006	0.000	0.000	0.000	0.000
146	A	157	GLY	0	0.072	0.033	24.410	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	158	THR	0	-0.080	-0.053	23.161	0.005	0.005	0.000	0.000	0.000	0.000
148	A	159	GLY	0	0.038	0.040	22.498	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	160	THR	0	-0.067	-0.040	21.745	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	161	TYR	0	0.026	-0.025	18.910	0.001	0.001	0.000	0.000	0.000	0.000
151	A	162	MET	0	-0.006	0.005	20.247	-0.008	-0.008	0.000	0.000	0.000	0.000
152	A	163	VAL	0	0.022	0.007	15.766	0.000	0.000	0.000	0.000	0.000	0.000
153	A	164	GLY	0	0.001	0.017	17.127	-0.024	-0.024	0.000	0.000	0.000	0.000

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