FMO DATABASE

FMODB ID: 4JGJN

Calculation Name: 4EM8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EM8

Chain ID: A

ChEMBL ID:

UniProt ID: Q2GK74

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	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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1350397.86754
FMO2-HF: Nuclear repulsion	1292564.388743
FMO2-HF: Total energy	-57833.478797
FMO2-MP2: Total energy	-57996.705649

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:-2:GLY)

Summations of interaction energy for fragment #1(A:-2:GLY)

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.
-5.157	-1.504	0.607	-1.875	-2.386	-0.002

Interaction energy analysis for fragmet #1(A:-2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.012

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	0	MET	0	-0.020	-0.010	3.826	-0.428	0.772	-0.006	-0.609	-0.586	0.003
4	A	1	VAL	0	-0.049	-0.023	6.480	0.677	0.677	0.000	0.000	0.000	0.000
5	A	2	VAL	0	0.027	0.028	8.583	0.353	0.353	0.000	0.000	0.000	0.000
6	A	3	LYS	1	0.869	0.943	10.000	1.256	1.256	0.000	0.000	0.000	0.000
7	A	4	ARG	1	0.921	0.966	12.899	0.672	0.672	0.000	0.000	0.000	0.000
8	A	5	VAL	0	-0.018	-0.012	13.772	-0.049	-0.049	0.000	0.000	0.000	0.000
9	A	6	PHE	0	0.054	0.032	16.890	0.047	0.047	0.000	0.000	0.000	0.000
10	A	7	LEU	0	-0.037	-0.023	17.287	-0.013	-0.013	0.000	0.000	0.000	0.000
11	A	8	SER	0	-0.012	-0.032	21.028	0.024	0.024	0.000	0.000	0.000	0.000
12	A	9	SER	0	-0.063	-0.046	23.576	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	10	ASP	-1	-0.768	-0.881	26.043	-0.162	-0.162	0.000	0.000	0.000	0.000
14	A	11	HIS	0	0.086	0.045	28.600	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	12	ALA	0	-0.062	-0.029	28.846	0.002	0.002	0.000	0.000	0.000	0.000
16	A	13	GLY	0	-0.007	-0.005	25.373	0.001	0.001	0.000	0.000	0.000	0.000
17	A	14	VAL	0	0.035	0.034	24.458	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	15	GLU	-1	-0.908	-0.953	24.708	-0.171	-0.171	0.000	0.000	0.000	0.000
19	A	16	LEU	0	0.021	0.003	18.860	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	17	ARG	1	0.848	0.916	20.288	0.227	0.227	0.000	0.000	0.000	0.000
21	A	18	LEU	0	-0.028	0.000	20.701	-0.046	-0.046	0.000	0.000	0.000	0.000
22	A	19	PHE	0	0.007	0.011	16.729	-0.033	-0.033	0.000	0.000	0.000	0.000
23	A	20	LEU	0	0.016	-0.007	14.856	-0.047	-0.047	0.000	0.000	0.000	0.000
24	A	21	SER	0	-0.023	-0.020	16.064	-0.092	-0.092	0.000	0.000	0.000	0.000
25	A	22	ALA	0	-0.039	-0.025	17.386	-0.045	-0.045	0.000	0.000	0.000	0.000
26	A	23	TYR	0	0.052	0.034	9.196	-0.130	-0.130	0.000	0.000	0.000	0.000
27	A	24	LEU	0	0.031	-0.004	11.625	-0.112	-0.112	0.000	0.000	0.000	0.000
28	A	25	ARG	1	0.942	0.965	13.343	0.349	0.349	0.000	0.000	0.000	0.000
29	A	26	ASP	-1	-0.929	-0.947	13.999	-0.513	-0.513	0.000	0.000	0.000	0.000
30	A	27	LEU	0	-0.036	-0.011	8.082	-0.084	-0.084	0.000	0.000	0.000	0.000
31	A	28	GLY	0	-0.015	-0.020	10.515	-0.243	-0.243	0.000	0.000	0.000	0.000
32	A	29	CYS	0	-0.152	-0.070	11.875	-0.124	-0.124	0.000	0.000	0.000	0.000
33	A	30	GLU	-1	-0.857	-0.927	13.876	-0.426	-0.426	0.000	0.000	0.000	0.000
34	A	31	VAL	0	-0.047	-0.035	16.368	-0.042	-0.042	0.000	0.000	0.000	0.000
35	A	32	PHE	0	-0.021	-0.006	18.694	0.057	0.057	0.000	0.000	0.000	0.000
36	A	33	ASP	-1	-0.875	-0.927	21.992	-0.300	-0.300	0.000	0.000	0.000	0.000
37	A	34	CYS	0	-0.015	-0.013	24.094	0.014	0.014	0.000	0.000	0.000	0.000
38	A	35	GLY	0	0.015	0.031	26.417	0.021	0.021	0.000	0.000	0.000	0.000
39	A	36	CYS	0	0.016	-0.005	26.815	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.803	-0.907	29.435	-0.171	-0.171	0.000	0.000	0.000	0.000
41	A	38	PRO	0	0.033	-0.004	28.948	0.007	0.007	0.000	0.000	0.000	0.000
42	A	39	LYS	1	0.843	0.922	31.405	0.151	0.151	0.000	0.000	0.000	0.000
43	A	40	GLU	-1	-0.959	-0.963	33.751	-0.120	-0.120	0.000	0.000	0.000	0.000
44	A	41	HIS	0	-0.053	-0.046	33.927	0.001	0.001	0.000	0.000	0.000	0.000
45	A	42	SER	0	-0.039	-0.031	35.555	0.004	0.004	0.000	0.000	0.000	0.000
46	A	43	VAL	0	-0.018	0.013	32.195	0.000	0.000	0.000	0.000	0.000	0.000
47	A	44	ASP	-1	-0.845	-0.918	34.344	-0.118	-0.118	0.000	0.000	0.000	0.000
48	A	45	TYR	0	-0.050	-0.039	28.865	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	46	PRO	0	-0.026	-0.029	29.954	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	47	ASP	-1	-0.882	-0.934	31.568	-0.151	-0.151	0.000	0.000	0.000	0.000
51	A	48	TYR	0	0.009	0.001	28.249	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	49	VAL	0	-0.024	0.013	26.225	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	50	HIS	0	-0.032	-0.022	26.755	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	51	ASP	-1	-0.825	-0.922	27.741	-0.238	-0.238	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.011	0.014	21.694	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	53	VAL	0	-0.031	-0.030	23.601	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	54	ARG	1	0.885	0.929	24.698	0.219	0.219	0.000	0.000	0.000	0.000
58	A	55	GLU	-1	-0.912	-0.945	23.215	-0.323	-0.323	0.000	0.000	0.000	0.000
59	A	56	VAL	0	-0.113	-0.037	18.770	-0.043	-0.043	0.000	0.000	0.000	0.000
60	A	57	SER	0	-0.045	-0.039	18.972	0.030	0.030	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.939	-0.966	16.760	-0.532	-0.532	0.000	0.000	0.000	0.000
62	A	59	THR	0	0.027	-0.026	15.347	-0.101	-0.101	0.000	0.000	0.000	0.000
63	A	60	SER	0	-0.065	0.009	16.282	-0.055	-0.055	0.000	0.000	0.000	0.000
64	A	61	PHE	0	0.063	0.039	11.100	0.043	0.043	0.000	0.000	0.000	0.000
65	A	62	GLY	0	0.034	0.017	16.340	0.030	0.030	0.000	0.000	0.000	0.000
66	A	63	VAL	0	-0.039	-0.021	15.794	-0.033	-0.033	0.000	0.000	0.000	0.000
67	A	64	LEU	0	0.025	0.009	18.531	0.036	0.036	0.000	0.000	0.000	0.000
68	A	65	ILE	0	-0.024	-0.010	20.013	0.007	0.007	0.000	0.000	0.000	0.000
69	A	66	CYS	0	0.007	0.040	23.295	0.014	0.014	0.000	0.000	0.000	0.000
70	A	67	GLY	0	0.041	0.015	25.623	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	68	THR	0	0.025	0.001	26.603	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	69	GLY	0	0.074	0.027	23.600	0.000	0.000	0.000	0.000	0.000	0.000
73	A	70	ILE	0	-0.003	-0.015	24.506	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	71	GLY	0	0.006	-0.006	26.920	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	72	MET	0	0.058	0.024	24.335	0.003	0.003	0.000	0.000	0.000	0.000
76	A	73	SER	0	0.006	0.001	23.106	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	74	ILE	0	-0.052	-0.025	24.689	0.000	0.000	0.000	0.000	0.000	0.000
78	A	75	ALA	0	-0.011	-0.009	28.234	0.002	0.002	0.000	0.000	0.000	0.000
79	A	76	ALA	0	0.037	0.015	23.553	0.000	0.000	0.000	0.000	0.000	0.000
80	A	77	ASN	0	0.008	-0.006	22.972	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	78	ARG	1	0.886	0.958	26.117	0.153	0.153	0.000	0.000	0.000	0.000
82	A	79	HIS	0	-0.004	0.016	26.482	0.011	0.011	0.000	0.000	0.000	0.000
83	A	80	LYS	1	0.903	0.929	26.060	0.129	0.129	0.000	0.000	0.000	0.000
84	A	81	ASN	0	0.006	0.016	23.576	0.020	0.020	0.000	0.000	0.000	0.000
85	A	82	ILE	0	-0.049	-0.003	21.540	-0.042	-0.042	0.000	0.000	0.000	0.000
86	A	83	ARG	1	0.858	0.936	17.219	0.403	0.403	0.000	0.000	0.000	0.000
87	A	84	ALA	0	-0.005	-0.012	18.667	-0.048	-0.048	0.000	0.000	0.000	0.000
88	A	85	ALA	0	0.011	-0.002	17.285	0.042	0.042	0.000	0.000	0.000	0.000
89	A	86	LEU	0	-0.014	0.019	18.457	-0.038	-0.038	0.000	0.000	0.000	0.000
90	A	87	CYS	0	-0.068	-0.013	15.506	0.022	0.022	0.000	0.000	0.000	0.000
91	A	88	SER	0	0.023	-0.001	17.542	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	89	SER	0	0.019	0.011	15.656	0.025	0.025	0.000	0.000	0.000	0.000
93	A	90	THR	0	0.091	0.036	10.209	-0.052	-0.052	0.000	0.000	0.000	0.000
94	A	91	MET	0	-0.001	0.013	11.664	-0.043	-0.043	0.000	0.000	0.000	0.000
95	A	92	LEU	0	0.026	-0.002	13.771	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	93	ALA	0	0.056	0.031	11.041	-0.022	-0.022	0.000	0.000	0.000	0.000
97	A	94	LYS	1	0.887	0.926	8.996	-0.307	-0.307	0.000	0.000	0.000	0.000
98	A	95	LEU	0	-0.031	-0.020	10.939	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	96	SER	0	-0.001	0.006	13.854	-0.032	-0.032	0.000	0.000	0.000	0.000
100	A	97	ARG	1	0.809	0.912	9.458	0.982	0.982	0.000	0.000	0.000	0.000
101	A	98	GLU	-1	-0.833	-0.918	10.049	0.225	0.225	0.000	0.000	0.000	0.000
102	A	99	HIS	0	-0.036	-0.031	12.331	0.011	0.011	0.000	0.000	0.000	0.000
103	A	100	ASN	0	-0.017	-0.031	15.879	0.019	0.019	0.000	0.000	0.000	0.000
104	A	101	ASP	-1	-0.833	-0.899	13.903	-0.559	-0.559	0.000	0.000	0.000	0.000
105	A	102	ALA	0	-0.024	-0.011	14.748	-0.016	-0.016	0.000	0.000	0.000	0.000
106	A	103	ASN	0	0.062	0.027	14.239	-0.079	-0.079	0.000	0.000	0.000	0.000
107	A	104	VAL	0	0.021	0.016	16.325	-0.031	-0.031	0.000	0.000	0.000	0.000
108	A	105	LEU	0	-0.009	0.012	13.055	0.041	0.041	0.000	0.000	0.000	0.000
109	A	106	CYS	0	-0.053	-0.018	16.843	0.023	0.023	0.000	0.000	0.000	0.000
110	A	107	PHE	0	0.075	0.016	14.546	0.013	0.013	0.000	0.000	0.000	0.000
111	A	108	GLY	0	0.022	-0.006	20.422	0.009	0.009	0.000	0.000	0.000	0.000
112	A	109	SER	0	-0.041	-0.033	23.059	0.013	0.013	0.000	0.000	0.000	0.000
113	A	110	ARG	1	0.930	0.961	24.067	0.123	0.123	0.000	0.000	0.000	0.000
114	A	111	TYR	0	-0.043	-0.023	24.783	0.014	0.014	0.000	0.000	0.000	0.000
115	A	112	ILE	0	-0.046	-0.002	17.235	0.010	0.010	0.000	0.000	0.000	0.000
116	A	113	ASP	-1	-0.778	-0.838	19.554	-0.102	-0.102	0.000	0.000	0.000	0.000
117	A	114	PRO	0	0.041	0.004	18.878	-0.021	-0.021	0.000	0.000	0.000	0.000
118	A	115	ASP	-1	-0.834	-0.906	16.319	-0.181	-0.181	0.000	0.000	0.000	0.000
119	A	116	THR	0	-0.073	-0.095	14.745	-0.014	-0.014	0.000	0.000	0.000	0.000
120	A	117	ALA	0	-0.047	-0.033	14.261	-0.048	-0.048	0.000	0.000	0.000	0.000
121	A	118	GLN	0	0.036	0.025	11.779	-0.087	-0.087	0.000	0.000	0.000	0.000
122	A	119	SER	0	-0.008	0.000	10.012	-0.145	-0.145	0.000	0.000	0.000	0.000
123	A	120	VAL	0	-0.078	-0.044	9.440	-0.142	-0.142	0.000	0.000	0.000	0.000
124	A	121	LEU	0	0.048	0.014	10.585	-0.106	-0.106	0.000	0.000	0.000	0.000
125	A	122	TYR	0	0.021	0.023	2.553	-2.703	-1.682	0.284	-0.585	-0.720	-0.003
126	A	123	THR	0	-0.022	-0.004	6.067	-0.672	-0.672	0.000	0.000	0.000	0.000
127	A	124	PHE	0	-0.045	-0.014	7.017	-0.257	-0.257	0.000	0.000	0.000	0.000
128	A	125	MET	0	0.003	0.000	7.596	0.113	0.113	0.000	0.000	0.000	0.000
129	A	126	THR	0	-0.042	-0.020	2.675	-0.762	0.111	0.310	-0.431	-0.752	0.000
130	A	127	THR	0	-0.072	-0.026	3.512	-0.321	0.238	0.019	-0.250	-0.328	-0.002
131	A	128	ALA	0	0.029	0.006	6.167	0.001	0.001	0.000	0.000	0.000	0.000
132	A	129	PHE	0	-0.010	0.002	7.926	0.225	0.225	0.000	0.000	0.000	0.000
133	A	130	LEU	0	-0.014	-0.019	10.901	0.042	0.042	0.000	0.000	0.000	0.000
134	A	131	GLY	0	0.005	0.028	13.124	0.036	0.036	0.000	0.000	0.000	0.000
135	A	132	GLY	0	0.028	-0.002	16.357	0.030	0.030	0.000	0.000	0.000	0.000
136	A	133	ARG	1	0.916	0.934	19.005	-0.031	-0.031	0.000	0.000	0.000	0.000
137	A	134	HIS	0	0.015	0.013	16.649	-0.016	-0.016	0.000	0.000	0.000	0.000
138	A	135	ALA	0	0.029	0.030	19.492	-0.020	-0.020	0.000	0.000	0.000	0.000
139	A	136	VAL	0	0.029	0.017	20.494	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	137	ARG	1	0.900	0.942	22.384	0.042	0.042	0.000	0.000	0.000	0.000
141	A	138	VAL	0	0.055	0.031	18.240	0.001	0.001	0.000	0.000	0.000	0.000
142	A	139	GLN	0	-0.006	0.003	21.640	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	140	LYS	1	0.973	0.971	24.169	0.077	0.077	0.000	0.000	0.000	0.000
144	A	141	LEU	0	-0.069	-0.025	21.686	0.004	0.004	0.000	0.000	0.000	0.000
145	A	142	GLY	0	0.031	0.034	25.555	-0.007	-0.007	0.000	0.000	0.000	0.000
146	A	143	GLU	-1	-0.972	-0.963	26.356	-0.111	-0.111	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:GLY)