FMO DATABASE

FMODB ID: GN2R1

Calculation Name: 4EXW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EXW

Chain ID: A

ChEMBL ID:

UniProt ID: Q1J1N6

Base Structure: X-ray

Registration Date: 2023-06-19

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1094559.729467
FMO2-HF: Nuclear repulsion	1043090.590247
FMO2-HF: Total energy	-51469.139221
FMO2-MP2: Total energy	-51621.404423

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:-5:GLY)

Summations of interaction energy for fragment #1(A:-5: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.
0.348	1.288	-0.001	-0.346	-0.593	0.001

Interaction energy analysis for fragmet #1(A:-5:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.026

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

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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	-3	ASP	-1	-0.795	-0.878	3.849	-0.728	0.212	-0.001	-0.346	-0.593	0.001
4	A	-2	PRO	0	-0.044	-0.031	6.163	0.289	0.289	0.000	0.000	0.000	0.000
5	A	-1	PHE	0	-0.054	-0.018	9.012	0.136	0.136	0.000	0.000	0.000	0.000
6	A	0	THR	0	-0.056	-0.046	9.940	0.000	0.000	0.000	0.000	0.000	0.000
7	A	1	MET	0	-0.019	0.000	12.291	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	2	LEU	0	-0.005	0.006	10.851	-0.032	-0.032	0.000	0.000	0.000	0.000
9	A	3	HIS	1	0.793	0.868	15.026	0.282	0.282	0.000	0.000	0.000	0.000
10	A	4	ILE	0	-0.004	0.013	17.952	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	5	GLU	-1	-0.795	-0.878	19.815	-0.108	-0.108	0.000	0.000	0.000	0.000
12	A	6	PHE	0	0.005	0.000	21.944	0.000	0.000	0.000	0.000	0.000	0.000
13	A	7	ILE	0	-0.017	0.005	25.920	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	8	THR	0	-0.003	-0.009	29.435	0.004	0.004	0.000	0.000	0.000	0.000
15	A	9	ASP	-1	-0.816	-0.912	31.278	-0.027	-0.027	0.000	0.000	0.000	0.000
16	A	10	LEU	0	-0.057	-0.025	34.173	0.001	0.001	0.000	0.000	0.000	0.000
17	A	11	GLY	0	-0.010	-0.001	34.188	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	12	ALA	0	-0.030	-0.005	33.240	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	13	LYS	1	0.843	0.901	27.278	0.112	0.112	0.000	0.000	0.000	0.000
20	A	14	VAL	0	0.002	-0.004	27.309	0.000	0.000	0.000	0.000	0.000	0.000
21	A	15	THR	0	-0.013	-0.008	22.594	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	16	VAL	0	-0.036	-0.015	22.054	0.012	0.012	0.000	0.000	0.000	0.000
23	A	17	ASP	-1	-0.801	-0.893	19.973	-0.173	-0.173	0.000	0.000	0.000	0.000
24	A	18	VAL	0	-0.037	-0.025	15.270	0.028	0.028	0.000	0.000	0.000	0.000
25	A	19	GLU	-1	-0.830	-0.891	15.453	0.022	0.022	0.000	0.000	0.000	0.000
26	A	20	SER	0	0.039	0.001	10.549	-0.039	-0.039	0.000	0.000	0.000	0.000
27	A	21	ALA	0	0.022	-0.006	8.284	0.039	0.039	0.000	0.000	0.000	0.000
28	A	22	ASP	-1	-0.888	-0.932	8.543	0.636	0.636	0.000	0.000	0.000	0.000
29	A	23	LYS	1	0.843	0.909	10.899	-0.088	-0.088	0.000	0.000	0.000	0.000
30	A	24	LEU	0	-0.018	-0.002	13.073	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	25	LEU	0	0.014	-0.006	12.807	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	26	ASP	-1	-0.880	-0.939	16.103	0.130	0.130	0.000	0.000	0.000	0.000
33	A	27	VAL	0	0.011	0.005	18.322	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	28	GLN	0	-0.015	-0.017	16.529	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	29	ARG	1	0.800	0.882	18.106	-0.091	-0.091	0.000	0.000	0.000	0.000
36	A	30	GLN	0	-0.021	0.006	22.247	0.010	0.010	0.000	0.000	0.000	0.000
37	A	31	TYR	0	0.007	-0.008	23.377	0.002	0.002	0.000	0.000	0.000	0.000
38	A	32	GLY	0	0.044	0.035	24.420	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	33	ARG	1	0.757	0.844	24.432	-0.031	-0.031	0.000	0.000	0.000	0.000
40	A	34	LEU	0	-0.044	-0.014	28.176	0.003	0.003	0.000	0.000	0.000	0.000
41	A	35	GLY	0	-0.030	-0.007	29.521	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	36	TRP	0	-0.044	-0.022	26.947	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	37	THR	0	-0.020	-0.005	26.158	0.003	0.003	0.000	0.000	0.000	0.000
44	A	38	SER	0	-0.025	-0.025	21.723	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	39	GLY	0	0.005	0.004	23.175	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	40	GLU	-1	-0.786	-0.868	24.023	-0.061	-0.061	0.000	0.000	0.000	0.000
47	A	41	VAL	0	-0.023	0.006	25.208	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	42	PRO	0	-0.028	0.003	24.012	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	43	VAL	0	0.065	0.018	26.818	0.009	0.009	0.000	0.000	0.000	0.000
50	A	44	GLY	0	0.019	0.013	29.122	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	45	GLY	0	-0.022	-0.009	28.485	0.008	0.008	0.000	0.000	0.000	0.000
52	A	46	TYR	0	-0.003	-0.022	22.703	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	47	GLN	0	-0.016	-0.007	22.932	0.015	0.015	0.000	0.000	0.000	0.000
54	A	48	PHE	0	0.016	0.011	20.411	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	49	PRO	0	0.027	0.004	19.329	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	50	LEU	0	-0.006	-0.001	22.375	0.003	0.003	0.000	0.000	0.000	0.000
57	A	51	GLU	-1	-0.846	-0.934	22.692	0.079	0.079	0.000	0.000	0.000	0.000
58	A	52	ASN	0	-0.007	-0.007	20.649	0.009	0.009	0.000	0.000	0.000	0.000
59	A	53	GLU	-1	-0.775	-0.833	24.032	0.018	0.018	0.000	0.000	0.000	0.000
60	A	54	PRO	0	-0.018	-0.009	27.118	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	55	ASP	-1	-0.806	-0.896	24.299	0.086	0.086	0.000	0.000	0.000	0.000
62	A	56	PHE	0	0.025	0.019	21.229	0.008	0.008	0.000	0.000	0.000	0.000
63	A	57	ASP	-1	-0.747	-0.828	22.376	0.040	0.040	0.000	0.000	0.000	0.000
64	A	58	TRP	0	0.028	-0.009	23.655	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	59	SER	0	-0.024	-0.015	24.304	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	60	LEU	0	-0.027	-0.010	18.785	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	61	ILE	0	-0.050	-0.020	21.812	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	62	GLY	0	0.035	0.021	24.543	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	63	ALA	0	-0.089	-0.039	27.223	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	64	ARG	1	0.927	0.960	28.902	0.004	0.004	0.000	0.000	0.000	0.000
71	A	65	LYS	1	0.924	0.951	31.433	-0.026	-0.026	0.000	0.000	0.000	0.000
72	A	66	TRP	0	-0.019	-0.031	33.998	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	67	THR	0	0.024	0.016	37.760	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	68	ASN	0	-0.056	-0.032	40.749	0.001	0.001	0.000	0.000	0.000	0.000
75	A	69	PRO	0	-0.024	-0.016	43.394	0.001	0.001	0.000	0.000	0.000	0.000
76	A	70	GLU	-1	-0.881	-0.929	47.125	0.000	0.000	0.000	0.000	0.000	0.000
77	A	71	GLY	0	-0.006	0.007	45.629	0.001	0.001	0.000	0.000	0.000	0.000
78	A	72	GLU	-1	-0.936	-0.971	41.220	0.002	0.002	0.000	0.000	0.000	0.000
79	A	73	GLU	-1	-0.830	-0.903	35.932	0.016	0.016	0.000	0.000	0.000	0.000
80	A	74	MET	0	-0.054	-0.013	37.523	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	75	ILE	0	-0.018	-0.008	30.974	0.003	0.003	0.000	0.000	0.000	0.000
82	A	76	LEU	0	-0.043	-0.025	33.934	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	77	HIS	0	0.023	-0.010	28.226	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	78	ARG	1	0.839	0.876	29.197	0.059	0.059	0.000	0.000	0.000	0.000
85	A	79	GLY	0	0.035	0.033	34.047	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	80	HIS	0	-0.059	-0.034	36.155	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	81	ALA	0	0.041	0.016	36.302	0.001	0.001	0.000	0.000	0.000	0.000
88	A	82	TYR	0	-0.039	-0.023	33.999	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	83	ARG	1	0.992	1.008	36.073	0.011	0.011	0.000	0.000	0.000	0.000
90	A	84	ARG	1	0.758	0.835	32.830	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	85	ARG	1	0.895	0.937	35.255	0.011	0.011	0.000	0.000	0.000	0.000
92	A	86	GLU	-1	-0.797	-0.882	34.887	0.015	0.015	0.000	0.000	0.000	0.000
93	A	87	LEU	0	-0.050	-0.032	33.998	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	88	GLU	-1	-0.797	-0.878	35.020	0.012	0.012	0.000	0.000	0.000	0.000
95	A	89	ALA	0	-0.117	-0.070	35.038	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	99	ALA	0	0.017	0.011	31.707	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	100	ALA	0	-0.077	-0.050	30.411	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	101	VAL	0	0.015	0.022	30.356	0.001	0.001	0.000	0.000	0.000	0.000
99	A	102	LYS	1	0.852	0.940	30.482	0.022	0.022	0.000	0.000	0.000	0.000
100	A	103	TYR	0	0.022	-0.015	30.523	0.002	0.002	0.000	0.000	0.000	0.000
101	A	104	SER	0	-0.068	-0.037	32.936	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	105	ARG	1	0.886	0.944	35.309	0.034	0.034	0.000	0.000	0.000	0.000
103	A	106	GLY	0	0.033	0.018	38.800	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	107	ALA	0	0.000	0.003	40.829	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	108	LYS	1	0.823	0.902	39.605	0.033	0.033	0.000	0.000	0.000	0.000
106	A	109	ASN	0	0.021	0.000	43.677	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	110	THR	0	-0.002	-0.001	42.412	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	111	ASP	-1	-0.786	-0.886	38.446	-0.034	-0.034	0.000	0.000	0.000	0.000
109	A	112	PRO	0	-0.040	-0.001	37.783	0.002	0.002	0.000	0.000	0.000	0.000
110	A	113	GLU	-1	-0.949	-0.965	36.286	-0.049	-0.049	0.000	0.000	0.000	0.000
111	A	124	GLU	-1	-0.906	-0.949	42.202	-0.022	-0.022	0.000	0.000	0.000	0.000
112	A	125	TYR	0	-0.055	-0.042	38.688	0.002	0.002	0.000	0.000	0.000	0.000
113	A	126	VAL	0	0.057	0.035	34.644	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	127	THR	0	-0.059	-0.054	31.189	0.006	0.006	0.000	0.000	0.000	0.000
115	A	128	LEU	0	0.029	0.041	28.907	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	129	ALA	0	0.000	-0.008	26.995	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	130	ILE	0	-0.044	-0.027	26.988	0.004	0.004	0.000	0.000	0.000	0.000
118	A	131	PHE	0	0.003	0.021	24.451	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	132	ARG	1	0.954	0.951	25.552	0.031	0.031	0.000	0.000	0.000	0.000
120	A	133	GLY	0	0.039	0.035	24.952	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	134	GLY	0	-0.005	-0.003	21.273	0.003	0.003	0.000	0.000	0.000	0.000
122	A	135	LYS	1	0.970	0.982	14.691	-0.082	-0.082	0.000	0.000	0.000	0.000
123	A	136	ARG	1	0.780	0.862	18.930	-0.109	-0.109	0.000	0.000	0.000	0.000
124	A	137	GLN	0	-0.050	-0.030	13.677	0.005	0.005	0.000	0.000	0.000	0.000
125	A	138	GLU	-1	-0.764	-0.876	16.670	0.147	0.147	0.000	0.000	0.000	0.000
126	A	139	ARG	1	0.871	0.943	12.154	-0.069	-0.069	0.000	0.000	0.000	0.000
127	A	140	TYR	0	-0.013	-0.020	15.862	-0.029	-0.029	0.000	0.000	0.000	0.000
128	A	141	ALA	0	0.045	0.044	18.972	-0.017	-0.017	0.000	0.000	0.000	0.000
129	A	142	VAL	0	0.002	0.009	21.256	0.004	0.004	0.000	0.000	0.000	0.000
130	A	143	PRO	0	-0.016	0.006	21.341	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-5:GLY)