FMO DATABASE

FMODB ID: VKQ81

Calculation Name: 1GRJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GRJ

Chain ID: A

ChEMBL ID:

UniProt ID: P0A6W5

Base Structure: X-ray

Registration Date: 2023-09-27

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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1340135.136064
FMO2-HF: Nuclear repulsion	1279036.87829
FMO2-HF: Total energy	-61098.257773
FMO2-MP2: Total energy	-61278.234199

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:GLN)

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

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.
-5.005	-2.766	5.755	-2.868	-5.126	0.026

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.031

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	4	ILE	0	0.005	-0.015	1.953	-2.013	-0.543	3.755	-1.896	-3.329	0.013
4	A	5	PRO	0	-0.026	-0.006	5.502	-0.546	-0.478	-0.001	-0.007	-0.060	0.000
5	A	6	MET	0	-0.025	0.001	9.093	-0.257	-0.257	0.000	0.000	0.000	0.000
6	A	7	THR	0	0.006	-0.003	11.753	0.028	0.028	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.015	0.003	15.432	0.032	0.032	0.000	0.000	0.000	0.000
8	A	9	ARG	0	0.072	0.061	17.745	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.031	0.024	16.207	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.019	-0.013	14.235	0.011	0.011	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.967	-0.988	15.623	0.380	0.380	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.856	0.933	18.736	-0.288	-0.288	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.013	-0.008	13.002	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.920	0.940	14.215	-0.736	-0.736	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.852	-0.902	18.488	0.216	0.216	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.820	-0.888	19.189	0.224	0.224	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.008	-0.006	16.468	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.869	-0.919	19.918	0.197	0.197	0.000	0.000	0.000	0.000
19	A	20	PHE	0	0.051	0.040	23.303	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.020	-0.011	20.472	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.801	0.872	18.531	-0.366	-0.366	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.090	-0.068	24.254	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	24	VAL	0	-0.012	-0.002	27.385	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.814	0.876	26.678	-0.098	-0.098	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.844	0.889	21.886	-0.178	-0.178	0.000	0.000	0.000	0.000
26	A	27	PRO	0	-0.031	-0.018	27.775	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.810	-0.894	31.231	0.074	0.074	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.021	0.001	27.631	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.043	-0.038	30.062	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.013	0.001	32.729	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.021	0.019	34.580	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.014	-0.013	31.452	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.110	-0.061	36.035	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.856	-0.925	38.286	0.023	0.023	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.082	0.055	38.852	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.879	0.928	35.333	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.972	-0.965	41.084	0.021	0.021	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.116	-0.061	43.682	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	40	GLY	0	-0.052	-0.012	43.959	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.877	-0.956	43.974	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.017	-0.021	38.682	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.810	0.899	39.719	0.024	0.024	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.819	-0.890	40.432	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.037	-0.002	40.344	0.003	0.003	0.000	0.000	0.000	0.000
45	A	46	ALA	0	0.059	0.026	39.111	0.000	0.000	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.849	-0.932	37.647	0.010	0.010	0.000	0.000	0.000	0.000
47	A	48	TYR	0	-0.009	-0.014	35.341	0.007	0.007	0.000	0.000	0.000	0.000
48	A	49	HIS	0	-0.066	-0.054	34.589	0.005	0.005	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.049	0.045	33.091	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.009	-0.002	32.057	0.005	0.005	0.000	0.000	0.000	0.000
51	A	52	ARG	1	0.840	0.899	29.847	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.915	-0.952	28.983	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	54	GLN	0	0.045	0.010	27.277	0.013	0.013	0.000	0.000	0.000	0.000
54	A	55	GLN	0	0.054	0.047	26.449	0.001	0.001	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.013	0.002	24.225	0.012	0.012	0.000	0.000	0.000	0.000
56	A	57	PHE	0	-0.043	-0.022	22.611	0.011	0.011	0.000	0.000	0.000	0.000
57	A	58	CYS	0	0.011	0.000	21.709	0.015	0.015	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.775	-0.840	21.570	0.172	0.172	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.067	-0.030	18.635	0.027	0.027	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.762	0.832	14.720	-0.246	-0.246	0.000	0.000	0.000	0.000
61	A	62	ILE	0	0.045	0.023	16.982	0.058	0.058	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.903	0.951	14.778	0.020	0.020	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.878	-0.919	12.451	0.392	0.392	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.041	0.027	12.017	0.166	0.166	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.805	-0.886	12.740	0.538	0.538	0.000	0.000	0.000	0.000
66	A	67	ALA	0	0.002	-0.001	9.057	0.161	0.161	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.824	0.882	8.387	0.140	0.140	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.047	-0.024	8.553	0.369	0.369	0.000	0.000	0.000	0.000
69	A	70	SER	0	-0.092	-0.033	8.977	-0.110	-0.110	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.120	-0.067	2.208	-3.943	-3.242	2.001	-0.965	-1.737	0.013
71	A	72	ALA	0	0.001	0.005	5.723	0.593	0.593	0.000	0.000	0.000	0.000
72	A	73	GLN	0	-0.031	-0.015	6.689	-0.416	-0.416	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.016	-0.031	9.288	-0.122	-0.122	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.026	0.008	11.298	-0.069	-0.069	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.760	-0.894	14.686	0.361	0.361	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.009	-0.014	17.991	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.030	0.031	19.961	-0.040	-0.040	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.796	0.891	20.959	-0.428	-0.428	0.000	0.000	0.000	0.000
79	A	80	MET	0	-0.049	-0.011	16.300	0.007	0.007	0.000	0.000	0.000	0.000
80	A	81	PRO	0	-0.015	0.000	22.462	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	82	ASN	0	0.014	-0.022	24.276	0.024	0.024	0.000	0.000	0.000	0.000
82	A	83	ASN	0	-0.013	-0.007	22.451	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	84	GLY	0	0.083	0.060	25.297	-0.018	-0.018	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.746	0.842	21.550	-0.171	-0.171	0.000	0.000	0.000	0.000
85	A	86	VAL	0	-0.005	0.004	19.282	0.035	0.035	0.000	0.000	0.000	0.000
86	A	87	ILE	0	0.008	0.012	16.534	0.020	0.020	0.000	0.000	0.000	0.000
87	A	88	PHE	0	0.000	-0.010	12.352	-0.028	-0.028	0.000	0.000	0.000	0.000
88	A	89	GLY	0	0.023	-0.009	15.185	0.058	0.058	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.079	-0.022	17.524	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	91	THR	0	0.017	-0.003	20.699	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	92	VAL	0	-0.030	-0.032	22.122	0.002	0.002	0.000	0.000	0.000	0.000
92	A	93	THR	0	0.056	0.049	24.857	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	94	VAL	0	-0.048	-0.033	25.444	0.001	0.001	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.041	0.033	28.426	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	96	ASN	0	-0.045	-0.003	30.197	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	97	LEU	0	0.056	0.012	32.060	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.930	-0.936	34.363	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	99	SER	0	-0.165	-0.115	34.193	0.003	0.003	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.874	-0.941	35.895	0.027	0.027	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-0.968	-0.973	30.648	0.023	0.023	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.874	-0.946	31.928	0.065	0.065	0.000	0.000	0.000	0.000
102	A	103	GLN	0	-0.057	-0.016	27.773	0.010	0.010	0.000	0.000	0.000	0.000
103	A	104	THR	0	-0.001	-0.012	26.531	0.004	0.004	0.000	0.000	0.000	0.000
104	A	105	TYR	0	-0.034	-0.013	22.003	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	106	ARG	1	0.849	0.909	18.585	-0.292	-0.292	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.023	-0.001	15.187	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	108	VAL	0	0.000	0.005	14.909	0.077	0.077	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.037	0.013	11.051	-0.043	-0.043	0.000	0.000	0.000	0.000
109	A	110	ASP	-1	-0.810	-0.896	8.954	-0.367	-0.367	0.000	0.000	0.000	0.000
110	A	111	ASP	-1	-0.853	-0.891	11.330	0.334	0.334	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.730	-0.853	13.079	0.408	0.408	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.064	-0.016	14.563	-0.028	-0.028	0.000	0.000	0.000	0.000
113	A	114	ASP	-1	-0.781	-0.884	16.290	0.043	0.043	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.017	-0.012	19.894	0.002	0.002	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.853	0.918	21.510	-0.037	-0.037	0.000	0.000	0.000	0.000
116	A	117	GLN	0	-0.063	-0.033	23.280	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	118	ASN	0	0.000	-0.005	23.742	0.010	0.010	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.034	0.006	19.235	0.021	0.021	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.027	0.005	18.164	-0.026	-0.026	0.000	0.000	0.000	0.000
120	A	121	SER	0	0.050	-0.002	12.047	0.061	0.061	0.000	0.000	0.000	0.000
121	A	122	VAL	0	0.003	-0.016	9.837	-0.033	-0.033	0.000	0.000	0.000	0.000
122	A	123	ASN	0	-0.152	-0.070	7.877	-0.087	-0.087	0.000	0.000	0.000	0.000
123	A	124	SER	0	0.013	-0.017	12.172	-0.024	-0.024	0.000	0.000	0.000	0.000
124	A	125	PRO	0	-0.022	-0.023	15.891	0.011	0.011	0.000	0.000	0.000	0.000
125	A	126	ILE	0	0.085	0.051	18.662	0.011	0.011	0.000	0.000	0.000	0.000
126	A	127	ALA	0	0.019	0.023	15.892	0.027	0.027	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.927	0.958	13.337	0.333	0.333	0.000	0.000	0.000	0.000
128	A	129	GLY	0	0.014	-0.006	17.059	0.020	0.020	0.000	0.000	0.000	0.000
129	A	130	LEU	0	0.046	0.026	20.129	0.016	0.016	0.000	0.000	0.000	0.000
130	A	131	ILE	0	-0.023	-0.008	14.963	0.037	0.037	0.000	0.000	0.000	0.000
131	A	132	GLY	0	-0.065	-0.046	18.444	-0.028	-0.028	0.000	0.000	0.000	0.000
132	A	133	LYS	1	0.816	0.935	19.604	-0.061	-0.061	0.000	0.000	0.000	0.000
133	A	134	GLU	-1	-0.812	-0.884	23.119	0.183	0.183	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.808	-0.893	25.795	0.120	0.120	0.000	0.000	0.000	0.000
135	A	136	ASP	-1	-0.906	-0.948	29.011	0.081	0.081	0.000	0.000	0.000	0.000
136	A	137	ASP	-1	-0.903	-0.942	26.147	0.082	0.082	0.000	0.000	0.000	0.000
137	A	138	VAL	0	0.025	0.013	29.110	0.000	0.000	0.000	0.000	0.000	0.000
138	A	139	VAL	0	-0.075	-0.052	24.611	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	140	VAL	0	0.011	0.002	27.390	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	141	ILE	0	-0.018	0.013	22.643	-0.018	-0.018	0.000	0.000	0.000	0.000
141	A	142	LYS	1	0.804	0.882	23.216	0.132	0.132	0.000	0.000	0.000	0.000
142	A	143	THR	0	-0.074	-0.030	23.361	-0.020	-0.020	0.000	0.000	0.000	0.000
143	A	144	PRO	0	0.026	0.018	24.416	-0.009	-0.009	0.000	0.000	0.000	0.000
144	A	145	GLY	0	-0.016	-0.007	26.454	-0.005	-0.005	0.000	0.000	0.000	0.000
145	A	146	GLY	0	-0.043	-0.039	27.547	0.008	0.008	0.000	0.000	0.000	0.000
146	A	147	GLU	-1	-0.825	-0.912	26.565	-0.120	-0.120	0.000	0.000	0.000	0.000
147	A	148	VAL	0	-0.025	-0.003	28.563	0.003	0.003	0.000	0.000	0.000	0.000
148	A	149	GLU	-1	-0.888	-0.929	28.850	-0.011	-0.011	0.000	0.000	0.000	0.000
149	A	150	PHE	0	-0.056	-0.023	27.473	-0.004	-0.004	0.000	0.000	0.000	0.000
150	A	151	GLU	-1	-0.871	-0.938	29.410	0.045	0.045	0.000	0.000	0.000	0.000
151	A	152	VAL	0	-0.029	-0.010	25.674	0.003	0.003	0.000	0.000	0.000	0.000
152	A	153	ILE	0	0.055	0.036	28.428	0.008	0.008	0.000	0.000	0.000	0.000
153	A	154	LYS	1	0.785	0.870	29.201	-0.108	-0.108	0.000	0.000	0.000	0.000
154	A	155	VAL	0	-0.028	-0.009	23.757	0.003	0.003	0.000	0.000	0.000	0.000
155	A	156	GLU	-1	-0.887	-0.938	25.761	0.165	0.165	0.000	0.000	0.000	0.000
156	A	157	TYR	0	-0.117	-0.073	21.738	0.028	0.028	0.000	0.000	0.000	0.000
157	A	158	LEU	0	-0.004	0.006	22.371	0.002	0.002	0.000	0.000	0.000	0.000

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