FMO DATABASE

FMODB ID: YNV62

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1340717.192268
FMO2-HF: Nuclear repulsion	1279620.803843
FMO2-HF: Total energy	-61096.388425
FMO2-MP2: Total energy	-61276.572919

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.
-5.738	-14.856	24.988	-7.533	-8.338	0.039

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 : -0.004 / q_NPA : -0.024

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	0.001	-0.018	1.534	-1.792	-6.999	15.297	-4.748	-5.342	0.008
4	A	5	PRO	0	-0.022	-0.003	5.119	-0.564	-0.509	-0.001	-0.014	-0.040	0.000
5	A	6	MET	0	-0.028	0.005	8.733	-0.309	-0.309	0.000	0.000	0.000	0.000
6	A	7	THR	0	0.001	0.012	11.275	0.042	0.042	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.011	-0.003	14.962	0.068	0.068	0.000	0.000	0.000	0.000
8	A	9	ARG	0	0.094	0.079	17.337	0.008	0.008	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.017	0.016	15.844	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.025	-0.012	13.765	0.034	0.034	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.967	-0.987	15.245	0.505	0.505	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.951	0.993	18.516	-0.391	-0.391	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.003	-0.006	12.556	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.901	0.925	14.086	-1.020	-1.020	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.908	-0.942	18.151	0.316	0.316	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.827	-0.924	19.031	0.369	0.369	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.029	-0.011	16.136	-0.044	-0.044	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.899	-0.944	19.660	0.295	0.295	0.000	0.000	0.000	0.000
19	A	20	PHE	0	0.055	0.041	23.023	-0.038	-0.038	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.034	-0.017	20.202	-0.037	-0.037	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.898	0.945	18.691	-0.549	-0.549	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.072	-0.046	24.044	-0.039	-0.039	0.000	0.000	0.000	0.000
23	A	24	VAL	0	0.008	0.010	27.153	-0.021	-0.021	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.881	0.918	26.561	-0.169	-0.169	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.852	0.906	21.685	-0.293	-0.293	0.000	0.000	0.000	0.000
26	A	27	PRO	0	-0.049	-0.024	27.622	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.847	-0.935	31.068	0.126	0.126	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.033	-0.011	27.580	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.030	-0.027	30.001	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.013	0.000	32.628	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.022	0.019	34.471	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.025	-0.022	31.610	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.096	-0.054	35.975	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.891	-0.966	38.211	0.052	0.052	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.060	0.059	38.890	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.866	0.925	35.021	-0.075	-0.075	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.969	-0.965	41.054	0.049	0.049	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.062	-0.023	43.791	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	40	GLY	0	-0.049	-0.012	43.969	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.862	-0.958	44.018	0.010	0.010	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.021	-0.016	38.567	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.814	0.912	39.970	0.009	0.009	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.847	-0.928	40.898	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.026	0.011	40.306	0.003	0.003	0.000	0.000	0.000	0.000
45	A	46	ALA	0	0.060	0.021	39.408	0.001	0.001	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.858	-0.937	38.003	0.038	0.038	0.000	0.000	0.000	0.000
47	A	48	TYR	0	-0.023	-0.016	35.211	0.012	0.012	0.000	0.000	0.000	0.000
48	A	49	HIS	0	-0.054	-0.039	34.850	0.010	0.010	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.075	0.064	33.454	0.002	0.002	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.017	-0.005	32.330	0.009	0.009	0.000	0.000	0.000	0.000
51	A	52	ARG	1	0.822	0.887	29.814	-0.061	-0.061	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.927	-0.953	29.134	0.029	0.029	0.000	0.000	0.000	0.000
53	A	54	GLN	0	0.056	-0.009	27.587	0.014	0.014	0.000	0.000	0.000	0.000
54	A	55	GLN	0	0.025	0.033	26.519	0.006	0.006	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.007	0.009	24.291	0.021	0.021	0.000	0.000	0.000	0.000
56	A	57	PHE	0	-0.030	-0.003	22.767	0.020	0.020	0.000	0.000	0.000	0.000
57	A	58	CYS	0	-0.007	-0.005	21.926	0.024	0.024	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.778	-0.843	21.464	0.289	0.289	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.050	-0.036	18.701	0.046	0.046	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.801	0.904	15.134	-0.389	-0.389	0.000	0.000	0.000	0.000
61	A	62	ILE	0	0.028	0.017	16.843	0.076	0.076	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.932	0.979	15.243	-0.090	-0.090	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.892	-0.954	12.828	0.734	0.734	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.052	0.035	11.874	0.253	0.253	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.880	-0.961	12.497	0.808	0.808	0.000	0.000	0.000	0.000
66	A	67	ALA	0	-0.001	-0.003	8.951	0.235	0.235	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.802	0.908	8.170	0.011	0.011	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.053	-0.028	8.237	0.556	0.556	0.000	0.000	0.000	0.000
69	A	70	SER	0	-0.105	-0.032	7.805	-0.218	-0.218	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.129	-0.073	1.822	-5.672	-9.676	9.693	-2.766	-2.924	0.031
71	A	72	ALA	0	-0.004	0.003	5.307	1.239	1.277	-0.001	-0.005	-0.032	0.000
72	A	73	GLN	0	-0.048	-0.018	6.958	-0.528	-0.528	0.000	0.000	0.000	0.000
73	A	74	VAL	0	0.001	-0.026	9.049	-0.234	-0.234	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.024	0.011	11.241	-0.105	-0.105	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.819	-0.932	14.704	0.457	0.457	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.006	-0.023	18.028	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.017	0.026	19.980	-0.056	-0.056	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.863	0.931	20.757	-0.489	-0.489	0.000	0.000	0.000	0.000
79	A	80	MET	0	-0.041	0.004	16.294	0.001	0.001	0.000	0.000	0.000	0.000
80	A	81	PRO	0	-0.028	-0.004	22.462	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	82	ASN	0	0.011	-0.011	24.276	0.012	0.012	0.000	0.000	0.000	0.000
82	A	83	ASN	0	-0.002	-0.003	22.796	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	84	GLY	0	0.096	0.061	25.415	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.802	0.888	21.665	-0.119	-0.119	0.000	0.000	0.000	0.000
85	A	86	VAL	0	-0.003	-0.002	18.908	0.042	0.042	0.000	0.000	0.000	0.000
86	A	87	ILE	0	0.005	0.013	16.501	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	88	PHE	0	0.003	-0.021	11.486	-0.036	-0.036	0.000	0.000	0.000	0.000
88	A	89	GLY	0	0.013	-0.011	14.780	0.084	0.084	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.072	-0.016	16.912	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	91	THR	0	0.013	-0.005	20.096	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	92	VAL	0	-0.036	-0.038	21.475	0.000	0.000	0.000	0.000	0.000	0.000
92	A	93	THR	0	0.021	0.022	24.281	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	94	VAL	0	-0.056	-0.047	24.727	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.043	0.033	27.934	0.001	0.001	0.000	0.000	0.000	0.000
95	A	96	ASN	0	-0.058	-0.018	30.811	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	97	LEU	0	0.061	0.011	31.678	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.908	-0.927	34.005	-0.053	-0.053	0.000	0.000	0.000	0.000
98	A	99	SER	0	-0.180	-0.104	34.115	0.004	0.004	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.865	-0.945	35.592	0.009	0.009	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-1.030	-1.011	30.516	0.004	0.004	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.860	-0.932	31.489	0.046	0.046	0.000	0.000	0.000	0.000
102	A	103	GLN	0	-0.003	0.013	27.325	0.015	0.015	0.000	0.000	0.000	0.000
103	A	104	THR	0	0.014	0.016	26.140	0.006	0.006	0.000	0.000	0.000	0.000
104	A	105	TYR	0	-0.037	0.001	21.496	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	106	ARG	1	0.831	0.886	18.304	-0.342	-0.342	0.000	0.000	0.000	0.000
106	A	107	ILE	0	-0.031	-0.003	14.621	-0.020	-0.020	0.000	0.000	0.000	0.000
107	A	108	VAL	0	-0.012	0.005	14.394	0.096	0.096	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.041	0.012	10.651	-0.093	-0.093	0.000	0.000	0.000	0.000
109	A	110	ASP	-1	-0.834	-0.937	8.832	-0.558	-0.558	0.000	0.000	0.000	0.000
110	A	111	ASP	-1	-0.855	-0.933	11.219	0.573	0.573	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.739	-0.855	13.038	0.476	0.476	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.063	-0.027	14.391	-0.046	-0.046	0.000	0.000	0.000	0.000
113	A	114	ASP	-1	-0.866	-0.939	16.114	0.094	0.094	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.025	-0.018	19.787	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.940	0.975	21.348	-0.025	-0.025	0.000	0.000	0.000	0.000
116	A	117	GLN	0	-0.027	-0.010	23.136	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	118	ASN	0	-0.018	-0.028	23.443	0.011	0.011	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.024	0.016	18.879	0.017	0.017	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.017	0.001	17.712	-0.026	-0.026	0.000	0.000	0.000	0.000
120	A	121	SER	0	0.059	0.027	12.048	0.033	0.033	0.000	0.000	0.000	0.000
121	A	122	VAL	0	0.013	-0.013	9.443	-0.040	-0.040	0.000	0.000	0.000	0.000
122	A	123	ASN	0	-0.154	-0.057	8.041	-0.285	-0.285	0.000	0.000	0.000	0.000
123	A	124	SER	0	0.015	-0.018	11.953	0.009	0.009	0.000	0.000	0.000	0.000
124	A	125	PRO	0	-0.021	-0.024	15.705	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	126	ILE	0	0.092	0.056	18.443	0.007	0.007	0.000	0.000	0.000	0.000
126	A	127	ALA	0	0.022	0.025	15.469	0.030	0.030	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.917	0.945	13.099	0.571	0.571	0.000	0.000	0.000	0.000
128	A	129	GLY	0	0.001	-0.014	16.639	0.018	0.018	0.000	0.000	0.000	0.000
129	A	130	LEU	0	0.035	0.011	19.644	0.022	0.022	0.000	0.000	0.000	0.000
130	A	131	ILE	0	-0.023	-0.010	14.800	0.044	0.044	0.000	0.000	0.000	0.000
131	A	132	GLY	0	-0.082	-0.047	17.980	-0.037	-0.037	0.000	0.000	0.000	0.000
132	A	133	LYS	1	0.860	0.955	19.620	0.055	0.055	0.000	0.000	0.000	0.000
133	A	134	GLU	-1	-0.889	-0.935	23.136	0.127	0.127	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.890	-0.959	25.812	0.103	0.103	0.000	0.000	0.000	0.000
135	A	136	ASP	-1	-0.905	-0.949	28.832	0.048	0.048	0.000	0.000	0.000	0.000
136	A	137	ASP	-1	-0.907	-0.937	26.214	0.020	0.020	0.000	0.000	0.000	0.000
137	A	138	VAL	0	0.031	0.016	28.577	0.000	0.000	0.000	0.000	0.000	0.000
138	A	139	VAL	0	-0.076	-0.066	23.776	-0.010	-0.010	0.000	0.000	0.000	0.000
139	A	140	VAL	0	0.009	0.005	26.602	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	141	ILE	0	-0.048	0.014	22.126	-0.025	-0.025	0.000	0.000	0.000	0.000
141	A	142	LYS	1	0.792	0.877	22.992	0.221	0.221	0.000	0.000	0.000	0.000
142	A	143	THR	0	-0.055	-0.021	23.297	-0.034	-0.034	0.000	0.000	0.000	0.000
143	A	144	PRO	0	0.019	0.012	24.440	-0.008	-0.008	0.000	0.000	0.000	0.000
144	A	145	GLY	0	0.002	-0.006	27.282	0.006	0.006	0.000	0.000	0.000	0.000
145	A	146	GLY	0	-0.052	-0.028	27.444	-0.011	-0.011	0.000	0.000	0.000	0.000
146	A	147	GLU	-1	-0.824	-0.913	26.644	-0.202	-0.202	0.000	0.000	0.000	0.000
147	A	148	VAL	0	-0.001	0.003	28.404	0.007	0.007	0.000	0.000	0.000	0.000
148	A	149	GLU	-1	-0.929	-0.944	28.520	-0.068	-0.068	0.000	0.000	0.000	0.000
149	A	150	PHE	0	-0.037	-0.017	26.972	0.000	0.000	0.000	0.000	0.000	0.000
150	A	151	GLU	-1	-0.870	-0.939	28.934	0.013	0.013	0.000	0.000	0.000	0.000
151	A	152	VAL	0	-0.035	0.002	25.300	0.004	0.004	0.000	0.000	0.000	0.000
152	A	153	ILE	0	0.069	0.037	27.853	0.009	0.009	0.000	0.000	0.000	0.000
153	A	154	LYS	1	0.904	0.937	28.597	-0.083	-0.083	0.000	0.000	0.000	0.000
154	A	155	VAL	0	-0.030	-0.002	23.377	0.000	0.000	0.000	0.000	0.000	0.000
155	A	156	GLU	-1	-0.875	-0.936	25.284	0.180	0.180	0.000	0.000	0.000	0.000
156	A	157	TYR	0	-0.119	-0.074	21.763	0.028	0.028	0.000	0.000	0.000	0.000
157	A	158	LEU	0	-0.016	-0.001	21.828	0.012	0.012	0.000	0.000	0.000	0.000

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