FMO DATABASE

FMODB ID: YZY72

Calculation Name: 3GGN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GGN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RZE3

Base Structure: X-ray

Registration Date: 2023-06-21

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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1129660.838051
FMO2-HF: Nuclear repulsion	1079239.076954
FMO2-HF: Total energy	-50421.761097
FMO2-MP2: Total energy	-50571.361546

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:3:THR)

Summations of interaction energy for fragment #1(A:3:THR)

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.
-24.456	-24.184	20.487	-9.956	-10.805	-0.062

Interaction energy analysis for fragmet #1(A:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / 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	5	VAL	0	0.042	0.035	3.880	-1.223	0.622	-0.013	-0.869	-0.964	0.002
4	A	6	ARG	1	0.865	0.939	6.256	-0.399	-0.399	0.000	0.000	0.000	0.000
5	A	7	ASP	-1	-0.771	-0.873	10.014	0.221	0.221	0.000	0.000	0.000	0.000
6	A	8	ALA	0	-0.049	-0.030	13.170	-0.012	-0.012	0.000	0.000	0.000	0.000
7	A	9	VAL	0	0.019	0.017	16.906	-0.004	-0.004	0.000	0.000	0.000	0.000
8	A	10	THR	0	-0.039	-0.009	20.198	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	11	ILE	0	0.021	0.012	22.083	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	12	GLY	0	-0.013	-0.008	25.807	0.000	0.000	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.859	0.937	28.517	-0.045	-0.045	0.000	0.000	0.000	0.000
12	A	14	PRO	0	0.013	-0.001	29.296	0.006	0.006	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.053	0.032	26.614	0.000	0.000	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.857	-0.945	26.693	0.045	0.045	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.038	-0.016	28.163	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.023	-0.013	23.859	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	19	TYR	0	-0.022	-0.046	23.342	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	20	ALA	0	0.022	-0.002	23.841	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.039	-0.018	23.062	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	22	TRP	0	0.033	0.004	15.379	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.813	0.895	20.530	0.004	0.004	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.881	-0.942	23.076	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	25	LEU	0	-0.016	-0.015	18.989	0.000	0.000	0.000	0.000	0.000	0.000
24	A	26	PRO	0	0.003	-0.006	20.030	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	27	GLY	0	0.051	0.039	21.896	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.021	-0.006	16.311	0.010	0.010	0.000	0.000	0.000	0.000
27	A	29	PRO	0	-0.006	-0.005	17.039	0.019	0.019	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.031	-0.011	18.084	0.011	0.011	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.072	-0.038	17.777	0.012	0.012	0.000	0.000	0.000	0.000
30	A	32	MET	0	-0.055	-0.024	11.852	0.029	0.029	0.000	0.000	0.000	0.000
31	A	33	THR	0	0.024	0.003	14.477	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	34	HIS	0	-0.030	-0.006	10.013	0.033	0.033	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.077	-0.037	12.007	-0.082	-0.082	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.862	0.913	14.506	0.159	0.159	0.000	0.000	0.000	0.000
35	A	37	SER	0	0.001	-0.020	17.310	0.018	0.018	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.043	-0.016	16.503	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.852	-0.904	19.209	-0.111	-0.111	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.016	0.000	21.596	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.079	-0.033	21.636	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.786	-0.876	24.959	-0.076	-0.076	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.910	-0.951	25.279	-0.037	-0.037	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.789	0.896	20.672	0.060	0.060	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.840	0.886	20.705	0.103	0.103	0.000	0.000	0.000	0.000
44	A	46	SER	0	0.028	0.011	18.695	0.011	0.011	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.813	0.889	18.429	0.127	0.127	0.000	0.000	0.000	0.000
46	A	48	TRP	0	0.003	-0.003	12.761	0.012	0.012	0.000	0.000	0.000	0.000
47	A	49	THR	0	-0.051	-0.037	15.186	-0.035	-0.035	0.000	0.000	0.000	0.000
48	A	50	VAL	0	0.030	0.027	10.874	0.030	0.030	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.751	-0.866	14.212	-0.173	-0.173	0.000	0.000	0.000	0.000
50	A	52	ALA	0	-0.049	-0.026	14.065	-0.056	-0.056	0.000	0.000	0.000	0.000
51	A	53	PRO	0	0.030	0.013	14.514	0.039	0.039	0.000	0.000	0.000	0.000
52	A	54	ALA	0	0.020	0.030	17.520	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	55	PRO	0	-0.022	-0.028	19.637	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	56	LEU	0	-0.015	-0.007	15.402	0.009	0.009	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.015	0.023	19.264	0.014	0.014	0.000	0.000	0.000	0.000
56	A	58	THR	0	-0.038	-0.029	16.927	0.012	0.012	0.000	0.000	0.000	0.000
57	A	59	VAL	0	-0.043	-0.024	11.977	-0.027	-0.027	0.000	0.000	0.000	0.000
58	A	60	SER	0	0.006	-0.002	14.724	0.017	0.017	0.000	0.000	0.000	0.000
59	A	61	TRP	0	-0.050	-0.022	10.630	-0.097	-0.097	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.744	-0.860	15.717	-0.129	-0.129	0.000	0.000	0.000	0.000
61	A	63	ALA	0	-0.011	-0.017	14.349	-0.056	-0.056	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.831	-0.899	16.220	-0.064	-0.064	0.000	0.000	0.000	0.000
63	A	65	LEU	0	0.006	0.004	16.759	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.074	-0.054	15.068	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.030	-0.020	18.236	0.016	0.016	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.786	-0.850	20.054	0.004	0.004	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.821	-0.878	22.850	0.076	0.076	0.000	0.000	0.000	0.000
68	A	70	PRO	0	0.064	0.021	24.895	0.007	0.007	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.051	0.033	26.866	0.003	0.003	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.799	0.894	24.558	-0.052	-0.052	0.000	0.000	0.000	0.000
71	A	73	ARG	1	0.771	0.850	18.528	-0.096	-0.096	0.000	0.000	0.000	0.000
72	A	74	ILE	0	0.033	0.038	18.221	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	75	ALA	0	0.010	0.002	15.351	0.020	0.020	0.000	0.000	0.000	0.000
74	A	76	TRP	0	0.039	0.032	11.681	0.017	0.017	0.000	0.000	0.000	0.000
75	A	77	ARG	1	0.916	0.943	10.231	0.048	0.048	0.000	0.000	0.000	0.000
76	A	78	SER	0	0.009	0.021	10.844	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	79	LEU	0	0.030	0.013	12.888	0.019	0.019	0.000	0.000	0.000	0.000
78	A	80	PRO	0	-0.024	-0.027	14.443	-0.070	-0.070	0.000	0.000	0.000	0.000
79	A	81	GLY	0	0.023	0.019	14.556	0.033	0.033	0.000	0.000	0.000	0.000
80	A	82	ALA	0	-0.037	-0.006	12.572	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.943	0.964	12.777	0.335	0.335	0.000	0.000	0.000	0.000
82	A	84	ILE	0	0.030	0.023	6.674	-0.118	-0.118	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.783	-0.818	6.998	-0.787	-0.787	0.000	0.000	0.000	0.000
84	A	86	ASN	0	-0.044	-0.047	6.013	-0.718	-0.718	0.000	0.000	0.000	0.000
85	A	87	SER	0	-0.037	-0.030	7.474	0.401	0.401	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.023	0.017	8.501	0.009	0.009	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.904	-0.940	11.082	0.159	0.159	0.000	0.000	0.000	0.000
88	A	90	VAL	0	0.010	0.016	13.770	0.037	0.037	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.034	-0.016	16.563	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	92	PHE	0	0.011	0.007	19.470	0.005	0.005	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.856	0.907	19.934	-0.166	-0.166	0.000	0.000	0.000	0.000
92	A	94	PRO	0	-0.009	-0.007	24.113	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.010	-0.004	25.856	0.007	0.007	0.000	0.000	0.000	0.000
94	A	96	PRO	0	0.007	-0.008	26.198	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	97	GLY	0	-0.013	0.010	29.154	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	98	ALA	0	0.033	0.006	30.986	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.896	0.964	29.281	-0.059	-0.059	0.000	0.000	0.000	0.000
98	A	100	GLY	0	0.001	-0.001	28.710	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	101	THR	0	-0.018	-0.021	24.398	0.001	0.001	0.000	0.000	0.000	0.000
100	A	102	GLU	-1	-0.803	-0.875	19.439	0.164	0.164	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.038	0.028	18.557	0.001	0.001	0.000	0.000	0.000	0.000
102	A	104	VAL	0	-0.064	-0.029	15.123	0.017	0.017	0.000	0.000	0.000	0.000
103	A	105	VAL	0	0.051	0.023	12.085	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	106	ARG	1	0.943	0.969	7.917	-0.447	-0.447	0.000	0.000	0.000	0.000
105	A	107	LEU	0	0.035	0.017	6.749	-0.081	-0.081	0.000	0.000	0.000	0.000
106	A	108	THR	0	-0.044	-0.032	4.537	0.091	0.343	-0.001	-0.084	-0.167	0.000
107	A	109	TYR	0	0.033	0.015	2.767	-2.867	1.067	2.604	-2.050	-4.488	0.002
108	A	110	ARG	1	0.848	0.896	1.848	-18.597	-24.356	17.897	-6.953	-5.186	-0.066
109	A	127	GLU	-1	-0.777	-0.845	7.793	0.368	0.368	0.000	0.000	0.000	0.000
110	A	128	PRO	0	-0.018	-0.032	5.948	0.019	0.019	0.000	0.000	0.000	0.000
111	A	129	SER	0	-0.061	-0.069	7.778	-0.058	-0.058	0.000	0.000	0.000	0.000
112	A	130	GLN	0	-0.043	-0.033	9.184	-0.043	-0.043	0.000	0.000	0.000	0.000
113	A	131	GLN	0	0.000	-0.005	11.473	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	132	LEU	0	0.009	0.000	10.122	-0.033	-0.033	0.000	0.000	0.000	0.000
115	A	133	ARG	1	0.870	0.921	12.686	-0.218	-0.218	0.000	0.000	0.000	0.000
116	A	134	ASP	-1	-0.846	-0.925	14.884	0.084	0.084	0.000	0.000	0.000	0.000
117	A	135	ASP	-1	-0.779	-0.840	15.001	0.080	0.080	0.000	0.000	0.000	0.000
118	A	136	LEU	0	-0.031	-0.020	15.074	-0.023	-0.023	0.000	0.000	0.000	0.000
119	A	137	MET	0	-0.037	-0.022	18.194	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	138	ARG	1	0.833	0.921	18.185	-0.074	-0.074	0.000	0.000	0.000	0.000
121	A	139	PHE	0	0.053	0.021	20.611	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	140	LYS	1	0.796	0.889	22.247	-0.084	-0.084	0.000	0.000	0.000	0.000
123	A	141	ARG	1	0.917	0.958	24.124	-0.042	-0.042	0.000	0.000	0.000	0.000
124	A	142	GLU	-1	-0.852	-0.933	25.310	0.027	0.027	0.000	0.000	0.000	0.000
125	A	143	GLN	0	0.025	0.021	25.405	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	144	GLU	-1	-0.852	-0.923	27.741	0.063	0.063	0.000	0.000	0.000	0.000
127	A	145	LEU	0	-0.020	-0.015	30.036	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	146	GLY	0	-0.026	0.007	31.175	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	147	LEU	0	-0.037	-0.015	27.972	-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:3:THR)