FMO DATABASE

FMODB ID: VR9Y1

Calculation Name: 3GIO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3GIO

Chain ID: A

ChEMBL ID:

UniProt ID: O25318

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1371679.05575
FMO2-HF: Nuclear repulsion	1311975.605297
FMO2-HF: Total energy	-59703.450454
FMO2-MP2: Total energy	-59877.558203

3D Structure Molmil

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:34:ASN)

Summations of interaction energy for fragment #1(A:34:ASN)

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.
-1.446	-3.928	12.281	-5.04	-4.758	-0.004

Interaction energy analysis for fragmet #1(A:34:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.005

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	36	PHE	0	-0.006	-0.005	3.815	-2.553	-0.081	0.001	-1.236	-1.237	0.007
4	A	37	LEU	0	-0.001	0.006	4.629	-0.194	-0.183	-0.001	-0.020	0.011	0.000
5	A	38	GLN	0	-0.012	-0.010	6.882	0.088	0.088	0.000	0.000	0.000	0.000
6	A	39	ASP	-1	-0.918	-0.957	10.033	0.209	0.209	0.000	0.000	0.000	0.000
7	A	40	VAL	0	-0.009	0.005	11.089	0.059	0.059	0.000	0.000	0.000	0.000
8	A	41	PRO	0	0.001	0.000	12.982	-0.030	-0.030	0.000	0.000	0.000	0.000
9	A	42	TYR	0	0.050	0.005	16.099	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	43	TRP	0	0.031	0.000	17.223	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	44	MET	0	-0.048	0.004	12.166	0.016	0.016	0.000	0.000	0.000	0.000
12	A	45	LEU	0	-0.033	-0.005	14.692	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	46	GLN	0	0.008	0.001	14.522	0.017	0.017	0.000	0.000	0.000	0.000
14	A	47	ASN	0	-0.014	-0.005	17.325	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	48	ARG	1	0.926	0.942	19.165	0.008	0.008	0.000	0.000	0.000	0.000
16	A	49	SER	0	0.027	0.013	22.167	0.002	0.002	0.000	0.000	0.000	0.000
17	A	50	GLU	-1	-1.003	-0.982	24.603	0.014	0.014	0.000	0.000	0.000	0.000
18	A	51	TYR	0	0.035	0.027	26.981	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	52	ILE	0	0.056	0.030	28.272	0.011	0.011	0.000	0.000	0.000	0.000
20	A	53	THR	0	0.005	0.001	29.781	0.009	0.009	0.000	0.000	0.000	0.000
21	A	54	GLN	0	-0.033	-0.029	25.457	0.000	0.000	0.000	0.000	0.000	0.000
22	A	55	GLY	0	0.001	0.006	24.257	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	56	VAL	0	0.003	-0.008	17.790	0.008	0.008	0.000	0.000	0.000	0.000
24	A	57	ASP	-1	-0.833	-0.899	18.701	0.281	0.281	0.000	0.000	0.000	0.000
25	A	58	SER	0	-0.040	-0.041	14.460	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	59	SER	0	-0.009	-0.012	16.062	-0.059	-0.059	0.000	0.000	0.000	0.000
27	A	60	HIS	0	-0.024	0.011	11.232	-0.093	-0.093	0.000	0.000	0.000	0.000
28	A	61	ILE	0	-0.012	-0.001	13.718	-0.143	-0.143	0.000	0.000	0.000	0.000
29	A	62	VAL	0	-0.032	-0.012	15.255	0.052	0.052	0.000	0.000	0.000	0.000
30	A	63	ASP	-1	-0.869	-0.928	17.904	0.572	0.572	0.000	0.000	0.000	0.000
31	A	64	GLY	0	-0.042	-0.032	20.099	-0.034	-0.034	0.000	0.000	0.000	0.000
32	A	65	LYS	1	0.853	0.928	20.599	-0.393	-0.393	0.000	0.000	0.000	0.000
33	A	66	LYS	1	0.910	0.960	20.090	-0.264	-0.264	0.000	0.000	0.000	0.000
34	A	67	THR	0	0.114	0.036	16.242	-0.027	-0.027	0.000	0.000	0.000	0.000
35	A	68	GLU	-1	-0.777	-0.868	18.788	0.279	0.279	0.000	0.000	0.000	0.000
36	A	69	GLU	-1	-0.858	-0.922	21.878	0.313	0.313	0.000	0.000	0.000	0.000
37	A	70	ILE	0	0.019	-0.003	16.820	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	71	GLU	-1	-0.799	-0.884	18.860	0.319	0.319	0.000	0.000	0.000	0.000
39	A	72	LYS	1	0.839	0.930	20.298	-0.294	-0.294	0.000	0.000	0.000	0.000
40	A	73	ILE	0	-0.030	-0.003	21.131	-0.027	-0.027	0.000	0.000	0.000	0.000
41	A	74	ALA	0	0.034	0.017	18.445	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	75	THR	0	-0.010	-0.035	20.427	-0.030	-0.030	0.000	0.000	0.000	0.000
43	A	76	LYS	1	0.937	0.975	23.307	-0.216	-0.216	0.000	0.000	0.000	0.000
44	A	77	ARG	1	0.903	0.942	18.862	-0.411	-0.411	0.000	0.000	0.000	0.000
45	A	78	ALA	0	0.027	0.021	21.735	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	79	THR	0	-0.015	-0.017	23.413	-0.024	-0.024	0.000	0.000	0.000	0.000
47	A	80	ILE	0	-0.004	-0.002	26.357	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	81	ARG	1	0.842	0.914	21.479	-0.225	-0.225	0.000	0.000	0.000	0.000
49	A	82	VAL	0	0.009	0.029	25.935	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	83	ALA	0	0.023	0.007	28.443	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	84	GLN	0	0.006	-0.009	26.129	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	85	ASN	0	-0.047	-0.009	26.332	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	86	ILE	0	0.007	0.003	29.719	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	87	VAL	0	0.010	0.002	32.624	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	88	HIS	0	-0.034	-0.037	29.601	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	89	LYS	1	0.918	0.971	32.794	-0.042	-0.042	0.000	0.000	0.000	0.000
57	A	90	LEU	0	0.008	-0.003	35.054	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	91	LYS	1	0.852	0.947	32.174	-0.079	-0.079	0.000	0.000	0.000	0.000
59	A	92	GLU	-1	-0.848	-0.910	33.665	0.029	0.029	0.000	0.000	0.000	0.000
60	A	93	ALA	0	-0.032	-0.016	37.652	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	94	TYR	0	-0.056	-0.043	40.509	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	95	LEU	0	-0.015	-0.025	37.777	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	96	SER	0	-0.014	0.020	41.556	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	97	LYS	1	0.999	0.988	43.071	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	98	THR	0	-0.079	-0.039	46.011	0.000	0.000	0.000	0.000	0.000	0.000
66	A	99	ASN	0	0.051	0.043	45.031	0.003	0.003	0.000	0.000	0.000	0.000
67	A	100	ARG	1	0.920	0.957	47.000	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	101	ILE	0	-0.033	-0.006	44.626	0.000	0.000	0.000	0.000	0.000	0.000
69	A	102	LYS	1	0.963	0.977	48.464	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	103	GLN	0	0.032	0.037	47.558	0.000	0.000	0.000	0.000	0.000	0.000
71	A	104	LYS	1	0.967	0.988	44.699	-0.036	-0.036	0.000	0.000	0.000	0.000
72	A	105	ILE	0	0.026	0.011	40.964	0.002	0.002	0.000	0.000	0.000	0.000
73	A	106	THR	0	-0.041	-0.055	39.953	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	107	ASN	0	0.026	0.005	33.206	0.003	0.003	0.000	0.000	0.000	0.000
75	A	108	GLU	-1	-0.796	-0.901	36.026	0.070	0.070	0.000	0.000	0.000	0.000
76	A	109	MET	0	0.023	0.038	37.195	0.004	0.004	0.000	0.000	0.000	0.000
77	A	110	PHE	0	0.022	-0.005	35.948	0.002	0.002	0.000	0.000	0.000	0.000
78	A	111	ILE	0	-0.016	-0.011	32.062	0.005	0.005	0.000	0.000	0.000	0.000
79	A	112	GLN	0	0.012	0.022	34.252	0.007	0.007	0.000	0.000	0.000	0.000
80	A	113	MET	0	0.006	0.010	36.858	0.002	0.002	0.000	0.000	0.000	0.000
81	A	114	THR	0	-0.037	-0.050	30.615	0.001	0.001	0.000	0.000	0.000	0.000
82	A	115	GLN	0	-0.089	-0.049	33.826	0.011	0.011	0.000	0.000	0.000	0.000
83	A	116	PRO	0	0.029	0.029	35.183	0.002	0.002	0.000	0.000	0.000	0.000
84	A	117	ILE	0	0.009	0.011	34.186	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	118	TYR	0	-0.010	-0.010	29.578	0.007	0.007	0.000	0.000	0.000	0.000
86	A	119	ASP	-1	-0.865	-0.927	33.731	0.119	0.119	0.000	0.000	0.000	0.000
87	A	120	SER	0	-0.065	-0.021	36.480	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	121	LEU	0	-0.041	-0.011	31.573	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	122	MET	0	0.010	0.001	35.500	0.004	0.004	0.000	0.000	0.000	0.000
90	A	123	ASN	0	-0.057	-0.030	34.832	0.001	0.001	0.000	0.000	0.000	0.000
91	A	124	VAL	0	0.020	0.008	28.709	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	125	ASP	-1	-0.804	-0.888	29.578	0.117	0.117	0.000	0.000	0.000	0.000
93	A	126	ARG	1	0.822	0.879	22.648	-0.261	-0.261	0.000	0.000	0.000	0.000
94	A	127	LEU	0	-0.017	-0.017	24.180	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	128	GLY	0	-0.005	0.003	20.828	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	129	ILE	0	-0.024	-0.007	16.771	0.006	0.006	0.000	0.000	0.000	0.000
97	A	130	TYR	0	0.024	0.003	9.205	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	131	ILE	0	0.000	0.001	10.661	0.020	0.020	0.000	0.000	0.000	0.000
99	A	132	ASN	0	0.021	0.030	5.451	-0.106	-0.106	0.000	0.000	0.000	0.000
100	A	133	PRO	0	0.038	0.001	6.054	0.220	0.220	0.000	0.000	0.000	0.000
101	A	134	ASN	0	-0.044	-0.008	2.070	-0.094	-5.237	12.280	-3.705	-3.433	-0.011
102	A	135	ASN	0	-0.029	-0.041	4.093	0.246	0.424	0.001	-0.079	-0.099	0.000
103	A	136	GLU	-1	-0.898	-0.935	7.276	0.920	0.920	0.000	0.000	0.000	0.000
104	A	137	GLU	-1	-0.824	-0.878	9.514	0.673	0.673	0.000	0.000	0.000	0.000
105	A	138	VAL	0	-0.019	-0.030	11.469	-0.069	-0.069	0.000	0.000	0.000	0.000
106	A	139	PHE	0	0.034	-0.005	10.580	-0.069	-0.069	0.000	0.000	0.000	0.000
107	A	140	ALA	0	-0.015	-0.007	15.618	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	141	LEU	0	-0.011	0.004	19.236	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	142	VAL	0	-0.058	-0.034	21.511	0.001	0.001	0.000	0.000	0.000	0.000
110	A	143	ARG	1	0.976	0.972	25.144	-0.088	-0.088	0.000	0.000	0.000	0.000
111	A	144	ALA	0	0.010	0.026	28.550	0.001	0.001	0.000	0.000	0.000	0.000
112	A	145	ARG	1	0.818	0.889	31.846	-0.099	-0.099	0.000	0.000	0.000	0.000
113	A	146	GLY	0	0.019	0.006	34.804	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	147	PHE	0	-0.037	-0.017	36.590	0.005	0.005	0.000	0.000	0.000	0.000
115	A	148	ASP	-1	-0.823	-0.913	38.783	0.069	0.069	0.000	0.000	0.000	0.000
116	A	149	LYS	1	0.858	0.903	41.847	-0.053	-0.053	0.000	0.000	0.000	0.000
117	A	150	ASP	-1	-0.791	-0.878	43.817	0.056	0.056	0.000	0.000	0.000	0.000
118	A	151	ALA	0	0.056	0.041	41.605	0.000	0.000	0.000	0.000	0.000	0.000
119	A	152	LEU	0	-0.033	-0.017	39.322	0.001	0.001	0.000	0.000	0.000	0.000
120	A	153	SER	0	-0.043	-0.050	42.171	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	154	GLU	-1	-0.942	-0.955	45.442	0.067	0.067	0.000	0.000	0.000	0.000
122	A	155	GLY	0	-0.023	-0.017	42.074	0.000	0.000	0.000	0.000	0.000	0.000
123	A	156	LEU	0	-0.008	-0.026	40.643	0.000	0.000	0.000	0.000	0.000	0.000
124	A	157	HIS	0	-0.007	-0.009	43.853	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	158	LYS	1	0.928	0.983	42.559	-0.088	-0.088	0.000	0.000	0.000	0.000
126	A	159	MET	0	-0.056	-0.008	40.083	0.003	0.003	0.000	0.000	0.000	0.000
127	A	160	SER	0	-0.095	-0.037	44.705	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	161	LEU	0	0.017	0.011	42.863	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	162	ASP	-1	-0.871	-0.950	47.483	0.038	0.038	0.000	0.000	0.000	0.000
130	A	163	ASN	0	0.028	-0.004	49.522	0.003	0.003	0.000	0.000	0.000	0.000
131	A	164	GLN	0	-0.016	-0.007	50.807	0.001	0.001	0.000	0.000	0.000	0.000
132	A	165	ALA	0	0.047	0.014	46.346	0.000	0.000	0.000	0.000	0.000	0.000
133	A	166	VAL	0	0.019	0.022	45.890	0.001	0.001	0.000	0.000	0.000	0.000
134	A	167	SER	0	-0.006	0.004	46.191	0.000	0.000	0.000	0.000	0.000	0.000
135	A	168	ILE	0	-0.006	-0.020	45.609	0.000	0.000	0.000	0.000	0.000	0.000
136	A	169	LEU	0	-0.021	-0.018	41.120	0.000	0.000	0.000	0.000	0.000	0.000
137	A	170	VAL	0	0.035	0.011	42.362	0.002	0.002	0.000	0.000	0.000	0.000
138	A	171	ALA	0	-0.006	0.001	43.418	0.001	0.001	0.000	0.000	0.000	0.000
139	A	172	LYS	1	0.818	0.878	41.210	-0.035	-0.035	0.000	0.000	0.000	0.000
140	A	173	VAL	0	0.012	0.018	37.672	0.000	0.000	0.000	0.000	0.000	0.000
141	A	174	GLU	-1	-0.864	-0.932	39.315	0.049	0.049	0.000	0.000	0.000	0.000
142	A	175	GLU	-1	-0.866	-0.913	41.285	0.033	0.033	0.000	0.000	0.000	0.000
143	A	176	ILE	0	0.013	0.011	35.054	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	177	PHE	0	-0.012	-0.018	34.676	0.001	0.001	0.000	0.000	0.000	0.000
145	A	178	LYS	1	0.844	0.917	37.915	-0.044	-0.044	0.000	0.000	0.000	0.000
146	A	179	ASP	-1	-0.902	-0.943	37.840	0.032	0.032	0.000	0.000	0.000	0.000
147	A	180	SER	0	-0.157	-0.062	34.117	0.001	0.001	0.000	0.000	0.000	0.000
148	A	181	VAL	0	-0.038	-0.013	36.057	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:34:ASN)