FMO DATABASE

FMODB ID: YY4R2

Calculation Name: 3GIO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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	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	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1372268.622935
FMO2-HF: Nuclear repulsion	1312566.281809
FMO2-HF: Total energy	-59702.341126
FMO2-MP2: Total energy	-59876.531955

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: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.
3.178	-4.924	20.229	-6.553	-5.573	-0.013

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 : 0.021 / q_NPA : 0.002

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	-0.008	-0.014	3.815	-1.372	1.008	0.010	-1.193	-1.196	0.006
4	A	37	LEU	0	-0.009	-0.001	4.790	-0.251	-0.250	-0.001	-0.018	0.018	0.000
5	A	38	GLN	0	0.002	-0.004	6.878	0.176	0.176	0.000	0.000	0.000	0.000
6	A	39	ASP	-1	-0.933	-0.958	9.975	0.152	0.152	0.000	0.000	0.000	0.000
7	A	40	VAL	0	-0.014	0.006	11.237	0.101	0.101	0.000	0.000	0.000	0.000
8	A	41	PRO	0	0.004	-0.004	13.025	-0.053	-0.053	0.000	0.000	0.000	0.000
9	A	42	TYR	0	0.057	0.007	16.189	0.007	0.007	0.000	0.000	0.000	0.000
10	A	43	TRP	0	0.029	0.002	17.404	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	44	MET	0	-0.059	0.001	12.506	0.019	0.019	0.000	0.000	0.000	0.000
12	A	45	LEU	0	-0.013	0.000	14.646	0.010	0.010	0.000	0.000	0.000	0.000
13	A	46	GLN	0	-0.006	-0.003	14.218	0.010	0.010	0.000	0.000	0.000	0.000
14	A	47	ASN	0	-0.012	0.001	17.364	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	48	ARG	1	0.933	0.939	19.256	-0.068	-0.068	0.000	0.000	0.000	0.000
16	A	49	SER	0	0.008	0.005	22.549	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	50	GLU	-1	-0.984	-0.975	24.770	0.046	0.046	0.000	0.000	0.000	0.000
18	A	51	TYR	0	0.018	0.026	27.160	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	52	ILE	0	0.051	0.026	28.454	0.015	0.015	0.000	0.000	0.000	0.000
20	A	53	THR	0	0.004	-0.002	29.972	0.013	0.013	0.000	0.000	0.000	0.000
21	A	54	GLN	0	-0.034	-0.033	25.649	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	55	GLY	0	-0.011	0.002	24.446	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	56	VAL	0	-0.001	-0.007	17.941	0.005	0.005	0.000	0.000	0.000	0.000
24	A	57	ASP	-1	-0.867	-0.933	18.879	0.459	0.459	0.000	0.000	0.000	0.000
25	A	58	SER	0	-0.048	-0.051	14.639	-0.031	-0.031	0.000	0.000	0.000	0.000
26	A	59	SER	0	-0.008	-0.022	16.226	-0.081	-0.081	0.000	0.000	0.000	0.000
27	A	60	HIS	0	0.018	0.030	11.032	-0.159	-0.159	0.000	0.000	0.000	0.000
28	A	61	ILE	0	-0.003	0.004	13.860	-0.192	-0.192	0.000	0.000	0.000	0.000
29	A	62	VAL	0	-0.031	-0.010	15.366	0.073	0.073	0.000	0.000	0.000	0.000
30	A	63	ASP	-1	-0.876	-0.932	18.004	0.730	0.730	0.000	0.000	0.000	0.000
31	A	64	GLY	0	-0.047	-0.037	20.025	-0.039	-0.039	0.000	0.000	0.000	0.000
32	A	65	LYS	1	0.910	0.971	20.845	-0.544	-0.544	0.000	0.000	0.000	0.000
33	A	66	LYS	1	0.974	1.011	20.149	-0.335	-0.335	0.000	0.000	0.000	0.000
34	A	67	THR	0	0.121	0.034	16.424	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	68	GLU	-1	-0.850	-0.924	18.843	0.363	0.363	0.000	0.000	0.000	0.000
36	A	69	GLU	-1	-0.902	-0.956	21.939	0.402	0.402	0.000	0.000	0.000	0.000
37	A	70	ILE	0	-0.026	-0.022	16.944	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	71	GLU	-1	-0.850	-0.933	18.693	0.439	0.439	0.000	0.000	0.000	0.000
39	A	72	LYS	1	0.846	0.929	20.408	-0.362	-0.362	0.000	0.000	0.000	0.000
40	A	73	ILE	0	-0.024	0.002	21.264	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	74	ALA	0	0.037	0.018	18.598	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	75	THR	0	0.000	-0.010	20.589	-0.041	-0.041	0.000	0.000	0.000	0.000
43	A	76	LYS	1	0.946	0.977	23.458	-0.311	-0.311	0.000	0.000	0.000	0.000
44	A	77	ARG	1	0.880	0.934	19.186	-0.580	-0.580	0.000	0.000	0.000	0.000
45	A	78	ALA	0	0.037	0.027	22.013	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	79	THR	0	-0.007	-0.012	23.597	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	80	ILE	0	-0.005	0.002	26.489	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	81	ARG	1	0.914	0.976	22.322	-0.335	-0.335	0.000	0.000	0.000	0.000
49	A	82	VAL	0	0.001	0.024	26.146	-0.019	-0.019	0.000	0.000	0.000	0.000
50	A	83	ALA	0	0.031	0.012	28.641	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	84	GLN	0	0.008	-0.015	26.290	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	85	ASN	0	-0.024	0.009	26.195	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	86	ILE	0	0.014	0.013	29.896	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	87	VAL	0	0.000	-0.002	32.632	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	88	HIS	0	-0.079	-0.072	29.027	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	89	LYS	1	1.018	1.028	32.833	-0.082	-0.082	0.000	0.000	0.000	0.000
57	A	90	LEU	0	-0.009	-0.010	35.096	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	91	LYS	1	0.877	0.961	32.131	-0.142	-0.142	0.000	0.000	0.000	0.000
59	A	92	GLU	-1	-0.915	-0.950	33.638	0.072	0.072	0.000	0.000	0.000	0.000
60	A	93	ALA	0	-0.044	-0.023	37.686	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	94	TYR	0	-0.042	-0.022	40.545	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	95	LEU	0	-0.009	-0.021	37.807	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	96	SER	0	-0.011	0.018	41.586	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	97	LYS	1	1.003	0.991	43.102	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	98	THR	0	-0.090	-0.040	45.719	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	99	ASN	0	0.038	0.027	45.085	0.004	0.004	0.000	0.000	0.000	0.000
67	A	100	ARG	1	0.921	0.953	47.035	-0.044	-0.044	0.000	0.000	0.000	0.000
68	A	101	ILE	0	-0.031	-0.003	44.657	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	102	LYS	1	0.965	0.980	48.498	-0.047	-0.047	0.000	0.000	0.000	0.000
70	A	103	GLN	0	0.057	0.056	47.209	0.000	0.000	0.000	0.000	0.000	0.000
71	A	104	LYS	1	0.950	0.970	44.692	-0.072	-0.072	0.000	0.000	0.000	0.000
72	A	105	ILE	0	0.020	0.007	40.976	0.003	0.003	0.000	0.000	0.000	0.000
73	A	106	THR	0	0.016	-0.009	40.297	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	107	ASN	0	0.063	0.020	32.852	0.000	0.000	0.000	0.000	0.000	0.000
75	A	108	GLU	-1	-0.868	-0.945	36.059	0.128	0.128	0.000	0.000	0.000	0.000
76	A	109	MET	0	0.003	0.020	37.226	0.006	0.006	0.000	0.000	0.000	0.000
77	A	110	PHE	0	0.026	-0.001	35.946	0.002	0.002	0.000	0.000	0.000	0.000
78	A	111	ILE	0	-0.027	-0.016	32.109	0.006	0.006	0.000	0.000	0.000	0.000
79	A	112	GLN	0	0.001	0.006	34.345	0.008	0.008	0.000	0.000	0.000	0.000
80	A	113	MET	0	0.022	0.015	36.948	0.002	0.002	0.000	0.000	0.000	0.000
81	A	114	THR	0	-0.029	-0.037	30.914	0.001	0.001	0.000	0.000	0.000	0.000
82	A	115	GLN	0	-0.002	0.004	34.040	0.013	0.013	0.000	0.000	0.000	0.000
83	A	116	PRO	0	0.017	0.024	35.396	0.001	0.001	0.000	0.000	0.000	0.000
84	A	117	ILE	0	-0.004	0.003	34.771	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	118	TYR	0	-0.020	-0.021	29.549	0.006	0.006	0.000	0.000	0.000	0.000
86	A	119	ASP	-1	-0.906	-0.962	33.929	0.172	0.172	0.000	0.000	0.000	0.000
87	A	120	SER	0	-0.081	-0.023	36.669	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	121	LEU	0	-0.046	-0.013	31.734	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	122	MET	0	0.020	0.004	35.675	0.004	0.004	0.000	0.000	0.000	0.000
90	A	123	ASN	0	-0.088	-0.037	35.019	0.000	0.000	0.000	0.000	0.000	0.000
91	A	124	VAL	0	0.030	0.011	28.821	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	125	ASP	-1	-0.856	-0.931	29.699	0.154	0.154	0.000	0.000	0.000	0.000
93	A	126	ARG	1	0.853	0.911	22.431	-0.336	-0.336	0.000	0.000	0.000	0.000
94	A	127	LEU	0	-0.017	-0.017	24.079	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	128	GLY	0	-0.007	0.001	20.918	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	129	ILE	0	-0.032	-0.010	16.802	0.013	0.013	0.000	0.000	0.000	0.000
97	A	130	TYR	0	0.043	0.008	8.934	0.012	0.012	0.000	0.000	0.000	0.000
98	A	131	ILE	0	0.005	0.004	10.750	0.037	0.037	0.000	0.000	0.000	0.000
99	A	132	ASN	0	0.016	0.037	5.512	0.275	0.275	0.000	0.000	0.000	0.000
100	A	133	PRO	0	0.027	-0.014	5.974	0.270	0.270	0.000	0.000	0.000	0.000
101	A	134	ASN	0	-0.019	0.001	1.957	2.931	-7.722	20.220	-5.269	-4.298	-0.019
102	A	135	ASN	0	-0.035	-0.028	4.164	0.071	0.241	0.000	-0.073	-0.097	0.000
103	A	136	GLU	-1	-0.908	-0.942	7.421	1.176	1.176	0.000	0.000	0.000	0.000
104	A	137	GLU	-1	-0.859	-0.901	9.637	0.959	0.959	0.000	0.000	0.000	0.000
105	A	138	VAL	0	-0.014	-0.031	11.628	-0.088	-0.088	0.000	0.000	0.000	0.000
106	A	139	PHE	0	0.031	-0.006	11.066	-0.105	-0.105	0.000	0.000	0.000	0.000
107	A	140	ALA	0	-0.022	-0.011	15.770	-0.036	-0.036	0.000	0.000	0.000	0.000
108	A	141	LEU	0	-0.017	0.003	19.378	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	142	VAL	0	-0.050	-0.033	21.653	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	143	ARG	1	0.982	0.970	25.292	-0.124	-0.124	0.000	0.000	0.000	0.000
111	A	144	ALA	0	0.010	0.026	28.699	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	145	ARG	1	0.900	0.948	32.005	-0.121	-0.121	0.000	0.000	0.000	0.000
113	A	146	GLY	0	0.009	-0.002	34.951	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	147	PHE	0	-0.040	-0.009	36.755	0.008	0.008	0.000	0.000	0.000	0.000
115	A	148	ASP	-1	-0.813	-0.912	38.956	0.098	0.098	0.000	0.000	0.000	0.000
116	A	149	LYS	1	0.950	0.960	42.021	-0.075	-0.075	0.000	0.000	0.000	0.000
117	A	150	ASP	-1	-0.860	-0.935	44.004	0.083	0.083	0.000	0.000	0.000	0.000
118	A	151	ALA	0	0.045	0.040	41.783	0.001	0.001	0.000	0.000	0.000	0.000
119	A	152	LEU	0	-0.043	-0.024	39.799	0.003	0.003	0.000	0.000	0.000	0.000
120	A	153	SER	0	-0.029	-0.040	42.371	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	154	GLU	-1	-0.949	-0.955	45.533	0.098	0.098	0.000	0.000	0.000	0.000
122	A	155	GLY	0	-0.014	-0.013	42.279	0.001	0.001	0.000	0.000	0.000	0.000
123	A	156	LEU	0	-0.023	-0.031	40.843	0.001	0.001	0.000	0.000	0.000	0.000
124	A	157	HIS	0	-0.006	-0.006	44.071	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	158	LYS	1	0.922	0.979	42.837	-0.129	-0.129	0.000	0.000	0.000	0.000
126	A	159	MET	0	-0.060	-0.006	40.206	0.004	0.004	0.000	0.000	0.000	0.000
127	A	160	SER	0	-0.095	-0.040	44.915	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	161	LEU	0	0.008	0.008	43.031	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	162	ASP	-1	-0.853	-0.947	47.556	0.065	0.065	0.000	0.000	0.000	0.000
130	A	163	ASN	0	0.021	-0.008	49.653	0.004	0.004	0.000	0.000	0.000	0.000
131	A	164	GLN	0	-0.003	0.004	50.686	0.001	0.001	0.000	0.000	0.000	0.000
132	A	165	ALA	0	0.029	0.004	46.353	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	166	VAL	0	0.041	0.028	46.120	0.002	0.002	0.000	0.000	0.000	0.000
134	A	167	SER	0	-0.012	-0.001	46.407	0.001	0.001	0.000	0.000	0.000	0.000
135	A	168	ILE	0	-0.020	-0.023	45.837	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	169	LEU	0	-0.022	-0.021	41.280	0.000	0.000	0.000	0.000	0.000	0.000
137	A	170	VAL	0	0.034	0.017	42.574	0.003	0.003	0.000	0.000	0.000	0.000
138	A	171	ALA	0	0.009	0.010	43.619	0.000	0.000	0.000	0.000	0.000	0.000
139	A	172	LYS	1	0.935	0.951	41.361	-0.064	-0.064	0.000	0.000	0.000	0.000
140	A	173	VAL	0	0.004	0.016	37.969	0.001	0.001	0.000	0.000	0.000	0.000
141	A	174	GLU	-1	-0.923	-0.973	39.506	0.075	0.075	0.000	0.000	0.000	0.000
142	A	175	GLU	-1	-0.986	-0.996	41.466	0.056	0.056	0.000	0.000	0.000	0.000
143	A	176	ILE	0	-0.009	0.013	35.354	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	177	PHE	0	0.002	-0.013	34.889	0.001	0.001	0.000	0.000	0.000	0.000
145	A	178	LYS	1	0.905	0.977	38.089	-0.064	-0.064	0.000	0.000	0.000	0.000
146	A	179	ASP	-1	-0.892	-0.940	37.929	0.057	0.057	0.000	0.000	0.000	0.000
147	A	180	SER	0	-0.170	-0.085	34.537	0.001	0.001	0.000	0.000	0.000	0.000
148	A	181	VAL	0	-0.043	-0.022	36.214	-0.003	-0.003	0.000	0.000	0.000	0.000

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