FMO DATABASE

FMODB ID: 6YG7Z

Calculation Name: 2IB0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IB0

Chain ID: A

ChEMBL ID:

UniProt ID: O05815

Base Structure: X-ray

Registration Date: 2023-09-22

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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1148013.61286
FMO2-HF: Nuclear repulsion	1095246.768925
FMO2-HF: Total energy	-52766.843934
FMO2-MP2: Total energy	-52920.020955

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:17:SER)

Summations of interaction energy for fragment #1(A:17:SER)

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.
-11.61	-6.681	4.899	-4.161	-5.665	0.022

Interaction energy analysis for fragmet #1(A:17:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.011

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	19	GLY	0	0.075	0.053	2.897	-2.964	0.069	0.303	-1.604	-1.733	0.004
4	A	20	SER	0	-0.118	-0.065	2.313	-7.278	-6.017	4.563	-2.327	-3.496	0.017
5	A	21	ALA	0	0.054	0.025	3.861	-1.612	-0.977	0.033	-0.230	-0.436	0.001
6	A	22	ASP	-1	-0.738	-0.845	5.604	0.300	0.300	0.000	0.000	0.000	0.000
7	A	23	ASN	0	0.004	-0.019	7.090	-0.111	-0.111	0.000	0.000	0.000	0.000
8	A	24	ALA	0	-0.019	0.004	7.707	-0.044	-0.044	0.000	0.000	0.000	0.000
9	A	25	ALA	0	0.053	0.038	9.383	0.029	0.029	0.000	0.000	0.000	0.000
10	A	26	LEU	0	-0.003	-0.012	11.448	0.036	0.036	0.000	0.000	0.000	0.000
11	A	27	CYS	0	-0.066	-0.041	12.121	0.022	0.022	0.000	0.000	0.000	0.000
12	A	28	ASP	-1	-0.879	-0.936	12.749	-0.247	-0.247	0.000	0.000	0.000	0.000
13	A	29	ALA	0	-0.033	-0.016	15.258	0.018	0.018	0.000	0.000	0.000	0.000
14	A	30	LEU	0	-0.015	-0.001	17.271	0.014	0.014	0.000	0.000	0.000	0.000
15	A	31	ALA	0	-0.013	-0.008	18.232	0.011	0.011	0.000	0.000	0.000	0.000
16	A	32	VAL	0	0.009	0.006	19.196	0.009	0.009	0.000	0.000	0.000	0.000
17	A	33	GLU	-1	-0.742	-0.849	21.424	-0.063	-0.063	0.000	0.000	0.000	0.000
18	A	34	HIS	0	-0.023	-0.019	21.905	0.008	0.008	0.000	0.000	0.000	0.000
19	A	35	ALA	0	-0.006	0.008	24.125	0.006	0.006	0.000	0.000	0.000	0.000
20	A	36	THR	0	-0.012	-0.012	25.281	0.004	0.004	0.000	0.000	0.000	0.000
21	A	37	ILE	0	-0.055	-0.031	26.699	0.005	0.005	0.000	0.000	0.000	0.000
22	A	38	TYR	0	-0.020	-0.012	28.893	0.004	0.004	0.000	0.000	0.000	0.000
23	A	39	GLY	0	0.042	0.006	29.899	0.003	0.003	0.000	0.000	0.000	0.000
24	A	40	TYR	0	-0.041	-0.073	30.480	0.004	0.004	0.000	0.000	0.000	0.000
25	A	41	GLY	0	-0.008	0.015	33.670	0.003	0.003	0.000	0.000	0.000	0.000
26	A	42	ILE	0	0.006	0.006	33.893	0.002	0.002	0.000	0.000	0.000	0.000
27	A	43	VAL	0	-0.018	-0.006	34.389	0.002	0.002	0.000	0.000	0.000	0.000
28	A	44	SER	0	-0.066	-0.022	37.239	0.002	0.002	0.000	0.000	0.000	0.000
29	A	45	ALA	0	-0.003	0.008	39.558	0.001	0.001	0.000	0.000	0.000	0.000
30	A	46	LEU	0	-0.035	-0.002	38.954	0.001	0.001	0.000	0.000	0.000	0.000
31	A	47	SER	0	-0.054	-0.067	40.086	0.000	0.000	0.000	0.000	0.000	0.000
32	A	48	PRO	0	-0.035	-0.013	42.651	0.001	0.001	0.000	0.000	0.000	0.000
33	A	49	PRO	0	0.080	0.029	44.483	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	50	GLY	0	-0.028	-0.002	46.171	0.000	0.000	0.000	0.000	0.000	0.000
35	A	51	VAL	0	0.007	0.010	41.017	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	52	ASN	0	0.011	-0.003	41.076	0.000	0.000	0.000	0.000	0.000	0.000
37	A	53	PHE	0	0.044	0.023	41.230	0.000	0.000	0.000	0.000	0.000	0.000
38	A	54	LEU	0	-0.007	0.012	36.619	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	55	VAL	0	0.028	0.013	36.764	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	56	ALA	0	-0.017	-0.004	36.188	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	57	ASP	-1	-0.901	-0.956	35.920	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	58	ALA	0	0.017	0.004	32.500	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	59	LEU	0	-0.026	-0.021	31.542	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	60	LYS	1	0.946	0.977	31.584	0.030	0.030	0.000	0.000	0.000	0.000
45	A	61	GLN	0	0.020	0.004	28.671	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	62	HIS	1	0.788	0.852	26.278	0.059	0.059	0.000	0.000	0.000	0.000
47	A	63	ARG	1	0.916	0.961	26.636	0.030	0.030	0.000	0.000	0.000	0.000
48	A	64	HIS	0	0.015	0.024	27.101	0.002	0.002	0.000	0.000	0.000	0.000
49	A	65	ARG	1	0.848	0.934	22.604	0.068	0.068	0.000	0.000	0.000	0.000
50	A	66	ARG	1	0.895	0.937	22.697	0.035	0.035	0.000	0.000	0.000	0.000
51	A	67	ASP	-1	-0.886	-0.944	22.390	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	68	ASP	-1	-0.837	-0.931	22.213	-0.030	-0.030	0.000	0.000	0.000	0.000
53	A	69	VAL	0	-0.010	-0.013	17.121	0.003	0.003	0.000	0.000	0.000	0.000
54	A	70	ILE	0	-0.035	-0.019	17.922	0.005	0.005	0.000	0.000	0.000	0.000
55	A	71	VAL	0	-0.013	0.001	18.881	0.005	0.005	0.000	0.000	0.000	0.000
56	A	72	MET	0	-0.015	-0.003	15.798	0.001	0.001	0.000	0.000	0.000	0.000
57	A	73	LEU	0	0.011	-0.003	12.991	0.014	0.014	0.000	0.000	0.000	0.000
58	A	74	SER	0	0.011	0.007	14.093	0.005	0.005	0.000	0.000	0.000	0.000
59	A	75	ALA	0	-0.060	-0.023	15.916	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	76	ARG	1	0.731	0.848	9.772	-0.101	-0.101	0.000	0.000	0.000	0.000
61	A	77	GLY	0	-0.040	-0.004	10.849	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	78	VAL	0	-0.052	-0.025	10.311	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	79	THR	0	-0.037	-0.023	13.058	0.001	0.001	0.000	0.000	0.000	0.000
64	A	80	ALA	0	0.021	0.003	15.974	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	81	PRO	0	0.026	0.023	15.927	0.003	0.003	0.000	0.000	0.000	0.000
66	A	82	ILE	0	0.007	0.004	18.833	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	83	ALA	0	-0.033	-0.016	22.609	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	84	ALA	0	0.007	0.007	24.822	0.004	0.004	0.000	0.000	0.000	0.000
69	A	85	ALA	0	-0.022	-0.023	26.329	0.000	0.000	0.000	0.000	0.000	0.000
70	A	86	GLY	0	0.003	0.005	29.797	0.001	0.001	0.000	0.000	0.000	0.000
71	A	87	TYR	0	0.025	0.014	23.657	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	88	GLN	0	0.013	0.021	27.734	0.006	0.006	0.000	0.000	0.000	0.000
73	A	89	LEU	0	-0.008	-0.021	28.068	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	90	PRO	0	0.016	0.009	27.311	0.001	0.001	0.000	0.000	0.000	0.000
75	A	91	MET	0	-0.058	-0.017	29.007	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	92	GLN	0	0.002	0.001	32.693	0.002	0.002	0.000	0.000	0.000	0.000
77	A	93	VAL	0	-0.041	-0.024	35.793	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	94	SER	0	-0.086	-0.042	38.523	0.002	0.002	0.000	0.000	0.000	0.000
79	A	95	SER	0	0.025	-0.001	41.909	0.002	0.002	0.000	0.000	0.000	0.000
80	A	96	ALA	0	0.084	0.028	41.843	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	97	ALA	0	0.009	-0.002	41.921	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	98	ASP	-1	-0.791	-0.888	38.521	-0.035	-0.035	0.000	0.000	0.000	0.000
83	A	99	ALA	0	0.014	0.020	37.227	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	100	ALA	0	0.065	0.027	36.249	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	101	ARG	1	0.919	0.955	35.594	0.035	0.035	0.000	0.000	0.000	0.000
86	A	102	LEU	0	0.006	0.007	31.458	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	103	ALA	0	0.039	0.009	31.572	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	104	VAL	0	-0.035	-0.013	31.163	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	105	ARG	1	0.851	0.929	26.187	0.072	0.072	0.000	0.000	0.000	0.000
90	A	106	MET	0	-0.019	0.009	27.212	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	107	GLU	-1	-0.739	-0.826	26.156	-0.069	-0.069	0.000	0.000	0.000	0.000
92	A	108	ASN	0	-0.002	-0.011	25.934	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	109	ASP	-1	-0.861	-0.930	23.098	-0.106	-0.106	0.000	0.000	0.000	0.000
94	A	110	GLY	0	0.026	0.011	21.602	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	111	ALA	0	-0.016	-0.020	21.450	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	112	THR	0	-0.084	-0.041	18.664	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	113	ALA	0	0.016	0.016	17.170	-0.027	-0.027	0.000	0.000	0.000	0.000
98	A	114	TRP	0	0.032	-0.005	16.566	-0.021	-0.021	0.000	0.000	0.000	0.000
99	A	115	ARG	1	0.927	0.957	17.657	0.165	0.165	0.000	0.000	0.000	0.000
100	A	116	ALA	0	0.031	0.023	13.119	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	117	VAL	0	0.039	0.025	12.874	-0.051	-0.051	0.000	0.000	0.000	0.000
102	A	118	VAL	0	-0.085	-0.050	13.832	0.012	0.012	0.000	0.000	0.000	0.000
103	A	119	GLU	-1	-1.026	-1.015	11.892	-0.446	-0.446	0.000	0.000	0.000	0.000
104	A	120	HIS	0	0.004	0.004	8.668	-0.189	-0.189	0.000	0.000	0.000	0.000
105	A	121	ALA	0	-0.009	0.017	9.415	0.093	0.093	0.000	0.000	0.000	0.000
106	A	122	GLU	-1	-0.897	-0.966	6.698	0.763	0.763	0.000	0.000	0.000	0.000
107	A	123	THR	0	-0.023	-0.017	10.794	-0.037	-0.037	0.000	0.000	0.000	0.000
108	A	124	ALA	0	-0.009	-0.023	14.055	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	125	ASP	-1	-0.894	-0.938	17.550	-0.025	-0.025	0.000	0.000	0.000	0.000
110	A	126	ASP	-1	-0.816	-0.903	13.661	0.014	0.014	0.000	0.000	0.000	0.000
111	A	127	ARG	1	0.890	0.955	14.315	0.080	0.080	0.000	0.000	0.000	0.000
112	A	128	VAL	0	-0.027	-0.007	17.146	-0.010	-0.010	0.000	0.000	0.000	0.000
113	A	129	PHE	0	-0.006	0.009	18.909	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	130	ALA	0	0.039	0.018	17.119	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	131	SER	0	-0.028	-0.012	19.241	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	132	THR	0	0.007	0.003	21.819	0.003	0.003	0.000	0.000	0.000	0.000
117	A	133	ALA	0	0.024	0.018	21.550	0.003	0.003	0.000	0.000	0.000	0.000
118	A	134	LEU	0	-0.039	-0.018	21.041	0.001	0.001	0.000	0.000	0.000	0.000
119	A	135	THR	0	-0.026	-0.023	23.362	0.003	0.003	0.000	0.000	0.000	0.000
120	A	136	GLU	-1	-0.907	-0.958	26.836	-0.050	-0.050	0.000	0.000	0.000	0.000
121	A	137	SER	0	-0.015	0.008	24.835	0.005	0.005	0.000	0.000	0.000	0.000
122	A	138	ALA	0	0.012	0.002	27.136	0.003	0.003	0.000	0.000	0.000	0.000
123	A	139	VAL	0	-0.018	-0.002	28.700	0.005	0.005	0.000	0.000	0.000	0.000
124	A	140	MET	0	-0.036	-0.010	30.344	0.006	0.006	0.000	0.000	0.000	0.000
125	A	141	ALA	0	0.069	0.032	29.890	0.004	0.004	0.000	0.000	0.000	0.000
126	A	142	THR	0	-0.097	-0.048	31.981	0.005	0.005	0.000	0.000	0.000	0.000
127	A	143	ARG	1	0.859	0.924	34.618	0.043	0.043	0.000	0.000	0.000	0.000
128	A	144	TRP	0	0.065	0.019	33.790	0.004	0.004	0.000	0.000	0.000	0.000
129	A	145	ASN	0	0.026	0.006	33.832	0.004	0.004	0.000	0.000	0.000	0.000
130	A	146	ARG	1	0.911	0.971	37.381	0.043	0.043	0.000	0.000	0.000	0.000
131	A	147	VAL	0	-0.025	-0.007	39.828	0.002	0.002	0.000	0.000	0.000	0.000
132	A	148	LEU	0	-0.022	-0.019	37.317	0.002	0.002	0.000	0.000	0.000	0.000
133	A	149	GLY	0	-0.012	0.003	41.301	0.001	0.001	0.000	0.000	0.000	0.000
134	A	150	ALA	0	-0.027	0.001	43.111	0.001	0.001	0.000	0.000	0.000	0.000
135	A	151	TRP	0	-0.056	-0.031	41.805	0.001	0.001	0.000	0.000	0.000	0.000
136	A	152	PRO	0	0.021	0.005	46.296	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	153	ILE	0	-0.002	0.010	43.143	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	154	THR	0	-0.016	-0.021	45.681	0.001	0.001	0.000	0.000	0.000	0.000
139	A	155	ALA	0	-0.024	-0.011	44.389	0.000	0.000	0.000	0.000	0.000	0.000
140	A	156	ALA	0	0.016	0.017	44.984	0.001	0.001	0.000	0.000	0.000	0.000
141	A	157	PHE	0	0.006	-0.010	46.509	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	158	PRO	0	-0.002	0.017	45.594	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:17:SER)