FMO DATABASE

FMODB ID: R8YM8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1153403.113116
FMO2-HF: Nuclear repulsion	1100635.254074
FMO2-HF: Total energy	-52767.859042
FMO2-MP2: Total energy	-52920.988328

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.
-3.628	0.316	1.695	-2.505	-3.133	0.009

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 : -0.002 / q_NPA : 0.001

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	0.113	0.064	3.855	-0.317	1.089	-0.011	-0.611	-0.784	0.003
4	A	20	SER	0	-0.093	-0.049	2.460	-2.979	-0.850	1.704	-1.758	-2.075	0.006
5	A	21	ALA	0	0.023	0.011	4.172	-0.543	-0.134	0.002	-0.136	-0.274	0.000
6	A	22	ASP	-1	-0.765	-0.834	5.967	0.332	0.332	0.000	0.000	0.000	0.000
7	A	23	ASN	0	0.025	-0.007	7.083	-0.122	-0.122	0.000	0.000	0.000	0.000
8	A	24	ALA	0	-0.003	0.020	7.998	0.042	0.042	0.000	0.000	0.000	0.000
9	A	25	ALA	0	0.055	0.033	9.643	0.101	0.101	0.000	0.000	0.000	0.000
10	A	26	LEU	0	-0.009	-0.014	11.890	0.080	0.080	0.000	0.000	0.000	0.000
11	A	27	CYS	0	-0.063	-0.033	12.246	0.066	0.066	0.000	0.000	0.000	0.000
12	A	28	ASP	-1	-0.898	-0.949	13.318	-0.348	-0.348	0.000	0.000	0.000	0.000
13	A	29	ALA	0	-0.028	-0.022	15.686	0.034	0.034	0.000	0.000	0.000	0.000
14	A	30	LEU	0	0.000	0.009	17.358	0.027	0.027	0.000	0.000	0.000	0.000
15	A	31	ALA	0	-0.003	-0.001	18.344	0.021	0.021	0.000	0.000	0.000	0.000
16	A	32	VAL	0	-0.005	-0.001	19.862	0.017	0.017	0.000	0.000	0.000	0.000
17	A	33	GLU	-1	-0.733	-0.817	21.711	-0.111	-0.111	0.000	0.000	0.000	0.000
18	A	34	HIS	0	-0.019	-0.026	21.530	0.014	0.014	0.000	0.000	0.000	0.000
19	A	35	ALA	0	-0.015	0.001	24.270	0.010	0.010	0.000	0.000	0.000	0.000
20	A	36	THR	0	-0.020	-0.028	25.487	0.007	0.007	0.000	0.000	0.000	0.000
21	A	37	ILE	0	-0.041	-0.031	26.684	0.010	0.010	0.000	0.000	0.000	0.000
22	A	38	TYR	0	-0.045	-0.019	28.928	0.009	0.009	0.000	0.000	0.000	0.000
23	A	39	GLY	0	0.035	0.001	30.085	0.005	0.005	0.000	0.000	0.000	0.000
24	A	40	TYR	0	-0.029	-0.067	30.796	0.007	0.007	0.000	0.000	0.000	0.000
25	A	41	GLY	0	-0.004	0.013	33.737	0.005	0.005	0.000	0.000	0.000	0.000
26	A	42	ILE	0	0.007	0.003	34.105	0.004	0.004	0.000	0.000	0.000	0.000
27	A	43	VAL	0	-0.025	-0.010	34.752	0.002	0.002	0.000	0.000	0.000	0.000
28	A	44	SER	0	-0.013	-0.008	37.557	0.003	0.003	0.000	0.000	0.000	0.000
29	A	45	ALA	0	-0.058	-0.018	39.681	0.003	0.003	0.000	0.000	0.000	0.000
30	A	46	LEU	0	-0.011	0.004	39.671	0.002	0.002	0.000	0.000	0.000	0.000
31	A	47	SER	0	-0.039	-0.033	40.331	0.000	0.000	0.000	0.000	0.000	0.000
32	A	48	PRO	0	0.000	0.001	42.906	0.003	0.003	0.000	0.000	0.000	0.000
33	A	49	PRO	0	0.066	0.017	45.151	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	50	GLY	0	-0.023	-0.005	46.447	0.000	0.000	0.000	0.000	0.000	0.000
35	A	51	VAL	0	0.002	0.001	41.610	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	52	ASN	0	-0.004	-0.007	41.509	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	53	PHE	0	0.022	0.012	41.276	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	54	LEU	0	-0.010	0.005	36.706	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	55	VAL	0	0.030	0.015	37.005	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	56	ALA	0	0.009	0.008	36.333	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	57	ASP	-1	-0.849	-0.902	36.438	-0.060	-0.060	0.000	0.000	0.000	0.000
42	A	58	ALA	0	0.070	0.034	32.897	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	59	LEU	0	-0.028	-0.019	31.843	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	60	LYS	1	0.852	0.922	31.892	0.052	0.052	0.000	0.000	0.000	0.000
45	A	61	GLN	0	-0.056	-0.031	29.296	0.000	0.000	0.000	0.000	0.000	0.000
46	A	62	HIS	1	0.801	0.849	26.302	0.106	0.106	0.000	0.000	0.000	0.000
47	A	63	ARG	1	0.923	0.966	26.884	0.050	0.050	0.000	0.000	0.000	0.000
48	A	64	HIS	0	-0.010	-0.004	26.974	0.003	0.003	0.000	0.000	0.000	0.000
49	A	65	ARG	1	0.775	0.867	23.215	0.126	0.126	0.000	0.000	0.000	0.000
50	A	66	ARG	1	0.817	0.871	23.001	0.052	0.052	0.000	0.000	0.000	0.000
51	A	67	ASP	-1	-0.812	-0.877	22.655	-0.044	-0.044	0.000	0.000	0.000	0.000
52	A	68	ASP	-1	-0.801	-0.896	22.757	-0.040	-0.040	0.000	0.000	0.000	0.000
53	A	69	VAL	0	0.009	-0.005	17.629	0.007	0.007	0.000	0.000	0.000	0.000
54	A	70	ILE	0	-0.016	-0.003	18.337	0.008	0.008	0.000	0.000	0.000	0.000
55	A	71	VAL	0	-0.014	0.011	19.356	0.016	0.016	0.000	0.000	0.000	0.000
56	A	72	MET	0	-0.021	-0.002	16.550	0.014	0.014	0.000	0.000	0.000	0.000
57	A	73	LEU	0	0.001	-0.005	13.294	0.030	0.030	0.000	0.000	0.000	0.000
58	A	74	SER	0	-0.022	-0.023	14.788	0.031	0.031	0.000	0.000	0.000	0.000
59	A	75	ALA	0	-0.064	-0.028	16.659	0.018	0.018	0.000	0.000	0.000	0.000
60	A	76	ARG	1	0.708	0.812	10.727	0.037	0.037	0.000	0.000	0.000	0.000
61	A	77	GLY	0	-0.022	0.004	11.480	0.058	0.058	0.000	0.000	0.000	0.000
62	A	78	VAL	0	-0.046	-0.024	10.792	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	79	THR	0	-0.033	-0.028	13.540	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	80	ALA	0	0.031	0.020	16.428	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	81	PRO	0	0.004	0.021	15.895	0.006	0.006	0.000	0.000	0.000	0.000
66	A	82	ILE	0	0.020	0.011	18.691	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	83	ALA	0	-0.019	-0.008	22.387	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	84	ALA	0	0.002	0.000	24.955	0.007	0.007	0.000	0.000	0.000	0.000
69	A	85	ALA	0	-0.018	-0.022	26.385	0.001	0.001	0.000	0.000	0.000	0.000
70	A	86	GLY	0	-0.013	-0.005	29.286	0.003	0.003	0.000	0.000	0.000	0.000
71	A	87	TYR	0	0.041	0.024	23.522	0.000	0.000	0.000	0.000	0.000	0.000
72	A	88	GLN	0	-0.015	-0.002	28.534	0.009	0.009	0.000	0.000	0.000	0.000
73	A	89	LEU	0	0.019	0.013	28.789	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	90	PRO	0	0.033	0.019	27.326	0.002	0.002	0.000	0.000	0.000	0.000
75	A	91	MET	0	-0.026	-0.008	29.209	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	92	GLN	0	0.008	0.007	32.805	0.004	0.004	0.000	0.000	0.000	0.000
77	A	93	VAL	0	-0.030	-0.023	36.136	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	94	SER	0	-0.051	-0.029	38.778	0.003	0.003	0.000	0.000	0.000	0.000
79	A	95	SER	0	0.007	-0.012	42.197	0.003	0.003	0.000	0.000	0.000	0.000
80	A	96	ALA	0	0.076	0.030	42.155	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	97	ALA	0	-0.009	-0.013	42.259	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	98	ASP	-1	-0.772	-0.860	38.947	-0.061	-0.061	0.000	0.000	0.000	0.000
83	A	99	ALA	0	0.005	0.024	37.666	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	100	ALA	0	0.054	0.022	36.770	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	101	ARG	1	0.875	0.932	35.939	0.058	0.058	0.000	0.000	0.000	0.000
86	A	102	LEU	0	0.034	0.006	31.885	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	103	ALA	0	0.026	0.009	31.954	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	104	VAL	0	-0.022	-0.015	31.400	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	105	ARG	1	0.764	0.878	25.534	0.126	0.126	0.000	0.000	0.000	0.000
90	A	106	MET	0	0.024	0.030	27.432	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	107	GLU	-1	-0.745	-0.823	26.470	-0.117	-0.117	0.000	0.000	0.000	0.000
92	A	108	ASN	0	-0.012	-0.009	26.309	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	109	ASP	-1	-0.855	-0.908	23.466	-0.173	-0.173	0.000	0.000	0.000	0.000
94	A	110	GLY	0	0.038	0.013	21.935	-0.023	-0.023	0.000	0.000	0.000	0.000
95	A	111	ALA	0	-0.014	-0.020	21.751	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	112	THR	0	-0.059	-0.038	19.286	-0.023	-0.023	0.000	0.000	0.000	0.000
97	A	113	ALA	0	0.021	0.016	17.548	-0.040	-0.040	0.000	0.000	0.000	0.000
98	A	114	TRP	0	0.032	-0.016	16.871	-0.045	-0.045	0.000	0.000	0.000	0.000
99	A	115	ARG	1	0.898	0.951	17.864	0.263	0.263	0.000	0.000	0.000	0.000
100	A	116	ALA	0	0.039	0.029	13.357	-0.029	-0.029	0.000	0.000	0.000	0.000
101	A	117	VAL	0	0.015	0.006	12.974	-0.090	-0.090	0.000	0.000	0.000	0.000
102	A	118	VAL	0	-0.064	-0.040	14.054	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	119	GLU	-1	-0.988	-0.977	12.011	-0.741	-0.741	0.000	0.000	0.000	0.000
104	A	120	HIS	0	-0.044	-0.032	8.191	-0.417	-0.417	0.000	0.000	0.000	0.000
105	A	121	ALA	0	-0.014	0.012	9.450	-0.029	-0.029	0.000	0.000	0.000	0.000
106	A	122	GLU	-1	-0.874	-0.949	6.922	0.692	0.692	0.000	0.000	0.000	0.000
107	A	123	THR	0	-0.039	-0.038	10.904	0.005	0.005	0.000	0.000	0.000	0.000
108	A	124	ALA	0	-0.011	-0.015	14.373	-0.055	-0.055	0.000	0.000	0.000	0.000
109	A	125	ASP	-1	-0.878	-0.944	17.735	-0.052	-0.052	0.000	0.000	0.000	0.000
110	A	126	ASP	-1	-0.776	-0.857	14.203	-0.037	-0.037	0.000	0.000	0.000	0.000
111	A	127	ARG	1	0.876	0.933	13.527	0.266	0.266	0.000	0.000	0.000	0.000
112	A	128	VAL	0	-0.013	0.019	17.565	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	129	PHE	0	-0.016	0.011	19.479	0.000	0.000	0.000	0.000	0.000	0.000
114	A	130	ALA	0	0.035	0.017	17.639	0.001	0.001	0.000	0.000	0.000	0.000
115	A	131	SER	0	-0.005	-0.034	19.703	0.003	0.003	0.000	0.000	0.000	0.000
116	A	132	THR	0	-0.034	-0.010	21.942	0.012	0.012	0.000	0.000	0.000	0.000
117	A	133	ALA	0	0.040	0.027	21.999	0.005	0.005	0.000	0.000	0.000	0.000
118	A	134	LEU	0	-0.030	0.003	20.480	0.005	0.005	0.000	0.000	0.000	0.000
119	A	135	THR	0	-0.024	-0.028	23.454	0.009	0.009	0.000	0.000	0.000	0.000
120	A	136	GLU	-1	-0.827	-0.897	26.850	-0.088	-0.088	0.000	0.000	0.000	0.000
121	A	137	SER	0	-0.005	-0.009	25.164	0.009	0.009	0.000	0.000	0.000	0.000
122	A	138	ALA	0	0.027	0.016	26.988	0.005	0.005	0.000	0.000	0.000	0.000
123	A	139	VAL	0	-0.015	-0.006	28.612	0.009	0.009	0.000	0.000	0.000	0.000
124	A	140	MET	0	0.024	0.031	30.478	0.011	0.011	0.000	0.000	0.000	0.000
125	A	141	ALA	0	0.054	0.032	29.829	0.007	0.007	0.000	0.000	0.000	0.000
126	A	142	THR	0	-0.063	-0.035	31.921	0.009	0.009	0.000	0.000	0.000	0.000
127	A	143	ARG	1	0.753	0.849	34.725	0.075	0.075	0.000	0.000	0.000	0.000
128	A	144	TRP	0	0.081	0.020	33.889	0.007	0.007	0.000	0.000	0.000	0.000
129	A	145	ASN	0	-0.001	-0.016	33.530	0.006	0.006	0.000	0.000	0.000	0.000
130	A	146	ARG	1	0.885	0.953	37.320	0.076	0.076	0.000	0.000	0.000	0.000
131	A	147	VAL	0	-0.028	-0.003	39.814	0.004	0.004	0.000	0.000	0.000	0.000
132	A	148	LEU	0	-0.009	-0.008	37.370	0.003	0.003	0.000	0.000	0.000	0.000
133	A	149	GLY	0	-0.013	-0.004	41.333	0.002	0.002	0.000	0.000	0.000	0.000
134	A	150	ALA	0	-0.042	-0.009	43.104	0.002	0.002	0.000	0.000	0.000	0.000
135	A	151	TRP	0	-0.044	-0.028	41.860	0.002	0.002	0.000	0.000	0.000	0.000
136	A	152	PRO	0	0.016	-0.005	46.388	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	153	ILE	0	0.029	0.025	43.116	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	154	THR	0	-0.038	-0.020	46.162	0.001	0.001	0.000	0.000	0.000	0.000
139	A	155	ALA	0	-0.030	-0.010	44.882	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	156	ALA	0	0.009	0.007	45.202	0.002	0.002	0.000	0.000	0.000	0.000
141	A	157	PHE	0	0.008	-0.002	46.584	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	158	PRO	0	-0.012	0.007	45.633	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)