FMO DATABASE

FMODB ID: ZVNLN

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	OptHSide
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	-1149256.958637
FMO2-HF: Nuclear repulsion	1096489.446265
FMO2-HF: Total energy	-52767.512372
FMO2-MP2: Total energy	-52920.676477

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.
-9.894	-4.287	2.957	-3.732	-4.833	0.015

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 : -0.013 / q_NPA : -0.015

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	0.087	0.060	2.968	-3.187	-0.306	0.152	-1.471	-1.562	0.005
4	A	20	SER	0	-0.111	-0.064	2.239	-6.292	-4.108	2.798	-2.071	-2.911	0.010
5	A	21	ALA	0	0.045	0.026	4.048	-1.015	-0.473	0.007	-0.190	-0.360	0.000
6	A	22	ASP	-1	-0.745	-0.829	5.559	0.475	0.475	0.000	0.000	0.000	0.000
7	A	23	ASN	0	0.033	-0.009	7.207	-0.178	-0.178	0.000	0.000	0.000	0.000
8	A	24	ALA	0	-0.010	0.015	7.651	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	25	ALA	0	0.045	0.028	9.376	0.049	0.049	0.000	0.000	0.000	0.000
10	A	26	LEU	0	0.000	-0.008	11.411	0.049	0.049	0.000	0.000	0.000	0.000
11	A	27	CYS	0	-0.078	-0.048	12.309	0.037	0.037	0.000	0.000	0.000	0.000
12	A	28	ASP	-1	-0.887	-0.940	12.903	-0.246	-0.246	0.000	0.000	0.000	0.000
13	A	29	ALA	0	-0.037	-0.015	15.242	0.019	0.019	0.000	0.000	0.000	0.000
14	A	30	LEU	0	0.000	0.000	17.255	0.015	0.015	0.000	0.000	0.000	0.000
15	A	31	ALA	0	-0.014	-0.006	18.224	0.012	0.012	0.000	0.000	0.000	0.000
16	A	32	VAL	0	0.011	0.006	19.241	0.008	0.008	0.000	0.000	0.000	0.000
17	A	33	GLU	-1	-0.731	-0.832	21.402	-0.060	-0.060	0.000	0.000	0.000	0.000
18	A	34	HIS	0	-0.029	-0.029	21.795	0.003	0.003	0.000	0.000	0.000	0.000
19	A	35	ALA	0	-0.006	0.007	24.114	0.005	0.005	0.000	0.000	0.000	0.000
20	A	36	THR	0	-0.036	-0.032	25.089	0.001	0.001	0.000	0.000	0.000	0.000
21	A	37	ILE	0	-0.032	-0.023	26.927	0.005	0.005	0.000	0.000	0.000	0.000
22	A	38	TYR	0	-0.023	-0.005	28.883	0.004	0.004	0.000	0.000	0.000	0.000
23	A	39	GLY	0	0.043	0.002	29.888	0.002	0.002	0.000	0.000	0.000	0.000
24	A	40	TYR	0	-0.044	-0.070	30.407	0.003	0.003	0.000	0.000	0.000	0.000
25	A	41	GLY	0	-0.003	0.017	33.647	0.002	0.002	0.000	0.000	0.000	0.000
26	A	42	ILE	0	0.004	0.003	33.879	0.002	0.002	0.000	0.000	0.000	0.000
27	A	43	VAL	0	-0.018	-0.006	34.417	0.001	0.001	0.000	0.000	0.000	0.000
28	A	44	SER	0	-0.025	-0.008	37.212	0.001	0.001	0.000	0.000	0.000	0.000
29	A	45	ALA	0	-0.058	-0.018	39.534	0.001	0.001	0.000	0.000	0.000	0.000
30	A	46	LEU	0	-0.023	-0.001	38.922	0.001	0.001	0.000	0.000	0.000	0.000
31	A	47	SER	0	-0.052	-0.054	40.082	0.000	0.000	0.000	0.000	0.000	0.000
32	A	48	PRO	0	-0.032	-0.014	42.619	0.002	0.002	0.000	0.000	0.000	0.000
33	A	49	PRO	0	0.092	0.043	44.448	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	50	GLY	0	-0.037	-0.010	46.135	0.000	0.000	0.000	0.000	0.000	0.000
35	A	51	VAL	0	0.004	0.001	41.018	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	52	ASN	0	0.002	-0.015	41.038	0.000	0.000	0.000	0.000	0.000	0.000
37	A	53	PHE	0	0.040	0.028	41.198	0.000	0.000	0.000	0.000	0.000	0.000
38	A	54	LEU	0	0.001	0.014	36.629	0.000	0.000	0.000	0.000	0.000	0.000
39	A	55	VAL	0	0.026	0.013	36.725	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	56	ALA	0	-0.002	0.003	36.158	0.000	0.000	0.000	0.000	0.000	0.000
41	A	57	ASP	-1	-0.826	-0.909	35.992	-0.031	-0.031	0.000	0.000	0.000	0.000
42	A	58	ALA	0	0.028	0.017	32.552	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	59	LEU	0	-0.023	-0.016	31.565	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	60	LYS	1	0.860	0.933	31.877	0.027	0.027	0.000	0.000	0.000	0.000
45	A	61	GLN	0	-0.032	-0.026	28.958	0.000	0.000	0.000	0.000	0.000	0.000
46	A	62	HIS	1	0.788	0.847	26.092	0.059	0.059	0.000	0.000	0.000	0.000
47	A	63	ARG	1	0.923	0.966	26.960	0.021	0.021	0.000	0.000	0.000	0.000
48	A	64	HIS	0	-0.015	0.000	26.836	0.003	0.003	0.000	0.000	0.000	0.000
49	A	65	ARG	1	0.802	0.888	22.918	0.071	0.071	0.000	0.000	0.000	0.000
50	A	66	ARG	1	0.832	0.886	23.018	0.014	0.014	0.000	0.000	0.000	0.000
51	A	67	ASP	-1	-0.840	-0.903	22.684	0.001	0.001	0.000	0.000	0.000	0.000
52	A	68	ASP	-1	-0.801	-0.902	22.481	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	69	VAL	0	-0.005	-0.015	17.399	0.009	0.009	0.000	0.000	0.000	0.000
54	A	70	ILE	0	-0.028	-0.010	18.233	0.015	0.015	0.000	0.000	0.000	0.000
55	A	71	VAL	0	-0.015	0.005	19.292	0.015	0.015	0.000	0.000	0.000	0.000
56	A	72	MET	0	-0.015	0.000	16.142	0.009	0.009	0.000	0.000	0.000	0.000
57	A	73	LEU	0	0.007	-0.004	13.269	0.031	0.031	0.000	0.000	0.000	0.000
58	A	74	SER	0	0.000	-0.005	14.464	0.027	0.027	0.000	0.000	0.000	0.000
59	A	75	ALA	0	-0.064	-0.025	16.208	0.009	0.009	0.000	0.000	0.000	0.000
60	A	76	ARG	1	0.732	0.834	10.381	-0.165	-0.165	0.000	0.000	0.000	0.000
61	A	77	GLY	0	-0.040	-0.002	11.119	0.038	0.038	0.000	0.000	0.000	0.000
62	A	78	VAL	0	-0.050	-0.026	10.722	0.006	0.006	0.000	0.000	0.000	0.000
63	A	79	THR	0	-0.036	-0.017	13.425	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	80	ALA	0	0.027	0.004	16.392	0.000	0.000	0.000	0.000	0.000	0.000
65	A	81	PRO	0	0.024	0.026	16.087	0.002	0.002	0.000	0.000	0.000	0.000
66	A	82	ILE	0	0.012	0.011	18.906	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	83	ALA	0	-0.032	-0.016	22.725	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	84	ALA	0	0.007	0.008	24.821	0.006	0.006	0.000	0.000	0.000	0.000
69	A	85	ALA	0	-0.017	-0.021	26.347	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	86	GLY	0	0.001	0.002	29.851	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	87	TYR	0	0.018	0.010	23.552	0.001	0.001	0.000	0.000	0.000	0.000
72	A	88	GLN	0	-0.007	0.008	27.736	0.007	0.007	0.000	0.000	0.000	0.000
73	A	89	LEU	0	0.004	-0.012	28.056	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	90	PRO	0	0.020	0.012	27.208	0.001	0.001	0.000	0.000	0.000	0.000
75	A	91	MET	0	-0.047	-0.011	28.980	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	92	GLN	0	0.004	0.004	32.664	0.004	0.004	0.000	0.000	0.000	0.000
77	A	93	VAL	0	-0.040	-0.026	35.830	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	94	SER	0	-0.072	-0.030	38.497	0.002	0.002	0.000	0.000	0.000	0.000
79	A	95	SER	0	0.005	-0.003	41.900	0.002	0.002	0.000	0.000	0.000	0.000
80	A	96	ALA	0	0.076	0.021	41.811	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	97	ALA	0	0.016	0.002	41.884	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	98	ASP	-1	-0.783	-0.880	38.584	-0.038	-0.038	0.000	0.000	0.000	0.000
83	A	99	ALA	0	0.023	0.028	37.190	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	100	ALA	0	0.063	0.025	36.211	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	101	ARG	1	0.903	0.940	35.559	0.038	0.038	0.000	0.000	0.000	0.000
86	A	102	LEU	0	0.008	0.003	31.358	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	103	ALA	0	0.041	0.009	31.533	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	104	VAL	0	-0.031	-0.011	31.118	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	105	ARG	1	0.821	0.896	25.346	0.085	0.085	0.000	0.000	0.000	0.000
90	A	106	MET	0	-0.002	0.021	27.187	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	107	GLU	-1	-0.750	-0.825	26.114	-0.072	-0.072	0.000	0.000	0.000	0.000
92	A	108	ASN	0	-0.013	-0.015	25.881	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	109	ASP	-1	-0.848	-0.908	23.068	-0.123	-0.123	0.000	0.000	0.000	0.000
94	A	110	GLY	0	0.038	0.021	21.553	-0.015	-0.015	0.000	0.000	0.000	0.000
95	A	111	ALA	0	-0.020	-0.024	21.398	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	112	THR	0	-0.076	-0.046	18.767	-0.020	-0.020	0.000	0.000	0.000	0.000
97	A	113	ALA	0	0.022	0.023	17.119	-0.035	-0.035	0.000	0.000	0.000	0.000
98	A	114	TRP	0	0.037	-0.008	16.512	-0.027	-0.027	0.000	0.000	0.000	0.000
99	A	115	ARG	1	0.915	0.953	17.593	0.208	0.208	0.000	0.000	0.000	0.000
100	A	116	ALA	0	0.032	0.026	13.100	-0.023	-0.023	0.000	0.000	0.000	0.000
101	A	117	VAL	0	0.051	0.029	12.804	-0.070	-0.070	0.000	0.000	0.000	0.000
102	A	118	VAL	0	-0.080	-0.051	13.890	0.007	0.007	0.000	0.000	0.000	0.000
103	A	119	GLU	-1	-0.984	-0.985	12.099	-0.627	-0.627	0.000	0.000	0.000	0.000
104	A	120	HIS	0	-0.044	-0.028	8.345	-0.321	-0.321	0.000	0.000	0.000	0.000
105	A	121	ALA	0	-0.014	0.021	9.606	0.083	0.083	0.000	0.000	0.000	0.000
106	A	122	GLU	-1	-0.866	-0.945	6.714	1.091	1.091	0.000	0.000	0.000	0.000
107	A	123	THR	0	-0.029	-0.011	10.910	-0.044	-0.044	0.000	0.000	0.000	0.000
108	A	124	ALA	0	-0.002	-0.016	14.151	-0.036	-0.036	0.000	0.000	0.000	0.000
109	A	125	ASP	-1	-0.898	-0.945	17.690	0.001	0.001	0.000	0.000	0.000	0.000
110	A	126	ASP	-1	-0.790	-0.888	13.721	0.073	0.073	0.000	0.000	0.000	0.000
111	A	127	ARG	1	0.837	0.905	13.929	0.108	0.108	0.000	0.000	0.000	0.000
112	A	128	VAL	0	-0.014	-0.001	17.358	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	129	PHE	0	-0.005	0.020	19.116	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	130	ALA	0	0.038	0.019	17.391	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	131	SER	0	-0.014	-0.010	19.523	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	132	THR	0	-0.011	-0.005	21.993	0.003	0.003	0.000	0.000	0.000	0.000
117	A	133	ALA	0	0.037	0.029	21.712	0.002	0.002	0.000	0.000	0.000	0.000
118	A	134	LEU	0	-0.034	-0.004	20.480	0.001	0.001	0.000	0.000	0.000	0.000
119	A	135	THR	0	-0.037	-0.038	23.300	0.002	0.002	0.000	0.000	0.000	0.000
120	A	136	GLU	-1	-0.833	-0.904	26.770	-0.047	-0.047	0.000	0.000	0.000	0.000
121	A	137	SER	0	-0.010	-0.006	24.850	0.007	0.007	0.000	0.000	0.000	0.000
122	A	138	ALA	0	0.018	0.010	27.066	0.003	0.003	0.000	0.000	0.000	0.000
123	A	139	VAL	0	-0.012	0.000	28.636	0.005	0.005	0.000	0.000	0.000	0.000
124	A	140	MET	0	-0.016	-0.001	30.283	0.007	0.007	0.000	0.000	0.000	0.000
125	A	141	ALA	0	0.068	0.030	29.838	0.005	0.005	0.000	0.000	0.000	0.000
126	A	142	THR	0	-0.064	-0.028	31.923	0.005	0.005	0.000	0.000	0.000	0.000
127	A	143	ARG	1	0.786	0.874	34.554	0.045	0.045	0.000	0.000	0.000	0.000
128	A	144	TRP	0	0.062	0.018	33.726	0.005	0.005	0.000	0.000	0.000	0.000
129	A	145	ASN	0	-0.006	-0.014	33.492	0.003	0.003	0.000	0.000	0.000	0.000
130	A	146	ARG	1	0.923	0.973	37.322	0.050	0.050	0.000	0.000	0.000	0.000
131	A	147	VAL	0	-0.021	-0.003	39.779	0.002	0.002	0.000	0.000	0.000	0.000
132	A	148	LEU	0	-0.026	-0.020	37.116	0.002	0.002	0.000	0.000	0.000	0.000
133	A	149	GLY	0	-0.007	0.004	41.245	0.001	0.001	0.000	0.000	0.000	0.000
134	A	150	ALA	0	-0.029	-0.001	43.050	0.001	0.001	0.000	0.000	0.000	0.000
135	A	151	TRP	0	-0.064	-0.037	41.674	0.002	0.002	0.000	0.000	0.000	0.000
136	A	152	PRO	0	0.023	0.006	46.240	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	153	ILE	0	0.001	0.012	43.026	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	154	THR	0	-0.018	-0.023	45.602	0.001	0.001	0.000	0.000	0.000	0.000
139	A	155	ALA	0	-0.023	-0.009	44.330	0.000	0.000	0.000	0.000	0.000	0.000
140	A	156	ALA	0	0.018	0.017	44.941	0.002	0.002	0.000	0.000	0.000	0.000
141	A	157	PHE	0	0.002	-0.010	46.457	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	158	PRO	0	0.006	0.020	45.455	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)