FMO DATABASE

FMODB ID: R5ZV8

Calculation Name: 1O6A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O6A

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-20

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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-502077.257552
FMO2-HF: Nuclear repulsion	468175.923801
FMO2-HF: Total energy	-33901.333751
FMO2-MP2: Total energy	-34001.021612

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:68:SER)

Summations of interaction energy for fragment #1(A:68: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.
-6.461	-2.518	0.4	-1.553	-2.79	0.007

Interaction energy analysis for fragmet #1(A:68:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.028

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

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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	70	LYS	1	0.921	0.958	2.970	-3.247	-1.054	0.085	-0.965	-1.313	0.004
4	A	71	LEU	0	-0.013	-0.011	2.909	-2.201	-0.782	0.315	-0.476	-1.259	0.003
5	A	72	GLU	-1	-0.855	-0.935	4.338	-2.492	-2.161	0.000	-0.112	-0.218	0.000
6	A	73	LEU	0	-0.047	-0.029	6.315	0.307	0.307	0.000	0.000	0.000	0.000
7	A	74	LEU	0	-0.066	-0.042	7.077	0.203	0.203	0.000	0.000	0.000	0.000
8	A	75	LEU	0	-0.056	-0.015	7.066	0.073	0.073	0.000	0.000	0.000	0.000
9	A	76	ASP	-1	-0.920	-0.947	10.218	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	77	ILE	0	-0.039	-0.007	12.256	-0.013	-0.013	0.000	0.000	0.000	0.000
11	A	78	PRO	0	-0.016	-0.009	15.084	0.029	0.029	0.000	0.000	0.000	0.000
12	A	79	LEU	0	-0.004	0.003	13.936	0.049	0.049	0.000	0.000	0.000	0.000
13	A	80	LYS	1	0.886	0.940	18.448	-0.266	-0.266	0.000	0.000	0.000	0.000
14	A	81	VAL	0	0.044	0.023	20.266	0.020	0.020	0.000	0.000	0.000	0.000
15	A	82	THR	0	-0.055	-0.033	22.595	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	83	VAL	0	0.034	0.011	25.261	0.013	0.013	0.000	0.000	0.000	0.000
17	A	84	GLU	-1	-0.839	-0.884	27.899	0.216	0.216	0.000	0.000	0.000	0.000
18	A	85	LEU	0	0.030	0.006	30.680	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	86	GLY	0	0.060	0.028	33.412	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	87	ARG	1	0.756	0.848	27.325	-0.232	-0.232	0.000	0.000	0.000	0.000
21	A	88	THR	0	0.050	0.016	35.051	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	89	ARG	1	0.899	0.947	37.087	-0.138	-0.138	0.000	0.000	0.000	0.000
23	A	90	MET	0	0.023	0.023	40.047	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	91	THR	0	0.018	0.004	42.896	0.004	0.004	0.000	0.000	0.000	0.000
25	A	92	LEU	0	0.063	0.020	44.605	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	93	LYS	1	0.817	0.889	46.084	-0.078	-0.078	0.000	0.000	0.000	0.000
27	A	94	ARG	1	0.945	0.978	46.878	-0.086	-0.086	0.000	0.000	0.000	0.000
28	A	95	VAL	0	0.011	-0.011	43.283	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	96	LEU	0	-0.023	-0.014	46.293	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	97	GLU	-1	-0.811	-0.871	49.440	0.071	0.071	0.000	0.000	0.000	0.000
31	A	98	MET	0	-0.096	-0.032	43.388	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	99	ILE	0	0.021	0.013	49.233	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	100	HIS	0	0.028	-0.003	50.173	0.002	0.002	0.000	0.000	0.000	0.000
34	A	101	GLY	0	0.039	0.024	49.900	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	102	SER	0	-0.069	-0.037	48.233	0.000	0.000	0.000	0.000	0.000	0.000
36	A	103	ILE	0	0.038	0.030	46.608	0.003	0.003	0.000	0.000	0.000	0.000
37	A	104	ILE	0	-0.045	-0.035	41.687	0.001	0.001	0.000	0.000	0.000	0.000
38	A	105	GLU	-1	-0.937	-0.954	42.912	0.091	0.091	0.000	0.000	0.000	0.000
39	A	106	LEU	0	-0.055	-0.042	37.042	0.005	0.005	0.000	0.000	0.000	0.000
40	A	107	ASP	-1	-0.826	-0.913	34.255	0.157	0.157	0.000	0.000	0.000	0.000
41	A	108	LYS	1	0.774	0.900	31.051	-0.165	-0.165	0.000	0.000	0.000	0.000
42	A	109	LEU	0	0.010	0.010	36.161	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	110	THR	0	-0.031	-0.031	37.428	0.001	0.001	0.000	0.000	0.000	0.000
44	A	111	GLY	0	0.001	-0.006	37.708	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	112	GLU	-1	-0.862	-0.907	32.669	0.153	0.153	0.000	0.000	0.000	0.000
46	A	113	PRO	0	-0.033	0.006	29.401	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	114	VAL	0	0.003	-0.002	29.375	0.006	0.006	0.000	0.000	0.000	0.000
48	A	115	ASP	-1	-0.792	-0.895	27.053	0.199	0.199	0.000	0.000	0.000	0.000
49	A	116	ILE	0	-0.031	-0.015	22.369	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	117	LEU	0	-0.011	-0.013	22.093	0.029	0.029	0.000	0.000	0.000	0.000
51	A	118	VAL	0	0.013	0.000	17.222	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	119	ASN	0	0.016	0.004	17.295	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	120	GLY	0	0.005	0.007	20.731	0.014	0.014	0.000	0.000	0.000	0.000
54	A	121	LYS	1	0.826	0.912	17.473	-0.604	-0.604	0.000	0.000	0.000	0.000
55	A	122	LEU	0	0.013	0.009	20.488	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	123	ILE	0	-0.017	-0.009	16.749	0.035	0.035	0.000	0.000	0.000	0.000
57	A	124	ALA	0	0.001	-0.010	19.584	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	125	ARG	1	0.789	0.861	22.057	-0.184	-0.184	0.000	0.000	0.000	0.000
59	A	126	GLY	0	0.049	0.017	25.533	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	127	GLU	-1	-0.829	-0.897	27.888	0.079	0.079	0.000	0.000	0.000	0.000
61	A	128	VAL	0	0.006	-0.008	30.612	0.001	0.001	0.000	0.000	0.000	0.000
62	A	129	VAL	0	-0.045	-0.018	30.534	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	130	VAL	0	0.010	-0.002	33.415	0.005	0.005	0.000	0.000	0.000	0.000
64	A	131	ILE	0	-0.053	-0.032	29.779	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	132	ASP	-1	-0.873	-0.936	33.056	0.027	0.027	0.000	0.000	0.000	0.000
66	A	133	GLU	-1	-0.946	-0.962	35.759	0.038	0.038	0.000	0.000	0.000	0.000
67	A	134	ASN	0	-0.101	-0.048	32.701	0.008	0.008	0.000	0.000	0.000	0.000
68	A	135	PHE	0	0.008	0.001	33.291	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	136	GLY	0	0.015	0.006	29.507	0.003	0.003	0.000	0.000	0.000	0.000
70	A	137	VAL	0	-0.039	-0.019	25.877	0.001	0.001	0.000	0.000	0.000	0.000
71	A	138	ARG	1	0.847	0.930	26.731	-0.067	-0.067	0.000	0.000	0.000	0.000
72	A	139	ILE	0	-0.017	-0.015	20.799	0.003	0.003	0.000	0.000	0.000	0.000
73	A	140	THR	0	0.006	-0.008	24.966	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	141	GLU	-1	-0.847	-0.885	24.319	0.181	0.181	0.000	0.000	0.000	0.000
75	A	142	ILE	0	-0.042	-0.030	17.539	0.010	0.010	0.000	0.000	0.000	0.000
76	A	143	VAL	0	0.038	0.055	15.872	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	144	SER	0	-0.005	-0.045	13.890	0.018	0.018	0.000	0.000	0.000	0.000
78	A	145	PRO	0	0.002	-0.033	10.276	0.061	0.061	0.000	0.000	0.000	0.000
79	A	146	LYS	1	0.832	0.906	9.059	-0.700	-0.700	0.000	0.000	0.000	0.000
80	A	147	GLU	-1	-0.761	-0.844	10.138	0.650	0.650	0.000	0.000	0.000	0.000
81	A	148	ARG	1	0.846	0.919	12.563	-0.382	-0.382	0.000	0.000	0.000	0.000
82	A	149	LEU	0	0.030	0.020	6.369	0.037	0.037	0.000	0.000	0.000	0.000
83	A	150	GLU	-1	-0.809	-0.882	10.059	1.081	1.081	0.000	0.000	0.000	0.000
84	A	151	LEU	0	0.020	0.010	11.612	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	152	LEU	0	-0.047	-0.031	12.633	-0.077	-0.077	0.000	0.000	0.000	0.000
86	A	153	ASN	0	-0.105	-0.059	9.356	0.286	0.286	0.000	0.000	0.000	0.000
87	A	154	GLU	-1	-0.911	-0.918	12.552	0.525	0.525	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:68:SER)