FMO DATABASE

FMODB ID: 72YRK

Calculation Name: 1O6D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O6D

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WZU8

Base Structure: X-ray

Registration Date: 2023-06-22

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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1468127.106614
FMO2-HF: Nuclear repulsion	1408712.781881
FMO2-HF: Total energy	-59414.324734
FMO2-MP2: Total energy	-59587.775844

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:1:LEU)

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

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.
-14.006	-2.822	7.288	-5.349	-13.122	-0.032

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.022

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	3	VAL	0	0.031	0.018	2.516	-2.975	-0.375	0.814	-1.252	-2.161	-0.001
4	A	4	ARG	1	0.801	0.877	4.776	-0.215	-0.156	-0.001	-0.009	-0.049	0.000
5	A	5	ILE	0	0.042	0.032	8.485	-0.088	-0.088	0.000	0.000	0.000	0.000
6	A	6	ALA	0	-0.008	0.003	11.236	0.064	0.064	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.005	-0.008	14.524	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.007	0.015	17.601	0.024	0.024	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.014	-0.012	21.315	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.739	0.859	22.066	-0.033	-0.033	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.014	0.000	17.948	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.876	-0.932	22.538	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.020	-0.018	23.412	0.002	0.002	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.123	0.040	23.595	0.004	0.004	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.005	0.024	19.294	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.953	0.975	19.257	-0.050	-0.050	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.959	-0.987	19.168	0.011	0.011	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.040	0.026	18.931	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.003	-0.009	13.893	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.936	0.983	14.607	-0.088	-0.088	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.031	-0.018	15.963	0.012	0.012	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.001	-0.037	12.637	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.877	-0.929	11.094	0.108	0.108	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.865	0.934	11.476	0.021	0.021	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.006	-0.011	12.931	0.014	0.014	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.007	0.011	7.284	-0.035	-0.035	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.846	0.918	7.302	-0.254	-0.254	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.808	0.893	7.534	0.313	0.313	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.012	-0.013	5.837	0.047	0.047	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.018	0.023	2.817	-1.968	-0.350	0.330	-0.532	-1.417	0.000
31	A	31	LYS	1	0.882	0.941	3.600	-0.562	-0.046	0.004	-0.075	-0.445	0.000
32	A	32	PRO	0	0.006	0.008	5.640	0.089	0.089	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.853	-0.925	7.492	0.809	0.809	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.074	0.043	10.292	-0.072	-0.072	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.048	-0.028	12.998	0.035	0.035	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.765	-0.849	15.555	0.014	0.014	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.018	-0.007	17.746	0.021	0.021	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.963	0.980	21.182	-0.079	-0.079	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.900	0.944	24.981	0.011	0.011	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.071	-0.039	27.026	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.016	-0.004	25.688	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.963	0.973	30.682	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.010	0.007	34.181	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.007	-0.024	35.799	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.069	0.024	32.075	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.821	-0.889	31.488	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.774	-0.853	30.829	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.079	-0.033	29.141	0.003	0.003	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.058	0.026	26.334	0.002	0.002	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.751	0.851	26.025	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.856	0.905	25.878	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.800	-0.907	23.912	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.019	-0.019	21.526	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.769	-0.844	20.845	0.013	0.013	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.833	-0.903	20.894	0.062	0.062	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.046	-0.009	16.788	0.019	0.019	0.000	0.000	0.000	0.000
57	A	57	THR	0	-0.028	-0.014	16.381	0.003	0.003	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.016	-0.011	16.657	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.772	0.859	14.651	-0.047	-0.047	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.001	0.020	11.613	0.022	0.022	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.003	0.008	6.856	0.084	0.084	0.000	0.000	0.000	0.000
62	A	62	PRO	0	0.031	0.018	10.298	-0.113	-0.113	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.024	0.016	10.147	0.094	0.094	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.065	-0.017	6.829	-0.153	-0.153	0.000	0.000	0.000	0.000
65	A	65	PHE	0	-0.013	-0.020	6.780	0.088	0.088	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.015	-0.003	8.105	-0.052	-0.052	0.000	0.000	0.000	0.000
67	A	67	MET	0	0.010	0.014	7.213	0.035	0.035	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.004	0.001	11.696	0.041	0.041	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.022	-0.003	13.878	-0.030	-0.030	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.755	-0.880	16.587	-0.092	-0.092	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.824	0.904	20.223	0.093	0.093	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.783	0.866	22.771	0.104	0.104	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.006	0.004	19.633	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.865	-0.908	17.319	-0.304	-0.304	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.817	-0.891	18.705	-0.173	-0.173	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.042	-0.009	14.701	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.004	-0.022	17.907	0.004	0.004	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.016	-0.063	15.325	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.903	-0.947	14.519	-0.341	-0.341	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.801	-0.883	14.937	-0.336	-0.336	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.057	-0.022	9.302	-0.090	-0.090	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.021	0.002	10.326	-0.135	-0.135	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.866	-0.921	10.339	-0.615	-0.615	0.000	0.000	0.000	0.000
84	A	84	PHE	0	-0.049	-0.038	9.500	-0.077	-0.077	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.016	-0.015	4.138	-0.385	-0.233	0.000	-0.014	-0.137	0.000
86	A	86	LYS	1	0.971	0.995	5.834	0.111	0.111	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.810	-0.889	7.217	-0.941	-0.941	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.020	-0.020	3.958	-0.163	0.022	0.000	-0.022	-0.163	0.000
89	A	89	GLU	-1	-0.876	-0.928	2.681	-3.704	-2.251	0.523	-0.724	-1.252	-0.004
90	A	90	MET	0	-0.057	-0.027	3.670	0.271	0.441	0.001	0.079	-0.250	0.000
91	A	91	LYS	1	0.758	0.859	5.729	1.019	1.019	0.000	0.000	0.000	0.000
92	A	92	GLY	0	-0.008	0.012	2.280	0.083	0.057	1.561	-0.758	-0.777	0.000
93	A	93	LYS	1	0.829	0.920	3.093	0.837	1.112	0.496	0.380	-1.150	-0.004
94	A	94	ASP	-1	-0.813	-0.909	2.321	-4.304	-1.232	3.371	-2.527	-3.916	-0.023
95	A	95	ILE	0	-0.004	-0.010	2.798	-0.235	0.333	0.153	0.189	-0.910	0.000
96	A	96	THR	0	-0.023	-0.016	5.221	0.357	0.343	-0.001	-0.001	0.016	0.000
97	A	97	ILE	0	-0.006	-0.005	7.449	-0.050	-0.050	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.024	-0.007	10.902	0.071	0.071	0.000	0.000	0.000	0.000
99	A	99	ILE	0	0.019	0.008	14.653	-0.019	-0.019	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.080	0.029	17.495	0.023	0.023	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.034	0.011	21.105	0.000	0.000	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.020	-0.009	24.199	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	103	TYR	0	-0.022	-0.030	27.251	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.026	0.036	24.800	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.022	-0.011	19.579	0.009	0.009	0.000	0.000	0.000	0.000
106	A	106	ASN	0	0.017	-0.015	24.016	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.868	-0.951	23.679	-0.079	-0.079	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.843	-0.903	22.798	-0.048	-0.048	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.016	-0.014	17.714	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.031	-0.026	18.908	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.007	0.024	19.288	-0.020	-0.020	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.774	0.874	16.845	0.052	0.052	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.037	-0.016	14.599	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	114	HIS	0	0.011	0.029	11.682	-0.032	-0.032	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.837	0.901	12.468	0.362	0.362	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.030	0.025	14.362	0.007	0.007	0.000	0.000	0.000	0.000
117	A	117	PHE	0	0.021	0.009	11.246	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	118	SER	0	0.016	0.019	16.561	0.024	0.024	0.000	0.000	0.000	0.000
119	A	119	LEU	0	0.004	-0.020	15.246	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	120	SER	0	0.020	0.008	19.104	0.007	0.007	0.000	0.000	0.000	0.000
121	A	121	LYS	1	0.900	0.928	22.871	0.148	0.148	0.000	0.000	0.000	0.000
122	A	122	MET	0	-0.032	-0.008	25.733	0.011	0.011	0.000	0.000	0.000	0.000
123	A	123	THR	0	-0.005	-0.005	24.856	-0.010	-0.010	0.000	0.000	0.000	0.000
124	A	124	PHE	0	0.041	0.030	20.875	0.008	0.008	0.000	0.000	0.000	0.000
125	A	125	THR	0	0.046	0.018	23.788	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	HIS	0	0.077	0.039	20.722	-0.022	-0.022	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.032	0.005	19.242	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	128	MET	0	-0.009	-0.015	19.150	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	129	THR	0	-0.003	-0.006	16.550	-0.019	-0.019	0.000	0.000	0.000	0.000
130	A	130	VAL	0	0.028	0.017	14.033	-0.024	-0.024	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.049	-0.021	14.319	-0.022	-0.022	0.000	0.000	0.000	0.000
132	A	132	ILE	0	0.006	0.013	15.451	-0.020	-0.020	0.000	0.000	0.000	0.000
133	A	133	VAL	0	0.025	0.012	10.633	-0.030	-0.030	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.001	-0.002	9.754	-0.052	-0.052	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.827	-0.881	11.221	-0.229	-0.229	0.000	0.000	0.000	0.000
136	A	136	GLN	0	0.016	0.007	12.694	-0.048	-0.048	0.000	0.000	0.000	0.000
137	A	137	ILE	0	0.029	0.026	6.231	-0.043	-0.043	0.000	0.000	0.000	0.000
138	A	138	PHE	0	-0.018	-0.019	8.963	-0.066	-0.066	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.875	0.925	10.749	0.236	0.236	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.040	0.028	9.481	0.015	0.015	0.000	0.000	0.000	0.000
141	A	141	PHE	0	0.038	0.004	3.195	-0.530	0.026	0.037	-0.083	-0.511	0.000
142	A	142	LYS	1	0.843	0.942	8.881	0.303	0.303	0.000	0.000	0.000	0.000
143	A	143	ILE	0	0.000	0.007	12.507	0.023	0.023	0.000	0.000	0.000	0.000
144	A	144	ILE	0	-0.029	-0.003	7.708	0.044	0.044	0.000	0.000	0.000	0.000
145	A	145	HIS	0	-0.108	-0.069	6.860	0.192	0.192	0.000	0.000	0.000	0.000
146	A	146	GLY	0	-0.004	0.027	12.025	0.061	0.061	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.895	-0.945	14.587	-0.203	-0.203	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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