FMO DATABASE

FMODB ID: R9LV8

Calculation Name: 5J08-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J08

Chain ID: A

ChEMBL ID:

UniProt ID: Q03769

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	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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1772220.767497
FMO2-HF: Nuclear repulsion	1705446.850242
FMO2-HF: Total energy	-66773.917255
FMO2-MP2: Total energy	-66971.473815

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:30:SER)

Summations of interaction energy for fragment #1(A:30: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.
-38.772	-39.872	15.58	-7.395	-7.086	0.04

Interaction energy analysis for fragmet #1(A:30:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.005

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	32	PRO	0	0.059	0.016	3.827	4.154	5.122	-0.006	-0.403	-0.560	0.001
4	A	33	TYR	0	0.117	0.049	6.479	1.498	1.498	0.000	0.000	0.000	0.000
5	A	34	GLN	0	0.046	0.026	2.251	-0.438	-0.010	2.497	-1.243	-1.683	-0.016
6	A	35	ILE	0	-0.058	-0.011	3.304	1.099	1.477	0.026	-0.082	-0.323	0.000
7	A	36	ASP	-1	-0.757	-0.861	6.036	0.229	0.229	0.000	0.000	0.000	0.000
8	A	37	ILE	0	0.022	0.015	8.777	-0.124	-0.124	0.000	0.000	0.000	0.000
9	A	38	ARG	1	0.837	0.904	1.918	-36.762	-39.706	13.064	-5.666	-4.453	0.055
10	A	39	ARG	1	0.835	0.914	9.534	-1.534	-1.534	0.000	0.000	0.000	0.000
11	A	40	ALA	0	-0.027	-0.011	11.628	-0.232	-0.232	0.000	0.000	0.000	0.000
12	A	41	THR	0	0.005	-0.012	12.057	-0.081	-0.081	0.000	0.000	0.000	0.000
13	A	42	ASN	0	0.065	0.049	13.163	0.015	0.015	0.000	0.000	0.000	0.000
14	A	43	THR	0	0.023	0.000	14.377	-0.107	-0.107	0.000	0.000	0.000	0.000
15	A	44	ASP	-1	-0.828	-0.909	17.055	0.628	0.628	0.000	0.000	0.000	0.000
16	A	45	ALA	0	-0.070	-0.039	18.986	0.005	0.005	0.000	0.000	0.000	0.000
17	A	46	TRP	0	0.007	0.017	21.441	-0.049	-0.049	0.000	0.000	0.000	0.000
18	A	47	GLY	0	-0.026	0.005	19.483	0.075	0.075	0.000	0.000	0.000	0.000
19	A	48	PRO	0	-0.010	-0.014	17.385	0.006	0.006	0.000	0.000	0.000	0.000
20	A	49	THR	0	0.032	0.000	19.013	-0.087	-0.087	0.000	0.000	0.000	0.000
21	A	50	PRO	0	0.108	0.028	19.958	0.042	0.042	0.000	0.000	0.000	0.000
22	A	51	LYS	1	1.004	1.007	18.369	-0.267	-0.267	0.000	0.000	0.000	0.000
23	A	52	HIS	0	-0.024	-0.014	15.816	0.028	0.028	0.000	0.000	0.000	0.000
24	A	53	LEU	0	0.063	0.035	15.678	0.068	0.068	0.000	0.000	0.000	0.000
25	A	54	ALA	0	0.020	0.016	17.524	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	55	LYS	1	0.806	0.909	11.581	-0.367	-0.367	0.000	0.000	0.000	0.000
27	A	56	VAL	0	0.008	0.004	12.481	-0.038	-0.038	0.000	0.000	0.000	0.000
28	A	57	LEU	0	0.035	0.019	13.904	-0.071	-0.071	0.000	0.000	0.000	0.000
29	A	58	ARG	1	0.919	0.955	15.946	-0.115	-0.115	0.000	0.000	0.000	0.000
30	A	59	ASN	0	-0.003	-0.026	10.881	-0.269	-0.269	0.000	0.000	0.000	0.000
31	A	60	ARG	1	0.874	0.945	13.452	-0.176	-0.176	0.000	0.000	0.000	0.000
32	A	61	TYR	0	-0.050	-0.015	16.011	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	62	GLN	0	-0.021	-0.016	12.796	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	63	VAL	0	-0.032	-0.003	9.724	-0.129	-0.129	0.000	0.000	0.000	0.000
35	A	64	PRO	0	0.056	0.033	12.681	0.113	0.113	0.000	0.000	0.000	0.000
36	A	65	LEU	0	0.099	0.017	13.612	0.080	0.080	0.000	0.000	0.000	0.000
37	A	66	TYR	0	-0.002	0.030	14.722	0.125	0.125	0.000	0.000	0.000	0.000
38	A	67	LEU	0	0.080	0.033	9.592	0.092	0.092	0.000	0.000	0.000	0.000
39	A	68	MET	0	-0.055	-0.008	10.709	0.221	0.221	0.000	0.000	0.000	0.000
40	A	69	THR	0	-0.013	-0.031	11.761	0.245	0.245	0.000	0.000	0.000	0.000
41	A	70	GLU	-1	-0.906	-0.964	11.885	0.422	0.422	0.000	0.000	0.000	0.000
42	A	71	TYR	0	-0.013	-0.006	5.625	0.837	0.907	-0.001	-0.001	-0.067	0.000
43	A	72	THR	0	-0.040	-0.029	9.898	0.359	0.359	0.000	0.000	0.000	0.000
44	A	73	LEU	0	0.000	-0.007	12.417	0.045	0.045	0.000	0.000	0.000	0.000
45	A	74	LYS	1	0.939	0.980	8.760	-1.715	-1.715	0.000	0.000	0.000	0.000
46	A	75	ARG	1	0.872	0.928	9.549	-2.502	-2.502	0.000	0.000	0.000	0.000
47	A	76	LEU	0	0.000	-0.014	11.989	-0.072	-0.072	0.000	0.000	0.000	0.000
48	A	77	VAL	0	0.040	0.013	15.498	-0.049	-0.049	0.000	0.000	0.000	0.000
49	A	78	ASP	-1	-0.850	-0.923	11.549	1.433	1.433	0.000	0.000	0.000	0.000
50	A	79	HIS	1	0.763	0.845	11.762	-1.759	-1.759	0.000	0.000	0.000	0.000
51	A	80	ILE	0	-0.029	-0.005	16.232	-0.102	-0.102	0.000	0.000	0.000	0.000
52	A	81	ALA	0	0.022	0.009	17.563	-0.075	-0.075	0.000	0.000	0.000	0.000
53	A	82	THR	0	-0.003	0.011	15.290	-0.066	-0.066	0.000	0.000	0.000	0.000
54	A	83	ARG	1	0.820	0.915	18.583	-0.622	-0.622	0.000	0.000	0.000	0.000
55	A	84	PRO	0	-0.010	0.021	22.023	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	85	LYS	1	0.958	0.959	25.120	-0.362	-0.362	0.000	0.000	0.000	0.000
57	A	86	ASN	0	-0.001	-0.018	27.758	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	87	LEU	0	0.083	0.028	29.678	0.023	0.023	0.000	0.000	0.000	0.000
59	A	88	TYR	0	0.062	0.040	30.765	0.006	0.006	0.000	0.000	0.000	0.000
60	A	89	GLU	-1	-0.738	-0.861	26.235	0.390	0.390	0.000	0.000	0.000	0.000
61	A	90	LYS	1	0.865	0.932	26.704	-0.387	-0.387	0.000	0.000	0.000	0.000
62	A	91	ALA	0	-0.045	-0.037	27.250	0.023	0.023	0.000	0.000	0.000	0.000
63	A	92	ARG	1	0.929	0.979	27.864	-0.270	-0.270	0.000	0.000	0.000	0.000
64	A	93	LYS	1	0.851	0.950	21.095	-0.639	-0.639	0.000	0.000	0.000	0.000
65	A	94	ASP	-1	-0.837	-0.921	19.210	0.716	0.716	0.000	0.000	0.000	0.000
66	A	95	TYR	0	-0.125	-0.076	19.152	-0.071	-0.071	0.000	0.000	0.000	0.000
67	A	96	VAL	0	0.124	0.067	16.008	-0.038	-0.038	0.000	0.000	0.000	0.000
68	A	97	ASN	0	-0.037	-0.035	15.118	0.071	0.071	0.000	0.000	0.000	0.000
69	A	98	TYR	0	0.055	0.025	19.564	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	99	GLY	0	0.013	0.017	22.750	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	100	SER	0	-0.067	-0.053	20.691	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	101	GLU	-1	-0.660	-0.812	17.309	1.231	1.231	0.000	0.000	0.000	0.000
73	A	102	TRP	0	-0.005	-0.005	19.594	0.048	0.048	0.000	0.000	0.000	0.000
74	A	103	ARG	1	0.929	0.973	19.840	-0.701	-0.701	0.000	0.000	0.000	0.000
75	A	104	VAL	0	0.014	0.022	14.322	0.015	0.015	0.000	0.000	0.000	0.000
76	A	105	VAL	0	0.043	0.028	17.188	0.023	0.023	0.000	0.000	0.000	0.000
77	A	106	LEU	0	0.014	0.002	19.192	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	107	LYS	1	0.807	0.908	17.256	-1.003	-1.003	0.000	0.000	0.000	0.000
79	A	108	CYS	0	-0.044	-0.012	14.821	0.062	0.062	0.000	0.000	0.000	0.000
80	A	109	LEU	0	0.012	0.008	16.820	-0.055	-0.055	0.000	0.000	0.000	0.000
81	A	110	VAL	0	-0.013	-0.001	20.132	-0.060	-0.060	0.000	0.000	0.000	0.000
82	A	111	VAL	0	0.000	-0.005	14.481	-0.051	-0.051	0.000	0.000	0.000	0.000
83	A	112	ILE	0	0.016	0.008	16.973	-0.060	-0.060	0.000	0.000	0.000	0.000
84	A	113	GLU	-1	-0.854	-0.939	19.065	0.315	0.315	0.000	0.000	0.000	0.000
85	A	114	PHE	0	0.004	-0.004	19.058	-0.043	-0.043	0.000	0.000	0.000	0.000
86	A	115	LEU	0	0.018	0.005	15.255	-0.054	-0.054	0.000	0.000	0.000	0.000
87	A	116	LEU	0	0.007	0.007	19.925	-0.059	-0.059	0.000	0.000	0.000	0.000
88	A	117	LEU	0	-0.008	0.000	23.015	-0.043	-0.043	0.000	0.000	0.000	0.000
89	A	118	ASN	0	-0.080	-0.050	21.978	-0.052	-0.052	0.000	0.000	0.000	0.000
90	A	119	VAL	0	-0.047	0.009	19.364	-0.021	-0.021	0.000	0.000	0.000	0.000
91	A	120	ASP	-1	-0.831	-0.907	22.311	0.037	0.037	0.000	0.000	0.000	0.000
92	A	121	THR	0	-0.066	-0.060	24.639	0.019	0.019	0.000	0.000	0.000	0.000
93	A	122	GLY	0	0.027	0.027	26.923	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	123	ASP	-1	-0.828	-0.915	21.722	-0.037	-0.037	0.000	0.000	0.000	0.000
95	A	124	GLU	-1	-0.729	-0.855	19.987	0.056	0.056	0.000	0.000	0.000	0.000
96	A	125	LEU	0	0.000	-0.004	20.850	0.035	0.035	0.000	0.000	0.000	0.000
97	A	126	ASN	0	0.004	-0.018	23.083	0.042	0.042	0.000	0.000	0.000	0.000
98	A	127	GLN	0	0.032	0.016	17.725	0.030	0.030	0.000	0.000	0.000	0.000
99	A	128	ILE	0	0.004	0.016	18.361	0.027	0.027	0.000	0.000	0.000	0.000
100	A	129	ARG	1	0.927	0.950	19.827	-0.106	-0.106	0.000	0.000	0.000	0.000
101	A	130	SER	0	-0.008	0.007	21.072	0.007	0.007	0.000	0.000	0.000	0.000
102	A	131	CYS	0	-0.017	0.011	15.737	0.026	0.026	0.000	0.000	0.000	0.000
103	A	132	LEU	0	0.005	-0.015	19.417	0.030	0.030	0.000	0.000	0.000	0.000
104	A	133	LEU	0	-0.014	-0.013	21.209	0.004	0.004	0.000	0.000	0.000	0.000
105	A	134	THR	0	-0.030	-0.009	20.390	-0.017	-0.017	0.000	0.000	0.000	0.000
106	A	135	HIS	0	-0.007	0.000	17.119	0.013	0.013	0.000	0.000	0.000	0.000
107	A	136	LYS	1	1.001	1.008	21.412	-0.159	-0.159	0.000	0.000	0.000	0.000
108	A	137	HIS	0	-0.025	-0.016	21.147	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	138	ILE	0	0.062	0.045	18.258	0.006	0.006	0.000	0.000	0.000	0.000
110	A	139	LEU	0	0.005	-0.010	22.605	0.018	0.018	0.000	0.000	0.000	0.000
111	A	140	THR	0	-0.037	-0.026	24.907	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	141	ARG	1	0.958	0.983	26.735	-0.247	-0.247	0.000	0.000	0.000	0.000
113	A	142	GLU	-1	-0.901	-0.946	21.374	0.543	0.543	0.000	0.000	0.000	0.000
114	A	143	ILE	0	-0.028	-0.031	21.674	0.013	0.013	0.000	0.000	0.000	0.000
115	A	144	ALA	0	0.022	0.024	25.472	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	145	GLN	0	-0.034	-0.018	28.703	-0.029	-0.029	0.000	0.000	0.000	0.000
117	A	146	PHE	0	-0.018	0.004	22.898	0.009	0.009	0.000	0.000	0.000	0.000
118	A	147	LYS	1	0.858	0.914	27.564	-0.330	-0.330	0.000	0.000	0.000	0.000
119	A	148	VAL	0	-0.063	-0.015	26.409	0.046	0.046	0.000	0.000	0.000	0.000
120	A	149	LYS	1	0.851	0.925	27.956	-0.412	-0.412	0.000	0.000	0.000	0.000
121	A	150	PHE	0	0.047	0.004	27.486	-0.019	-0.019	0.000	0.000	0.000	0.000
122	A	151	SER	0	-0.043	-0.036	27.018	0.038	0.038	0.000	0.000	0.000	0.000
123	A	152	ASN	0	0.002	-0.018	24.808	-0.054	-0.054	0.000	0.000	0.000	0.000
124	A	153	ASP	-1	-0.800	-0.886	28.602	0.406	0.406	0.000	0.000	0.000	0.000
125	A	154	GLY	0	0.041	0.025	31.207	-0.021	-0.021	0.000	0.000	0.000	0.000
126	A	155	LYS	1	0.877	0.952	31.246	-0.340	-0.340	0.000	0.000	0.000	0.000
127	A	156	MET	0	0.022	0.010	29.980	0.017	0.017	0.000	0.000	0.000	0.000
128	A	157	GLU	-1	-0.853	-0.912	30.828	0.292	0.292	0.000	0.000	0.000	0.000
129	A	158	ILE	0	-0.007	-0.015	30.901	0.004	0.004	0.000	0.000	0.000	0.000
130	A	159	HIS	1	0.810	0.900	26.814	-0.431	-0.431	0.000	0.000	0.000	0.000
131	A	160	GLU	-1	-0.700	-0.832	27.669	0.362	0.362	0.000	0.000	0.000	0.000
132	A	161	ARG	1	0.989	1.001	29.256	-0.269	-0.269	0.000	0.000	0.000	0.000
133	A	162	GLY	0	-0.036	-0.020	28.351	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	163	ILE	0	-0.024	-0.014	23.719	0.008	0.008	0.000	0.000	0.000	0.000
135	A	164	ARG	1	0.915	0.949	26.203	-0.314	-0.314	0.000	0.000	0.000	0.000
136	A	165	LYS	1	0.965	0.988	28.739	-0.284	-0.284	0.000	0.000	0.000	0.000
137	A	166	LYS	1	0.858	0.947	23.586	-0.425	-0.425	0.000	0.000	0.000	0.000
138	A	167	GLY	0	0.031	0.000	25.204	0.002	0.002	0.000	0.000	0.000	0.000
139	A	168	GLU	-1	-0.917	-0.958	26.153	0.253	0.253	0.000	0.000	0.000	0.000
140	A	169	LEU	0	-0.014	0.009	27.152	-0.016	-0.016	0.000	0.000	0.000	0.000
141	A	170	ILE	0	-0.034	-0.023	22.095	-0.013	-0.013	0.000	0.000	0.000	0.000
142	A	171	LEU	0	0.001	-0.007	26.151	-0.014	-0.014	0.000	0.000	0.000	0.000
143	A	172	GLN	0	0.070	0.039	28.437	-0.008	-0.008	0.000	0.000	0.000	0.000
144	A	173	TYR	0	-0.087	-0.039	25.985	-0.025	-0.025	0.000	0.000	0.000	0.000
145	A	174	LEU	0	-0.075	-0.043	24.385	-0.015	-0.015	0.000	0.000	0.000	0.000
146	A	175	GLU	-1	-0.945	-0.963	28.523	0.182	0.182	0.000	0.000	0.000	0.000
147	A	176	ASP	-1	-0.838	-0.921	32.150	0.112	0.112	0.000	0.000	0.000	0.000
148	A	177	SER	0	0.012	-0.014	31.812	0.004	0.004	0.000	0.000	0.000	0.000
149	A	178	GLN	0	-0.022	-0.008	32.878	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	179	PHE	0	0.038	0.022	31.678	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	180	LEU	0	0.034	0.019	26.828	0.002	0.002	0.000	0.000	0.000	0.000
152	A	181	LYS	1	0.936	0.964	30.791	-0.071	-0.071	0.000	0.000	0.000	0.000
153	A	182	LYS	1	0.838	0.922	32.626	-0.149	-0.149	0.000	0.000	0.000	0.000
154	A	183	GLU	-1	-0.849	-0.927	30.739	0.175	0.175	0.000	0.000	0.000	0.000
155	A	184	ARG	1	0.815	0.884	25.111	-0.145	-0.145	0.000	0.000	0.000	0.000
156	A	185	ALA	0	-0.058	-0.020	30.113	-0.006	-0.006	0.000	0.000	0.000	0.000
157	A	186	LYS	1	0.917	0.950	33.314	-0.149	-0.149	0.000	0.000	0.000	0.000
158	A	187	ASN	0	-0.033	-0.012	26.560	0.011	0.011	0.000	0.000	0.000	0.000
159	A	188	LYS	1	0.959	0.980	29.339	-0.086	-0.086	0.000	0.000	0.000	0.000
160	A	189	LYS	1	0.922	0.986	31.508	-0.136	-0.136	0.000	0.000	0.000	0.000
161	A	190	ASN	0	-0.019	-0.030	32.928	-0.004	-0.004	0.000	0.000	0.000	0.000
162	A	191	ALA	0	0.010	0.009	29.599	0.008	0.008	0.000	0.000	0.000	0.000
163	A	192	LEU	0	-0.010	0.015	29.455	-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:30:SER)