FMO DATABASE

FMODB ID: K9VM3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1777628.359481
FMO2-HF: Nuclear repulsion	1710853.522324
FMO2-HF: Total energy	-66774.837156
FMO2-MP2: Total energy	-66972.411324

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.
-40.992	-50.111	26.415	-9.245	-8.049	0.032

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 : 0.007 / q_NPA : 0.011

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	0.053	0.013	3.857	3.844	4.745	-0.010	-0.411	-0.481	0.001
4	A	33	TYR	0	0.097	0.049	6.519	1.010	1.010	0.000	0.000	0.000	0.000
5	A	34	GLN	0	0.055	0.032	2.009	-2.663	-3.688	5.261	-2.125	-2.110	-0.027
6	A	35	ILE	0	-0.057	-0.004	4.090	1.803	2.060	0.000	-0.048	-0.209	0.000
7	A	36	ASP	-1	-0.767	-0.851	6.512	0.107	0.107	0.000	0.000	0.000	0.000
8	A	37	ILE	0	0.031	0.020	8.348	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	38	ARG	1	0.829	0.887	1.912	-37.107	-46.468	21.165	-6.652	-5.151	0.058
10	A	39	ARG	1	0.818	0.906	9.157	-1.488	-1.488	0.000	0.000	0.000	0.000
11	A	40	ALA	0	-0.030	-0.019	11.851	-0.211	-0.211	0.000	0.000	0.000	0.000
12	A	41	THR	0	0.022	-0.011	11.834	-0.094	-0.094	0.000	0.000	0.000	0.000
13	A	42	ASN	0	0.054	0.042	13.441	0.061	0.061	0.000	0.000	0.000	0.000
14	A	43	THR	0	0.032	0.011	14.302	-0.126	-0.126	0.000	0.000	0.000	0.000
15	A	44	ASP	-1	-0.799	-0.893	16.926	0.633	0.633	0.000	0.000	0.000	0.000
16	A	45	ALA	0	-0.068	-0.030	19.237	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	46	TRP	0	0.010	0.019	21.514	-0.062	-0.062	0.000	0.000	0.000	0.000
18	A	47	GLY	0	-0.014	0.011	19.782	0.088	0.088	0.000	0.000	0.000	0.000
19	A	48	PRO	0	0.018	0.003	17.084	0.015	0.015	0.000	0.000	0.000	0.000
20	A	49	THR	0	0.020	-0.013	19.018	-0.088	-0.088	0.000	0.000	0.000	0.000
21	A	50	PRO	0	0.095	0.025	19.963	0.028	0.028	0.000	0.000	0.000	0.000
22	A	51	LYS	1	0.997	1.006	19.097	-0.291	-0.291	0.000	0.000	0.000	0.000
23	A	52	HIS	0	0.000	0.010	15.835	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	53	LEU	0	0.041	0.029	15.738	0.032	0.032	0.000	0.000	0.000	0.000
25	A	54	ALA	0	0.037	0.018	17.250	-0.040	-0.040	0.000	0.000	0.000	0.000
26	A	55	LYS	1	0.786	0.892	11.606	-0.210	-0.210	0.000	0.000	0.000	0.000
27	A	56	VAL	0	0.004	-0.008	11.952	-0.069	-0.069	0.000	0.000	0.000	0.000
28	A	57	LEU	0	0.044	0.022	13.692	-0.115	-0.115	0.000	0.000	0.000	0.000
29	A	58	ARG	1	0.938	0.970	16.085	-0.035	-0.035	0.000	0.000	0.000	0.000
30	A	59	ASN	0	-0.017	-0.034	10.880	-0.256	-0.256	0.000	0.000	0.000	0.000
31	A	60	ARG	1	0.809	0.875	13.542	-0.028	-0.028	0.000	0.000	0.000	0.000
32	A	61	TYR	0	-0.032	-0.007	16.207	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	62	GLN	0	-0.036	-0.024	12.447	0.000	0.000	0.000	0.000	0.000	0.000
34	A	63	VAL	0	-0.024	-0.008	9.579	-0.198	-0.198	0.000	0.000	0.000	0.000
35	A	64	PRO	0	0.056	0.032	12.691	0.160	0.160	0.000	0.000	0.000	0.000
36	A	65	LEU	0	0.090	0.022	13.390	0.024	0.024	0.000	0.000	0.000	0.000
37	A	66	TYR	0	0.006	0.032	14.837	0.111	0.111	0.000	0.000	0.000	0.000
38	A	67	LEU	0	0.072	0.035	10.010	0.096	0.096	0.000	0.000	0.000	0.000
39	A	68	MET	0	-0.067	-0.018	10.197	0.146	0.146	0.000	0.000	0.000	0.000
40	A	69	THR	0	-0.007	-0.016	11.443	0.273	0.273	0.000	0.000	0.000	0.000
41	A	70	GLU	-1	-0.811	-0.913	11.973	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	71	TYR	0	-0.016	-0.002	4.342	0.358	0.467	-0.001	-0.009	-0.098	0.000
43	A	72	THR	0	-0.038	-0.028	9.432	0.426	0.426	0.000	0.000	0.000	0.000
44	A	73	LEU	0	-0.010	-0.010	11.912	0.077	0.077	0.000	0.000	0.000	0.000
45	A	74	LYS	1	0.869	0.929	9.071	-1.106	-1.106	0.000	0.000	0.000	0.000
46	A	75	ARG	1	0.873	0.917	9.166	-2.317	-2.317	0.000	0.000	0.000	0.000
47	A	76	LEU	0	0.003	-0.009	11.463	0.002	0.002	0.000	0.000	0.000	0.000
48	A	77	VAL	0	0.050	0.018	15.243	0.004	0.004	0.000	0.000	0.000	0.000
49	A	78	ASP	-1	-0.819	-0.899	10.820	1.384	1.384	0.000	0.000	0.000	0.000
50	A	79	HIS	1	0.785	0.861	11.515	-1.643	-1.643	0.000	0.000	0.000	0.000
51	A	80	ILE	0	-0.021	0.001	16.162	-0.070	-0.070	0.000	0.000	0.000	0.000
52	A	81	ALA	0	0.024	0.020	17.200	-0.064	-0.064	0.000	0.000	0.000	0.000
53	A	82	THR	0	-0.034	-0.023	15.232	-0.064	-0.064	0.000	0.000	0.000	0.000
54	A	83	ARG	1	0.818	0.917	18.252	-0.561	-0.561	0.000	0.000	0.000	0.000
55	A	84	PRO	0	0.011	0.026	21.881	-0.034	-0.034	0.000	0.000	0.000	0.000
56	A	85	LYS	1	0.931	0.955	24.875	-0.340	-0.340	0.000	0.000	0.000	0.000
57	A	86	ASN	0	-0.019	-0.016	27.565	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	87	LEU	0	0.097	0.033	29.397	0.026	0.026	0.000	0.000	0.000	0.000
59	A	88	TYR	0	0.049	0.030	30.989	0.013	0.013	0.000	0.000	0.000	0.000
60	A	89	GLU	-1	-0.724	-0.861	26.271	0.362	0.362	0.000	0.000	0.000	0.000
61	A	90	LYS	1	0.898	0.948	26.249	-0.422	-0.422	0.000	0.000	0.000	0.000
62	A	91	ALA	0	-0.048	-0.034	27.182	0.027	0.027	0.000	0.000	0.000	0.000
63	A	92	ARG	1	0.902	0.965	27.942	-0.280	-0.280	0.000	0.000	0.000	0.000
64	A	93	LYS	1	0.879	0.955	20.137	-0.673	-0.673	0.000	0.000	0.000	0.000
65	A	94	ASP	-1	-0.806	-0.906	19.018	0.799	0.799	0.000	0.000	0.000	0.000
66	A	95	TYR	0	-0.101	-0.063	19.206	-0.073	-0.073	0.000	0.000	0.000	0.000
67	A	96	VAL	0	0.096	0.060	15.921	-0.033	-0.033	0.000	0.000	0.000	0.000
68	A	97	ASN	0	-0.026	-0.024	14.938	0.049	0.049	0.000	0.000	0.000	0.000
69	A	98	TYR	0	0.063	0.039	19.365	-0.045	-0.045	0.000	0.000	0.000	0.000
70	A	99	GLY	0	0.012	0.026	22.818	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	100	SER	0	-0.069	-0.057	20.585	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	101	GLU	-1	-0.688	-0.822	16.626	1.256	1.256	0.000	0.000	0.000	0.000
73	A	102	TRP	0	0.003	-0.005	19.092	0.028	0.028	0.000	0.000	0.000	0.000
74	A	103	ARG	1	0.873	0.936	19.361	-0.744	-0.744	0.000	0.000	0.000	0.000
75	A	104	VAL	0	0.021	0.024	13.933	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	105	VAL	0	0.040	0.026	16.605	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	106	LEU	0	0.013	0.004	18.641	-0.038	-0.038	0.000	0.000	0.000	0.000
78	A	107	LYS	1	0.794	0.901	16.959	-0.946	-0.946	0.000	0.000	0.000	0.000
79	A	108	CYS	0	-0.044	-0.021	14.173	0.042	0.042	0.000	0.000	0.000	0.000
80	A	109	LEU	0	0.010	0.009	16.105	-0.070	-0.070	0.000	0.000	0.000	0.000
81	A	110	VAL	0	0.006	0.003	19.511	-0.058	-0.058	0.000	0.000	0.000	0.000
82	A	111	VAL	0	-0.010	-0.006	13.828	-0.050	-0.050	0.000	0.000	0.000	0.000
83	A	112	ILE	0	0.009	0.010	16.472	-0.075	-0.075	0.000	0.000	0.000	0.000
84	A	113	GLU	-1	-0.786	-0.878	18.527	0.246	0.246	0.000	0.000	0.000	0.000
85	A	114	PHE	0	0.015	0.001	18.914	-0.038	-0.038	0.000	0.000	0.000	0.000
86	A	115	LEU	0	0.026	0.011	14.801	-0.052	-0.052	0.000	0.000	0.000	0.000
87	A	116	LEU	0	0.018	0.007	19.528	-0.054	-0.054	0.000	0.000	0.000	0.000
88	A	117	LEU	0	-0.004	0.001	22.622	-0.034	-0.034	0.000	0.000	0.000	0.000
89	A	118	ASN	0	-0.082	-0.038	21.728	-0.032	-0.032	0.000	0.000	0.000	0.000
90	A	119	VAL	0	0.011	0.030	19.395	-0.021	-0.021	0.000	0.000	0.000	0.000
91	A	120	ASP	-1	-0.784	-0.864	22.147	-0.039	-0.039	0.000	0.000	0.000	0.000
92	A	121	THR	0	-0.048	-0.031	24.726	0.004	0.004	0.000	0.000	0.000	0.000
93	A	122	GLY	0	0.059	0.027	26.250	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	123	ASP	-1	-0.835	-0.900	21.420	-0.247	-0.247	0.000	0.000	0.000	0.000
95	A	124	GLU	-1	-0.736	-0.847	20.034	-0.121	-0.121	0.000	0.000	0.000	0.000
96	A	125	LEU	0	0.008	-0.001	20.517	0.023	0.023	0.000	0.000	0.000	0.000
97	A	126	ASN	0	0.031	0.012	22.879	0.046	0.046	0.000	0.000	0.000	0.000
98	A	127	GLN	0	0.015	0.014	17.403	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	128	ILE	0	-0.005	0.008	17.948	0.017	0.017	0.000	0.000	0.000	0.000
100	A	129	ARG	1	0.892	0.931	19.440	0.014	0.014	0.000	0.000	0.000	0.000
101	A	130	SER	0	0.020	-0.002	21.495	0.007	0.007	0.000	0.000	0.000	0.000
102	A	131	CYS	0	-0.042	0.018	16.359	0.035	0.035	0.000	0.000	0.000	0.000
103	A	132	LEU	0	-0.003	-0.017	19.091	0.032	0.032	0.000	0.000	0.000	0.000
104	A	133	LEU	0	0.010	0.001	20.942	0.015	0.015	0.000	0.000	0.000	0.000
105	A	134	THR	0	-0.031	-0.018	20.206	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	135	HIS	0	-0.024	-0.034	16.163	0.040	0.040	0.000	0.000	0.000	0.000
107	A	136	LYS	1	0.914	0.962	20.724	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	137	HIS	0	-0.005	0.017	20.905	-0.015	-0.015	0.000	0.000	0.000	0.000
109	A	138	ILE	0	0.033	0.023	17.707	0.016	0.016	0.000	0.000	0.000	0.000
110	A	139	LEU	0	-0.009	-0.012	22.036	0.021	0.021	0.000	0.000	0.000	0.000
111	A	140	THR	0	0.004	-0.029	24.250	0.000	0.000	0.000	0.000	0.000	0.000
112	A	141	ARG	1	0.943	0.984	25.987	-0.167	-0.167	0.000	0.000	0.000	0.000
113	A	142	GLU	-1	-0.882	-0.941	20.793	0.426	0.426	0.000	0.000	0.000	0.000
114	A	143	ILE	0	-0.042	-0.030	21.099	0.027	0.027	0.000	0.000	0.000	0.000
115	A	144	ALA	0	0.018	0.019	24.962	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	145	GLN	0	-0.027	-0.030	28.063	-0.020	-0.020	0.000	0.000	0.000	0.000
117	A	146	PHE	0	-0.038	-0.003	22.484	0.015	0.015	0.000	0.000	0.000	0.000
118	A	147	LYS	1	0.895	0.936	27.269	-0.290	-0.290	0.000	0.000	0.000	0.000
119	A	148	VAL	0	-0.066	-0.026	25.985	0.042	0.042	0.000	0.000	0.000	0.000
120	A	149	LYS	1	0.836	0.894	27.547	-0.381	-0.381	0.000	0.000	0.000	0.000
121	A	150	PHE	0	0.060	0.015	27.473	-0.017	-0.017	0.000	0.000	0.000	0.000
122	A	151	SER	0	-0.037	-0.039	26.825	0.033	0.033	0.000	0.000	0.000	0.000
123	A	152	ASN	0	-0.010	-0.025	24.362	-0.055	-0.055	0.000	0.000	0.000	0.000
124	A	153	ASP	-1	-0.764	-0.833	28.234	0.391	0.391	0.000	0.000	0.000	0.000
125	A	154	GLY	0	0.052	0.027	30.871	-0.022	-0.022	0.000	0.000	0.000	0.000
126	A	155	LYS	1	0.856	0.919	30.933	-0.361	-0.361	0.000	0.000	0.000	0.000
127	A	156	MET	0	-0.006	0.018	29.820	0.014	0.014	0.000	0.000	0.000	0.000
128	A	157	GLU	-1	-0.826	-0.915	30.141	0.271	0.271	0.000	0.000	0.000	0.000
129	A	158	ILE	0	-0.018	-0.009	31.020	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	159	HIS	1	0.803	0.883	26.397	-0.416	-0.416	0.000	0.000	0.000	0.000
131	A	160	GLU	-1	-0.721	-0.840	27.152	0.317	0.317	0.000	0.000	0.000	0.000
132	A	161	ARG	1	0.969	0.993	28.576	-0.240	-0.240	0.000	0.000	0.000	0.000
133	A	162	GLY	0	0.003	0.006	27.919	-0.013	-0.013	0.000	0.000	0.000	0.000
134	A	163	ILE	0	-0.021	-0.016	23.145	0.002	0.002	0.000	0.000	0.000	0.000
135	A	164	ARG	1	0.882	0.943	25.538	-0.270	-0.270	0.000	0.000	0.000	0.000
136	A	165	LYS	1	0.825	0.894	28.243	-0.222	-0.222	0.000	0.000	0.000	0.000
137	A	166	LYS	1	0.774	0.875	23.003	-0.340	-0.340	0.000	0.000	0.000	0.000
138	A	167	GLY	0	0.035	0.005	24.727	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	168	GLU	-1	-0.793	-0.881	25.661	0.190	0.190	0.000	0.000	0.000	0.000
140	A	169	LEU	0	0.005	0.017	27.597	-0.017	-0.017	0.000	0.000	0.000	0.000
141	A	170	ILE	0	-0.027	-0.028	21.590	-0.015	-0.015	0.000	0.000	0.000	0.000
142	A	171	LEU	0	-0.004	0.007	25.635	-0.017	-0.017	0.000	0.000	0.000	0.000
143	A	172	GLN	0	0.065	0.031	27.957	-0.011	-0.011	0.000	0.000	0.000	0.000
144	A	173	TYR	0	-0.061	-0.037	25.304	-0.024	-0.024	0.000	0.000	0.000	0.000
145	A	174	LEU	0	-0.070	-0.043	24.183	-0.019	-0.019	0.000	0.000	0.000	0.000
146	A	175	GLU	-1	-0.934	-0.965	28.262	0.105	0.105	0.000	0.000	0.000	0.000
147	A	176	ASP	-1	-0.796	-0.897	31.827	0.047	0.047	0.000	0.000	0.000	0.000
148	A	177	SER	0	0.023	-0.005	31.143	0.001	0.001	0.000	0.000	0.000	0.000
149	A	178	GLN	0	0.029	0.014	32.176	-0.006	-0.006	0.000	0.000	0.000	0.000
150	A	179	PHE	0	0.054	0.030	31.227	0.000	0.000	0.000	0.000	0.000	0.000
151	A	180	LEU	0	0.018	0.017	26.448	0.004	0.004	0.000	0.000	0.000	0.000
152	A	181	LYS	1	0.889	0.945	30.407	-0.011	-0.011	0.000	0.000	0.000	0.000
153	A	182	LYS	1	0.796	0.895	32.150	-0.089	-0.089	0.000	0.000	0.000	0.000
154	A	183	GLU	-1	-0.771	-0.867	30.365	0.109	0.109	0.000	0.000	0.000	0.000
155	A	184	ARG	1	0.802	0.870	24.870	-0.026	-0.026	0.000	0.000	0.000	0.000
156	A	185	ALA	0	-0.028	-0.005	29.780	-0.004	-0.004	0.000	0.000	0.000	0.000
157	A	186	LYS	1	0.824	0.895	32.978	-0.104	-0.104	0.000	0.000	0.000	0.000
158	A	187	ASN	0	-0.063	-0.040	26.010	0.014	0.014	0.000	0.000	0.000	0.000
159	A	188	LYS	1	0.912	0.939	27.718	0.008	0.008	0.000	0.000	0.000	0.000
160	A	189	LYS	1	0.920	0.986	31.039	-0.091	-0.091	0.000	0.000	0.000	0.000
161	A	190	ASN	0	0.004	-0.018	32.344	0.002	0.002	0.000	0.000	0.000	0.000
162	A	191	ALA	0	-0.009	0.009	29.052	0.007	0.007	0.000	0.000	0.000	0.000
163	A	192	LEU	0	-0.038	0.000	29.176	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:30:SER)