FMO DATABASE

FMODB ID: JLYJ9

Calculation Name: 3P9V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P9V

Chain ID: A

ChEMBL ID:

UniProt ID: A1U5H9

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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1470033.883788
FMO2-HF: Nuclear repulsion	1409629.723609
FMO2-HF: Total energy	-60404.160179
FMO2-MP2: Total energy	-60582.765693

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-7.122	-2.589	9.721	-6.451	-7.802	-0.052

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.023

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	4	THR	0	0.031	0.021	3.825	0.429	2.140	-0.023	-0.862	-0.826	0.001
4	A	5	VAL	0	-0.052	-0.016	6.442	-0.389	-0.389	0.000	0.000	0.000	0.000
5	A	6	SER	0	0.022	0.010	9.603	0.074	0.074	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.082	-0.053	12.903	-0.090	-0.090	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.885	-0.944	15.869	0.146	0.146	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.086	-0.017	19.493	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	10	ASN	0	0.033	0.000	22.254	0.012	0.012	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.792	0.886	23.022	0.008	0.008	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.861	-0.923	28.307	0.021	0.021	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.057	-0.037	30.959	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.926	-0.957	34.242	0.006	0.006	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.018	-0.018	33.491	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	16	PRO	0	-0.033	-0.001	37.750	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.064	0.018	40.257	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	18	SER	0	0.009	-0.016	41.621	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.015	-0.034	38.962	0.001	0.001	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.898	-0.953	40.202	0.020	0.020	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.869	-0.900	40.569	0.007	0.007	0.000	0.000	0.000	0.000
21	A	22	VAL	0	-0.026	-0.017	35.830	0.000	0.000	0.000	0.000	0.000	0.000
22	A	23	PHE	0	-0.004	-0.018	35.640	0.002	0.002	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.839	-0.916	35.639	0.025	0.025	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.063	-0.017	33.284	0.001	0.001	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.039	-0.031	30.567	0.001	0.001	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.039	-0.016	30.830	0.005	0.005	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.893	-0.927	32.375	0.027	0.027	0.000	0.000	0.000	0.000
28	A	29	VAL	0	0.001	-0.002	25.879	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.038	0.003	28.228	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.930	0.982	29.517	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.026	0.023	28.712	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.019	-0.005	25.276	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	34	SER	0	-0.088	-0.029	26.354	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	35	HIS	0	-0.011	-0.022	28.766	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.036	-0.030	19.901	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	37	PRO	0	-0.029	-0.007	22.377	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.928	0.959	19.671	0.135	0.135	0.000	0.000	0.000	0.000
38	A	39	VAL	0	0.018	0.011	19.839	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.943	-0.962	19.550	-0.067	-0.067	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.896	0.939	20.708	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.027	0.021	21.288	0.006	0.006	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.098	-0.052	21.877	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.824	-0.920	24.438	0.058	0.058	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.091	-0.049	22.113	0.000	0.000	0.000	0.000	0.000	0.000
45	A	46	GLY	0	0.035	0.030	26.805	0.003	0.003	0.000	0.000	0.000	0.000
46	A	47	ASN	0	-0.049	-0.045	28.837	0.002	0.002	0.000	0.000	0.000	0.000
47	A	48	ASN	0	0.020	0.021	29.470	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.020	0.023	24.534	0.007	0.007	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.057	0.016	23.804	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.847	0.916	17.522	-0.067	-0.067	0.000	0.000	0.000	0.000
51	A	52	TRP	0	-0.004	-0.003	18.096	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.858	-0.932	16.550	0.044	0.044	0.000	0.000	0.000	0.000
53	A	54	MET	0	0.023	0.021	15.221	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.883	-0.942	16.575	-0.111	-0.111	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.912	0.963	14.374	0.146	0.146	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.013	0.011	12.704	0.012	0.012	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.092	0.022	12.517	-0.085	-0.085	0.000	0.000	0.000	0.000
58	A	59	VAL	0	-0.075	-0.031	14.503	0.041	0.041	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.893	-0.959	14.520	-0.248	-0.248	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.945	0.966	12.636	0.170	0.170	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.022	0.000	10.059	-0.118	-0.118	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.092	-0.024	10.242	-0.088	-0.088	0.000	0.000	0.000	0.000
63	A	64	ILE	0	-0.011	-0.010	7.362	-0.078	-0.078	0.000	0.000	0.000	0.000
64	A	65	GLN	0	0.009	-0.024	9.849	0.062	0.062	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.037	0.016	10.562	0.053	0.053	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.048	0.016	11.820	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	68	TYR	0	0.047	0.021	12.925	0.073	0.073	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.049	0.031	15.444	-0.042	-0.042	0.000	0.000	0.000	0.000
69	A	70	CYS	0	-0.061	-0.011	18.857	0.027	0.027	0.000	0.000	0.000	0.000
70	A	71	THR	0	0.001	-0.005	21.429	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	72	TYR	0	0.003	-0.007	23.263	0.007	0.007	0.000	0.000	0.000	0.000
72	A	73	HIS	0	0.005	0.005	27.538	0.000	0.000	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.008	0.005	30.680	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.862	-0.932	33.509	0.047	0.047	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.852	0.906	36.537	-0.025	-0.025	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.958	-0.953	38.923	0.035	0.035	0.000	0.000	0.000	0.000
77	A	78	ALA	0	-0.011	0.000	37.300	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	79	GLY	0	0.017	0.031	37.463	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.861	0.925	29.748	-0.068	-0.068	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.038	0.033	29.162	0.002	0.002	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.053	-0.041	27.327	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	TRP	0	0.040	0.039	21.616	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.022	-0.010	22.066	0.010	0.010	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.041	0.025	17.597	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.048	-0.022	18.848	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.933	0.942	16.801	-0.188	-0.188	0.000	0.000	0.000	0.000
87	A	88	GLY	0	-0.004	0.000	14.411	-0.031	-0.031	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.929	-0.946	15.286	0.171	0.171	0.000	0.000	0.000	0.000
89	A	90	GLY	0	-0.029	-0.010	12.662	0.008	0.008	0.000	0.000	0.000	0.000
90	A	91	ASN	0	-0.053	-0.041	7.482	0.104	0.104	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.032	0.017	8.812	0.131	0.131	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.032	-0.014	11.520	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	94	VAL	0	0.018	0.004	14.164	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.049	-0.029	17.091	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.076	0.026	20.606	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	97	SER	0	-0.091	-0.048	23.430	0.002	0.002	0.000	0.000	0.000	0.000
97	A	98	TRP	0	0.086	0.039	27.155	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	99	THR	0	-0.060	-0.040	30.069	0.005	0.005	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.001	0.000	33.174	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	101	SER	0	-0.015	-0.008	36.243	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.061	0.031	39.886	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.886	0.946	41.293	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.022	0.014	44.100	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.908	-0.969	46.244	0.009	0.009	0.000	0.000	0.000	0.000
105	A	106	ASN	0	-0.047	-0.030	45.576	0.001	0.001	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.006	0.015	42.241	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.004	0.001	37.714	0.003	0.003	0.000	0.000	0.000	0.000
108	A	109	ALA	0	-0.039	-0.009	37.733	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	110	VAL	0	-0.005	-0.011	31.775	0.004	0.004	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.935	0.973	31.055	-0.035	-0.035	0.000	0.000	0.000	0.000
111	A	112	PHE	0	0.013	0.005	22.963	0.005	0.005	0.000	0.000	0.000	0.000
112	A	113	GLN	0	0.005	-0.012	22.075	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	114	THR	0	-0.018	-0.018	18.866	0.002	0.002	0.000	0.000	0.000	0.000
114	A	115	SER	0	0.008	0.016	18.445	-0.020	-0.020	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.014	-0.017	14.583	0.012	0.012	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.884	-0.918	11.038	0.491	0.491	0.000	0.000	0.000	0.000
117	A	118	LEU	0	0.006	-0.001	9.264	0.027	0.027	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.016	-0.006	3.755	-0.509	-0.182	0.027	-0.134	-0.220	0.001
119	A	120	VAL	0	0.020	0.002	4.160	-0.483	-0.196	-0.001	-0.083	-0.202	0.000
120	A	121	PRO	0	0.007	0.001	2.339	-7.532	-5.007	2.545	-2.711	-2.359	-0.028
121	A	122	LEU	0	0.029	0.012	2.871	0.897	1.618	0.240	-0.066	-0.896	-0.003
122	A	123	PRO	0	0.041	0.003	2.351	-0.604	-2.613	6.227	-2.093	-2.125	-0.021
123	A	124	SER	0	0.083	0.045	2.462	-1.115	-0.282	0.689	-0.501	-1.021	-0.002
124	A	125	LEU	0	-0.022	-0.005	3.644	0.346	0.484	0.017	-0.001	-0.153	0.000
125	A	126	LEU	0	-0.005	-0.011	6.124	0.200	0.200	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.995	1.002	6.589	0.397	0.397	0.000	0.000	0.000	0.000
127	A	128	LEU	0	-0.009	-0.028	7.790	0.134	0.134	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.011	0.017	11.007	0.064	0.064	0.000	0.000	0.000	0.000
129	A	130	ILE	0	0.030	0.013	7.535	0.073	0.073	0.000	0.000	0.000	0.000
130	A	131	SER	0	-0.004	-0.007	9.455	0.101	0.101	0.000	0.000	0.000	0.000
131	A	132	PRO	0	-0.002	-0.006	11.371	0.075	0.075	0.000	0.000	0.000	0.000
132	A	133	VAL	0	0.046	0.029	13.810	0.047	0.047	0.000	0.000	0.000	0.000
133	A	134	ILE	0	0.021	0.019	9.666	0.034	0.034	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.920	0.953	13.023	0.085	0.085	0.000	0.000	0.000	0.000
135	A	136	HIS	0	-0.017	0.008	15.286	0.036	0.036	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.877	-0.946	15.669	-0.143	-0.143	0.000	0.000	0.000	0.000
137	A	138	PHE	0	0.004	-0.004	15.312	0.024	0.024	0.000	0.000	0.000	0.000
138	A	139	ASN	0	-0.004	-0.022	17.378	0.035	0.035	0.000	0.000	0.000	0.000
139	A	140	SER	0	0.027	0.034	20.416	0.015	0.015	0.000	0.000	0.000	0.000
140	A	141	LEU	0	0.003	-0.002	17.549	0.010	0.010	0.000	0.000	0.000	0.000
141	A	142	VAL	0	0.021	0.007	20.606	0.011	0.011	0.000	0.000	0.000	0.000
142	A	143	ASP	-1	-0.859	-0.923	23.134	-0.035	-0.035	0.000	0.000	0.000	0.000
143	A	144	THR	0	-0.053	-0.029	25.002	0.003	0.003	0.000	0.000	0.000	0.000
144	A	145	TYR	0	-0.036	-0.015	24.724	0.006	0.006	0.000	0.000	0.000	0.000
145	A	146	MET	0	-0.028	-0.005	26.084	0.006	0.006	0.000	0.000	0.000	0.000
146	A	147	ALA	0	-0.025	-0.016	29.205	0.002	0.002	0.000	0.000	0.000	0.000
147	A	148	ASN	0	-0.066	-0.045	28.338	0.000	0.000	0.000	0.000	0.000	0.000
148	A	149	LEU	0	0.018	0.011	28.914	0.002	0.002	0.000	0.000	0.000	0.000
149	A	150	LYS	1	0.900	0.962	32.500	0.013	0.013	0.000	0.000	0.000	0.000
150	A	151	LYS	1	0.900	0.942	33.841	0.028	0.028	0.000	0.000	0.000	0.000
151	A	152	ALA	0	0.078	0.060	34.464	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	153	PHE	0	-0.027	-0.035	36.476	0.001	0.001	0.000	0.000	0.000	0.000
153	A	154	LEU	0	-0.075	0.003	39.372	0.000	0.000	0.000	0.000	0.000	0.000
154	A	155	GLU	-1	-0.890	-0.966	37.864	-0.014	-0.014	0.000	0.000	0.000	0.000
155	A	156	HIS	0	-0.021	-0.015	42.020	0.002	0.002	0.000	0.000	0.000	0.000
156	A	157	HIS	0	-0.016	-0.009	39.416	0.003	0.003	0.000	0.000	0.000	0.000
157	A	158	HIS	1	0.943	0.979	37.406	-0.003	-0.003	0.000	0.000	0.000	0.000
158	A	159	HIS	0	0.060	0.054	33.326	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)