FMO DATABASE

FMODB ID: 4J8ZN

Calculation Name: 3PH9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PH9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TD06

Base Structure: X-ray

Registration Date: 2023-09-23

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1316798.055555
FMO2-HF: Nuclear repulsion	1261451.249396
FMO2-HF: Total energy	-55346.80616
FMO2-MP2: Total energy	-55506.145603

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:31:PRO)

Summations of interaction energy for fragment #1(A:31:PRO)

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.
-0.708	0.891	-0.015	-0.664	-0.92	0.003

Interaction energy analysis for fragmet #1(A:31:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : -0.002

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	33	THR	0	0.069	0.048	3.834	-0.524	1.075	-0.015	-0.664	-0.920	0.003
4	A	34	LEU	0	0.028	0.001	6.069	0.273	0.273	0.000	0.000	0.000	0.000
5	A	35	SER	0	-0.009	-0.020	9.275	0.051	0.051	0.000	0.000	0.000	0.000
6	A	36	ARG	1	0.899	0.964	8.212	0.998	0.998	0.000	0.000	0.000	0.000
7	A	37	GLY	0	0.029	-0.001	9.435	0.173	0.173	0.000	0.000	0.000	0.000
8	A	38	TRP	0	-0.011	-0.014	11.224	0.170	0.170	0.000	0.000	0.000	0.000
9	A	39	GLY	0	0.077	0.013	13.180	0.099	0.099	0.000	0.000	0.000	0.000
10	A	40	ASP	-1	-0.888	-0.920	9.813	-1.271	-1.271	0.000	0.000	0.000	0.000
11	A	41	ASP	-1	-0.908	-0.932	12.240	-0.490	-0.490	0.000	0.000	0.000	0.000
12	A	42	ILE	0	-0.054	-0.025	15.141	0.071	0.071	0.000	0.000	0.000	0.000
13	A	43	THR	0	-0.056	-0.024	14.762	-0.053	-0.053	0.000	0.000	0.000	0.000
14	A	44	TRP	0	-0.064	-0.027	13.074	0.054	0.054	0.000	0.000	0.000	0.000
15	A	45	VAL	0	-0.003	0.002	15.793	0.010	0.010	0.000	0.000	0.000	0.000
16	A	46	GLN	0	-0.054	-0.039	13.745	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	47	THR	0	-0.001	0.002	15.926	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	48	TYR	0	0.016	-0.017	18.890	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	49	GLU	-1	-0.861	-0.942	21.695	-0.092	-0.092	0.000	0.000	0.000	0.000
20	A	50	GLU	-1	-0.853	-0.924	18.783	-0.212	-0.212	0.000	0.000	0.000	0.000
21	A	51	GLY	0	0.034	0.000	22.093	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	52	LEU	0	-0.004	-0.008	23.182	0.004	0.004	0.000	0.000	0.000	0.000
23	A	53	PHE	0	-0.047	-0.006	25.677	0.010	0.010	0.000	0.000	0.000	0.000
24	A	54	TYR	0	0.019	-0.011	22.753	0.010	0.010	0.000	0.000	0.000	0.000
25	A	55	ALA	0	0.019	0.031	26.353	0.001	0.001	0.000	0.000	0.000	0.000
26	A	56	GLN	0	0.037	0.018	27.924	0.005	0.005	0.000	0.000	0.000	0.000
27	A	57	LYS	1	0.871	0.945	29.288	0.089	0.089	0.000	0.000	0.000	0.000
28	A	58	SER	0	-0.071	-0.055	27.943	0.002	0.002	0.000	0.000	0.000	0.000
29	A	59	LYS	1	0.935	0.970	30.158	0.086	0.086	0.000	0.000	0.000	0.000
30	A	60	LYS	1	0.942	0.990	25.786	0.180	0.180	0.000	0.000	0.000	0.000
31	A	61	PRO	0	0.011	0.007	28.195	0.003	0.003	0.000	0.000	0.000	0.000
32	A	62	LEU	0	-0.008	0.003	22.220	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	63	MET	0	-0.034	-0.003	22.284	0.013	0.013	0.000	0.000	0.000	0.000
34	A	64	VAL	0	0.011	0.007	20.683	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	65	ILE	0	-0.016	-0.012	17.658	0.021	0.021	0.000	0.000	0.000	0.000
36	A	66	HIS	0	0.017	0.009	17.545	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	67	HIS	0	-0.050	-0.058	11.595	0.036	0.036	0.000	0.000	0.000	0.000
38	A	68	LEU	0	0.045	0.016	13.857	0.020	0.020	0.000	0.000	0.000	0.000
39	A	69	GLU	-1	-0.816	-0.933	8.048	-1.155	-1.155	0.000	0.000	0.000	0.000
40	A	70	ASP	-1	-0.919	-0.939	11.576	-0.114	-0.114	0.000	0.000	0.000	0.000
41	A	71	CYS	0	-0.082	0.016	13.958	0.043	0.043	0.000	0.000	0.000	0.000
42	A	72	GLN	0	0.046	0.000	16.476	-0.049	-0.049	0.000	0.000	0.000	0.000
43	A	73	TYR	0	0.036	0.008	18.379	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	74	SER	0	0.063	-0.007	15.820	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	75	GLN	0	-0.035	-0.023	10.908	-0.067	-0.067	0.000	0.000	0.000	0.000
46	A	76	ALA	0	-0.018	-0.010	15.610	-0.026	-0.026	0.000	0.000	0.000	0.000
47	A	77	LEU	0	-0.018	-0.015	18.736	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	78	LYS	1	0.891	0.964	10.395	0.860	0.860	0.000	0.000	0.000	0.000
49	A	79	LYS	1	0.971	1.000	15.748	0.335	0.335	0.000	0.000	0.000	0.000
50	A	80	VAL	0	-0.046	-0.032	16.591	0.010	0.010	0.000	0.000	0.000	0.000
51	A	81	PHE	0	-0.016	-0.006	18.171	0.022	0.022	0.000	0.000	0.000	0.000
52	A	82	ALA	0	-0.015	-0.010	15.407	0.015	0.015	0.000	0.000	0.000	0.000
53	A	83	GLN	0	-0.019	-0.006	15.915	0.035	0.035	0.000	0.000	0.000	0.000
54	A	84	ASN	0	-0.022	0.005	19.763	0.039	0.039	0.000	0.000	0.000	0.000
55	A	85	GLU	-1	-0.853	-0.940	22.679	-0.233	-0.233	0.000	0.000	0.000	0.000
56	A	86	GLU	-1	-0.882	-0.939	24.385	-0.166	-0.166	0.000	0.000	0.000	0.000
57	A	87	ILE	0	-0.031	-0.032	21.845	0.006	0.006	0.000	0.000	0.000	0.000
58	A	88	GLN	0	0.004	-0.006	17.715	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	89	GLU	-1	-0.885	-0.931	21.744	-0.194	-0.194	0.000	0.000	0.000	0.000
60	A	90	MET	0	-0.013	-0.018	24.573	0.013	0.013	0.000	0.000	0.000	0.000
61	A	91	ALA	0	-0.018	-0.016	20.462	0.009	0.009	0.000	0.000	0.000	0.000
62	A	92	GLN	0	-0.011	0.001	19.537	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	93	ASN	0	-0.048	-0.023	21.790	0.007	0.007	0.000	0.000	0.000	0.000
64	A	94	LYS	1	0.863	0.924	25.372	0.176	0.176	0.000	0.000	0.000	0.000
65	A	95	PHE	0	-0.037	-0.011	23.809	0.017	0.017	0.000	0.000	0.000	0.000
66	A	96	ILE	0	-0.035	0.010	21.976	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	97	MET	0	0.024	0.016	18.533	0.021	0.021	0.000	0.000	0.000	0.000
68	A	98	LEU	0	0.042	0.023	16.899	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	99	ASN	0	-0.008	-0.002	12.880	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	100	LEU	0	-0.020	-0.003	14.717	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	101	MET	0	-0.016	-0.007	9.193	-0.029	-0.029	0.000	0.000	0.000	0.000
72	A	102	HIS	0	-0.019	-0.011	14.586	0.069	0.069	0.000	0.000	0.000	0.000
73	A	103	GLU	-1	-0.814	-0.891	17.171	-0.146	-0.146	0.000	0.000	0.000	0.000
74	A	104	THR	0	0.016	0.014	20.846	0.018	0.018	0.000	0.000	0.000	0.000
75	A	105	THR	0	-0.011	-0.016	22.557	0.007	0.007	0.000	0.000	0.000	0.000
76	A	106	ASP	-1	-0.793	-0.888	25.819	-0.072	-0.072	0.000	0.000	0.000	0.000
77	A	107	LYS	1	0.994	0.977	27.343	0.023	0.023	0.000	0.000	0.000	0.000
78	A	108	ASN	0	-0.033	-0.014	29.542	0.000	0.000	0.000	0.000	0.000	0.000
79	A	109	LEU	0	-0.013	0.003	23.943	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	110	SER	0	-0.027	-0.020	25.871	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	111	PRO	0	-0.024	0.003	27.733	0.009	0.009	0.000	0.000	0.000	0.000
82	A	112	ASP	-1	-0.759	-0.864	30.153	-0.087	-0.087	0.000	0.000	0.000	0.000
83	A	113	GLY	0	0.000	0.009	28.644	0.001	0.001	0.000	0.000	0.000	0.000
84	A	114	GLN	0	-0.009	-0.019	23.515	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	115	TYR	0	-0.103	-0.060	22.927	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	116	VAL	0	0.007	0.029	18.251	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	117	PRO	0	-0.004	-0.020	19.224	0.011	0.011	0.000	0.000	0.000	0.000
88	A	118	ARG	1	0.752	0.862	20.604	0.157	0.157	0.000	0.000	0.000	0.000
89	A	119	ILE	0	-0.028	-0.008	21.502	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	120	MET	0	-0.020	0.019	23.645	0.019	0.019	0.000	0.000	0.000	0.000
91	A	121	PHE	0	0.056	0.007	25.158	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	122	VAL	0	-0.014	-0.004	26.547	0.013	0.013	0.000	0.000	0.000	0.000
93	A	123	ASP	-1	-0.730	-0.859	29.162	-0.107	-0.107	0.000	0.000	0.000	0.000
94	A	124	PRO	0	0.015	0.007	31.077	0.002	0.002	0.000	0.000	0.000	0.000
95	A	125	SER	0	-0.113	-0.077	32.082	0.005	0.005	0.000	0.000	0.000	0.000
96	A	126	LEU	0	-0.006	-0.008	30.362	0.006	0.006	0.000	0.000	0.000	0.000
97	A	127	THR	0	-0.015	0.014	32.135	0.003	0.003	0.000	0.000	0.000	0.000
98	A	128	VAL	0	0.022	0.005	29.179	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	129	ARG	1	0.806	0.874	31.021	0.109	0.109	0.000	0.000	0.000	0.000
100	A	130	ALA	0	0.036	0.020	32.004	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	131	ASP	-1	-0.795	-0.859	33.396	-0.094	-0.094	0.000	0.000	0.000	0.000
102	A	132	ILE	0	-0.129	-0.056	30.721	0.001	0.001	0.000	0.000	0.000	0.000
103	A	133	ALA	0	0.044	0.023	30.963	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	134	GLY	0	-0.002	-0.002	30.265	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	135	ARG	1	0.894	0.930	31.209	0.123	0.123	0.000	0.000	0.000	0.000
106	A	136	TYR	0	-0.037	-0.012	28.663	0.013	0.013	0.000	0.000	0.000	0.000
107	A	137	SER	0	0.033	0.011	32.941	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	138	ASN	0	-0.043	-0.021	33.324	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	139	ARG	1	0.964	0.974	25.309	0.103	0.103	0.000	0.000	0.000	0.000
110	A	140	LEU	0	0.034	0.029	29.664	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	141	TYR	0	0.020	-0.003	26.940	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	142	THR	0	-0.084	-0.034	23.984	-0.018	-0.018	0.000	0.000	0.000	0.000
113	A	143	TYR	0	-0.001	-0.006	24.414	0.012	0.012	0.000	0.000	0.000	0.000
114	A	144	GLU	-1	-0.870	-0.941	23.937	-0.153	-0.153	0.000	0.000	0.000	0.000
115	A	145	PRO	0	0.038	0.001	22.176	0.003	0.003	0.000	0.000	0.000	0.000
116	A	146	ARG	1	0.858	0.940	24.664	0.124	0.124	0.000	0.000	0.000	0.000
117	A	147	ASP	-1	-0.840	-0.912	27.416	-0.133	-0.133	0.000	0.000	0.000	0.000
118	A	148	LEU	0	0.028	0.008	23.435	0.002	0.002	0.000	0.000	0.000	0.000
119	A	149	PRO	0	0.021	0.006	27.493	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	150	LEU	0	0.022	0.027	30.940	0.004	0.004	0.000	0.000	0.000	0.000
121	A	151	LEU	0	0.005	0.008	23.661	0.003	0.003	0.000	0.000	0.000	0.000
122	A	152	ILE	0	0.014	0.009	27.512	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	153	GLU	-1	-0.924	-0.972	29.315	-0.121	-0.121	0.000	0.000	0.000	0.000
124	A	154	ASN	0	-0.041	-0.047	30.084	0.013	0.013	0.000	0.000	0.000	0.000
125	A	155	MET	0	-0.018	0.000	24.293	0.002	0.002	0.000	0.000	0.000	0.000
126	A	156	LYS	1	0.917	0.956	29.241	0.149	0.149	0.000	0.000	0.000	0.000
127	A	157	LYS	1	0.855	0.935	32.438	0.109	0.109	0.000	0.000	0.000	0.000
128	A	158	ALA	0	-0.006	-0.010	30.024	0.008	0.008	0.000	0.000	0.000	0.000
129	A	159	LEU	0	-0.023	-0.010	29.278	0.005	0.005	0.000	0.000	0.000	0.000
130	A	160	ARG	1	0.870	0.962	32.743	0.111	0.111	0.000	0.000	0.000	0.000
131	A	161	LEU	0	-0.008	-0.009	33.029	0.003	0.003	0.000	0.000	0.000	0.000
132	A	162	ILE	0	0.003	0.005	35.904	0.005	0.005	0.000	0.000	0.000	0.000
133	A	163	GLN	0	-0.084	-0.030	38.442	0.008	0.008	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:31:PRO)