FMO DATABASE

FMODB ID: 98Y22

Calculation Name: 3R0A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R0A

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PXX2

Base Structure: X-ray

Registration Date: 2023-09-20

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-967124.475235
FMO2-HF: Nuclear repulsion	918141.58291
FMO2-HF: Total energy	-48982.892325
FMO2-MP2: Total energy	-49125.962159

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:SER)

Summations of interaction energy for fragment #1(A:-2: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.
-5.888	1.47	1.667	-3.704	-5.32	-0.01

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.007

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	0	ALA	0	0.018	0.025	2.890	-2.170	1.467	0.373	-1.736	-2.274	0.003
4	A	1	MET	0	0.004	0.015	4.390	-1.391	-1.148	0.000	-0.035	-0.208	0.000
5	A	2	ILE	0	-0.040	-0.027	7.084	0.431	0.431	0.000	0.000	0.000	0.000
6	A	3	ASP	-1	-0.857	-0.917	9.182	0.115	0.115	0.000	0.000	0.000	0.000
7	A	4	PHE	0	-0.011	-0.009	12.772	0.041	0.041	0.000	0.000	0.000	0.000
8	A	5	ALA	0	-0.007	-0.013	14.689	-0.041	-0.041	0.000	0.000	0.000	0.000
9	A	6	CYS	0	-0.014	-0.007	17.872	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	7	LYS	1	0.972	0.985	15.520	0.094	0.094	0.000	0.000	0.000	0.000
11	A	8	GLU	-1	-0.855	-0.929	11.297	0.163	0.163	0.000	0.000	0.000	0.000
12	A	9	PHE	0	-0.071	-0.033	9.313	-0.134	-0.134	0.000	0.000	0.000	0.000
13	A	10	LYS	1	0.919	0.941	5.182	1.266	1.266	0.000	0.000	0.000	0.000
14	A	11	VAL	0	0.044	0.004	3.091	-0.950	-0.385	0.067	-0.178	-0.453	0.001
15	A	12	GLU	-1	-0.875	-0.959	2.589	-8.202	-5.404	1.229	-1.737	-2.290	-0.014
16	A	13	ASP	-1	-0.846	-0.906	4.568	-0.757	-0.708	-0.001	-0.009	-0.039	0.000
17	A	14	VAL	0	0.021	0.023	7.141	0.223	0.223	0.000	0.000	0.000	0.000
18	A	15	ILE	0	0.017	0.009	4.840	0.153	0.153	0.000	0.000	0.000	0.000
19	A	16	LYS	1	0.871	0.938	8.419	1.444	1.444	0.000	0.000	0.000	0.000
20	A	17	CYS	0	-0.006	0.023	10.487	0.160	0.160	0.000	0.000	0.000	0.000
21	A	18	ALA	0	0.018	0.025	11.858	0.081	0.081	0.000	0.000	0.000	0.000
22	A	19	LEU	0	0.024	-0.004	11.002	0.069	0.069	0.000	0.000	0.000	0.000
23	A	20	ASN	0	-0.010	0.022	14.089	0.028	0.028	0.000	0.000	0.000	0.000
24	A	21	LEU	0	-0.037	-0.009	10.855	0.026	0.026	0.000	0.000	0.000	0.000
25	A	22	THR	0	0.045	0.015	13.172	-0.081	-0.081	0.000	0.000	0.000	0.000
26	A	23	LYS	1	0.984	0.966	10.541	0.910	0.910	0.000	0.000	0.000	0.000
27	A	24	ALA	0	0.014	0.014	11.537	-0.099	-0.099	0.000	0.000	0.000	0.000
28	A	25	ASP	-1	-0.683	-0.825	13.439	-0.523	-0.523	0.000	0.000	0.000	0.000
29	A	26	LEU	0	-0.020	0.001	6.451	0.083	0.083	0.000	0.000	0.000	0.000
30	A	27	ASN	0	-0.001	-0.022	9.145	-0.235	-0.235	0.000	0.000	0.000	0.000
31	A	28	VAL	0	0.005	0.024	10.632	0.070	0.070	0.000	0.000	0.000	0.000
32	A	29	MET	0	0.010	0.004	9.181	0.097	0.097	0.000	0.000	0.000	0.000
33	A	30	LYS	1	0.875	0.929	4.461	2.812	2.878	-0.001	-0.009	-0.056	0.000
34	A	31	SER	0	0.021	0.010	9.557	0.136	0.136	0.000	0.000	0.000	0.000
35	A	32	PHE	0	-0.035	-0.025	12.596	0.080	0.080	0.000	0.000	0.000	0.000
36	A	33	LEU	0	-0.049	-0.025	8.111	0.061	0.061	0.000	0.000	0.000	0.000
37	A	34	ASN	0	-0.011	-0.011	9.077	0.118	0.118	0.000	0.000	0.000	0.000
38	A	35	GLU	-1	-0.924	-0.964	11.405	-0.057	-0.057	0.000	0.000	0.000	0.000
39	A	36	PRO	0	-0.043	-0.011	13.749	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.895	-0.974	15.820	0.067	0.067	0.000	0.000	0.000	0.000
41	A	38	ARG	1	0.918	0.979	16.798	0.184	0.184	0.000	0.000	0.000	0.000
42	A	39	TRP	0	-0.004	-0.003	19.872	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	40	ILE	0	-0.029	-0.019	19.189	0.001	0.001	0.000	0.000	0.000	0.000
44	A	41	ASP	-1	-0.801	-0.912	22.395	-0.152	-0.152	0.000	0.000	0.000	0.000
45	A	42	THR	0	0.020	-0.017	22.644	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	43	ASP	-1	-0.841	-0.932	22.989	-0.188	-0.188	0.000	0.000	0.000	0.000
47	A	44	ALA	0	0.010	0.048	23.940	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	45	LEU	0	-0.040	-0.013	16.741	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	46	SER	0	-0.052	-0.063	19.226	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	47	LYS	1	1.001	1.001	20.744	0.144	0.144	0.000	0.000	0.000	0.000
51	A	48	SER	0	-0.043	-0.020	17.449	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	49	LEU	0	-0.034	-0.018	13.845	-0.035	-0.035	0.000	0.000	0.000	0.000
53	A	50	LYS	1	0.880	0.956	16.984	0.297	0.297	0.000	0.000	0.000	0.000
54	A	51	LEU	0	-0.042	-0.014	15.548	-0.031	-0.031	0.000	0.000	0.000	0.000
55	A	52	ASP	-1	-0.782	-0.897	20.102	-0.249	-0.249	0.000	0.000	0.000	0.000
56	A	53	VAL	0	0.085	0.024	22.574	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	54	SER	0	0.007	0.013	23.942	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	55	THR	0	-0.083	-0.040	18.805	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	56	VAL	0	0.004	-0.003	19.026	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	57	GLN	0	0.003	0.009	20.209	0.002	0.002	0.000	0.000	0.000	0.000
61	A	58	ARG	1	0.967	0.972	21.205	0.326	0.326	0.000	0.000	0.000	0.000
62	A	59	SER	0	-0.068	-0.058	16.752	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	60	VAL	0	-0.002	0.001	18.694	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	61	LYS	1	0.935	0.976	19.955	0.206	0.206	0.000	0.000	0.000	0.000
65	A	62	LYS	1	0.886	0.940	17.357	0.449	0.449	0.000	0.000	0.000	0.000
66	A	63	LEU	0	-0.036	-0.027	14.453	0.004	0.004	0.000	0.000	0.000	0.000
67	A	64	HIS	0	-0.035	-0.022	18.380	0.030	0.030	0.000	0.000	0.000	0.000
68	A	65	GLU	-1	-0.889	-0.954	21.582	-0.182	-0.182	0.000	0.000	0.000	0.000
69	A	66	LYS	1	0.795	0.894	17.273	0.328	0.328	0.000	0.000	0.000	0.000
70	A	67	GLU	-1	-0.923	-0.947	19.296	-0.086	-0.086	0.000	0.000	0.000	0.000
71	A	68	ILE	0	-0.025	-0.006	14.281	0.013	0.013	0.000	0.000	0.000	0.000
72	A	69	LEU	0	-0.043	-0.028	16.912	0.010	0.010	0.000	0.000	0.000	0.000
73	A	70	GLN	0	0.004	0.014	19.560	0.017	0.017	0.000	0.000	0.000	0.000
74	A	71	ARG	1	0.923	0.962	22.761	0.108	0.108	0.000	0.000	0.000	0.000
75	A	72	SER	0	0.015	0.008	25.396	0.013	0.013	0.000	0.000	0.000	0.000
76	A	73	GLN	0	0.022	-0.007	28.106	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	74	GLN	0	0.013	0.022	28.979	0.006	0.006	0.000	0.000	0.000	0.000
78	A	75	ASN	0	-0.015	-0.013	31.771	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	76	LEU	0	-0.002	-0.006	33.177	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	77	ASP	-1	-0.871	-0.935	36.882	-0.052	-0.052	0.000	0.000	0.000	0.000
81	A	78	GLY	0	-0.053	-0.022	40.030	0.003	0.003	0.000	0.000	0.000	0.000
82	A	79	GLY	0	-0.002	0.009	40.613	0.000	0.000	0.000	0.000	0.000	0.000
83	A	80	GLY	0	-0.028	-0.006	37.802	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	81	TYR	0	-0.027	-0.029	31.791	0.004	0.004	0.000	0.000	0.000	0.000
85	A	82	VAL	0	0.025	0.017	29.205	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	83	TYR	0	-0.054	-0.032	26.865	0.004	0.004	0.000	0.000	0.000	0.000
87	A	84	ILE	0	0.005	0.010	24.980	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	85	TYR	0	-0.023	-0.028	20.804	0.005	0.005	0.000	0.000	0.000	0.000
89	A	86	LYS	1	0.967	1.009	19.622	0.005	0.005	0.000	0.000	0.000	0.000
90	A	87	ILE	0	-0.057	-0.007	13.605	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	88	TYR	0	0.029	0.021	17.027	0.039	0.039	0.000	0.000	0.000	0.000
92	A	89	SER	0	0.059	0.021	16.482	0.013	0.013	0.000	0.000	0.000	0.000
93	A	90	LYS	1	1.020	0.997	12.655	-0.443	-0.443	0.000	0.000	0.000	0.000
94	A	91	ASN	0	-0.021	-0.029	14.146	0.061	0.061	0.000	0.000	0.000	0.000
95	A	92	GLN	0	-0.006	0.008	16.768	0.016	0.016	0.000	0.000	0.000	0.000
96	A	93	ILE	0	0.012	0.010	11.218	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	94	ARG	1	0.977	0.980	10.780	-0.589	-0.589	0.000	0.000	0.000	0.000
98	A	95	ASN	0	0.011	0.006	13.172	0.017	0.017	0.000	0.000	0.000	0.000
99	A	96	ILE	0	0.011	0.024	15.421	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	97	ILE	0	-0.007	-0.008	9.516	-0.032	-0.032	0.000	0.000	0.000	0.000
101	A	98	GLN	0	0.038	0.020	13.484	0.001	0.001	0.000	0.000	0.000	0.000
102	A	99	LYS	1	0.949	0.975	15.217	-0.028	-0.028	0.000	0.000	0.000	0.000
103	A	100	ILE	0	0.014	0.015	15.214	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	101	VAL	0	0.010	0.008	12.445	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	102	GLN	0	-0.080	-0.040	15.774	0.035	0.035	0.000	0.000	0.000	0.000
106	A	103	SER	0	-0.039	-0.010	19.030	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	104	TRP	0	-0.019	-0.033	12.589	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	105	ALA	0	-0.016	-0.001	19.325	0.002	0.002	0.000	0.000	0.000	0.000
109	A	106	ASP	-1	-0.843	-0.932	20.885	0.017	0.017	0.000	0.000	0.000	0.000
110	A	107	ARG	1	0.930	0.962	21.797	0.109	0.109	0.000	0.000	0.000	0.000
111	A	108	LEU	0	-0.020	-0.010	21.105	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	109	GLY	0	0.040	0.022	24.235	0.006	0.006	0.000	0.000	0.000	0.000
113	A	110	GLN	0	-0.050	-0.031	26.856	0.004	0.004	0.000	0.000	0.000	0.000
114	A	111	GLU	-1	-0.901	-0.952	26.737	-0.053	-0.053	0.000	0.000	0.000	0.000
115	A	112	LEU	0	-0.017	0.010	26.694	0.003	0.003	0.000	0.000	0.000	0.000
116	A	113	LYS	1	0.849	0.929	30.211	0.003	0.003	0.000	0.000	0.000	0.000
117	A	114	GLU	-1	-0.976	-1.017	32.627	-0.033	-0.033	0.000	0.000	0.000	0.000
118	A	115	TRP	0	-0.040	0.003	31.611	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	116	GLU	-1	-0.950	-0.984	33.666	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	117	ASN	0	-0.070	-0.008	36.689	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:-2:SER)