FMO DATABASE

FMODB ID: MNM2Z

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	OptHSide
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	-966689.731608
FMO2-HF: Nuclear repulsion	917705.589767
FMO2-HF: Total energy	-48984.141841
FMO2-MP2: Total energy	-49127.103891

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.
-10.018	-2.605	2.699	-4.195	-5.915	-0.012

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 : -0.002 / 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	0	ALA	0	0.016	0.018	2.623	-2.577	0.703	0.487	-1.544	-2.222	0.000
4	A	1	MET	0	0.009	0.019	4.033	1.846	2.101	-0.001	-0.018	-0.237	0.000
5	A	2	ILE	0	-0.049	-0.036	6.738	-0.077	-0.077	0.000	0.000	0.000	0.000
6	A	3	ASP	-1	-0.856	-0.920	8.945	0.752	0.752	0.000	0.000	0.000	0.000
7	A	4	PHE	0	-0.019	-0.011	12.667	-0.050	-0.050	0.000	0.000	0.000	0.000
8	A	5	ALA	0	0.000	-0.008	14.729	-0.017	-0.017	0.000	0.000	0.000	0.000
9	A	6	CYS	0	-0.011	-0.010	17.839	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	7	LYS	1	0.959	0.989	16.324	-0.553	-0.553	0.000	0.000	0.000	0.000
11	A	8	GLU	-1	-0.839	-0.924	11.748	1.256	1.256	0.000	0.000	0.000	0.000
12	A	9	PHE	0	-0.075	-0.040	10.081	-0.075	-0.075	0.000	0.000	0.000	0.000
13	A	10	LYS	1	0.969	0.980	6.144	-1.398	-1.398	0.000	0.000	0.000	0.000
14	A	11	VAL	0	0.042	0.012	3.325	-1.214	-0.484	0.083	-0.289	-0.524	0.002
15	A	12	GLU	-1	-0.810	-0.910	2.509	-4.871	-1.871	2.133	-2.324	-2.810	-0.014
16	A	13	ASP	-1	-0.846	-0.926	5.090	0.531	0.543	-0.001	-0.002	-0.008	0.000
17	A	14	VAL	0	0.041	0.035	7.693	-0.498	-0.498	0.000	0.000	0.000	0.000
18	A	15	ILE	0	0.019	0.008	4.690	-0.512	-0.464	-0.001	-0.001	-0.045	0.000
19	A	16	LYS	1	0.832	0.914	8.552	-1.701	-1.701	0.000	0.000	0.000	0.000
20	A	17	CYS	0	-0.016	0.015	10.678	-0.252	-0.252	0.000	0.000	0.000	0.000
21	A	18	ALA	0	0.025	0.026	11.722	-0.136	-0.136	0.000	0.000	0.000	0.000
22	A	19	LEU	0	0.018	-0.007	11.045	-0.126	-0.126	0.000	0.000	0.000	0.000
23	A	20	ASN	0	-0.030	0.011	14.064	-0.077	-0.077	0.000	0.000	0.000	0.000
24	A	21	LEU	0	-0.039	-0.015	10.865	-0.089	-0.089	0.000	0.000	0.000	0.000
25	A	22	THR	0	0.025	-0.014	13.497	0.080	0.080	0.000	0.000	0.000	0.000
26	A	23	LYS	1	1.005	0.980	10.482	-0.200	-0.200	0.000	0.000	0.000	0.000
27	A	24	ALA	0	0.012	0.010	11.523	-0.043	-0.043	0.000	0.000	0.000	0.000
28	A	25	ASP	-1	-0.687	-0.814	13.431	0.211	0.211	0.000	0.000	0.000	0.000
29	A	26	LEU	0	-0.004	0.013	6.364	-0.078	-0.078	0.000	0.000	0.000	0.000
30	A	27	ASN	0	-0.006	-0.021	8.955	-0.100	-0.100	0.000	0.000	0.000	0.000
31	A	28	VAL	0	0.014	0.021	10.631	-0.116	-0.116	0.000	0.000	0.000	0.000
32	A	29	MET	0	0.011	0.006	9.179	-0.047	-0.047	0.000	0.000	0.000	0.000
33	A	30	LYS	1	0.822	0.891	3.964	-0.114	-0.026	-0.001	-0.017	-0.069	0.000
34	A	31	SER	0	0.005	0.005	9.553	-0.139	-0.139	0.000	0.000	0.000	0.000
35	A	32	PHE	0	-0.011	-0.019	12.604	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	33	LEU	0	-0.039	-0.017	8.235	0.007	0.007	0.000	0.000	0.000	0.000
37	A	34	ASN	0	-0.023	-0.013	8.997	-0.186	-0.186	0.000	0.000	0.000	0.000
38	A	35	GLU	-1	-0.867	-0.928	11.413	-0.388	-0.388	0.000	0.000	0.000	0.000
39	A	36	PRO	0	-0.013	-0.001	13.575	0.064	0.064	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.855	-0.930	15.807	-0.205	-0.205	0.000	0.000	0.000	0.000
41	A	38	ARG	1	0.859	0.947	16.102	0.349	0.349	0.000	0.000	0.000	0.000
42	A	39	TRP	0	-0.004	0.000	19.865	0.013	0.013	0.000	0.000	0.000	0.000
43	A	40	ILE	0	-0.043	-0.030	19.136	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	41	ASP	-1	-0.770	-0.883	22.395	-0.085	-0.085	0.000	0.000	0.000	0.000
45	A	42	THR	0	0.029	-0.008	22.649	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	43	ASP	-1	-0.859	-0.937	22.997	-0.052	-0.052	0.000	0.000	0.000	0.000
47	A	44	ALA	0	-0.013	0.005	23.951	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	45	LEU	0	-0.024	-0.011	16.697	-0.024	-0.024	0.000	0.000	0.000	0.000
49	A	46	SER	0	-0.068	-0.046	19.237	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	47	LYS	1	1.003	1.002	20.753	0.103	0.103	0.000	0.000	0.000	0.000
51	A	48	SER	0	-0.002	0.000	17.521	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	49	LEU	0	-0.058	-0.029	13.266	-0.044	-0.044	0.000	0.000	0.000	0.000
53	A	50	LYS	1	0.867	0.948	16.993	0.268	0.268	0.000	0.000	0.000	0.000
54	A	51	LEU	0	-0.035	-0.006	15.659	0.029	0.029	0.000	0.000	0.000	0.000
55	A	52	ASP	-1	-0.771	-0.878	20.104	0.020	0.020	0.000	0.000	0.000	0.000
56	A	53	VAL	0	0.066	0.013	22.572	0.010	0.010	0.000	0.000	0.000	0.000
57	A	54	SER	0	0.012	0.012	23.940	0.007	0.007	0.000	0.000	0.000	0.000
58	A	55	THR	0	-0.074	-0.053	18.880	0.027	0.027	0.000	0.000	0.000	0.000
59	A	56	VAL	0	0.026	0.012	18.563	0.018	0.018	0.000	0.000	0.000	0.000
60	A	57	GLN	0	0.014	0.020	20.207	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	58	ARG	1	0.933	0.952	21.714	-0.111	-0.111	0.000	0.000	0.000	0.000
62	A	59	SER	0	-0.064	-0.045	16.700	0.011	0.011	0.000	0.000	0.000	0.000
63	A	60	VAL	0	-0.003	-0.001	18.684	0.014	0.014	0.000	0.000	0.000	0.000
64	A	61	LYS	1	0.822	0.904	19.951	-0.100	-0.100	0.000	0.000	0.000	0.000
65	A	62	LYS	1	0.864	0.924	17.369	-0.298	-0.298	0.000	0.000	0.000	0.000
66	A	63	LEU	0	-0.043	-0.028	14.279	0.018	0.018	0.000	0.000	0.000	0.000
67	A	64	HIS	0	0.010	-0.002	18.239	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	65	GLU	-1	-0.796	-0.881	21.462	0.110	0.110	0.000	0.000	0.000	0.000
69	A	66	LYS	1	0.826	0.907	17.025	-0.327	-0.327	0.000	0.000	0.000	0.000
70	A	67	GLU	-1	-0.943	-0.960	19.205	0.090	0.090	0.000	0.000	0.000	0.000
71	A	68	ILE	0	-0.025	-0.010	14.039	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	69	LEU	0	-0.041	-0.027	16.666	-0.043	-0.043	0.000	0.000	0.000	0.000
73	A	70	GLN	0	0.011	0.023	19.487	0.008	0.008	0.000	0.000	0.000	0.000
74	A	71	ARG	1	0.857	0.916	22.737	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	72	SER	0	0.018	0.012	25.371	0.004	0.004	0.000	0.000	0.000	0.000
76	A	73	GLN	0	0.014	-0.008	28.086	0.002	0.002	0.000	0.000	0.000	0.000
77	A	74	GLN	0	0.005	0.026	29.284	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	75	ASN	0	-0.001	-0.016	31.765	0.007	0.007	0.000	0.000	0.000	0.000
79	A	76	LEU	0	0.003	-0.001	33.237	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	77	ASP	-1	-0.890	-0.946	36.882	-0.051	-0.051	0.000	0.000	0.000	0.000
81	A	78	GLY	0	-0.033	-0.014	40.024	0.002	0.002	0.000	0.000	0.000	0.000
82	A	79	GLY	0	-0.005	0.008	40.592	0.004	0.004	0.000	0.000	0.000	0.000
83	A	80	GLY	0	-0.028	-0.007	37.807	0.003	0.003	0.000	0.000	0.000	0.000
84	A	81	TYR	0	-0.029	-0.033	31.945	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	82	VAL	0	0.021	0.017	29.367	0.005	0.005	0.000	0.000	0.000	0.000
86	A	83	TYR	0	-0.022	-0.016	26.969	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	84	ILE	0	-0.006	0.008	24.975	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	85	TYR	0	-0.010	-0.026	20.783	0.021	0.021	0.000	0.000	0.000	0.000
89	A	86	LYS	1	0.871	0.938	19.562	0.162	0.162	0.000	0.000	0.000	0.000
90	A	87	ILE	0	-0.061	-0.011	13.630	0.036	0.036	0.000	0.000	0.000	0.000
91	A	88	TYR	0	0.034	0.020	17.001	-0.027	-0.027	0.000	0.000	0.000	0.000
92	A	89	SER	0	0.065	0.021	16.446	-0.027	-0.027	0.000	0.000	0.000	0.000
93	A	90	LYS	1	1.025	1.002	12.822	0.468	0.468	0.000	0.000	0.000	0.000
94	A	91	ASN	0	-0.010	-0.023	14.099	0.001	0.001	0.000	0.000	0.000	0.000
95	A	92	GLN	0	0.025	0.035	16.801	0.041	0.041	0.000	0.000	0.000	0.000
96	A	93	ILE	0	0.004	-0.004	11.299	0.047	0.047	0.000	0.000	0.000	0.000
97	A	94	ARG	1	0.945	0.970	11.156	0.247	0.247	0.000	0.000	0.000	0.000
98	A	95	ASN	0	0.008	0.003	13.215	0.070	0.070	0.000	0.000	0.000	0.000
99	A	96	ILE	0	0.012	0.020	15.349	0.030	0.030	0.000	0.000	0.000	0.000
100	A	97	ILE	0	-0.008	-0.003	9.397	0.040	0.040	0.000	0.000	0.000	0.000
101	A	98	GLN	0	0.028	0.011	13.453	0.093	0.093	0.000	0.000	0.000	0.000
102	A	99	LYS	1	0.955	0.978	15.233	-0.172	-0.172	0.000	0.000	0.000	0.000
103	A	100	ILE	0	0.005	0.013	15.417	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	101	VAL	0	0.006	0.015	12.394	0.015	0.015	0.000	0.000	0.000	0.000
105	A	102	GLN	0	-0.084	-0.053	15.746	0.007	0.007	0.000	0.000	0.000	0.000
106	A	103	SER	0	-0.041	-0.012	19.029	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	104	TRP	0	-0.009	-0.028	12.656	0.021	0.021	0.000	0.000	0.000	0.000
108	A	105	ALA	0	-0.011	0.002	19.256	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	106	ASP	-1	-0.825	-0.917	20.870	0.236	0.236	0.000	0.000	0.000	0.000
110	A	107	ARG	1	0.802	0.884	23.134	-0.335	-0.335	0.000	0.000	0.000	0.000
111	A	108	LEU	0	-0.010	-0.005	21.452	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	109	GLY	0	0.040	0.024	24.395	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	110	GLN	0	-0.039	-0.029	26.887	-0.031	-0.031	0.000	0.000	0.000	0.000
114	A	111	GLU	-1	-0.807	-0.881	26.182	0.256	0.256	0.000	0.000	0.000	0.000
115	A	112	LEU	0	0.006	0.015	27.161	0.000	0.000	0.000	0.000	0.000	0.000
116	A	113	LYS	1	0.857	0.934	30.445	-0.180	-0.180	0.000	0.000	0.000	0.000
117	A	114	GLU	-1	-0.974	-1.025	33.037	0.162	0.162	0.000	0.000	0.000	0.000
118	A	115	TRP	0	-0.051	-0.006	31.982	0.006	0.006	0.000	0.000	0.000	0.000
119	A	116	GLU	-1	-0.961	-0.983	34.042	0.137	0.137	0.000	0.000	0.000	0.000
120	A	117	ASN	0	-0.071	-0.004	36.432	-0.013	-0.013	0.000	0.000	0.000	0.000

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