FMO DATABASE

FMODB ID: 2NJMR

Calculation Name: 2QR3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QR3

Chain ID: A

ChEMBL ID:

UniProt ID: Q64UD2

Base Structure: X-ray

Registration Date: 2023-09-21

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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1081176.006668
FMO2-HF: Nuclear repulsion	1033289.957765
FMO2-HF: Total energy	-47886.048903
FMO2-MP2: Total energy	-48029.197656

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:0:SER)

Summations of interaction energy for fragment #1(A:0: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.
-7.712	-5.787	-0.01	-0.894	-1.02	0.003

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.006

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

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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	2	GLY	0	0.032	0.022	3.865	1.807	3.521	-0.007	-0.825	-0.882	0.003
4	A	3	THR	0	-0.036	-0.034	5.238	0.672	0.735	-0.001	-0.001	-0.061	0.000
5	A	4	ILE	0	0.004	0.026	8.860	-0.154	-0.154	0.000	0.000	0.000	0.000
6	A	5	ILE	0	-0.023	-0.012	11.472	0.225	0.225	0.000	0.000	0.000	0.000
7	A	6	ILE	0	-0.009	-0.003	15.052	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	7	VAL	0	-0.004	0.000	18.096	0.063	0.063	0.000	0.000	0.000	0.000
9	A	8	ASP	-1	-0.730	-0.886	21.523	-0.404	-0.404	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.743	-0.851	24.656	-0.277	-0.277	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.026	0.006	27.689	0.028	0.028	0.000	0.000	0.000	0.000
12	A	11	LYS	1	0.891	0.921	26.262	0.255	0.255	0.000	0.000	0.000	0.000
13	A	12	GLY	0	0.019	0.029	26.002	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	13	VAL	0	0.000	0.001	23.672	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	14	LEU	0	-0.032	-0.007	21.388	-0.038	-0.038	0.000	0.000	0.000	0.000
16	A	15	THR	0	-0.029	-0.030	21.135	-0.033	-0.033	0.000	0.000	0.000	0.000
17	A	16	ALA	0	0.001	0.003	21.870	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	17	VAL	0	0.030	0.009	17.468	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	18	GLN	0	-0.029	-0.022	16.549	-0.083	-0.083	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.032	-0.014	17.492	0.012	0.012	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.037	-0.019	17.434	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	21	LEU	0	0.043	0.006	13.054	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.810	0.911	12.091	0.319	0.319	0.000	0.000	0.000	0.000
24	A	23	ASN	0	-0.032	-0.017	11.485	0.096	0.096	0.000	0.000	0.000	0.000
25	A	24	HIS	0	-0.005	0.006	8.603	0.068	0.068	0.000	0.000	0.000	0.000
26	A	25	PHE	0	0.020	0.012	6.934	-0.499	-0.499	0.000	0.000	0.000	0.000
27	A	26	SER	0	-0.047	-0.035	4.307	0.959	1.063	-0.001	-0.005	-0.098	0.000
28	A	27	LYS	1	0.768	0.866	6.974	1.081	1.081	0.000	0.000	0.000	0.000
29	A	28	VAL	0	0.042	0.032	10.151	-0.225	-0.225	0.000	0.000	0.000	0.000
30	A	29	ILE	0	0.003	0.015	13.078	0.186	0.186	0.000	0.000	0.000	0.000
31	A	30	THR	0	0.005	0.007	15.901	-0.039	-0.039	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.067	-0.025	19.385	0.062	0.062	0.000	0.000	0.000	0.000
33	A	32	SER	0	0.017	-0.029	22.415	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	33	SER	0	0.017	0.007	24.675	0.033	0.033	0.000	0.000	0.000	0.000
35	A	34	PRO	0	0.084	0.038	24.573	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	35	VAL	0	0.030	0.027	24.862	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	36	SER	0	0.017	0.008	22.702	0.002	0.002	0.000	0.000	0.000	0.000
38	A	37	LEU	0	0.025	0.017	19.277	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	38	SER	0	-0.056	-0.041	19.954	-0.029	-0.029	0.000	0.000	0.000	0.000
40	A	39	THR	0	-0.032	-0.012	20.427	0.014	0.014	0.000	0.000	0.000	0.000
41	A	40	VAL	0	0.012	-0.009	16.345	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	41	LEU	0	-0.015	-0.016	15.501	-0.073	-0.073	0.000	0.000	0.000	0.000
43	A	42	ARG	1	0.813	0.933	15.836	0.252	0.252	0.000	0.000	0.000	0.000
44	A	43	GLU	-1	-0.847	-0.924	15.956	-0.253	-0.253	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.826	-0.894	12.928	-0.507	-0.507	0.000	0.000	0.000	0.000
46	A	45	ASN	0	-0.079	-0.030	9.286	-0.127	-0.127	0.000	0.000	0.000	0.000
47	A	46	PRO	0	-0.026	-0.003	8.835	-0.313	-0.313	0.000	0.000	0.000	0.000
48	A	47	GLU	-1	-0.781	-0.889	4.012	-8.614	-8.570	-0.001	-0.063	0.021	0.000
49	A	48	VAL	0	-0.022	-0.017	8.828	0.187	0.187	0.000	0.000	0.000	0.000
50	A	49	VAL	0	-0.016	-0.010	12.100	0.047	0.047	0.000	0.000	0.000	0.000
51	A	50	LEU	0	-0.016	0.011	15.475	0.039	0.039	0.000	0.000	0.000	0.000
52	A	51	LEU	0	-0.017	-0.022	17.971	0.042	0.042	0.000	0.000	0.000	0.000
53	A	52	ASP	-1	-0.823	-0.922	21.366	-0.343	-0.343	0.000	0.000	0.000	0.000
54	A	53	MET	0	-0.022	0.005	24.755	0.002	0.002	0.000	0.000	0.000	0.000
55	A	54	ASN	0	-0.014	-0.016	27.387	0.006	0.006	0.000	0.000	0.000	0.000
56	A	55	PHE	0	-0.003	0.013	25.378	0.016	0.016	0.000	0.000	0.000	0.000
57	A	56	THR	0	-0.068	-0.038	28.107	0.013	0.013	0.000	0.000	0.000	0.000
58	A	57	SER	0	0.008	0.021	30.977	0.021	0.021	0.000	0.000	0.000	0.000
59	A	58	GLY	0	0.012	-0.001	33.666	0.003	0.003	0.000	0.000	0.000	0.000
60	A	59	ILE	0	-0.037	-0.023	37.207	0.003	0.003	0.000	0.000	0.000	0.000
61	A	60	ASN	0	-0.067	-0.037	34.580	0.014	0.014	0.000	0.000	0.000	0.000
62	A	61	ASN	0	-0.055	-0.034	36.204	0.000	0.000	0.000	0.000	0.000	0.000
63	A	62	GLY	0	0.033	0.014	35.849	0.011	0.011	0.000	0.000	0.000	0.000
64	A	63	ASN	0	-0.080	-0.036	32.455	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.752	-0.876	30.516	-0.241	-0.241	0.000	0.000	0.000	0.000
66	A	65	GLY	0	0.008	0.004	26.508	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	66	LEU	0	-0.008	-0.005	25.993	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	67	PHE	0	-0.012	0.006	27.564	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	68	TRP	0	0.010	-0.026	24.480	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	69	LEU	0	0.013	0.011	21.700	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	70	HIS	0	0.000	0.013	23.142	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	71	GLU	-1	-0.756	-0.849	25.057	-0.273	-0.273	0.000	0.000	0.000	0.000
73	A	72	ILE	0	-0.040	-0.011	18.585	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	73	LYS	1	0.843	0.918	17.986	0.636	0.636	0.000	0.000	0.000	0.000
75	A	74	ARG	1	0.782	0.851	21.826	0.271	0.271	0.000	0.000	0.000	0.000
76	A	75	GLN	0	-0.078	-0.035	20.822	0.042	0.042	0.000	0.000	0.000	0.000
77	A	76	TYR	0	0.002	-0.009	16.708	0.018	0.018	0.000	0.000	0.000	0.000
78	A	77	ARG	1	0.876	0.912	17.895	0.315	0.315	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.848	-0.900	15.305	-0.490	-0.490	0.000	0.000	0.000	0.000
80	A	79	LEU	0	-0.006	0.021	12.566	-0.106	-0.106	0.000	0.000	0.000	0.000
81	A	80	PRO	0	0.015	0.010	11.904	0.177	0.177	0.000	0.000	0.000	0.000
82	A	81	VAL	0	-0.014	-0.008	14.876	-0.034	-0.034	0.000	0.000	0.000	0.000
83	A	82	VAL	0	-0.006	0.012	16.357	0.058	0.058	0.000	0.000	0.000	0.000
84	A	83	LEU	0	0.013	0.011	18.944	0.017	0.017	0.000	0.000	0.000	0.000
85	A	84	PHE	0	0.015	-0.011	21.956	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	85	THR	0	0.050	0.013	23.848	0.029	0.029	0.000	0.000	0.000	0.000
87	A	86	ALA	0	0.040	0.031	27.583	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	87	TYR	0	0.008	-0.024	29.269	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	88	ALA	0	-0.051	-0.015	32.534	0.008	0.008	0.000	0.000	0.000	0.000
90	A	89	ASP	-1	-0.792	-0.878	31.372	-0.248	-0.248	0.000	0.000	0.000	0.000
91	A	90	ILE	0	-0.021	-0.022	29.622	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	91	ASP	-1	-0.880	-0.938	30.760	-0.243	-0.243	0.000	0.000	0.000	0.000
93	A	92	LEU	0	0.016	0.009	31.080	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	93	ALA	0	0.033	0.015	26.703	-0.017	-0.017	0.000	0.000	0.000	0.000
95	A	94	VAL	0	-0.035	-0.022	27.241	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	95	ARG	1	0.762	0.858	29.196	0.253	0.253	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.082	0.018	26.691	0.000	0.000	0.000	0.000	0.000	0.000
98	A	97	ILE	0	-0.043	-0.007	22.866	-0.017	-0.017	0.000	0.000	0.000	0.000
99	A	98	LYS	1	0.881	0.945	25.477	0.247	0.247	0.000	0.000	0.000	0.000
100	A	99	GLU	-1	-0.836	-0.894	27.473	-0.261	-0.261	0.000	0.000	0.000	0.000
101	A	100	GLY	0	0.004	0.009	23.632	0.000	0.000	0.000	0.000	0.000	0.000
102	A	101	ALA	0	-0.067	-0.029	21.137	-0.051	-0.051	0.000	0.000	0.000	0.000
103	A	102	SER	0	-0.028	-0.028	16.999	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	103	ASP	-1	-0.819	-0.913	18.275	-0.620	-0.620	0.000	0.000	0.000	0.000
105	A	104	PHE	0	-0.081	-0.055	20.179	0.012	0.012	0.000	0.000	0.000	0.000
106	A	105	VAL	0	-0.013	0.004	19.689	0.012	0.012	0.000	0.000	0.000	0.000
107	A	106	VAL	0	-0.032	-0.013	22.845	0.013	0.013	0.000	0.000	0.000	0.000
108	A	107	LYS	1	0.788	0.906	25.522	0.385	0.385	0.000	0.000	0.000	0.000
109	A	108	PRO	0	-0.015	-0.037	27.791	0.020	0.020	0.000	0.000	0.000	0.000
110	A	109	TRP	0	0.013	0.000	22.279	0.007	0.007	0.000	0.000	0.000	0.000
111	A	110	ASP	-1	-0.807	-0.904	22.356	-0.379	-0.379	0.000	0.000	0.000	0.000
112	A	111	ASN	0	-0.018	-0.021	20.234	-0.064	-0.064	0.000	0.000	0.000	0.000
113	A	112	GLN	0	-0.018	-0.010	16.016	-0.055	-0.055	0.000	0.000	0.000	0.000
114	A	113	LYS	1	1.015	0.997	17.556	0.386	0.386	0.000	0.000	0.000	0.000
115	A	114	LEU	0	-0.038	0.001	17.798	-0.067	-0.067	0.000	0.000	0.000	0.000
116	A	115	LEU	0	0.005	0.008	11.756	-0.098	-0.098	0.000	0.000	0.000	0.000
117	A	116	GLU	-1	-0.836	-0.915	13.735	-0.745	-0.745	0.000	0.000	0.000	0.000
118	A	117	THR	0	-0.069	-0.044	13.938	-0.073	-0.073	0.000	0.000	0.000	0.000
119	A	118	LEU	0	-0.012	-0.011	13.248	-0.064	-0.064	0.000	0.000	0.000	0.000
120	A	119	LEU	0	0.011	0.011	8.515	-0.276	-0.276	0.000	0.000	0.000	0.000
121	A	120	ASN	0	-0.020	-0.012	9.547	-0.334	-0.334	0.000	0.000	0.000	0.000
122	A	121	ALA	0	-0.034	-0.008	11.790	-0.008	-0.008	0.000	0.000	0.000	0.000
123	A	122	ALA	0	0.006	-0.001	8.006	0.114	0.114	0.000	0.000	0.000	0.000
124	A	123	SER	0	-0.059	-0.029	7.321	-0.641	-0.641	0.000	0.000	0.000	0.000
125	A	124	GLN	0	-0.080	-0.040	8.242	0.577	0.577	0.000	0.000	0.000	0.000
126	A	125	ALA	0	-0.018	-0.003	10.197	-0.083	-0.083	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)