FMO DATABASE

FMODB ID: 22QRR

Calculation Name: 2NRK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NRK

Chain ID: A

ChEMBL ID:

UniProt ID: Q837C3

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1851289.525388
FMO2-HF: Nuclear repulsion	1783335.341188
FMO2-HF: Total energy	-67954.1842
FMO2-MP2: Total energy	-68156.31866

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:4:ILE)

Summations of interaction energy for fragment #1(A:4:ILE)

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.
-28.636	-26.291	7.534	-4.23	-5.649	0.04

Interaction energy analysis for fragmet #1(A:4:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.015

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	6	THR	0	-0.006	-0.003	3.490	-2.757	-0.496	0.024	-1.005	-1.280	-0.001
4	A	7	GLU	-1	-0.740	-0.872	5.544	-0.243	-0.243	0.000	0.000	0.000	0.000
5	A	8	TYR	0	-0.013	0.007	8.684	-0.126	-0.126	0.000	0.000	0.000	0.000
6	A	9	GLN	0	0.023	-0.002	6.543	0.087	0.087	0.000	0.000	0.000	0.000
7	A	10	PRO	0	0.023	0.005	11.687	0.071	0.071	0.000	0.000	0.000	0.000
8	A	11	ALA	0	0.086	0.054	13.357	0.041	0.041	0.000	0.000	0.000	0.000
9	A	12	TRP	0	-0.069	-0.035	7.196	0.105	0.105	0.000	0.000	0.000	0.000
10	A	13	VAL	0	0.009	0.006	13.692	0.065	0.065	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.894	-0.947	17.321	-0.168	-0.168	0.000	0.000	0.000	0.000
12	A	15	GLN	0	0.009	-0.007	11.800	0.054	0.054	0.000	0.000	0.000	0.000
13	A	16	PHE	0	-0.012	-0.001	16.491	0.045	0.045	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.928	-0.978	18.142	0.017	0.017	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.960	-0.968	19.839	-0.040	-0.040	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.716	-0.833	17.657	0.171	0.171	0.000	0.000	0.000	0.000
17	A	20	ALA	0	-0.027	-0.024	20.294	0.018	0.018	0.000	0.000	0.000	0.000
18	A	21	GLN	0	-0.060	-0.021	22.321	0.001	0.001	0.000	0.000	0.000	0.000
19	A	22	ALA	0	0.041	0.023	22.527	0.002	0.002	0.000	0.000	0.000	0.000
20	A	23	LEU	0	0.002	-0.007	19.756	0.007	0.007	0.000	0.000	0.000	0.000
21	A	24	LYS	1	0.935	0.966	24.163	-0.081	-0.081	0.000	0.000	0.000	0.000
22	A	25	GLN	0	-0.033	-0.013	27.466	0.001	0.001	0.000	0.000	0.000	0.000
23	A	26	ILE	0	-0.029	0.000	24.632	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.027	-0.036	25.062	0.001	0.001	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.866	0.949	29.166	-0.092	-0.092	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.870	-0.948	32.229	0.078	0.078	0.000	0.000	0.000	0.000
27	A	30	ASN	0	0.012	0.010	31.111	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	31	CYS	0	-0.051	-0.027	28.238	0.014	0.014	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.022	0.030	30.319	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.823	0.899	26.951	-0.107	-0.107	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.033	0.011	22.249	0.014	0.014	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.825	-0.885	22.652	0.097	0.097	0.000	0.000	0.000	0.000
33	A	36	HIS	0	0.008	0.028	14.446	0.009	0.009	0.000	0.000	0.000	0.000
34	A	37	ILE	0	0.007	-0.011	16.958	-0.024	-0.024	0.000	0.000	0.000	0.000
35	A	38	GLY	0	0.065	0.039	13.940	0.020	0.020	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.028	-0.022	11.003	-0.089	-0.089	0.000	0.000	0.000	0.000
37	A	40	THR	0	0.032	0.011	9.997	-0.101	-0.101	0.000	0.000	0.000	0.000
38	A	41	SER	0	-0.032	0.010	12.643	-0.086	-0.086	0.000	0.000	0.000	0.000
39	A	42	VAL	0	0.030	0.006	15.503	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.039	0.012	15.625	-0.034	-0.034	0.000	0.000	0.000	0.000
41	A	44	ASN	0	-0.010	-0.015	15.179	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	45	LEU	0	-0.070	-0.006	12.798	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.032	0.021	9.402	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	47	ALA	0	0.011	-0.005	8.067	0.304	0.304	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.928	0.973	2.165	-27.556	-28.216	7.504	-3.099	-3.746	0.041
46	A	49	PRO	0	-0.023	0.002	3.748	-0.421	0.073	0.005	-0.089	-0.409	0.000
47	A	50	ILE	0	-0.027	-0.020	5.690	0.268	0.268	0.000	0.000	0.000	0.000
48	A	51	ILE	0	-0.013	0.014	8.734	-0.040	-0.040	0.000	0.000	0.000	0.000
49	A	52	ASP	-1	-0.805	-0.894	12.501	0.905	0.905	0.000	0.000	0.000	0.000
50	A	53	PHE	0	0.000	-0.012	14.492	-0.080	-0.080	0.000	0.000	0.000	0.000
51	A	54	LEU	0	-0.020	0.002	18.138	0.033	0.033	0.000	0.000	0.000	0.000
52	A	55	VAL	0	-0.008	-0.017	21.066	-0.032	-0.032	0.000	0.000	0.000	0.000
53	A	56	ILE	0	-0.013	-0.001	24.095	0.013	0.013	0.000	0.000	0.000	0.000
54	A	57	VAL	0	-0.006	-0.002	27.651	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.833	-0.911	30.418	0.101	0.101	0.000	0.000	0.000	0.000
56	A	59	GLU	-1	-0.834	-0.909	33.211	0.109	0.109	0.000	0.000	0.000	0.000
57	A	60	ILE	0	-0.017	-0.024	26.640	0.002	0.002	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.919	-0.958	30.096	0.158	0.158	0.000	0.000	0.000	0.000
59	A	62	LYS	1	0.760	0.867	32.516	-0.108	-0.108	0.000	0.000	0.000	0.000
60	A	63	VAL	0	-0.026	-0.017	26.373	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.750	-0.829	28.470	0.213	0.213	0.000	0.000	0.000	0.000
62	A	65	LEU	0	-0.046	-0.017	29.857	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.022	-0.009	28.511	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	67	GLN	0	-0.036	-0.020	25.622	0.000	0.000	0.000	0.000	0.000	0.000
65	A	68	TRP	0	0.037	0.005	25.539	0.005	0.005	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.843	-0.905	27.073	0.083	0.083	0.000	0.000	0.000	0.000
67	A	70	PHE	0	-0.001	-0.006	22.244	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	71	GLU	-1	-0.860	-0.923	22.125	0.204	0.204	0.000	0.000	0.000	0.000
69	A	72	ARG	1	0.816	0.908	22.702	-0.090	-0.090	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.047	-0.013	21.315	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	74	GLY	0	-0.010	-0.012	18.685	0.002	0.002	0.000	0.000	0.000	0.000
72	A	75	TYR	0	-0.115	-0.101	16.357	0.061	0.061	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.770	-0.865	14.847	0.603	0.603	0.000	0.000	0.000	0.000
74	A	77	TYR	0	0.010	-0.037	18.969	0.040	0.040	0.000	0.000	0.000	0.000
75	A	78	MET	0	-0.054	-0.027	17.917	0.002	0.002	0.000	0.000	0.000	0.000
76	A	79	GLY	0	0.057	0.033	21.387	0.000	0.000	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.733	-0.864	22.962	0.280	0.280	0.000	0.000	0.000	0.000
78	A	81	PHE	0	-0.033	-0.016	16.379	0.043	0.043	0.000	0.000	0.000	0.000
79	A	82	GLY	0	0.022	0.006	20.450	0.050	0.050	0.000	0.000	0.000	0.000
80	A	83	LEU	0	-0.054	-0.023	20.103	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	84	SER	0	-0.035	-0.031	23.955	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	85	GLY	0	0.031	0.019	27.396	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	86	ARG	1	0.809	0.902	18.149	-0.487	-0.487	0.000	0.000	0.000	0.000
84	A	87	ARG	1	0.802	0.880	23.965	-0.233	-0.233	0.000	0.000	0.000	0.000
85	A	88	TYR	0	-0.046	-0.017	13.456	0.029	0.029	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.028	0.025	18.629	-0.016	-0.016	0.000	0.000	0.000	0.000
87	A	90	ARG	1	0.795	0.886	13.467	-0.586	-0.586	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.833	0.941	13.649	-0.227	-0.227	0.000	0.000	0.000	0.000
89	A	92	GLY	0	0.056	0.019	11.937	0.080	0.080	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.030	-0.001	12.419	0.079	0.079	0.000	0.000	0.000	0.000
91	A	94	ILE	0	-0.008	0.006	11.801	0.011	0.011	0.000	0.000	0.000	0.000
92	A	95	LYS	1	0.970	0.977	7.374	0.499	0.499	0.000	0.000	0.000	0.000
93	A	96	ARG	1	0.869	0.949	7.475	-1.119	-1.119	0.000	0.000	0.000	0.000
94	A	97	THR	0	-0.052	-0.028	7.349	0.024	0.024	0.000	0.000	0.000	0.000
95	A	98	HIS	0	0.013	0.009	9.638	-0.102	-0.102	0.000	0.000	0.000	0.000
96	A	99	HIS	0	-0.062	-0.030	10.279	0.189	0.189	0.000	0.000	0.000	0.000
97	A	100	VAL	0	0.020	0.020	14.336	-0.049	-0.049	0.000	0.000	0.000	0.000
98	A	101	HIS	0	-0.044	-0.036	14.947	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	102	ILE	0	0.031	0.017	20.085	-0.030	-0.030	0.000	0.000	0.000	0.000
100	A	103	TYR	0	-0.012	-0.046	21.546	0.031	0.031	0.000	0.000	0.000	0.000
101	A	104	GLN	0	0.026	0.010	26.550	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	105	PHE	0	-0.007	-0.020	30.068	0.008	0.008	0.000	0.000	0.000	0.000
103	A	106	ASP	-1	-0.830	-0.889	31.879	0.152	0.152	0.000	0.000	0.000	0.000
104	A	107	ASN	0	-0.023	0.010	27.642	0.000	0.000	0.000	0.000	0.000	0.000
105	A	108	THR	0	-0.008	-0.034	28.594	0.016	0.016	0.000	0.000	0.000	0.000
106	A	109	GLN	0	0.010	0.010	28.659	0.001	0.001	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.750	-0.826	22.535	0.389	0.389	0.000	0.000	0.000	0.000
108	A	111	ILE	0	-0.012	-0.001	24.048	0.018	0.018	0.000	0.000	0.000	0.000
109	A	112	LEU	0	0.002	-0.006	25.092	0.000	0.000	0.000	0.000	0.000	0.000
110	A	113	ARG	1	0.777	0.869	19.366	-0.407	-0.407	0.000	0.000	0.000	0.000
111	A	114	HIS	0	-0.009	-0.018	18.218	0.015	0.015	0.000	0.000	0.000	0.000
112	A	115	LEU	0	-0.011	-0.009	21.230	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	116	ALA	0	0.004	0.009	23.687	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	117	PHE	0	0.002	-0.005	16.018	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.770	0.865	19.426	-0.165	-0.165	0.000	0.000	0.000	0.000
116	A	119	ASN	0	0.028	0.003	20.539	-0.027	-0.027	0.000	0.000	0.000	0.000
117	A	120	TYR	0	-0.023	-0.025	22.791	-0.027	-0.027	0.000	0.000	0.000	0.000
118	A	121	LEU	0	-0.009	-0.011	16.805	-0.019	-0.019	0.000	0.000	0.000	0.000
119	A	122	ARG	1	0.823	0.909	19.815	-0.108	-0.108	0.000	0.000	0.000	0.000
120	A	123	GLU	-1	-0.892	-0.939	22.027	0.019	0.019	0.000	0.000	0.000	0.000
121	A	124	ASN	0	-0.083	-0.035	23.364	-0.014	-0.014	0.000	0.000	0.000	0.000
122	A	125	PRO	0	0.098	0.040	20.794	0.011	0.011	0.000	0.000	0.000	0.000
123	A	126	ALA	0	0.025	0.030	20.155	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	127	ILE	0	0.027	0.024	19.436	0.001	0.001	0.000	0.000	0.000	0.000
125	A	128	ALA	0	0.036	0.021	16.997	0.028	0.028	0.000	0.000	0.000	0.000
126	A	129	THR	0	-0.013	-0.024	15.612	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	130	THR	0	-0.032	-0.013	15.628	-0.022	-0.022	0.000	0.000	0.000	0.000
128	A	131	TYR	0	0.059	0.017	12.748	0.075	0.075	0.000	0.000	0.000	0.000
129	A	132	GLY	0	0.001	-0.011	11.326	0.081	0.081	0.000	0.000	0.000	0.000
130	A	133	THR	0	-0.043	-0.029	10.634	-0.093	-0.093	0.000	0.000	0.000	0.000
131	A	134	LEU	0	0.010	0.012	11.567	-0.014	-0.014	0.000	0.000	0.000	0.000
132	A	135	LYS	1	0.796	0.893	7.753	-0.258	-0.258	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.829	0.891	7.043	0.702	0.702	0.000	0.000	0.000	0.000
134	A	137	GLN	0	0.011	-0.002	7.932	-0.061	-0.061	0.000	0.000	0.000	0.000
135	A	138	LEU	0	-0.005	-0.004	8.714	0.006	0.006	0.000	0.000	0.000	0.000
136	A	139	ALA	0	-0.039	-0.024	3.743	0.085	0.243	0.002	-0.032	-0.128	0.000
137	A	140	GLN	0	-0.043	-0.017	5.502	-0.172	-0.172	0.000	0.000	0.000	0.000
138	A	141	ALA	0	-0.035	-0.003	8.149	-0.023	-0.023	0.000	0.000	0.000	0.000
139	A	142	HIS	0	-0.003	-0.003	8.245	-0.077	-0.077	0.000	0.000	0.000	0.000
140	A	143	PRO	0	-0.010	-0.010	4.681	0.451	0.543	-0.001	-0.005	-0.086	0.000
141	A	144	ASP	-1	-0.822	-0.886	5.245	0.903	0.903	0.000	0.000	0.000	0.000
142	A	145	SER	0	-0.017	-0.017	8.026	0.051	0.051	0.000	0.000	0.000	0.000
143	A	146	ILE	0	0.009	-0.012	5.482	0.490	0.490	0.000	0.000	0.000	0.000
144	A	147	ASP	-1	-0.874	-0.932	8.019	1.255	1.255	0.000	0.000	0.000	0.000
145	A	148	LYS	1	0.885	0.935	10.903	-0.768	-0.768	0.000	0.000	0.000	0.000
146	A	149	TYR	0	-0.024	-0.009	6.035	0.318	0.318	0.000	0.000	0.000	0.000
147	A	150	MET	0	0.006	0.017	9.078	-0.092	-0.092	0.000	0.000	0.000	0.000
148	A	151	ASP	-1	-0.888	-0.937	11.167	0.473	0.473	0.000	0.000	0.000	0.000
149	A	152	GLY	0	0.037	0.021	12.940	-0.104	-0.104	0.000	0.000	0.000	0.000
150	A	153	LYS	1	0.775	0.864	9.192	-1.393	-1.393	0.000	0.000	0.000	0.000
151	A	154	ASP	-1	-0.829	-0.896	13.374	0.468	0.468	0.000	0.000	0.000	0.000
152	A	155	ALA	0	0.039	0.016	16.413	-0.062	-0.062	0.000	0.000	0.000	0.000
153	A	156	PHE	0	-0.021	-0.011	16.148	-0.054	-0.054	0.000	0.000	0.000	0.000
154	A	157	ILE	0	-0.008	-0.006	13.583	-0.028	-0.028	0.000	0.000	0.000	0.000
155	A	158	LYS	1	0.884	0.932	17.893	-0.534	-0.534	0.000	0.000	0.000	0.000
156	A	159	LYS	1	0.824	0.901	21.287	-0.196	-0.196	0.000	0.000	0.000	0.000
157	A	160	ILE	0	0.009	-0.001	19.471	-0.029	-0.029	0.000	0.000	0.000	0.000
158	A	161	GLU	-1	-0.821	-0.914	20.324	0.376	0.376	0.000	0.000	0.000	0.000
159	A	162	LYS	1	0.932	0.971	22.894	-0.205	-0.205	0.000	0.000	0.000	0.000
160	A	163	GLU	-1	-0.868	-0.899	24.886	0.131	0.131	0.000	0.000	0.000	0.000
161	A	164	ALA	0	0.027	0.013	23.706	-0.017	-0.017	0.000	0.000	0.000	0.000
162	A	165	LEU	0	-0.004	-0.004	25.852	-0.013	-0.013	0.000	0.000	0.000	0.000
163	A	166	LYS	1	0.901	0.959	28.324	-0.136	-0.136	0.000	0.000	0.000	0.000
164	A	167	LYS	1	0.840	0.891	28.192	-0.091	-0.091	0.000	0.000	0.000	0.000
165	A	168	TYR	0	-0.033	-0.018	27.896	-0.007	-0.007	0.000	0.000	0.000	0.000
166	A	169	TRP	0	-0.011	-0.005	30.509	-0.008	-0.008	0.000	0.000	0.000	0.000
167	A	170	GLU	-1	-0.864	-0.886	32.578	0.069	0.069	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ILE)