FMO DATABASE

FMODB ID: 7G7NK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1844740.102643
FMO2-HF: Nuclear repulsion	1776786.233437
FMO2-HF: Total energy	-67953.869206
FMO2-MP2: Total energy	-68156.072626

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.
-14.028	-8.996	0.517	-2.117	-3.432	0.015

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 : 0.015 / 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

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	0.014	3.193	-2.836	-0.509	0.047	-0.987	-1.388	0.001
4	A	7	GLU	-1	-0.758	-0.882	5.100	-0.182	-0.107	-0.001	-0.004	-0.069	0.000
5	A	8	TYR	0	0.017	0.019	8.465	-0.109	-0.109	0.000	0.000	0.000	0.000
6	A	9	GLN	0	0.013	-0.009	6.546	0.080	0.080	0.000	0.000	0.000	0.000
7	A	10	PRO	0	0.028	0.008	11.505	0.073	0.073	0.000	0.000	0.000	0.000
8	A	11	ALA	0	0.076	0.046	13.143	0.039	0.039	0.000	0.000	0.000	0.000
9	A	12	TRP	0	-0.074	-0.035	7.203	0.129	0.129	0.000	0.000	0.000	0.000
10	A	13	VAL	0	0.005	0.002	13.746	0.062	0.062	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.885	-0.938	17.313	-0.152	-0.152	0.000	0.000	0.000	0.000
12	A	15	GLN	0	0.014	-0.005	11.855	0.051	0.051	0.000	0.000	0.000	0.000
13	A	16	PHE	0	-0.023	-0.004	16.298	0.040	0.040	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.930	-0.972	17.488	0.026	0.026	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.964	-0.971	19.329	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.734	-0.843	17.358	0.156	0.156	0.000	0.000	0.000	0.000
17	A	20	ALA	0	-0.026	-0.019	19.834	0.016	0.016	0.000	0.000	0.000	0.000
18	A	21	GLN	0	-0.060	-0.026	21.964	0.000	0.000	0.000	0.000	0.000	0.000
19	A	22	ALA	0	0.049	0.030	22.014	0.000	0.000	0.000	0.000	0.000	0.000
20	A	23	LEU	0	-0.003	-0.011	19.628	0.005	0.005	0.000	0.000	0.000	0.000
21	A	24	LYS	1	0.947	0.965	23.974	-0.082	-0.082	0.000	0.000	0.000	0.000
22	A	25	GLN	0	-0.053	-0.012	27.094	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	26	ILE	0	-0.028	-0.010	24.699	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.038	-0.026	25.079	0.000	0.000	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.921	0.969	29.259	-0.073	-0.073	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.860	-0.942	31.950	0.071	0.071	0.000	0.000	0.000	0.000
27	A	30	ASN	0	0.001	0.017	30.926	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	31	CYS	0	-0.050	-0.022	28.049	0.014	0.014	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.018	0.020	30.031	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.839	0.899	26.594	-0.106	-0.106	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.010	0.007	21.836	0.013	0.013	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.837	-0.898	22.491	0.101	0.101	0.000	0.000	0.000	0.000
33	A	36	HIS	0	0.017	0.031	14.365	0.003	0.003	0.000	0.000	0.000	0.000
34	A	37	ILE	0	0.002	-0.011	16.961	-0.024	-0.024	0.000	0.000	0.000	0.000
35	A	38	GLY	0	0.063	0.037	14.259	0.028	0.028	0.000	0.000	0.000	0.000
36	A	39	SER	0	0.007	-0.010	11.037	-0.069	-0.069	0.000	0.000	0.000	0.000
37	A	40	THR	0	0.038	0.026	10.122	-0.117	-0.117	0.000	0.000	0.000	0.000
38	A	41	SER	0	-0.029	0.006	12.727	-0.089	-0.089	0.000	0.000	0.000	0.000
39	A	42	VAL	0	0.025	0.004	15.552	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.027	0.005	15.580	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	44	ASN	0	-0.015	-0.019	14.929	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	45	LEU	0	-0.062	0.005	12.501	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.036	0.018	8.921	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	47	ALA	0	-0.002	-0.023	7.880	0.312	0.312	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.960	0.998	2.916	-12.609	-10.664	0.466	-1.009	-1.402	0.014
46	A	49	PRO	0	-0.010	0.016	3.389	-0.448	0.028	0.006	-0.093	-0.390	0.000
47	A	50	ILE	0	-0.054	-0.033	5.722	0.218	0.218	0.000	0.000	0.000	0.000
48	A	51	ILE	0	-0.020	0.002	8.386	0.000	0.000	0.000	0.000	0.000	0.000
49	A	52	ASP	-1	-0.835	-0.910	12.066	0.853	0.853	0.000	0.000	0.000	0.000
50	A	53	PHE	0	0.009	-0.014	14.399	-0.077	-0.077	0.000	0.000	0.000	0.000
51	A	54	LEU	0	-0.014	0.005	18.041	0.034	0.034	0.000	0.000	0.000	0.000
52	A	55	VAL	0	0.011	0.002	21.120	-0.031	-0.031	0.000	0.000	0.000	0.000
53	A	56	ILE	0	-0.002	0.006	23.929	0.011	0.011	0.000	0.000	0.000	0.000
54	A	57	VAL	0	0.015	0.000	27.374	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.905	-0.958	30.103	0.091	0.091	0.000	0.000	0.000	0.000
56	A	59	GLU	-1	-0.837	-0.910	33.145	0.097	0.097	0.000	0.000	0.000	0.000
57	A	60	ILE	0	-0.023	-0.028	26.854	0.001	0.001	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.916	-0.955	30.433	0.135	0.135	0.000	0.000	0.000	0.000
59	A	62	LYS	1	0.828	0.904	32.740	-0.098	-0.098	0.000	0.000	0.000	0.000
60	A	63	VAL	0	-0.040	-0.022	26.337	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.746	-0.827	28.755	0.183	0.183	0.000	0.000	0.000	0.000
62	A	65	LEU	0	-0.036	-0.008	30.109	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.029	-0.016	28.427	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	67	GLN	0	-0.036	-0.011	25.813	0.003	0.003	0.000	0.000	0.000	0.000
65	A	68	TRP	0	0.036	-0.001	25.717	0.005	0.005	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.850	-0.907	27.066	0.073	0.073	0.000	0.000	0.000	0.000
67	A	70	PHE	0	-0.026	-0.026	22.408	0.000	0.000	0.000	0.000	0.000	0.000
68	A	71	GLU	-1	-0.871	-0.932	22.226	0.172	0.172	0.000	0.000	0.000	0.000
69	A	72	ARG	1	0.812	0.915	22.784	-0.077	-0.077	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.067	-0.026	21.293	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	74	GLY	0	-0.032	-0.027	18.825	0.003	0.003	0.000	0.000	0.000	0.000
72	A	75	TYR	0	-0.091	-0.092	16.297	0.054	0.054	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.780	-0.855	15.811	0.442	0.442	0.000	0.000	0.000	0.000
74	A	77	TYR	0	0.011	-0.043	19.284	0.041	0.041	0.000	0.000	0.000	0.000
75	A	78	MET	0	-0.063	-0.030	17.982	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	79	GLY	0	0.051	0.033	21.436	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.796	-0.905	23.072	0.246	0.246	0.000	0.000	0.000	0.000
78	A	81	PHE	0	-0.049	-0.032	16.435	0.043	0.043	0.000	0.000	0.000	0.000
79	A	82	GLY	0	0.022	0.003	20.910	0.041	0.041	0.000	0.000	0.000	0.000
80	A	83	LEU	0	-0.058	-0.018	20.556	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	84	SER	0	0.010	0.005	24.331	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	85	GLY	0	0.021	0.004	27.598	0.002	0.002	0.000	0.000	0.000	0.000
83	A	86	ARG	1	0.807	0.926	18.008	-0.448	-0.448	0.000	0.000	0.000	0.000
84	A	87	ARG	1	0.809	0.885	24.005	-0.208	-0.208	0.000	0.000	0.000	0.000
85	A	88	TYR	0	-0.041	-0.019	13.626	0.030	0.030	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.026	0.026	18.645	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	90	ARG	1	0.748	0.846	13.560	-0.470	-0.470	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.868	0.980	13.676	-0.226	-0.226	0.000	0.000	0.000	0.000
89	A	92	GLY	0	0.049	0.017	11.832	0.098	0.098	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.029	0.001	12.849	0.066	0.066	0.000	0.000	0.000	0.000
91	A	94	ILE	0	-0.005	0.006	11.886	0.013	0.013	0.000	0.000	0.000	0.000
92	A	95	LYS	1	0.989	0.987	7.326	0.545	0.545	0.000	0.000	0.000	0.000
93	A	96	ARG	1	0.887	0.944	7.251	-1.031	-1.031	0.000	0.000	0.000	0.000
94	A	97	THR	0	-0.048	-0.044	7.377	0.051	0.051	0.000	0.000	0.000	0.000
95	A	98	HIS	0	0.025	0.017	9.808	-0.070	-0.070	0.000	0.000	0.000	0.000
96	A	99	HIS	0	-0.026	0.001	10.134	0.118	0.118	0.000	0.000	0.000	0.000
97	A	100	VAL	0	0.026	0.014	14.087	-0.035	-0.035	0.000	0.000	0.000	0.000
98	A	101	HIS	0	-0.055	-0.044	14.876	-0.023	-0.023	0.000	0.000	0.000	0.000
99	A	102	ILE	0	0.009	0.009	19.939	-0.027	-0.027	0.000	0.000	0.000	0.000
100	A	103	TYR	0	-0.009	-0.045	21.579	0.025	0.025	0.000	0.000	0.000	0.000
101	A	104	GLN	0	0.060	0.028	26.454	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	105	PHE	0	0.002	-0.018	30.005	0.008	0.008	0.000	0.000	0.000	0.000
103	A	106	ASP	-1	-0.870	-0.905	31.729	0.134	0.134	0.000	0.000	0.000	0.000
104	A	107	ASN	0	-0.001	0.007	27.757	0.001	0.001	0.000	0.000	0.000	0.000
105	A	108	THR	0	0.023	-0.013	28.702	0.015	0.015	0.000	0.000	0.000	0.000
106	A	109	GLN	0	0.007	0.007	28.561	0.002	0.002	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.762	-0.834	22.615	0.354	0.354	0.000	0.000	0.000	0.000
108	A	111	ILE	0	-0.010	0.000	24.082	0.018	0.018	0.000	0.000	0.000	0.000
109	A	112	LEU	0	0.000	-0.011	24.860	0.003	0.003	0.000	0.000	0.000	0.000
110	A	113	ARG	1	0.785	0.884	19.069	-0.384	-0.384	0.000	0.000	0.000	0.000
111	A	114	HIS	0	-0.009	-0.021	18.437	0.022	0.022	0.000	0.000	0.000	0.000
112	A	115	LEU	0	-0.012	-0.010	21.224	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	116	ALA	0	0.004	0.005	23.601	-0.015	-0.015	0.000	0.000	0.000	0.000
114	A	117	PHE	0	0.004	-0.001	15.945	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.779	0.869	19.395	-0.164	-0.164	0.000	0.000	0.000	0.000
116	A	119	ASN	0	0.005	-0.011	20.506	-0.022	-0.022	0.000	0.000	0.000	0.000
117	A	120	TYR	0	0.022	-0.003	22.427	-0.024	-0.024	0.000	0.000	0.000	0.000
118	A	121	LEU	0	-0.021	-0.017	16.557	-0.014	-0.014	0.000	0.000	0.000	0.000
119	A	122	ARG	1	0.831	0.904	19.784	-0.116	-0.116	0.000	0.000	0.000	0.000
120	A	123	GLU	-1	-0.910	-0.937	21.933	0.029	0.029	0.000	0.000	0.000	0.000
121	A	124	ASN	0	-0.104	-0.046	23.059	-0.016	-0.016	0.000	0.000	0.000	0.000
122	A	125	PRO	0	0.103	0.046	20.699	0.012	0.012	0.000	0.000	0.000	0.000
123	A	126	ALA	0	0.019	0.021	19.991	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	127	ILE	0	0.042	0.027	19.515	0.004	0.004	0.000	0.000	0.000	0.000
125	A	128	ALA	0	0.031	0.013	16.976	0.030	0.030	0.000	0.000	0.000	0.000
126	A	129	THR	0	-0.009	-0.018	15.538	0.000	0.000	0.000	0.000	0.000	0.000
127	A	130	THR	0	-0.037	-0.006	15.562	-0.011	-0.011	0.000	0.000	0.000	0.000
128	A	131	TYR	0	0.054	0.018	12.570	0.085	0.085	0.000	0.000	0.000	0.000
129	A	132	GLY	0	0.000	-0.017	11.218	0.079	0.079	0.000	0.000	0.000	0.000
130	A	133	THR	0	-0.036	-0.031	10.603	-0.053	-0.053	0.000	0.000	0.000	0.000
131	A	134	LEU	0	0.009	0.016	11.856	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	135	LYS	1	0.817	0.909	7.598	-0.374	-0.374	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.813	0.890	7.154	0.629	0.629	0.000	0.000	0.000	0.000
134	A	137	GLN	0	0.019	-0.002	8.114	-0.063	-0.063	0.000	0.000	0.000	0.000
135	A	138	LEU	0	-0.008	0.001	8.754	0.014	0.014	0.000	0.000	0.000	0.000
136	A	139	ALA	0	-0.018	-0.006	4.086	-0.004	0.117	0.000	-0.019	-0.101	0.000
137	A	140	GLN	0	-0.065	-0.026	5.920	-0.117	-0.117	0.000	0.000	0.000	0.000
138	A	141	ALA	0	-0.027	-0.006	8.559	-0.066	-0.066	0.000	0.000	0.000	0.000
139	A	142	HIS	0	-0.039	-0.025	8.580	-0.073	-0.073	0.000	0.000	0.000	0.000
140	A	143	PRO	0	-0.009	-0.002	4.798	0.334	0.422	-0.001	-0.005	-0.082	0.000
141	A	144	ASP	-1	-0.803	-0.887	5.313	0.716	0.716	0.000	0.000	0.000	0.000
142	A	145	SER	0	-0.044	-0.029	8.176	0.093	0.093	0.000	0.000	0.000	0.000
143	A	146	ILE	0	0.024	-0.016	5.971	0.417	0.417	0.000	0.000	0.000	0.000
144	A	147	ASP	-1	-0.876	-0.930	8.550	0.946	0.946	0.000	0.000	0.000	0.000
145	A	148	LYS	1	0.901	0.948	11.502	-0.554	-0.554	0.000	0.000	0.000	0.000
146	A	149	TYR	0	-0.027	-0.003	6.040	0.340	0.340	0.000	0.000	0.000	0.000
147	A	150	MET	0	-0.017	-0.011	9.339	0.013	0.013	0.000	0.000	0.000	0.000
148	A	151	ASP	-1	-0.890	-0.930	11.285	0.426	0.426	0.000	0.000	0.000	0.000
149	A	152	GLY	0	0.064	0.038	12.676	-0.092	-0.092	0.000	0.000	0.000	0.000
150	A	153	LYS	1	0.803	0.888	9.115	-1.264	-1.264	0.000	0.000	0.000	0.000
151	A	154	ASP	-1	-0.849	-0.914	13.581	0.425	0.425	0.000	0.000	0.000	0.000
152	A	155	ALA	0	0.049	0.019	16.550	-0.048	-0.048	0.000	0.000	0.000	0.000
153	A	156	PHE	0	-0.026	-0.016	16.136	-0.041	-0.041	0.000	0.000	0.000	0.000
154	A	157	ILE	0	0.012	-0.001	13.351	-0.021	-0.021	0.000	0.000	0.000	0.000
155	A	158	LYS	1	0.887	0.949	17.793	-0.467	-0.467	0.000	0.000	0.000	0.000
156	A	159	LYS	1	0.834	0.909	21.209	-0.193	-0.193	0.000	0.000	0.000	0.000
157	A	160	ILE	0	0.006	-0.010	19.200	-0.028	-0.028	0.000	0.000	0.000	0.000
158	A	161	GLU	-1	-0.819	-0.907	20.113	0.354	0.354	0.000	0.000	0.000	0.000
159	A	162	LYS	1	0.928	0.970	22.643	-0.188	-0.188	0.000	0.000	0.000	0.000
160	A	163	GLU	-1	-0.873	-0.912	24.640	0.132	0.132	0.000	0.000	0.000	0.000
161	A	164	ALA	0	0.014	0.006	23.366	-0.016	-0.016	0.000	0.000	0.000	0.000
162	A	165	LEU	0	0.006	0.005	25.518	-0.013	-0.013	0.000	0.000	0.000	0.000
163	A	166	LYS	1	0.894	0.943	28.014	-0.132	-0.132	0.000	0.000	0.000	0.000
164	A	167	LYS	1	0.841	0.901	28.123	-0.090	-0.090	0.000	0.000	0.000	0.000
165	A	168	TYR	0	-0.040	-0.017	27.928	-0.007	-0.007	0.000	0.000	0.000	0.000
166	A	169	TRP	0	-0.014	-0.010	30.217	-0.007	-0.007	0.000	0.000	0.000	0.000
167	A	170	GLU	-1	-0.862	-0.884	32.757	0.066	0.066	0.000	0.000	0.000	0.000

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