FMO DATABASE

FMODB ID: M3Y8Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1842635.339958
FMO2-HF: Nuclear repulsion	1774682.216319
FMO2-HF: Total energy	-67953.123639
FMO2-MP2: Total energy	-68155.325583

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.
-9.554	-4.901	0.419	-1.866	-3.203	0

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 : 0.017 / q_NPA : -0.004

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	0.011	0.011	2.851	-3.878	-0.736	0.385	-1.388	-2.138	-0.002
4	A	7	GLU	-1	-0.806	-0.917	4.641	-0.187	-0.093	-0.001	-0.012	-0.081	0.000
5	A	8	TYR	0	0.019	0.024	8.096	-0.118	-0.118	0.000	0.000	0.000	0.000
6	A	9	GLN	0	0.010	-0.010	6.496	0.088	0.088	0.000	0.000	0.000	0.000
7	A	10	PRO	0	0.037	0.014	11.271	0.069	0.069	0.000	0.000	0.000	0.000
8	A	11	ALA	0	0.077	0.036	13.088	0.040	0.040	0.000	0.000	0.000	0.000
9	A	12	TRP	0	-0.065	-0.031	6.996	0.120	0.120	0.000	0.000	0.000	0.000
10	A	13	VAL	0	0.008	0.001	13.637	0.058	0.058	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.905	-0.942	17.232	-0.165	-0.165	0.000	0.000	0.000	0.000
12	A	15	GLN	0	0.023	-0.002	11.659	0.066	0.066	0.000	0.000	0.000	0.000
13	A	16	PHE	0	-0.033	-0.007	16.260	0.040	0.040	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.930	-0.973	17.435	0.006	0.006	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.959	-0.964	19.192	-0.060	-0.060	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.775	-0.875	17.385	0.106	0.106	0.000	0.000	0.000	0.000
17	A	20	ALA	0	-0.030	-0.021	19.790	0.018	0.018	0.000	0.000	0.000	0.000
18	A	21	GLN	0	-0.045	-0.023	21.911	0.002	0.002	0.000	0.000	0.000	0.000
19	A	22	ALA	0	0.045	0.029	21.980	0.002	0.002	0.000	0.000	0.000	0.000
20	A	23	LEU	0	-0.004	-0.011	19.616	0.006	0.006	0.000	0.000	0.000	0.000
21	A	24	LYS	1	0.933	0.958	23.924	-0.056	-0.056	0.000	0.000	0.000	0.000
22	A	25	GLN	0	-0.062	-0.018	27.050	0.000	0.000	0.000	0.000	0.000	0.000
23	A	26	ILE	0	-0.028	-0.005	24.653	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.025	-0.021	25.125	0.001	0.001	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.919	0.969	29.205	-0.053	-0.053	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.857	-0.947	31.892	0.057	0.057	0.000	0.000	0.000	0.000
27	A	30	ASN	0	-0.017	0.012	31.147	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	31	CYS	0	-0.068	-0.024	27.108	0.012	0.012	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.046	0.033	29.964	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.881	0.938	26.434	-0.078	-0.078	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.004	0.003	21.821	0.012	0.012	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.898	-0.958	22.420	0.080	0.080	0.000	0.000	0.000	0.000
33	A	36	HIS	0	0.006	0.019	14.403	0.011	0.011	0.000	0.000	0.000	0.000
34	A	37	ILE	0	0.006	-0.015	16.883	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	38	GLY	0	0.058	0.035	14.179	0.021	0.021	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.019	-0.029	11.002	-0.029	-0.029	0.000	0.000	0.000	0.000
37	A	40	THR	0	0.063	0.046	9.992	-0.103	-0.103	0.000	0.000	0.000	0.000
38	A	41	SER	0	-0.013	0.015	12.659	-0.076	-0.076	0.000	0.000	0.000	0.000
39	A	42	VAL	0	0.014	-0.004	15.253	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.018	0.000	15.176	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	44	ASN	0	-0.005	-0.015	14.491	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	45	LEU	0	-0.060	0.008	12.187	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.037	0.018	8.327	-0.031	-0.031	0.000	0.000	0.000	0.000
44	A	47	ALA	0	-0.046	-0.058	7.418	0.342	0.342	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.964	1.001	3.605	-7.257	-6.475	0.026	-0.341	-0.466	0.002
46	A	49	PRO	0	-0.008	0.016	3.310	-0.415	0.103	0.009	-0.106	-0.421	0.000
47	A	50	ILE	0	-0.050	-0.031	5.859	0.216	0.216	0.000	0.000	0.000	0.000
48	A	51	ILE	0	-0.019	0.003	8.323	0.015	0.015	0.000	0.000	0.000	0.000
49	A	52	ASP	-1	-0.859	-0.925	12.003	0.751	0.751	0.000	0.000	0.000	0.000
50	A	53	PHE	0	0.009	-0.013	14.328	-0.067	-0.067	0.000	0.000	0.000	0.000
51	A	54	LEU	0	-0.017	0.004	17.972	0.035	0.035	0.000	0.000	0.000	0.000
52	A	55	VAL	0	0.012	0.002	21.047	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	56	ILE	0	0.001	0.007	23.860	0.011	0.011	0.000	0.000	0.000	0.000
54	A	57	VAL	0	0.005	-0.003	27.303	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.914	-0.962	30.034	0.077	0.077	0.000	0.000	0.000	0.000
56	A	59	GLU	-1	-0.927	-0.976	33.107	0.085	0.085	0.000	0.000	0.000	0.000
57	A	60	ILE	0	-0.029	-0.037	26.751	0.001	0.001	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.914	-0.956	30.372	0.120	0.120	0.000	0.000	0.000	0.000
59	A	62	LYS	1	0.965	0.983	32.684	-0.081	-0.081	0.000	0.000	0.000	0.000
60	A	63	VAL	0	-0.066	-0.027	26.233	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.729	-0.820	28.772	0.159	0.159	0.000	0.000	0.000	0.000
62	A	65	LEU	0	-0.053	-0.019	30.058	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.019	-0.008	28.316	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	67	GLN	0	-0.027	-0.003	25.703	0.001	0.001	0.000	0.000	0.000	0.000
65	A	68	TRP	0	0.040	-0.002	25.680	0.004	0.004	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.936	-0.964	27.037	0.059	0.059	0.000	0.000	0.000	0.000
67	A	70	PHE	0	-0.025	-0.031	22.374	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	71	GLU	-1	-0.893	-0.943	22.193	0.148	0.148	0.000	0.000	0.000	0.000
69	A	72	ARG	1	0.919	0.986	22.762	-0.053	-0.053	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.073	-0.029	21.318	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	74	GLY	0	-0.031	-0.027	18.806	0.000	0.000	0.000	0.000	0.000	0.000
72	A	75	TYR	0	-0.091	-0.091	16.361	0.046	0.046	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.788	-0.872	16.327	0.372	0.372	0.000	0.000	0.000	0.000
74	A	77	TYR	0	0.013	-0.035	19.242	0.036	0.036	0.000	0.000	0.000	0.000
75	A	78	MET	0	-0.056	-0.029	17.924	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	79	GLY	0	0.047	0.032	21.391	0.000	0.000	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.825	-0.917	23.014	0.224	0.224	0.000	0.000	0.000	0.000
78	A	81	PHE	0	-0.070	-0.040	16.264	0.038	0.038	0.000	0.000	0.000	0.000
79	A	82	GLY	0	0.030	0.008	20.910	0.039	0.039	0.000	0.000	0.000	0.000
80	A	83	LEU	0	-0.061	-0.025	20.440	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	84	SER	0	0.027	0.018	24.331	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	85	GLY	0	0.017	-0.001	27.598	0.002	0.002	0.000	0.000	0.000	0.000
83	A	86	ARG	1	0.821	0.938	18.133	-0.408	-0.408	0.000	0.000	0.000	0.000
84	A	87	ARG	1	0.808	0.878	23.943	-0.185	-0.185	0.000	0.000	0.000	0.000
85	A	88	TYR	0	-0.030	-0.017	13.620	0.035	0.035	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.023	0.026	18.513	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	90	ARG	1	0.790	0.880	13.475	-0.440	-0.440	0.000	0.000	0.000	0.000
88	A	91	LYS	1	0.912	1.003	13.629	-0.167	-0.167	0.000	0.000	0.000	0.000
89	A	92	GLY	0	0.034	0.010	11.809	0.078	0.078	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.024	0.004	12.837	0.061	0.061	0.000	0.000	0.000	0.000
91	A	94	ILE	0	-0.001	0.004	11.806	0.012	0.012	0.000	0.000	0.000	0.000
92	A	95	LYS	1	0.994	0.989	7.321	0.597	0.597	0.000	0.000	0.000	0.000
93	A	96	ARG	1	0.879	0.932	7.185	-0.942	-0.942	0.000	0.000	0.000	0.000
94	A	97	THR	0	-0.053	-0.038	7.346	0.019	0.019	0.000	0.000	0.000	0.000
95	A	98	HIS	0	0.032	0.020	9.771	-0.061	-0.061	0.000	0.000	0.000	0.000
96	A	99	HIS	0	-0.017	0.006	10.040	0.113	0.113	0.000	0.000	0.000	0.000
97	A	100	VAL	0	0.025	0.018	14.025	-0.032	-0.032	0.000	0.000	0.000	0.000
98	A	101	HIS	0	-0.066	-0.042	14.898	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	102	ILE	0	0.012	0.006	19.869	-0.025	-0.025	0.000	0.000	0.000	0.000
100	A	103	TYR	0	-0.002	-0.030	21.711	0.024	0.024	0.000	0.000	0.000	0.000
101	A	104	GLN	0	0.061	0.036	26.383	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	105	PHE	0	0.011	-0.012	29.931	0.008	0.008	0.000	0.000	0.000	0.000
103	A	106	ASP	-1	-0.868	-0.911	31.654	0.117	0.117	0.000	0.000	0.000	0.000
104	A	107	ASN	0	-0.014	0.001	27.735	0.002	0.002	0.000	0.000	0.000	0.000
105	A	108	THR	0	0.017	-0.018	28.625	0.014	0.014	0.000	0.000	0.000	0.000
106	A	109	GLN	0	0.010	0.008	28.577	0.002	0.002	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.759	-0.849	22.793	0.314	0.314	0.000	0.000	0.000	0.000
108	A	111	ILE	0	-0.007	0.003	24.012	0.016	0.016	0.000	0.000	0.000	0.000
109	A	112	LEU	0	0.006	-0.008	24.781	0.003	0.003	0.000	0.000	0.000	0.000
110	A	113	ARG	1	0.763	0.884	18.862	-0.356	-0.356	0.000	0.000	0.000	0.000
111	A	114	HIS	0	-0.008	-0.016	18.450	0.016	0.016	0.000	0.000	0.000	0.000
112	A	115	LEU	0	-0.004	-0.007	21.144	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	116	ALA	0	0.000	0.004	23.522	-0.015	-0.015	0.000	0.000	0.000	0.000
114	A	117	PHE	0	0.009	0.000	15.966	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.801	0.896	19.157	-0.132	-0.132	0.000	0.000	0.000	0.000
116	A	119	ASN	0	0.019	-0.003	20.429	-0.023	-0.023	0.000	0.000	0.000	0.000
117	A	120	TYR	0	0.017	-0.004	22.345	-0.023	-0.023	0.000	0.000	0.000	0.000
118	A	121	LEU	0	-0.019	-0.017	16.547	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	122	ARG	1	0.830	0.910	19.786	-0.085	-0.085	0.000	0.000	0.000	0.000
120	A	123	GLU	-1	-0.913	-0.940	21.557	0.016	0.016	0.000	0.000	0.000	0.000
121	A	124	ASN	0	-0.102	-0.041	22.929	-0.013	-0.013	0.000	0.000	0.000	0.000
122	A	125	PRO	0	0.095	0.044	20.247	0.011	0.011	0.000	0.000	0.000	0.000
123	A	126	ALA	0	0.021	0.011	19.716	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	127	ILE	0	0.041	0.022	19.500	0.005	0.005	0.000	0.000	0.000	0.000
125	A	128	ALA	0	0.027	0.010	16.677	0.028	0.028	0.000	0.000	0.000	0.000
126	A	129	THR	0	-0.002	-0.010	15.538	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	130	THR	0	-0.030	-0.004	15.557	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	131	TYR	0	0.033	0.009	12.816	0.091	0.091	0.000	0.000	0.000	0.000
129	A	132	GLY	0	0.013	-0.008	11.219	0.075	0.075	0.000	0.000	0.000	0.000
130	A	133	THR	0	-0.037	-0.018	10.598	-0.053	-0.053	0.000	0.000	0.000	0.000
131	A	134	LEU	0	0.015	0.018	11.847	0.001	0.001	0.000	0.000	0.000	0.000
132	A	135	LYS	1	0.841	0.925	7.590	-0.367	-0.367	0.000	0.000	0.000	0.000
133	A	136	LYS	1	0.865	0.929	7.133	0.613	0.613	0.000	0.000	0.000	0.000
134	A	137	GLN	0	0.019	-0.005	8.068	-0.053	-0.053	0.000	0.000	0.000	0.000
135	A	138	LEU	0	-0.021	-0.005	8.641	0.022	0.022	0.000	0.000	0.000	0.000
136	A	139	ALA	0	-0.017	-0.006	4.089	0.001	0.118	0.000	-0.019	-0.097	0.000
137	A	140	GLN	0	-0.070	-0.028	5.912	-0.055	-0.055	0.000	0.000	0.000	0.000
138	A	141	ALA	0	-0.026	-0.006	8.482	-0.074	-0.074	0.000	0.000	0.000	0.000
139	A	142	HIS	0	-0.040	-0.022	8.651	-0.083	-0.083	0.000	0.000	0.000	0.000
140	A	143	PRO	0	-0.015	-0.003	5.297	0.438	0.438	0.000	0.000	0.000	0.000
141	A	144	ASP	-1	-0.854	-0.926	5.529	0.628	0.628	0.000	0.000	0.000	0.000
142	A	145	SER	0	-0.052	-0.023	8.379	0.068	0.068	0.000	0.000	0.000	0.000
143	A	146	ILE	0	0.017	-0.015	5.975	0.363	0.363	0.000	0.000	0.000	0.000
144	A	147	ASP	-1	-0.877	-0.932	8.568	0.873	0.873	0.000	0.000	0.000	0.000
145	A	148	LYS	1	0.981	0.980	11.796	-0.506	-0.506	0.000	0.000	0.000	0.000
146	A	149	TYR	0	-0.027	0.004	6.252	0.328	0.328	0.000	0.000	0.000	0.000
147	A	150	MET	0	-0.055	-0.052	9.351	0.055	0.055	0.000	0.000	0.000	0.000
148	A	151	ASP	-1	-0.896	-0.929	11.284	0.411	0.411	0.000	0.000	0.000	0.000
149	A	152	GLY	0	0.063	0.033	12.780	-0.091	-0.091	0.000	0.000	0.000	0.000
150	A	153	LYS	1	0.854	0.926	9.625	-1.190	-1.190	0.000	0.000	0.000	0.000
151	A	154	ASP	-1	-0.904	-0.939	13.592	0.385	0.385	0.000	0.000	0.000	0.000
152	A	155	ALA	0	0.044	0.016	16.565	-0.049	-0.049	0.000	0.000	0.000	0.000
153	A	156	PHE	0	-0.033	-0.017	15.889	-0.041	-0.041	0.000	0.000	0.000	0.000
154	A	157	ILE	0	0.028	0.005	13.347	-0.024	-0.024	0.000	0.000	0.000	0.000
155	A	158	LYS	1	0.956	0.986	17.806	-0.423	-0.423	0.000	0.000	0.000	0.000
156	A	159	LYS	1	0.907	0.968	21.223	-0.178	-0.178	0.000	0.000	0.000	0.000
157	A	160	ILE	0	-0.001	-0.012	19.181	-0.027	-0.027	0.000	0.000	0.000	0.000
158	A	161	GLU	-1	-0.821	-0.913	19.845	0.325	0.325	0.000	0.000	0.000	0.000
159	A	162	LYS	1	0.926	0.968	22.658	-0.170	-0.170	0.000	0.000	0.000	0.000
160	A	163	GLU	-1	-0.943	-0.965	24.745	0.114	0.114	0.000	0.000	0.000	0.000
161	A	164	ALA	0	0.010	0.003	23.390	-0.015	-0.015	0.000	0.000	0.000	0.000
162	A	165	LEU	0	0.005	0.002	25.530	-0.013	-0.013	0.000	0.000	0.000	0.000
163	A	166	LYS	1	0.884	0.938	28.028	-0.124	-0.124	0.000	0.000	0.000	0.000
164	A	167	LYS	1	0.903	0.951	28.130	-0.076	-0.076	0.000	0.000	0.000	0.000
165	A	168	TYR	0	-0.040	-0.019	28.069	-0.008	-0.008	0.000	0.000	0.000	0.000
166	A	169	TRP	0	-0.010	-0.005	30.230	-0.006	-0.006	0.000	0.000	0.000	0.000
167	A	170	GLU	-1	-0.914	-0.930	33.034	0.059	0.059	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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