FMO DATABASE

FMODB ID: 765NK

Calculation Name: 3CNU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CNU

Chain ID: A

ChEMBL ID:

UniProt ID: O28738

Base Structure: X-ray

Registration Date: 2023-09-23

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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-843241.324723
FMO2-HF: Nuclear repulsion	798286.847256
FMO2-HF: Total energy	-44954.477467
FMO2-MP2: Total energy	-45081.05286

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:1:MET)

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

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.
-18.057	-10.099	12.879	-7.02	-13.817	-0.027

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.017

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	3	GLU	-1	-0.730	-0.875	3.023	-3.632	-0.751	0.205	-1.527	-1.559	0.000
4	A	4	ALA	0	-0.002	-0.001	5.732	1.067	1.067	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.874	0.943	2.379	-4.726	-3.595	4.733	-1.300	-4.564	0.001
6	A	6	GLU	-1	-0.890	-0.933	2.941	0.507	1.852	0.174	-0.436	-1.083	-0.002
7	A	7	LEU	0	-0.010	-0.010	4.137	0.364	0.522	0.006	-0.017	-0.147	0.000
8	A	8	ILE	0	0.014	0.004	6.972	0.082	0.082	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.831	0.921	2.190	-6.003	-7.194	5.132	-1.104	-2.837	0.006
10	A	10	LYS	1	0.902	0.937	6.857	-1.082	-1.082	0.000	0.000	0.000	0.000
11	A	11	MET	0	-0.019	-0.003	9.370	-0.301	-0.301	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.020	-0.015	9.684	-0.137	-0.137	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.913	-0.949	9.073	1.680	1.680	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.047	-0.019	12.032	-0.181	-0.181	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.015	-0.007	14.800	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.006	-0.023	12.689	-0.163	-0.163	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.085	-0.040	15.929	-0.067	-0.067	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.013	0.002	18.131	-0.076	-0.076	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.786	-0.890	20.628	0.226	0.226	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.912	-0.956	23.604	0.194	0.194	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.026	0.009	18.406	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.027	-0.013	19.978	0.001	0.001	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.773	0.866	22.005	-0.221	-0.221	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.975	-0.977	23.575	0.200	0.200	0.000	0.000	0.000	0.000
25	A	25	MET	0	-0.070	-0.023	18.175	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.042	-0.005	22.659	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.063	-0.034	24.758	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	28	TRP	0	-0.056	-0.035	19.080	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.016	-0.012	21.586	0.020	0.020	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.038	-0.014	20.064	-0.041	-0.041	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.013	0.013	14.893	0.050	0.050	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.001	0.007	14.300	-0.075	-0.075	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.001	-0.013	11.168	0.176	0.176	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.006	-0.003	9.640	-0.162	-0.162	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.886	0.950	10.754	0.012	0.012	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.029	-0.021	6.987	-0.035	-0.035	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.843	-0.937	8.419	-1.049	-1.049	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.051	-0.027	9.720	-0.095	-0.095	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.820	-0.878	2.567	-5.692	-3.850	1.109	-1.425	-1.527	-0.016
40	A	40	GLU	-1	-0.863	-0.941	7.302	0.294	0.294	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.015	-0.018	5.896	0.548	0.548	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.030	-0.006	8.000	-0.255	-0.255	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.032	0.016	9.753	0.266	0.266	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.914	-0.965	12.047	0.470	0.470	0.000	0.000	0.000	0.000
45	A	45	TYR	0	0.025	-0.001	14.520	0.061	0.061	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.898	0.936	16.936	-0.580	-0.580	0.000	0.000	0.000	0.000
47	A	47	SER	0	0.027	0.001	20.221	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.867	-0.907	21.227	0.367	0.367	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.052	0.027	21.277	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.066	-0.029	17.520	0.045	0.045	0.000	0.000	0.000	0.000
51	A	51	CYS	0	-0.057	-0.045	13.935	0.017	0.017	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.843	-0.887	11.807	0.693	0.693	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.064	0.040	4.278	-0.028	0.315	0.006	-0.072	-0.276	0.000
54	A	54	LYS	1	0.815	0.909	7.665	-0.835	-0.835	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.787	-0.899	2.654	0.736	2.185	1.514	-1.139	-1.824	-0.016
56	A	56	GLY	0	0.010	0.009	6.379	-0.196	-0.196	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.012	-0.010	9.118	0.056	0.056	0.000	0.000	0.000	0.000
58	A	58	HIS	0	0.055	0.039	12.587	-0.044	-0.044	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.004	-0.007	14.880	-0.036	-0.036	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.115	-0.074	18.428	-0.047	-0.047	0.000	0.000	0.000	0.000
61	A	61	PRO	0	0.004	0.032	16.646	0.005	0.005	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.019	-0.013	18.721	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.002	-0.011	17.620	-0.034	-0.034	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.003	-0.001	15.324	0.068	0.068	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.003	0.004	13.825	-0.056	-0.056	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.059	-0.031	13.862	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.031	-0.002	12.938	0.001	0.001	0.000	0.000	0.000	0.000
68	A	68	PRO	0	0.068	0.037	12.164	-0.059	-0.059	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.029	0.018	8.033	0.099	0.099	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.908	-0.951	10.006	-1.416	-1.416	0.000	0.000	0.000	0.000
71	A	71	PHE	0	-0.009	-0.010	12.171	0.128	0.128	0.000	0.000	0.000	0.000
72	A	72	TRP	0	0.044	0.006	9.787	0.048	0.048	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.028	0.001	8.753	0.161	0.161	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.032	0.016	11.092	0.128	0.128	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.037	-0.015	14.498	0.082	0.082	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.045	-0.015	9.451	0.071	0.071	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.777	0.875	11.442	0.820	0.820	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.008	0.007	15.273	0.014	0.014	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.079	-0.049	16.376	-0.047	-0.047	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.824	-0.892	17.855	-0.256	-0.256	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.734	-0.832	19.045	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	82	PRO	0	0.039	0.014	17.866	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.008	0.008	19.924	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.023	-0.055	23.656	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	85	GLY	0	0.010	-0.002	20.995	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.033	-0.013	21.383	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	87	MET	0	-0.063	-0.032	22.775	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	MET	0	-0.048	-0.016	23.940	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	89	GLY	0	-0.009	0.018	23.558	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.747	0.846	19.576	0.210	0.210	0.000	0.000	0.000	0.000
91	A	91	TYR	0	-0.076	-0.050	16.851	-0.040	-0.040	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.838	0.901	18.222	0.107	0.107	0.000	0.000	0.000	0.000
93	A	93	ILE	0	0.040	0.021	18.288	0.009	0.009	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.848	-0.896	18.849	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.058	0.023	21.108	0.032	0.032	0.000	0.000	0.000	0.000
96	A	96	ASN	0	-0.009	-0.022	23.825	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.000	0.010	24.161	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	98	MET	0	0.061	0.034	23.898	0.008	0.008	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.831	-0.918	26.684	0.096	0.096	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.017	-0.007	29.776	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	101	GLN	0	0.005	-0.008	25.423	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.953	0.983	28.421	-0.125	-0.125	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.010	0.000	32.055	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.012	0.013	33.414	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	105	GLY	0	-0.004	-0.007	33.955	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.039	-0.031	35.063	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	107	ILE	0	0.023	0.006	37.903	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.953	0.984	36.039	-0.116	-0.116	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.899	0.965	35.674	-0.104	-0.104	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.057	-0.011	41.148	-0.006	-0.006	0.000	0.000	0.000	0.000

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