FMO DATABASE

FMODB ID: 1NNKZ

Calculation Name: 1NQ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NQ3

Chain ID: A

ChEMBL ID:

UniProt ID: P80601

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	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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1034679.751343
FMO2-HF: Nuclear repulsion	986631.268073
FMO2-HF: Total energy	-48048.48327
FMO2-MP2: Total energy	-48190.666772

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:3:SER)

Summations of interaction energy for fragment #1(A:3: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.
0.134	1.553	-0.021	-0.663	-0.736	0.002

Interaction energy analysis for fragmet #1(A:3:SER)

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 : -0.023

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	5	VAL	0	0.027	0.019	3.818	1.489	2.908	-0.021	-0.663	-0.736	0.002
4	A	6	ARG	1	0.973	0.981	6.127	-0.918	-0.918	0.000	0.000	0.000	0.000
5	A	7	ARG	1	0.905	0.948	9.072	0.047	0.047	0.000	0.000	0.000	0.000
6	A	8	ILE	0	0.000	-0.002	12.123	-0.030	-0.030	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.010	0.004	15.531	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.008	-0.011	18.359	0.001	0.001	0.000	0.000	0.000	0.000
9	A	11	THR	0	-0.011	-0.023	21.549	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.019	0.007	24.838	0.001	0.001	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.871	0.942	28.014	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	14	ALA	0	0.082	0.044	27.124	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	15	PRO	0	0.003	0.022	28.795	0.004	0.004	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.031	0.023	27.323	0.003	0.003	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.021	-0.006	24.068	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	18	ILE	0	-0.015	0.006	25.875	0.007	0.007	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.035	0.007	26.787	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	20	PRO	0	-0.046	-0.026	23.455	0.007	0.007	0.000	0.000	0.000	0.000
19	A	21	TYR	0	-0.014	-0.002	21.432	0.003	0.003	0.000	0.000	0.000	0.000
20	A	22	SER	0	0.027	0.013	18.948	0.009	0.009	0.000	0.000	0.000	0.000
21	A	23	GLN	0	0.029	0.016	21.038	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.067	0.024	19.408	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.051	-0.006	13.399	0.028	0.028	0.000	0.000	0.000	0.000
24	A	26	LEU	0	0.021	0.024	12.298	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	27	VAL	0	-0.010	-0.022	8.440	0.105	0.105	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.904	-0.942	8.086	-0.760	-0.760	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.838	0.894	9.223	0.239	0.239	0.000	0.000	0.000	0.000
28	A	30	THR	0	-0.010	0.013	12.645	0.034	0.034	0.000	0.000	0.000	0.000
29	A	31	ILE	0	-0.038	-0.029	14.366	0.025	0.025	0.000	0.000	0.000	0.000
30	A	32	TYR	0	0.017	0.004	14.221	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	33	ILE	0	-0.011	-0.014	18.548	0.018	0.018	0.000	0.000	0.000	0.000
32	A	34	SER	0	-0.018	-0.023	21.739	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.025	0.019	23.757	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	36	GLN	0	-0.065	-0.037	26.637	0.003	0.003	0.000	0.000	0.000	0.000
35	A	37	LEU	0	0.062	0.022	29.636	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	38	GLY	0	0.034	0.017	33.324	0.000	0.000	0.000	0.000	0.000	0.000
37	A	39	MET	0	-0.085	-0.042	32.840	0.001	0.001	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.794	-0.881	34.556	0.014	0.014	0.000	0.000	0.000	0.000
39	A	41	PRO	0	-0.022	-0.006	31.804	0.003	0.003	0.000	0.000	0.000	0.000
40	A	42	ALA	0	-0.008	-0.001	33.151	0.003	0.003	0.000	0.000	0.000	0.000
41	A	43	SER	0	-0.071	-0.056	35.145	0.001	0.001	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.035	0.000	34.478	0.002	0.002	0.000	0.000	0.000	0.000
43	A	45	GLN	0	-0.055	-0.035	35.327	0.001	0.001	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.029	-0.006	37.401	0.000	0.000	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.024	0.020	39.205	0.000	0.000	0.000	0.000	0.000	0.000
46	A	48	PRO	0	-0.018	-0.006	41.051	0.000	0.000	0.000	0.000	0.000	0.000
47	A	49	GLY	0	0.056	0.010	44.349	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	50	GLY	0	-0.003	0.008	44.336	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	51	VAL	0	0.059	0.018	40.527	0.000	0.000	0.000	0.000	0.000	0.000
50	A	52	VAL	0	0.021	0.008	40.626	0.000	0.000	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.884	-0.941	41.022	0.002	0.002	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.851	-0.927	38.143	0.010	0.010	0.000	0.000	0.000	0.000
53	A	55	ALA	0	0.016	0.006	36.577	0.001	0.001	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.950	0.979	35.858	0.000	0.000	0.000	0.000	0.000	0.000
55	A	57	GLN	0	-0.014	0.015	34.094	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	58	ALA	0	0.007	0.003	32.597	0.001	0.001	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.000	-0.010	31.284	0.000	0.000	0.000	0.000	0.000	0.000
58	A	60	THR	0	-0.013	-0.002	31.170	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	61	ASN	0	0.008	-0.001	29.650	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	62	ILE	0	-0.020	-0.009	26.192	0.002	0.002	0.000	0.000	0.000	0.000
61	A	63	GLY	0	0.007	0.003	26.421	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.911	-0.973	27.049	0.000	0.000	0.000	0.000	0.000	0.000
63	A	65	ILE	0	-0.032	-0.006	22.276	0.002	0.002	0.000	0.000	0.000	0.000
64	A	66	LEU	0	-0.019	-0.016	22.382	0.000	0.000	0.000	0.000	0.000	0.000
65	A	67	LYS	1	1.001	1.024	22.389	0.002	0.002	0.000	0.000	0.000	0.000
66	A	68	ALA	0	-0.071	-0.025	21.707	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	69	ALA	0	-0.035	-0.021	18.154	0.006	0.006	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.064	-0.031	18.577	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	71	CYS	0	-0.107	-0.053	19.799	-0.014	-0.014	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.747	-0.804	22.634	-0.030	-0.030	0.000	0.000	0.000	0.000
71	A	73	PHE	0	0.025	-0.023	25.343	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	74	THR	0	-0.125	-0.107	26.416	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	75	ASN	0	0.006	-0.001	21.042	0.001	0.001	0.000	0.000	0.000	0.000
74	A	76	VAL	0	-0.026	-0.008	22.099	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.025	0.012	20.502	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.883	0.952	23.223	0.024	0.024	0.000	0.000	0.000	0.000
77	A	79	ALA	0	0.002	0.008	25.035	0.003	0.003	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.025	-0.018	27.291	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.010	-0.007	29.585	0.002	0.002	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.018	0.013	30.317	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.022	0.001	34.304	0.001	0.001	0.000	0.000	0.000	0.000
82	A	84	ALA	0	0.012	0.011	38.027	0.000	0.000	0.000	0.000	0.000	0.000
83	A	85	ASP	-1	-0.865	-0.933	40.578	0.002	0.002	0.000	0.000	0.000	0.000
84	A	86	ILE	0	-0.004	-0.014	40.457	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	87	ASN	0	-0.054	-0.037	42.673	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.898	-0.938	42.327	0.002	0.002	0.000	0.000	0.000	0.000
87	A	89	PHE	0	-0.025	-0.027	37.005	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	90	SER	0	0.026	0.000	40.981	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	91	ALA	0	0.050	0.036	42.978	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	92	VAL	0	0.020	0.007	37.211	0.000	0.000	0.000	0.000	0.000	0.000
91	A	93	ASN	0	-0.019	-0.001	38.162	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.881	-0.956	39.082	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	95	VAL	0	0.040	0.020	37.627	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	96	TYR	0	0.004	-0.017	30.253	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.817	0.916	35.170	0.008	0.008	0.000	0.000	0.000	0.000
96	A	98	GLN	0	-0.068	-0.027	37.249	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	99	TYR	0	-0.039	-0.012	32.514	0.000	0.000	0.000	0.000	0.000	0.000
98	A	100	PHE	0	-0.030	-0.013	28.634	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	101	GLN	0	0.031	0.014	32.979	0.001	0.001	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.032	-0.019	32.673	0.000	0.000	0.000	0.000	0.000	0.000
101	A	103	SER	0	-0.022	-0.005	28.311	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	104	PHE	0	-0.016	-0.009	28.822	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	105	PRO	0	0.022	0.030	26.779	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	106	ALA	0	0.016	0.016	26.468	0.003	0.003	0.000	0.000	0.000	0.000
105	A	107	ARG	1	0.881	0.920	28.278	0.016	0.016	0.000	0.000	0.000	0.000
106	A	108	ALA	0	-0.011	-0.002	30.389	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	109	ALA	0	0.009	0.004	32.001	0.001	0.001	0.000	0.000	0.000	0.000
108	A	110	TYR	0	-0.004	-0.003	31.380	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	111	GLN	0	0.038	0.041	36.804	0.000	0.000	0.000	0.000	0.000	0.000
110	A	112	VAL	0	-0.007	0.004	34.238	0.000	0.000	0.000	0.000	0.000	0.000
111	A	113	ALA	0	-0.016	-0.016	37.631	0.000	0.000	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.006	-0.019	37.970	0.000	0.000	0.000	0.000	0.000	0.000
113	A	115	LEU	0	-0.016	0.026	33.992	0.001	0.001	0.000	0.000	0.000	0.000
114	A	116	PRO	0	0.020	-0.002	32.288	0.000	0.000	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.893	0.935	34.977	-0.028	-0.028	0.000	0.000	0.000	0.000
116	A	118	GLY	0	0.013	0.023	38.408	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	119	GLY	0	-0.014	0.010	37.663	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	120	ARG	1	0.918	0.928	38.733	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	121	VAL	0	-0.021	-0.019	35.313	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.881	-0.952	29.871	0.022	0.022	0.000	0.000	0.000	0.000
121	A	123	ILE	0	-0.033	-0.008	29.099	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.890	-0.926	25.119	0.012	0.012	0.000	0.000	0.000	0.000
123	A	125	ALA	0	-0.015	-0.026	24.541	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	126	ILE	0	-0.013	0.001	18.934	0.004	0.004	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.021	0.010	19.855	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	128	VAL	0	0.007	0.008	15.997	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	129	GLN	0	0.015	0.005	14.730	-0.012	-0.012	0.000	0.000	0.000	0.000
128	A	130	GLY	0	0.034	0.052	17.013	-0.018	-0.018	0.000	0.000	0.000	0.000
129	A	131	PRO	0	-0.014	-0.032	17.716	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	132	LEU	0	0.046	0.004	19.090	-0.012	-0.012	0.000	0.000	0.000	0.000
131	A	133	THR	0	-0.037	-0.010	21.570	0.005	0.005	0.000	0.000	0.000	0.000
132	A	134	THR	0	0.011	0.015	23.915	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	135	ALA	0	0.011	0.013	26.329	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)