FMO DATABASE

FMODB ID: 9Y522

Calculation Name: 1NIG-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NIG

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HIT9

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	149
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1475693.885379
FMO2-HF: Nuclear repulsion	1414569.70042
FMO2-HF: Total energy	-61124.18496
FMO2-MP2: Total energy	-61302.657518

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.
0.178	1.822	0.007	-0.672	-0.98	0

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 : -0.018 / 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].
3	A	3	ILE	0	-0.030	-0.013	3.621	0.067	1.642	0.007	-0.665	-0.917
4	A	4	LYS	1	0.944	0.979	5.137	0.445	0.514	0.000	-0.007	-0.063
5	A	5	ARG	1	0.896	0.951	7.373	0.360	0.360	0.000	0.000	0.000
6	A	6	TYR	0	0.004	-0.011	10.821	0.028	0.028	0.000	0.000	0.000
7	A	7	CYS	0	-0.076	-0.012	13.819	-0.026	-0.026	0.000	0.000	0.000
8	A	8	PRO	0	0.010	-0.024	16.723	0.024	0.024	0.000	0.000	0.000
9	A	9	VAL	0	-0.026	-0.008	20.017	0.011	0.011	0.000	0.000	0.000
10	A	10	THR	0	0.052	0.018	17.450	0.010	0.010	0.000	0.000	0.000
11	A	11	ASP	-1	-0.885	-0.892	18.839	0.022	0.022	0.000	0.000	0.000
12	A	12	SER	0	-0.030	-0.027	14.971	0.027	0.027	0.000	0.000	0.000
13	A	13	GLU	-1	-0.920	-0.975	9.824	-0.193	-0.193	0.000	0.000	0.000
14	A	14	LEU	0	-0.025	-0.006	11.820	0.044	0.044	0.000	0.000	0.000
15	A	15	PRO	0	0.065	0.027	8.839	-0.052	-0.052	0.000	0.000	0.000
16	A	16	ALA	0	-0.006	-0.016	8.865	0.100	0.100	0.000	0.000	0.000
17	A	17	ASP	-1	-0.991	-0.997	10.607	-0.689	-0.689	0.000	0.000	0.000
18	A	18	HIS	0	0.032	0.028	12.720	0.075	0.075	0.000	0.000	0.000
19	A	19	VAL	0	-0.005	0.002	15.064	0.013	0.013	0.000	0.000	0.000
20	A	20	TYR	0	0.079	0.025	17.183	0.029	0.029	0.000	0.000	0.000
21	A	21	PHE	0	-0.040	-0.026	13.087	0.028	0.028	0.000	0.000	0.000
22	A	22	LYS	1	0.864	0.957	18.114	0.266	0.266	0.000	0.000	0.000
23	A	23	PHE	0	0.063	0.029	20.644	0.024	0.024	0.000	0.000	0.000
24	A	24	ARG	1	0.946	0.983	17.219	0.217	0.217	0.000	0.000	0.000
25	A	25	SER	0	-0.092	-0.053	21.111	0.011	0.011	0.000	0.000	0.000
26	A	26	GLU	-1	-0.851	-0.952	23.044	-0.172	-0.172	0.000	0.000	0.000
27	A	27	ILE	0	0.004	0.011	26.026	0.015	0.015	0.000	0.000	0.000
28	A	28	GLU	-1	-0.934	-0.976	23.068	-0.150	-0.150	0.000	0.000	0.000
29	A	29	ALA	0	0.005	0.015	27.013	0.010	0.010	0.000	0.000	0.000
30	A	30	ALA	0	0.014	0.003	28.706	0.010	0.010	0.000	0.000	0.000
31	A	31	GLH	0	-0.073	-0.077	30.315	0.011	0.011	0.000	0.000	0.000
32	A	32	ALA	0	0.005	0.006	29.762	0.008	0.008	0.000	0.000	0.000
33	A	33	TYR	0	-0.035	-0.026	31.453	0.005	0.005	0.000	0.000	0.000
34	A	34	LEU	0	0.043	0.020	34.494	0.007	0.007	0.000	0.000	0.000
35	A	35	GLY	0	0.004	0.013	35.022	0.006	0.006	0.000	0.000	0.000
36	A	36	LEU	0	-0.007	0.000	34.193	0.005	0.005	0.000	0.000	0.000
37	A	37	ALA	0	-0.012	0.019	37.548	0.005	0.005	0.000	0.000	0.000
38	A	38	ILE	0	-0.032	-0.028	38.273	0.005	0.005	0.000	0.000	0.000
39	A	39	SER	0	-0.149	-0.101	39.094	0.004	0.004	0.000	0.000	0.000
40	A	40	GLU	-1	-0.869	-0.955	41.213	-0.057	-0.057	0.000	0.000	0.000
41	A	41	GLY	0	-0.055	-0.002	44.059	0.002	0.002	0.000	0.000	0.000
42	A	42	ILE	0	-0.010	-0.005	46.154	0.002	0.002	0.000	0.000	0.000
43	A	43	LYS	1	0.865	0.956	46.051	0.049	0.049	0.000	0.000	0.000
44	A	44	VAL	0	0.027	0.023	44.091	-0.002	-0.002	0.000	0.000	0.000
45	A	45	ARG	1	0.939	0.964	44.554	0.035	0.035	0.000	0.000	0.000
46	A	46	GLU	-1	-0.829	-0.925	45.037	-0.044	-0.044	0.000	0.000	0.000
47	A	47	THR	0	-0.017	-0.027	40.282	-0.003	-0.003	0.000	0.000	0.000
48	A	48	ARG	1	0.936	0.957	40.312	0.043	0.043	0.000	0.000	0.000
49	A	49	GLU	-1	-0.891	-0.935	40.386	-0.043	-0.043	0.000	0.000	0.000
50	A	50	ILE	0	0.007	0.002	38.973	-0.001	-0.001	0.000	0.000	0.000
51	A	51	LEU	0	-0.011	-0.008	34.036	-0.004	-0.004	0.000	0.000	0.000
52	A	52	ASP	-1	-0.899	-0.935	35.804	-0.052	-0.052	0.000	0.000	0.000
53	A	53	ILE	0	-0.056	-0.034	36.801	0.000	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.013	-0.015	32.397	-0.002	-0.002	0.000	0.000	0.000
55	A	55	ASP	-1	-0.774	-0.869	30.882	-0.080	-0.080	0.000	0.000	0.000
56	A	56	THR	0	-0.018	0.002	31.999	0.001	0.001	0.000	0.000	0.000
57	A	57	VAL	0	-0.006	0.000	32.507	0.001	0.001	0.000	0.000	0.000
58	A	58	TYR	0	-0.044	-0.007	24.497	-0.009	-0.009	0.000	0.000	0.000
59	A	59	ASN	0	0.021	0.000	28.285	-0.005	-0.005	0.000	0.000	0.000
60	A	60	SER	0	-0.098	-0.044	29.557	0.005	0.005	0.000	0.000	0.000
61	A	61	LEU	0	-0.048	-0.035	24.635	0.001	0.001	0.000	0.000	0.000
62	A	62	SER	0	-0.011	-0.004	25.012	-0.003	-0.003	0.000	0.000	0.000
63	A	63	ASP	-1	-0.906	-0.930	27.064	-0.032	-0.032	0.000	0.000	0.000
64	A	64	PRO	0	-0.004	-0.024	30.266	-0.001	-0.001	0.000	0.000	0.000
65	A	65	GLU	-1	-0.884	-0.930	33.350	-0.024	-0.024	0.000	0.000	0.000
66	A	66	SER	0	-0.003	0.020	32.582	0.001	0.001	0.000	0.000	0.000
67	A	67	LYS	1	0.774	0.861	34.557	0.025	0.025	0.000	0.000	0.000
68	A	68	LEU	0	-0.027	-0.011	37.668	0.001	0.001	0.000	0.000	0.000
69	A	69	ASN	0	0.035	0.014	40.135	0.002	0.002	0.000	0.000	0.000
70	A	70	ASP	-1	-0.771	-0.886	43.709	-0.033	-0.033	0.000	0.000	0.000
71	A	71	PHE	0	-0.005	-0.003	46.535	-0.001	-0.001	0.000	0.000	0.000
72	A	72	GLN	0	0.033	0.007	41.094	0.000	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.813	-0.910	41.586	-0.048	-0.048	0.000	0.000	0.000
74	A	74	LYS	1	0.811	0.892	43.984	0.031	0.031	0.000	0.000	0.000
75	A	75	ARG	1	0.859	0.928	44.125	0.049	0.049	0.000	0.000	0.000
76	A	76	LEU	0	-0.012	-0.004	39.525	-0.002	-0.002	0.000	0.000	0.000
77	A	77	ASN	0	-0.014	-0.022	43.717	-0.004	-0.004	0.000	0.000	0.000
78	A	78	PHE	0	-0.060	-0.017	45.868	0.001	0.001	0.000	0.000	0.000
79	A	79	THR	0	-0.066	-0.013	43.616	0.000	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.919	-0.954	45.550	-0.051	-0.051	0.000	0.000	0.000
81	A	81	GLU	-1	-0.933	-0.974	41.499	-0.080	-0.080	0.000	0.000	0.000
82	A	82	ASP	-1	-0.890	-0.940	45.374	-0.053	-0.053	0.000	0.000	0.000
83	A	83	TRP	0	-0.010	-0.015	46.844	-0.003	-0.003	0.000	0.000	0.000
84	A	84	TYR	0	-0.038	-0.046	42.102	-0.001	-0.001	0.000	0.000	0.000
85	A	85	ASP	-1	-0.834	-0.909	47.345	-0.068	-0.068	0.000	0.000	0.000
86	A	86	ILE	0	0.007	0.002	41.597	0.001	0.001	0.000	0.000	0.000
87	A	87	LYS	1	0.936	0.971	45.092	0.065	0.065	0.000	0.000	0.000
88	A	88	GLU	-1	-0.906	-0.954	46.583	-0.056	-0.056	0.000	0.000	0.000
89	A	89	LYS	1	0.826	0.917	45.631	0.061	0.061	0.000	0.000	0.000
90	A	90	ALA	0	0.006	0.004	43.795	0.000	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.067	-0.043	45.479	0.000	0.000	0.000	0.000	0.000
92	A	92	ASN	0	0.004	0.004	48.421	0.003	0.003	0.000	0.000	0.000
93	A	93	GLY	0	0.028	0.034	45.990	0.001	0.001	0.000	0.000	0.000
94	A	94	ASN	0	-0.023	-0.011	46.992	0.001	0.001	0.000	0.000	0.000
95	A	95	ARG	1	1.006	0.993	42.720	0.059	0.059	0.000	0.000	0.000
96	A	96	TRP	0	0.068	0.047	42.287	-0.004	-0.004	0.000	0.000	0.000
97	A	97	SER	0	-0.041	-0.037	42.462	-0.002	-0.002	0.000	0.000	0.000
98	A	98	LEU	0	-0.008	-0.008	41.001	-0.003	-0.003	0.000	0.000	0.000
99	A	99	TYR	0	-0.015	-0.003	37.484	-0.007	-0.007	0.000	0.000	0.000
100	A	100	MET	0	0.007	0.020	37.753	-0.005	-0.005	0.000	0.000	0.000
101	A	101	PHE	0	0.028	0.001	38.704	-0.003	-0.003	0.000	0.000	0.000
102	A	102	LEU	0	-0.032	-0.003	34.508	-0.005	-0.005	0.000	0.000	0.000
103	A	103	ALA	0	0.028	0.009	34.190	-0.007	-0.007	0.000	0.000	0.000
104	A	104	ARG	1	0.889	0.942	34.319	0.084	0.084	0.000	0.000	0.000
105	A	105	SER	0	-0.004	0.007	33.770	-0.004	-0.004	0.000	0.000	0.000
106	A	106	ALA	0	0.009	0.022	30.234	-0.007	-0.007	0.000	0.000	0.000
107	A	107	VAL	0	-0.014	-0.011	30.339	-0.007	-0.007	0.000	0.000	0.000
108	A	108	ASP	-1	-0.854	-0.934	31.878	-0.106	-0.106	0.000	0.000	0.000
109	A	109	SER	0	-0.085	-0.038	28.240	-0.008	-0.008	0.000	0.000	0.000
110	A	110	ALA	0	-0.005	-0.004	27.292	-0.013	-0.013	0.000	0.000	0.000
111	A	111	VAL	0	0.015	0.006	28.046	-0.005	-0.005	0.000	0.000	0.000
112	A	112	TYR	0	0.013	0.012	25.451	0.002	0.002	0.000	0.000	0.000
113	A	113	TRP	0	0.001	-0.028	21.852	-0.016	-0.016	0.000	0.000	0.000
114	A	114	SER	0	-0.028	-0.010	24.764	-0.005	-0.005	0.000	0.000	0.000
115	A	115	TYR	0	-0.030	-0.022	26.552	0.002	0.002	0.000	0.000	0.000
116	A	116	ARG	1	0.882	0.950	23.043	0.179	0.179	0.000	0.000	0.000
117	A	117	MET	0	-0.017	-0.002	21.291	-0.016	-0.016	0.000	0.000	0.000
118	A	118	LYS	1	0.946	0.981	22.758	0.097	0.097	0.000	0.000	0.000
119	A	119	GLU	-1	-0.980	-0.969	24.196	-0.121	-0.121	0.000	0.000	0.000
120	A	120	THR	0	-0.062	-0.033	19.181	-0.009	-0.009	0.000	0.000	0.000
121	A	121	GLU	-1	-0.843	-0.936	18.902	-0.059	-0.059	0.000	0.000	0.000
122	A	122	GLU	-1	-0.892	-0.950	15.746	-0.168	-0.168	0.000	0.000	0.000
123	A	123	PHE	0	-0.006	-0.030	18.191	0.010	0.010	0.000	0.000	0.000
124	A	124	LYS	1	0.844	0.943	22.864	0.079	0.079	0.000	0.000	0.000
125	A	125	GLU	-1	-0.953	-0.975	25.472	-0.044	-0.044	0.000	0.000	0.000
126	A	126	ILE	0	-0.049	-0.003	24.075	0.006	0.006	0.000	0.000	0.000
127	A	127	VAL	0	-0.016	-0.006	25.283	0.002	0.002	0.000	0.000	0.000
128	A	128	LYS	1	0.967	0.991	27.958	0.056	0.056	0.000	0.000	0.000
129	A	129	GLU	-1	-0.823	-0.947	31.719	-0.087	-0.087	0.000	0.000	0.000
130	A	130	GLU	-1	-0.937	-0.973	33.990	-0.050	-0.050	0.000	0.000	0.000
131	A	131	MET	0	0.000	0.008	28.707	0.001	0.001	0.000	0.000	0.000
132	A	132	ILE	0	0.061	0.025	29.857	-0.001	-0.001	0.000	0.000	0.000
133	A	133	SER	0	-0.044	-0.018	33.204	0.000	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.851	0.910	36.060	0.053	0.053	0.000	0.000	0.000
135	A	135	LEU	0	0.023	0.010	30.239	0.001	0.001	0.000	0.000	0.000
136	A	136	LEU	0	0.010	0.013	34.768	0.000	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.940	0.979	36.821	0.059	0.059	0.000	0.000	0.000
138	A	138	ALA	0	0.018	0.010	36.742	0.003	0.003	0.000	0.000	0.000
139	A	139	GLY	0	0.040	0.020	37.728	0.001	0.001	0.000	0.000	0.000
140	A	140	TYR	0	0.013	-0.007	38.348	0.003	0.003	0.000	0.000	0.000
141	A	141	VAL	0	-0.002	0.003	41.581	0.003	0.003	0.000	0.000	0.000
142	A	142	ILE	0	-0.011	-0.005	37.201	0.003	0.003	0.000	0.000	0.000
143	A	143	LEU	0	-0.019	0.010	41.450	0.001	0.001	0.000	0.000	0.000
144	A	144	ARG	1	1.003	1.021	43.235	0.053	0.053	0.000	0.000	0.000
145	A	145	GLU	-1	-0.885	-0.967	43.885	-0.052	-0.052	0.000	0.000	0.000
146	A	146	SER	0	-0.066	-0.029	43.220	0.001	0.001	0.000	0.000	0.000
147	A	147	LEU	0	-0.013	-0.018	45.337	0.001	0.001	0.000	0.000	0.000
148	A	148	GLY	0	-0.074	-0.024	48.389	0.002	0.002	0.000	0.000	0.000
149	A	149	NME	0	-0.012	0.001	49.723	0.002	0.002	0.000	0.000	0.000

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