FMO DATABASE

FMODB ID: 3QVVL

Calculation Name: 1NIG-A-Xray372

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: 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	OptAll
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	148
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1479149.649195
FMO2-HF: Nuclear repulsion	1418042.383113
FMO2-HF: Total energy	-61107.266082
FMO2-MP2: Total energy	-61285.618068

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.
-0.459	1.035	-0.004	-0.631	-0.859	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 : -0.023 / q_NPA : -0.031

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	-0.017	-0.007	3.713	-0.484	1.010	-0.004	-0.631	-0.859
4	A	4	LYS	1	0.851	0.925	5.753	0.595	0.595	0.000	0.000	0.000
5	A	5	ARG	1	0.923	0.962	7.727	0.329	0.329	0.000	0.000	0.000
6	A	6	TYR	0	-0.016	-0.014	11.290	0.025	0.025	0.000	0.000	0.000
7	A	7	CYS	0	-0.070	-0.014	14.213	-0.031	-0.031	0.000	0.000	0.000
8	A	8	PRO	0	0.017	0.001	17.218	0.023	0.023	0.000	0.000	0.000
9	A	9	VAL	0	-0.015	-0.019	20.548	0.012	0.012	0.000	0.000	0.000
10	A	10	THR	0	0.020	-0.004	17.576	-0.001	-0.001	0.000	0.000	0.000
11	A	11	ASP	-1	-0.883	-0.885	19.280	0.012	0.012	0.000	0.000	0.000
12	A	12	SER	0	-0.035	-0.036	15.132	0.021	0.021	0.000	0.000	0.000
13	A	13	GLU	-1	-0.885	-0.963	10.027	-0.219	-0.219	0.000	0.000	0.000
14	A	14	LEU	0	0.000	0.016	11.596	0.045	0.045	0.000	0.000	0.000
15	A	15	PRO	0	0.013	-0.007	9.402	-0.048	-0.048	0.000	0.000	0.000
16	A	16	ALA	0	-0.009	-0.012	9.499	0.115	0.115	0.000	0.000	0.000
17	A	17	ASP	-1	-0.959	-0.981	11.304	-0.760	-0.760	0.000	0.000	0.000
18	A	18	HIS	0	-0.031	-0.010	13.174	0.058	0.058	0.000	0.000	0.000
19	A	19	VAL	0	0.014	0.004	15.609	0.016	0.016	0.000	0.000	0.000
20	A	20	TYR	0	0.057	0.017	17.627	0.026	0.026	0.000	0.000	0.000
21	A	21	PHE	0	-0.020	-0.019	13.856	0.025	0.025	0.000	0.000	0.000
22	A	22	LYS	1	0.775	0.891	18.831	0.258	0.258	0.000	0.000	0.000
23	A	23	PHE	0	0.050	0.005	21.288	0.022	0.022	0.000	0.000	0.000
24	A	24	ARG	1	0.817	0.883	19.931	0.188	0.188	0.000	0.000	0.000
25	A	25	SER	0	-0.004	-0.005	21.987	0.009	0.009	0.000	0.000	0.000
26	A	26	GLU	-1	-0.850	-0.911	23.895	-0.178	-0.178	0.000	0.000	0.000
27	A	27	ILE	0	0.016	0.018	26.876	0.014	0.014	0.000	0.000	0.000
28	A	28	GLU	-1	-0.813	-0.878	23.215	-0.165	-0.165	0.000	0.000	0.000
29	A	29	ALA	0	-0.006	0.003	27.618	0.010	0.010	0.000	0.000	0.000
30	A	30	ALA	0	0.005	-0.001	29.391	0.010	0.010	0.000	0.000	0.000
31	A	31	GLH	0	-0.067	-0.075	30.901	0.009	0.009	0.000	0.000	0.000
32	A	32	ALA	0	0.002	0.008	30.507	0.008	0.008	0.000	0.000	0.000
33	A	33	TYR	0	-0.021	-0.016	31.393	0.008	0.008	0.000	0.000	0.000
34	A	34	LEU	0	0.036	0.014	35.273	0.006	0.006	0.000	0.000	0.000
35	A	35	GLY	0	0.009	0.009	35.775	0.006	0.006	0.000	0.000	0.000
36	A	36	LEU	0	-0.011	-0.002	34.976	0.005	0.005	0.000	0.000	0.000
37	A	37	ALA	0	-0.015	0.006	38.279	0.005	0.005	0.000	0.000	0.000
38	A	38	ILE	0	-0.050	-0.035	39.018	0.005	0.005	0.000	0.000	0.000
39	A	39	SER	0	-0.083	-0.050	40.221	0.003	0.003	0.000	0.000	0.000
40	A	40	GLU	-1	-0.804	-0.886	42.243	-0.061	-0.061	0.000	0.000	0.000
41	A	41	GLY	0	-0.020	0.001	44.908	0.002	0.002	0.000	0.000	0.000
42	A	42	ILE	0	-0.036	-0.024	46.649	0.003	0.003	0.000	0.000	0.000
43	A	43	LYS	1	0.851	0.913	46.467	0.047	0.047	0.000	0.000	0.000
44	A	44	VAL	0	0.033	0.040	44.771	-0.001	-0.001	0.000	0.000	0.000
45	A	45	ARG	1	0.840	0.911	44.923	0.036	0.036	0.000	0.000	0.000
46	A	46	GLU	-1	-0.776	-0.888	45.423	-0.043	-0.043	0.000	0.000	0.000
47	A	47	THR	0	0.009	-0.021	40.819	-0.003	-0.003	0.000	0.000	0.000
48	A	48	ARG	1	0.909	0.966	40.876	0.044	0.044	0.000	0.000	0.000
49	A	49	GLU	-1	-0.758	-0.851	40.758	-0.045	-0.045	0.000	0.000	0.000
50	A	50	ILE	0	-0.020	-0.006	39.494	-0.001	-0.001	0.000	0.000	0.000
51	A	51	LEU	0	0.014	0.010	34.466	-0.004	-0.004	0.000	0.000	0.000
52	A	52	ASP	-1	-0.897	-0.955	36.390	-0.052	-0.052	0.000	0.000	0.000
53	A	53	ILE	0	-0.056	-0.021	37.444	0.001	0.001	0.000	0.000	0.000
54	A	54	ILE	0	0.021	0.006	33.045	-0.001	-0.001	0.000	0.000	0.000
55	A	55	ASP	-1	-0.801	-0.876	31.123	-0.081	-0.081	0.000	0.000	0.000
56	A	56	THR	0	-0.032	-0.009	32.441	0.001	0.001	0.000	0.000	0.000
57	A	57	VAL	0	-0.004	-0.010	33.191	0.001	0.001	0.000	0.000	0.000
58	A	58	TYR	0	-0.016	0.008	24.923	-0.008	-0.008	0.000	0.000	0.000
59	A	59	ASN	0	0.001	-0.010	28.921	-0.004	-0.004	0.000	0.000	0.000
60	A	60	SER	0	-0.076	-0.042	29.825	0.005	0.005	0.000	0.000	0.000
61	A	61	LEU	0	-0.041	-0.024	25.976	0.002	0.002	0.000	0.000	0.000
62	A	62	SER	0	-0.022	-0.017	25.296	-0.003	-0.003	0.000	0.000	0.000
63	A	63	ASP	-1	-0.850	-0.919	27.336	-0.026	-0.026	0.000	0.000	0.000
64	A	64	PRO	0	-0.028	-0.008	30.562	-0.002	-0.002	0.000	0.000	0.000
65	A	65	GLU	-1	-0.891	-0.941	33.212	-0.025	-0.025	0.000	0.000	0.000
66	A	66	SER	0	-0.007	0.016	33.039	0.001	0.001	0.000	0.000	0.000
67	A	67	LYS	1	0.733	0.843	35.099	0.027	0.027	0.000	0.000	0.000
68	A	68	LEU	0	-0.034	0.000	37.998	0.001	0.001	0.000	0.000	0.000
69	A	69	ASN	0	0.028	0.011	40.641	0.003	0.003	0.000	0.000	0.000
70	A	70	ASP	-1	-0.756	-0.883	44.260	-0.033	-0.033	0.000	0.000	0.000
71	A	71	PHE	0	-0.010	0.005	47.070	-0.001	-0.001	0.000	0.000	0.000
72	A	72	GLN	0	0.039	0.015	41.227	0.000	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.755	-0.870	41.250	-0.050	-0.050	0.000	0.000	0.000
74	A	74	LYS	1	0.783	0.874	44.480	0.031	0.031	0.000	0.000	0.000
75	A	75	ARG	1	0.707	0.823	44.939	0.047	0.047	0.000	0.000	0.000
76	A	76	LEU	0	-0.006	0.012	39.796	-0.002	-0.002	0.000	0.000	0.000
77	A	77	ASN	0	-0.057	-0.044	43.660	-0.003	-0.003	0.000	0.000	0.000
78	A	78	PHE	0	-0.045	-0.009	46.083	0.001	0.001	0.000	0.000	0.000
79	A	79	THR	0	-0.071	-0.028	44.657	0.001	0.001	0.000	0.000	0.000
80	A	80	GLU	-1	-0.912	-0.948	45.941	-0.051	-0.051	0.000	0.000	0.000
81	A	81	GLU	-1	-0.838	-0.922	41.942	-0.080	-0.080	0.000	0.000	0.000
82	A	82	ASP	-1	-0.848	-0.923	46.095	-0.052	-0.052	0.000	0.000	0.000
83	A	83	TRP	0	0.006	-0.003	47.160	-0.002	-0.002	0.000	0.000	0.000
84	A	84	TYR	0	-0.027	-0.035	41.607	0.000	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.843	-0.915	46.802	-0.069	-0.069	0.000	0.000	0.000
86	A	86	ILE	0	0.013	0.009	41.229	0.002	0.002	0.000	0.000	0.000
87	A	87	LYS	1	0.847	0.917	44.684	0.061	0.061	0.000	0.000	0.000
88	A	88	GLU	-1	-0.788	-0.894	46.332	-0.058	-0.058	0.000	0.000	0.000
89	A	89	LYS	1	0.853	0.948	45.296	0.062	0.062	0.000	0.000	0.000
90	A	90	ALA	0	0.017	0.007	43.370	0.001	0.001	0.000	0.000	0.000
91	A	91	ASN	0	-0.077	-0.053	45.100	0.000	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.032	-0.022	48.226	0.004	0.004	0.000	0.000	0.000
93	A	93	GLY	0	0.001	0.016	45.862	0.002	0.002	0.000	0.000	0.000
94	A	94	ASN	0	-0.008	-0.009	46.684	-0.001	-0.001	0.000	0.000	0.000
95	A	95	ARG	1	0.928	0.950	42.946	0.059	0.059	0.000	0.000	0.000
96	A	96	TRP	0	0.012	0.017	42.856	-0.004	-0.004	0.000	0.000	0.000
97	A	97	SER	0	-0.011	-0.012	43.009	-0.003	-0.003	0.000	0.000	0.000
98	A	98	LEU	0	0.010	0.003	41.242	-0.003	-0.003	0.000	0.000	0.000
99	A	99	TYR	0	-0.042	-0.039	38.673	-0.007	-0.007	0.000	0.000	0.000
100	A	100	MET	0	0.007	0.022	38.284	-0.005	-0.005	0.000	0.000	0.000
101	A	101	PHE	0	0.035	0.009	39.290	-0.003	-0.003	0.000	0.000	0.000
102	A	102	LEU	0	-0.040	0.005	34.535	-0.005	-0.005	0.000	0.000	0.000
103	A	103	ALA	0	0.018	0.004	34.832	-0.007	-0.007	0.000	0.000	0.000
104	A	104	ARG	1	0.748	0.854	35.001	0.087	0.087	0.000	0.000	0.000
105	A	105	SER	0	-0.024	-0.020	34.255	-0.003	-0.003	0.000	0.000	0.000
106	A	106	ALA	0	-0.001	0.016	30.768	-0.008	-0.008	0.000	0.000	0.000
107	A	107	VAL	0	0.015	0.004	30.996	-0.007	-0.007	0.000	0.000	0.000
108	A	108	ASP	-1	-0.799	-0.891	32.631	-0.104	-0.104	0.000	0.000	0.000
109	A	109	SER	0	-0.042	-0.024	28.530	-0.008	-0.008	0.000	0.000	0.000
110	A	110	ALA	0	-0.009	-0.008	28.049	-0.012	-0.012	0.000	0.000	0.000
111	A	111	VAL	0	0.012	0.005	28.916	-0.002	-0.002	0.000	0.000	0.000
112	A	112	TYR	0	0.002	0.009	25.448	0.002	0.002	0.000	0.000	0.000
113	A	113	TRP	0	0.019	-0.016	22.238	-0.014	-0.014	0.000	0.000	0.000
114	A	114	SER	0	-0.012	-0.005	25.199	-0.005	-0.005	0.000	0.000	0.000
115	A	115	TYR	0	-0.015	-0.043	27.084	0.001	0.001	0.000	0.000	0.000
116	A	116	ARG	1	0.737	0.856	23.476	0.165	0.165	0.000	0.000	0.000
117	A	117	MET	0	-0.015	0.015	21.752	-0.014	-0.014	0.000	0.000	0.000
118	A	118	LYS	1	0.827	0.921	23.487	0.092	0.092	0.000	0.000	0.000
119	A	119	GLU	-1	-0.821	-0.891	23.410	-0.126	-0.126	0.000	0.000	0.000
120	A	120	THR	0	-0.064	-0.036	19.617	-0.010	-0.010	0.000	0.000	0.000
121	A	121	GLU	-1	-0.797	-0.899	19.382	-0.051	-0.051	0.000	0.000	0.000
122	A	122	GLU	-1	-0.846	-0.925	16.069	-0.159	-0.159	0.000	0.000	0.000
123	A	123	PHE	0	0.019	-0.015	18.433	0.008	0.008	0.000	0.000	0.000
124	A	124	LYS	1	0.782	0.911	23.252	0.066	0.066	0.000	0.000	0.000
125	A	125	GLU	-1	-0.902	-0.956	26.006	-0.046	-0.046	0.000	0.000	0.000
126	A	126	ILE	0	-0.032	0.004	24.225	0.005	0.005	0.000	0.000	0.000
127	A	127	VAL	0	-0.003	-0.004	25.835	0.002	0.002	0.000	0.000	0.000
128	A	128	LYS	1	0.875	0.928	28.564	0.053	0.053	0.000	0.000	0.000
129	A	129	GLU	-1	-0.804	-0.907	32.329	-0.082	-0.082	0.000	0.000	0.000
130	A	130	GLU	-1	-0.837	-0.886	34.263	-0.050	-0.050	0.000	0.000	0.000
131	A	131	MET	0	0.020	0.028	29.310	0.000	0.000	0.000	0.000	0.000
132	A	132	ILE	0	0.060	0.027	30.607	0.000	0.000	0.000	0.000	0.000
133	A	133	SER	0	-0.061	-0.040	33.664	0.001	0.001	0.000	0.000	0.000
134	A	134	LYS	1	0.792	0.872	36.825	0.052	0.052	0.000	0.000	0.000
135	A	135	LEU	0	0.032	0.019	31.937	0.001	0.001	0.000	0.000	0.000
136	A	136	LEU	0	0.023	0.003	35.369	-0.001	-0.001	0.000	0.000	0.000
137	A	137	LYS	1	0.888	0.944	37.250	0.058	0.058	0.000	0.000	0.000
138	A	138	ALA	0	0.021	0.006	37.240	0.003	0.003	0.000	0.000	0.000
139	A	139	GLY	0	0.048	0.024	38.138	0.001	0.001	0.000	0.000	0.000
140	A	140	TYR	0	-0.019	-0.009	38.919	0.002	0.002	0.000	0.000	0.000
141	A	141	VAL	0	0.020	0.009	42.253	0.003	0.003	0.000	0.000	0.000
142	A	142	ILE	0	-0.017	-0.015	37.820	0.002	0.002	0.000	0.000	0.000
143	A	143	LEU	0	-0.025	0.008	41.998	0.001	0.001	0.000	0.000	0.000
144	A	144	ARG	1	0.916	0.959	43.909	0.054	0.054	0.000	0.000	0.000
145	A	145	GLU	-1	-0.780	-0.869	45.132	-0.049	-0.049	0.000	0.000	0.000
146	A	146	SER	0	-0.072	-0.028	43.706	0.001	0.001	0.000	0.000	0.000
147	A	147	LEU	0	-0.037	-0.033	45.828	0.001	0.001	0.000	0.000	0.000
148	A	148	GLY	0	-0.064	-0.021	48.961	0.003	0.003	0.000	0.000	0.000

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