FMO DATABASE

FMODB ID: N1GGQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1474469.766773
FMO2-HF: Nuclear repulsion	1413364.70557
FMO2-HF: Total energy	-61105.061203
FMO2-MP2: Total energy	-61283.451693

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.
0.258	1.889	0.003	-0.649	-0.985	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 : -0.019 / 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	-0.029	-0.012	3.649	0.194	1.755	0.004	-0.643	-0.922
4	A	4	LYS	1	0.944	0.978	5.152	0.379	0.449	-0.001	-0.006	-0.063
5	A	5	ARG	1	0.896	0.952	7.393	0.348	0.348	0.000	0.000	0.000
6	A	6	TYR	0	0.004	-0.011	10.836	0.024	0.024	0.000	0.000	0.000
7	A	7	CYS	0	-0.069	-0.008	13.834	-0.028	-0.028	0.000	0.000	0.000
8	A	8	PRO	0	0.003	-0.026	16.742	0.024	0.024	0.000	0.000	0.000
9	A	9	VAL	0	-0.032	-0.012	20.034	0.011	0.011	0.000	0.000	0.000
10	A	10	THR	0	0.057	0.020	17.478	0.010	0.010	0.000	0.000	0.000
11	A	11	ASP	-1	-0.889	-0.894	18.857	0.026	0.026	0.000	0.000	0.000
12	A	12	SER	0	-0.028	-0.025	14.995	0.028	0.028	0.000	0.000	0.000
13	A	13	GLU	-1	-0.921	-0.975	9.844	-0.172	-0.172	0.000	0.000	0.000
14	A	14	LEU	0	-0.022	-0.005	11.844	0.046	0.046	0.000	0.000	0.000
15	A	15	PRO	0	0.063	0.026	8.867	-0.039	-0.039	0.000	0.000	0.000
16	A	16	ALA	0	-0.002	-0.015	8.888	0.100	0.100	0.000	0.000	0.000
17	A	17	ASP	-1	-0.992	-0.997	10.627	-0.692	-0.692	0.000	0.000	0.000
18	A	18	HIS	0	0.033	0.029	12.710	0.070	0.070	0.000	0.000	0.000
19	A	19	VAL	0	-0.005	0.003	15.090	0.011	0.011	0.000	0.000	0.000
20	A	20	TYR	0	0.081	0.025	17.203	0.028	0.028	0.000	0.000	0.000
21	A	21	PHE	0	-0.042	-0.028	13.110	0.028	0.028	0.000	0.000	0.000
22	A	22	LYS	1	0.866	0.958	18.133	0.265	0.265	0.000	0.000	0.000
23	A	23	PHE	0	0.062	0.029	20.663	0.023	0.023	0.000	0.000	0.000
24	A	24	ARG	1	0.941	0.981	17.231	0.214	0.214	0.000	0.000	0.000
25	A	25	SER	0	-0.089	-0.053	21.125	0.011	0.011	0.000	0.000	0.000
26	A	26	GLU	-1	-0.847	-0.951	23.058	-0.172	-0.172	0.000	0.000	0.000
27	A	27	ILE	0	0.002	0.012	26.043	0.014	0.014	0.000	0.000	0.000
28	A	28	GLU	-1	-0.936	-0.978	23.078	-0.149	-0.149	0.000	0.000	0.000
29	A	29	ALA	0	0.006	0.016	27.026	0.010	0.010	0.000	0.000	0.000
30	A	30	ALA	0	0.012	0.003	28.718	0.010	0.010	0.000	0.000	0.000
31	A	31	GLH	0	-0.073	-0.077	30.326	0.010	0.010	0.000	0.000	0.000
32	A	32	ALA	0	0.007	0.006	29.769	0.008	0.008	0.000	0.000	0.000
33	A	33	TYR	0	-0.036	-0.025	31.465	0.005	0.005	0.000	0.000	0.000
34	A	34	LEU	0	0.045	0.021	34.503	0.006	0.006	0.000	0.000	0.000
35	A	35	GLY	0	0.003	0.011	35.031	0.006	0.006	0.000	0.000	0.000
36	A	36	LEU	0	-0.007	0.001	34.198	0.005	0.005	0.000	0.000	0.000
37	A	37	ALA	0	-0.013	0.019	37.554	0.005	0.005	0.000	0.000	0.000
38	A	38	ILE	0	-0.032	-0.028	38.282	0.005	0.005	0.000	0.000	0.000
39	A	39	SER	0	-0.148	-0.101	39.098	0.004	0.004	0.000	0.000	0.000
40	A	40	GLU	-1	-0.868	-0.956	41.217	-0.057	-0.057	0.000	0.000	0.000
41	A	41	GLY	0	-0.055	-0.002	44.065	0.002	0.002	0.000	0.000	0.000
42	A	42	ILE	0	-0.009	-0.004	46.162	0.002	0.002	0.000	0.000	0.000
43	A	43	LYS	1	0.870	0.958	46.065	0.049	0.049	0.000	0.000	0.000
44	A	44	VAL	0	0.028	0.023	44.099	-0.002	-0.002	0.000	0.000	0.000
45	A	45	ARG	1	0.934	0.962	44.565	0.035	0.035	0.000	0.000	0.000
46	A	46	GLU	-1	-0.829	-0.925	45.050	-0.043	-0.043	0.000	0.000	0.000
47	A	47	THR	0	-0.016	-0.027	40.293	-0.003	-0.003	0.000	0.000	0.000
48	A	48	ARG	1	0.934	0.957	40.324	0.043	0.043	0.000	0.000	0.000
49	A	49	GLU	-1	-0.890	-0.934	40.399	-0.043	-0.043	0.000	0.000	0.000
50	A	50	ILE	0	0.006	0.002	38.989	-0.001	-0.001	0.000	0.000	0.000
51	A	51	LEU	0	-0.011	-0.009	34.048	-0.004	-0.004	0.000	0.000	0.000
52	A	52	ASP	-1	-0.898	-0.934	35.819	-0.052	-0.052	0.000	0.000	0.000
53	A	53	ILE	0	-0.054	-0.032	36.817	0.000	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.011	-0.014	32.414	-0.002	-0.002	0.000	0.000	0.000
55	A	55	ASP	-1	-0.776	-0.870	30.896	-0.079	-0.079	0.000	0.000	0.000
56	A	56	THR	0	-0.013	0.004	32.016	0.001	0.001	0.000	0.000	0.000
57	A	57	VAL	0	0.002	0.003	32.529	0.001	0.001	0.000	0.000	0.000
58	A	58	TYR	0	-0.045	-0.006	24.513	-0.008	-0.008	0.000	0.000	0.000
59	A	59	ASN	0	0.002	-0.007	28.301	-0.005	-0.005	0.000	0.000	0.000
60	A	60	SER	0	-0.097	-0.043	29.577	0.005	0.005	0.000	0.000	0.000
61	A	61	LEU	0	-0.027	-0.030	24.659	0.002	0.002	0.000	0.000	0.000
62	A	62	SER	0	-0.011	-0.006	25.033	-0.003	-0.003	0.000	0.000	0.000
63	A	63	ASP	-1	-0.869	-0.916	27.085	-0.024	-0.024	0.000	0.000	0.000
64	A	64	PRO	0	0.011	0.018	30.172	-0.001	-0.001	0.000	0.000	0.000
65	A	65	GLU	-1	-0.972	-0.998	32.834	-0.022	-0.022	0.000	0.000	0.000
66	A	66	SER	0	0.048	0.032	32.602	0.001	0.001	0.000	0.000	0.000
67	A	67	LYS	1	0.748	0.857	34.576	0.027	0.027	0.000	0.000	0.000
68	A	68	LEU	0	-0.041	-0.010	37.689	0.001	0.001	0.000	0.000	0.000
69	A	69	ASN	0	0.042	0.017	40.155	0.002	0.002	0.000	0.000	0.000
70	A	70	ASP	-1	-0.772	-0.887	43.729	-0.033	-0.033	0.000	0.000	0.000
71	A	71	PHE	0	-0.005	-0.004	46.591	-0.001	-0.001	0.000	0.000	0.000
72	A	72	GLN	0	0.032	0.007	41.111	0.000	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.815	-0.910	41.609	-0.047	-0.047	0.000	0.000	0.000
74	A	74	LYS	1	0.809	0.891	44.006	0.031	0.031	0.000	0.000	0.000
75	A	75	ARG	1	0.864	0.929	44.144	0.048	0.048	0.000	0.000	0.000
76	A	76	LEU	0	-0.016	-0.005	39.546	-0.002	-0.002	0.000	0.000	0.000
77	A	77	ASN	0	-0.010	-0.021	43.738	-0.004	-0.004	0.000	0.000	0.000
78	A	78	PHE	0	-0.061	-0.017	45.891	0.001	0.001	0.000	0.000	0.000
79	A	79	THR	0	-0.067	-0.014	43.638	0.000	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.919	-0.953	45.573	-0.051	-0.051	0.000	0.000	0.000
81	A	81	GLU	-1	-0.933	-0.975	41.520	-0.080	-0.080	0.000	0.000	0.000
82	A	82	ASP	-1	-0.889	-0.939	45.395	-0.053	-0.053	0.000	0.000	0.000
83	A	83	TRP	0	-0.010	-0.015	46.864	-0.003	-0.003	0.000	0.000	0.000
84	A	84	TYR	0	-0.040	-0.048	42.094	-0.001	-0.001	0.000	0.000	0.000
85	A	85	ASP	-1	-0.834	-0.908	47.299	-0.068	-0.068	0.000	0.000	0.000
86	A	86	ILE	0	0.010	0.003	41.586	0.001	0.001	0.000	0.000	0.000
87	A	87	LYS	1	0.933	0.971	45.025	0.064	0.064	0.000	0.000	0.000
88	A	88	GLU	-1	-0.909	-0.957	46.518	-0.057	-0.057	0.000	0.000	0.000
89	A	89	LYS	1	0.828	0.929	45.556	0.061	0.061	0.000	0.000	0.000
90	A	90	ALA	0	0.008	0.005	43.729	0.000	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.068	-0.043	45.412	0.000	0.000	0.000	0.000	0.000
92	A	92	ASN	0	0.003	0.004	48.356	0.003	0.003	0.000	0.000	0.000
93	A	93	GLY	0	0.026	0.033	45.998	0.001	0.001	0.000	0.000	0.000
94	A	94	ASN	0	-0.019	-0.009	46.999	0.001	0.001	0.000	0.000	0.000
95	A	95	ARG	1	1.003	0.992	42.724	0.059	0.059	0.000	0.000	0.000
96	A	96	TRP	0	0.064	0.044	42.295	-0.004	-0.004	0.000	0.000	0.000
97	A	97	SER	0	-0.025	-0.027	42.472	-0.002	-0.002	0.000	0.000	0.000
98	A	98	LEU	0	-0.010	-0.011	41.010	-0.003	-0.003	0.000	0.000	0.000
99	A	99	TYR	0	-0.019	-0.005	37.492	-0.007	-0.007	0.000	0.000	0.000
100	A	100	MET	0	0.016	0.024	37.764	-0.005	-0.005	0.000	0.000	0.000
101	A	101	PHE	0	0.017	-0.003	38.718	-0.003	-0.003	0.000	0.000	0.000
102	A	102	LEU	0	-0.033	-0.003	34.519	-0.005	-0.005	0.000	0.000	0.000
103	A	103	ALA	0	0.027	0.010	34.204	-0.007	-0.007	0.000	0.000	0.000
104	A	104	ARG	1	0.889	0.942	34.335	0.084	0.084	0.000	0.000	0.000
105	A	105	SER	0	-0.001	0.007	33.786	-0.003	-0.003	0.000	0.000	0.000
106	A	106	ALA	0	0.007	0.021	30.249	-0.007	-0.007	0.000	0.000	0.000
107	A	107	VAL	0	-0.013	-0.011	30.357	-0.007	-0.007	0.000	0.000	0.000
108	A	108	ASP	-1	-0.853	-0.935	31.898	-0.106	-0.106	0.000	0.000	0.000
109	A	109	SER	0	-0.089	-0.039	28.259	-0.008	-0.008	0.000	0.000	0.000
110	A	110	ALA	0	-0.001	-0.003	27.313	-0.013	-0.013	0.000	0.000	0.000
111	A	111	VAL	0	0.013	0.005	28.069	-0.005	-0.005	0.000	0.000	0.000
112	A	112	TYR	0	0.014	0.011	25.441	0.002	0.002	0.000	0.000	0.000
113	A	113	TRP	0	0.000	-0.028	21.842	-0.016	-0.016	0.000	0.000	0.000
114	A	114	SER	0	-0.022	-0.008	24.790	-0.005	-0.005	0.000	0.000	0.000
115	A	115	TYR	0	-0.032	-0.023	26.580	0.002	0.002	0.000	0.000	0.000
116	A	116	ARG	1	0.884	0.950	23.031	0.179	0.179	0.000	0.000	0.000
117	A	117	MET	0	-0.027	-0.005	21.317	-0.016	-0.016	0.000	0.000	0.000
118	A	118	LYS	1	0.955	0.982	22.787	0.095	0.095	0.000	0.000	0.000
119	A	119	GLU	-1	-0.981	-0.969	24.184	-0.120	-0.120	0.000	0.000	0.000
120	A	120	THR	0	-0.063	-0.032	19.194	-0.009	-0.009	0.000	0.000	0.000
121	A	121	GLU	-1	-0.840	-0.935	18.902	-0.059	-0.059	0.000	0.000	0.000
122	A	122	GLU	-1	-0.892	-0.951	15.777	-0.164	-0.164	0.000	0.000	0.000
123	A	123	PHE	0	-0.006	-0.030	18.218	0.010	0.010	0.000	0.000	0.000
124	A	124	LYS	1	0.843	0.943	22.893	0.077	0.077	0.000	0.000	0.000
125	A	125	GLU	-1	-0.951	-0.974	25.504	-0.043	-0.043	0.000	0.000	0.000
126	A	126	ILE	0	-0.052	-0.004	24.102	0.006	0.006	0.000	0.000	0.000
127	A	127	VAL	0	-0.019	-0.007	25.311	0.002	0.002	0.000	0.000	0.000
128	A	128	LYS	1	0.970	0.993	27.986	0.054	0.054	0.000	0.000	0.000
129	A	129	GLU	-1	-0.824	-0.946	31.747	-0.086	-0.086	0.000	0.000	0.000
130	A	130	GLU	-1	-0.935	-0.973	34.018	-0.049	-0.049	0.000	0.000	0.000
131	A	131	MET	0	-0.004	0.006	28.730	0.001	0.001	0.000	0.000	0.000
132	A	132	ILE	0	0.061	0.026	29.884	-0.001	-0.001	0.000	0.000	0.000
133	A	133	SER	0	-0.046	-0.019	33.229	0.000	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.852	0.910	36.083	0.052	0.052	0.000	0.000	0.000
135	A	135	LEU	0	0.021	0.010	30.260	0.001	0.001	0.000	0.000	0.000
136	A	136	LEU	0	0.009	0.012	34.790	0.000	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.940	0.980	36.844	0.059	0.059	0.000	0.000	0.000
138	A	138	ALA	0	0.021	0.011	36.762	0.003	0.003	0.000	0.000	0.000
139	A	139	GLY	0	0.039	0.020	37.748	0.001	0.001	0.000	0.000	0.000
140	A	140	TYR	0	0.010	-0.008	38.367	0.002	0.002	0.000	0.000	0.000
141	A	141	VAL	0	0.007	0.006	41.599	0.003	0.003	0.000	0.000	0.000
142	A	142	ILE	0	-0.013	-0.006	37.217	0.003	0.003	0.000	0.000	0.000
143	A	143	LEU	0	-0.025	0.008	41.467	0.001	0.001	0.000	0.000	0.000
144	A	144	ARG	1	1.006	1.014	43.253	0.052	0.052	0.000	0.000	0.000
145	A	145	GLU	-1	-0.887	-0.968	43.901	-0.051	-0.051	0.000	0.000	0.000
146	A	146	SER	0	-0.058	-0.021	43.234	0.001	0.001	0.000	0.000	0.000
147	A	147	LEU	0	-0.027	-0.032	45.351	0.001	0.001	0.000	0.000	0.000
148	A	148	GLY	0	-0.075	-0.019	48.405	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)