FMO DATABASE

FMODB ID: J3999

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1475484.756001
FMO2-HF: Nuclear repulsion	1414378.217654
FMO2-HF: Total energy	-61106.538347
FMO2-MP2: Total energy	-61284.944782

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.
0.17	1.803	-0.001	-0.626	-1.004	0.001

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 : -0.024 / q_NPA : -0.028

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	ILE	0	-0.016	-0.012	3.723	0.308	1.855	0.000	-0.620	-0.926	0.001
4	A	4	LYS	1	0.864	0.929	5.197	0.179	0.265	-0.001	-0.006	-0.078	0.000
5	A	5	ARG	1	0.896	0.947	7.448	0.257	0.257	0.000	0.000	0.000	0.000
6	A	6	TYR	0	0.004	-0.006	10.879	0.019	0.019	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.081	-0.022	13.876	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.007	-0.017	16.795	0.022	0.022	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.039	-0.020	20.082	0.009	0.009	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.043	0.008	17.617	0.006	0.006	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.892	-0.890	18.853	0.053	0.053	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.028	-0.023	15.102	0.031	0.031	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.895	-0.963	9.897	-0.090	-0.090	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.011	0.005	11.910	0.044	0.044	0.000	0.000	0.000	0.000
15	A	15	PRO	0	0.046	0.013	8.940	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.000	-0.012	8.958	0.070	0.070	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.990	-0.998	10.682	-0.649	-0.649	0.000	0.000	0.000	0.000
18	A	18	HIS	0	0.003	0.014	12.786	0.047	0.047	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.004	0.007	15.159	0.006	0.006	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.079	0.018	17.163	0.025	0.025	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.026	-0.018	13.338	0.019	0.019	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.789	0.907	18.186	0.229	0.229	0.000	0.000	0.000	0.000
23	A	23	PHE	0	0.069	0.021	20.715	0.020	0.020	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.858	0.915	18.764	0.153	0.153	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.045	-0.017	21.182	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.856	-0.929	23.098	-0.158	-0.158	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.007	0.008	26.097	0.012	0.012	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.857	-0.918	22.766	-0.133	-0.133	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.012	0.018	27.062	0.008	0.008	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.008	0.003	28.751	0.008	0.008	0.000	0.000	0.000	0.000
31	A	31	GLH	0	-0.060	-0.073	30.346	0.008	0.008	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.004	0.010	29.725	0.007	0.007	0.000	0.000	0.000	0.000
33	A	33	TYR	0	-0.020	-0.023	31.225	0.006	0.006	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.041	0.024	34.533	0.005	0.005	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.003	0.010	35.060	0.005	0.005	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.007	0.000	34.313	0.004	0.004	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.010	0.006	37.575	0.004	0.004	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.038	-0.024	38.141	0.005	0.005	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.135	-0.084	39.164	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.850	-0.950	41.235	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.047	0.000	44.084	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.011	-0.006	46.190	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.809	0.910	46.157	0.041	0.041	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.021	0.021	44.274	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.876	0.919	44.597	0.029	0.029	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.784	-0.888	45.088	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.015	0.000	40.302	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.941	0.955	40.356	0.035	0.035	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.821	-0.887	40.437	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.009	-0.005	38.999	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.010	-0.010	34.021	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.883	-0.935	35.862	-0.041	-0.041	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.052	-0.020	36.863	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.003	-0.011	32.572	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.780	-0.865	30.832	-0.061	-0.061	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.032	-0.006	32.065	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.022	0.002	32.649	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	TYR	0	-0.045	-0.001	24.588	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.003	-0.011	28.517	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.097	-0.053	29.632	0.005	0.005	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.031	-0.029	25.152	0.002	0.002	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.011	-0.007	25.058	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.866	-0.924	27.144	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.017	0.025	30.254	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.959	-0.992	32.862	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.045	0.039	32.689	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.725	0.843	34.630	0.016	0.016	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.052	-0.010	37.746	0.000	0.000	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.037	0.008	40.212	0.002	0.002	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.779	-0.891	43.784	-0.025	-0.025	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.008	0.003	46.403	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	72	GLN	0	0.035	0.014	40.809	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.787	-0.892	40.949	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.804	0.879	44.066	0.024	0.024	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.755	0.867	44.399	0.039	0.039	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.016	-0.002	39.686	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.010	-0.004	43.798	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	78	PHE	0	-0.057	-0.016	45.955	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.053	-0.012	43.838	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.920	-0.950	45.635	-0.044	-0.044	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.893	-0.952	41.628	-0.070	-0.070	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.816	-0.897	45.455	-0.045	-0.045	0.000	0.000	0.000	0.000
83	A	83	TRP	0	-0.029	-0.022	46.919	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.033	-0.041	41.635	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.844	-0.914	47.293	-0.061	-0.061	0.000	0.000	0.000	0.000
86	A	86	ILE	0	0.015	0.003	41.586	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.858	0.924	45.040	0.056	0.056	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.811	-0.897	46.535	-0.051	-0.051	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.844	0.936	45.658	0.053	0.053	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.013	0.005	43.779	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.090	-0.048	45.426	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.040	-0.023	48.371	0.003	0.003	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.033	0.037	46.016	0.001	0.001	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.032	-0.015	47.023	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.983	0.990	42.823	0.051	0.051	0.000	0.000	0.000	0.000
96	A	96	TRP	0	0.048	0.028	42.321	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.021	-0.018	42.503	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	98	LEU	0	0.008	-0.005	41.018	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	99	TYR	0	-0.023	-0.006	38.003	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	100	MET	0	0.024	0.023	37.798	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	101	PHE	0	0.034	0.010	38.758	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.037	0.004	34.553	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.021	0.006	34.240	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.785	0.870	34.379	0.077	0.077	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.011	-0.010	34.202	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	106	ALA	0	0.010	0.019	30.260	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.002	-0.006	30.407	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.812	-0.902	31.954	-0.091	-0.091	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.067	-0.036	28.398	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.002	-0.004	27.372	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	111	VAL	0	0.015	0.010	28.131	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	112	TYR	0	0.015	0.018	25.575	0.002	0.002	0.000	0.000	0.000	0.000
113	A	113	TRP	0	0.016	-0.025	22.208	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	114	SER	0	-0.027	-0.017	24.858	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	115	TYR	0	-0.039	-0.042	26.653	0.002	0.002	0.000	0.000	0.000	0.000
116	A	116	ARG	1	0.783	0.876	23.244	0.148	0.148	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.038	0.004	21.364	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.877	0.955	22.865	0.075	0.075	0.000	0.000	0.000	0.000
119	A	119	GLU	-1	-0.824	-0.889	23.794	-0.107	-0.107	0.000	0.000	0.000	0.000
120	A	120	THR	0	-0.081	-0.048	19.265	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.796	-0.891	19.059	-0.036	-0.036	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.872	-0.936	15.712	-0.116	-0.116	0.000	0.000	0.000	0.000
123	A	123	PHE	0	0.016	-0.022	18.296	0.009	0.009	0.000	0.000	0.000	0.000
124	A	124	LYS	1	0.788	0.903	22.971	0.049	0.049	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.911	-0.961	25.585	-0.031	-0.031	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.048	-0.007	23.842	0.005	0.005	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.012	0.004	25.327	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.895	0.940	28.060	0.038	0.038	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.783	-0.903	31.822	-0.071	-0.071	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.848	-0.909	34.093	-0.038	-0.038	0.000	0.000	0.000	0.000
131	A	131	MET	0	0.025	0.020	28.968	0.000	0.000	0.000	0.000	0.000	0.000
132	A	132	ILE	0	0.052	0.024	30.010	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	133	SER	0	-0.064	-0.032	33.297	0.000	0.000	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.794	0.876	36.190	0.040	0.040	0.000	0.000	0.000	0.000
135	A	135	LEU	0	0.018	0.014	30.778	0.001	0.001	0.000	0.000	0.000	0.000
136	A	136	LEU	0	0.018	0.013	34.850	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.917	0.957	36.906	0.048	0.048	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.016	0.007	36.815	0.002	0.002	0.000	0.000	0.000	0.000
139	A	139	GLY	0	0.034	0.019	37.803	0.001	0.001	0.000	0.000	0.000	0.000
140	A	140	TYR	0	0.000	-0.009	38.421	0.002	0.002	0.000	0.000	0.000	0.000
141	A	141	VAL	0	0.011	0.004	41.713	0.003	0.003	0.000	0.000	0.000	0.000
142	A	142	ILE	0	-0.025	-0.011	37.263	0.002	0.002	0.000	0.000	0.000	0.000
143	A	143	LEU	0	-0.021	0.015	41.514	0.001	0.001	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.927	0.957	43.301	0.046	0.046	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.795	-0.900	44.411	-0.042	-0.042	0.000	0.000	0.000	0.000
146	A	146	SER	0	-0.058	-0.019	43.263	0.001	0.001	0.000	0.000	0.000	0.000
147	A	147	LEU	0	-0.006	-0.018	45.392	0.001	0.001	0.000	0.000	0.000	0.000
148	A	148	GLY	0	-0.078	-0.020	48.447	0.003	0.003	0.000	0.000	0.000	0.000

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