FMO DATABASE

FMODB ID: 2N9VR

Calculation Name: 1NG6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NG6

Chain ID: A

ChEMBL ID:

UniProt ID: P54464

Base Structure: X-ray

Registration Date: 2023-09-23

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	-1333767.566501
FMO2-HF: Nuclear repulsion	1274232.183385
FMO2-HF: Total energy	-59535.383115
FMO2-MP2: Total energy	-59706.348476

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.
-19.735	-11.52	10.082	-6.828	-11.471	-0.042

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 : -0.026 / q_NPA : 0.001

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	LEU	0	0.046	0.023	2.989	-2.884	0.170	0.173	-1.748	-1.480	-0.001
4	A	4	LEU	0	0.049	0.021	5.717	0.969	0.969	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.828	-0.865	2.294	-8.184	-5.174	4.469	-3.245	-4.234	-0.027
6	A	6	ARG	1	0.886	0.947	2.318	2.678	4.771	1.375	-1.087	-2.381	-0.003
7	A	7	LEU	0	0.022	0.014	3.131	1.279	0.924	0.051	0.671	-0.368	0.000
8	A	8	ASN	0	-0.028	-0.027	6.603	0.228	0.228	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.019	-0.008	2.663	-4.980	-4.567	4.014	-1.419	-3.008	-0.011
10	A	10	ASP	-1	-0.736	-0.856	5.988	-0.823	-0.823	0.000	0.000	0.000	0.000
11	A	11	MET	0	-0.049	-0.013	7.580	-0.114	-0.114	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.974	0.982	9.365	-1.387	-1.387	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.017	0.009	7.986	-0.084	-0.084	0.000	0.000	0.000	0.000
14	A	14	TYR	0	0.002	-0.031	8.913	-0.063	-0.063	0.000	0.000	0.000	0.000
15	A	15	MET	0	-0.031	-0.017	13.039	-0.039	-0.039	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.885	0.954	12.504	-0.662	-0.662	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.007	-0.016	13.240	0.024	0.024	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.953	0.980	16.025	-0.278	-0.278	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.777	-0.848	14.986	0.006	0.006	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.880	0.917	16.408	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.827	-0.895	18.454	-0.047	-0.047	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.890	0.930	13.338	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.001	-0.002	13.555	-0.037	-0.037	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.062	-0.040	14.599	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.050	0.031	13.985	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.012	0.017	9.498	-0.053	-0.053	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.898	0.933	12.188	-0.029	-0.029	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.034	-0.009	14.173	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.063	0.035	12.100	-0.027	-0.027	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.889	0.935	10.589	-0.130	-0.130	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.015	-0.002	12.568	-0.037	-0.037	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.033	-0.045	16.072	0.007	0.007	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.018	-0.003	10.529	0.012	0.012	0.000	0.000	0.000	0.000
34	A	34	GLN	0	0.005	-0.012	12.952	0.038	0.038	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.002	0.001	15.218	0.051	0.051	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.770	-0.864	17.268	-0.435	-0.435	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.020	0.017	15.403	0.019	0.019	0.000	0.000	0.000	0.000
38	A	38	ILE	0	0.046	0.022	17.561	0.053	0.053	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.818	0.909	20.263	0.445	0.445	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.045	-0.033	19.431	0.040	0.040	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.784	0.898	22.078	0.281	0.281	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.845	0.918	17.311	0.716	0.716	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.889	-0.942	14.656	-0.440	-0.440	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.056	-0.030	11.450	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.032	-0.014	12.595	0.138	0.138	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.010	-0.022	12.251	-0.172	-0.172	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.861	-0.943	7.652	-2.671	-2.671	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.769	-0.869	11.587	-0.987	-0.987	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.794	-0.843	15.248	-0.676	-0.676	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.854	-0.946	9.127	-2.367	-2.367	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.020	0.008	12.820	0.129	0.129	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.055	-0.018	14.868	0.163	0.163	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.030	-0.023	15.335	0.097	0.097	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.012	0.005	10.890	0.097	0.097	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.011	-0.014	15.410	0.097	0.097	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.809	0.905	18.638	0.563	0.563	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.798	-0.866	16.573	-0.349	-0.349	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.024	0.002	17.364	0.061	0.061	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.797	0.890	19.473	0.349	0.349	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.007	-0.015	21.070	0.018	0.018	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.795	0.886	18.555	0.368	0.368	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.870	0.921	21.145	0.438	0.438	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.828	-0.892	25.093	-0.259	-0.259	0.000	0.000	0.000	0.000
64	A	64	SER	0	0.001	-0.024	26.078	0.024	0.024	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.030	0.000	25.372	0.021	0.021	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.010	0.002	28.183	0.012	0.012	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.948	-0.970	31.078	-0.152	-0.152	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.017	-0.031	27.594	0.015	0.015	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.016	0.003	32.341	0.012	0.012	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.027	-0.001	34.024	0.009	0.009	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.038	-0.016	35.343	0.008	0.008	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.045	-0.024	36.954	0.010	0.010	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.818	0.887	33.303	0.079	0.079	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.073	0.015	32.481	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.759	-0.841	31.056	-0.078	-0.078	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.055	-0.023	28.746	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.012	0.014	27.687	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.805	-0.888	26.976	-0.110	-0.110	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.836	0.920	23.743	0.138	0.138	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.030	-0.023	23.099	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.003	-0.016	22.418	-0.024	-0.024	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.859	0.924	20.954	0.078	0.078	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.877	-0.933	18.479	-0.228	-0.228	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.016	-0.004	17.616	-0.055	-0.055	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.834	-0.908	17.622	-0.261	-0.261	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.089	-0.032	13.373	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.003	-0.012	13.241	-0.079	-0.079	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.783	-0.905	13.629	-0.546	-0.546	0.000	0.000	0.000	0.000
89	A	89	VAL	0	-0.022	0.012	10.305	-0.068	-0.068	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.141	-0.104	7.191	-0.164	-0.164	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.026	0.001	10.416	-0.218	-0.218	0.000	0.000	0.000	0.000
92	A	92	PRO	0	-0.033	-0.005	13.199	0.017	0.017	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.912	-0.965	15.266	-0.387	-0.387	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.040	-0.032	17.773	0.039	0.039	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.032	-0.006	20.707	0.035	0.035	0.000	0.000	0.000	0.000
96	A	96	SER	0	0.003	-0.033	24.217	0.011	0.011	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.766	-0.900	27.397	-0.240	-0.240	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.915	-0.953	29.941	-0.190	-0.190	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.783	-0.842	26.647	-0.306	-0.306	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.008	0.000	25.851	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.846	0.890	28.575	0.211	0.211	0.000	0.000	0.000	0.000
102	A	102	THR	0	-0.022	-0.007	30.999	0.012	0.012	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.021	0.006	25.108	0.005	0.005	0.000	0.000	0.000	0.000
104	A	104	VAL	0	-0.020	0.003	29.278	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	ASN	0	0.012	0.007	31.254	0.006	0.006	0.000	0.000	0.000	0.000
106	A	106	GLH	0	-0.025	-0.040	29.508	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	THR	0	0.000	-0.013	28.531	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.017	-0.012	31.119	0.003	0.003	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.003	0.004	34.512	0.009	0.009	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.814	-0.853	29.239	-0.289	-0.289	0.000	0.000	0.000	0.000
111	A	111	VAL	0	-0.025	-0.010	31.327	0.005	0.005	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.026	0.018	34.369	0.006	0.006	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.089	-0.037	35.896	0.003	0.003	0.000	0.000	0.000	0.000
114	A	114	SER	0	-0.017	-0.011	37.855	0.007	0.007	0.000	0.000	0.000	0.000
115	A	115	SER	0	-0.016	0.004	39.777	0.005	0.005	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.889	0.914	38.087	0.177	0.177	0.000	0.000	0.000	0.000
117	A	117	ALA	0	0.012	0.017	37.862	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.747	-0.867	36.232	-0.196	-0.196	0.000	0.000	0.000	0.000
119	A	119	MET	0	0.002	0.010	32.753	-0.017	-0.017	0.000	0.000	0.000	0.000
120	A	120	GLY	0	0.017	0.006	31.081	-0.018	-0.018	0.000	0.000	0.000	0.000
121	A	121	LYS	1	0.822	0.921	30.124	0.185	0.185	0.000	0.000	0.000	0.000
122	A	122	VAL	0	0.024	0.007	30.419	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	123	MET	0	-0.008	-0.012	26.722	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	124	GLY	0	0.000	0.000	25.881	-0.034	-0.034	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.011	0.009	25.095	-0.030	-0.030	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.014	0.000	25.525	-0.018	-0.018	0.000	0.000	0.000	0.000
127	A	127	MET	0	0.025	0.013	21.350	-0.021	-0.021	0.000	0.000	0.000	0.000
128	A	128	PRO	0	-0.020	-0.015	19.566	-0.063	-0.063	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.786	0.877	19.488	0.295	0.295	0.000	0.000	0.000	0.000
130	A	130	VAL	0	0.002	-0.007	21.456	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.834	0.912	15.298	0.974	0.974	0.000	0.000	0.000	0.000
132	A	132	GLY	0	0.011	0.004	16.782	-0.068	-0.068	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.921	0.966	17.732	0.612	0.612	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.031	0.016	19.906	0.064	0.064	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.765	-0.866	21.913	-0.434	-0.434	0.000	0.000	0.000	0.000
136	A	136	GLY	0	0.032	0.022	23.360	0.018	0.018	0.000	0.000	0.000	0.000
137	A	137	SER	0	-0.028	-0.048	24.764	0.025	0.025	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.040	-0.009	26.757	0.027	0.027	0.000	0.000	0.000	0.000
139	A	139	ILE	0	0.035	0.016	23.377	0.025	0.025	0.000	0.000	0.000	0.000
140	A	140	ASN	0	-0.027	-0.028	27.247	0.033	0.033	0.000	0.000	0.000	0.000
141	A	141	LYS	1	0.899	0.960	30.248	0.263	0.263	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.039	-0.006	30.081	0.022	0.022	0.000	0.000	0.000	0.000
143	A	143	VAL	0	0.039	0.013	29.849	0.015	0.015	0.000	0.000	0.000	0.000
144	A	144	SER	0	0.014	-0.004	32.947	0.019	0.019	0.000	0.000	0.000	0.000
145	A	145	SER	0	-0.065	-0.051	35.650	0.017	0.017	0.000	0.000	0.000	0.000
146	A	146	GLN	0	-0.063	-0.020	36.002	0.018	0.018	0.000	0.000	0.000	0.000
147	A	147	LEU	0	-0.009	0.012	34.927	0.003	0.003	0.000	0.000	0.000	0.000
148	A	148	SER	0	-0.019	-0.024	39.109	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:1:MET)