FMO DATABASE

FMODB ID: 89RYY

Calculation Name: 1NOG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NOG

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HIA7

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	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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1446837.379974
FMO2-HF: Nuclear repulsion	1388226.848317
FMO2-HF: Total energy	-58610.531657
FMO2-MP2: Total energy	-58783.164743

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:23:SER)

Summations of interaction energy for fragment #1(A:23:SER)

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.
2.059	-24.096	33.56	3.455	-10.862	-0.031

Interaction energy analysis for fragmet #1(A:23:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.056 / q_NPA : 0.026

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	25	VAL	0	0.085	0.015	2.426	8.084	-1.462	4.023	8.636	-3.113	-0.030
4	A	26	VAL	0	0.054	0.022	2.039	-0.147	-11.530	20.721	-4.428	-4.911	0.002
5	A	27	GLU	-1	-0.873	-0.950	1.865	-4.131	-9.505	8.793	-0.760	-2.659	-0.003
6	A	28	VAL	0	-0.025	-0.012	3.499	-0.592	-0.444	0.023	0.007	-0.179	0.000
7	A	29	GLN	0	-0.028	-0.009	5.716	-0.692	-0.692	0.000	0.000	0.000	0.000
8	A	30	GLY	0	0.041	0.030	6.202	-0.370	-0.370	0.000	0.000	0.000	0.000
9	A	31	THR	0	-0.019	-0.019	7.498	-0.211	-0.211	0.000	0.000	0.000	0.000
10	A	32	ILE	0	-0.050	-0.013	9.628	-0.087	-0.087	0.000	0.000	0.000	0.000
11	A	33	ASP	-1	-0.919	-0.954	10.961	0.056	0.056	0.000	0.000	0.000	0.000
12	A	34	GLU	-1	-0.803	-0.878	11.911	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	35	LEU	0	-0.035	-0.010	13.539	-0.027	-0.027	0.000	0.000	0.000	0.000
14	A	36	ASN	0	0.040	0.004	15.326	-0.039	-0.039	0.000	0.000	0.000	0.000
15	A	37	SER	0	-0.042	-0.030	16.665	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	38	PHE	0	0.004	-0.014	16.930	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	39	ILE	0	-0.025	-0.013	19.427	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	40	GLY	0	0.026	0.012	21.215	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	41	TYR	0	-0.041	-0.015	22.697	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	42	ALA	0	0.040	0.002	24.086	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	43	LEU	0	-0.063	-0.014	25.564	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	44	VAL	0	-0.049	-0.033	27.350	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	45	LEU	0	-0.019	-0.008	28.195	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	46	SER	0	-0.018	0.005	30.092	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	47	ARG	1	0.870	0.911	31.876	-0.022	-0.022	0.000	0.000	0.000	0.000
26	A	48	TRP	0	0.045	0.016	33.942	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	49	ASP	-1	-0.835	-0.924	33.865	0.028	0.028	0.000	0.000	0.000	0.000
28	A	50	ASP	-1	-0.840	-0.893	33.499	0.034	0.034	0.000	0.000	0.000	0.000
29	A	51	ILE	0	0.010	-0.001	29.346	0.003	0.003	0.000	0.000	0.000	0.000
30	A	52	ARG	1	0.921	0.958	29.210	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	53	ASN	0	0.016	0.002	29.032	0.004	0.004	0.000	0.000	0.000	0.000
32	A	54	ASP	-1	-0.803	-0.851	27.260	0.052	0.052	0.000	0.000	0.000	0.000
33	A	55	LEU	0	0.006	-0.001	24.517	0.007	0.007	0.000	0.000	0.000	0.000
34	A	56	PHE	0	0.054	0.033	24.089	0.008	0.008	0.000	0.000	0.000	0.000
35	A	57	ARG	1	0.913	0.969	24.601	-0.043	-0.043	0.000	0.000	0.000	0.000
36	A	58	ILE	0	0.033	0.020	20.232	0.007	0.007	0.000	0.000	0.000	0.000
37	A	59	GLN	0	-0.041	-0.016	20.116	0.008	0.008	0.000	0.000	0.000	0.000
38	A	60	ASN	0	-0.055	-0.038	19.765	0.012	0.012	0.000	0.000	0.000	0.000
39	A	61	ASP	-1	-0.793	-0.886	19.973	0.107	0.107	0.000	0.000	0.000	0.000
40	A	62	LEU	0	-0.049	-0.031	15.105	0.024	0.024	0.000	0.000	0.000	0.000
41	A	63	PHE	0	0.000	0.008	15.083	0.049	0.049	0.000	0.000	0.000	0.000
42	A	64	VAL	0	-0.011	0.006	15.964	0.022	0.022	0.000	0.000	0.000	0.000
43	A	65	LEU	0	-0.041	-0.022	12.173	0.018	0.018	0.000	0.000	0.000	0.000
44	A	66	GLY	0	0.045	0.017	11.348	0.061	0.061	0.000	0.000	0.000	0.000
45	A	67	GLU	-1	-0.750	-0.881	11.531	0.215	0.215	0.000	0.000	0.000	0.000
46	A	68	ASP	-1	-0.799	-0.871	13.699	0.185	0.185	0.000	0.000	0.000	0.000
47	A	69	VAL	0	-0.039	-0.029	7.667	0.013	0.013	0.000	0.000	0.000	0.000
48	A	70	SER	0	-0.073	-0.066	9.196	0.127	0.127	0.000	0.000	0.000	0.000
49	A	71	THR	0	-0.084	-0.051	10.213	-0.121	-0.121	0.000	0.000	0.000	0.000
50	A	72	GLY	0	0.001	0.003	11.848	-0.065	-0.065	0.000	0.000	0.000	0.000
51	A	73	GLY	0	0.004	0.004	12.950	-0.034	-0.034	0.000	0.000	0.000	0.000
52	A	74	LYS	1	0.874	0.934	15.979	0.008	0.008	0.000	0.000	0.000	0.000
53	A	75	GLY	0	0.001	0.013	17.002	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	76	ARG	1	0.886	0.945	18.689	-0.077	-0.077	0.000	0.000	0.000	0.000
55	A	77	THR	0	0.005	0.003	17.528	0.020	0.020	0.000	0.000	0.000	0.000
56	A	78	VAL	0	-0.020	-0.013	16.445	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	79	THR	0	0.031	0.006	19.194	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	80	ARG	1	0.875	0.939	22.793	-0.062	-0.062	0.000	0.000	0.000	0.000
59	A	81	GLU	-1	-0.812	-0.914	24.756	0.057	0.057	0.000	0.000	0.000	0.000
60	A	82	MET	0	-0.031	0.011	19.749	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	83	ILE	0	-0.051	-0.030	20.460	0.001	0.001	0.000	0.000	0.000	0.000
62	A	84	ASP	-1	-0.815	-0.930	23.769	0.055	0.055	0.000	0.000	0.000	0.000
63	A	85	TYR	0	-0.080	-0.055	26.488	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	86	LEU	0	0.006	0.001	21.850	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	87	GLU	-1	-0.876	-0.932	25.953	0.059	0.059	0.000	0.000	0.000	0.000
66	A	88	ALA	0	-0.007	-0.005	28.021	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	89	ARG	1	0.838	0.898	28.975	-0.046	-0.046	0.000	0.000	0.000	0.000
68	A	90	VAL	0	-0.021	0.004	26.821	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	91	LYS	1	0.909	0.948	30.082	-0.037	-0.037	0.000	0.000	0.000	0.000
70	A	92	GLU	-1	-0.898	-0.952	33.239	0.031	0.031	0.000	0.000	0.000	0.000
71	A	93	MET	0	0.079	0.043	29.287	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	94	LYS	1	0.914	0.952	30.038	-0.046	-0.046	0.000	0.000	0.000	0.000
73	A	95	ALA	0	-0.053	-0.010	34.889	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	96	GLU	-1	-0.812	-0.889	37.163	0.027	0.027	0.000	0.000	0.000	0.000
75	A	97	ILE	0	-0.061	-0.035	34.441	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	98	GLY	0	0.012	0.017	37.778	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	99	LYS	1	0.904	0.930	37.548	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	100	ILE	0	0.027	0.011	32.281	0.000	0.000	0.000	0.000	0.000	0.000
79	A	101	GLU	-1	-0.944	-0.963	35.196	0.026	0.026	0.000	0.000	0.000	0.000
80	A	102	LEU	0	-0.016	-0.020	30.993	0.001	0.001	0.000	0.000	0.000	0.000
81	A	103	PHE	0	-0.017	-0.009	30.195	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	104	VAL	0	0.057	0.037	30.743	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	105	VAL	0	-0.032	-0.019	30.330	0.002	0.002	0.000	0.000	0.000	0.000
84	A	106	PRO	0	-0.052	-0.020	26.973	0.000	0.000	0.000	0.000	0.000	0.000
85	A	107	GLY	0	0.044	0.003	29.463	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	108	GLY	0	0.004	0.014	31.363	0.001	0.001	0.000	0.000	0.000	0.000
87	A	109	SER	0	0.053	0.027	33.393	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	110	VAL	0	0.017	0.005	30.201	0.001	0.001	0.000	0.000	0.000	0.000
89	A	111	GLU	-1	-0.750	-0.872	29.819	0.025	0.025	0.000	0.000	0.000	0.000
90	A	112	SER	0	0.000	-0.019	29.262	0.003	0.003	0.000	0.000	0.000	0.000
91	A	113	ALA	0	-0.049	-0.021	28.212	0.003	0.003	0.000	0.000	0.000	0.000
92	A	114	SER	0	-0.007	-0.007	25.425	0.003	0.003	0.000	0.000	0.000	0.000
93	A	115	LEU	0	0.039	0.023	24.077	0.005	0.005	0.000	0.000	0.000	0.000
94	A	116	HIS	0	0.000	-0.001	23.877	0.008	0.008	0.000	0.000	0.000	0.000
95	A	117	MET	0	-0.043	-0.013	21.622	0.002	0.002	0.000	0.000	0.000	0.000
96	A	118	ALA	0	0.055	0.030	19.738	0.004	0.004	0.000	0.000	0.000	0.000
97	A	119	ARG	1	0.920	0.966	19.089	-0.047	-0.047	0.000	0.000	0.000	0.000
98	A	120	ALA	0	-0.051	-0.025	19.176	0.006	0.006	0.000	0.000	0.000	0.000
99	A	121	VAL	0	0.009	0.008	14.113	0.001	0.001	0.000	0.000	0.000	0.000
100	A	122	SER	0	0.064	0.004	14.506	0.013	0.013	0.000	0.000	0.000	0.000
101	A	123	ARG	1	0.946	0.972	15.209	-0.057	-0.057	0.000	0.000	0.000	0.000
102	A	124	ARG	1	0.766	0.871	11.311	-0.028	-0.028	0.000	0.000	0.000	0.000
103	A	125	LEU	0	0.067	0.026	9.865	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	126	GLU	-1	-0.824	-0.898	10.765	0.123	0.123	0.000	0.000	0.000	0.000
105	A	127	ARG	1	0.898	0.953	12.033	-0.051	-0.051	0.000	0.000	0.000	0.000
106	A	128	ARG	1	0.882	0.951	6.682	0.100	0.100	0.000	0.000	0.000	0.000
107	A	129	ILE	0	0.042	0.029	7.193	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	130	VAL	0	-0.016	-0.003	9.220	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	131	ALA	0	-0.053	-0.019	7.564	0.005	0.005	0.000	0.000	0.000	0.000
110	A	132	ALA	0	0.043	0.019	4.977	0.012	0.012	0.000	0.000	0.000	0.000
111	A	133	SER	0	-0.038	-0.031	6.486	0.024	0.024	0.000	0.000	0.000	0.000
112	A	134	LYS	1	0.913	0.960	9.759	-0.146	-0.146	0.000	0.000	0.000	0.000
113	A	135	LEU	0	-0.052	-0.024	5.584	0.021	0.021	0.000	0.000	0.000	0.000
114	A	136	THR	0	-0.022	-0.011	6.500	-0.084	-0.084	0.000	0.000	0.000	0.000
115	A	137	GLU	-1	-0.940	-0.955	9.320	0.103	0.103	0.000	0.000	0.000	0.000
116	A	138	ILE	0	-0.025	-0.020	7.638	0.052	0.052	0.000	0.000	0.000	0.000
117	A	139	ASN	0	0.038	0.021	12.078	-0.047	-0.047	0.000	0.000	0.000	0.000
118	A	140	LYS	1	0.962	0.968	14.910	-0.067	-0.067	0.000	0.000	0.000	0.000
119	A	141	ASN	0	-0.012	-0.027	17.202	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	142	VAL	0	0.066	0.050	11.815	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	143	LEU	0	0.021	0.010	13.537	0.000	0.000	0.000	0.000	0.000	0.000
122	A	144	ILE	0	-0.041	-0.018	15.129	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	145	TYR	0	-0.005	-0.034	17.351	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	146	ALA	0	0.031	0.013	14.570	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	147	ASN	0	-0.072	-0.030	16.665	-0.019	-0.019	0.000	0.000	0.000	0.000
126	A	148	ARG	1	0.818	0.896	19.115	-0.087	-0.087	0.000	0.000	0.000	0.000
127	A	149	LEU	0	0.032	0.030	17.437	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	150	SER	0	0.022	-0.013	18.377	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	151	SER	0	-0.102	-0.038	20.884	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	152	ILE	0	0.050	0.014	23.477	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	153	LEU	0	0.034	0.030	20.586	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	154	PHE	0	-0.032	-0.025	24.804	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	155	MET	0	-0.044	-0.014	26.683	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	156	HIS	0	0.040	-0.001	26.456	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	157	ALA	0	-0.002	0.014	27.948	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	158	LEU	0	0.013	0.021	29.898	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	159	ILE	0	-0.021	-0.005	32.660	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	160	SER	0	-0.030	-0.027	31.725	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	161	ASN	0	0.002	-0.008	33.612	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	162	LYS	1	0.908	0.974	36.083	-0.026	-0.026	0.000	0.000	0.000	0.000
141	A	163	ARG	1	0.714	0.830	36.025	-0.031	-0.031	0.000	0.000	0.000	0.000
142	A	164	LEU	0	-0.048	-0.010	35.962	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	165	ASN	0	-0.061	-0.024	39.846	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	166	ILE	0	-0.031	-0.007	37.199	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	167	PRO	0	-0.025	-0.018	38.587	0.001	0.001	0.000	0.000	0.000	0.000
146	A	168	GLU	-1	-0.818	-0.906	33.985	0.030	0.030	0.000	0.000	0.000	0.000
147	A	169	LYS	1	0.927	0.964	35.776	-0.022	-0.022	0.000	0.000	0.000	0.000
148	A	170	ILE	0	0.010	0.012	35.130	0.002	0.002	0.000	0.000	0.000	0.000
149	A	171	TRP	0	-0.038	-0.016	32.837	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:23:SER)