FMO DATABASE

FMODB ID: Z63NN

Calculation Name: 1NYE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYE

Chain ID: A

ChEMBL ID:

UniProt ID: P0C0L2

Base Structure: X-ray

Registration Date: 2023-09-20

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1074902.32178
FMO2-HF: Nuclear repulsion	1021641.84992
FMO2-HF: Total energy	-53260.47186
FMO2-MP2: Total energy	-53414.780515

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:21:MET)

Summations of interaction energy for fragment #1(A:21: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.
-0.969	1.067	-0.022	-1.077	-0.937	0.01

Interaction energy analysis for fragmet #1(A:21:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.039

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	23	ILE	0	0.027	0.001	3.811	0.876	2.912	-0.022	-1.077	-0.937	0.010
4	A	24	HIS	0	-0.003	0.001	5.902	-0.521	-0.521	0.000	0.000	0.000	0.000
5	A	25	LYS	1	0.940	0.948	8.459	-0.311	-0.311	0.000	0.000	0.000	0.000
6	A	26	LYS	1	0.912	0.953	11.469	-1.229	-1.229	0.000	0.000	0.000	0.000
7	A	27	GLY	0	0.036	0.024	14.704	-0.047	-0.047	0.000	0.000	0.000	0.000
8	A	28	GLN	0	-0.051	-0.041	18.429	0.009	0.009	0.000	0.000	0.000	0.000
9	A	29	ALA	0	0.019	0.010	21.250	-0.033	-0.033	0.000	0.000	0.000	0.000
10	A	30	HIS	0	-0.068	-0.030	24.978	0.030	0.030	0.000	0.000	0.000	0.000
11	A	31	TRP	0	-0.053	-0.019	28.102	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	32	GLU	-1	-0.875	-0.906	31.383	0.170	0.170	0.000	0.000	0.000	0.000
13	A	33	GLY	0	-0.001	-0.015	34.672	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	34	ASP	-1	-0.898	-0.962	36.836	0.084	0.084	0.000	0.000	0.000	0.000
15	A	35	ILE	0	0.041	0.048	36.678	0.003	0.003	0.000	0.000	0.000	0.000
16	A	36	LYS	1	0.998	0.995	38.200	-0.058	-0.058	0.000	0.000	0.000	0.000
17	A	37	ARG	1	0.888	0.933	40.967	-0.075	-0.075	0.000	0.000	0.000	0.000
18	A	38	GLY	0	0.001	-0.006	37.396	0.001	0.001	0.000	0.000	0.000	0.000
19	A	39	LYS	1	0.930	0.971	35.657	-0.100	-0.100	0.000	0.000	0.000	0.000
20	A	40	GLY	0	0.079	0.042	31.683	0.008	0.008	0.000	0.000	0.000	0.000
21	A	41	THR	0	-0.049	-0.027	28.492	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	42	VAL	0	0.009	0.009	25.036	0.015	0.015	0.000	0.000	0.000	0.000
23	A	43	SER	0	-0.021	-0.062	22.201	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	44	THR	0	-0.054	-0.010	18.263	0.000	0.000	0.000	0.000	0.000	0.000
25	A	45	GLU	-1	-0.854	-0.911	12.385	0.770	0.770	0.000	0.000	0.000	0.000
26	A	46	SER	0	-0.029	-0.022	16.478	0.021	0.021	0.000	0.000	0.000	0.000
27	A	47	GLY	0	0.041	0.020	17.256	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	48	VAL	0	-0.047	-0.029	20.646	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	49	LEU	0	0.009	0.021	22.333	-0.022	-0.022	0.000	0.000	0.000	0.000
30	A	50	ASN	0	0.015	0.002	22.999	0.036	0.036	0.000	0.000	0.000	0.000
31	A	51	GLN	0	0.047	0.025	24.935	0.023	0.023	0.000	0.000	0.000	0.000
32	A	52	GLN	0	0.021	0.034	27.604	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	53	PRO	0	0.013	0.007	29.505	0.008	0.008	0.000	0.000	0.000	0.000
34	A	54	TYR	0	-0.048	-0.022	28.711	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	55	GLY	0	0.074	0.021	32.684	0.008	0.008	0.000	0.000	0.000	0.000
36	A	56	PHE	0	-0.006	-0.013	35.084	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	57	ASN	0	0.063	0.032	37.207	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	58	THR	0	0.008	-0.001	34.000	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	59	ARG	1	0.720	0.852	30.344	-0.060	-0.060	0.000	0.000	0.000	0.000
40	A	60	PHE	0	-0.063	-0.052	35.242	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	61	GLU	-1	-0.985	-0.971	38.509	0.045	0.045	0.000	0.000	0.000	0.000
42	A	62	GLY	0	0.003	0.002	39.917	0.000	0.000	0.000	0.000	0.000	0.000
43	A	63	GLU	-1	-0.928	-0.949	39.703	0.054	0.054	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.945	0.964	36.446	-0.045	-0.045	0.000	0.000	0.000	0.000
45	A	65	GLY	0	0.007	-0.006	34.448	0.005	0.005	0.000	0.000	0.000	0.000
46	A	66	THR	0	0.031	0.031	27.978	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	67	ASN	0	-0.016	-0.005	29.808	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	68	PRO	0	0.008	-0.012	27.010	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	69	GLU	-1	-0.695	-0.827	26.935	0.040	0.040	0.000	0.000	0.000	0.000
50	A	70	GLU	-1	-0.833	-0.926	28.297	0.043	0.043	0.000	0.000	0.000	0.000
51	A	71	LEU	0	-0.020	-0.008	24.049	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	72	ILE	0	-0.035	-0.004	23.673	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	73	GLY	0	0.049	0.011	24.359	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	74	ALA	0	-0.023	-0.006	24.557	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	75	ALA	0	-0.012	-0.011	20.119	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	76	HIS	0	0.002	-0.028	21.086	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	77	ALA	0	0.045	0.031	23.071	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	78	ALA	0	-0.011	0.005	20.893	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	79	CYS	0	-0.075	-0.006	17.617	-0.038	-0.038	0.000	0.000	0.000	0.000
60	A	80	PHE	0	0.060	0.022	19.765	-0.038	-0.038	0.000	0.000	0.000	0.000
61	A	81	SER	0	0.025	0.002	22.650	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	82	MET	0	-0.050	-0.018	16.245	-0.032	-0.032	0.000	0.000	0.000	0.000
63	A	83	ALA	0	-0.006	-0.012	19.670	-0.027	-0.027	0.000	0.000	0.000	0.000
64	A	84	LEU	0	0.008	0.004	20.537	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	85	SER	0	-0.025	-0.011	21.897	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	86	LEU	0	0.002	0.000	17.545	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	87	MET	0	0.000	-0.001	20.958	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	88	LEU	0	-0.033	-0.007	23.515	0.013	0.013	0.000	0.000	0.000	0.000
69	A	89	GLY	0	0.039	0.032	23.201	0.012	0.012	0.000	0.000	0.000	0.000
70	A	90	GLU	-1	-0.989	-1.005	19.819	-0.455	-0.455	0.000	0.000	0.000	0.000
71	A	91	ALA	0	-0.031	-0.012	23.871	0.006	0.006	0.000	0.000	0.000	0.000
72	A	92	GLY	0	-0.052	-0.012	26.786	0.015	0.015	0.000	0.000	0.000	0.000
73	A	93	PHE	0	-0.045	-0.038	27.691	0.022	0.022	0.000	0.000	0.000	0.000
74	A	94	THR	0	-0.005	-0.021	26.447	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	95	PRO	0	-0.029	0.006	26.227	0.015	0.015	0.000	0.000	0.000	0.000
76	A	96	THR	0	-0.024	-0.024	28.670	0.001	0.001	0.000	0.000	0.000	0.000
77	A	97	SER	0	0.000	-0.008	30.336	0.010	0.010	0.000	0.000	0.000	0.000
78	A	98	ILE	0	-0.036	-0.018	25.970	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	99	ASP	-1	-0.883	-0.921	28.891	-0.057	-0.057	0.000	0.000	0.000	0.000
80	A	100	THR	0	-0.045	-0.025	27.360	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	101	THR	0	-0.015	-0.024	29.436	0.012	0.012	0.000	0.000	0.000	0.000
82	A	102	ALA	0	-0.014	-0.002	27.702	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	103	ASP	-1	-0.939	-0.954	29.812	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	104	VAL	0	-0.024	-0.017	28.652	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	105	SER	0	-0.005	-0.003	31.717	0.006	0.006	0.000	0.000	0.000	0.000
86	A	106	LEU	0	-0.011	-0.002	32.352	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	107	ASP	-1	-0.845	-0.941	34.773	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	108	LYS	1	0.882	0.946	37.188	0.007	0.007	0.000	0.000	0.000	0.000
89	A	109	VAL	0	-0.026	-0.019	37.198	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	110	ASP	-1	-0.891	-0.947	38.469	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	111	ALA	0	-0.063	-0.031	39.582	0.002	0.002	0.000	0.000	0.000	0.000
92	A	112	GLY	0	-0.015	-0.014	37.324	0.007	0.007	0.000	0.000	0.000	0.000
93	A	113	PHE	0	0.013	0.002	35.278	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	114	ALA	0	-0.007	0.000	32.352	0.004	0.004	0.000	0.000	0.000	0.000
95	A	115	ILE	0	-0.004	0.002	28.591	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	116	THR	0	-0.040	-0.011	30.595	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	117	LYS	1	0.983	0.987	31.922	0.047	0.047	0.000	0.000	0.000	0.000
98	A	118	ILE	0	0.000	0.018	26.712	0.010	0.010	0.000	0.000	0.000	0.000
99	A	119	ALA	0	-0.005	0.001	30.670	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	120	LEU	0	-0.018	-0.006	26.234	0.006	0.006	0.000	0.000	0.000	0.000
101	A	121	LYS	1	0.991	0.995	30.781	0.052	0.052	0.000	0.000	0.000	0.000
102	A	122	SER	0	-0.028	-0.028	29.497	0.004	0.004	0.000	0.000	0.000	0.000
103	A	123	GLU	-1	-0.945	-0.959	32.115	-0.057	-0.057	0.000	0.000	0.000	0.000
104	A	124	VAL	0	-0.004	-0.006	30.427	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	125	ALA	0	-0.042	-0.017	32.440	0.005	0.005	0.000	0.000	0.000	0.000
106	A	126	VAL	0	0.052	0.017	30.934	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	127	PRO	0	-0.029	-0.019	32.496	0.004	0.004	0.000	0.000	0.000	0.000
108	A	128	GLY	0	0.013	0.011	35.391	0.007	0.007	0.000	0.000	0.000	0.000
109	A	129	ILE	0	-0.041	0.005	32.323	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	130	ASP	-1	-0.811	-0.852	35.689	-0.134	-0.134	0.000	0.000	0.000	0.000
111	A	131	ALA	0	0.047	-0.008	36.313	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	132	SER	0	-0.049	-0.010	36.630	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	133	THR	0	0.010	-0.060	33.179	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	134	PHE	0	0.050	0.017	30.742	-0.013	-0.013	0.000	0.000	0.000	0.000
115	A	135	ASP	-1	-0.846	-0.859	31.514	-0.141	-0.141	0.000	0.000	0.000	0.000
116	A	136	GLY	0	0.056	0.005	31.726	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	137	ILE	0	-0.048	-0.021	26.587	-0.017	-0.017	0.000	0.000	0.000	0.000
118	A	138	ILE	0	-0.029	0.011	27.140	-0.015	-0.015	0.000	0.000	0.000	0.000
119	A	139	GLN	0	0.011	0.008	27.574	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	140	LYS	1	0.936	0.976	24.389	0.300	0.300	0.000	0.000	0.000	0.000
121	A	141	ALA	0	0.000	0.010	23.010	-0.021	-0.021	0.000	0.000	0.000	0.000
122	A	142	LYS	1	0.872	0.922	23.289	0.140	0.140	0.000	0.000	0.000	0.000
123	A	143	ALA	0	-0.035	-0.028	24.789	0.006	0.006	0.000	0.000	0.000	0.000
124	A	144	GLY	0	0.020	0.026	21.524	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	145	CYS	0	-0.026	0.007	18.962	-0.040	-0.040	0.000	0.000	0.000	0.000
126	A	146	PRO	0	0.045	-0.011	14.882	0.025	0.025	0.000	0.000	0.000	0.000
127	A	147	VAL	0	0.026	-0.002	17.241	0.023	0.023	0.000	0.000	0.000	0.000
128	A	148	SER	0	0.024	-0.010	19.585	0.034	0.034	0.000	0.000	0.000	0.000
129	A	149	GLN	0	-0.083	-0.026	18.926	0.028	0.028	0.000	0.000	0.000	0.000
130	A	150	VAL	0	-0.063	-0.016	17.266	0.007	0.007	0.000	0.000	0.000	0.000
131	A	151	LEU	0	-0.036	-0.008	20.210	0.035	0.035	0.000	0.000	0.000	0.000
132	A	152	LYS	1	0.951	0.978	23.783	0.037	0.037	0.000	0.000	0.000	0.000
133	A	153	ALA	0	-0.026	-0.002	26.464	0.008	0.008	0.000	0.000	0.000	0.000
134	A	154	GLU	-1	-0.914	-0.953	28.925	-0.085	-0.085	0.000	0.000	0.000	0.000
135	A	155	ILE	0	0.008	-0.006	25.957	0.004	0.004	0.000	0.000	0.000	0.000
136	A	156	THR	0	0.009	0.014	30.224	-0.008	-0.008	0.000	0.000	0.000	0.000
137	A	157	LEU	0	-0.035	-0.030	30.022	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	158	ASP	-1	-0.908	-0.925	32.548	-0.070	-0.070	0.000	0.000	0.000	0.000
139	A	159	TYR	0	-0.090	-0.140	33.068	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	160	GLN	0	-0.007	0.008	35.079	0.004	0.004	0.000	0.000	0.000	0.000
141	A	161	LEU	0	-0.009	0.004	34.396	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	162	LYS	1	0.902	0.950	36.047	0.080	0.080	0.000	0.000	0.000	0.000
143	A	163	SER	0	0.045	0.023	37.237	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:21:MET)