FMO DATABASE

FMODB ID: QYQNY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1074337.06261
FMO2-HF: Nuclear repulsion	1021074.66258
FMO2-HF: Total energy	-53262.40003
FMO2-MP2: Total energy	-53416.559794

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.
-0.453	1.107	-0.011	-0.765	-0.784	0.001

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 : -0.010 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	23	ILE	0	-0.012	0.004	3.847	0.588	2.148	-0.011	-0.765	-0.784	0.001
4	A	24	HIS	0	-0.008	0.000	5.560	-0.256	-0.256	0.000	0.000	0.000	0.000
5	A	25	LYS	1	0.906	0.947	8.444	-0.201	-0.201	0.000	0.000	0.000	0.000
6	A	26	LYS	1	0.929	0.976	10.532	-0.603	-0.603	0.000	0.000	0.000	0.000
7	A	27	GLY	0	0.054	0.033	14.751	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	28	GLN	0	-0.063	-0.044	18.391	0.012	0.012	0.000	0.000	0.000	0.000
9	A	29	ALA	0	0.015	0.003	21.020	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	30	HIS	0	-0.027	-0.010	24.760	0.014	0.014	0.000	0.000	0.000	0.000
11	A	31	TRP	0	-0.065	-0.040	27.721	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	32	GLU	-1	-0.879	-0.906	31.290	0.083	0.083	0.000	0.000	0.000	0.000
13	A	33	GLY	0	0.007	-0.006	34.614	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	34	ASP	-1	-0.821	-0.918	36.859	0.036	0.036	0.000	0.000	0.000	0.000
15	A	35	ILE	0	0.014	0.016	35.613	0.001	0.001	0.000	0.000	0.000	0.000
16	A	36	LYS	1	0.818	0.897	37.845	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	37	ARG	1	0.915	0.942	40.623	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	38	GLY	0	-0.005	0.010	37.617	0.001	0.001	0.000	0.000	0.000	0.000
19	A	39	LYS	1	0.843	0.915	35.548	-0.046	-0.046	0.000	0.000	0.000	0.000
20	A	40	GLY	0	0.092	0.050	31.373	0.004	0.004	0.000	0.000	0.000	0.000
21	A	41	THR	0	-0.057	-0.017	28.542	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	42	VAL	0	0.017	0.009	24.940	0.006	0.006	0.000	0.000	0.000	0.000
23	A	43	SER	0	-0.004	-0.021	21.903	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	44	THR	0	-0.058	-0.044	17.843	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	45	GLU	-1	-0.822	-0.916	12.287	0.338	0.338	0.000	0.000	0.000	0.000
26	A	46	SER	0	-0.016	-0.010	16.537	0.008	0.008	0.000	0.000	0.000	0.000
27	A	47	GLY	0	0.005	0.005	17.706	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	48	VAL	0	-0.034	-0.022	20.844	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	49	LEU	0	0.003	0.017	22.298	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	50	ASN	0	0.021	0.010	22.895	0.011	0.011	0.000	0.000	0.000	0.000
31	A	51	GLN	0	0.023	0.005	24.639	0.009	0.009	0.000	0.000	0.000	0.000
32	A	52	GLN	0	0.016	0.026	27.227	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	53	PRO	0	0.033	0.014	29.268	0.002	0.002	0.000	0.000	0.000	0.000
34	A	54	TYR	0	-0.052	-0.008	28.894	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	55	GLY	0	0.066	0.019	32.979	0.004	0.004	0.000	0.000	0.000	0.000
36	A	56	PHE	0	0.002	0.002	35.470	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	57	ASN	0	0.002	-0.020	37.396	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	58	THR	0	-0.036	-0.029	33.864	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	59	ARG	1	0.775	0.897	30.156	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	60	PHE	0	-0.025	-0.025	35.129	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	61	GLU	-1	-0.837	-0.902	38.510	0.018	0.018	0.000	0.000	0.000	0.000
42	A	62	GLY	0	0.023	0.023	39.685	0.000	0.000	0.000	0.000	0.000	0.000
43	A	63	GLU	-1	-0.870	-0.912	39.651	0.024	0.024	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.962	0.985	35.315	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	65	GLY	0	-0.043	-0.041	34.910	0.002	0.002	0.000	0.000	0.000	0.000
46	A	66	THR	0	0.047	0.011	28.417	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	67	ASN	0	-0.006	0.007	30.319	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	68	PRO	0	0.017	-0.004	26.750	0.000	0.000	0.000	0.000	0.000	0.000
49	A	69	GLU	-1	-0.735	-0.866	26.877	0.004	0.004	0.000	0.000	0.000	0.000
50	A	70	GLU	-1	-0.892	-0.943	28.714	0.015	0.015	0.000	0.000	0.000	0.000
51	A	71	LEU	0	-0.031	-0.017	23.594	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	72	ILE	0	-0.022	-0.008	24.042	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	73	GLY	0	0.067	0.025	24.998	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	74	ALA	0	-0.022	-0.008	25.400	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	75	ALA	0	-0.014	-0.010	20.790	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	76	HIS	0	0.008	-0.020	21.812	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	77	ALA	0	0.042	0.025	23.791	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	78	ALA	0	0.013	0.027	21.779	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	79	CYS	0	-0.064	-0.013	17.868	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	80	PHE	0	0.059	0.014	20.458	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	81	SER	0	0.019	-0.008	23.305	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	82	MET	0	-0.047	-0.022	16.915	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	83	ALA	0	0.006	-0.001	19.824	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	84	LEU	0	0.026	0.010	20.696	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	85	SER	0	0.016	0.002	22.203	0.003	0.003	0.000	0.000	0.000	0.000
66	A	86	LEU	0	-0.064	-0.017	17.551	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	87	MET	0	-0.017	0.008	20.813	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	88	LEU	0	0.004	-0.008	23.351	0.003	0.003	0.000	0.000	0.000	0.000
69	A	89	GLY	0	0.030	0.026	22.784	0.005	0.005	0.000	0.000	0.000	0.000
70	A	90	GLU	-1	-0.909	-0.977	20.187	-0.242	-0.242	0.000	0.000	0.000	0.000
71	A	91	ALA	0	-0.051	-0.019	23.609	0.002	0.002	0.000	0.000	0.000	0.000
72	A	92	GLY	0	-0.016	0.011	26.391	0.008	0.008	0.000	0.000	0.000	0.000
73	A	93	PHE	0	-0.034	-0.026	27.542	0.011	0.011	0.000	0.000	0.000	0.000
74	A	94	THR	0	-0.018	-0.030	26.773	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	95	PRO	0	-0.020	0.006	26.708	0.005	0.005	0.000	0.000	0.000	0.000
76	A	96	THR	0	-0.027	-0.031	29.353	0.001	0.001	0.000	0.000	0.000	0.000
77	A	97	SER	0	-0.043	-0.044	30.758	0.006	0.006	0.000	0.000	0.000	0.000
78	A	98	ILE	0	-0.027	-0.018	26.181	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	99	ASP	-1	-0.845	-0.872	29.052	-0.031	-0.031	0.000	0.000	0.000	0.000
80	A	100	THR	0	-0.021	-0.033	27.469	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	101	THR	0	-0.064	-0.042	30.347	0.008	0.008	0.000	0.000	0.000	0.000
82	A	102	ALA	0	-0.016	0.006	28.426	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	103	ASP	-1	-0.880	-0.931	30.509	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	104	VAL	0	-0.033	-0.021	29.125	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	105	SER	0	0.024	0.016	32.180	0.004	0.004	0.000	0.000	0.000	0.000
86	A	106	LEU	0	-0.044	-0.012	32.138	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	107	ASP	-1	-0.810	-0.889	34.331	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	108	LYS	1	0.795	0.869	36.964	0.016	0.016	0.000	0.000	0.000	0.000
89	A	109	VAL	0	-0.018	-0.016	37.021	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	110	ASP	-1	-0.893	-0.951	38.660	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	111	ALA	0	-0.038	-0.018	39.243	0.002	0.002	0.000	0.000	0.000	0.000
92	A	112	GLY	0	-0.026	-0.011	36.996	0.004	0.004	0.000	0.000	0.000	0.000
93	A	113	PHE	0	0.004	0.000	35.277	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	114	ALA	0	-0.014	-0.005	32.171	0.001	0.001	0.000	0.000	0.000	0.000
95	A	115	ILE	0	0.010	0.009	28.439	0.000	0.000	0.000	0.000	0.000	0.000
96	A	116	THR	0	-0.025	-0.002	30.978	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	117	LYS	1	0.821	0.893	32.558	0.041	0.041	0.000	0.000	0.000	0.000
98	A	118	ILE	0	-0.010	-0.003	27.341	0.005	0.005	0.000	0.000	0.000	0.000
99	A	119	ALA	0	-0.002	0.005	31.373	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	120	LEU	0	-0.024	-0.004	27.212	0.005	0.005	0.000	0.000	0.000	0.000
101	A	121	LYS	1	0.898	0.948	31.369	0.032	0.032	0.000	0.000	0.000	0.000
102	A	122	SER	0	-0.023	-0.029	30.824	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	123	GLU	-1	-0.856	-0.921	32.696	-0.032	-0.032	0.000	0.000	0.000	0.000
104	A	124	VAL	0	0.011	0.010	30.691	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	125	ALA	0	-0.003	0.012	32.777	0.002	0.002	0.000	0.000	0.000	0.000
106	A	126	VAL	0	0.065	0.013	30.855	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	127	PRO	0	-0.045	-0.013	32.957	0.001	0.001	0.000	0.000	0.000	0.000
108	A	128	GLY	0	0.016	0.009	35.589	0.004	0.004	0.000	0.000	0.000	0.000
109	A	129	ILE	0	-0.031	0.010	32.417	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	130	ASP	-1	-0.783	-0.853	35.869	-0.075	-0.075	0.000	0.000	0.000	0.000
111	A	131	ALA	0	0.042	-0.003	36.256	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	132	SER	0	-0.008	0.006	36.591	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	133	THR	0	-0.069	-0.079	32.860	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	134	PHE	0	0.034	0.013	31.049	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	135	ASP	-1	-0.791	-0.862	31.655	-0.085	-0.085	0.000	0.000	0.000	0.000
116	A	136	GLY	0	0.052	0.019	31.548	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	137	ILE	0	-0.022	-0.006	26.649	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	138	ILE	0	-0.017	-0.002	27.133	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	139	GLN	0	-0.021	-0.020	28.012	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	140	LYS	1	0.832	0.907	21.631	0.210	0.210	0.000	0.000	0.000	0.000
121	A	141	ALA	0	-0.020	0.000	23.191	-0.015	-0.015	0.000	0.000	0.000	0.000
122	A	142	LYS	1	0.888	0.948	23.352	0.088	0.088	0.000	0.000	0.000	0.000
123	A	143	ALA	0	-0.033	-0.009	25.005	0.002	0.002	0.000	0.000	0.000	0.000
124	A	144	GLY	0	0.026	0.019	21.287	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	145	CYS	0	-0.051	0.004	19.291	-0.026	-0.026	0.000	0.000	0.000	0.000
126	A	146	PRO	0	0.032	-0.013	15.134	0.010	0.010	0.000	0.000	0.000	0.000
127	A	147	VAL	0	0.025	0.004	17.520	0.004	0.004	0.000	0.000	0.000	0.000
128	A	148	SER	0	0.014	-0.022	20.174	0.015	0.015	0.000	0.000	0.000	0.000
129	A	149	GLN	0	-0.082	-0.027	18.398	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	150	VAL	0	-0.045	-0.009	17.394	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	151	LEU	0	-0.028	-0.013	20.695	0.018	0.018	0.000	0.000	0.000	0.000
132	A	152	LYS	1	0.963	0.996	24.146	0.053	0.053	0.000	0.000	0.000	0.000
133	A	153	ALA	0	-0.035	-0.019	26.548	0.008	0.008	0.000	0.000	0.000	0.000
134	A	154	GLU	-1	-0.818	-0.896	29.464	-0.062	-0.062	0.000	0.000	0.000	0.000
135	A	155	ILE	0	0.020	0.009	26.272	0.004	0.004	0.000	0.000	0.000	0.000
136	A	156	THR	0	-0.027	-0.024	30.621	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	157	LEU	0	-0.008	-0.024	30.000	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	158	ASP	-1	-0.887	-0.899	32.770	-0.050	-0.050	0.000	0.000	0.000	0.000
139	A	159	TYR	0	-0.069	-0.086	33.646	0.003	0.003	0.000	0.000	0.000	0.000
140	A	160	GLN	0	-0.004	0.001	35.582	0.002	0.002	0.000	0.000	0.000	0.000
141	A	161	LEU	0	-0.016	0.011	34.191	0.001	0.001	0.000	0.000	0.000	0.000
142	A	162	LYS	1	0.830	0.912	36.473	0.042	0.042	0.000	0.000	0.000	0.000
143	A	163	SER	0	0.030	0.005	37.196	-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:21:MET)