FMO DATABASE

FMODB ID: R9RY8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1074792.162222
FMO2-HF: Nuclear repulsion	1021530.42709
FMO2-HF: Total energy	-53261.735132
FMO2-MP2: Total energy	-53415.936552

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.
-0.141	1.483	0.01	-0.727	-0.906	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 : -0.022 / q_NPA : -0.032

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	-0.008	3.547	1.136	2.760	0.010	-0.727	-0.906	0.001
4	A	24	HIS	0	-0.015	-0.005	4.960	-0.265	-0.265	0.000	0.000	0.000	0.000
5	A	25	LYS	1	0.926	0.966	8.134	-0.161	-0.161	0.000	0.000	0.000	0.000
6	A	26	LYS	1	0.918	0.962	11.026	-0.875	-0.875	0.000	0.000	0.000	0.000
7	A	27	GLY	0	0.037	0.023	14.562	-0.024	-0.024	0.000	0.000	0.000	0.000
8	A	28	GLN	0	-0.054	-0.041	18.282	0.005	0.005	0.000	0.000	0.000	0.000
9	A	29	ALA	0	0.018	0.007	21.009	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	30	HIS	0	-0.054	-0.024	24.640	0.019	0.019	0.000	0.000	0.000	0.000
11	A	31	TRP	0	-0.055	-0.014	27.720	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	32	GLU	-1	-0.875	-0.903	30.843	0.110	0.110	0.000	0.000	0.000	0.000
13	A	33	GLY	0	-0.003	-0.017	34.150	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	34	ASP	-1	-0.837	-0.931	36.065	0.043	0.043	0.000	0.000	0.000	0.000
15	A	35	ILE	0	0.007	0.034	35.465	0.002	0.002	0.000	0.000	0.000	0.000
16	A	36	LYS	1	0.854	0.921	37.534	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	37	ARG	1	0.906	0.935	40.312	-0.041	-0.041	0.000	0.000	0.000	0.000
18	A	38	GLY	0	0.001	-0.002	36.829	0.002	0.002	0.000	0.000	0.000	0.000
19	A	39	LYS	1	0.857	0.929	35.444	-0.059	-0.059	0.000	0.000	0.000	0.000
20	A	40	GLY	0	0.090	0.043	31.343	0.005	0.005	0.000	0.000	0.000	0.000
21	A	41	THR	0	-0.061	-0.037	28.715	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	42	VAL	0	0.014	0.013	25.029	0.008	0.008	0.000	0.000	0.000	0.000
23	A	43	SER	0	-0.018	-0.036	22.030	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	44	THR	0	-0.053	-0.031	18.237	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	45	GLU	-1	-0.838	-0.919	12.374	0.487	0.487	0.000	0.000	0.000	0.000
26	A	46	SER	0	-0.029	-0.022	16.486	0.018	0.018	0.000	0.000	0.000	0.000
27	A	47	GLY	0	0.036	0.021	17.461	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	48	VAL	0	-0.050	-0.031	20.815	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	49	LEU	0	0.007	0.023	22.379	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	50	ASN	0	0.009	-0.003	23.064	0.019	0.019	0.000	0.000	0.000	0.000
31	A	51	GLN	0	0.048	0.017	25.018	0.010	0.010	0.000	0.000	0.000	0.000
32	A	52	GLN	0	0.017	0.027	27.585	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	53	PRO	0	0.027	0.013	29.471	0.004	0.004	0.000	0.000	0.000	0.000
34	A	54	TYR	0	-0.051	-0.020	28.379	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	55	GLY	0	0.085	0.026	32.570	0.006	0.006	0.000	0.000	0.000	0.000
36	A	56	PHE	0	0.001	-0.007	34.752	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	57	ASN	0	-0.006	-0.025	36.700	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	58	THR	0	0.003	-0.004	33.856	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	59	ARG	1	0.750	0.882	29.793	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	60	PHE	0	-0.039	-0.041	34.445	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	61	GLU	-1	-0.862	-0.909	38.000	0.019	0.019	0.000	0.000	0.000	0.000
42	A	62	GLY	0	0.015	0.007	39.748	0.001	0.001	0.000	0.000	0.000	0.000
43	A	63	GLU	-1	-0.875	-0.904	39.617	0.027	0.027	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.947	0.964	36.091	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	65	GLY	0	0.009	-0.006	34.535	0.005	0.005	0.000	0.000	0.000	0.000
46	A	66	THR	0	0.017	0.026	28.437	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	67	ASN	0	0.014	0.009	29.758	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	68	PRO	0	0.016	-0.005	26.480	0.000	0.000	0.000	0.000	0.000	0.000
49	A	69	GLU	-1	-0.721	-0.858	26.612	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	70	GLU	-1	-0.864	-0.932	28.143	0.008	0.008	0.000	0.000	0.000	0.000
51	A	71	LEU	0	-0.018	-0.010	23.717	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	72	ILE	0	-0.029	-0.005	23.470	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	73	GLY	0	0.054	0.015	24.587	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	74	ALA	0	-0.024	-0.009	24.885	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	75	ALA	0	-0.016	-0.011	20.425	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	76	HIS	0	0.009	-0.024	21.524	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	77	ALA	0	0.054	0.036	23.490	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	78	ALA	0	-0.011	0.012	21.380	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	79	CYS	0	-0.067	-0.021	17.601	-0.028	-0.028	0.000	0.000	0.000	0.000
60	A	80	PHE	0	0.069	0.022	20.147	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	81	SER	0	0.014	-0.012	22.984	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	82	MET	0	-0.046	-0.018	16.614	-0.020	-0.020	0.000	0.000	0.000	0.000
63	A	83	ALA	0	-0.005	-0.012	19.912	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	84	LEU	0	0.015	0.004	20.788	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	85	SER	0	0.016	0.002	22.111	0.008	0.008	0.000	0.000	0.000	0.000
66	A	86	LEU	0	-0.053	-0.017	17.866	0.001	0.001	0.000	0.000	0.000	0.000
67	A	87	MET	0	-0.012	-0.008	21.118	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	88	LEU	0	-0.005	0.000	23.637	0.010	0.010	0.000	0.000	0.000	0.000
69	A	89	GLY	0	0.038	0.034	23.292	0.010	0.010	0.000	0.000	0.000	0.000
70	A	90	GLU	-1	-0.995	-1.006	19.842	-0.346	-0.346	0.000	0.000	0.000	0.000
71	A	91	ALA	0	-0.035	-0.015	23.891	0.004	0.004	0.000	0.000	0.000	0.000
72	A	92	GLY	0	-0.046	-0.008	26.829	0.011	0.011	0.000	0.000	0.000	0.000
73	A	93	PHE	0	-0.054	-0.042	27.771	0.017	0.017	0.000	0.000	0.000	0.000
74	A	94	THR	0	-0.008	-0.022	26.533	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	95	PRO	0	-0.019	0.010	26.510	0.011	0.011	0.000	0.000	0.000	0.000
76	A	96	THR	0	-0.022	-0.026	28.907	0.001	0.001	0.000	0.000	0.000	0.000
77	A	97	SER	0	-0.027	-0.017	30.639	0.008	0.008	0.000	0.000	0.000	0.000
78	A	98	ILE	0	-0.031	-0.014	26.314	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	99	ASP	-1	-0.870	-0.917	29.251	-0.052	-0.052	0.000	0.000	0.000	0.000
80	A	100	THR	0	-0.059	-0.032	27.384	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	101	THR	0	-0.028	-0.020	29.851	0.010	0.010	0.000	0.000	0.000	0.000
82	A	102	ALA	0	-0.005	0.001	28.128	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	103	ASP	-1	-0.929	-0.949	30.233	-0.031	-0.031	0.000	0.000	0.000	0.000
84	A	104	VAL	0	-0.032	-0.019	28.654	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	105	SER	0	-0.009	-0.007	31.849	0.006	0.006	0.000	0.000	0.000	0.000
86	A	106	LEU	0	-0.006	-0.002	31.920	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	107	ASP	-1	-0.814	-0.900	34.359	-0.028	-0.028	0.000	0.000	0.000	0.000
88	A	108	LYS	1	0.805	0.878	36.776	0.027	0.027	0.000	0.000	0.000	0.000
89	A	109	VAL	0	-0.016	-0.006	36.857	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	110	ASP	-1	-0.882	-0.943	37.996	-0.032	-0.032	0.000	0.000	0.000	0.000
91	A	111	ALA	0	-0.059	-0.027	39.120	0.003	0.003	0.000	0.000	0.000	0.000
92	A	112	GLY	0	-0.011	-0.011	36.835	0.005	0.005	0.000	0.000	0.000	0.000
93	A	113	PHE	0	0.005	-0.002	34.633	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	114	ALA	0	-0.004	0.001	31.900	0.001	0.001	0.000	0.000	0.000	0.000
95	A	115	ILE	0	-0.003	0.004	28.380	0.000	0.000	0.000	0.000	0.000	0.000
96	A	116	THR	0	-0.027	-0.009	30.437	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	117	LYS	1	0.849	0.907	32.074	0.063	0.063	0.000	0.000	0.000	0.000
98	A	118	ILE	0	0.011	0.021	26.960	0.007	0.007	0.000	0.000	0.000	0.000
99	A	119	ALA	0	-0.001	0.012	31.041	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	120	LEU	0	-0.015	-0.007	26.849	0.005	0.005	0.000	0.000	0.000	0.000
101	A	121	LYS	1	0.940	0.967	31.143	0.055	0.055	0.000	0.000	0.000	0.000
102	A	122	SER	0	-0.023	-0.026	30.452	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	123	GLU	-1	-0.877	-0.932	32.458	-0.052	-0.052	0.000	0.000	0.000	0.000
104	A	124	VAL	0	0.005	0.001	30.602	0.000	0.000	0.000	0.000	0.000	0.000
105	A	125	ALA	0	-0.006	0.002	32.731	0.004	0.004	0.000	0.000	0.000	0.000
106	A	126	VAL	0	0.057	0.015	30.905	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	127	PRO	0	-0.037	-0.020	32.728	0.002	0.002	0.000	0.000	0.000	0.000
108	A	128	GLY	0	0.015	0.014	35.524	0.005	0.005	0.000	0.000	0.000	0.000
109	A	129	ILE	0	-0.046	-0.001	32.399	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	130	ASP	-1	-0.811	-0.858	35.812	-0.106	-0.106	0.000	0.000	0.000	0.000
111	A	131	ALA	0	0.052	-0.005	36.442	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	132	SER	0	-0.006	0.006	36.784	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	133	THR	0	-0.043	-0.072	33.155	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	134	PHE	0	0.050	0.021	30.959	-0.011	-0.011	0.000	0.000	0.000	0.000
115	A	135	ASP	-1	-0.836	-0.880	31.677	-0.121	-0.121	0.000	0.000	0.000	0.000
116	A	136	GLY	0	0.010	-0.005	31.843	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	137	ILE	0	-0.052	-0.026	26.793	-0.015	-0.015	0.000	0.000	0.000	0.000
118	A	138	ILE	0	-0.008	-0.002	27.307	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	139	GLN	0	0.028	0.017	27.790	-0.013	-0.013	0.000	0.000	0.000	0.000
120	A	140	LYS	1	0.937	0.974	23.928	0.258	0.258	0.000	0.000	0.000	0.000
121	A	141	ALA	0	0.000	0.007	23.211	-0.020	-0.020	0.000	0.000	0.000	0.000
122	A	142	LYS	1	0.895	0.950	23.530	0.129	0.129	0.000	0.000	0.000	0.000
123	A	143	ALA	0	-0.032	-0.013	25.053	0.001	0.001	0.000	0.000	0.000	0.000
124	A	144	GLY	0	0.021	0.025	21.694	-0.013	-0.013	0.000	0.000	0.000	0.000
125	A	145	CYS	0	-0.037	0.023	19.189	-0.039	-0.039	0.000	0.000	0.000	0.000
126	A	146	PRO	0	0.054	-0.004	15.076	0.017	0.017	0.000	0.000	0.000	0.000
127	A	147	VAL	0	0.025	0.004	17.532	0.012	0.012	0.000	0.000	0.000	0.000
128	A	148	SER	0	-0.002	-0.039	19.946	0.023	0.023	0.000	0.000	0.000	0.000
129	A	149	GLN	0	-0.086	-0.039	19.049	0.008	0.008	0.000	0.000	0.000	0.000
130	A	150	VAL	0	-0.057	-0.016	17.068	0.000	0.000	0.000	0.000	0.000	0.000
131	A	151	LEU	0	-0.038	-0.007	20.210	0.027	0.027	0.000	0.000	0.000	0.000
132	A	152	LYS	1	0.959	0.982	23.783	0.077	0.077	0.000	0.000	0.000	0.000
133	A	153	ALA	0	-0.028	-0.004	26.464	0.009	0.009	0.000	0.000	0.000	0.000
134	A	154	GLU	-1	-0.825	-0.897	28.995	-0.090	-0.090	0.000	0.000	0.000	0.000
135	A	155	ILE	0	0.020	-0.002	26.057	0.004	0.004	0.000	0.000	0.000	0.000
136	A	156	THR	0	-0.005	0.007	30.538	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	157	LEU	0	-0.034	-0.026	30.242	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	158	ASP	-1	-0.906	-0.925	32.846	-0.070	-0.070	0.000	0.000	0.000	0.000
139	A	159	TYR	0	-0.071	-0.093	33.386	0.000	0.000	0.000	0.000	0.000	0.000
140	A	160	GLN	0	-0.021	-0.005	35.377	0.004	0.004	0.000	0.000	0.000	0.000
141	A	161	LEU	0	-0.002	0.009	34.243	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	162	LYS	1	0.841	0.923	36.647	0.063	0.063	0.000	0.000	0.000	0.000
143	A	163	SER	0	0.060	0.029	37.463	-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:21:MET)