FMO DATABASE

FMODB ID: 94282

Calculation Name: 4NYL-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NYL

Chain ID: E

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1430880.282335
FMO2-HF: Nuclear repulsion	1369376.97128
FMO2-HF: Total energy	-61503.311055
FMO2-MP2: Total energy	-61683.195951

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(E:1:GLU)

Summations of interaction energy for fragment #1(E:1:GLU)

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.
35.776	39.944	0.418	-1.739	-2.846	-0.004

Interaction energy analysis for fragmet #1(E:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.931 / q_NPA : -0.967

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	E	3	GLN	0	-0.033	-0.015	2.800	-5.576	-2.425	0.411	-1.473	-2.089	-0.004
4	E	4	LEU	0	-0.009	-0.005	5.358	-2.951	-2.885	-0.001	-0.004	-0.061	0.000
5	E	5	VAL	0	0.007	0.002	9.007	0.008	0.008	0.000	0.000	0.000	0.000
6	E	6	GLU	-1	-0.761	-0.878	11.410	20.001	20.001	0.000	0.000	0.000	0.000
7	E	7	SER	0	-0.068	-0.045	14.916	-0.368	-0.368	0.000	0.000	0.000	0.000
8	E	8	GLY	0	0.013	0.000	18.119	-0.123	-0.123	0.000	0.000	0.000	0.000
9	E	9	GLY	0	0.029	0.023	20.996	-0.458	-0.458	0.000	0.000	0.000	0.000
10	E	10	GLY	0	-0.012	-0.010	22.640	-0.140	-0.140	0.000	0.000	0.000	0.000
11	E	11	LEU	0	-0.047	-0.016	25.744	-0.055	-0.055	0.000	0.000	0.000	0.000
12	E	12	VAL	0	0.003	0.010	29.209	-0.058	-0.058	0.000	0.000	0.000	0.000
13	E	13	GLN	0	-0.014	0.001	31.351	-0.188	-0.188	0.000	0.000	0.000	0.000
14	E	14	PRO	0	0.056	0.010	34.444	0.130	0.130	0.000	0.000	0.000	0.000
15	E	15	GLY	0	-0.036	0.001	35.917	-0.177	-0.177	0.000	0.000	0.000	0.000
16	E	16	ARG	1	0.840	0.908	34.162	-8.139	-8.139	0.000	0.000	0.000	0.000
17	E	17	SER	0	-0.003	-0.009	31.137	0.058	0.058	0.000	0.000	0.000	0.000
18	E	18	LEU	0	-0.018	0.001	24.371	-0.135	-0.135	0.000	0.000	0.000	0.000
19	E	19	ARG	1	0.896	0.956	22.859	-12.615	-12.615	0.000	0.000	0.000	0.000
20	E	20	LEU	0	0.038	0.040	20.163	0.194	0.194	0.000	0.000	0.000	0.000
21	E	21	SER	0	-0.011	-0.021	17.780	-0.322	-0.322	0.000	0.000	0.000	0.000
22	E	22	CYS	0	-0.035	-0.010	13.421	0.067	0.067	0.000	0.000	0.000	0.000
23	E	23	ALA	0	0.007	0.035	12.646	-0.248	-0.248	0.000	0.000	0.000	0.000
24	E	24	ALA	0	0.019	0.001	9.998	1.383	1.383	0.000	0.000	0.000	0.000
25	E	25	SER	0	-0.012	-0.007	6.337	-0.952	-0.952	0.000	0.000	0.000	0.000
26	E	26	GLY	0	0.064	0.022	3.919	2.276	2.551	0.008	-0.172	-0.110	0.000
27	E	27	PHE	0	-0.030	-0.021	4.547	3.484	3.744	-0.001	-0.020	-0.239	0.000
28	E	28	THR	0	0.010	-0.028	7.663	-1.016	-1.016	0.000	0.000	0.000	0.000
29	E	29	PHE	0	0.007	0.007	11.457	-1.050	-1.050	0.000	0.000	0.000	0.000
30	E	30	ASP	-1	-0.857	-0.938	12.961	16.987	16.987	0.000	0.000	0.000	0.000
31	E	31	ASP	-1	-0.837	-0.885	14.260	19.446	19.446	0.000	0.000	0.000	0.000
32	E	32	TYR	0	-0.045	-0.022	11.593	-0.078	-0.078	0.000	0.000	0.000	0.000
33	E	33	ALA	0	-0.026	-0.009	15.526	-0.666	-0.666	0.000	0.000	0.000	0.000
34	E	34	MET	0	-0.052	-0.007	12.421	1.823	1.823	0.000	0.000	0.000	0.000
35	E	35	HIS	0	0.072	0.021	16.316	-1.674	-1.674	0.000	0.000	0.000	0.000
36	E	36	TRP	0	-0.015	-0.006	17.015	1.095	1.095	0.000	0.000	0.000	0.000
37	E	37	VAL	0	-0.006	-0.001	18.304	-0.786	-0.786	0.000	0.000	0.000	0.000
38	E	38	ARG	1	0.778	0.863	19.604	-11.102	-11.102	0.000	0.000	0.000	0.000
39	E	39	GLN	0	0.007	-0.005	20.963	0.491	0.491	0.000	0.000	0.000	0.000
40	E	40	ALA	0	0.030	0.024	23.088	-0.046	-0.046	0.000	0.000	0.000	0.000
41	E	41	PRO	0	0.014	-0.012	26.048	0.106	0.106	0.000	0.000	0.000	0.000
42	E	42	GLY	0	0.000	0.005	26.244	-0.428	-0.428	0.000	0.000	0.000	0.000
43	E	43	LYS	1	0.912	0.969	27.185	-10.204	-10.204	0.000	0.000	0.000	0.000
44	E	44	GLY	0	0.038	0.018	25.464	0.422	0.422	0.000	0.000	0.000	0.000
45	E	45	LEU	0	-0.012	-0.005	19.402	-0.090	-0.090	0.000	0.000	0.000	0.000
46	E	46	GLU	-1	-0.813	-0.868	23.262	10.790	10.790	0.000	0.000	0.000	0.000
47	E	47	TRP	0	-0.031	-0.021	20.763	0.188	0.188	0.000	0.000	0.000	0.000
48	E	48	VAL	0	-0.016	-0.008	22.651	-0.591	-0.591	0.000	0.000	0.000	0.000
49	E	49	SER	0	0.025	-0.002	22.757	-0.496	-0.496	0.000	0.000	0.000	0.000
50	E	50	ALA	0	-0.020	0.003	20.991	0.874	0.874	0.000	0.000	0.000	0.000
51	E	51	ILE	0	0.007	0.011	19.921	-0.738	-0.738	0.000	0.000	0.000	0.000
52	E	52	THR	0	-0.006	-0.021	19.989	0.901	0.901	0.000	0.000	0.000	0.000
53	E	53	TRP	0	0.011	0.001	18.862	-0.021	-0.021	0.000	0.000	0.000	0.000
54	E	54	ASN	0	0.024	0.013	19.827	0.364	0.364	0.000	0.000	0.000	0.000
55	E	55	SER	0	-0.018	-0.019	22.781	-0.320	-0.320	0.000	0.000	0.000	0.000
56	E	56	GLY	0	-0.025	0.004	24.662	-0.475	-0.475	0.000	0.000	0.000	0.000
57	E	57	HIS	0	0.001	-0.015	25.870	-0.297	-0.297	0.000	0.000	0.000	0.000
58	E	58	ILE	0	-0.005	0.011	25.022	0.721	0.721	0.000	0.000	0.000	0.000
59	E	59	ASP	-1	-0.896	-0.927	24.945	11.965	11.965	0.000	0.000	0.000	0.000
60	E	60	TYR	0	0.030	-0.004	25.892	0.664	0.664	0.000	0.000	0.000	0.000
61	E	61	ALA	0	0.024	0.026	27.554	-0.193	-0.193	0.000	0.000	0.000	0.000
62	E	62	ASP	-1	-0.857	-0.950	29.188	9.252	9.252	0.000	0.000	0.000	0.000
63	E	63	SER	0	-0.080	-0.042	29.402	-0.219	-0.219	0.000	0.000	0.000	0.000
64	E	64	VAL	0	-0.068	-0.060	27.663	-0.123	-0.123	0.000	0.000	0.000	0.000
65	E	65	GLU	-1	-0.891	-0.937	31.166	9.642	9.642	0.000	0.000	0.000	0.000
66	E	66	GLY	0	0.000	0.018	32.706	0.025	0.025	0.000	0.000	0.000	0.000
67	E	67	ARG	1	0.679	0.799	31.243	-9.921	-9.921	0.000	0.000	0.000	0.000
68	E	68	PHE	0	-0.004	-0.007	26.030	0.066	0.066	0.000	0.000	0.000	0.000
69	E	69	THR	0	-0.023	-0.016	27.427	-0.299	-0.299	0.000	0.000	0.000	0.000
70	E	70	ILE	0	-0.003	0.024	20.288	0.231	0.231	0.000	0.000	0.000	0.000
71	E	71	SER	0	-0.022	-0.022	22.521	-0.424	-0.424	0.000	0.000	0.000	0.000
72	E	72	ARG	1	0.813	0.894	16.572	-16.593	-16.593	0.000	0.000	0.000	0.000
73	E	73	ASP	-1	-0.825	-0.903	19.247	12.893	12.893	0.000	0.000	0.000	0.000
74	E	74	ASN	0	0.040	0.023	17.297	0.716	0.716	0.000	0.000	0.000	0.000
75	E	75	ALA	0	-0.006	0.011	16.842	0.704	0.704	0.000	0.000	0.000	0.000
76	E	76	LYS	1	0.791	0.887	16.829	-13.424	-13.424	0.000	0.000	0.000	0.000
77	E	77	ASN	0	-0.034	-0.022	12.064	1.899	1.899	0.000	0.000	0.000	0.000
78	E	78	SER	0	0.003	0.003	13.402	1.280	1.280	0.000	0.000	0.000	0.000
79	E	79	LEU	0	-0.015	-0.001	15.770	-0.823	-0.823	0.000	0.000	0.000	0.000
80	E	80	TYR	0	-0.024	-0.037	17.714	-0.160	-0.160	0.000	0.000	0.000	0.000
81	E	81	LEU	0	0.028	0.021	20.584	-0.095	-0.095	0.000	0.000	0.000	0.000
82	E	82	GLN	0	-0.041	-0.017	22.964	-0.023	-0.023	0.000	0.000	0.000	0.000
83	E	83	MET	0	0.000	0.014	25.432	0.013	0.013	0.000	0.000	0.000	0.000
84	E	84	ASN	0	0.024	-0.007	28.393	-0.328	-0.328	0.000	0.000	0.000	0.000
85	E	85	SER	0	0.035	0.019	32.228	-0.028	-0.028	0.000	0.000	0.000	0.000
86	E	86	LEU	0	-0.019	0.016	28.995	0.016	0.016	0.000	0.000	0.000	0.000
87	E	87	ARG	1	0.923	0.947	32.732	-9.085	-9.085	0.000	0.000	0.000	0.000
88	E	88	ALA	0	0.036	0.018	32.538	0.266	0.266	0.000	0.000	0.000	0.000
89	E	89	GLU	-1	-0.853	-0.939	32.052	9.143	9.143	0.000	0.000	0.000	0.000
90	E	90	ASP	-1	-0.761	-0.824	28.669	10.402	10.402	0.000	0.000	0.000	0.000
91	E	91	THR	0	-0.030	0.001	27.414	0.424	0.424	0.000	0.000	0.000	0.000
92	E	92	ALA	0	-0.015	-0.011	24.215	-0.117	-0.117	0.000	0.000	0.000	0.000
93	E	93	VAL	0	0.005	0.016	18.648	-0.099	-0.099	0.000	0.000	0.000	0.000
94	E	94	TYR	0	-0.026	-0.036	19.817	-0.172	-0.172	0.000	0.000	0.000	0.000
95	E	95	TYR	0	0.029	0.011	14.512	-0.071	-0.071	0.000	0.000	0.000	0.000
96	E	97	ALA	0	0.013	-0.010	12.578	1.417	1.417	0.000	0.000	0.000	0.000
97	E	98	LYS	1	0.809	0.889	8.636	-32.479	-32.479	0.000	0.000	0.000	0.000
98	E	99	VAL	0	-0.016	0.000	12.165	-0.116	-0.116	0.000	0.000	0.000	0.000
99	E	100	SER	0	-0.002	0.006	11.819	1.342	1.342	0.000	0.000	0.000	0.000
100	E	101	TYR	0	-0.009	-0.011	12.443	1.362	1.362	0.000	0.000	0.000	0.000
101	E	102	LEU	0	0.029	0.024	15.070	-0.410	-0.410	0.000	0.000	0.000	0.000
102	E	103	SER	0	-0.016	-0.026	17.631	-1.286	-1.286	0.000	0.000	0.000	0.000
103	E	104	THR	0	0.035	0.014	18.701	0.824	0.824	0.000	0.000	0.000	0.000
104	E	105	ALA	0	-0.031	0.007	20.542	0.086	0.086	0.000	0.000	0.000	0.000
105	E	106	SER	0	-0.035	-0.028	16.695	0.604	0.604	0.000	0.000	0.000	0.000
106	E	107	SER	0	0.050	0.023	14.313	-0.556	-0.556	0.000	0.000	0.000	0.000
107	E	108	LEU	0	0.005	-0.005	14.035	0.744	0.744	0.000	0.000	0.000	0.000
108	E	109	ASP	-1	-0.829	-0.899	9.062	31.834	31.834	0.000	0.000	0.000	0.000
109	E	110	TYR	0	0.010	-0.003	3.633	-1.129	-0.713	0.001	-0.070	-0.347	0.000
110	E	111	TRP	0	-0.021	-0.021	8.866	-4.160	-4.160	0.000	0.000	0.000	0.000
111	E	112	GLY	0	0.063	0.042	9.138	2.506	2.506	0.000	0.000	0.000	0.000
112	E	113	GLN	0	-0.051	-0.037	10.208	0.347	0.347	0.000	0.000	0.000	0.000
113	E	114	GLY	0	0.005	0.007	12.287	-1.249	-1.249	0.000	0.000	0.000	0.000
114	E	115	THR	0	-0.068	-0.036	15.586	-0.506	-0.506	0.000	0.000	0.000	0.000
115	E	116	LEU	0	-0.014	0.004	18.655	-0.233	-0.233	0.000	0.000	0.000	0.000
116	E	117	VAL	0	0.014	0.007	22.307	-0.165	-0.165	0.000	0.000	0.000	0.000
117	E	118	THR	0	-0.016	-0.015	25.319	-0.153	-0.153	0.000	0.000	0.000	0.000
118	E	119	VAL	0	0.016	0.011	28.786	-0.184	-0.184	0.000	0.000	0.000	0.000
119	E	120	SER	0	0.007	-0.005	31.785	-0.351	-0.351	0.000	0.000	0.000	0.000
120	E	121	SER	0	0.023	-0.012	34.797	0.098	0.098	0.000	0.000	0.000	0.000
121	E	122	ALA	0	-0.027	0.009	36.398	-0.154	-0.154	0.000	0.000	0.000	0.000
122	E	123	SER	0	0.060	0.026	35.639	0.224	0.224	0.000	0.000	0.000	0.000
123	E	124	THR	0	0.049	0.031	32.161	0.017	0.017	0.000	0.000	0.000	0.000
124	E	125	LYS	1	0.783	0.882	33.939	-8.376	-8.376	0.000	0.000	0.000	0.000
125	E	126	GLY	0	0.052	0.024	33.234	0.302	0.302	0.000	0.000	0.000	0.000
126	E	127	PRO	0	-0.034	0.006	31.857	-0.314	-0.314	0.000	0.000	0.000	0.000
127	E	151	LYS	1	0.848	0.903	33.935	-7.684	-7.684	0.000	0.000	0.000	0.000
128	E	152	ASP	-1	-0.834	-0.915	35.991	7.796	7.796	0.000	0.000	0.000	0.000
129	E	153	TYR	0	-0.031	-0.029	29.131	-0.196	-0.196	0.000	0.000	0.000	0.000
130	E	154	PHE	0	0.044	0.012	32.408	-0.007	-0.007	0.000	0.000	0.000	0.000
131	E	155	PRO	0	-0.014	0.002	28.372	-0.233	-0.233	0.000	0.000	0.000	0.000
132	E	156	GLU	-1	-0.792	-0.887	26.407	11.066	11.066	0.000	0.000	0.000	0.000
133	E	157	PRO	0	-0.016	-0.009	22.157	0.030	0.030	0.000	0.000	0.000	0.000
134	E	158	VAL	0	0.010	-0.009	25.285	-0.075	-0.075	0.000	0.000	0.000	0.000
135	E	159	THR	0	-0.001	0.008	20.440	0.103	0.103	0.000	0.000	0.000	0.000
136	E	160	VAL	0	0.000	-0.006	23.551	-0.285	-0.285	0.000	0.000	0.000	0.000
137	E	161	SER	0	0.012	0.006	20.954	0.254	0.254	0.000	0.000	0.000	0.000
138	E	162	TRP	0	-0.014	-0.025	23.559	-0.347	-0.347	0.000	0.000	0.000	0.000
139	E	163	ASN	0	0.019	0.001	25.339	-0.182	-0.182	0.000	0.000	0.000	0.000
140	E	164	SER	0	0.015	0.003	22.251	-0.058	-0.058	0.000	0.000	0.000	0.000
141	E	165	GLY	0	-0.049	-0.002	21.285	0.459	0.459	0.000	0.000	0.000	0.000
142	E	166	ALA	0	-0.017	-0.011	19.852	0.565	0.565	0.000	0.000	0.000	0.000
143	E	167	LEU	0	0.031	0.016	22.636	0.318	0.318	0.000	0.000	0.000	0.000
144	E	168	THR	0	0.011	-0.009	19.866	-0.460	-0.460	0.000	0.000	0.000	0.000
145	E	169	SER	0	-0.022	-0.002	23.298	-0.032	-0.032	0.000	0.000	0.000	0.000
146	E	170	GLY	0	0.023	0.001	25.674	-0.417	-0.417	0.000	0.000	0.000	0.000
147	E	171	VAL	0	-0.030	0.006	24.859	-0.280	-0.280	0.000	0.000	0.000	0.000
148	E	172	HIS	0	-0.030	-0.025	26.480	0.099	0.099	0.000	0.000	0.000	0.000
149	E	173	THR	0	-0.006	0.000	24.866	-0.477	-0.477	0.000	0.000	0.000	0.000
150	E	174	PHE	0	0.016	0.016	26.601	0.297	0.297	0.000	0.000	0.000	0.000
151	E	175	PRO	0	0.017	0.002	27.433	0.130	0.130	0.000	0.000	0.000	0.000
152	E	176	ALA	0	0.002	0.021	28.676	-0.360	-0.360	0.000	0.000	0.000	0.000
153	E	177	VAL	0	-0.004	-0.004	30.738	-0.014	-0.014	0.000	0.000	0.000	0.000
154	E	178	LEU	0	-0.021	-0.013	34.223	-0.007	-0.007	0.000	0.000	0.000	0.000
155	E	179	GLN	0	-0.008	-0.005	35.613	-0.333	-0.333	0.000	0.000	0.000	0.000
156	E	180	SER	0	-0.006	-0.023	39.127	0.043	0.043	0.000	0.000	0.000	0.000
157	E	181	SER	0	-0.044	-0.011	40.516	-0.128	-0.128	0.000	0.000	0.000	0.000
158	E	182	GLY	0	0.044	0.005	39.566	-0.162	-0.162	0.000	0.000	0.000	0.000
159	E	183	LEU	0	-0.094	-0.017	36.315	0.157	0.157	0.000	0.000	0.000	0.000
160	E	184	TYR	0	0.043	0.018	31.224	-0.089	-0.089	0.000	0.000	0.000	0.000
161	E	185	SER	0	0.021	0.023	31.771	-0.231	-0.231	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:1:GLU)