FMO DATABASE

FMODB ID: 394JL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1428589.481512
FMO2-HF: Nuclear repulsion	1367087.332723
FMO2-HF: Total energy	-61502.14879
FMO2-MP2: Total energy	-61682.05769

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.
38.373	42.582	0.314	-1.73	-2.793	-0.001

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 : -0.976 / q_NPA : -0.996

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	-0.026	-0.013	2.934	-1.002	1.864	0.274	-1.243	-1.897	-0.003
4	E	4	LEU	0	-0.003	-0.011	5.104	-3.474	-3.402	-0.001	-0.006	-0.065	0.000
5	E	5	VAL	0	-0.011	0.001	8.751	-0.502	-0.502	0.000	0.000	0.000	0.000
6	E	6	GLU	-1	-0.758	-0.912	11.047	19.446	19.446	0.000	0.000	0.000	0.000
7	E	7	SER	0	-0.079	-0.029	14.561	-0.539	-0.539	0.000	0.000	0.000	0.000
8	E	8	GLY	0	0.015	-0.006	17.650	0.021	0.021	0.000	0.000	0.000	0.000
9	E	9	GLY	0	0.021	0.020	20.635	-0.524	-0.524	0.000	0.000	0.000	0.000
10	E	10	GLY	0	0.005	0.006	22.435	-0.196	-0.196	0.000	0.000	0.000	0.000
11	E	11	LEU	0	-0.031	-0.027	25.227	-0.149	-0.149	0.000	0.000	0.000	0.000
12	E	12	VAL	0	0.004	0.010	28.658	-0.040	-0.040	0.000	0.000	0.000	0.000
13	E	13	GLN	0	-0.008	-0.004	30.939	-0.263	-0.263	0.000	0.000	0.000	0.000
14	E	14	PRO	0	0.098	0.035	34.012	0.135	0.135	0.000	0.000	0.000	0.000
15	E	15	GLY	0	-0.033	0.012	35.542	-0.209	-0.209	0.000	0.000	0.000	0.000
16	E	16	ARG	1	0.858	0.909	33.827	-8.115	-8.115	0.000	0.000	0.000	0.000
17	E	17	SER	0	-0.003	0.003	30.464	0.086	0.086	0.000	0.000	0.000	0.000
18	E	18	LEU	0	0.008	0.014	23.824	-0.098	-0.098	0.000	0.000	0.000	0.000
19	E	19	ARG	1	0.900	0.956	22.910	-12.499	-12.499	0.000	0.000	0.000	0.000
20	E	20	LEU	0	0.018	0.024	19.662	0.128	0.128	0.000	0.000	0.000	0.000
21	E	21	SER	0	0.001	-0.025	17.340	-0.429	-0.429	0.000	0.000	0.000	0.000
22	E	22	CYS	0	-0.008	0.021	13.105	0.325	0.325	0.000	0.000	0.000	0.000
23	E	23	ALA	0	-0.003	0.028	12.573	-0.234	-0.234	0.000	0.000	0.000	0.000
24	E	24	ALA	0	0.026	0.011	9.653	1.528	1.528	0.000	0.000	0.000	0.000
25	E	25	SER	0	-0.033	-0.015	6.118	-1.184	-1.184	0.000	0.000	0.000	0.000
26	E	26	GLY	0	0.051	0.024	3.379	2.526	2.851	0.033	-0.222	-0.136	0.001
27	E	27	PHE	0	0.011	-0.016	4.181	4.315	4.527	-0.001	-0.020	-0.191	0.000
28	E	28	THR	0	0.021	0.015	7.390	-0.881	-0.881	0.000	0.000	0.000	0.000
29	E	29	PHE	0	0.019	0.017	11.025	-0.832	-0.832	0.000	0.000	0.000	0.000
30	E	30	ASP	-1	-0.934	-0.978	12.525	16.985	16.985	0.000	0.000	0.000	0.000
31	E	31	ASP	-1	-0.874	-0.935	14.265	18.068	18.068	0.000	0.000	0.000	0.000
32	E	32	TYR	0	-0.071	-0.028	11.842	0.016	0.016	0.000	0.000	0.000	0.000
33	E	33	ALA	0	-0.005	-0.005	15.362	-0.802	-0.802	0.000	0.000	0.000	0.000
34	E	34	MET	0	-0.070	-0.023	12.273	1.892	1.892	0.000	0.000	0.000	0.000
35	E	35	HIS	0	0.056	0.005	15.909	-1.549	-1.549	0.000	0.000	0.000	0.000
36	E	36	TRP	0	0.002	0.005	16.746	1.048	1.048	0.000	0.000	0.000	0.000
37	E	37	VAL	0	-0.018	-0.009	17.917	-0.876	-0.876	0.000	0.000	0.000	0.000
38	E	38	ARG	1	0.802	0.889	19.116	-11.218	-11.218	0.000	0.000	0.000	0.000
39	E	39	GLN	0	0.004	-0.006	20.682	0.485	0.485	0.000	0.000	0.000	0.000
40	E	40	ALA	0	0.010	0.009	22.948	-0.018	-0.018	0.000	0.000	0.000	0.000
41	E	41	PRO	0	0.059	0.012	25.534	0.156	0.156	0.000	0.000	0.000	0.000
42	E	42	GLY	0	-0.030	0.003	25.645	-0.465	-0.465	0.000	0.000	0.000	0.000
43	E	43	LYS	1	0.926	0.965	27.283	-10.226	-10.226	0.000	0.000	0.000	0.000
44	E	44	GLY	0	0.036	0.016	25.165	0.422	0.422	0.000	0.000	0.000	0.000
45	E	45	LEU	0	-0.009	-0.004	18.862	-0.006	-0.006	0.000	0.000	0.000	0.000
46	E	46	GLU	-1	-0.816	-0.899	22.857	10.850	10.850	0.000	0.000	0.000	0.000
47	E	47	TRP	0	-0.011	0.006	20.863	0.267	0.267	0.000	0.000	0.000	0.000
48	E	48	VAL	0	-0.024	-0.012	22.430	-0.621	-0.621	0.000	0.000	0.000	0.000
49	E	49	SER	0	0.040	0.006	22.514	-0.487	-0.487	0.000	0.000	0.000	0.000
50	E	50	ALA	0	-0.016	0.007	20.811	0.879	0.879	0.000	0.000	0.000	0.000
51	E	51	ILE	0	0.012	0.024	20.138	-0.756	-0.756	0.000	0.000	0.000	0.000
52	E	52	THR	0	0.034	0.013	20.083	0.977	0.977	0.000	0.000	0.000	0.000
53	E	53	TRP	0	0.023	0.010	18.671	-0.171	-0.171	0.000	0.000	0.000	0.000
54	E	54	ASN	0	0.009	0.002	19.710	0.215	0.215	0.000	0.000	0.000	0.000
55	E	55	SER	0	0.002	-0.015	22.775	-0.292	-0.292	0.000	0.000	0.000	0.000
56	E	56	GLY	0	-0.049	-0.005	24.532	-0.452	-0.452	0.000	0.000	0.000	0.000
57	E	57	HIS	0	-0.022	-0.040	25.889	-0.361	-0.361	0.000	0.000	0.000	0.000
58	E	58	ILE	0	-0.018	0.004	25.038	0.658	0.658	0.000	0.000	0.000	0.000
59	E	59	ASP	-1	-0.911	-0.941	25.088	11.857	11.857	0.000	0.000	0.000	0.000
60	E	60	TYR	0	0.026	-0.011	25.769	0.715	0.715	0.000	0.000	0.000	0.000
61	E	61	ALA	0	0.014	0.013	26.955	-0.314	-0.314	0.000	0.000	0.000	0.000
62	E	62	ASP	-1	-0.868	-0.940	28.693	9.075	9.075	0.000	0.000	0.000	0.000
63	E	63	SER	0	-0.080	-0.027	29.152	-0.181	-0.181	0.000	0.000	0.000	0.000
64	E	64	VAL	0	-0.136	-0.090	27.803	-0.119	-0.119	0.000	0.000	0.000	0.000
65	E	65	GLU	-1	-0.857	-0.908	30.392	9.698	9.698	0.000	0.000	0.000	0.000
66	E	66	GLY	0	0.003	-0.007	32.483	0.101	0.101	0.000	0.000	0.000	0.000
67	E	67	ARG	1	0.703	0.820	30.977	-9.992	-9.992	0.000	0.000	0.000	0.000
68	E	68	PHE	0	0.000	-0.010	25.812	0.030	0.030	0.000	0.000	0.000	0.000
69	E	69	THR	0	0.001	0.004	27.067	-0.236	-0.236	0.000	0.000	0.000	0.000
70	E	70	ILE	0	-0.021	0.013	20.016	0.277	0.277	0.000	0.000	0.000	0.000
71	E	71	SER	0	-0.023	-0.027	22.314	-0.488	-0.488	0.000	0.000	0.000	0.000
72	E	72	ARG	1	0.843	0.927	16.262	-16.621	-16.621	0.000	0.000	0.000	0.000
73	E	73	ASP	-1	-0.851	-0.926	18.923	13.002	13.002	0.000	0.000	0.000	0.000
74	E	74	ASN	0	0.056	0.014	17.077	1.141	1.141	0.000	0.000	0.000	0.000
75	E	75	ALA	0	0.034	0.029	16.377	0.680	0.680	0.000	0.000	0.000	0.000
76	E	76	LYS	1	0.806	0.894	16.723	-12.833	-12.833	0.000	0.000	0.000	0.000
77	E	77	ASN	0	-0.030	-0.006	12.145	1.910	1.910	0.000	0.000	0.000	0.000
78	E	78	SER	0	0.031	0.007	13.342	1.136	1.136	0.000	0.000	0.000	0.000
79	E	79	LEU	0	-0.021	0.009	15.886	-0.859	-0.859	0.000	0.000	0.000	0.000
80	E	80	TYR	0	-0.058	-0.044	17.503	-0.078	-0.078	0.000	0.000	0.000	0.000
81	E	81	LEU	0	0.062	0.038	20.469	-0.192	-0.192	0.000	0.000	0.000	0.000
82	E	82	GLN	0	-0.051	-0.008	22.662	0.069	0.069	0.000	0.000	0.000	0.000
83	E	83	MET	0	0.007	0.013	24.986	-0.046	-0.046	0.000	0.000	0.000	0.000
84	E	84	ASN	0	0.055	0.013	27.819	-0.280	-0.280	0.000	0.000	0.000	0.000
85	E	85	SER	0	-0.006	-0.011	31.555	-0.043	-0.043	0.000	0.000	0.000	0.000
86	E	86	LEU	0	-0.038	0.004	28.886	0.022	0.022	0.000	0.000	0.000	0.000
87	E	87	ARG	1	0.947	0.971	32.261	-9.274	-9.274	0.000	0.000	0.000	0.000
88	E	88	ALA	0	0.035	0.013	32.039	0.255	0.255	0.000	0.000	0.000	0.000
89	E	89	GLU	-1	-0.867	-0.949	31.504	9.263	9.263	0.000	0.000	0.000	0.000
90	E	90	ASP	-1	-0.769	-0.845	28.359	10.495	10.495	0.000	0.000	0.000	0.000
91	E	91	THR	0	-0.038	-0.011	27.117	0.445	0.445	0.000	0.000	0.000	0.000
92	E	92	ALA	0	-0.031	-0.028	24.169	-0.106	-0.106	0.000	0.000	0.000	0.000
93	E	93	VAL	0	0.009	0.018	18.598	-0.124	-0.124	0.000	0.000	0.000	0.000
94	E	94	TYR	0	-0.055	-0.058	19.454	-0.126	-0.126	0.000	0.000	0.000	0.000
95	E	95	TYR	0	0.027	0.018	13.962	0.362	0.362	0.000	0.000	0.000	0.000
96	E	97	ALA	0	0.027	-0.005	12.266	1.460	1.460	0.000	0.000	0.000	0.000
97	E	98	LYS	1	0.904	0.953	8.049	-34.102	-34.102	0.000	0.000	0.000	0.000
98	E	99	VAL	0	-0.069	-0.022	12.129	0.562	0.562	0.000	0.000	0.000	0.000
99	E	100	SER	0	-0.046	-0.017	11.743	0.865	0.865	0.000	0.000	0.000	0.000
100	E	101	TYR	0	0.017	-0.006	12.857	0.818	0.818	0.000	0.000	0.000	0.000
101	E	102	LEU	0	0.031	0.029	14.845	-0.482	-0.482	0.000	0.000	0.000	0.000
102	E	103	SER	0	-0.045	-0.023	17.758	-1.278	-1.278	0.000	0.000	0.000	0.000
103	E	104	THR	0	0.076	0.012	18.791	0.837	0.837	0.000	0.000	0.000	0.000
104	E	105	ALA	0	-0.047	-0.008	20.551	0.120	0.120	0.000	0.000	0.000	0.000
105	E	106	SER	0	-0.038	-0.010	16.829	0.490	0.490	0.000	0.000	0.000	0.000
106	E	107	SER	0	0.053	0.025	14.548	-0.472	-0.472	0.000	0.000	0.000	0.000
107	E	108	LEU	0	-0.002	-0.008	13.824	0.683	0.683	0.000	0.000	0.000	0.000
108	E	109	ASP	-1	-0.874	-0.941	9.272	31.680	31.680	0.000	0.000	0.000	0.000
109	E	110	TYR	0	0.040	0.011	3.646	-2.035	-1.301	0.009	-0.239	-0.504	0.001
110	E	111	TRP	0	-0.016	-0.008	8.540	-3.740	-3.740	0.000	0.000	0.000	0.000
111	E	112	GLY	0	0.054	0.044	8.943	2.788	2.788	0.000	0.000	0.000	0.000
112	E	113	GLN	0	-0.037	-0.043	10.077	0.420	0.420	0.000	0.000	0.000	0.000
113	E	114	GLY	0	0.016	0.025	12.307	-1.275	-1.275	0.000	0.000	0.000	0.000
114	E	115	THR	0	-0.060	-0.023	15.339	-0.625	-0.625	0.000	0.000	0.000	0.000
115	E	116	LEU	0	-0.003	0.002	18.278	-0.209	-0.209	0.000	0.000	0.000	0.000
116	E	117	VAL	0	-0.008	-0.002	21.825	-0.193	-0.193	0.000	0.000	0.000	0.000
117	E	118	THR	0	-0.008	-0.007	24.707	-0.142	-0.142	0.000	0.000	0.000	0.000
118	E	119	VAL	0	0.010	0.005	28.168	-0.155	-0.155	0.000	0.000	0.000	0.000
119	E	120	SER	0	-0.014	-0.013	31.217	-0.355	-0.355	0.000	0.000	0.000	0.000
120	E	121	SER	0	0.022	-0.005	34.172	-0.003	-0.003	0.000	0.000	0.000	0.000
121	E	122	ALA	0	-0.068	-0.010	35.694	-0.172	-0.172	0.000	0.000	0.000	0.000
122	E	123	SER	0	0.022	0.009	35.300	0.156	0.156	0.000	0.000	0.000	0.000
123	E	124	THR	0	-0.012	-0.028	31.723	0.063	0.063	0.000	0.000	0.000	0.000
124	E	125	LYS	1	0.902	0.969	33.838	-7.990	-7.990	0.000	0.000	0.000	0.000
125	E	126	GLY	0	0.050	0.018	33.004	0.290	0.290	0.000	0.000	0.000	0.000
126	E	127	PRO	0	-0.019	0.019	31.578	-0.219	-0.219	0.000	0.000	0.000	0.000
127	E	151	LYS	1	0.834	0.889	34.242	-7.723	-7.723	0.000	0.000	0.000	0.000
128	E	152	ASP	-1	-0.821	-0.903	35.435	7.803	7.803	0.000	0.000	0.000	0.000
129	E	153	TYR	0	-0.011	0.000	28.967	-0.132	-0.132	0.000	0.000	0.000	0.000
130	E	154	PHE	0	-0.019	-0.012	31.934	-0.023	-0.023	0.000	0.000	0.000	0.000
131	E	155	PRO	0	-0.011	-0.004	27.999	-0.174	-0.174	0.000	0.000	0.000	0.000
132	E	156	GLU	-1	-0.852	-0.930	25.923	11.352	11.352	0.000	0.000	0.000	0.000
133	E	157	PRO	0	0.007	0.000	21.800	-0.015	-0.015	0.000	0.000	0.000	0.000
134	E	158	VAL	0	0.027	0.000	24.827	-0.138	-0.138	0.000	0.000	0.000	0.000
135	E	159	THR	0	-0.018	-0.006	20.115	0.238	0.238	0.000	0.000	0.000	0.000
136	E	160	VAL	0	0.009	-0.002	23.113	-0.371	-0.371	0.000	0.000	0.000	0.000
137	E	161	SER	0	-0.014	0.001	21.377	0.668	0.668	0.000	0.000	0.000	0.000
138	E	162	TRP	0	-0.023	-0.009	23.358	-0.518	-0.518	0.000	0.000	0.000	0.000
139	E	163	ASN	0	0.030	-0.013	25.221	-0.174	-0.174	0.000	0.000	0.000	0.000
140	E	164	SER	0	-0.030	-0.015	22.526	0.084	0.084	0.000	0.000	0.000	0.000
141	E	165	GLY	0	-0.022	0.021	20.599	0.483	0.483	0.000	0.000	0.000	0.000
142	E	166	ALA	0	0.015	-0.003	19.168	0.593	0.593	0.000	0.000	0.000	0.000
143	E	167	LEU	0	-0.003	-0.010	22.280	0.218	0.218	0.000	0.000	0.000	0.000
144	E	168	THR	0	0.044	0.020	19.590	-0.402	-0.402	0.000	0.000	0.000	0.000
145	E	169	SER	0	0.043	0.024	23.046	-0.229	-0.229	0.000	0.000	0.000	0.000
146	E	170	GLY	0	-0.005	0.004	25.598	-0.171	-0.171	0.000	0.000	0.000	0.000
147	E	171	VAL	0	-0.041	-0.017	23.941	-0.266	-0.266	0.000	0.000	0.000	0.000
148	E	172	HIS	0	-0.034	-0.039	26.615	0.002	0.002	0.000	0.000	0.000	0.000
149	E	173	THR	0	-0.012	0.006	24.743	-0.494	-0.494	0.000	0.000	0.000	0.000
150	E	174	PHE	0	0.015	0.011	26.523	0.263	0.263	0.000	0.000	0.000	0.000
151	E	175	PRO	0	0.006	-0.005	27.447	0.186	0.186	0.000	0.000	0.000	0.000
152	E	176	ALA	0	0.030	0.032	28.470	-0.226	-0.226	0.000	0.000	0.000	0.000
153	E	177	VAL	0	-0.035	-0.005	30.742	-0.018	-0.018	0.000	0.000	0.000	0.000
154	E	178	LEU	0	0.011	-0.001	34.189	0.003	0.003	0.000	0.000	0.000	0.000
155	E	179	GLN	0	-0.019	-0.007	35.502	-0.340	-0.340	0.000	0.000	0.000	0.000
156	E	180	SER	0	0.004	-0.023	38.868	-0.024	-0.024	0.000	0.000	0.000	0.000
157	E	181	SER	0	-0.049	-0.002	40.073	-0.136	-0.136	0.000	0.000	0.000	0.000
158	E	182	GLY	0	0.059	0.012	39.184	-0.172	-0.172	0.000	0.000	0.000	0.000
159	E	183	LEU	0	-0.111	-0.024	35.941	0.210	0.210	0.000	0.000	0.000	0.000
160	E	184	TYR	0	0.056	0.023	31.004	-0.159	-0.159	0.000	0.000	0.000	0.000
161	E	185	SER	0	0.017	0.009	31.371	-0.189	-0.189	0.000	0.000	0.000	0.000

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