FMO DATABASE

FMODB ID: LZ6N9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1429073.020945
FMO2-HF: Nuclear repulsion	1367570.374631
FMO2-HF: Total energy	-61502.646314
FMO2-MP2: Total energy	-61682.532888

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.
38.679	42.689	0.278	-1.565	-2.723	0

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 : -0.970 / q_NPA : -0.997

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	-0.029	-0.013	2.959	-2.728	0.108	0.245	-1.172	-1.909	-0.002
4	E	4	LEU	0	-0.009	-0.011	5.206	-3.377	-3.304	-0.001	-0.005	-0.066	0.000
5	E	5	VAL	0	-0.003	0.008	8.839	-0.564	-0.564	0.000	0.000	0.000	0.000
6	E	6	GLU	-1	-0.750	-0.893	11.178	20.423	20.423	0.000	0.000	0.000	0.000
7	E	7	SER	0	-0.069	-0.027	14.678	-0.600	-0.600	0.000	0.000	0.000	0.000
8	E	8	GLY	0	0.029	-0.007	17.786	0.040	0.040	0.000	0.000	0.000	0.000
9	E	9	GLY	0	0.014	0.016	20.764	-0.513	-0.513	0.000	0.000	0.000	0.000
10	E	10	GLY	0	0.005	0.007	22.551	-0.191	-0.191	0.000	0.000	0.000	0.000
11	E	11	LEU	0	-0.053	-0.028	25.347	-0.132	-0.132	0.000	0.000	0.000	0.000
12	E	12	VAL	0	0.013	0.012	28.880	-0.036	-0.036	0.000	0.000	0.000	0.000
13	E	13	GLN	0	-0.010	0.004	31.050	-0.224	-0.224	0.000	0.000	0.000	0.000
14	E	14	PRO	0	0.090	0.031	34.111	0.123	0.123	0.000	0.000	0.000	0.000
15	E	15	GLY	0	-0.030	0.013	35.627	-0.208	-0.208	0.000	0.000	0.000	0.000
16	E	16	ARG	1	0.845	0.896	33.939	-8.114	-8.114	0.000	0.000	0.000	0.000
17	E	17	SER	0	-0.005	-0.001	30.579	0.065	0.065	0.000	0.000	0.000	0.000
18	E	18	LEU	0	-0.010	0.008	23.807	-0.090	-0.090	0.000	0.000	0.000	0.000
19	E	19	ARG	1	0.916	0.964	23.178	-12.653	-12.653	0.000	0.000	0.000	0.000
20	E	20	LEU	0	0.024	0.033	19.678	0.147	0.147	0.000	0.000	0.000	0.000
21	E	21	SER	0	-0.007	-0.031	17.513	-0.376	-0.376	0.000	0.000	0.000	0.000
22	E	22	CYS	0	-0.036	-0.006	13.150	0.292	0.292	0.000	0.000	0.000	0.000
23	E	23	ALA	0	-0.004	0.031	12.684	-0.218	-0.218	0.000	0.000	0.000	0.000
24	E	24	ALA	0	0.031	0.012	9.741	1.516	1.516	0.000	0.000	0.000	0.000
25	E	25	SER	0	-0.020	-0.009	6.243	-1.190	-1.190	0.000	0.000	0.000	0.000
26	E	26	GLY	0	0.054	0.024	3.447	2.671	2.998	0.032	-0.230	-0.130	0.001
27	E	27	PHE	0	0.012	-0.017	4.247	4.484	4.696	-0.001	-0.021	-0.190	0.000
28	E	28	THR	0	-0.011	-0.026	7.390	-0.968	-0.968	0.000	0.000	0.000	0.000
29	E	29	PHE	0	0.022	0.020	11.025	-0.945	-0.945	0.000	0.000	0.000	0.000
30	E	30	ASP	-1	-0.920	-0.983	12.592	17.132	17.132	0.000	0.000	0.000	0.000
31	E	31	ASP	-1	-0.844	-0.895	14.230	18.802	18.802	0.000	0.000	0.000	0.000
32	E	32	TYR	0	-0.046	-0.018	11.444	0.045	0.045	0.000	0.000	0.000	0.000
33	E	33	ALA	0	-0.010	-0.002	15.306	-0.816	-0.816	0.000	0.000	0.000	0.000
34	E	34	MET	0	-0.064	-0.016	12.231	1.904	1.904	0.000	0.000	0.000	0.000
35	E	35	HIS	0	0.059	0.007	15.805	-1.545	-1.545	0.000	0.000	0.000	0.000
36	E	36	TRP	0	-0.014	-0.002	16.752	1.067	1.067	0.000	0.000	0.000	0.000
37	E	37	VAL	0	-0.011	-0.004	17.746	-0.883	-0.883	0.000	0.000	0.000	0.000
38	E	38	ARG	1	0.801	0.872	19.133	-11.234	-11.234	0.000	0.000	0.000	0.000
39	E	39	GLN	0	0.018	0.002	20.703	0.495	0.495	0.000	0.000	0.000	0.000
40	E	40	ALA	0	0.014	0.011	22.961	-0.022	-0.022	0.000	0.000	0.000	0.000
41	E	41	PRO	0	0.059	0.009	25.547	0.134	0.134	0.000	0.000	0.000	0.000
42	E	42	GLY	0	-0.033	0.005	25.661	-0.462	-0.462	0.000	0.000	0.000	0.000
43	E	43	LYS	1	0.921	0.962	27.324	-10.179	-10.179	0.000	0.000	0.000	0.000
44	E	44	GLY	0	0.036	0.015	25.191	0.410	0.410	0.000	0.000	0.000	0.000
45	E	45	LEU	0	-0.010	-0.002	19.040	-0.017	-0.017	0.000	0.000	0.000	0.000
46	E	46	GLU	-1	-0.808	-0.865	22.859	10.946	10.946	0.000	0.000	0.000	0.000
47	E	47	TRP	0	-0.023	-0.007	20.651	0.236	0.236	0.000	0.000	0.000	0.000
48	E	48	VAL	0	-0.012	-0.005	22.374	-0.609	-0.609	0.000	0.000	0.000	0.000
49	E	49	SER	0	0.022	0.004	22.447	-0.534	-0.534	0.000	0.000	0.000	0.000
50	E	50	ALA	0	-0.006	0.005	20.692	0.890	0.890	0.000	0.000	0.000	0.000
51	E	51	ILE	0	0.019	0.027	19.945	-0.777	-0.777	0.000	0.000	0.000	0.000
52	E	52	THR	0	0.002	-0.011	19.933	0.892	0.892	0.000	0.000	0.000	0.000
53	E	53	TRP	0	0.018	0.003	18.730	-0.161	-0.161	0.000	0.000	0.000	0.000
54	E	54	ASN	0	0.002	-0.006	19.653	0.250	0.250	0.000	0.000	0.000	0.000
55	E	55	SER	0	-0.002	-0.011	22.806	-0.298	-0.298	0.000	0.000	0.000	0.000
56	E	56	GLY	0	-0.034	0.004	24.532	-0.471	-0.471	0.000	0.000	0.000	0.000
57	E	57	HIS	0	-0.002	-0.027	25.758	-0.332	-0.332	0.000	0.000	0.000	0.000
58	E	58	ILE	0	-0.012	0.008	24.886	0.709	0.709	0.000	0.000	0.000	0.000
59	E	59	ASP	-1	-0.915	-0.939	24.957	11.927	11.927	0.000	0.000	0.000	0.000
60	E	60	TYR	0	0.026	-0.015	25.665	0.724	0.724	0.000	0.000	0.000	0.000
61	E	61	ALA	0	0.008	0.010	26.858	-0.318	-0.318	0.000	0.000	0.000	0.000
62	E	62	ASP	-1	-0.872	-0.947	28.616	9.192	9.192	0.000	0.000	0.000	0.000
63	E	63	SER	0	-0.094	-0.046	29.081	-0.210	-0.210	0.000	0.000	0.000	0.000
64	E	64	VAL	0	-0.119	-0.084	27.868	-0.117	-0.117	0.000	0.000	0.000	0.000
65	E	65	GLU	-1	-0.859	-0.908	30.405	9.709	9.709	0.000	0.000	0.000	0.000
66	E	66	GLY	0	0.013	0.002	32.504	0.098	0.098	0.000	0.000	0.000	0.000
67	E	67	ARG	1	0.690	0.807	31.005	-10.049	-10.049	0.000	0.000	0.000	0.000
68	E	68	PHE	0	-0.002	-0.011	26.042	0.047	0.047	0.000	0.000	0.000	0.000
69	E	69	THR	0	0.003	0.004	27.134	-0.246	-0.246	0.000	0.000	0.000	0.000
70	E	70	ILE	0	-0.003	0.020	20.090	0.284	0.284	0.000	0.000	0.000	0.000
71	E	71	SER	0	-0.007	-0.019	22.364	-0.504	-0.504	0.000	0.000	0.000	0.000
72	E	72	ARG	1	0.817	0.912	16.284	-16.749	-16.749	0.000	0.000	0.000	0.000
73	E	73	ASP	-1	-0.858	-0.913	18.998	13.085	13.085	0.000	0.000	0.000	0.000
74	E	74	ASN	0	0.054	0.025	17.150	0.937	0.937	0.000	0.000	0.000	0.000
75	E	75	ALA	0	0.012	0.022	16.439	0.758	0.758	0.000	0.000	0.000	0.000
76	E	76	LYS	1	0.825	0.894	16.778	-12.951	-12.951	0.000	0.000	0.000	0.000
77	E	77	ASN	0	-0.032	-0.016	11.628	2.023	2.023	0.000	0.000	0.000	0.000
78	E	78	SER	0	-0.012	-0.002	13.402	1.147	1.147	0.000	0.000	0.000	0.000
79	E	79	LEU	0	-0.018	0.002	15.718	-0.851	-0.851	0.000	0.000	0.000	0.000
80	E	80	TYR	0	-0.052	-0.045	17.567	-0.155	-0.155	0.000	0.000	0.000	0.000
81	E	81	LEU	0	0.061	0.039	20.543	-0.163	-0.163	0.000	0.000	0.000	0.000
82	E	82	GLN	0	-0.061	-0.011	22.728	0.038	0.038	0.000	0.000	0.000	0.000
83	E	83	MET	0	0.011	0.011	24.958	-0.054	-0.054	0.000	0.000	0.000	0.000
84	E	84	ASN	0	0.033	-0.009	27.893	-0.338	-0.338	0.000	0.000	0.000	0.000
85	E	85	SER	0	0.017	0.009	31.632	-0.035	-0.035	0.000	0.000	0.000	0.000
86	E	86	LEU	0	-0.030	0.001	28.888	0.024	0.024	0.000	0.000	0.000	0.000
87	E	87	ARG	1	0.929	0.959	32.322	-9.211	-9.211	0.000	0.000	0.000	0.000
88	E	88	ALA	0	0.038	0.016	32.104	0.248	0.248	0.000	0.000	0.000	0.000
89	E	89	GLU	-1	-0.862	-0.953	31.560	9.278	9.278	0.000	0.000	0.000	0.000
90	E	90	ASP	-1	-0.757	-0.816	28.409	10.534	10.534	0.000	0.000	0.000	0.000
91	E	91	THR	0	-0.019	0.002	27.176	0.434	0.434	0.000	0.000	0.000	0.000
92	E	92	ALA	0	-0.047	-0.031	24.170	-0.104	-0.104	0.000	0.000	0.000	0.000
93	E	93	VAL	0	0.007	0.010	18.641	-0.128	-0.128	0.000	0.000	0.000	0.000
94	E	94	TYR	0	-0.045	-0.056	19.505	-0.113	-0.113	0.000	0.000	0.000	0.000
95	E	95	TYR	0	0.001	0.003	14.292	-0.055	-0.055	0.000	0.000	0.000	0.000
96	E	97	ALA	0	0.017	-0.007	12.206	1.441	1.441	0.000	0.000	0.000	0.000
97	E	98	LYS	1	0.858	0.920	8.072	-34.126	-34.126	0.000	0.000	0.000	0.000
98	E	99	VAL	0	-0.037	-0.013	11.992	0.514	0.514	0.000	0.000	0.000	0.000
99	E	100	SER	0	-0.038	-0.002	11.670	0.894	0.894	0.000	0.000	0.000	0.000
100	E	101	TYR	0	0.024	-0.006	12.631	0.817	0.817	0.000	0.000	0.000	0.000
101	E	102	LEU	0	0.035	0.031	14.674	-0.512	-0.512	0.000	0.000	0.000	0.000
102	E	103	SER	0	-0.042	-0.030	17.605	-1.305	-1.305	0.000	0.000	0.000	0.000
103	E	104	THR	0	0.060	0.012	18.588	0.851	0.851	0.000	0.000	0.000	0.000
104	E	105	ALA	0	-0.046	-0.007	20.375	0.144	0.144	0.000	0.000	0.000	0.000
105	E	106	SER	0	-0.037	-0.011	16.624	0.491	0.491	0.000	0.000	0.000	0.000
106	E	107	SER	0	0.058	0.028	14.422	-0.514	-0.514	0.000	0.000	0.000	0.000
107	E	108	LEU	0	0.002	-0.006	13.686	0.718	0.718	0.000	0.000	0.000	0.000
108	E	109	ASP	-1	-0.860	-0.923	9.272	31.787	31.787	0.000	0.000	0.000	0.000
109	E	110	TYR	0	0.038	0.004	3.664	-1.083	-0.521	0.003	-0.137	-0.428	0.001
110	E	111	TRP	0	-0.031	-0.020	8.464	-3.863	-3.863	0.000	0.000	0.000	0.000
111	E	112	GLY	0	0.068	0.052	8.948	2.756	2.756	0.000	0.000	0.000	0.000
112	E	113	GLN	0	-0.042	-0.036	10.208	0.477	0.477	0.000	0.000	0.000	0.000
113	E	114	GLY	0	0.002	0.011	12.371	-1.340	-1.340	0.000	0.000	0.000	0.000
114	E	115	THR	0	-0.055	-0.021	15.411	-0.622	-0.622	0.000	0.000	0.000	0.000
115	E	116	LEU	0	-0.004	0.004	18.374	-0.206	-0.206	0.000	0.000	0.000	0.000
116	E	117	VAL	0	-0.003	-0.004	21.914	-0.184	-0.184	0.000	0.000	0.000	0.000
117	E	118	THR	0	-0.008	-0.003	24.797	-0.181	-0.181	0.000	0.000	0.000	0.000
118	E	119	VAL	0	0.017	0.007	28.258	-0.157	-0.157	0.000	0.000	0.000	0.000
119	E	120	SER	0	-0.005	-0.008	31.304	-0.358	-0.358	0.000	0.000	0.000	0.000
120	E	121	SER	0	0.024	-0.009	34.268	0.090	0.090	0.000	0.000	0.000	0.000
121	E	122	ALA	0	-0.055	-0.006	35.815	-0.175	-0.175	0.000	0.000	0.000	0.000
122	E	123	SER	0	0.033	0.013	35.416	0.146	0.146	0.000	0.000	0.000	0.000
123	E	124	THR	0	0.010	-0.001	31.807	0.069	0.069	0.000	0.000	0.000	0.000
124	E	125	LYS	1	0.884	0.944	33.969	-7.982	-7.982	0.000	0.000	0.000	0.000
125	E	126	GLY	0	0.052	0.020	33.135	0.290	0.290	0.000	0.000	0.000	0.000
126	E	127	PRO	0	-0.029	0.015	31.669	-0.217	-0.217	0.000	0.000	0.000	0.000
127	E	151	LYS	1	0.853	0.909	33.581	-7.772	-7.772	0.000	0.000	0.000	0.000
128	E	152	ASP	-1	-0.843	-0.923	35.540	7.810	7.810	0.000	0.000	0.000	0.000
129	E	153	TYR	0	-0.028	-0.029	28.736	-0.191	-0.191	0.000	0.000	0.000	0.000
130	E	154	PHE	0	-0.018	-0.011	32.046	-0.026	-0.026	0.000	0.000	0.000	0.000
131	E	155	PRO	0	-0.010	-0.003	28.018	-0.176	-0.176	0.000	0.000	0.000	0.000
132	E	156	GLU	-1	-0.811	-0.892	25.978	11.263	11.263	0.000	0.000	0.000	0.000
133	E	157	PRO	0	-0.018	-0.011	21.861	0.004	0.004	0.000	0.000	0.000	0.000
134	E	158	VAL	0	0.027	-0.001	24.931	-0.138	-0.138	0.000	0.000	0.000	0.000
135	E	159	THR	0	-0.017	0.001	20.172	0.206	0.206	0.000	0.000	0.000	0.000
136	E	160	VAL	0	0.004	-0.010	23.226	-0.373	-0.373	0.000	0.000	0.000	0.000
137	E	161	SER	0	-0.006	0.006	20.936	0.503	0.503	0.000	0.000	0.000	0.000
138	E	162	TRP	0	-0.011	-0.011	23.553	-0.531	-0.531	0.000	0.000	0.000	0.000
139	E	163	ASN	0	0.020	-0.018	25.372	-0.146	-0.146	0.000	0.000	0.000	0.000
140	E	164	SER	0	-0.017	-0.006	22.716	0.074	0.074	0.000	0.000	0.000	0.000
141	E	165	GLY	0	-0.028	0.019	20.813	0.478	0.478	0.000	0.000	0.000	0.000
142	E	166	ALA	0	0.008	-0.006	19.350	0.583	0.583	0.000	0.000	0.000	0.000
143	E	167	LEU	0	0.001	-0.008	22.423	0.217	0.217	0.000	0.000	0.000	0.000
144	E	168	THR	0	0.042	0.020	19.679	-0.395	-0.395	0.000	0.000	0.000	0.000
145	E	169	SER	0	0.048	0.029	23.152	-0.212	-0.212	0.000	0.000	0.000	0.000
146	E	170	GLY	0	-0.025	-0.008	25.673	-0.170	-0.170	0.000	0.000	0.000	0.000
147	E	171	VAL	0	-0.029	-0.015	24.538	-0.270	-0.270	0.000	0.000	0.000	0.000
148	E	172	HIS	0	-0.030	-0.033	26.699	0.033	0.033	0.000	0.000	0.000	0.000
149	E	173	THR	0	-0.025	0.002	25.069	-0.498	-0.498	0.000	0.000	0.000	0.000
150	E	174	PHE	0	0.008	0.010	26.623	0.251	0.251	0.000	0.000	0.000	0.000
151	E	175	PRO	0	0.022	0.002	27.505	0.201	0.201	0.000	0.000	0.000	0.000
152	E	176	ALA	0	0.029	0.025	28.525	-0.220	-0.220	0.000	0.000	0.000	0.000
153	E	177	VAL	0	-0.029	-0.002	30.809	-0.016	-0.016	0.000	0.000	0.000	0.000
154	E	178	LEU	0	0.004	-0.005	34.198	0.004	0.004	0.000	0.000	0.000	0.000
155	E	179	GLN	0	-0.016	-0.008	35.571	-0.332	-0.332	0.000	0.000	0.000	0.000
156	E	180	SER	0	0.002	-0.021	38.945	-0.020	-0.020	0.000	0.000	0.000	0.000
157	E	181	SER	0	-0.052	-0.004	40.149	-0.131	-0.131	0.000	0.000	0.000	0.000
158	E	182	GLY	0	0.065	0.013	39.272	-0.173	-0.173	0.000	0.000	0.000	0.000
159	E	183	LEU	0	-0.111	-0.025	36.032	0.202	0.202	0.000	0.000	0.000	0.000
160	E	184	TYR	0	0.056	0.023	31.065	-0.139	-0.139	0.000	0.000	0.000	0.000
161	E	185	SER	0	0.022	0.013	31.208	-0.223	-0.223	0.000	0.000	0.000	0.000

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