FMO DATABASE

FMODB ID: GNK41

Calculation Name: 4Y66-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y66

Chain ID: F

ChEMBL ID:

UniProt ID: E2RTU1

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1122500.34548
FMO2-HF: Nuclear repulsion	1055646.433973
FMO2-HF: Total energy	-66853.911508
FMO2-MP2: Total energy	-67046.682154

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(F:3:ALA)

Summations of interaction energy for fragment #1(F:3:ALA)

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.
-9.354	-5.605	1.297	-2.236	-2.811	0.008

Interaction energy analysis for fragmet #1(F:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.011

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	F	5	TYR	0	-0.011	-0.007	3.169	-3.867	-1.144	0.108	-1.386	-1.445	0.009
4	F	6	LYS	1	0.983	0.991	2.582	-3.024	-2.185	1.186	-0.808	-1.217	-0.001
5	F	7	GLU	-1	-0.913	-0.960	3.944	-1.917	-1.730	0.003	-0.042	-0.149	0.000
6	F	8	ALA	0	-0.007	0.006	6.228	0.027	0.027	0.000	0.000	0.000	0.000
7	F	9	PHE	0	0.000	0.001	7.343	-0.122	-0.122	0.000	0.000	0.000	0.000
8	F	10	ALA	0	-0.013	-0.016	7.988	-0.149	-0.149	0.000	0.000	0.000	0.000
9	F	11	ALA	0	0.056	0.037	9.847	-0.097	-0.097	0.000	0.000	0.000	0.000
10	F	12	VAL	0	-0.007	-0.008	11.809	-0.042	-0.042	0.000	0.000	0.000	0.000
11	F	13	LYS	1	0.808	0.904	12.024	-0.190	-0.190	0.000	0.000	0.000	0.000
12	F	14	GLU	-1	-0.861	-0.903	14.060	0.036	0.036	0.000	0.000	0.000	0.000
13	F	15	LEU	0	-0.028	-0.017	15.832	-0.020	-0.020	0.000	0.000	0.000	0.000
14	F	16	MET	0	-0.027	-0.037	17.651	-0.024	-0.024	0.000	0.000	0.000	0.000
15	F	17	GLN	0	-0.001	0.000	16.913	0.006	0.006	0.000	0.000	0.000	0.000
16	F	18	THR	0	-0.005	0.011	19.920	-0.020	-0.020	0.000	0.000	0.000	0.000
17	F	19	SER	0	-0.094	-0.091	21.680	-0.011	-0.011	0.000	0.000	0.000	0.000
18	F	20	ASN	0	0.011	0.054	23.522	0.019	0.019	0.000	0.000	0.000	0.000
19	F	21	LYS	1	0.939	0.965	25.314	-0.090	-0.090	0.000	0.000	0.000	0.000
20	F	22	PRO	0	-0.007	0.022	24.398	0.012	0.012	0.000	0.000	0.000	0.000
21	F	23	GLN	0	0.047	0.001	20.820	-0.004	-0.004	0.000	0.000	0.000	0.000
22	F	24	ASN	0	0.007	-0.016	22.263	0.012	0.012	0.000	0.000	0.000	0.000
23	F	25	VAL	0	0.038	0.025	18.025	0.002	0.002	0.000	0.000	0.000	0.000
24	F	26	GLN	0	0.048	0.024	19.138	0.037	0.037	0.000	0.000	0.000	0.000
25	F	27	THR	0	0.015	0.012	21.154	-0.004	-0.004	0.000	0.000	0.000	0.000
26	F	28	ALA	0	0.070	0.034	16.985	-0.014	-0.014	0.000	0.000	0.000	0.000
27	F	29	ILE	0	0.003	0.012	16.062	-0.009	-0.009	0.000	0.000	0.000	0.000
28	F	30	ASN	0	-0.001	-0.001	17.727	-0.024	-0.024	0.000	0.000	0.000	0.000
29	F	31	ASN	0	-0.031	-0.027	20.241	-0.012	-0.012	0.000	0.000	0.000	0.000
30	F	32	THR	0	-0.023	-0.007	14.739	-0.010	-0.010	0.000	0.000	0.000	0.000
31	F	33	GLY	0	-0.026	-0.018	15.973	-0.023	-0.023	0.000	0.000	0.000	0.000
32	F	34	SER	0	-0.036	-0.023	17.967	-0.017	-0.017	0.000	0.000	0.000	0.000
33	F	35	LYS	1	0.970	1.000	12.941	0.040	0.040	0.000	0.000	0.000	0.000
34	F	36	TYR	0	0.006	0.008	9.157	0.059	0.059	0.000	0.000	0.000	0.000
35	F	37	GLY	0	0.058	0.032	12.625	-0.048	-0.048	0.000	0.000	0.000	0.000
36	F	38	LYS	1	0.944	0.954	14.412	-0.231	-0.231	0.000	0.000	0.000	0.000
37	F	39	THR	0	0.023	-0.007	13.842	0.042	0.042	0.000	0.000	0.000	0.000
38	F	40	THR	0	0.031	0.019	9.189	-0.029	-0.029	0.000	0.000	0.000	0.000
39	F	41	VAL	0	0.066	0.041	11.550	0.099	0.099	0.000	0.000	0.000	0.000
40	F	42	GLN	0	-0.005	-0.010	13.680	0.055	0.055	0.000	0.000	0.000	0.000
41	F	43	LYS	1	0.849	0.941	11.332	-0.698	-0.698	0.000	0.000	0.000	0.000
42	F	44	ALA	0	0.088	0.045	10.590	-0.007	-0.007	0.000	0.000	0.000	0.000
43	F	45	LEU	0	-0.044	-0.029	12.149	-0.094	-0.094	0.000	0.000	0.000	0.000
44	F	46	ASP	-1	-0.827	-0.944	15.854	0.363	0.363	0.000	0.000	0.000	0.000
45	F	47	GLU	-1	-0.913	-0.932	10.339	1.107	1.107	0.000	0.000	0.000	0.000
46	F	48	LEU	0	-0.001	-0.011	13.950	-0.063	-0.063	0.000	0.000	0.000	0.000
47	F	49	VAL	0	-0.037	-0.022	15.937	-0.049	-0.049	0.000	0.000	0.000	0.000
48	F	50	ALA	0	-0.052	-0.009	16.304	-0.037	-0.037	0.000	0.000	0.000	0.000
49	F	51	GLN	0	-0.058	-0.029	13.384	0.025	0.025	0.000	0.000	0.000	0.000
50	F	52	ASN	0	0.015	0.002	17.891	-0.028	-0.028	0.000	0.000	0.000	0.000
51	F	53	LEU	0	0.018	0.012	16.696	-0.026	-0.026	0.000	0.000	0.000	0.000
52	F	54	CYS	0	-0.095	-0.037	19.231	-0.002	-0.002	0.000	0.000	0.000	0.000
53	F	55	ILE	0	0.046	0.047	21.094	0.008	0.008	0.000	0.000	0.000	0.000
54	F	56	TYR	0	-0.004	-0.032	22.941	0.018	0.018	0.000	0.000	0.000	0.000
55	F	57	THR	0	0.009	0.009	24.936	-0.015	-0.015	0.000	0.000	0.000	0.000
56	F	58	GLU	-1	-0.900	-0.947	27.520	0.193	0.193	0.000	0.000	0.000	0.000
57	F	59	ILE	0	0.038	0.022	29.208	-0.010	-0.010	0.000	0.000	0.000	0.000
58	F	60	GLY	0	0.046	0.008	32.133	0.002	0.002	0.000	0.000	0.000	0.000
59	F	61	LYS	1	0.846	0.921	29.623	-0.162	-0.162	0.000	0.000	0.000	0.000
60	F	62	THR	0	-0.020	0.007	30.402	0.003	0.003	0.000	0.000	0.000	0.000
61	F	63	GLY	0	0.020	0.005	27.336	0.008	0.008	0.000	0.000	0.000	0.000
62	F	64	LYS	1	0.875	0.954	21.159	-0.309	-0.309	0.000	0.000	0.000	0.000
63	F	65	LEU	0	-0.054	-0.024	24.677	0.008	0.008	0.000	0.000	0.000	0.000
64	F	66	TYR	0	-0.021	-0.021	19.930	-0.009	-0.009	0.000	0.000	0.000	0.000
65	F	67	LEU	0	0.009	-0.006	22.913	-0.012	-0.012	0.000	0.000	0.000	0.000
66	F	68	TRP	0	0.117	0.055	17.596	0.026	0.026	0.000	0.000	0.000	0.000
67	F	69	ASN	0	-0.021	-0.010	22.435	-0.027	-0.027	0.000	0.000	0.000	0.000
68	F	70	GLN	0	0.086	0.024	24.499	-0.001	-0.001	0.000	0.000	0.000	0.000
69	F	71	ASN	0	-0.047	-0.023	27.637	-0.017	-0.017	0.000	0.000	0.000	0.000
70	F	72	LEU	0	-0.033	-0.009	22.786	-0.003	-0.003	0.000	0.000	0.000	0.000
71	F	73	LEU	0	-0.072	-0.020	25.867	-0.005	-0.005	0.000	0.000	0.000	0.000
72	F	74	GLU	-1	-0.942	-0.961	28.663	0.046	0.046	0.000	0.000	0.000	0.000
73	F	75	VAL	0	-0.013	-0.007	31.670	-0.001	-0.001	0.000	0.000	0.000	0.000
74	F	76	LEU	0	-0.002	-0.006	34.729	-0.003	-0.003	0.000	0.000	0.000	0.000
75	F	77	SER	0	0.015	-0.011	37.257	-0.001	-0.001	0.000	0.000	0.000	0.000
76	F	78	ASP	-1	-0.814	-0.911	40.763	0.035	0.035	0.000	0.000	0.000	0.000
77	F	79	ALA	0	-0.020	-0.026	43.582	-0.002	-0.002	0.000	0.000	0.000	0.000
78	F	80	GLN	0	-0.021	0.011	38.141	-0.002	-0.002	0.000	0.000	0.000	0.000
79	F	81	LEU	0	0.022	0.009	38.589	-0.002	-0.002	0.000	0.000	0.000	0.000
80	F	82	MET	0	-0.062	-0.028	40.815	-0.002	-0.002	0.000	0.000	0.000	0.000
81	F	83	GLU	-1	-0.886	-0.922	40.158	0.013	0.013	0.000	0.000	0.000	0.000
82	F	84	VAL	0	0.062	0.024	36.862	-0.002	-0.002	0.000	0.000	0.000	0.000
83	F	85	ASN	0	-0.039	-0.034	39.793	-0.001	-0.001	0.000	0.000	0.000	0.000
84	F	86	ALA	0	-0.004	0.017	42.091	-0.001	-0.001	0.000	0.000	0.000	0.000
85	F	87	GLN	0	-0.002	-0.012	38.035	-0.001	-0.001	0.000	0.000	0.000	0.000
86	F	88	ILE	0	-0.042	-0.014	37.741	-0.001	-0.001	0.000	0.000	0.000	0.000
87	F	89	ASN	0	-0.037	-0.039	40.614	0.000	0.000	0.000	0.000	0.000	0.000
88	F	90	ASP	-1	-0.871	-0.917	43.168	0.003	0.003	0.000	0.000	0.000	0.000
89	F	91	LEU	0	0.008	-0.013	37.747	-0.001	-0.001	0.000	0.000	0.000	0.000
90	F	92	LYS	1	0.942	0.968	41.347	-0.021	-0.021	0.000	0.000	0.000	0.000
91	F	93	ALA	0	0.030	0.019	42.723	-0.001	-0.001	0.000	0.000	0.000	0.000
92	F	94	GLN	0	-0.134	-0.067	42.716	-0.003	-0.003	0.000	0.000	0.000	0.000
93	F	95	VAL	0	0.060	0.031	39.426	-0.002	-0.002	0.000	0.000	0.000	0.000
94	F	96	GLU	-1	-0.902	-0.908	42.695	0.002	0.002	0.000	0.000	0.000	0.000
95	F	97	LYS	1	0.951	0.974	45.632	0.002	0.002	0.000	0.000	0.000	0.000
96	F	98	LEU	0	0.004	-0.015	41.637	-0.001	-0.001	0.000	0.000	0.000	0.000
97	F	99	THR	0	-0.026	-0.024	42.935	-0.002	-0.002	0.000	0.000	0.000	0.000
98	F	100	GLN	0	-0.013	-0.009	44.376	-0.002	-0.002	0.000	0.000	0.000	0.000
99	F	101	GLN	0	-0.039	-0.015	46.924	-0.001	-0.001	0.000	0.000	0.000	0.000
100	F	102	GLY	0	0.023	0.007	44.745	-0.001	-0.001	0.000	0.000	0.000	0.000
101	F	103	GLU	-1	-0.956	-0.992	45.699	-0.002	-0.002	0.000	0.000	0.000	0.000
102	F	104	THR	0	-0.015	0.000	47.535	0.000	0.000	0.000	0.000	0.000	0.000
103	F	105	LEU	0	-0.016	-0.015	46.362	-0.001	-0.001	0.000	0.000	0.000	0.000
104	F	106	ARG	1	0.954	0.984	43.262	0.007	0.007	0.000	0.000	0.000	0.000
105	F	107	ILE	0	-0.028	-0.011	47.709	-0.001	-0.001	0.000	0.000	0.000	0.000
106	F	108	THR	0	-0.014	-0.014	51.282	0.000	0.000	0.000	0.000	0.000	0.000
107	F	109	GLN	0	-0.020	-0.015	44.673	0.000	0.000	0.000	0.000	0.000	0.000
108	F	110	ARG	1	0.978	0.993	49.453	0.008	0.008	0.000	0.000	0.000	0.000
109	F	111	ASN	0	-0.069	-0.047	50.749	0.000	0.000	0.000	0.000	0.000	0.000
110	F	112	LEU	0	-0.053	-0.024	52.722	0.000	0.000	0.000	0.000	0.000	0.000
111	F	113	GLU	-1	-0.928	-0.940	48.130	-0.018	-0.018	0.000	0.000	0.000	0.000
112	F	114	ALA	0	-0.049	-0.014	52.156	0.000	0.000	0.000	0.000	0.000	0.000
113	F	115	ALA	0	-0.014	-0.014	54.972	0.000	0.000	0.000	0.000	0.000	0.000
114	F	116	PRO	0	0.052	0.039	55.406	-0.001	-0.001	0.000	0.000	0.000	0.000
115	F	117	ILE	0	0.012	-0.006	53.540	0.001	0.001	0.000	0.000	0.000	0.000
116	F	118	THR	0	0.050	0.009	57.172	0.000	0.000	0.000	0.000	0.000	0.000
117	F	119	GLU	-1	-0.985	-0.997	58.846	-0.021	-0.021	0.000	0.000	0.000	0.000
118	F	120	VAL	0	0.053	0.019	56.368	0.000	0.000	0.000	0.000	0.000	0.000
119	F	121	LEU	0	0.036	0.036	59.778	0.001	0.001	0.000	0.000	0.000	0.000
120	F	122	LYS	1	0.894	0.937	61.974	0.017	0.017	0.000	0.000	0.000	0.000
121	F	123	GLN	0	0.055	0.025	60.821	0.000	0.000	0.000	0.000	0.000	0.000
122	F	124	GLU	-1	-0.905	-0.937	60.938	-0.014	-0.014	0.000	0.000	0.000	0.000
123	F	125	VAL	0	-0.011	-0.018	64.004	0.001	0.001	0.000	0.000	0.000	0.000
124	F	126	ASP	-1	-0.866	-0.919	67.175	-0.014	-0.014	0.000	0.000	0.000	0.000
125	F	127	GLU	-1	-0.969	-0.983	63.592	-0.016	-0.016	0.000	0.000	0.000	0.000
126	F	128	LEU	0	-0.034	-0.015	66.834	0.001	0.001	0.000	0.000	0.000	0.000
127	F	129	ARG	1	0.803	0.894	69.059	0.013	0.013	0.000	0.000	0.000	0.000
128	F	130	GLN	0	-0.018	-0.011	71.297	0.000	0.000	0.000	0.000	0.000	0.000
129	F	131	GLN	0	-0.025	-0.026	67.409	0.001	0.001	0.000	0.000	0.000	0.000
130	F	132	VAL	0	0.037	0.026	72.763	0.000	0.000	0.000	0.000	0.000	0.000
131	F	133	SER	0	0.001	0.015	75.246	0.000	0.000	0.000	0.000	0.000	0.000
132	F	134	ALA	0	-0.008	-0.007	75.119	0.000	0.000	0.000	0.000	0.000	0.000
133	F	135	ASN	0	-0.021	-0.028	73.936	0.000	0.000	0.000	0.000	0.000	0.000
134	F	136	ASP	-1	-0.780	-0.916	77.735	-0.008	-0.008	0.000	0.000	0.000	0.000
135	F	137	GLU	-1	-0.864	-0.918	80.387	-0.009	-0.009	0.000	0.000	0.000	0.000
136	F	138	LYS	1	0.858	0.916	79.221	0.010	0.010	0.000	0.000	0.000	0.000
137	F	139	LEU	0	-0.032	0.001	80.856	0.000	0.000	0.000	0.000	0.000	0.000
138	F	140	ARG	1	0.790	0.905	81.586	0.009	0.009	0.000	0.000	0.000	0.000
139	F	141	LEU	0	-0.078	-0.027	83.802	0.000	0.000	0.000	0.000	0.000	0.000
140	F	142	VAL	0	-0.041	-0.002	84.300	0.000	0.000	0.000	0.000	0.000	0.000
141	F	153	ASP	-1	-0.805	-0.884	95.888	-0.003	-0.003	0.000	0.000	0.000	0.000
142	F	154	MET	0	0.011	0.000	92.891	0.000	0.000	0.000	0.000	0.000	0.000
143	F	155	LEU	0	0.025	0.014	95.829	0.000	0.000	0.000	0.000	0.000	0.000
144	F	156	THR	0	0.006	-0.035	98.276	0.000	0.000	0.000	0.000	0.000	0.000
145	F	157	LEU	0	-0.028	-0.007	97.121	0.000	0.000	0.000	0.000	0.000	0.000
146	F	158	GLN	0	0.001	-0.009	97.690	0.000	0.000	0.000	0.000	0.000	0.000
147	F	159	LYS	1	0.776	0.868	100.050	0.002	0.002	0.000	0.000	0.000	0.000
148	F	160	ASN	0	-0.035	-0.013	103.324	0.000	0.000	0.000	0.000	0.000	0.000
149	F	161	TYR	0	0.060	0.016	102.051	0.000	0.000	0.000	0.000	0.000	0.000
150	F	162	LYS	1	0.874	0.942	102.005	0.002	0.002	0.000	0.000	0.000	0.000
151	F	163	ASP	-1	-0.814	-0.892	104.794	-0.002	-0.002	0.000	0.000	0.000	0.000
152	F	164	ALA	0	-0.070	-0.010	106.834	0.000	0.000	0.000	0.000	0.000	0.000
153	F	165	MET	0	-0.043	-0.012	105.501	0.000	0.000	0.000	0.000	0.000	0.000
154	F	205	MET	0	0.081	0.028	110.674	0.000	0.000	0.000	0.000	0.000	0.000
155	F	206	THR	0	0.015	0.015	107.764	0.000	0.000	0.000	0.000	0.000	0.000
156	F	207	THR	0	0.079	0.038	105.606	0.000	0.000	0.000	0.000	0.000	0.000
157	F	208	TYR	0	0.014	-0.003	104.955	0.000	0.000	0.000	0.000	0.000	0.000
158	F	209	THR	0	-0.054	-0.036	104.271	0.000	0.000	0.000	0.000	0.000	0.000
159	F	210	GLU	-1	-0.924	-0.964	101.338	-0.002	-0.002	0.000	0.000	0.000	0.000
160	F	211	MET	0	0.033	0.017	99.358	0.000	0.000	0.000	0.000	0.000	0.000
161	F	212	LYS	1	0.912	0.968	100.264	0.002	0.002	0.000	0.000	0.000	0.000
162	F	213	LYS	1	0.895	0.954	98.403	0.001	0.001	0.000	0.000	0.000	0.000
163	F	214	ALA	0	-0.020	-0.010	96.060	0.000	0.000	0.000	0.000	0.000	0.000
164	F	215	LEU	0	-0.028	-0.005	96.130	0.000	0.000	0.000	0.000	0.000	0.000
165	F	216	PRO	0	0.021	0.003	95.060	0.000	0.000	0.000	0.000	0.000	0.000
166	F	217	PRO	0	-0.009	-0.002	98.398	0.000	0.000	0.000	0.000	0.000	0.000
167	F	218	VAL	0	0.025	0.020	98.215	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:3:ALA)