FMO DATABASE

FMODB ID: KGZZ3

Calculation Name: 1Y6K-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y6K

Chain ID: L

ChEMBL ID:

UniProt ID: Q13651

Base Structure: X-ray

Registration Date: 2023-09-23

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1218379.425011
FMO2-HF: Nuclear repulsion	1156975.593038
FMO2-HF: Total energy	-61403.831973
FMO2-MP2: Total energy	-61577.099337

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(L:12:CYS)

Summations of interaction energy for fragment #1(L:12:CYS)

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.
-40.998	-32.11	16.314	-8.391	-16.812	-0.03

Interaction energy analysis for fragmet #1(L:12:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.012

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	L	14	HIS	0	0.018	-0.009	2.547	-4.992	-5.045	7.853	-3.329	-4.471	0.010
4	L	15	PHE	0	-0.006	-0.028	2.815	-2.910	-2.947	7.920	-0.842	-7.041	-0.013
5	L	16	PRO	0	-0.067	-0.017	4.206	-1.457	-1.650	0.033	0.325	-0.166	0.001
6	L	17	GLY	0	0.084	0.038	7.470	-0.543	-0.543	0.000	0.000	0.000	0.000
7	L	18	ASN	0	-0.043	-0.024	6.841	-0.481	-0.481	0.000	0.000	0.000	0.000
8	L	19	LEU	0	0.039	0.024	4.688	-0.329	-0.227	-0.002	-0.004	-0.095	0.000
9	L	20	PRO	0	0.046	0.039	8.554	-0.181	-0.181	0.000	0.000	0.000	0.000
10	L	21	ASN	0	0.011	0.000	12.231	-0.067	-0.067	0.000	0.000	0.000	0.000
11	L	22	MET	0	0.008	0.007	8.900	-0.214	-0.214	0.000	0.000	0.000	0.000
12	L	23	LEU	0	0.002	0.009	11.492	-0.098	-0.098	0.000	0.000	0.000	0.000
13	L	24	ARG	1	0.882	0.954	13.782	0.319	0.319	0.000	0.000	0.000	0.000
14	L	25	ASP	-1	-0.841	-0.912	14.788	-0.496	-0.496	0.000	0.000	0.000	0.000
15	L	26	LEU	0	-0.010	0.000	13.851	0.011	0.011	0.000	0.000	0.000	0.000
16	L	27	ARG	1	0.927	0.948	16.796	0.828	0.828	0.000	0.000	0.000	0.000
17	L	28	ASP	-1	-0.879	-0.945	19.598	-0.364	-0.364	0.000	0.000	0.000	0.000
18	L	29	ALA	0	-0.013	0.003	19.700	0.057	0.057	0.000	0.000	0.000	0.000
19	L	30	PHE	0	0.027	0.008	21.065	0.038	0.038	0.000	0.000	0.000	0.000
20	L	31	SER	0	-0.073	-0.049	22.779	0.058	0.058	0.000	0.000	0.000	0.000
21	L	32	ARG	1	0.903	0.949	24.648	0.385	0.385	0.000	0.000	0.000	0.000
22	L	33	VAL	0	0.018	0.008	25.117	0.022	0.022	0.000	0.000	0.000	0.000
23	L	34	LYS	1	0.906	0.971	26.662	0.409	0.409	0.000	0.000	0.000	0.000
24	L	35	THR	0	0.039	-0.004	28.102	-0.002	-0.002	0.000	0.000	0.000	0.000
25	L	36	PHE	0	0.048	0.033	30.964	0.012	0.012	0.000	0.000	0.000	0.000
26	L	37	PHE	0	0.057	0.003	27.389	0.010	0.010	0.000	0.000	0.000	0.000
27	L	38	GLN	0	-0.052	-0.021	27.833	0.024	0.024	0.000	0.000	0.000	0.000
28	L	39	MET	0	-0.043	0.001	31.998	0.018	0.018	0.000	0.000	0.000	0.000
29	L	40	LYS	1	0.932	0.965	33.674	0.320	0.320	0.000	0.000	0.000	0.000
30	L	41	ASP	-1	-0.960	-0.980	32.014	-0.401	-0.401	0.000	0.000	0.000	0.000
31	L	42	GLN	0	-0.015	-0.012	34.298	0.001	0.001	0.000	0.000	0.000	0.000
32	L	43	LEU	0	-0.059	-0.006	34.873	0.018	0.018	0.000	0.000	0.000	0.000
33	L	44	ASP	-1	-0.847	-0.917	34.905	-0.304	-0.304	0.000	0.000	0.000	0.000
34	L	45	ASN	0	-0.099	-0.041	33.132	0.006	0.006	0.000	0.000	0.000	0.000
35	L	46	LEU	0	0.016	0.014	26.689	-0.010	-0.010	0.000	0.000	0.000	0.000
36	L	47	LEU	0	0.056	0.021	26.722	0.011	0.011	0.000	0.000	0.000	0.000
37	L	48	LEU	0	-0.002	-0.003	22.018	-0.014	-0.014	0.000	0.000	0.000	0.000
38	L	49	LYS	1	0.886	0.922	25.139	0.455	0.455	0.000	0.000	0.000	0.000
39	L	50	GLU	-1	-0.891	-0.952	24.217	-0.556	-0.556	0.000	0.000	0.000	0.000
40	L	51	SER	0	0.046	0.018	24.189	-0.011	-0.011	0.000	0.000	0.000	0.000
41	L	52	LEU	0	0.030	0.019	20.168	-0.025	-0.025	0.000	0.000	0.000	0.000
42	L	53	LEU	0	-0.046	-0.012	18.676	-0.112	-0.112	0.000	0.000	0.000	0.000
43	L	54	GLU	-1	-0.876	-0.957	19.547	-0.657	-0.657	0.000	0.000	0.000	0.000
44	L	55	ASP	-1	-0.886	-0.943	19.883	-0.822	-0.822	0.000	0.000	0.000	0.000
45	L	56	PHE	0	-0.125	-0.071	15.517	-0.149	-0.149	0.000	0.000	0.000	0.000
46	L	57	LYS	1	0.873	0.939	15.490	0.559	0.559	0.000	0.000	0.000	0.000
47	L	58	GLY	0	0.058	0.056	17.704	0.079	0.079	0.000	0.000	0.000	0.000
48	L	59	TYR	0	-0.007	-0.014	16.945	-0.118	-0.118	0.000	0.000	0.000	0.000
49	L	60	LEU	0	0.010	-0.004	17.498	0.010	0.010	0.000	0.000	0.000	0.000
50	L	61	GLY	0	0.008	0.017	15.000	-0.095	-0.095	0.000	0.000	0.000	0.000
51	L	62	CYS	0	-0.063	-0.010	8.209	-0.070	-0.070	0.000	0.000	0.000	0.000
52	L	63	GLN	0	0.034	0.023	12.465	-0.342	-0.342	0.000	0.000	0.000	0.000
53	L	64	ALA	0	0.083	0.047	15.097	0.000	0.000	0.000	0.000	0.000	0.000
54	L	65	LEU	0	-0.044	-0.020	10.606	-0.026	-0.026	0.000	0.000	0.000	0.000
55	L	66	SER	0	-0.011	-0.047	12.019	-0.230	-0.230	0.000	0.000	0.000	0.000
56	L	67	GLU	-1	-0.899	-0.947	13.190	-1.029	-1.029	0.000	0.000	0.000	0.000
57	L	68	MET	0	0.015	0.032	16.401	0.117	0.117	0.000	0.000	0.000	0.000
58	L	69	ILE	0	-0.060	-0.026	11.158	0.014	0.014	0.000	0.000	0.000	0.000
59	L	70	GLN	0	-0.015	-0.025	15.070	-0.095	-0.095	0.000	0.000	0.000	0.000
60	L	71	PHE	0	0.029	0.024	16.927	0.112	0.112	0.000	0.000	0.000	0.000
61	L	72	TYR	0	-0.016	-0.028	18.296	0.121	0.121	0.000	0.000	0.000	0.000
62	L	73	LEU	0	-0.052	-0.048	14.358	0.068	0.068	0.000	0.000	0.000	0.000
63	L	74	GLU	-1	-0.941	-0.950	18.797	-1.006	-1.006	0.000	0.000	0.000	0.000
64	L	75	GLU	-1	-0.893	-0.948	21.296	-0.678	-0.678	0.000	0.000	0.000	0.000
65	L	76	VAL	0	-0.015	-0.004	22.861	0.052	0.052	0.000	0.000	0.000	0.000
66	L	77	MET	0	-0.062	-0.035	19.967	0.006	0.006	0.000	0.000	0.000	0.000
67	L	78	PRO	0	0.027	0.030	22.537	0.072	0.072	0.000	0.000	0.000	0.000
68	L	79	GLN	0	-0.036	-0.024	25.382	0.030	0.030	0.000	0.000	0.000	0.000
69	L	80	ALA	0	0.018	0.018	27.053	0.042	0.042	0.000	0.000	0.000	0.000
70	L	81	GLU	-1	-0.907	-0.959	23.852	-0.641	-0.641	0.000	0.000	0.000	0.000
71	L	82	ASN	0	-0.063	-0.049	28.101	0.045	0.045	0.000	0.000	0.000	0.000
72	L	83	GLN	0	-0.022	-0.012	30.602	0.011	0.011	0.000	0.000	0.000	0.000
73	L	84	ASP	-1	-0.877	-0.920	32.073	-0.323	-0.323	0.000	0.000	0.000	0.000
74	L	85	PRO	0	-0.028	-0.049	31.850	-0.014	-0.014	0.000	0.000	0.000	0.000
75	L	86	ASP	-1	-0.916	-0.937	32.161	-0.295	-0.295	0.000	0.000	0.000	0.000
76	L	87	ILE	0	-0.014	-0.017	28.790	0.000	0.000	0.000	0.000	0.000	0.000
77	L	88	LYS	1	0.896	0.993	27.918	0.371	0.371	0.000	0.000	0.000	0.000
78	L	89	ALA	0	-0.014	0.007	26.439	-0.034	-0.034	0.000	0.000	0.000	0.000
79	L	90	HIS	0	0.038	0.001	24.975	-0.061	-0.061	0.000	0.000	0.000	0.000
80	L	91	VAL	0	-0.004	0.004	23.714	-0.045	-0.045	0.000	0.000	0.000	0.000
81	L	92	ASN	0	0.049	0.034	21.494	-0.100	-0.100	0.000	0.000	0.000	0.000
82	L	93	SER	0	-0.031	-0.039	20.354	-0.065	-0.065	0.000	0.000	0.000	0.000
83	L	94	LEU	0	-0.032	0.010	19.026	-0.084	-0.084	0.000	0.000	0.000	0.000
84	L	95	GLY	0	0.068	0.019	17.588	-0.149	-0.149	0.000	0.000	0.000	0.000
85	L	96	GLU	-1	-0.930	-0.963	16.037	-1.234	-1.234	0.000	0.000	0.000	0.000
86	L	97	ASN	0	-0.058	-0.048	14.368	-0.206	-0.206	0.000	0.000	0.000	0.000
87	L	98	LEU	0	0.037	0.033	12.879	-0.287	-0.287	0.000	0.000	0.000	0.000
88	L	99	LYS	1	0.959	0.983	11.636	0.614	0.614	0.000	0.000	0.000	0.000
89	L	100	THR	0	-0.020	-0.025	10.029	-0.630	-0.630	0.000	0.000	0.000	0.000
90	L	101	LEU	0	-0.005	-0.006	7.944	-0.387	-0.387	0.000	0.000	0.000	0.000
91	L	102	ARG	1	0.918	0.954	7.140	1.133	1.133	0.000	0.000	0.000	0.000
92	L	103	LEU	0	-0.059	-0.033	6.051	-2.398	-2.398	0.000	0.000	0.000	0.000
93	L	104	ARG	1	0.911	0.938	3.982	-4.676	-4.375	0.009	-0.114	-0.196	-0.001
94	L	105	LEU	0	-0.001	0.008	3.068	-6.725	-4.406	0.123	-1.068	-1.374	-0.009
95	L	106	ARG	1	0.975	1.007	2.786	-4.013	0.045	0.374	-2.429	-2.003	-0.023
98	L	110	ARG	1	0.981	0.972	3.842	-2.988	-1.339	-0.015	-0.828	-0.807	0.005
99	L	111	PHE	0	-0.025	0.027	3.225	1.176	1.839	0.021	-0.099	-0.585	0.000
100	L	112	LEU	0	0.059	0.015	5.178	1.129	1.129	0.000	0.000	0.000	0.000
101	L	113	PRO	0	-0.024	-0.020	6.823	0.023	0.023	0.000	0.000	0.000	0.000
102	L	115	GLU	-1	-0.832	-0.911	8.167	-3.979	-3.979	0.000	0.000	0.000	0.000
103	L	116	ASN	0	-0.069	-0.033	4.824	-1.313	-1.234	-0.002	-0.003	-0.074	0.000
104	L	117	LYS	1	0.950	0.976	8.305	1.343	1.343	0.000	0.000	0.000	0.000
105	L	118	SER	0	0.034	0.020	10.280	0.366	0.366	0.000	0.000	0.000	0.000
106	L	119	LYS	1	1.009	0.987	10.863	-1.545	-1.545	0.000	0.000	0.000	0.000
107	L	120	ALA	0	0.048	0.028	12.963	-0.065	-0.065	0.000	0.000	0.000	0.000
108	L	121	VAL	0	0.039	0.008	16.018	-0.050	-0.050	0.000	0.000	0.000	0.000
109	L	122	GLU	-1	-0.916	-0.949	14.552	-0.107	-0.107	0.000	0.000	0.000	0.000
110	L	123	GLN	0	0.004	-0.019	16.182	-0.054	-0.054	0.000	0.000	0.000	0.000
111	L	124	VAL	0	0.027	0.024	18.645	-0.028	-0.028	0.000	0.000	0.000	0.000
112	L	125	LYS	1	0.957	0.986	18.673	0.236	0.236	0.000	0.000	0.000	0.000
113	L	126	ASN	0	0.030	0.020	18.256	-0.034	-0.034	0.000	0.000	0.000	0.000
114	L	127	ALA	0	-0.056	-0.028	22.112	-0.007	-0.007	0.000	0.000	0.000	0.000
115	L	128	PHE	0	0.018	0.007	24.368	-0.010	-0.010	0.000	0.000	0.000	0.000
116	L	129	ASN	0	-0.005	-0.017	23.164	-0.008	-0.008	0.000	0.000	0.000	0.000
117	L	130	LYS	1	0.883	0.938	22.130	-0.219	-0.219	0.000	0.000	0.000	0.000
118	L	131	LEU	0	-0.053	0.004	27.743	0.007	0.007	0.000	0.000	0.000	0.000
119	L	132	GLN	0	0.010	-0.004	29.902	-0.008	-0.008	0.000	0.000	0.000	0.000
120	L	133	GLU	-1	-0.887	-0.929	31.541	-0.004	-0.004	0.000	0.000	0.000	0.000
121	L	134	LYS	1	0.938	0.953	33.953	-0.047	-0.047	0.000	0.000	0.000	0.000
122	L	135	GLY	0	0.008	-0.004	30.536	0.009	0.009	0.000	0.000	0.000	0.000
123	L	136	ILE	0	0.004	0.002	31.055	-0.003	-0.003	0.000	0.000	0.000	0.000
124	L	137	TYR	0	0.006	-0.010	32.618	-0.003	-0.003	0.000	0.000	0.000	0.000
125	L	138	LYS	1	0.952	0.994	30.437	-0.088	-0.088	0.000	0.000	0.000	0.000
126	L	139	ALA	0	0.018	0.007	28.770	0.005	0.005	0.000	0.000	0.000	0.000
127	L	140	MET	0	-0.013	-0.009	30.073	-0.008	-0.008	0.000	0.000	0.000	0.000
128	L	141	SER	0	-0.023	-0.014	33.073	-0.002	-0.002	0.000	0.000	0.000	0.000
129	L	142	GLU	-1	-0.909	-0.945	28.962	0.103	0.103	0.000	0.000	0.000	0.000
130	L	143	PHE	0	-0.005	0.000	30.474	0.000	0.000	0.000	0.000	0.000	0.000
131	L	144	ASP	-1	-0.857	-0.930	30.927	0.018	0.018	0.000	0.000	0.000	0.000
132	L	145	ILE	0	0.020	0.014	27.544	0.004	0.004	0.000	0.000	0.000	0.000
133	L	146	PHE	0	-0.068	-0.030	24.063	-0.002	-0.002	0.000	0.000	0.000	0.000
134	L	147	ILE	0	0.015	-0.007	27.265	-0.009	-0.009	0.000	0.000	0.000	0.000
135	L	148	ASN	0	0.054	0.027	29.333	-0.015	-0.015	0.000	0.000	0.000	0.000
136	L	149	TYR	0	-0.082	-0.031	23.931	0.024	0.024	0.000	0.000	0.000	0.000
137	L	150	ILE	0	-0.047	-0.024	24.909	-0.007	-0.007	0.000	0.000	0.000	0.000
138	L	151	GLU	-1	-0.917	-0.965	25.943	-0.034	-0.034	0.000	0.000	0.000	0.000
139	L	152	ALA	0	-0.019	-0.014	25.437	-0.001	-0.001	0.000	0.000	0.000	0.000
140	L	153	TYR	0	-0.084	-0.045	18.944	-0.012	-0.012	0.000	0.000	0.000	0.000
141	L	154	MET	0	-0.002	-0.014	23.578	-0.012	-0.012	0.000	0.000	0.000	0.000
142	L	155	THR	0	-0.093	-0.007	25.814	-0.014	-0.014	0.000	0.000	0.000	0.000
143	L	156	MET	0	-0.065	-0.030	20.272	0.028	0.028	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:12:CYS)