FMO DATABASE

FMODB ID: 6G6GZ

Calculation Name: 2YZI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YZI

Chain ID: A

ChEMBL ID:

UniProt ID: O57847

Base Structure: X-ray

Registration Date: 2023-09-26

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1137559.133371
FMO2-HF: Nuclear repulsion	1085021.982271
FMO2-HF: Total energy	-52537.1511
FMO2-MP2: Total energy	-52688.239617

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(A:4:MET)

Summations of interaction energy for fragment #1(A:4:MET)

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.
-25.43	-15.203	19.116	-9.34	-20.002	-0.079

Interaction energy analysis for fragmet #1(A:4:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : 0.002

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	A	6	MET	0	-0.029	-0.019	2.537	-0.368	2.482	1.640	-1.519	-2.971	0.009
4	A	7	LYS	1	0.919	0.948	6.194	1.439	1.439	0.000	0.000	0.000	0.000
5	A	8	ALA	0	0.059	0.050	5.358	0.239	0.239	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.044	-0.017	7.445	0.535	0.535	0.000	0.000	0.000	0.000
7	A	10	ILE	0	0.062	0.022	8.041	0.174	0.174	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.919	0.938	9.223	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	12	VAL	0	-0.087	-0.036	6.245	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	13	TYR	0	-0.016	-0.027	2.331	-1.598	0.172	1.990	-1.253	-2.507	-0.008
11	A	14	MET	0	-0.050	0.024	7.462	0.137	0.137	0.000	0.000	0.000	0.000
12	A	15	THR	0	0.048	0.040	10.910	-0.208	-0.208	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.992	0.968	13.934	-0.532	-0.532	0.000	0.000	0.000	0.000
14	A	17	LYS	1	0.868	0.976	17.094	-0.564	-0.564	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.030	-0.015	18.670	0.032	0.032	0.000	0.000	0.000	0.000
16	A	19	LEU	0	0.022	0.004	20.235	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	20	GLY	0	0.038	-0.004	23.855	0.017	0.017	0.000	0.000	0.000	0.000
18	A	21	VAL	0	-0.037	-0.004	26.572	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	22	LYS	1	1.013	1.017	29.890	-0.181	-0.181	0.000	0.000	0.000	0.000
20	A	23	PRO	0	0.061	0.022	33.033	0.005	0.005	0.000	0.000	0.000	0.000
21	A	24	SER	0	0.014	-0.004	33.955	0.003	0.003	0.000	0.000	0.000	0.000
22	A	25	THR	0	-0.032	-0.019	31.964	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	26	SER	0	0.075	0.050	34.024	0.008	0.008	0.000	0.000	0.000	0.000
24	A	27	VAL	0	0.025	0.000	30.405	0.014	0.014	0.000	0.000	0.000	0.000
25	A	28	GLN	0	0.000	0.005	30.967	0.011	0.011	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.840	-0.918	32.108	0.221	0.221	0.000	0.000	0.000	0.000
27	A	30	ALA	0	0.021	0.000	28.338	0.013	0.013	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.022	-0.026	27.449	0.027	0.027	0.000	0.000	0.000	0.000
29	A	32	ARG	1	0.810	0.905	27.790	-0.209	-0.209	0.000	0.000	0.000	0.000
30	A	33	LEU	0	-0.016	-0.009	28.156	0.009	0.009	0.000	0.000	0.000	0.000
31	A	34	MET	0	-0.067	-0.033	23.687	0.028	0.028	0.000	0.000	0.000	0.000
32	A	35	MET	0	-0.053	-0.031	23.917	0.044	0.044	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.871	-0.906	25.954	0.249	0.249	0.000	0.000	0.000	0.000
34	A	37	PHE	0	-0.062	-0.045	24.004	0.017	0.017	0.000	0.000	0.000	0.000
35	A	38	ASP	-1	-0.929	-0.955	19.806	0.570	0.570	0.000	0.000	0.000	0.000
36	A	39	VAL	0	-0.003	0.013	19.256	0.062	0.062	0.000	0.000	0.000	0.000
37	A	40	GLY	0	-0.025	-0.024	18.191	-0.042	-0.042	0.000	0.000	0.000	0.000
38	A	41	SER	0	0.006	-0.022	18.938	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	42	LEU	0	-0.013	0.006	20.750	0.007	0.007	0.000	0.000	0.000	0.000
40	A	43	VAL	0	0.016	0.008	22.178	0.006	0.006	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.034	-0.012	24.756	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	45	ILE	0	0.001	0.010	26.839	0.008	0.008	0.000	0.000	0.000	0.000
43	A	46	ASN	0	0.012	0.005	30.111	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.859	-0.947	33.445	0.161	0.161	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.965	-0.973	34.088	0.150	0.150	0.000	0.000	0.000	0.000
46	A	49	GLY	0	-0.026	-0.011	31.520	0.001	0.001	0.000	0.000	0.000	0.000
47	A	50	ASN	0	-0.038	-0.021	28.921	0.025	0.025	0.000	0.000	0.000	0.000
48	A	51	VAL	0	-0.023	-0.018	24.337	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	52	VAL	0	-0.018	-0.009	27.585	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	53	GLY	0	-0.008	-0.027	27.064	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	54	PHE	0	-0.003	-0.005	18.345	0.019	0.019	0.000	0.000	0.000	0.000
52	A	55	PHE	0	0.006	0.011	23.580	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	56	THR	0	0.042	0.010	18.596	0.015	0.015	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.995	0.986	20.502	-0.486	-0.486	0.000	0.000	0.000	0.000
55	A	58	SER	0	0.002	-0.002	20.237	-0.030	-0.030	0.000	0.000	0.000	0.000
56	A	59	ASP	-1	-0.853	-0.923	22.296	0.352	0.352	0.000	0.000	0.000	0.000
57	A	60	ILE	0	0.021	0.018	24.574	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	61	ILE	0	0.017	-0.001	24.042	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	62	ARG	1	0.890	0.920	23.935	-0.310	-0.310	0.000	0.000	0.000	0.000
60	A	63	ARG	1	0.845	0.905	25.950	-0.285	-0.285	0.000	0.000	0.000	0.000
61	A	64	VAL	0	0.017	0.022	30.304	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	65	ILE	0	-0.012	-0.004	29.475	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	66	VAL	0	-0.034	-0.012	30.088	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	67	PRO	0	-0.088	-0.021	32.299	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	68	GLY	0	0.050	0.025	35.170	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	69	LEU	0	-0.082	-0.038	35.368	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	70	PRO	0	0.058	0.049	36.525	0.005	0.005	0.000	0.000	0.000	0.000
68	A	71	TYR	0	0.041	-0.005	34.499	0.007	0.007	0.000	0.000	0.000	0.000
69	A	72	ASP	-1	-0.915	-0.966	35.029	0.158	0.158	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.004	0.011	34.114	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	74	PRO	0	0.052	0.019	35.295	0.011	0.011	0.000	0.000	0.000	0.000
72	A	75	VAL	0	0.014	0.014	29.870	0.002	0.002	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.901	-0.970	30.933	0.180	0.180	0.000	0.000	0.000	0.000
74	A	77	ARG	1	0.927	0.963	33.033	-0.157	-0.157	0.000	0.000	0.000	0.000
75	A	78	ILE	0	-0.014	0.000	28.788	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	79	MET	0	-0.071	0.027	27.467	0.024	0.024	0.000	0.000	0.000	0.000
77	A	80	THR	0	-0.049	-0.026	23.654	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	81	ARG	1	0.998	0.989	26.437	-0.194	-0.194	0.000	0.000	0.000	0.000
79	A	82	ASN	0	-0.024	-0.008	25.486	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.005	-0.003	22.659	0.022	0.022	0.000	0.000	0.000	0.000
81	A	84	ILE	0	0.004	0.029	18.408	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	85	THR	0	-0.035	-0.020	18.048	0.043	0.043	0.000	0.000	0.000	0.000
83	A	86	ALA	0	-0.012	-0.015	14.372	-0.026	-0.026	0.000	0.000	0.000	0.000
84	A	87	ASN	0	0.065	0.046	16.114	0.001	0.001	0.000	0.000	0.000	0.000
85	A	88	VAL	0	0.052	0.018	14.186	0.099	0.099	0.000	0.000	0.000	0.000
86	A	89	ASN	0	-0.003	-0.017	12.868	0.052	0.052	0.000	0.000	0.000	0.000
87	A	90	THR	0	-0.033	0.000	12.463	-0.122	-0.122	0.000	0.000	0.000	0.000
88	A	91	PRO	0	0.009	0.019	9.597	0.194	0.194	0.000	0.000	0.000	0.000
89	A	92	LEU	0	0.059	0.017	3.130	-0.670	-0.518	1.471	-0.326	-1.296	0.005
90	A	93	GLY	0	0.034	0.008	7.476	0.129	0.129	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.879	-0.924	8.766	0.308	0.308	0.000	0.000	0.000	0.000
92	A	95	VAL	0	-0.007	-0.004	9.512	-0.063	-0.063	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.013	-0.002	4.600	-0.282	-0.172	-0.001	-0.010	-0.100	0.000
94	A	97	ARG	1	0.805	0.899	9.098	-0.498	-0.498	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.937	0.983	12.286	-0.509	-0.509	0.000	0.000	0.000	0.000
96	A	99	MET	0	-0.027	-0.026	10.466	0.020	0.020	0.000	0.000	0.000	0.000
97	A	100	ALA	0	-0.005	0.002	11.655	-0.065	-0.065	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.912	-0.942	13.322	0.215	0.215	0.000	0.000	0.000	0.000
99	A	102	HIS	0	-0.034	-0.032	16.394	-0.040	-0.040	0.000	0.000	0.000	0.000
100	A	103	ARG	1	0.891	0.964	15.760	-0.294	-0.294	0.000	0.000	0.000	0.000
101	A	104	ILE	0	-0.009	0.013	14.532	-0.024	-0.024	0.000	0.000	0.000	0.000
102	A	105	LYS	1	0.929	0.949	12.492	-0.499	-0.499	0.000	0.000	0.000	0.000
103	A	106	HIS	0	-0.007	-0.020	12.879	0.103	0.103	0.000	0.000	0.000	0.000
104	A	107	ILE	0	-0.006	0.010	12.349	-0.112	-0.112	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.026	0.013	14.878	0.082	0.082	0.000	0.000	0.000	0.000
106	A	109	ILE	0	-0.004	-0.011	12.954	0.025	0.025	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.850	-0.927	16.733	0.295	0.295	0.000	0.000	0.000	0.000
108	A	111	GLU	-1	-0.927	-0.965	18.486	0.306	0.306	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.920	-0.948	20.684	0.137	0.137	0.000	0.000	0.000	0.000
110	A	113	GLY	0	-0.022	-0.029	22.921	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	114	LYS	1	0.908	0.948	23.708	-0.195	-0.195	0.000	0.000	0.000	0.000
112	A	115	ILE	0	-0.025	-0.016	20.520	0.025	0.025	0.000	0.000	0.000	0.000
113	A	116	VAL	0	0.035	0.020	17.575	-0.016	-0.016	0.000	0.000	0.000	0.000
114	A	117	GLY	0	-0.004	-0.008	16.694	0.017	0.017	0.000	0.000	0.000	0.000
115	A	118	ILE	0	-0.043	-0.020	14.792	-0.052	-0.052	0.000	0.000	0.000	0.000
116	A	119	PHE	0	0.058	0.035	5.901	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	120	THR	0	-0.002	-0.009	11.054	-0.158	-0.158	0.000	0.000	0.000	0.000
118	A	121	LEU	0	0.033	-0.003	7.820	0.320	0.320	0.000	0.000	0.000	0.000
119	A	122	SER	0	0.014	0.004	7.752	0.163	0.163	0.000	0.000	0.000	0.000
120	A	123	ASP	-1	-0.797	-0.898	8.732	1.721	1.721	0.000	0.000	0.000	0.000
121	A	124	LEU	0	-0.022	-0.007	2.428	0.064	0.663	0.863	-0.239	-1.223	0.000
122	A	125	LEU	0	-0.013	0.015	4.074	1.449	1.897	0.023	-0.151	-0.320	-0.001
123	A	126	GLU	-1	-0.870	-0.955	6.165	1.746	1.746	0.000	0.000	0.000	0.000
124	A	127	ALA	0	-0.046	-0.024	3.274	-1.308	-0.732	1.012	-0.407	-1.182	0.002
125	A	128	SER	0	-0.042	-0.047	2.314	-4.679	-2.354	5.908	-3.219	-5.014	-0.021
126	A	129	ARG	1	0.902	0.959	3.168	-0.677	-2.707	0.020	2.539	-0.529	-0.002
127	A	130	ARG	1	0.865	0.950	3.826	-2.453	-2.201	0.000	-0.031	-0.220	0.000
128	A	131	ARG	1	0.956	0.972	4.577	0.095	0.288	-0.001	-0.007	-0.185	0.000
129	A	132	LEU	0	-0.016	0.005	6.040	-0.541	-0.541	0.000	0.000	0.000	0.000
130	A	133	GLU	-1	-0.820	-0.910	2.029	-20.008	-17.063	6.192	-4.716	-4.421	-0.063
131	A	134	THR	0	-0.057	-0.038	5.257	0.756	0.793	-0.001	-0.001	-0.034	0.000
132	A	135	ALA	0	0.012	0.013	7.682	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:MET)