FMO DATABASE

FMODB ID: 6NKMZ

Calculation Name: 2YZ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YZ1

Chain ID: A

ChEMBL ID:

UniProt ID: P97797

Base Structure: X-ray

Registration Date: 2023-09-19

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-849664.049363
FMO2-HF: Nuclear repulsion	805957.082101
FMO2-HF: Total energy	-43706.967261
FMO2-MP2: Total energy	-43834.619459

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:7:GLU)

Summations of interaction energy for fragment #1(A:7: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.
-109.285	-109.206	19.432	-10.189	-9.32	0.102

Interaction energy analysis for fragmet #1(A:7:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.810 / q_NPA : -0.892

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	9	LYS	1	0.889	0.926	1.680	-108.883	-109.967	19.436	-9.690	-8.662	0.101
4	A	10	VAL	0	0.014	0.001	4.581	-5.345	-5.279	-0.001	-0.015	-0.050	0.000
5	A	11	THR	0	-0.005	-0.006	8.344	1.658	1.658	0.000	0.000	0.000	0.000
6	A	12	GLN	0	0.024	-0.004	10.082	-0.664	-0.664	0.000	0.000	0.000	0.000
7	A	13	PRO	0	-0.045	-0.025	13.809	0.370	0.370	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.885	-0.927	13.466	21.256	21.256	0.000	0.000	0.000	0.000
9	A	15	LYS	1	0.941	0.955	17.049	-14.820	-14.820	0.000	0.000	0.000	0.000
10	A	16	SER	0	-0.031	-0.017	20.693	0.305	0.305	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.081	-0.045	23.750	-0.151	-0.151	0.000	0.000	0.000	0.000
12	A	18	SER	0	0.027	0.013	25.615	-0.150	-0.150	0.000	0.000	0.000	0.000
13	A	19	VAL	0	-0.019	-0.013	29.339	-0.053	-0.053	0.000	0.000	0.000	0.000
14	A	20	ALA	0	0.055	0.033	31.311	-0.084	-0.084	0.000	0.000	0.000	0.000
15	A	21	ALA	0	0.046	0.014	34.418	0.139	0.139	0.000	0.000	0.000	0.000
16	A	22	GLY	0	-0.025	-0.007	35.366	-0.251	-0.251	0.000	0.000	0.000	0.000
17	A	23	ASP	-1	-0.876	-0.918	32.972	8.841	8.841	0.000	0.000	0.000	0.000
18	A	24	SER	0	-0.040	-0.025	30.445	0.129	0.129	0.000	0.000	0.000	0.000
19	A	25	THR	0	-0.022	-0.010	25.733	0.116	0.116	0.000	0.000	0.000	0.000
20	A	26	VAL	0	-0.046	-0.022	21.886	-0.082	-0.082	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.001	0.021	20.095	0.218	0.218	0.000	0.000	0.000	0.000
22	A	28	ASN	0	0.016	-0.010	16.837	-0.226	-0.226	0.000	0.000	0.000	0.000
23	A	29	CYS	0	-0.023	-0.005	13.542	0.284	0.284	0.000	0.000	0.000	0.000
24	A	30	THR	0	-0.029	0.004	10.624	-1.379	-1.379	0.000	0.000	0.000	0.000
25	A	31	LEU	0	-0.008	-0.002	8.648	1.694	1.694	0.000	0.000	0.000	0.000
26	A	32	THR	0	-0.005	-0.013	3.924	-2.963	-2.153	-0.001	-0.457	-0.352	0.001
27	A	33	SER	0	0.019	-0.010	4.536	-2.487	-2.388	-0.001	-0.012	-0.085	0.000
28	A	34	LEU	0	-0.017	-0.016	6.632	0.037	0.037	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.039	0.018	7.261	-1.584	-1.584	0.000	0.000	0.000	0.000
30	A	36	PRO	0	0.067	0.013	7.264	2.951	2.951	0.000	0.000	0.000	0.000
31	A	37	VAL	0	0.043	0.009	10.232	0.421	0.421	0.000	0.000	0.000	0.000
32	A	38	GLY	0	0.025	0.008	13.419	-0.084	-0.084	0.000	0.000	0.000	0.000
33	A	39	PRO	0	-0.006	0.022	14.979	0.698	0.698	0.000	0.000	0.000	0.000
34	A	40	ILE	0	-0.005	0.010	13.323	1.459	1.459	0.000	0.000	0.000	0.000
35	A	41	LYS	1	0.823	0.903	16.241	-17.109	-17.109	0.000	0.000	0.000	0.000
36	A	42	TRP	0	0.006	-0.014	17.596	1.131	1.131	0.000	0.000	0.000	0.000
37	A	43	TYR	0	0.008	0.001	18.710	-0.558	-0.558	0.000	0.000	0.000	0.000
38	A	44	ARG	1	0.857	0.936	20.951	-10.876	-10.876	0.000	0.000	0.000	0.000
39	A	45	GLY	0	0.007	0.009	22.896	-0.374	-0.374	0.000	0.000	0.000	0.000
40	A	46	VAL	0	0.008	-0.007	21.412	0.712	0.712	0.000	0.000	0.000	0.000
41	A	47	GLY	0	0.025	0.015	21.930	-0.589	-0.589	0.000	0.000	0.000	0.000
42	A	48	GLN	0	0.012	-0.013	21.473	0.732	0.732	0.000	0.000	0.000	0.000
43	A	49	SER	0	-0.024	-0.008	23.936	-0.052	-0.052	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.816	0.919	16.598	-18.241	-18.241	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.045	0.019	24.030	-0.056	-0.056	0.000	0.000	0.000	0.000
46	A	52	LEU	0	-0.035	-0.018	22.230	0.491	0.491	0.000	0.000	0.000	0.000
47	A	53	ILE	0	-0.029	-0.007	23.425	-0.528	-0.528	0.000	0.000	0.000	0.000
48	A	54	TYR	0	0.017	0.002	21.723	-0.626	-0.626	0.000	0.000	0.000	0.000
49	A	55	SER	0	0.009	0.003	21.347	0.921	0.921	0.000	0.000	0.000	0.000
50	A	56	PHE	0	-0.036	-0.015	18.565	-0.668	-0.668	0.000	0.000	0.000	0.000
51	A	57	THR	0	0.013	-0.013	19.048	0.907	0.907	0.000	0.000	0.000	0.000
52	A	58	GLY	0	0.014	0.014	19.101	0.586	0.586	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.797	-0.903	17.699	14.290	14.290	0.000	0.000	0.000	0.000
54	A	60	HIS	0	0.021	0.010	20.639	0.676	0.676	0.000	0.000	0.000	0.000
55	A	61	PHE	0	0.004	0.014	15.900	-0.303	-0.303	0.000	0.000	0.000	0.000
56	A	62	PRO	0	0.003	-0.006	19.534	0.004	0.004	0.000	0.000	0.000	0.000
57	A	63	ARG	1	0.896	0.945	20.878	-11.033	-11.033	0.000	0.000	0.000	0.000
58	A	64	VAL	0	-0.034	-0.018	22.185	-0.579	-0.579	0.000	0.000	0.000	0.000
59	A	65	THR	0	-0.024	-0.022	18.284	0.390	0.390	0.000	0.000	0.000	0.000
60	A	66	ASN	0	0.007	0.008	18.086	0.518	0.518	0.000	0.000	0.000	0.000
61	A	67	VAL	0	-0.015	-0.005	20.009	-0.440	-0.440	0.000	0.000	0.000	0.000
62	A	68	SER	0	-0.014	-0.012	17.404	0.647	0.647	0.000	0.000	0.000	0.000
63	A	69	ASP	-1	-0.828	-0.897	18.939	12.970	12.970	0.000	0.000	0.000	0.000
64	A	70	ALA	0	-0.019	-0.015	19.892	0.394	0.394	0.000	0.000	0.000	0.000
65	A	71	THR	0	-0.057	-0.053	22.370	-0.401	-0.401	0.000	0.000	0.000	0.000
66	A	72	LYS	1	0.802	0.931	16.255	-16.919	-16.919	0.000	0.000	0.000	0.000
67	A	73	ARG	1	0.894	0.931	20.463	-13.668	-13.668	0.000	0.000	0.000	0.000
68	A	74	ASN	0	0.025	0.000	14.667	0.704	0.704	0.000	0.000	0.000	0.000
69	A	75	ASN	0	0.047	0.015	13.021	0.036	0.036	0.000	0.000	0.000	0.000
70	A	76	MET	0	-0.018	0.016	8.849	-0.040	-0.040	0.000	0.000	0.000	0.000
71	A	77	ASP	-1	-0.790	-0.857	13.044	16.682	16.682	0.000	0.000	0.000	0.000
72	A	78	PHE	0	0.020	-0.005	13.154	-0.556	-0.556	0.000	0.000	0.000	0.000
73	A	79	SER	0	0.012	-0.020	16.936	0.050	0.050	0.000	0.000	0.000	0.000
74	A	80	ILE	0	-0.022	0.009	19.185	-0.530	-0.530	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.951	0.964	22.406	-10.832	-10.832	0.000	0.000	0.000	0.000
76	A	82	ILE	0	0.005	0.019	24.805	-0.098	-0.098	0.000	0.000	0.000	0.000
77	A	83	SER	0	0.009	-0.025	27.930	0.006	0.006	0.000	0.000	0.000	0.000
78	A	84	ASN	0	-0.109	-0.055	31.475	-0.073	-0.073	0.000	0.000	0.000	0.000
79	A	85	VAL	0	0.002	0.008	29.543	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	86	THR	0	0.026	0.004	32.320	-0.385	-0.385	0.000	0.000	0.000	0.000
81	A	87	PRO	0	0.060	0.004	32.798	0.344	0.344	0.000	0.000	0.000	0.000
82	A	88	GLU	-1	-0.888	-0.944	32.905	9.151	9.151	0.000	0.000	0.000	0.000
83	A	89	ASP	-1	-0.871	-0.916	29.025	10.781	10.781	0.000	0.000	0.000	0.000
84	A	90	ALA	0	-0.003	0.024	28.021	0.545	0.545	0.000	0.000	0.000	0.000
85	A	91	GLY	0	0.006	-0.001	26.145	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	92	THR	0	-0.005	-0.002	19.636	-0.134	-0.134	0.000	0.000	0.000	0.000
87	A	93	TYR	0	-0.010	-0.024	20.581	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	94	TYR	0	-0.008	0.006	15.402	0.218	0.218	0.000	0.000	0.000	0.000
89	A	96	VAL	0	0.027	0.010	13.364	1.936	1.936	0.000	0.000	0.000	0.000
90	A	97	LYS	1	0.805	0.901	9.717	-25.834	-25.834	0.000	0.000	0.000	0.000
91	A	98	PHE	0	0.023	-0.014	12.227	0.843	0.843	0.000	0.000	0.000	0.000
92	A	99	GLN	0	-0.027	-0.007	12.307	1.702	1.702	0.000	0.000	0.000	0.000
93	A	100	LYS	1	0.854	0.902	14.176	-15.757	-15.757	0.000	0.000	0.000	0.000
94	A	101	GLY	0	-0.001	0.009	17.597	0.365	0.365	0.000	0.000	0.000	0.000
95	A	102	PRO	0	-0.012	-0.031	18.840	-0.476	-0.476	0.000	0.000	0.000	0.000
96	A	103	SER	0	-0.020	-0.007	22.211	-0.765	-0.765	0.000	0.000	0.000	0.000
97	A	104	GLU	-1	-0.870	-0.908	22.082	14.674	14.674	0.000	0.000	0.000	0.000
98	A	105	PRO	0	-0.019	-0.015	21.706	-0.443	-0.443	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.758	-0.861	17.761	16.397	16.397	0.000	0.000	0.000	0.000
100	A	107	THR	0	-0.029	-0.012	14.279	-0.382	-0.382	0.000	0.000	0.000	0.000
101	A	108	GLU	-1	-0.821	-0.885	12.927	22.548	22.548	0.000	0.000	0.000	0.000
102	A	109	ILE	0	-0.059	-0.044	8.564	0.113	0.113	0.000	0.000	0.000	0.000
103	A	110	GLN	0	-0.042	-0.022	4.600	-2.161	-1.973	-0.001	-0.015	-0.171	0.000
104	A	111	SER	0	0.041	0.013	9.025	-4.445	-4.445	0.000	0.000	0.000	0.000
105	A	112	GLY	0	-0.028	-0.001	9.644	2.819	2.819	0.000	0.000	0.000	0.000
106	A	113	GLY	0	0.022	0.011	11.682	-0.528	-0.528	0.000	0.000	0.000	0.000
107	A	114	GLY	0	-0.020	-0.010	13.260	-1.187	-1.187	0.000	0.000	0.000	0.000
108	A	115	THR	0	-0.047	-0.032	16.784	0.246	0.246	0.000	0.000	0.000	0.000
109	A	116	GLU	-1	-0.899	-0.915	19.363	12.122	12.122	0.000	0.000	0.000	0.000
110	A	117	VAL	0	-0.011	-0.002	22.968	-0.100	-0.100	0.000	0.000	0.000	0.000
111	A	118	TYR	0	0.031	0.010	25.900	-0.199	-0.199	0.000	0.000	0.000	0.000
112	A	119	VAL	0	-0.003	-0.003	29.186	-0.060	-0.060	0.000	0.000	0.000	0.000
113	A	120	LEU	0	-0.045	-0.017	32.313	-0.244	-0.244	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:GLU)