FMO DATABASE

FMODB ID: 3QM3L

Calculation Name: 2ZV3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZV3

Chain ID: A

ChEMBL ID:

UniProt ID: Q60363

Base Structure: X-ray

Registration Date: 2023-03-14

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	OptAll
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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-844986.742494
FMO2-HF: Nuclear repulsion	802920.643919
FMO2-HF: Total energy	-42066.098576
FMO2-MP2: Total energy	-42187.667444

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-34.221	-33.912	42.897	-15.584	-27.622	-0.043

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.056

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	3	MET	0	-0.013	0.013	3.852	-1.689	1.364	-0.025	-1.707	-1.321	0.007
4	A	4	VAL	0	-0.015	-0.004	6.962	-0.085	-0.085	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.004	-0.008	9.757	0.211	0.211	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.004	0.002	13.341	0.006	0.006	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.002	-0.010	16.328	0.068	0.068	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.823	0.883	19.853	0.305	0.305	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.014	-0.026	23.299	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.800	-0.881	25.190	-0.290	-0.290	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.026	-0.005	26.097	0.018	0.018	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.010	0.020	28.943	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.044	-0.016	23.709	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.085	0.040	27.337	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.978	0.968	25.390	0.381	0.381	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.050	0.031	24.402	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.868	0.924	24.838	0.266	0.266	0.000	0.000	0.000	0.000
18	A	18	MET	0	-0.002	0.004	22.041	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.002	0.003	20.103	-0.044	-0.044	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.003	0.009	20.044	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	21	GLN	0	-0.002	0.005	20.988	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.065	0.024	17.781	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.009	0.002	16.349	-0.079	-0.079	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.021	0.001	16.627	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.014	0.014	15.551	0.009	0.009	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.017	0.001	11.600	-0.058	-0.058	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.003	0.007	12.028	-0.052	-0.052	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.731	-0.848	13.522	-0.258	-0.258	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.052	-0.002	10.205	0.061	0.061	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.028	0.001	8.534	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.009	-0.003	9.277	0.112	0.112	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.778	-0.878	11.380	-0.155	-0.155	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.022	0.012	5.784	0.122	0.122	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.760	0.862	7.878	-0.043	-0.043	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.792	0.855	9.135	0.326	0.326	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.845	0.937	9.254	0.160	0.160	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.004	-0.010	6.112	0.228	0.228	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.056	0.024	6.267	-0.074	-0.074	0.000	0.000	0.000	0.000
39	A	39	ARG	1	1.019	1.004	7.219	-1.994	-1.994	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.016	0.016	2.180	0.600	0.737	1.226	-0.269	-1.095	0.002
41	A	41	VAL	0	0.008	0.010	2.576	-2.091	-0.854	1.115	-1.004	-1.349	-0.016
42	A	42	ASP	-1	-0.810	-0.895	4.855	0.478	0.491	-0.001	-0.005	-0.008	0.000
43	A	43	GLU	-1	-0.855	-0.924	2.701	8.440	9.323	4.154	-1.710	-3.328	-0.014
44	A	44	TRP	0	-0.017	-0.014	2.859	-2.415	-0.457	0.335	-0.571	-1.721	0.000
45	A	45	LEU	0	-0.051	-0.035	4.063	-1.164	-0.997	0.007	-0.026	-0.148	0.000
46	A	46	ARG	1	0.787	0.889	6.308	-2.757	-2.757	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.897	-0.928	3.599	-1.464	-0.626	0.012	-0.312	-0.537	-0.002
48	A	48	GLY	0	0.009	0.004	6.233	-0.861	-0.861	0.000	0.000	0.000	0.000
49	A	49	GLN	0	0.010	0.014	6.363	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.877	0.944	3.085	8.160	8.737	0.005	-0.212	-0.370	0.001
51	A	51	LYS	1	0.852	0.914	6.529	1.229	1.229	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.020	0.015	8.323	0.130	0.130	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.001	0.004	11.055	0.079	0.079	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.010	0.012	13.728	0.087	0.087	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.860	0.937	16.156	0.509	0.509	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.006	0.010	19.115	0.002	0.002	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.070	-0.064	21.685	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	SER	0	0.046	0.026	24.972	0.034	0.034	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.800	-0.872	24.914	-0.250	-0.250	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.902	0.925	25.008	0.176	0.176	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.795	-0.889	21.600	-0.372	-0.372	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.013	-0.005	19.446	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.017	0.004	20.105	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.862	-0.907	20.941	-0.204	-0.204	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.051	-0.019	15.471	0.012	0.012	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.049	0.031	15.915	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.025	-0.002	16.556	0.019	0.019	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.956	0.999	16.387	0.295	0.295	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.041	0.023	12.356	0.050	0.050	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.824	0.890	13.049	0.335	0.335	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.077	-0.040	15.385	0.061	0.061	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.819	-0.893	12.230	0.200	0.200	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.009	-0.001	11.898	0.086	0.086	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.035	-0.011	7.773	0.037	0.037	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.008	0.001	6.050	0.014	0.014	0.000	0.000	0.000	0.000
76	A	76	CYS	0	-0.065	-0.039	9.202	-0.163	-0.163	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.051	-0.028	11.783	0.106	0.106	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.036	0.000	14.988	-0.041	-0.041	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.025	0.009	18.125	0.034	0.034	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.891	0.940	20.959	0.194	0.194	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.793	-0.868	24.785	-0.261	-0.261	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.026	0.011	27.089	0.024	0.024	0.000	0.000	0.000	0.000
83	A	90	GLY	0	0.005	0.012	30.465	0.002	0.002	0.000	0.000	0.000	0.000
84	A	91	THR	0	-0.054	-0.049	27.956	0.005	0.005	0.000	0.000	0.000	0.000
85	A	92	LEU	0	0.027	0.001	23.417	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	93	THR	0	-0.016	-0.033	23.267	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	94	ALA	0	0.009	-0.004	18.505	-0.029	-0.029	0.000	0.000	0.000	0.000
88	A	95	VAL	0	0.000	0.006	14.986	0.051	0.051	0.000	0.000	0.000	0.000
89	A	96	ALA	0	-0.017	-0.001	11.609	-0.088	-0.088	0.000	0.000	0.000	0.000
90	A	97	ILE	0	0.013	0.004	8.960	0.178	0.178	0.000	0.000	0.000	0.000
91	A	98	GLY	0	0.018	0.026	5.982	-0.447	-0.447	0.000	0.000	0.000	0.000
92	A	99	PRO	0	-0.041	-0.038	3.098	0.012	0.442	0.041	-0.091	-0.379	0.000
93	A	100	GLU	-1	-0.797	-0.913	2.078	0.961	1.168	4.105	-1.599	-2.713	-0.012
94	A	101	LYS	1	0.849	0.899	2.011	-25.641	-33.457	28.179	-8.818	-11.544	0.026
95	A	102	ASP	-1	-0.724	-0.859	2.124	-14.882	-16.529	3.743	0.773	-2.869	-0.035
96	A	103	GLU	-1	-0.782	-0.911	4.118	1.823	2.030	0.002	-0.030	-0.179	0.000
97	A	104	LYS	1	0.861	0.923	5.826	-1.526	-1.526	0.000	0.000	0.000	0.000
98	A	105	ILE	0	-0.019	-0.004	4.756	-0.125	-0.060	-0.001	-0.003	-0.061	0.000
99	A	106	ASP	-1	-0.837	-0.913	7.990	-1.592	-1.592	0.000	0.000	0.000	0.000
100	A	107	LYS	1	0.798	0.891	10.106	-0.056	-0.056	0.000	0.000	0.000	0.000
101	A	108	ILE	0	-0.066	-0.023	11.361	0.066	0.066	0.000	0.000	0.000	0.000
102	A	109	THR	0	0.020	-0.018	11.293	0.016	0.016	0.000	0.000	0.000	0.000
103	A	110	GLY	0	0.002	0.009	12.920	-0.054	-0.054	0.000	0.000	0.000	0.000
104	A	111	HIS	0	-0.020	0.003	13.585	0.004	0.004	0.000	0.000	0.000	0.000
105	A	112	LEU	0	-0.041	-0.014	15.559	0.045	0.045	0.000	0.000	0.000	0.000
106	A	113	LYS	1	0.931	0.960	17.026	0.423	0.423	0.000	0.000	0.000	0.000
107	A	114	LEU	0	0.060	0.021	13.958	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	115	LEU	0	-0.033	-0.018	17.628	0.097	0.097	0.000	0.000	0.000	0.000

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