FMO DATABASE

FMODB ID: J3V69

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

Total energy (hartree)

FMO2-HF: Electronic energy	-845200.825927
FMO2-HF: Nuclear repulsion	803134.991983
FMO2-HF: Total energy	-42065.833944
FMO2-MP2: Total energy	-42187.389496

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.
-26.199	-10.713	13.783	-8.389	-20.878	-0.052

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 : 0.001 / q_NPA : 0.028

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

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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	-0.005	0.010	3.762	-3.079	1.575	-0.047	-2.620	-1.988	0.013
4	A	4	VAL	0	-0.033	-0.009	6.657	-0.146	-0.146	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.009	-0.013	9.932	0.192	0.192	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.000	-0.009	13.191	-0.003	-0.003	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.009	-0.006	16.324	0.059	0.059	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.817	0.885	19.617	0.196	0.196	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.034	-0.043	23.076	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.797	-0.874	25.104	-0.198	-0.198	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.019	-0.008	25.789	0.013	0.013	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.018	0.028	28.861	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.051	-0.017	23.204	0.012	0.012	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.083	0.041	27.600	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.995	0.972	25.236	0.285	0.285	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.039	0.022	24.300	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.881	0.928	24.719	0.177	0.177	0.000	0.000	0.000	0.000
18	A	18	MET	0	0.022	0.016	21.642	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.001	0.008	19.959	-0.030	-0.030	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.008	0.009	19.804	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	21	GLN	0	0.013	0.014	20.776	0.004	0.004	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.062	0.021	17.473	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.015	0.006	16.130	-0.041	-0.041	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.010	-0.006	16.655	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.009	0.004	15.327	0.019	0.019	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.006	-0.014	11.418	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.000	0.003	11.832	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.854	-0.941	13.183	-0.052	-0.052	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.060	-0.003	9.768	0.062	0.062	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.037	0.010	8.029	0.070	0.070	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.019	-0.012	8.947	0.132	0.132	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.785	-0.871	10.860	0.146	0.146	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.021	-0.003	5.391	0.103	0.103	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.806	0.889	7.433	-0.308	-0.308	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.926	0.960	8.504	0.041	0.041	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.852	0.929	8.723	-0.162	-0.162	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.005	-0.010	5.565	0.199	0.199	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.051	0.022	5.635	0.112	0.112	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.995	0.997	7.115	-1.443	-1.443	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.016	0.014	2.205	0.113	0.021	2.002	-0.430	-1.480	0.001
41	A	41	VAL	0	0.001	0.003	2.909	0.068	1.420	1.118	-0.805	-1.664	-0.014
42	A	42	ASP	-1	-0.824	-0.908	4.345	0.705	0.731	-0.001	-0.008	-0.017	0.000
43	A	43	GLU	-1	-0.896	-0.932	3.397	2.689	4.289	0.483	-0.559	-1.525	-0.003
44	A	44	TRP	0	-0.006	0.000	2.783	-3.701	-1.142	0.772	-0.934	-2.396	0.002
45	A	45	LEU	0	-0.053	-0.033	3.592	-1.638	-1.545	0.024	0.056	-0.173	0.001
46	A	46	ARG	1	0.825	0.908	6.911	-1.879	-1.879	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.953	-0.968	2.995	-5.398	-3.800	0.084	-0.753	-0.929	-0.007
48	A	48	GLY	0	0.012	0.013	6.408	-0.486	-0.486	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.016	-0.004	5.795	0.043	0.043	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.912	0.963	4.166	5.610	5.841	-0.001	-0.035	-0.195	0.000
51	A	51	LYS	1	0.869	0.912	6.561	1.081	1.081	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.002	0.006	8.399	0.086	0.086	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.006	0.000	11.021	0.095	0.095	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.025	0.021	13.578	0.043	0.043	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.890	0.957	16.091	0.385	0.385	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.005	0.007	19.059	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.068	-0.061	21.545	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	SER	0	0.057	0.033	24.772	0.024	0.024	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.781	-0.880	24.761	-0.149	-0.149	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.898	0.926	24.687	0.105	0.105	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.833	-0.916	21.558	-0.248	-0.248	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.026	-0.004	19.207	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.017	-0.004	19.809	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.865	-0.901	20.786	-0.104	-0.104	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.040	-0.018	15.625	0.015	0.015	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.049	0.030	15.809	0.012	0.012	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.011	-0.004	16.602	0.032	0.032	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.965	0.996	16.512	0.148	0.148	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.036	0.018	12.361	0.038	0.038	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.847	0.898	13.093	0.091	0.091	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.056	-0.024	15.254	0.038	0.038	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.848	-0.910	12.289	0.210	0.210	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.014	0.010	12.098	0.079	0.079	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.051	-0.024	7.672	0.092	0.092	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.021	0.006	6.023	-0.035	-0.035	0.000	0.000	0.000	0.000
76	A	76	CYS	0	-0.060	-0.044	9.270	-0.128	-0.128	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.034	-0.006	11.689	0.057	0.057	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.038	0.004	14.890	-0.040	-0.040	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.020	0.006	17.630	0.027	0.027	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.961	0.982	20.556	0.098	0.098	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.840	-0.899	24.354	-0.163	-0.163	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.004	-0.001	26.586	0.016	0.016	0.000	0.000	0.000	0.000
83	A	90	GLY	0	0.006	-0.011	30.600	0.004	0.004	0.000	0.000	0.000	0.000
84	A	91	THR	0	-0.086	-0.043	27.341	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	92	LEU	0	0.028	0.011	23.001	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	93	THR	0	-0.010	-0.036	22.810	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	94	ALA	0	0.009	-0.006	18.177	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	95	VAL	0	0.001	0.009	14.607	0.044	0.044	0.000	0.000	0.000	0.000
89	A	96	ALA	0	-0.008	0.015	11.484	-0.078	-0.078	0.000	0.000	0.000	0.000
90	A	97	ILE	0	0.000	-0.002	8.610	0.133	0.133	0.000	0.000	0.000	0.000
91	A	98	GLY	0	0.025	0.041	5.670	-0.333	-0.333	0.000	0.000	0.000	0.000
92	A	99	PRO	0	-0.040	-0.047	2.460	-0.617	0.111	0.479	-0.239	-0.967	0.001
93	A	100	GLU	-1	-0.798	-0.916	2.089	1.142	1.339	4.435	-1.760	-2.872	-0.007
94	A	101	LYS	1	0.960	0.983	2.267	-8.734	-7.568	3.025	0.192	-4.383	-0.018
95	A	102	ASP	-1	-0.745	-0.881	2.535	-11.003	-9.800	1.409	-0.469	-2.142	-0.021
96	A	103	GLU	-1	-0.809	-0.915	4.175	1.294	1.465	0.001	-0.025	-0.147	0.000
97	A	104	LYS	1	0.854	0.922	6.051	-1.208	-1.208	0.000	0.000	0.000	0.000
98	A	105	ILE	0	-0.030	-0.013	5.295	-0.053	-0.053	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.836	-0.902	7.979	-1.251	-1.251	0.000	0.000	0.000	0.000
100	A	107	LYS	1	0.795	0.899	9.946	-0.097	-0.097	0.000	0.000	0.000	0.000
101	A	108	ILE	0	-0.074	-0.035	11.442	0.026	0.026	0.000	0.000	0.000	0.000
102	A	109	THR	0	0.041	-0.010	11.184	0.011	0.011	0.000	0.000	0.000	0.000
103	A	110	GLY	0	0.000	0.018	12.649	-0.057	-0.057	0.000	0.000	0.000	0.000
104	A	111	HIS	0	-0.025	-0.006	13.378	-0.022	-0.022	0.000	0.000	0.000	0.000
105	A	112	LEU	0	-0.052	-0.016	15.483	0.029	0.029	0.000	0.000	0.000	0.000
106	A	113	LYS	1	0.950	0.973	16.739	0.297	0.297	0.000	0.000	0.000	0.000
107	A	114	LEU	0	0.061	0.022	14.025	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	115	LEU	0	-0.035	-0.019	17.794	0.058	0.058	0.000	0.000	0.000	0.000

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