FMO DATABASE

FMODB ID: J3559

Calculation Name: 3ZII-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZII

Chain ID: A

ChEMBL ID:

UniProt ID: O31728

Base Structure: X-ray

Registration Date: 2023-06-20

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-524989.671774
FMO2-HF: Nuclear repulsion	493427.025565
FMO2-HF: Total energy	-31562.646209
FMO2-MP2: Total energy	-31656.143919

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:61:SER)

Summations of interaction energy for fragment #1(A:61:SER)

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.
-4.16	-1.97	-0.025	-1.269	-0.895	0.003

Interaction energy analysis for fragmet #1(A:61:SER)

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 : -0.013

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	63	LYS	1	0.945	0.961	3.829	-2.951	-0.761	-0.025	-1.269	-0.895	0.003
4	A	64	VAL	0	0.048	0.032	6.826	-0.565	-0.565	0.000	0.000	0.000	0.000
5	A	65	VAL	0	-0.039	-0.013	10.033	0.125	0.125	0.000	0.000	0.000	0.000
6	A	66	LEU	0	0.006	0.010	13.133	-0.121	-0.121	0.000	0.000	0.000	0.000
7	A	67	SER	0	0.013	0.005	16.172	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	68	GLU	-1	-0.718	-0.827	19.483	0.264	0.264	0.000	0.000	0.000	0.000
9	A	69	PRO	0	-0.011	0.000	22.849	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	70	ARG	1	0.844	0.899	25.365	-0.294	-0.294	0.000	0.000	0.000	0.000
11	A	71	VAL	0	-0.034	-0.015	28.403	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	72	TYR	0	0.007	-0.016	28.192	0.010	0.010	0.000	0.000	0.000	0.000
13	A	73	ALA	0	0.033	0.004	27.856	0.005	0.005	0.000	0.000	0.000	0.000
14	A	74	GLU	-1	-0.744	-0.863	24.463	0.285	0.285	0.000	0.000	0.000	0.000
15	A	75	ALA	0	-0.011	-0.013	23.287	0.027	0.027	0.000	0.000	0.000	0.000
16	A	76	GLN	0	-0.046	-0.038	23.410	0.000	0.000	0.000	0.000	0.000	0.000
17	A	77	GLU	-1	-0.904	-0.936	21.036	0.340	0.340	0.000	0.000	0.000	0.000
18	A	78	ILE	0	-0.059	-0.026	18.412	0.045	0.045	0.000	0.000	0.000	0.000
19	A	79	ALA	0	0.038	0.016	18.099	0.019	0.019	0.000	0.000	0.000	0.000
20	A	80	ASP	-1	-0.841	-0.907	18.180	0.253	0.253	0.000	0.000	0.000	0.000
21	A	81	HIS	0	0.027	0.021	14.024	0.112	0.112	0.000	0.000	0.000	0.000
22	A	82	LEU	0	0.011	0.021	13.532	0.022	0.022	0.000	0.000	0.000	0.000
23	A	83	LYS	1	0.892	0.937	14.817	-0.261	-0.261	0.000	0.000	0.000	0.000
24	A	84	ASN	0	-0.149	-0.079	12.097	-0.046	-0.046	0.000	0.000	0.000	0.000
25	A	85	ARG	1	0.805	0.867	9.791	0.299	0.299	0.000	0.000	0.000	0.000
26	A	86	ARG	1	0.841	0.923	8.998	-0.850	-0.850	0.000	0.000	0.000	0.000
27	A	87	ALA	0	0.073	0.040	10.386	-0.127	-0.127	0.000	0.000	0.000	0.000
28	A	88	VAL	0	-0.050	-0.031	12.422	0.181	0.181	0.000	0.000	0.000	0.000
29	A	89	VAL	0	0.018	0.016	14.675	-0.081	-0.081	0.000	0.000	0.000	0.000
30	A	90	VAL	0	0.005	-0.009	17.116	0.029	0.029	0.000	0.000	0.000	0.000
31	A	91	ASN	0	0.005	-0.001	20.618	-0.054	-0.054	0.000	0.000	0.000	0.000
32	A	92	LEU	0	0.004	-0.023	23.214	0.004	0.004	0.000	0.000	0.000	0.000
33	A	93	GLN	0	0.026	0.004	25.744	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	94	ARG	1	0.773	0.885	27.225	-0.249	-0.249	0.000	0.000	0.000	0.000
35	A	95	ILE	0	-0.038	-0.008	28.667	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	96	GLN	0	0.039	0.024	31.379	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	97	HIS	0	0.149	0.052	33.768	0.008	0.008	0.000	0.000	0.000	0.000
38	A	98	ASP	-1	-0.854	-0.917	34.199	0.084	0.084	0.000	0.000	0.000	0.000
39	A	99	GLN	0	-0.012	-0.010	33.314	0.002	0.002	0.000	0.000	0.000	0.000
40	A	100	ALA	0	0.033	0.029	29.964	0.006	0.006	0.000	0.000	0.000	0.000
41	A	101	LYS	1	0.882	0.921	29.848	-0.087	-0.087	0.000	0.000	0.000	0.000
42	A	102	ARG	1	0.883	0.948	31.243	-0.113	-0.113	0.000	0.000	0.000	0.000
43	A	103	ILE	0	-0.005	0.005	26.219	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	104	VAL	0	0.047	0.026	26.439	0.004	0.004	0.000	0.000	0.000	0.000
45	A	105	ASP	-1	-0.810	-0.864	27.079	0.067	0.067	0.000	0.000	0.000	0.000
46	A	106	PHE	0	0.009	-0.004	24.376	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	107	LEU	0	-0.009	-0.014	21.687	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	108	SER	0	0.020	-0.003	23.397	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	109	LYS	1	0.779	0.870	25.237	-0.080	-0.080	0.000	0.000	0.000	0.000
50	A	110	THR	0	-0.064	-0.032	21.057	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	111	VAL	0	0.012	-0.003	19.197	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	112	TYR	0	0.011	0.025	21.146	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	113	ALA	0	-0.049	-0.021	23.631	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	114	ILE	0	-0.084	-0.040	17.269	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	115	GLY	0	0.000	0.011	18.639	-0.023	-0.023	0.000	0.000	0.000	0.000
56	A	116	GLY	0	-0.029	-0.028	17.473	-0.026	-0.026	0.000	0.000	0.000	0.000
57	A	117	ASP	-1	-0.866	-0.926	18.185	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	118	ILE	0	-0.058	-0.048	19.277	0.050	0.050	0.000	0.000	0.000	0.000
59	A	119	GLN	0	0.031	0.025	19.029	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	120	ARG	1	0.808	0.888	21.995	-0.072	-0.072	0.000	0.000	0.000	0.000
61	A	121	ILE	0	-0.009	-0.013	18.777	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	122	GLY	0	0.051	0.014	22.777	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	123	SER	0	-0.047	-0.023	25.541	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	124	ASP	-1	-0.904	-0.950	27.220	0.161	0.161	0.000	0.000	0.000	0.000
65	A	125	ILE	0	-0.041	0.001	20.207	0.025	0.025	0.000	0.000	0.000	0.000
66	A	126	PHE	0	0.019	0.000	22.017	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	127	LEU	0	-0.006	0.008	14.694	0.061	0.061	0.000	0.000	0.000	0.000
68	A	128	CYS	0	-0.029	-0.004	17.655	-0.057	-0.057	0.000	0.000	0.000	0.000
69	A	129	THR	0	0.047	0.003	13.705	0.108	0.108	0.000	0.000	0.000	0.000
70	A	130	PRO	0	-0.017	0.013	11.917	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	131	ASP	-1	-0.705	-0.838	14.175	-0.220	-0.220	0.000	0.000	0.000	0.000
72	A	132	ASN	0	-0.073	-0.026	8.428	0.028	0.028	0.000	0.000	0.000	0.000
73	A	133	VAL	0	-0.086	-0.050	9.335	-0.124	-0.124	0.000	0.000	0.000	0.000
74	A	134	ASP	-1	-0.895	-0.934	11.363	-0.249	-0.249	0.000	0.000	0.000	0.000
75	A	135	VAL	0	-0.035	-0.015	13.046	0.035	0.035	0.000	0.000	0.000	0.000
76	A	136	SER	0	0.016	0.013	15.040	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	137	GLY	0	-0.008	0.000	17.476	0.035	0.035	0.000	0.000	0.000	0.000
78	A	138	THR	0	-0.050	-0.047	20.123	0.000	0.000	0.000	0.000	0.000	0.000
79	A	139	ILE	0	0.002	0.011	20.590	0.003	0.003	0.000	0.000	0.000	0.000
80	A	140	SER	0	0.011	0.015	24.508	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	141	GLU	-1	-0.857	-0.908	28.278	0.087	0.087	0.000	0.000	0.000	0.000
82	A	142	LEU	0	-0.016	-0.007	30.643	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:61:SER)