FMO DATABASE

FMODB ID: N1YYQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-524427.414698
FMO2-HF: Nuclear repulsion	492865.187037
FMO2-HF: Total energy	-31562.227662
FMO2-MP2: Total energy	-31655.714306

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.
1.626	3.696	-0.025	-1.193	-0.852	0.002

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 : -0.009 / q_NPA : -0.015

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	0.944	0.960	3.829	0.815	2.885	-0.025	-1.193	-0.852	0.002
4	A	64	VAL	0	0.054	0.034	6.313	0.026	0.026	0.000	0.000	0.000	0.000
5	A	65	VAL	0	-0.040	-0.016	9.849	-0.047	-0.047	0.000	0.000	0.000	0.000
6	A	66	LEU	0	0.002	0.006	12.611	0.042	0.042	0.000	0.000	0.000	0.000
7	A	67	SER	0	0.011	0.003	15.837	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	68	GLU	-1	-0.817	-0.887	18.992	0.058	0.058	0.000	0.000	0.000	0.000
9	A	69	PRO	0	-0.022	-0.001	22.385	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	70	ARG	1	0.931	0.950	24.754	0.009	0.009	0.000	0.000	0.000	0.000
11	A	71	VAL	0	-0.015	-0.004	27.614	0.002	0.002	0.000	0.000	0.000	0.000
12	A	72	TYR	0	-0.003	-0.019	27.463	0.001	0.001	0.000	0.000	0.000	0.000
13	A	73	ALA	0	0.026	0.001	27.149	0.000	0.000	0.000	0.000	0.000	0.000
14	A	74	GLU	-1	-0.763	-0.867	23.727	-0.046	-0.046	0.000	0.000	0.000	0.000
15	A	75	ALA	0	-0.025	-0.014	22.535	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	76	GLN	0	-0.049	-0.041	22.855	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	77	GLU	-1	-0.882	-0.930	20.372	-0.116	-0.116	0.000	0.000	0.000	0.000
18	A	78	ILE	0	-0.061	-0.021	18.071	-0.025	-0.025	0.000	0.000	0.000	0.000
19	A	79	ALA	0	0.032	0.011	17.702	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	80	ASP	-1	-0.895	-0.939	17.737	-0.204	-0.204	0.000	0.000	0.000	0.000
21	A	81	HIS	0	0.022	0.004	13.425	-0.111	-0.111	0.000	0.000	0.000	0.000
22	A	82	LEU	0	0.009	0.020	13.349	-0.061	-0.061	0.000	0.000	0.000	0.000
23	A	83	LYS	1	0.950	0.974	14.792	0.179	0.179	0.000	0.000	0.000	0.000
24	A	84	ASN	0	-0.140	-0.062	12.005	-0.070	-0.070	0.000	0.000	0.000	0.000
25	A	85	ARG	1	0.854	0.914	9.500	0.179	0.179	0.000	0.000	0.000	0.000
26	A	86	ARG	1	0.843	0.925	8.548	0.468	0.468	0.000	0.000	0.000	0.000
27	A	87	ALA	0	0.082	0.046	10.365	0.042	0.042	0.000	0.000	0.000	0.000
28	A	88	VAL	0	-0.046	-0.028	12.140	-0.036	-0.036	0.000	0.000	0.000	0.000
29	A	89	VAL	0	0.017	0.014	14.881	0.029	0.029	0.000	0.000	0.000	0.000
30	A	90	VAL	0	0.002	-0.009	17.073	-0.032	-0.032	0.000	0.000	0.000	0.000
31	A	91	ASN	0	0.019	0.004	20.421	0.004	0.004	0.000	0.000	0.000	0.000
32	A	92	LEU	0	0.004	-0.025	23.110	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	93	GLN	0	0.014	-0.005	26.042	0.000	0.000	0.000	0.000	0.000	0.000
34	A	94	ARG	1	0.794	0.897	27.469	-0.034	-0.034	0.000	0.000	0.000	0.000
35	A	95	ILE	0	-0.037	-0.008	28.165	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	96	GLN	0	0.018	0.012	31.010	0.008	0.008	0.000	0.000	0.000	0.000
37	A	97	HIS	0	0.108	0.026	33.472	0.000	0.000	0.000	0.000	0.000	0.000
38	A	98	ASP	-1	-0.873	-0.930	34.018	0.025	0.025	0.000	0.000	0.000	0.000
39	A	99	GLN	0	-0.039	-0.018	32.777	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	100	ALA	0	0.048	0.036	29.746	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	101	LYS	1	0.982	0.983	29.582	-0.035	-0.035	0.000	0.000	0.000	0.000
42	A	102	ARG	1	0.881	0.934	31.078	0.006	0.006	0.000	0.000	0.000	0.000
43	A	103	ILE	0	0.008	0.016	25.810	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	104	VAL	0	0.041	0.021	26.215	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	105	ASP	-1	-0.866	-0.918	27.079	0.012	0.012	0.000	0.000	0.000	0.000
46	A	106	PHE	0	0.011	-0.002	24.217	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	107	LEU	0	-0.015	-0.024	21.583	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	108	SER	0	0.014	-0.001	23.397	0.004	0.004	0.000	0.000	0.000	0.000
49	A	109	LYS	1	0.845	0.922	25.237	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	110	THR	0	-0.059	-0.025	20.994	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	111	VAL	0	0.010	-0.004	19.232	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	112	TYR	0	0.019	0.028	21.222	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	113	ALA	0	-0.049	-0.022	23.729	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	114	ILE	0	-0.098	-0.048	17.465	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	115	GLY	0	0.016	0.019	18.715	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	116	GLY	0	-0.030	-0.027	17.604	0.015	0.015	0.000	0.000	0.000	0.000
57	A	117	ASP	-1	-0.836	-0.915	18.287	0.143	0.143	0.000	0.000	0.000	0.000
58	A	118	ILE	0	-0.081	-0.057	19.277	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	119	GLN	0	0.029	0.026	19.478	0.004	0.004	0.000	0.000	0.000	0.000
60	A	120	ARG	1	0.926	0.968	21.993	-0.093	-0.093	0.000	0.000	0.000	0.000
61	A	121	ILE	0	-0.007	-0.012	18.752	0.011	0.011	0.000	0.000	0.000	0.000
62	A	122	GLY	0	0.053	0.015	22.688	0.011	0.011	0.000	0.000	0.000	0.000
63	A	123	SER	0	-0.054	-0.027	25.491	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	124	ASP	-1	-0.887	-0.938	27.463	0.069	0.069	0.000	0.000	0.000	0.000
65	A	125	ILE	0	-0.040	-0.002	20.195	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	126	PHE	0	0.001	-0.007	22.147	0.009	0.009	0.000	0.000	0.000	0.000
67	A	127	LEU	0	0.008	0.013	14.621	0.001	0.001	0.000	0.000	0.000	0.000
68	A	128	CYS	0	-0.033	-0.009	17.619	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	129	THR	0	0.020	-0.006	13.781	0.007	0.007	0.000	0.000	0.000	0.000
70	A	130	PRO	0	-0.013	0.011	11.955	-0.021	-0.021	0.000	0.000	0.000	0.000
71	A	131	ASP	-1	-0.746	-0.879	14.312	-0.061	-0.061	0.000	0.000	0.000	0.000
72	A	132	ASN	0	-0.070	-0.025	8.477	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	133	VAL	0	-0.096	-0.056	9.466	0.130	0.130	0.000	0.000	0.000	0.000
74	A	134	ASP	-1	-0.886	-0.931	11.532	0.375	0.375	0.000	0.000	0.000	0.000
75	A	135	VAL	0	-0.029	-0.009	13.103	0.117	0.117	0.000	0.000	0.000	0.000
76	A	136	SER	0	0.009	0.008	15.332	-0.043	-0.043	0.000	0.000	0.000	0.000
77	A	137	GLY	0	-0.010	-0.004	17.665	0.012	0.012	0.000	0.000	0.000	0.000
78	A	138	THR	0	-0.040	-0.039	20.341	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	139	ILE	0	-0.006	0.005	20.669	0.008	0.008	0.000	0.000	0.000	0.000
80	A	140	SER	0	0.000	0.005	24.521	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	141	GLU	-1	-0.973	-0.984	28.292	0.096	0.096	0.000	0.000	0.000	0.000
82	A	142	LEU	0	-0.021	-0.008	30.592	-0.004	-0.004	0.000	0.000	0.000	0.000

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