FMO DATABASE

FMODB ID: 6611Z

Calculation Name: 3ZIE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZIE

Chain ID: A

ChEMBL ID:

UniProt ID: O29476

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	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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-547931.421615
FMO2-HF: Nuclear repulsion	515660.680998
FMO2-HF: Total energy	-32270.740617
FMO2-MP2: Total energy	-32366.636551

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:37:VAL)

Summations of interaction energy for fragment #1(A:37:VAL)

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.
-11.469	-2.475	3.826	-5.085	-7.737	-0.03

Interaction energy analysis for fragmet #1(A:37:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : 0.012

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	39	ILE	0	-0.014	-0.015	3.298	-1.862	1.435	0.061	-1.732	-1.627	0.005
4	A	40	ARG	1	0.770	0.857	5.619	0.762	0.762	0.000	0.000	0.000	0.000
5	A	41	VAL	0	0.013	0.007	8.988	0.110	0.110	0.000	0.000	0.000	0.000
6	A	42	ALA	0	-0.021	-0.015	12.326	-0.020	-0.020	0.000	0.000	0.000	0.000
7	A	43	GLU	-1	-0.864	-0.939	14.906	-0.305	-0.305	0.000	0.000	0.000	0.000
8	A	44	VAL	0	-0.048	-0.014	17.173	0.016	0.016	0.000	0.000	0.000	0.000
9	A	45	THR	0	-0.048	-0.041	19.742	0.023	0.023	0.000	0.000	0.000	0.000
10	A	46	GLY	0	0.000	-0.017	22.360	0.019	0.019	0.000	0.000	0.000	0.000
11	A	47	LEU	0	-0.011	-0.016	21.853	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	48	ASN	0	-0.039	-0.013	21.603	0.013	0.013	0.000	0.000	0.000	0.000
13	A	49	GLU	-1	-0.748	-0.866	17.699	-0.192	-0.192	0.000	0.000	0.000	0.000
14	A	50	VAL	0	0.022	0.013	16.600	-0.028	-0.028	0.000	0.000	0.000	0.000
15	A	51	PRO	0	-0.024	-0.023	16.034	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	52	GLU	-1	-0.801	-0.863	13.491	-0.385	-0.385	0.000	0.000	0.000	0.000
17	A	53	ILE	0	0.015	0.005	11.612	-0.053	-0.053	0.000	0.000	0.000	0.000
18	A	54	LYS	1	0.849	0.916	11.225	0.013	0.013	0.000	0.000	0.000	0.000
19	A	55	ARG	1	0.865	0.937	11.827	0.241	0.241	0.000	0.000	0.000	0.000
20	A	56	GLU	-1	-0.671	-0.796	7.139	-1.203	-1.203	0.000	0.000	0.000	0.000
21	A	57	ILE	0	-0.042	-0.012	6.787	-0.102	-0.102	0.000	0.000	0.000	0.000
22	A	58	TYR	0	-0.086	-0.059	7.924	0.112	0.112	0.000	0.000	0.000	0.000
23	A	59	ASP	-1	-0.932	-0.958	7.130	0.025	0.025	0.000	0.000	0.000	0.000
24	A	60	GLY	0	-0.038	-0.011	4.045	0.380	0.541	-0.001	-0.035	-0.126	0.000
25	A	61	ASN	0	-0.025	-0.018	2.339	-8.269	-4.216	3.271	-3.226	-4.099	-0.036
26	A	62	ILE	0	-0.015	-0.017	3.024	0.278	0.928	0.182	0.112	-0.944	0.001
27	A	63	VAL	0	-0.013	-0.003	5.032	-0.248	-0.246	-0.001	-0.002	0.001	0.000
28	A	64	VAL	0	-0.033	-0.026	8.725	0.122	0.122	0.000	0.000	0.000	0.000
29	A	65	ALA	0	0.035	0.020	11.655	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	66	ASP	-1	-0.798	-0.888	15.021	-0.201	-0.201	0.000	0.000	0.000	0.000
31	A	67	ILE	0	-0.010	-0.023	18.123	0.008	0.008	0.000	0.000	0.000	0.000
32	A	68	ALA	0	0.033	0.018	21.041	0.022	0.022	0.000	0.000	0.000	0.000
33	A	69	PHE	0	-0.076	-0.031	20.789	0.021	0.021	0.000	0.000	0.000	0.000
34	A	70	ILE	0	0.018	0.008	21.861	0.013	0.013	0.000	0.000	0.000	0.000
35	A	71	LYS	1	0.738	0.878	23.761	0.111	0.111	0.000	0.000	0.000	0.000
36	A	72	HIS	0	-0.003	-0.022	26.187	0.016	0.016	0.000	0.000	0.000	0.000
37	A	73	ASP	-1	-0.835	-0.880	28.917	-0.072	-0.072	0.000	0.000	0.000	0.000
38	A	74	LYS	1	0.969	0.967	28.216	0.063	0.063	0.000	0.000	0.000	0.000
39	A	75	LEU	0	0.018	0.033	28.290	0.003	0.003	0.000	0.000	0.000	0.000
40	A	76	THR	0	-0.036	-0.054	25.064	0.003	0.003	0.000	0.000	0.000	0.000
41	A	77	LEU	0	-0.006	0.006	22.660	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	78	ASP	-1	-0.881	-0.948	23.406	-0.060	-0.060	0.000	0.000	0.000	0.000
43	A	79	ARG	1	0.853	0.931	24.463	0.070	0.070	0.000	0.000	0.000	0.000
44	A	80	VAL	0	0.058	0.029	19.175	0.003	0.003	0.000	0.000	0.000	0.000
45	A	81	LEU	0	-0.015	-0.016	19.309	0.001	0.001	0.000	0.000	0.000	0.000
46	A	82	LYS	1	0.798	0.896	20.160	0.053	0.053	0.000	0.000	0.000	0.000
47	A	83	ASP	-1	-0.831	-0.901	19.432	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	84	LEU	0	-0.006	-0.005	14.546	0.003	0.003	0.000	0.000	0.000	0.000
49	A	85	ARG	1	0.955	0.968	15.565	0.047	0.047	0.000	0.000	0.000	0.000
50	A	86	GLN	0	-0.013	-0.007	17.288	0.011	0.011	0.000	0.000	0.000	0.000
51	A	87	LEU	0	-0.018	0.003	11.991	0.020	0.020	0.000	0.000	0.000	0.000
52	A	88	ALA	0	0.028	0.010	12.825	0.024	0.024	0.000	0.000	0.000	0.000
53	A	89	GLU	-1	-0.966	-0.989	13.906	0.087	0.087	0.000	0.000	0.000	0.000
54	A	90	ASP	-1	-0.865	-0.926	15.238	0.067	0.067	0.000	0.000	0.000	0.000
55	A	91	VAL	0	-0.046	-0.016	10.277	0.035	0.035	0.000	0.000	0.000	0.000
56	A	92	LYS	1	0.924	0.969	11.967	-0.136	-0.136	0.000	0.000	0.000	0.000
57	A	93	GLY	0	0.030	0.038	10.409	0.069	0.069	0.000	0.000	0.000	0.000
58	A	94	ASP	-1	-0.827	-0.880	10.606	0.053	0.053	0.000	0.000	0.000	0.000
59	A	95	ILE	0	0.005	-0.003	11.609	-0.044	-0.044	0.000	0.000	0.000	0.000
60	A	96	VAL	0	-0.086	-0.039	13.650	0.026	0.026	0.000	0.000	0.000	0.000
61	A	97	GLY	0	0.039	0.031	15.636	-0.029	-0.029	0.000	0.000	0.000	0.000
62	A	98	LEU	0	-0.045	-0.032	14.025	0.015	0.015	0.000	0.000	0.000	0.000
63	A	99	GLY	0	-0.004	-0.008	17.657	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	100	GLU	-1	-0.831	-0.902	21.275	-0.087	-0.087	0.000	0.000	0.000	0.000
65	A	101	ASP	-1	-0.878	-0.951	21.257	-0.146	-0.146	0.000	0.000	0.000	0.000
66	A	102	TYR	0	-0.018	-0.014	16.009	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	103	VAL	0	-0.058	-0.029	14.812	0.034	0.034	0.000	0.000	0.000	0.000
68	A	104	ILE	0	-0.018	0.001	9.850	-0.043	-0.043	0.000	0.000	0.000	0.000
69	A	105	MET	0	0.003	-0.001	10.247	0.062	0.062	0.000	0.000	0.000	0.000
70	A	106	THR	0	-0.027	-0.036	6.674	-0.145	-0.145	0.000	0.000	0.000	0.000
71	A	107	PRO	0	0.041	0.036	3.679	-0.101	0.091	0.002	-0.030	-0.163	0.000
72	A	108	THR	0	0.001	-0.030	6.985	0.082	0.082	0.000	0.000	0.000	0.000
73	A	109	GLY	0	-0.057	-0.018	7.038	0.198	0.198	0.000	0.000	0.000	0.000
74	A	110	ILE	0	-0.011	0.004	2.917	-0.696	-0.057	0.312	-0.172	-0.779	0.000
75	A	111	LYS	1	0.936	0.976	7.098	-0.359	-0.359	0.000	0.000	0.000	0.000
76	A	112	VAL	0	0.019	0.007	9.240	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	113	ASP	-1	-0.820	-0.898	11.737	0.058	0.058	0.000	0.000	0.000	0.000
78	A	114	ARG	1	0.794	0.857	14.551	-0.054	-0.054	0.000	0.000	0.000	0.000
79	A	115	ASN	0	-0.094	-0.057	17.738	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	116	LYS	1	0.914	0.963	18.514	0.059	0.059	0.000	0.000	0.000	0.000
81	A	117	ILE	0	0.069	0.035	16.947	0.007	0.007	0.000	0.000	0.000	0.000
82	A	118	ARG	1	0.917	0.955	20.532	0.039	0.039	0.000	0.000	0.000	0.000
83	A	119	SER	0	0.033	0.029	24.192	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:37:VAL)