FMO DATABASE

FMODB ID: ZYZNN

Calculation Name: 3D0W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D0W

Chain ID: A

ChEMBL ID:

UniProt ID: O34306

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-567942.672743
FMO2-HF: Nuclear repulsion	534045.968648
FMO2-HF: Total energy	-33896.704095
FMO2-MP2: Total energy	-33997.306384

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:19:GLY)

Summations of interaction energy for fragment #1(A:19:GLY)

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.
-6.787	-3.456	0.184	-1.67	-1.844	-0.001

Interaction energy analysis for fragmet #1(A:19:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.005

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	21	ILE	0	-0.020	-0.002	2.851	-2.645	-0.334	0.149	-1.091	-1.369	0.003
4	A	22	LYS	1	0.849	0.901	3.272	-2.160	-1.359	0.026	-0.521	-0.306	-0.004
5	A	23	GLU	-1	-0.870	-0.936	6.027	-1.304	-1.304	0.000	0.000	0.000	0.000
6	A	24	ASP	-1	-0.794	-0.886	6.739	-0.747	-0.747	0.000	0.000	0.000	0.000
7	A	25	ILE	0	0.028	0.017	7.985	0.154	0.154	0.000	0.000	0.000	0.000
8	A	26	LEU	0	-0.040	-0.015	3.263	0.060	0.279	0.009	-0.058	-0.169	0.000
9	A	27	LYS	1	0.820	0.891	7.919	0.582	0.582	0.000	0.000	0.000	0.000
10	A	28	ASP	-1	-0.824	-0.901	11.056	-0.286	-0.286	0.000	0.000	0.000	0.000
11	A	29	PHE	0	0.013	0.011	10.621	0.116	0.116	0.000	0.000	0.000	0.000
12	A	30	GLU	-1	-0.803	-0.905	10.763	0.017	0.017	0.000	0.000	0.000	0.000
13	A	31	GLU	-1	-0.869	-0.920	13.326	-0.255	-0.255	0.000	0.000	0.000	0.000
14	A	32	PHE	0	0.013	0.019	15.591	0.041	0.041	0.000	0.000	0.000	0.000
15	A	33	LYS	1	0.776	0.879	13.247	0.030	0.030	0.000	0.000	0.000	0.000
16	A	34	GLY	0	0.008	-0.005	17.323	0.020	0.020	0.000	0.000	0.000	0.000
17	A	35	TYR	0	-0.014	-0.042	19.201	0.012	0.012	0.000	0.000	0.000	0.000
18	A	36	LEU	0	0.035	0.026	19.591	0.012	0.012	0.000	0.000	0.000	0.000
19	A	37	LYS	1	0.845	0.912	19.655	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	38	LYS	1	0.763	0.894	22.949	0.074	0.074	0.000	0.000	0.000	0.000
21	A	39	GLN	0	0.051	0.029	25.475	0.002	0.002	0.000	0.000	0.000	0.000
22	A	40	VAL	0	0.035	0.022	25.261	0.005	0.005	0.000	0.000	0.000	0.000
23	A	41	ASN	0	0.005	-0.006	26.075	0.007	0.007	0.000	0.000	0.000	0.000
24	A	42	ARG	1	0.969	0.983	28.489	0.032	0.032	0.000	0.000	0.000	0.000
25	A	43	GLY	0	0.054	0.033	30.852	0.001	0.001	0.000	0.000	0.000	0.000
26	A	44	LYS	1	0.852	0.911	28.720	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	45	LYS	1	0.777	0.909	31.013	0.009	0.009	0.000	0.000	0.000	0.000
28	A	46	LEU	0	0.073	0.028	34.845	0.001	0.001	0.000	0.000	0.000	0.000
29	A	47	GLY	0	0.009	0.017	36.219	0.001	0.001	0.000	0.000	0.000	0.000
30	A	48	LEU	0	-0.035	-0.011	36.624	0.002	0.002	0.000	0.000	0.000	0.000
31	A	49	ASP	-1	-0.911	-0.973	38.301	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	50	ASP	-1	-0.837	-0.899	40.710	0.000	0.000	0.000	0.000	0.000	0.000
33	A	51	GLY	0	-0.013	0.008	41.821	0.001	0.001	0.000	0.000	0.000	0.000
34	A	52	LYS	1	0.740	0.846	40.236	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	53	LEU	0	0.000	-0.005	36.722	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	54	VAL	0	0.031	0.026	33.515	0.003	0.003	0.000	0.000	0.000	0.000
37	A	55	LYS	1	0.974	0.978	32.163	-0.033	-0.033	0.000	0.000	0.000	0.000
38	A	56	SER	0	0.032	-0.008	26.922	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	57	ALA	0	0.072	0.039	27.960	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	58	ALA	0	0.028	0.030	28.953	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	59	ILE	0	-0.012	0.006	29.420	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	60	LEU	0	-0.014	-0.014	24.114	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	61	GLY	0	0.059	0.035	27.764	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	62	ASP	-1	-0.893	-0.959	30.436	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	63	TYR	0	-0.141	-0.066	23.905	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	64	LEU	0	0.072	0.040	24.930	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	65	ALA	0	-0.051	-0.012	29.010	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	66	LYS	1	0.828	0.903	31.399	0.016	0.016	0.000	0.000	0.000	0.000
49	A	67	HIS	0	-0.031	-0.013	30.149	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	68	GLU	-1	-0.848	-0.914	27.696	-0.047	-0.047	0.000	0.000	0.000	0.000
51	A	69	GLU	-1	-0.894	-0.942	27.526	-0.075	-0.075	0.000	0.000	0.000	0.000
52	A	70	PRO	0	-0.043	-0.021	23.239	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	71	GLN	0	-0.063	-0.037	22.171	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	72	ASN	0	-0.050	-0.027	17.276	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	73	GLY	0	0.036	0.013	17.384	0.019	0.019	0.000	0.000	0.000	0.000
56	A	74	GLU	-1	-0.915	-0.964	13.815	-0.129	-0.129	0.000	0.000	0.000	0.000
57	A	75	GLU	-1	-0.808	-0.909	17.881	-0.074	-0.074	0.000	0.000	0.000	0.000
58	A	76	MET	0	-0.007	0.010	21.126	0.010	0.010	0.000	0.000	0.000	0.000
59	A	77	LEU	0	-0.019	-0.005	18.217	0.014	0.014	0.000	0.000	0.000	0.000
60	A	78	LEU	0	-0.026	-0.021	20.795	0.015	0.015	0.000	0.000	0.000	0.000
61	A	79	GLN	0	0.024	0.007	23.186	0.008	0.008	0.000	0.000	0.000	0.000
62	A	80	GLU	-1	-0.915	-0.950	24.716	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	81	LEU	0	-0.016	-0.003	22.114	0.007	0.007	0.000	0.000	0.000	0.000
64	A	82	TRP	0	-0.006	-0.007	26.358	0.006	0.006	0.000	0.000	0.000	0.000
65	A	83	SER	0	-0.086	-0.057	28.759	0.000	0.000	0.000	0.000	0.000	0.000
66	A	84	VAL	0	-0.049	-0.029	28.858	0.000	0.000	0.000	0.000	0.000	0.000
67	A	85	ALA	0	-0.020	0.016	29.183	0.003	0.003	0.000	0.000	0.000	0.000
68	A	86	ASP	-1	-0.845	-0.926	31.225	0.036	0.036	0.000	0.000	0.000	0.000
69	A	87	GLU	-1	-0.971	-1.003	33.435	0.023	0.023	0.000	0.000	0.000	0.000
70	A	88	ASP	-1	-0.870	-0.939	34.431	0.052	0.052	0.000	0.000	0.000	0.000
71	A	89	GLU	-1	-0.886	-0.948	30.078	0.059	0.059	0.000	0.000	0.000	0.000
72	A	90	LYS	1	0.818	0.916	29.349	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	91	GLU	-1	-0.943	-0.959	29.569	0.038	0.038	0.000	0.000	0.000	0.000
74	A	92	HIS	0	-0.055	-0.031	28.391	0.010	0.010	0.000	0.000	0.000	0.000
75	A	93	LEU	0	-0.012	-0.002	23.404	0.011	0.011	0.000	0.000	0.000	0.000
76	A	94	ALA	0	0.031	0.014	24.757	0.002	0.002	0.000	0.000	0.000	0.000
77	A	95	GLN	0	-0.056	-0.050	25.779	0.000	0.000	0.000	0.000	0.000	0.000
78	A	96	LEU	0	-0.052	-0.022	20.580	0.009	0.009	0.000	0.000	0.000	0.000
79	A	97	LEU	0	0.041	0.025	20.054	0.012	0.012	0.000	0.000	0.000	0.000
80	A	98	VAL	0	-0.010	-0.007	21.302	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	99	LYS	1	0.899	0.953	20.793	-0.153	-0.153	0.000	0.000	0.000	0.000
82	A	100	LEU	0	-0.005	0.017	15.952	0.023	0.023	0.000	0.000	0.000	0.000
83	A	101	VAL	0	0.019	0.004	17.134	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	102	ASP	-1	-0.932	-0.969	19.009	0.025	0.025	0.000	0.000	0.000	0.000
85	A	103	LYS	1	0.921	0.984	11.628	-0.356	-0.356	0.000	0.000	0.000	0.000
86	A	104	GLN	0	-0.024	-0.013	10.088	0.031	0.031	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:GLY)