FMO DATABASE

FMODB ID: G5VV1

Calculation Name: 2W9P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W9P

Chain ID: A

ChEMBL ID:

UniProt ID: P37842

Base Structure: X-ray

Registration Date: 2023-09-23

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-628164.635537
FMO2-HF: Nuclear repulsion	593443.488075
FMO2-HF: Total energy	-34721.147463
FMO2-MP2: Total energy	-34825.127854

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:4:GLY)

Summations of interaction energy for fragment #1(A:4: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.
-0.012	1.337	0.009	-0.523	-0.835	0.001

Interaction energy analysis for fragmet #1(A:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.001

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	6	VAL	0	0.059	0.045	3.488	1.127	2.308	0.010	-0.465	-0.726	0.001
4	A	7	ASN	0	-0.034	-0.042	5.633	0.284	0.284	0.000	0.000	0.000	0.000
5	A	8	VAL	0	0.041	0.021	9.302	-0.044	-0.044	0.000	0.000	0.000	0.000
6	A	9	PRO	0	0.018	-0.001	11.636	0.068	0.068	0.000	0.000	0.000	0.000
7	A	10	ASN	0	0.034	0.021	14.317	0.041	0.041	0.000	0.000	0.000	0.000
8	A	11	PRO	0	0.003	-0.012	15.309	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	12	ASN	0	0.097	0.024	16.968	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	13	ASN	0	-0.065	-0.013	19.470	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	14	THR	0	0.083	0.029	20.902	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.974	1.017	15.193	0.366	0.366	0.000	0.000	0.000	0.000
13	A	16	PHE	0	-0.016	-0.025	14.304	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	17	GLN	0	0.005	0.010	18.651	0.012	0.012	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.916	-0.966	21.960	-0.133	-0.133	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.050	-0.018	15.794	0.001	0.001	0.000	0.000	0.000	0.000
17	A	20	ALA	0	-0.001	0.006	20.344	0.009	0.009	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.943	0.980	21.570	0.091	0.091	0.000	0.000	0.000	0.000
19	A	22	PHE	0	0.000	0.005	20.809	0.007	0.007	0.000	0.000	0.000	0.000
20	A	23	ALA	0	-0.016	-0.017	20.892	0.007	0.007	0.000	0.000	0.000	0.000
21	A	24	ILE	0	0.004	0.017	22.956	0.010	0.010	0.000	0.000	0.000	0.000
22	A	25	GLN	0	-0.012	-0.008	25.976	0.003	0.003	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.877	-0.951	24.826	-0.097	-0.097	0.000	0.000	0.000	0.000
24	A	27	TYR	0	0.036	0.008	25.794	0.007	0.007	0.000	0.000	0.000	0.000
25	A	28	ASN	0	0.014	0.009	27.365	0.009	0.009	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.911	0.959	30.623	0.060	0.060	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.870	0.941	27.208	0.090	0.090	0.000	0.000	0.000	0.000
28	A	31	GLN	0	-0.028	-0.021	28.444	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	32	ASN	0	-0.078	-0.020	31.520	0.003	0.003	0.000	0.000	0.000	0.000
30	A	33	ALA	0	0.016	-0.009	32.910	0.004	0.004	0.000	0.000	0.000	0.000
31	A	34	HIS	0	-0.024	-0.008	32.071	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	35	LEU	0	0.010	0.017	27.846	0.004	0.004	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.948	-0.987	31.011	-0.040	-0.040	0.000	0.000	0.000	0.000
34	A	37	PHE	0	-0.026	-0.049	27.348	0.002	0.002	0.000	0.000	0.000	0.000
35	A	38	VAL	0	-0.062	0.007	26.284	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.885	-0.940	23.636	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.036	-0.028	18.649	0.017	0.017	0.000	0.000	0.000	0.000
38	A	41	LEU	0	0.040	0.027	19.802	0.008	0.008	0.000	0.000	0.000	0.000
39	A	42	ASN	0	-0.056	-0.046	13.296	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	43	VAL	0	-0.008	0.014	12.774	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.880	0.956	8.327	-0.245	-0.245	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.900	-0.954	5.837	-1.861	-1.861	0.000	0.000	0.000	0.000
43	A	46	GLN	0	0.105	0.073	3.809	-0.466	-0.409	0.000	-0.051	-0.006	0.000
44	A	47	VAL	0	0.072	0.033	4.734	0.509	0.620	-0.001	-0.007	-0.103	0.000
45	A	48	VAL	0	-0.019	0.004	6.721	0.059	0.059	0.000	0.000	0.000	0.000
46	A	49	ALA	0	0.004	-0.005	9.349	0.040	0.040	0.000	0.000	0.000	0.000
47	A	50	GLY	0	0.012	0.004	11.984	0.061	0.061	0.000	0.000	0.000	0.000
48	A	51	ILE	0	-0.015	0.006	8.846	-0.121	-0.121	0.000	0.000	0.000	0.000
49	A	52	MET	0	-0.078	-0.019	9.224	0.203	0.203	0.000	0.000	0.000	0.000
50	A	53	TYR	0	0.042	0.015	9.451	-0.164	-0.164	0.000	0.000	0.000	0.000
51	A	54	TYR	0	-0.080	-0.076	7.297	0.277	0.277	0.000	0.000	0.000	0.000
52	A	55	ILE	0	0.031	0.016	12.484	0.020	0.020	0.000	0.000	0.000	0.000
53	A	56	THR	0	-0.092	-0.047	15.674	0.041	0.041	0.000	0.000	0.000	0.000
54	A	57	LEU	0	0.015	0.009	17.884	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	58	ALA	0	-0.035	-0.027	21.049	0.013	0.013	0.000	0.000	0.000	0.000
56	A	59	ALA	0	0.056	0.030	24.803	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	60	THR	0	-0.055	-0.044	27.905	0.008	0.008	0.000	0.000	0.000	0.000
58	A	61	ASP	-1	-0.835	-0.895	31.562	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.857	-0.952	34.494	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	63	ALA	0	0.008	0.021	37.471	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	64	GLY	0	0.036	0.019	35.174	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.773	0.889	35.069	0.011	0.011	0.000	0.000	0.000	0.000
63	A	66	LYS	1	1.021	1.011	28.746	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.932	0.956	27.448	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	68	ILE	0	0.003	0.015	22.037	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	69	TYR	0	0.087	0.037	22.442	0.010	0.010	0.000	0.000	0.000	0.000
67	A	70	LYS	1	0.920	0.962	13.508	-0.035	-0.035	0.000	0.000	0.000	0.000
68	A	71	ALA	0	0.030	0.021	17.360	0.007	0.007	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.893	0.965	12.582	0.076	0.076	0.000	0.000	0.000	0.000
70	A	73	ILE	0	0.005	-0.001	14.506	0.031	0.031	0.000	0.000	0.000	0.000
71	A	74	TRP	0	-0.010	-0.012	12.980	-0.029	-0.029	0.000	0.000	0.000	0.000
72	A	75	VAL	0	-0.016	-0.011	13.670	0.061	0.061	0.000	0.000	0.000	0.000
73	A	76	LYS	1	0.929	0.953	14.413	0.186	0.186	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.804	-0.930	14.661	-0.373	-0.373	0.000	0.000	0.000	0.000
75	A	78	TRP	0	-0.036	0.001	16.113	0.031	0.031	0.000	0.000	0.000	0.000
76	A	79	GLU	-1	-0.877	-0.954	19.735	-0.199	-0.199	0.000	0.000	0.000	0.000
77	A	80	ASP	-1	-0.923	-0.941	21.227	-0.147	-0.147	0.000	0.000	0.000	0.000
78	A	81	PHE	0	-0.047	-0.013	18.976	0.008	0.008	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.941	0.963	18.738	0.147	0.147	0.000	0.000	0.000	0.000
80	A	83	LYS	1	0.929	0.967	18.549	0.183	0.183	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.031	0.023	18.344	-0.030	-0.030	0.000	0.000	0.000	0.000
82	A	85	VAL	0	-0.055	-0.031	15.561	0.013	0.013	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.908	-0.967	17.380	-0.038	-0.038	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.008	-0.011	18.760	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	88	LYS	1	0.956	0.986	19.197	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.008	0.021	21.978	0.002	0.002	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.048	-0.030	20.598	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:4:GLY)