FMO DATABASE

FMODB ID: NNLLQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-628948.575515
FMO2-HF: Nuclear repulsion	594225.707248
FMO2-HF: Total energy	-34722.868267
FMO2-MP2: Total energy	-34826.69636

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.
-0.026	1.059	-0.007	-0.445	-0.633	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 : 0.034 / q_NPA : 0.004

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	0.070	0.041	3.862	1.105	2.094	-0.006	-0.400	-0.583	0.001
4	A	7	ASN	0	0.003	0.001	5.753	0.338	0.338	0.000	0.000	0.000	0.000
5	A	8	VAL	0	0.023	0.013	9.404	-0.038	-0.038	0.000	0.000	0.000	0.000
6	A	9	PRO	0	0.011	0.001	11.927	0.071	0.071	0.000	0.000	0.000	0.000
7	A	10	ASN	0	0.009	-0.003	14.448	0.044	0.044	0.000	0.000	0.000	0.000
8	A	11	PRO	0	0.027	0.002	15.201	-0.021	-0.021	0.000	0.000	0.000	0.000
9	A	12	ASN	0	0.056	0.025	17.234	-0.012	-0.012	0.000	0.000	0.000	0.000
10	A	13	ASN	0	-0.001	0.013	19.379	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	14	THR	0	0.046	0.019	20.994	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.944	0.976	15.112	0.380	0.380	0.000	0.000	0.000	0.000
13	A	16	PHE	0	-0.012	-0.021	14.510	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	17	GLN	0	0.023	0.015	18.816	0.016	0.016	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.901	-0.948	22.324	-0.129	-0.129	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.023	-0.015	16.622	0.003	0.003	0.000	0.000	0.000	0.000
17	A	20	ALA	0	-0.011	0.002	20.601	0.007	0.007	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.860	0.927	21.633	0.082	0.082	0.000	0.000	0.000	0.000
19	A	22	PHE	0	0.013	0.014	21.161	0.007	0.007	0.000	0.000	0.000	0.000
20	A	23	ALA	0	-0.005	-0.015	21.033	0.006	0.006	0.000	0.000	0.000	0.000
21	A	24	ILE	0	-0.003	0.005	23.154	0.010	0.010	0.000	0.000	0.000	0.000
22	A	25	GLN	0	-0.008	0.005	26.125	0.004	0.004	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.811	-0.891	25.145	-0.090	-0.090	0.000	0.000	0.000	0.000
24	A	27	TYR	0	0.001	-0.005	25.487	0.008	0.008	0.000	0.000	0.000	0.000
25	A	28	ASN	0	0.017	0.006	27.311	0.008	0.008	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.858	0.930	30.389	0.050	0.050	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.774	0.871	26.319	0.089	0.089	0.000	0.000	0.000	0.000
28	A	31	GLN	0	-0.013	-0.015	28.024	0.000	0.000	0.000	0.000	0.000	0.000
29	A	32	ASN	0	-0.065	-0.016	31.490	0.002	0.002	0.000	0.000	0.000	0.000
30	A	33	ALA	0	0.055	0.027	33.176	0.004	0.004	0.000	0.000	0.000	0.000
31	A	34	HIS	0	-0.044	-0.022	32.498	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	35	LEU	0	0.006	0.012	27.989	0.003	0.003	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.925	-0.960	31.393	-0.034	-0.034	0.000	0.000	0.000	0.000
34	A	37	PHE	0	0.021	-0.028	27.458	0.001	0.001	0.000	0.000	0.000	0.000
35	A	38	VAL	0	-0.039	0.003	26.500	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.892	-0.942	23.720	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.021	-0.028	18.845	0.012	0.012	0.000	0.000	0.000	0.000
38	A	41	LEU	0	0.009	0.001	20.029	0.008	0.008	0.000	0.000	0.000	0.000
39	A	42	ASN	0	-0.070	-0.052	13.463	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	43	VAL	0	-0.003	0.014	13.033	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.866	0.939	7.141	-0.509	-0.509	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.901	-0.963	7.164	-1.634	-1.634	0.000	0.000	0.000	0.000
43	A	46	GLN	0	0.046	0.030	3.908	-0.248	-0.152	-0.001	-0.045	-0.050	0.000
44	A	47	VAL	0	0.069	0.048	5.580	0.563	0.563	0.000	0.000	0.000	0.000
45	A	48	VAL	0	-0.026	-0.026	7.014	-0.151	-0.151	0.000	0.000	0.000	0.000
46	A	49	ALA	0	0.009	0.019	9.877	0.043	0.043	0.000	0.000	0.000	0.000
47	A	50	GLY	0	-0.002	-0.007	12.050	0.095	0.095	0.000	0.000	0.000	0.000
48	A	51	ILE	0	-0.009	0.008	9.669	-0.140	-0.140	0.000	0.000	0.000	0.000
49	A	52	MET	0	-0.006	0.004	9.385	0.210	0.210	0.000	0.000	0.000	0.000
50	A	53	TYR	0	0.012	-0.001	10.018	-0.123	-0.123	0.000	0.000	0.000	0.000
51	A	54	TYR	0	-0.072	-0.055	6.921	0.209	0.209	0.000	0.000	0.000	0.000
52	A	55	ILE	0	0.028	0.019	12.438	0.029	0.029	0.000	0.000	0.000	0.000
53	A	56	THR	0	-0.047	-0.024	15.674	0.053	0.053	0.000	0.000	0.000	0.000
54	A	57	LEU	0	0.019	0.021	17.956	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	58	ALA	0	0.002	0.002	21.370	0.015	0.015	0.000	0.000	0.000	0.000
56	A	59	ALA	0	0.028	0.015	25.066	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	60	THR	0	0.002	-0.016	28.041	0.008	0.008	0.000	0.000	0.000	0.000
58	A	61	ASP	-1	-0.871	-0.921	31.807	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.871	-0.953	34.411	0.001	0.001	0.000	0.000	0.000	0.000
60	A	63	ALA	0	0.041	0.036	37.720	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	64	GLY	0	0.033	0.019	35.517	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.772	0.880	35.110	0.001	0.001	0.000	0.000	0.000	0.000
63	A	66	LYS	1	1.001	1.000	29.462	-0.032	-0.032	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.890	0.947	27.552	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	68	ILE	0	0.007	0.007	22.374	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	69	TYR	0	0.034	0.009	22.638	0.008	0.008	0.000	0.000	0.000	0.000
67	A	70	LYS	1	0.860	0.922	14.259	-0.093	-0.093	0.000	0.000	0.000	0.000
68	A	71	ALA	0	0.016	0.009	17.289	0.002	0.002	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.801	0.896	12.832	0.028	0.028	0.000	0.000	0.000	0.000
70	A	73	ILE	0	0.013	0.006	14.559	0.026	0.026	0.000	0.000	0.000	0.000
71	A	74	TRP	0	-0.009	0.005	14.046	-0.037	-0.037	0.000	0.000	0.000	0.000
72	A	75	VAL	0	-0.007	-0.014	14.409	0.058	0.058	0.000	0.000	0.000	0.000
73	A	76	LYS	1	0.804	0.887	15.096	0.189	0.189	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.734	-0.869	15.494	-0.357	-0.357	0.000	0.000	0.000	0.000
75	A	78	TRP	0	0.001	0.005	16.120	0.033	0.033	0.000	0.000	0.000	0.000
76	A	79	GLU	-1	-0.821	-0.900	20.611	-0.209	-0.209	0.000	0.000	0.000	0.000
77	A	80	ASP	-1	-0.843	-0.913	22.184	-0.157	-0.157	0.000	0.000	0.000	0.000
78	A	81	PHE	0	-0.001	0.023	19.140	0.009	0.009	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.818	0.892	19.529	0.144	0.144	0.000	0.000	0.000	0.000
80	A	83	LYS	1	0.919	0.954	19.207	0.179	0.179	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.045	0.035	18.478	-0.026	-0.026	0.000	0.000	0.000	0.000
82	A	85	VAL	0	-0.061	-0.034	15.771	0.009	0.009	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.838	-0.915	17.335	0.012	0.012	0.000	0.000	0.000	0.000
84	A	87	PHE	0	0.041	0.018	18.945	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	88	LYS	1	0.945	0.988	19.049	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.065	0.038	22.210	0.002	0.002	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.044	-0.019	20.928	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)