FMO DATABASE

FMODB ID: 89J2Y

Calculation Name: 3DWM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DWM

Chain ID: A

ChEMBL ID:

UniProt ID: P9WP33

Base Structure: X-ray

Registration Date: 2023-09-20

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	89
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-548311.886446
FMO2-HF: Nuclear repulsion	516145.90279
FMO2-HF: Total energy	-32165.983656
FMO2-MP2: Total energy	-32260.992902

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:2:ASN)

Summations of interaction energy for fragment #1(A:2:ASN)

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.
-41.603	-38.886	17.347	-10.386	-9.677	-0.039

Interaction energy analysis for fragmet #1(A:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : 0.002

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	4	THR	0	-0.013	-0.004	3.867	3.945	5.982	-0.018	-0.959	-1.060	0.005
4	A	5	VAL	0	0.039	0.014	6.249	-1.108	-1.108	0.000	0.000	0.000	0.000
5	A	6	SER	0	-0.024	0.005	9.267	0.527	0.527	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.059	0.029	11.740	-0.153	-0.153	0.000	0.000	0.000	0.000
7	A	8	PRO	0	0.036	0.033	15.017	-0.023	-0.023	0.000	0.000	0.000	0.000
8	A	9	THR	0	0.015	-0.025	18.839	0.062	0.062	0.000	0.000	0.000	0.000
9	A	10	ILE	0	0.004	0.003	21.065	0.047	0.047	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.040	0.010	17.632	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.876	0.948	16.599	-0.553	-0.553	0.000	0.000	0.000	0.000
12	A	13	PRO	0	-0.039	-0.015	18.102	0.097	0.097	0.000	0.000	0.000	0.000
13	A	14	HIS	0	-0.013	0.013	17.210	-0.045	-0.045	0.000	0.000	0.000	0.000
14	A	15	THR	0	0.002	0.011	13.101	0.022	0.022	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.033	0.023	15.018	0.173	0.173	0.000	0.000	0.000	0.000
16	A	17	GLY	0	-0.039	-0.022	17.754	-0.037	-0.037	0.000	0.000	0.000	0.000
17	A	18	GLN	0	-0.077	-0.041	11.348	0.155	0.155	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.941	0.942	14.317	-0.724	-0.724	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.050	-0.039	9.720	-0.216	-0.216	0.000	0.000	0.000	0.000
20	A	21	VAL	0	0.001	0.009	8.356	0.007	0.007	0.000	0.000	0.000	0.000
21	A	22	SER	0	0.002	0.007	1.911	-12.091	-12.780	5.781	-2.465	-2.626	0.026
22	A	23	ALA	0	-0.003	-0.002	3.803	-1.535	-1.330	0.000	-0.039	-0.165	0.000
23	A	24	SER	0	-0.053	-0.032	2.910	-3.259	-1.386	0.442	-1.135	-1.180	-0.009
24	A	25	GLY	0	0.053	0.000	3.841	0.555	0.667	0.001	-0.019	-0.095	0.000
25	A	26	ASP	-1	-0.883	-0.939	6.407	-1.839	-1.839	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.025	-0.023	8.678	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.048	0.028	9.922	0.117	0.117	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.032	-0.021	11.673	0.207	0.207	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.026	0.016	9.455	0.171	0.171	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.066	0.046	6.298	0.342	0.342	0.000	0.000	0.000	0.000
31	A	32	ILE	0	-0.031	-0.026	8.752	0.438	0.438	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.082	-0.048	11.514	0.150	0.150	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.739	-0.864	6.689	3.058	3.058	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.023	-0.014	9.192	0.300	0.300	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.816	-0.891	11.157	0.758	0.758	0.000	0.000	0.000	0.000
36	A	37	ALA	0	-0.029	-0.015	12.340	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.085	-0.037	9.287	0.225	0.225	0.000	0.000	0.000	0.000
38	A	39	TYR	0	-0.033	-0.032	9.355	-0.159	-0.159	0.000	0.000	0.000	0.000
39	A	40	SER	0	-0.001	-0.001	14.847	-0.162	-0.162	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.031	0.012	17.857	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.045	-0.021	14.533	-0.086	-0.086	0.000	0.000	0.000	0.000
42	A	43	SER	0	0.039	0.008	16.432	-0.120	-0.120	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.929	-0.977	17.889	0.310	0.310	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.800	0.898	20.520	-0.484	-0.484	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.018	-0.004	15.378	-0.036	-0.036	0.000	0.000	0.000	0.000
46	A	47	MET	0	-0.017	0.008	19.412	-0.085	-0.085	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.812	-0.895	21.643	0.043	0.043	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.018	-0.004	25.298	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	50	SER	0	-0.044	-0.023	27.433	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.069	-0.053	27.434	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	52	PRO	0	0.064	0.027	24.166	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.003	0.007	20.733	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.796	0.900	20.704	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.063	0.025	17.373	0.038	0.038	0.000	0.000	0.000	0.000
55	A	56	HIS	0	0.035	0.017	21.503	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.941	0.962	24.164	-0.027	-0.027	0.000	0.000	0.000	0.000
57	A	58	PHE	0	-0.027	-0.028	26.237	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.008	0.022	19.844	0.026	0.026	0.000	0.000	0.000	0.000
59	A	60	ASN	0	0.017	0.028	20.955	-0.035	-0.035	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.015	-0.007	14.485	0.076	0.076	0.000	0.000	0.000	0.000
61	A	62	TYR	0	-0.057	-0.032	15.981	0.008	0.008	0.000	0.000	0.000	0.000
62	A	63	VAL	0	0.023	-0.003	10.925	0.073	0.073	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.025	-0.019	10.628	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.959	-0.971	13.774	-0.810	-0.810	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.798	-0.881	16.894	-0.517	-0.517	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.867	-0.929	17.262	-0.314	-0.314	0.000	0.000	0.000	0.000
67	A	68	VAL	0	0.027	0.005	14.934	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.757	0.858	17.984	0.168	0.168	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.056	-0.020	21.132	0.053	0.053	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.026	0.020	17.651	-0.038	-0.038	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.026	0.019	18.337	-0.054	-0.054	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.033	-0.013	18.438	0.062	0.062	0.000	0.000	0.000	0.000
73	A	74	LEU	0	0.003	-0.018	15.392	-0.066	-0.066	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.022	-0.012	14.728	-0.035	-0.035	0.000	0.000	0.000	0.000
75	A	76	THR	0	-0.022	-0.005	13.476	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.009	-0.009	12.030	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.051	-0.015	6.060	0.129	0.129	0.000	0.000	0.000	0.000
78	A	79	ALA	0	-0.024	-0.007	7.532	0.164	0.164	0.000	0.000	0.000	0.000
79	A	80	ASP	-1	-0.874	-0.951	1.813	-30.206	-31.791	11.140	-5.567	-3.988	-0.061
80	A	81	GLY	0	-0.019	-0.014	3.647	1.775	2.309	0.002	-0.189	-0.347	0.000
81	A	82	ASP	-1	-0.820	-0.880	4.479	-1.385	-1.155	-0.001	-0.013	-0.216	0.000
82	A	83	SER	0	-0.078	-0.049	6.707	0.121	0.121	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.052	0.018	8.519	0.097	0.097	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.059	-0.035	11.004	0.363	0.363	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.014	0.025	13.287	-0.075	-0.075	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.006	-0.010	16.423	0.079	0.079	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.001	-0.006	20.128	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	89	ALA	0	-0.014	0.010	23.588	-0.032	-0.032	0.000	0.000	0.000	0.000
89	A	90	VAL	0	-0.024	-0.011	25.825	0.014	0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASN)