FMO DATABASE

FMODB ID: M3L9Z

Calculation Name: 3D33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D33

Chain ID: A

ChEMBL ID:

UniProt ID: A6KX32

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-666591.396435
FMO2-HF: Nuclear repulsion	629601.000213
FMO2-HF: Total energy	-36990.396222
FMO2-MP2: Total energy	-37097.852939

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:34:PRO)

Summations of interaction energy for fragment #1(A:34:PRO)

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.
-5.329	-2.701	0.124	-1.456	-1.296	-0.002

Interaction energy analysis for fragmet #1(A:34:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.026

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

Sort

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	36	LYS	1	0.887	0.937	3.041	-1.910	0.718	0.124	-1.456	-1.296	-0.002
4	A	37	ASP	-1	-0.877	-0.945	5.745	-0.540	-0.540	0.000	0.000	0.000	0.000
5	A	38	VAL	0	-0.106	-0.056	7.792	0.005	0.005	0.000	0.000	0.000	0.000
6	A	39	GLU	-1	-0.884	-0.929	11.459	-0.547	-0.547	0.000	0.000	0.000	0.000
7	A	40	LEU	0	-0.077	-0.041	13.379	0.052	0.052	0.000	0.000	0.000	0.000
8	A	41	ASP	-1	-0.875	-0.923	16.690	-0.371	-0.371	0.000	0.000	0.000	0.000
9	A	42	GLY	0	-0.019	-0.028	20.012	0.009	0.009	0.000	0.000	0.000	0.000
10	A	43	ARG	1	0.747	0.843	23.314	0.156	0.156	0.000	0.000	0.000	0.000
11	A	44	TRP	0	0.055	0.005	23.012	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	45	ASP	-1	-0.828	-0.871	24.960	-0.141	-0.141	0.000	0.000	0.000	0.000
13	A	46	ASP	-1	-0.913	-0.943	27.407	-0.106	-0.106	0.000	0.000	0.000	0.000
14	A	54	ASN	0	-0.034	-0.035	15.983	-0.019	-0.019	0.000	0.000	0.000	0.000
15	A	55	CYS	0	0.017	0.030	17.864	0.028	0.028	0.000	0.000	0.000	0.000
16	A	56	PRO	0	0.037	0.023	17.679	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	57	ILE	0	-0.004	0.005	17.087	0.001	0.001	0.000	0.000	0.000	0.000
18	A	58	THR	0	0.009	0.008	11.815	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	59	VAL	0	0.038	0.000	12.276	0.062	0.062	0.000	0.000	0.000	0.000
20	A	60	PHE	0	-0.010	0.006	7.157	-0.052	-0.052	0.000	0.000	0.000	0.000
21	A	61	THR	0	-0.001	-0.006	8.345	0.385	0.385	0.000	0.000	0.000	0.000
22	A	62	ASP	-1	-0.932	-0.967	6.237	-1.716	-1.716	0.000	0.000	0.000	0.000
23	A	63	GLY	0	0.020	0.010	7.468	0.485	0.485	0.000	0.000	0.000	0.000
24	A	64	TYR	0	-0.073	-0.058	9.475	-0.086	-0.086	0.000	0.000	0.000	0.000
25	A	65	LEU	0	-0.013	0.000	11.783	0.138	0.138	0.000	0.000	0.000	0.000
26	A	66	LEU	0	0.018	0.016	11.333	-0.190	-0.190	0.000	0.000	0.000	0.000
27	A	67	THR	0	-0.009	-0.017	11.381	0.203	0.203	0.000	0.000	0.000	0.000
28	A	68	LEU	0	0.022	0.016	12.712	-0.097	-0.097	0.000	0.000	0.000	0.000
29	A	69	LYS	1	0.903	0.946	11.737	0.219	0.219	0.000	0.000	0.000	0.000
30	A	70	ASN	0	0.086	0.039	15.877	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	71	ALA	0	-0.047	-0.031	17.530	0.028	0.028	0.000	0.000	0.000	0.000
32	A	72	SER	0	-0.069	-0.048	19.296	0.025	0.025	0.000	0.000	0.000	0.000
33	A	73	PRO	0	-0.027	-0.010	22.276	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	74	ASP	-1	-0.801	-0.857	24.634	-0.126	-0.126	0.000	0.000	0.000	0.000
35	A	75	ARG	1	0.761	0.852	26.674	0.149	0.149	0.000	0.000	0.000	0.000
36	A	76	ASP	-1	-0.857	-0.916	27.381	-0.113	-0.113	0.000	0.000	0.000	0.000
37	A	77	MET	0	-0.049	-0.033	21.275	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	78	THR	0	-0.030	-0.018	25.986	0.011	0.011	0.000	0.000	0.000	0.000
39	A	79	ILE	0	-0.047	-0.010	19.782	-0.020	-0.020	0.000	0.000	0.000	0.000
40	A	80	ARG	1	0.863	0.911	23.222	0.213	0.213	0.000	0.000	0.000	0.000
41	A	81	ILE	0	-0.010	0.000	19.086	-0.032	-0.032	0.000	0.000	0.000	0.000
42	A	82	THR	0	-0.030	-0.022	22.657	0.039	0.039	0.000	0.000	0.000	0.000
43	A	83	ASP	-1	-0.776	-0.883	23.412	-0.275	-0.275	0.000	0.000	0.000	0.000
44	A	84	MET	0	0.007	-0.003	22.165	0.033	0.033	0.000	0.000	0.000	0.000
45	A	85	ALA	0	-0.042	0.007	25.208	0.016	0.016	0.000	0.000	0.000	0.000
46	A	86	LYS	1	0.822	0.882	27.575	0.194	0.194	0.000	0.000	0.000	0.000
47	A	87	GLY	0	0.010	0.023	28.345	0.014	0.014	0.000	0.000	0.000	0.000
48	A	88	GLY	0	-0.035	-0.016	28.838	0.013	0.013	0.000	0.000	0.000	0.000
49	A	89	VAL	0	-0.010	-0.006	26.864	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	90	VAL	0	-0.043	-0.021	22.862	0.017	0.017	0.000	0.000	0.000	0.000
51	A	91	TYR	0	-0.017	-0.019	22.655	0.004	0.004	0.000	0.000	0.000	0.000
52	A	92	GLU	-1	-0.844	-0.911	25.168	-0.184	-0.184	0.000	0.000	0.000	0.000
53	A	93	ASN	0	-0.053	-0.026	23.802	0.028	0.028	0.000	0.000	0.000	0.000
54	A	94	ASP	-1	-0.820	-0.876	26.272	-0.162	-0.162	0.000	0.000	0.000	0.000
55	A	95	ILE	0	-0.047	-0.032	22.968	0.007	0.007	0.000	0.000	0.000	0.000
56	A	96	PRO	0	0.011	0.002	27.053	0.000	0.000	0.000	0.000	0.000	0.000
57	A	97	GLU	-1	-0.879	-0.929	27.437	-0.092	-0.092	0.000	0.000	0.000	0.000
58	A	98	VAL	0	-0.039	-0.020	26.680	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	99	GLN	0	-0.068	-0.043	25.408	0.000	0.000	0.000	0.000	0.000	0.000
60	A	100	SER	0	-0.029	-0.030	23.308	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	101	ALA	0	0.031	0.018	20.623	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	102	TYR	0	-0.056	-0.044	14.262	-0.019	-0.019	0.000	0.000	0.000	0.000
63	A	103	ILE	0	0.022	0.030	17.561	0.024	0.024	0.000	0.000	0.000	0.000
64	A	104	THR	0	-0.020	0.000	14.546	-0.035	-0.035	0.000	0.000	0.000	0.000
65	A	105	ILE	0	-0.017	-0.008	16.150	0.047	0.047	0.000	0.000	0.000	0.000
66	A	106	SER	0	-0.010	0.003	16.216	-0.077	-0.077	0.000	0.000	0.000	0.000
67	A	107	ILE	0	0.043	0.019	13.373	0.030	0.030	0.000	0.000	0.000	0.000
68	A	108	ALA	0	0.008	0.002	16.906	0.000	0.000	0.000	0.000	0.000	0.000
69	A	109	ASN	0	-0.044	-0.029	17.777	0.017	0.017	0.000	0.000	0.000	0.000
70	A	110	PHE	0	0.037	0.029	19.264	0.024	0.024	0.000	0.000	0.000	0.000
71	A	111	PRO	0	0.005	-0.002	20.447	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	112	ALA	0	-0.009	0.009	19.193	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	113	GLU	-1	-0.846	-0.911	19.212	-0.288	-0.288	0.000	0.000	0.000	0.000
74	A	114	GLU	-1	-0.952	-0.987	18.424	-0.559	-0.559	0.000	0.000	0.000	0.000
75	A	115	TYR	0	-0.055	-0.054	18.694	0.077	0.077	0.000	0.000	0.000	0.000
76	A	116	LYS	1	0.888	0.935	19.077	0.224	0.224	0.000	0.000	0.000	0.000
77	A	117	LEU	0	-0.041	-0.026	16.074	0.020	0.020	0.000	0.000	0.000	0.000
78	A	118	GLU	-1	-0.815	-0.900	19.839	-0.258	-0.258	0.000	0.000	0.000	0.000
79	A	119	ILE	0	-0.008	-0.010	18.091	0.006	0.006	0.000	0.000	0.000	0.000
80	A	120	THR	0	0.012	-0.001	22.405	0.002	0.002	0.000	0.000	0.000	0.000
81	A	121	GLY	0	0.002	0.002	25.880	0.001	0.001	0.000	0.000	0.000	0.000
82	A	122	THR	0	-0.044	0.013	27.673	0.005	0.005	0.000	0.000	0.000	0.000
83	A	123	PRO	0	-0.012	-0.033	31.343	0.005	0.005	0.000	0.000	0.000	0.000
84	A	124	SER	0	-0.026	-0.027	30.721	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	125	GLY	0	0.045	0.029	26.651	0.001	0.001	0.000	0.000	0.000	0.000
86	A	126	HIS	0	-0.072	-0.047	25.203	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	127	LEU	0	0.020	0.024	19.289	0.000	0.000	0.000	0.000	0.000	0.000
88	A	128	THR	0	0.000	-0.016	20.718	0.010	0.010	0.000	0.000	0.000	0.000
89	A	129	GLY	0	0.084	0.050	16.699	-0.018	-0.018	0.000	0.000	0.000	0.000
90	A	130	TYR	0	-0.012	-0.006	16.249	0.065	0.065	0.000	0.000	0.000	0.000
91	A	131	PHE	0	-0.026	-0.015	13.637	-0.116	-0.116	0.000	0.000	0.000	0.000
92	A	132	THR	0	0.061	0.028	14.327	0.070	0.070	0.000	0.000	0.000	0.000
93	A	133	LYS	1	0.741	0.896	13.938	0.250	0.250	0.000	0.000	0.000	0.000
94	A	134	GLU	-1	-0.873	-0.935	13.542	-0.383	-0.383	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:34:PRO)