FMO DATABASE

FMODB ID: 53LGZ

Calculation Name: 1YVW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YVW

Chain ID: A

ChEMBL ID:

UniProt ID: Q81G00

Base Structure: X-ray

Registration Date: 2023-06-21

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-645023.199088
FMO2-HF: Nuclear repulsion	607154.988488
FMO2-HF: Total energy	-37868.210599
FMO2-MP2: Total energy	-37976.850453

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:ALA)

Summations of interaction energy for fragment #1(A:4:ALA)

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.
-10.919	-7.45	1.514	-2.225	-2.759	0.008

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.010

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	LYS	1	0.976	0.969	3.310	-6.483	-4.133	0.062	-1.193	-1.220	0.008
4	A	7	LEU	0	0.017	0.011	2.303	-2.436	-1.702	1.452	-0.870	-1.315	0.000
5	A	8	LEU	0	0.050	0.050	3.955	-0.457	-0.072	0.000	-0.162	-0.224	0.000
6	A	9	TYR	0	0.028	0.002	5.881	0.220	0.220	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.945	0.970	7.370	-1.281	-1.281	0.000	0.000	0.000	0.000
8	A	11	THR	0	0.043	0.014	7.316	-0.111	-0.111	0.000	0.000	0.000	0.000
9	A	12	ILE	0	-0.045	-0.021	9.871	-0.028	-0.028	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.921	-0.973	11.779	0.274	0.274	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.973	-0.987	11.462	0.113	0.113	0.000	0.000	0.000	0.000
12	A	15	ARG	1	0.913	0.960	14.233	0.113	0.113	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.928	0.992	16.239	-0.108	-0.108	0.000	0.000	0.000	0.000
14	A	17	GLY	0	-0.021	0.003	17.942	0.000	0.000	0.000	0.000	0.000	0.000
15	A	18	SER	0	-0.039	-0.014	18.644	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	19	PRO	0	-0.065	-0.035	19.416	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.027	0.008	18.498	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	21	PRO	0	-0.028	-0.019	21.514	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.874	-0.944	22.350	-0.074	-0.074	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.077	-0.035	17.685	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	24	TYR	0	0.048	-0.002	16.058	0.031	0.031	0.000	0.000	0.000	0.000
22	A	25	THR	0	0.057	0.023	14.078	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	26	ASN	0	0.025	0.029	17.164	0.008	0.008	0.000	0.000	0.000	0.000
24	A	27	TYR	0	0.013	0.020	20.194	0.017	0.017	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.017	-0.011	17.074	0.015	0.015	0.000	0.000	0.000	0.000
26	A	29	PHE	0	0.006	0.002	15.966	0.009	0.009	0.000	0.000	0.000	0.000
27	A	30	SER	0	-0.100	-0.042	21.506	0.008	0.008	0.000	0.000	0.000	0.000
28	A	31	LYS	1	0.861	0.923	24.456	0.036	0.036	0.000	0.000	0.000	0.000
29	A	32	GLY	0	0.073	0.048	24.032	0.004	0.004	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.803	-0.911	22.948	0.040	0.040	0.000	0.000	0.000	0.000
31	A	34	ASP	-1	-0.871	-0.936	23.535	0.001	0.001	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.843	0.929	22.997	0.051	0.051	0.000	0.000	0.000	0.000
33	A	36	ILE	0	0.033	0.008	18.190	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	37	LEU	0	0.013	0.007	20.289	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.896	0.947	22.393	0.018	0.018	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.954	0.992	19.031	0.117	0.117	0.000	0.000	0.000	0.000
37	A	40	ILE	0	0.013	0.022	17.157	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	41	GLY	0	-0.046	-0.020	19.370	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.941	-0.979	21.976	-0.104	-0.104	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.797	-0.910	16.340	-0.173	-0.173	0.000	0.000	0.000	0.000
41	A	44	CYS	0	-0.089	-0.042	18.979	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	45	ALA	0	-0.024	-0.020	20.075	0.000	0.000	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.867	-0.935	19.736	-0.150	-0.150	0.000	0.000	0.000	0.000
44	A	47	VAL	0	-0.011	0.008	16.582	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	48	ILE	0	-0.083	-0.040	19.388	0.004	0.004	0.000	0.000	0.000	0.000
46	A	49	ILE	0	-0.011	-0.014	22.704	0.003	0.003	0.000	0.000	0.000	0.000
47	A	50	ALA	0	0.060	0.038	19.888	0.004	0.004	0.000	0.000	0.000	0.000
48	A	51	CYS	0	-0.062	-0.038	20.534	0.001	0.001	0.000	0.000	0.000	0.000
49	A	52	LYS	1	0.868	0.931	21.940	0.076	0.076	0.000	0.000	0.000	0.000
50	A	53	ASN	0	0.009	0.014	24.346	0.015	0.015	0.000	0.000	0.000	0.000
51	A	54	ASN	0	-0.120	-0.055	23.386	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	55	ASP	-1	-0.838	-0.909	20.620	-0.197	-0.197	0.000	0.000	0.000	0.000
53	A	56	LYS	1	0.953	0.945	17.548	0.156	0.156	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.955	-0.974	15.826	-0.299	-0.299	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.873	-0.930	15.428	-0.277	-0.277	0.000	0.000	0.000	0.000
56	A	59	VAL	0	-0.032	-0.011	15.567	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.068	-0.033	10.612	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.921	0.958	11.704	0.274	0.274	0.000	0.000	0.000	0.000
59	A	62	GLU	-1	-0.712	-0.862	13.010	-0.257	-0.257	0.000	0.000	0.000	0.000
60	A	63	MET	0	-0.073	-0.036	11.739	0.019	0.019	0.000	0.000	0.000	0.000
61	A	64	VAL	0	-0.070	-0.042	7.826	-0.035	-0.035	0.000	0.000	0.000	0.000
62	A	65	ASP	-1	-0.833	-0.897	10.110	-0.327	-0.327	0.000	0.000	0.000	0.000
63	A	66	VAL	0	-0.004	0.008	12.926	0.047	0.047	0.000	0.000	0.000	0.000
64	A	67	PHE	0	-0.053	-0.041	8.137	0.067	0.067	0.000	0.000	0.000	0.000
65	A	68	TYR	0	-0.020	-0.017	10.011	0.082	0.082	0.000	0.000	0.000	0.000
66	A	69	HIS	0	0.070	0.023	10.922	0.105	0.105	0.000	0.000	0.000	0.000
67	A	70	CYS	0	-0.032	-0.012	13.076	0.060	0.060	0.000	0.000	0.000	0.000
68	A	71	PHE	0	-0.047	-0.041	6.731	0.121	0.121	0.000	0.000	0.000	0.000
69	A	72	VAL	0	0.020	0.013	12.344	0.058	0.058	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.007	0.007	14.915	0.027	0.027	0.000	0.000	0.000	0.000
71	A	74	LEU	0	-0.050	-0.024	12.561	0.028	0.028	0.000	0.000	0.000	0.000
72	A	75	ALA	0	0.032	0.017	14.554	0.012	0.012	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.943	-0.977	16.369	0.046	0.046	0.000	0.000	0.000	0.000
74	A	77	LYS	1	0.780	0.883	19.369	-0.087	-0.087	0.000	0.000	0.000	0.000
75	A	78	ASN	0	-0.049	-0.013	19.197	0.015	0.015	0.000	0.000	0.000	0.000
76	A	79	ILE	0	0.002	0.011	16.702	0.009	0.009	0.000	0.000	0.000	0.000
77	A	80	ALA	0	0.063	0.026	15.384	0.033	0.033	0.000	0.000	0.000	0.000
78	A	81	LEU	0	0.032	0.010	7.526	0.111	0.111	0.000	0.000	0.000	0.000
79	A	82	GLU	-1	-0.941	-0.988	12.213	0.636	0.636	0.000	0.000	0.000	0.000
80	A	83	ASP	-1	-0.831	-0.915	13.193	0.345	0.345	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.021	0.019	12.112	-0.033	-0.033	0.000	0.000	0.000	0.000
82	A	85	MET	0	-0.063	-0.047	8.362	0.110	0.110	0.000	0.000	0.000	0.000
83	A	86	ARG	1	0.833	0.924	12.174	-0.455	-0.455	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.840	-0.906	15.715	0.197	0.197	0.000	0.000	0.000	0.000
85	A	88	VAL	0	-0.047	-0.026	11.309	-0.039	-0.039	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.898	0.937	11.998	-0.816	-0.816	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.910	-0.941	15.331	0.166	0.166	0.000	0.000	0.000	0.000
88	A	91	ARG	1	0.930	0.954	16.982	-0.167	-0.167	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.034	-0.037	13.501	-0.066	-0.066	0.000	0.000	0.000	0.000
90	A	93	GLY	0	0.002	0.015	17.407	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.882	0.947	20.357	-0.172	-0.172	0.000	0.000	0.000	0.000
92	A	95	LEU	0	-0.044	0.004	18.518	-0.025	-0.025	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ALA)