FMO DATABASE

FMODB ID: VQR21

Calculation Name: 5D1I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D1I

Chain ID: A

ChEMBL ID:

UniProt ID: Q57AQ0

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:

Apendix: None

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	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-906659.943839
FMO2-HF: Nuclear repulsion	862281.502053
FMO2-HF: Total energy	-44378.441787
FMO2-MP2: Total energy	-44509.666169

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:ALA)

Summations of interaction energy for fragment #1(A:2: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.
-12.378	-4.637	4.685	-5.41	-7.016	-0.041

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.022

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	ASP	-1	-0.903	-0.962	2.900	-3.638	-1.051	0.151	-1.189	-1.550	0.003
4	A	5	ASP	-1	-0.902	-0.956	2.280	-14.170	-10.092	4.480	-3.806	-4.752	-0.043
5	A	6	ASP	-1	-0.848	-0.932	3.844	-2.548	-1.925	0.004	-0.235	-0.391	0.000
6	A	7	ILE	0	-0.030	-0.020	5.608	1.108	1.108	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.948	0.984	7.055	2.376	2.376	0.000	0.000	0.000	0.000
8	A	9	ILE	0	-0.030	-0.017	6.787	0.464	0.464	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.002	0.000	9.467	0.365	0.365	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.030	0.011	11.544	0.194	0.194	0.000	0.000	0.000	0.000
11	A	12	THR	0	-0.113	-0.060	12.816	0.127	0.127	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.045	-0.009	13.939	0.093	0.093	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.062	0.027	16.561	0.016	0.016	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.035	-0.018	19.506	0.021	0.021	0.000	0.000	0.000	0.000
15	A	16	PHE	0	-0.073	-0.049	14.580	0.039	0.039	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.927	-0.944	17.792	-0.385	-0.385	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.035	-0.017	19.184	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	19	PHE	0	-0.018	-0.006	16.484	0.028	0.028	0.000	0.000	0.000	0.000
19	A	20	THR	0	0.046	0.023	17.610	-0.047	-0.047	0.000	0.000	0.000	0.000
20	A	21	PRO	0	0.049	-0.004	13.534	-0.040	-0.040	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.985	-0.985	13.495	-0.325	-0.325	0.000	0.000	0.000	0.000
22	A	23	GLN	0	0.060	0.024	15.384	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.026	0.015	12.020	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.967	0.997	8.784	0.540	0.540	0.000	0.000	0.000	0.000
25	A	26	LEU	0	0.007	-0.002	11.619	0.025	0.025	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.024	-0.007	12.996	0.063	0.063	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.008	-0.015	7.896	0.031	0.031	0.000	0.000	0.000	0.000
28	A	29	PHE	0	-0.071	-0.035	9.430	0.113	0.113	0.000	0.000	0.000	0.000
29	A	30	GLY	0	-0.050	-0.018	11.222	0.125	0.125	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.042	-0.015	10.091	0.068	0.068	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.859	-0.900	11.676	0.138	0.138	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.823	0.897	3.187	1.705	2.158	0.050	-0.180	-0.323	-0.001
33	A	34	LEU	0	-0.030	-0.017	10.054	0.105	0.105	0.000	0.000	0.000	0.000
34	A	35	VAL	0	0.062	0.034	10.683	-0.060	-0.060	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.083	-0.050	12.908	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	37	ARG	1	1.013	0.999	15.954	-0.263	-0.263	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.047	0.023	18.419	-0.029	-0.029	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.001	-0.004	20.491	0.012	0.012	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.903	0.962	17.950	-0.096	-0.096	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.854	-0.931	21.198	-0.040	-0.040	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.064	-0.020	16.810	0.015	0.015	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.069	-0.044	20.233	0.001	0.001	0.000	0.000	0.000	0.000
43	A	44	ARG	1	1.015	1.013	24.016	0.027	0.027	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.724	-0.853	27.615	-0.086	-0.086	0.000	0.000	0.000	0.000
45	A	46	GLY	0	-0.009	-0.009	29.157	0.009	0.009	0.000	0.000	0.000	0.000
46	A	47	GLN	0	-0.027	0.003	25.812	0.004	0.004	0.000	0.000	0.000	0.000
47	A	48	SER	0	0.006	-0.007	28.283	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	49	ALA	0	-0.012	-0.006	24.139	0.004	0.004	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.918	-0.958	23.063	-0.092	-0.092	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.059	-0.017	18.603	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.026	0.023	17.366	0.015	0.015	0.000	0.000	0.000	0.000
52	A	53	TYR	0	0.019	-0.005	14.752	0.008	0.008	0.000	0.000	0.000	0.000
53	A	54	ILE	0	0.031	0.019	10.969	0.020	0.020	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.014	0.010	11.188	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.001	0.012	5.237	-0.170	-0.170	0.000	0.000	0.000	0.000
56	A	57	THR	0	0.007	-0.008	7.440	0.003	0.003	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.067	0.036	10.150	0.102	0.102	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.059	-0.035	13.808	-0.066	-0.066	0.000	0.000	0.000	0.000
59	A	60	ILE	0	0.005	0.015	16.083	0.042	0.042	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.036	-0.008	19.163	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.058	-0.028	21.166	0.008	0.008	0.000	0.000	0.000	0.000
62	A	63	PHE	0	-0.025	-0.022	24.515	0.003	0.003	0.000	0.000	0.000	0.000
63	A	64	HIS	1	0.853	0.898	28.126	0.091	0.091	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.924	-0.977	31.155	-0.035	-0.035	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.018	-0.002	33.369	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.917	-0.963	36.678	-0.035	-0.035	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.992	-0.996	39.348	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.012	0.003	35.738	0.004	0.004	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.865	0.934	27.032	0.020	0.020	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.035	0.026	32.263	0.002	0.002	0.000	0.000	0.000	0.000
71	A	72	THR	0	-0.023	-0.020	27.440	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	73	ILE	0	-0.068	-0.016	27.113	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.960	0.964	22.157	0.221	0.221	0.000	0.000	0.000	0.000
74	A	75	PRO	0	0.045	0.039	21.409	0.001	0.001	0.000	0.000	0.000	0.000
75	A	76	VAL	0	-0.061	-0.035	18.256	-0.023	-0.023	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.075	0.022	15.652	0.038	0.038	0.000	0.000	0.000	0.000
77	A	78	PRO	0	-0.019	-0.021	10.946	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	79	GLY	0	0.000	0.008	11.805	0.020	0.020	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.042	0.001	13.130	0.049	0.049	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.052	0.019	14.810	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.052	-0.024	16.790	0.058	0.058	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.029	-0.009	19.019	0.004	0.004	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.819	-0.917	19.653	-0.361	-0.361	0.000	0.000	0.000	0.000
84	A	85	MET	0	0.030	0.006	20.922	0.016	0.016	0.000	0.000	0.000	0.000
85	A	86	ALA	0	-0.022	0.002	22.666	0.016	0.016	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.051	-0.020	18.229	0.023	0.023	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.000	-0.001	22.874	0.007	0.007	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.006	0.013	26.080	0.013	0.013	0.000	0.000	0.000	0.000
89	A	90	GLN	0	-0.025	-0.008	27.863	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.016	-0.008	26.766	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	92	THR	0	0.009	-0.003	28.603	0.005	0.005	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.807	0.912	21.100	0.131	0.131	0.000	0.000	0.000	0.000
93	A	94	LEU	0	0.057	0.024	26.672	0.009	0.009	0.000	0.000	0.000	0.000
94	A	95	THR	0	-0.046	-0.032	25.158	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.040	0.023	26.258	0.001	0.001	0.000	0.000	0.000	0.000
96	A	97	ALA	0	-0.014	-0.005	21.040	-0.019	-0.019	0.000	0.000	0.000	0.000
97	A	98	VAL	0	0.002	0.005	22.067	0.016	0.016	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.003	0.011	17.862	-0.023	-0.023	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.833	-0.883	19.523	-0.060	-0.060	0.000	0.000	0.000	0.000
100	A	101	VAL	0	-0.023	-0.023	16.270	0.025	0.025	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.984	-0.982	13.576	0.418	0.418	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.022	-0.035	13.058	-0.043	-0.043	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.883	-0.897	6.157	1.011	1.011	0.000	0.000	0.000	0.000
104	A	105	VAL	0	-0.031	-0.029	10.090	-0.211	-0.211	0.000	0.000	0.000	0.000
105	A	106	ILE	0	0.034	0.013	6.498	0.160	0.160	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.843	0.893	10.424	0.070	0.070	0.000	0.000	0.000	0.000
107	A	108	ILE	0	0.045	0.022	12.301	0.014	0.014	0.000	0.000	0.000	0.000
108	A	109	SER	0	0.016	-0.002	15.589	0.021	0.021	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.971	0.972	18.967	0.109	0.109	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.063	-0.037	21.767	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	112	ILE	0	0.018	0.017	15.859	0.011	0.011	0.000	0.000	0.000	0.000
112	A	113	PHE	0	0.080	0.027	18.808	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.925	0.958	19.839	0.109	0.109	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.910	0.947	20.828	0.094	0.094	0.000	0.000	0.000	0.000
115	A	116	ILE	0	-0.021	0.012	16.425	0.008	0.008	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.048	-0.009	20.877	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.967	-0.971	23.875	-0.101	-0.101	0.000	0.000	0.000	0.000

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