FMO DATABASE

FMODB ID: YVN62

Calculation Name: 3R0P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R0P

Chain ID: A

ChEMBL ID:

UniProt ID: D8VN48

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1004052.90722
FMO2-HF: Nuclear repulsion	957110.148475
FMO2-HF: Total energy	-46942.758745
FMO2-MP2: Total energy	-47079.8439

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:3:ASN)

Summations of interaction energy for fragment #1(A:3: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.
-1.017	1.641	0.091	-1.276	-1.475	0.004

Interaction energy analysis for fragmet #1(A:3:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.018

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	5	ALA	0	0.020	0.022	3.805	-1.744	0.055	-0.020	-0.902	-0.878	0.002
4	A	6	ILE	0	-0.014	-0.014	6.056	0.411	0.411	0.000	0.000	0.000	0.000
5	A	7	ILE	0	-0.036	-0.012	9.648	-0.310	-0.310	0.000	0.000	0.000	0.000
6	A	8	HIS	0	0.011	0.001	12.421	0.062	0.062	0.000	0.000	0.000	0.000
7	A	9	SER	0	0.007	-0.006	15.516	-0.101	-0.101	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.902	-0.947	18.643	0.302	0.302	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.059	-0.030	21.791	-0.018	-0.018	0.000	0.000	0.000	0.000
10	A	12	ALA	0	-0.002	0.002	20.976	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	13	PRO	0	0.001	-0.003	22.908	0.006	0.006	0.000	0.000	0.000	0.000
12	A	14	ALA	0	0.034	0.031	21.296	0.049	0.049	0.000	0.000	0.000	0.000
13	A	15	ALA	0	-0.010	-0.004	18.293	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	16	ILE	0	-0.009	0.004	20.031	0.027	0.027	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.022	0.001	21.310	0.015	0.015	0.000	0.000	0.000	0.000
16	A	18	THR	0	-0.026	-0.021	17.609	0.016	0.016	0.000	0.000	0.000	0.000
17	A	19	TYR	0	-0.037	-0.009	15.383	0.116	0.116	0.000	0.000	0.000	0.000
18	A	20	SER	0	0.018	0.014	12.672	0.030	0.030	0.000	0.000	0.000	0.000
19	A	21	GLN	0	0.026	0.013	14.720	0.004	0.004	0.000	0.000	0.000	0.000
20	A	22	ALA	0	0.048	0.016	13.403	-0.073	-0.073	0.000	0.000	0.000	0.000
21	A	23	VAL	0	-0.038	-0.003	6.957	0.224	0.224	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.913	0.960	7.900	0.380	0.380	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.006	-0.017	3.397	-0.483	0.376	0.111	-0.374	-0.597	0.002
24	A	26	ASN	0	-0.016	-0.011	4.993	-0.567	-0.567	0.000	0.000	0.000	0.000
25	A	27	ASN	0	0.009	-0.006	6.700	0.222	0.222	0.000	0.000	0.000	0.000
26	A	28	THR	0	0.016	0.035	9.259	0.098	0.098	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.034	-0.037	9.546	0.311	0.311	0.000	0.000	0.000	0.000
28	A	30	TYR	0	-0.004	-0.005	8.512	-0.137	-0.137	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.007	-0.009	12.508	0.107	0.107	0.000	0.000	0.000	0.000
30	A	32	SER	0	0.006	-0.020	15.711	0.036	0.036	0.000	0.000	0.000	0.000
31	A	33	GLY	0	-0.010	0.005	17.438	-0.080	-0.080	0.000	0.000	0.000	0.000
32	A	34	GLN	0	-0.016	-0.009	20.359	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	35	ILE	0	0.050	0.019	23.463	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	36	PRO	0	-0.046	-0.013	27.090	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.027	-0.017	26.557	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	38	ASP	-1	-0.731	-0.856	28.906	0.196	0.196	0.000	0.000	0.000	0.000
37	A	39	PRO	0	-0.046	-0.023	25.643	0.011	0.011	0.000	0.000	0.000	0.000
38	A	40	VAL	0	-0.028	-0.002	27.669	0.008	0.008	0.000	0.000	0.000	0.000
39	A	41	THR	0	-0.038	-0.049	30.330	0.009	0.009	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.050	-0.011	25.504	0.010	0.010	0.000	0.000	0.000	0.000
41	A	43	GLN	0	0.017	0.025	30.397	0.020	0.020	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.035	-0.009	31.318	0.002	0.002	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.021	-0.002	32.801	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.938	-0.962	35.237	0.147	0.147	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.000	-0.016	38.911	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.883	-0.943	39.383	0.134	0.134	0.000	0.000	0.000	0.000
47	A	49	PHE	0	0.036	0.008	33.567	0.007	0.007	0.000	0.000	0.000	0.000
48	A	50	ALA	0	0.043	0.014	35.778	0.010	0.010	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.007	0.004	35.527	0.004	0.004	0.000	0.000	0.000	0.000
50	A	52	GLN	0	0.082	0.028	33.275	0.022	0.022	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.014	0.003	31.447	0.017	0.017	0.000	0.000	0.000	0.000
52	A	54	HIS	0	0.038	0.026	30.626	0.011	0.011	0.000	0.000	0.000	0.000
53	A	55	GLN	0	-0.010	0.011	28.475	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	56	VAL	0	-0.003	0.007	25.911	0.016	0.016	0.000	0.000	0.000	0.000
55	A	57	PHE	0	0.019	-0.009	25.890	0.022	0.022	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.893	0.943	25.882	-0.159	-0.159	0.000	0.000	0.000	0.000
57	A	59	ASN	0	0.030	0.015	24.351	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	60	LEU	0	0.003	0.001	20.733	0.019	0.019	0.000	0.000	0.000	0.000
59	A	61	ARG	1	0.878	0.941	20.919	-0.089	-0.089	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.045	0.045	21.158	-0.020	-0.020	0.000	0.000	0.000	0.000
61	A	63	VAL	0	-0.009	-0.006	16.458	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	64	CYS	0	-0.060	-0.049	16.656	0.006	0.006	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.830	-0.913	16.948	0.032	0.032	0.000	0.000	0.000	0.000
64	A	66	ALA	0	-0.016	0.003	15.761	-0.061	-0.061	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.057	-0.021	12.798	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.056	-0.030	12.941	-0.144	-0.144	0.000	0.000	0.000	0.000
67	A	69	GLY	0	0.002	0.007	15.046	-0.070	-0.070	0.000	0.000	0.000	0.000
68	A	70	GLY	0	0.005	-0.009	17.728	0.021	0.021	0.000	0.000	0.000	0.000
69	A	71	LEU	0	0.030	-0.002	20.359	0.012	0.012	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.836	0.926	22.768	0.016	0.016	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.787	-0.885	17.803	-0.102	-0.102	0.000	0.000	0.000	0.000
72	A	74	ILE	0	-0.040	-0.023	18.656	0.027	0.027	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.016	-0.007	17.267	-0.033	-0.033	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.819	0.913	19.118	-0.387	-0.387	0.000	0.000	0.000	0.000
75	A	77	LEU	0	0.010	0.008	20.236	0.040	0.040	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.072	-0.053	20.338	-0.086	-0.086	0.000	0.000	0.000	0.000
77	A	79	VAL	0	0.022	0.001	23.785	0.010	0.010	0.000	0.000	0.000	0.000
78	A	80	TYR	0	-0.044	-0.032	21.950	-0.033	-0.033	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.003	0.000	28.547	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	82	THR	0	0.005	0.010	32.207	0.001	0.001	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.809	-0.910	34.711	0.154	0.154	0.000	0.000	0.000	0.000
82	A	84	LEU	0	0.009	-0.005	33.379	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	85	ALA	0	-0.003	0.015	36.952	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	86	ASN	0	-0.028	-0.025	36.619	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	87	PHE	0	-0.021	-0.023	31.014	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	88	PRO	0	-0.017	-0.014	35.711	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	89	ILE	0	0.089	0.048	36.735	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	90	VAL	0	0.009	0.017	30.952	0.000	0.000	0.000	0.000	0.000	0.000
89	A	91	ASN	0	-0.012	-0.002	32.981	0.004	0.004	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.927	-0.948	34.546	0.082	0.082	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.003	-0.008	32.115	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	94	MET	0	-0.010	0.009	27.507	0.002	0.002	0.000	0.000	0.000	0.000
93	A	95	GLY	0	0.007	0.011	31.115	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	96	GLN	0	-0.039	-0.028	33.690	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	97	TYR	0	-0.092	-0.057	28.104	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	98	PHE	0	-0.049	-0.018	23.959	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	99	GLN	0	-0.002	-0.005	28.594	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	100	ALA	0	0.011	0.027	28.899	0.002	0.002	0.000	0.000	0.000	0.000
99	A	101	PRO	0	-0.052	-0.037	26.433	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	102	TYR	0	0.031	-0.001	26.996	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	103	PRO	0	-0.008	0.020	23.276	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.015	0.011	23.041	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.846	0.882	24.338	-0.139	-0.139	0.000	0.000	0.000	0.000
104	A	106	ALA	0	-0.028	-0.002	25.261	-0.014	-0.014	0.000	0.000	0.000	0.000
105	A	107	ALA	0	0.000	0.007	26.984	0.017	0.017	0.000	0.000	0.000	0.000
106	A	108	ILE	0	0.000	-0.005	27.406	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	109	GLY	0	0.021	0.019	30.453	0.004	0.004	0.000	0.000	0.000	0.000
108	A	110	ILE	0	-0.036	-0.021	28.823	0.005	0.005	0.000	0.000	0.000	0.000
109	A	111	ASN	0	0.007	-0.005	32.261	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	112	GLN	0	-0.024	-0.022	31.772	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.004	0.020	27.752	0.022	0.022	0.000	0.000	0.000	0.000
112	A	114	PRO	0	0.069	0.030	25.731	-0.023	-0.023	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.833	0.899	29.001	-0.327	-0.327	0.000	0.000	0.000	0.000
114	A	116	ALA	0	0.008	0.017	31.840	-0.018	-0.018	0.000	0.000	0.000	0.000
115	A	117	SER	0	-0.011	-0.013	30.327	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	118	LEU	0	0.015	0.004	32.476	0.002	0.002	0.000	0.000	0.000	0.000
117	A	119	ILE	0	-0.017	-0.026	29.081	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.868	-0.940	23.528	0.500	0.500	0.000	0.000	0.000	0.000
119	A	121	ALA	0	-0.022	-0.012	24.433	-0.017	-0.017	0.000	0.000	0.000	0.000
120	A	122	ASP	-1	-0.758	-0.838	19.088	0.615	0.615	0.000	0.000	0.000	0.000
121	A	123	GLY	0	0.045	0.004	18.273	-0.083	-0.083	0.000	0.000	0.000	0.000
122	A	124	ILE	0	-0.048	-0.012	13.728	0.123	0.123	0.000	0.000	0.000	0.000
123	A	125	MET	0	0.000	0.022	14.823	-0.126	-0.126	0.000	0.000	0.000	0.000
124	A	126	VAL	0	-0.019	-0.008	13.664	0.079	0.079	0.000	0.000	0.000	0.000
125	A	127	ILE	0	-0.004	0.012	12.546	-0.080	-0.080	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASN)