FMO DATABASE

FMODB ID: 5JN9Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1003801.548208
FMO2-HF: Nuclear repulsion	956859.250302
FMO2-HF: Total energy	-46942.297906
FMO2-MP2: Total energy	-47079.412802

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.
-0.104	2.113	0.002	-1.034	-1.184	0.003

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 : 0.002 / q_NPA : -0.017

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	5	ALA	0	0.017	0.023	3.805	-1.376	0.365	-0.021	-0.859	-0.860	0.002
4	A	6	ILE	0	-0.013	-0.012	6.033	0.414	0.414	0.000	0.000	0.000	0.000
5	A	7	ILE	0	-0.039	-0.014	9.623	-0.298	-0.298	0.000	0.000	0.000	0.000
6	A	8	HIS	0	0.018	0.006	12.399	0.086	0.086	0.000	0.000	0.000	0.000
7	A	9	SER	0	-0.004	-0.011	15.493	-0.095	-0.095	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.890	-0.946	18.623	0.259	0.259	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.056	-0.032	21.757	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	12	ALA	0	-0.011	-0.003	20.985	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	13	PRO	0	-0.005	-0.003	22.885	0.008	0.008	0.000	0.000	0.000	0.000
12	A	14	ALA	0	0.042	0.038	21.273	0.042	0.042	0.000	0.000	0.000	0.000
13	A	15	ALA	0	-0.015	-0.005	18.236	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	16	ILE	0	-0.016	0.002	19.935	0.030	0.030	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.014	-0.001	21.219	0.015	0.015	0.000	0.000	0.000	0.000
16	A	18	THR	0	-0.021	-0.019	17.495	0.013	0.013	0.000	0.000	0.000	0.000
17	A	19	TYR	0	-0.031	-0.010	15.377	0.113	0.113	0.000	0.000	0.000	0.000
18	A	20	SER	0	0.013	0.013	12.722	0.048	0.048	0.000	0.000	0.000	0.000
19	A	21	GLN	0	0.043	0.031	14.770	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	22	ALA	0	0.051	0.019	13.517	-0.069	-0.069	0.000	0.000	0.000	0.000
21	A	23	VAL	0	-0.030	0.003	7.160	0.207	0.207	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.927	0.970	7.862	0.736	0.736	0.000	0.000	0.000	0.000
23	A	25	VAL	0	0.001	-0.013	3.662	-0.519	-0.043	0.023	-0.175	-0.324	0.001
24	A	26	ASN	0	-0.016	-0.014	4.988	-0.269	-0.269	0.000	0.000	0.000	0.000
25	A	27	ASN	0	0.018	-0.001	6.699	0.328	0.328	0.000	0.000	0.000	0.000
26	A	28	THR	0	0.015	0.034	9.254	0.174	0.174	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.030	-0.031	9.723	0.219	0.219	0.000	0.000	0.000	0.000
28	A	30	TYR	0	-0.010	-0.010	8.975	-0.044	-0.044	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.011	-0.016	12.627	0.097	0.097	0.000	0.000	0.000	0.000
30	A	32	SER	0	0.002	-0.026	15.827	0.052	0.052	0.000	0.000	0.000	0.000
31	A	33	GLY	0	-0.011	0.003	17.519	-0.081	-0.081	0.000	0.000	0.000	0.000
32	A	34	GLN	0	-0.017	-0.009	20.207	-0.026	-0.026	0.000	0.000	0.000	0.000
33	A	35	ILE	0	0.046	0.015	23.557	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	36	PRO	0	-0.040	-0.013	27.176	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.042	-0.025	26.576	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	38	ASP	-1	-0.814	-0.915	28.884	0.157	0.157	0.000	0.000	0.000	0.000
37	A	39	PRO	0	-0.037	-0.025	25.616	0.015	0.015	0.000	0.000	0.000	0.000
38	A	40	VAL	0	-0.005	0.012	27.647	0.009	0.009	0.000	0.000	0.000	0.000
39	A	41	THR	0	0.008	-0.004	30.307	0.011	0.011	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.023	0.000	25.845	0.012	0.012	0.000	0.000	0.000	0.000
41	A	43	GLN	0	0.003	-0.003	30.372	0.019	0.019	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.042	-0.012	31.550	0.000	0.000	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.020	-0.001	32.715	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.937	-0.964	35.262	0.130	0.130	0.000	0.000	0.000	0.000
45	A	47	GLY	0	-0.003	-0.018	39.011	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.890	-0.941	39.484	0.111	0.111	0.000	0.000	0.000	0.000
47	A	49	PHE	0	0.029	-0.003	33.694	0.005	0.005	0.000	0.000	0.000	0.000
48	A	50	ALA	0	0.054	0.021	35.891	0.008	0.008	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.005	0.012	35.656	0.001	0.001	0.000	0.000	0.000	0.000
50	A	52	GLN	0	0.091	0.031	33.356	0.018	0.018	0.000	0.000	0.000	0.000
51	A	53	ALA	0	0.020	0.006	31.560	0.014	0.014	0.000	0.000	0.000	0.000
52	A	54	HIS	0	0.030	0.033	30.757	0.006	0.006	0.000	0.000	0.000	0.000
53	A	55	GLN	0	-0.045	-0.009	28.599	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	56	VAL	0	0.007	0.015	26.035	0.011	0.011	0.000	0.000	0.000	0.000
55	A	57	PHE	0	0.016	-0.010	26.020	0.016	0.016	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.900	0.956	25.867	-0.130	-0.130	0.000	0.000	0.000	0.000
57	A	59	ASN	0	0.040	0.018	24.255	-0.027	-0.027	0.000	0.000	0.000	0.000
58	A	60	LEU	0	0.003	-0.001	20.648	0.012	0.012	0.000	0.000	0.000	0.000
59	A	61	ARG	1	0.955	0.980	20.904	-0.054	-0.054	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.030	0.034	21.145	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	63	VAL	0	-0.005	-0.006	16.486	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	64	CYS	0	-0.060	-0.037	16.641	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.909	-0.957	16.938	-0.064	-0.064	0.000	0.000	0.000	0.000
64	A	66	ALA	0	-0.020	0.001	15.622	-0.063	-0.063	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.073	-0.029	12.787	-0.045	-0.045	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.059	-0.038	12.935	-0.166	-0.166	0.000	0.000	0.000	0.000
67	A	69	GLY	0	0.007	0.011	15.041	-0.067	-0.067	0.000	0.000	0.000	0.000
68	A	70	GLY	0	0.016	-0.002	17.724	0.031	0.031	0.000	0.000	0.000	0.000
69	A	71	LEU	0	0.023	-0.004	20.368	0.006	0.006	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.827	0.917	22.776	0.075	0.075	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.798	-0.890	17.742	-0.219	-0.219	0.000	0.000	0.000	0.000
72	A	74	ILE	0	-0.046	-0.023	18.657	0.017	0.017	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.005	-0.003	17.286	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.859	0.933	19.275	-0.314	-0.314	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.001	0.003	20.364	0.034	0.034	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.072	-0.039	20.434	-0.075	-0.075	0.000	0.000	0.000	0.000
77	A	79	VAL	0	0.012	0.004	23.877	0.007	0.007	0.000	0.000	0.000	0.000
78	A	80	TYR	0	0.001	0.005	22.441	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.001	-0.007	28.618	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	82	THR	0	0.007	0.013	32.280	0.002	0.002	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.814	-0.910	34.768	0.140	0.140	0.000	0.000	0.000	0.000
82	A	84	LEU	0	-0.002	-0.013	33.487	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	85	ALA	0	-0.006	0.014	37.031	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	86	ASN	0	0.007	-0.006	36.679	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	87	PHE	0	-0.029	-0.031	31.178	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	88	PRO	0	-0.013	-0.012	35.828	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	89	ILE	0	0.094	0.051	36.625	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	90	VAL	0	0.001	0.013	31.067	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	91	ASN	0	0.011	0.000	33.117	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.945	-0.957	34.682	0.056	0.056	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.015	-0.015	32.166	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	94	MET	0	-0.017	-0.001	27.665	0.001	0.001	0.000	0.000	0.000	0.000
93	A	95	GLY	0	0.023	0.020	31.264	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	96	GLN	0	-0.023	-0.017	33.683	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	97	TYR	0	-0.103	-0.079	28.254	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	98	PHE	0	-0.051	-0.020	24.218	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	99	GLN	0	0.010	0.002	28.595	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	100	ALA	0	0.008	0.023	28.902	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	101	PRO	0	-0.040	-0.022	26.299	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	102	TYR	0	0.034	-0.006	26.952	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	103	PRO	0	-0.004	0.020	23.372	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.011	0.010	23.031	0.004	0.004	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.857	0.904	24.465	-0.105	-0.105	0.000	0.000	0.000	0.000
104	A	106	ALA	0	-0.026	-0.002	25.386	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	107	ALA	0	-0.008	0.003	27.074	0.014	0.014	0.000	0.000	0.000	0.000
106	A	108	ILE	0	-0.003	-0.005	27.581	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	109	GLY	0	0.020	0.019	30.516	0.003	0.003	0.000	0.000	0.000	0.000
108	A	110	ILE	0	-0.037	-0.023	28.898	0.007	0.007	0.000	0.000	0.000	0.000
109	A	111	ASN	0	-0.014	-0.019	32.298	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	112	GLN	0	0.007	-0.003	32.016	-0.020	-0.020	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.003	0.013	27.755	0.021	0.021	0.000	0.000	0.000	0.000
112	A	114	PRO	0	0.065	0.029	25.792	-0.020	-0.020	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.841	0.916	29.035	-0.308	-0.308	0.000	0.000	0.000	0.000
114	A	116	ALA	0	0.013	0.021	31.881	-0.017	-0.017	0.000	0.000	0.000	0.000
115	A	117	SER	0	-0.016	-0.014	30.425	-0.021	-0.021	0.000	0.000	0.000	0.000
116	A	118	LEU	0	0.014	0.003	32.541	0.003	0.003	0.000	0.000	0.000	0.000
117	A	119	ILE	0	-0.015	-0.026	29.100	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.865	-0.938	23.544	0.460	0.460	0.000	0.000	0.000	0.000
119	A	121	ALA	0	-0.029	-0.015	24.532	-0.017	-0.017	0.000	0.000	0.000	0.000
120	A	122	ASP	-1	-0.803	-0.897	19.109	0.562	0.562	0.000	0.000	0.000	0.000
121	A	123	GLY	0	0.012	-0.008	18.378	-0.074	-0.074	0.000	0.000	0.000	0.000
122	A	124	ILE	0	-0.044	-0.008	13.995	0.111	0.111	0.000	0.000	0.000	0.000
123	A	125	MET	0	0.014	0.022	15.048	-0.102	-0.102	0.000	0.000	0.000	0.000
124	A	126	VAL	0	-0.025	-0.012	13.666	0.050	0.050	0.000	0.000	0.000	0.000
125	A	127	ILE	0	-0.005	0.013	12.764	-0.062	-0.062	0.000	0.000	0.000	0.000

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