FMO DATABASE

FMODB ID: J3V59

Calculation Name: 3U28-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U28

Chain ID: C

ChEMBL ID:

UniProt ID: P33322

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	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-647625.817257
FMO2-HF: Nuclear repulsion	611555.248295
FMO2-HF: Total energy	-36070.568962
FMO2-MP2: Total energy	-36175.056494

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(C:33:PRO)

Summations of interaction energy for fragment #1(C:33: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.
-6.153	-0.558	1.354	-2.385	-4.566	-0.004

Interaction energy analysis for fragmet #1(C:33:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / 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

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	C	35	ASP	-1	-0.865	-0.921	3.800	-3.417	-1.898	0.018	-0.672	-0.866	0.003
4	C	36	THR	0	-0.066	-0.036	6.035	0.039	0.039	0.000	0.000	0.000	0.000
5	C	37	VAL	0	-0.022	-0.001	5.419	0.239	0.239	0.000	0.000	0.000	0.000
6	C	38	LEU	0	0.000	-0.008	7.447	-0.096	-0.096	0.000	0.000	0.000	0.000
7	C	39	GLU	-1	-0.762	-0.869	11.091	0.058	0.058	0.000	0.000	0.000	0.000
8	C	40	MET	0	-0.014	0.007	12.552	0.019	0.019	0.000	0.000	0.000	0.000
9	C	41	GLY	0	0.017	0.004	14.305	-0.009	-0.009	0.000	0.000	0.000	0.000
10	C	42	ALA	0	0.004	0.007	15.829	-0.014	-0.014	0.000	0.000	0.000	0.000
11	C	43	PHE	0	0.021	-0.005	18.002	0.010	0.010	0.000	0.000	0.000	0.000
12	C	44	LEU	0	-0.023	0.004	19.552	-0.013	-0.013	0.000	0.000	0.000	0.000
13	C	45	HIS	1	0.893	0.917	22.536	-0.087	-0.087	0.000	0.000	0.000	0.000
14	C	46	PRO	0	0.030	0.015	21.764	0.011	0.011	0.000	0.000	0.000	0.000
15	C	47	CYS	0	-0.041	-0.018	22.586	-0.013	-0.013	0.000	0.000	0.000	0.000
16	C	48	GLU	-1	-0.923	-0.956	23.570	0.095	0.095	0.000	0.000	0.000	0.000
17	C	49	GLY	0	-0.006	0.005	21.777	0.005	0.005	0.000	0.000	0.000	0.000
18	C	50	ASP	-1	-0.799	-0.891	18.908	0.208	0.208	0.000	0.000	0.000	0.000
19	C	51	ILE	0	-0.058	-0.023	14.841	-0.026	-0.026	0.000	0.000	0.000	0.000
20	C	52	VAL	0	-0.005	-0.001	18.743	0.018	0.018	0.000	0.000	0.000	0.000
21	C	53	CYS	0	-0.017	0.006	17.315	-0.012	-0.012	0.000	0.000	0.000	0.000
22	C	54	ARG	1	0.870	0.924	19.800	-0.057	-0.057	0.000	0.000	0.000	0.000
23	C	55	SER	0	-0.010	-0.014	18.783	0.010	0.010	0.000	0.000	0.000	0.000
24	C	56	ILE	0	-0.052	-0.029	16.024	-0.019	-0.019	0.000	0.000	0.000	0.000
25	C	57	ASN	0	-0.005	-0.009	14.950	-0.015	-0.015	0.000	0.000	0.000	0.000
26	C	58	THR	0	-0.024	-0.017	18.284	0.003	0.003	0.000	0.000	0.000	0.000
27	C	59	LYS	1	0.881	0.953	17.679	-0.097	-0.097	0.000	0.000	0.000	0.000
28	C	60	ILE	0	0.034	0.011	18.943	0.006	0.006	0.000	0.000	0.000	0.000
29	C	61	PRO	0	0.039	0.027	15.124	0.012	0.012	0.000	0.000	0.000	0.000
30	C	62	TYR	0	-0.052	-0.038	14.825	-0.034	-0.034	0.000	0.000	0.000	0.000
31	C	63	PHE	0	0.071	0.028	15.875	0.038	0.038	0.000	0.000	0.000	0.000
32	C	64	ASN	0	-0.037	-0.019	14.416	0.023	0.023	0.000	0.000	0.000	0.000
33	C	65	ALA	0	0.002	0.015	11.736	0.098	0.098	0.000	0.000	0.000	0.000
34	C	66	PRO	0	-0.003	-0.006	6.796	-0.102	-0.102	0.000	0.000	0.000	0.000
35	C	67	ILE	0	0.000	0.006	8.799	-0.012	-0.012	0.000	0.000	0.000	0.000
36	C	68	TYR	0	-0.053	-0.032	2.815	-1.190	-0.124	0.180	-0.328	-0.917	0.001
37	C	69	LEU	0	0.077	0.041	7.242	-0.100	-0.100	0.000	0.000	0.000	0.000
38	C	70	GLU	-1	-0.833	-0.891	7.249	-0.238	-0.238	0.000	0.000	0.000	0.000
39	C	71	ASN	0	-0.044	-0.029	7.672	-0.106	-0.106	0.000	0.000	0.000	0.000
40	C	72	LYS	1	0.825	0.892	2.262	0.506	1.702	0.727	-0.536	-1.387	0.000
41	C	73	THR	0	0.015	0.016	3.004	-1.856	-0.201	0.430	-0.823	-1.263	-0.008
42	C	74	GLN	0	-0.071	-0.044	4.067	0.302	0.461	-0.001	-0.026	-0.133	0.000
43	C	75	VAL	0	0.010	0.000	5.457	-0.172	-0.172	0.000	0.000	0.000	0.000
44	C	76	GLY	0	0.076	0.037	8.946	-0.095	-0.095	0.000	0.000	0.000	0.000
45	C	77	LYS	1	0.850	0.938	9.563	-0.182	-0.182	0.000	0.000	0.000	0.000
46	C	78	VAL	0	-0.003	0.010	12.084	-0.082	-0.082	0.000	0.000	0.000	0.000
47	C	79	ASP	-1	-0.889	-0.949	15.047	0.242	0.242	0.000	0.000	0.000	0.000
48	C	80	GLU	-1	-0.882	-0.939	18.289	0.146	0.146	0.000	0.000	0.000	0.000
49	C	81	ILE	0	-0.046	-0.021	19.176	0.008	0.008	0.000	0.000	0.000	0.000
50	C	82	LEU	0	-0.011	-0.007	22.353	-0.013	-0.013	0.000	0.000	0.000	0.000
51	C	83	GLY	0	0.047	0.032	25.041	0.001	0.001	0.000	0.000	0.000	0.000
52	C	84	PRO	0	-0.015	0.000	27.705	0.002	0.002	0.000	0.000	0.000	0.000
53	C	85	LEU	0	0.037	-0.008	27.722	0.003	0.003	0.000	0.000	0.000	0.000
54	C	86	ASN	0	-0.048	-0.022	26.907	0.005	0.005	0.000	0.000	0.000	0.000
55	C	87	GLU	-1	-0.843	-0.907	26.006	0.053	0.053	0.000	0.000	0.000	0.000
56	C	88	VAL	0	0.003	0.018	21.428	0.003	0.003	0.000	0.000	0.000	0.000
57	C	89	PHE	0	0.004	-0.005	22.071	-0.004	-0.004	0.000	0.000	0.000	0.000
58	C	90	PHE	0	-0.028	-0.013	14.850	0.009	0.009	0.000	0.000	0.000	0.000
59	C	91	THR	0	0.000	-0.009	19.123	-0.009	-0.009	0.000	0.000	0.000	0.000
60	C	92	ILE	0	-0.023	-0.009	12.801	0.039	0.039	0.000	0.000	0.000	0.000
61	C	93	LYS	1	0.885	0.956	15.433	-0.252	-0.252	0.000	0.000	0.000	0.000
62	C	94	CYS	0	-0.057	-0.032	13.706	0.056	0.056	0.000	0.000	0.000	0.000
63	C	95	GLY	0	0.007	-0.008	11.339	0.008	0.008	0.000	0.000	0.000	0.000
64	C	96	ASP	-1	-0.915	-0.972	12.408	0.105	0.105	0.000	0.000	0.000	0.000
65	C	97	GLY	0	-0.001	0.006	12.819	-0.002	-0.002	0.000	0.000	0.000	0.000
66	C	98	VAL	0	-0.041	-0.001	11.156	-0.026	-0.026	0.000	0.000	0.000	0.000
67	C	99	GLN	0	-0.007	-0.005	14.424	0.000	0.000	0.000	0.000	0.000	0.000
68	C	100	ALA	0	0.065	0.023	17.578	-0.009	-0.009	0.000	0.000	0.000	0.000
69	C	101	THR	0	-0.050	-0.044	18.713	-0.005	-0.005	0.000	0.000	0.000	0.000
70	C	102	SER	0	-0.073	-0.033	17.239	-0.012	-0.012	0.000	0.000	0.000	0.000
71	C	103	PHE	0	0.001	0.011	12.968	-0.007	-0.007	0.000	0.000	0.000	0.000
72	C	104	LYS	1	0.856	0.905	18.872	0.009	0.009	0.000	0.000	0.000	0.000
73	C	105	GLU	-1	-0.912	-0.975	20.525	0.045	0.045	0.000	0.000	0.000	0.000
74	C	106	GLY	0	-0.052	-0.020	20.845	-0.010	-0.010	0.000	0.000	0.000	0.000
75	C	107	ASP	-1	-0.818	-0.872	16.350	-0.002	-0.002	0.000	0.000	0.000	0.000
76	C	108	LYS	1	0.818	0.891	14.264	0.034	0.034	0.000	0.000	0.000	0.000
77	C	109	PHE	0	-0.007	-0.002	11.540	-0.007	-0.007	0.000	0.000	0.000	0.000
78	C	110	TYR	0	-0.052	-0.062	8.118	-0.018	-0.018	0.000	0.000	0.000	0.000
79	C	111	ILE	0	0.018	0.012	8.664	0.193	0.193	0.000	0.000	0.000	0.000
80	C	112	ALA	0	0.051	0.031	6.973	-0.125	-0.125	0.000	0.000	0.000	0.000
81	C	113	ALA	0	0.045	0.006	8.528	-0.067	-0.067	0.000	0.000	0.000	0.000
82	C	114	ASP	-1	-0.846	-0.913	10.212	0.573	0.573	0.000	0.000	0.000	0.000
83	C	115	LYS	1	0.823	0.902	9.481	-0.677	-0.677	0.000	0.000	0.000	0.000
84	C	116	LEU	0	0.010	0.016	13.163	-0.017	-0.017	0.000	0.000	0.000	0.000
85	C	117	LEU	0	-0.011	-0.011	15.909	-0.022	-0.022	0.000	0.000	0.000	0.000
86	C	118	PRO	0	-0.015	0.001	19.687	-0.004	-0.004	0.000	0.000	0.000	0.000
87	C	119	ILE	0	0.103	0.029	22.427	0.004	0.004	0.000	0.000	0.000	0.000
88	C	120	GLU	-1	-0.918	-0.963	24.787	0.067	0.067	0.000	0.000	0.000	0.000
89	C	121	ARG	1	0.893	0.952	22.229	-0.123	-0.123	0.000	0.000	0.000	0.000
90	C	122	PHE	0	-0.019	-0.010	22.337	0.002	0.002	0.000	0.000	0.000	0.000
91	C	123	LEU	0	-0.039	-0.008	28.137	-0.005	-0.005	0.000	0.000	0.000	0.000
92	C	124	PRO	0	0.005	0.013	31.225	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:33:PRO)