FMO DATABASE

FMODB ID: 3QM1L

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	OptAll
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	-646462.908409
FMO2-HF: Nuclear repulsion	610392.097178
FMO2-HF: Total energy	-36070.811231
FMO2-MP2: Total energy	-36175.275175

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.
-7.727	-1.622	3.892	-3.594	-6.403	-0.005

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 : 0.028 / q_NPA : -0.009

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	C	35	ASP	-1	-0.863	-0.913	3.942	-2.465	-1.228	-0.009	-0.566	-0.662	0.002
4	C	36	THR	0	-0.049	-0.026	6.651	-0.064	-0.064	0.000	0.000	0.000	0.000
5	C	37	VAL	0	-0.011	-0.003	5.312	0.337	0.337	0.000	0.000	0.000	0.000
6	C	38	LEU	0	-0.006	-0.001	7.420	-0.186	-0.186	0.000	0.000	0.000	0.000
7	C	39	GLU	-1	-0.764	-0.865	10.693	0.122	0.122	0.000	0.000	0.000	0.000
8	C	40	MET	0	-0.028	0.002	12.423	0.040	0.040	0.000	0.000	0.000	0.000
9	C	41	GLY	0	0.037	-0.007	14.191	-0.021	-0.021	0.000	0.000	0.000	0.000
10	C	42	ALA	0	-0.016	0.000	15.609	-0.013	-0.013	0.000	0.000	0.000	0.000
11	C	43	PHE	0	0.009	-0.004	17.734	0.009	0.009	0.000	0.000	0.000	0.000
12	C	44	LEU	0	-0.030	0.000	19.329	-0.013	-0.013	0.000	0.000	0.000	0.000
13	C	45	HIS	1	0.886	0.914	22.076	-0.096	-0.096	0.000	0.000	0.000	0.000
14	C	46	PRO	0	0.030	0.017	21.192	0.014	0.014	0.000	0.000	0.000	0.000
15	C	47	CYS	0	-0.044	-0.020	22.020	-0.010	-0.010	0.000	0.000	0.000	0.000
16	C	48	GLU	-1	-0.922	-0.961	22.930	0.101	0.101	0.000	0.000	0.000	0.000
17	C	49	GLY	0	0.007	0.014	21.255	-0.004	-0.004	0.000	0.000	0.000	0.000
18	C	50	ASP	-1	-0.783	-0.869	18.099	0.222	0.222	0.000	0.000	0.000	0.000
19	C	51	ILE	0	-0.018	-0.003	14.527	-0.030	-0.030	0.000	0.000	0.000	0.000
20	C	52	VAL	0	-0.008	0.000	18.337	0.024	0.024	0.000	0.000	0.000	0.000
21	C	53	CYS	0	-0.024	-0.001	16.988	-0.016	-0.016	0.000	0.000	0.000	0.000
22	C	54	ARG	1	0.867	0.925	19.412	-0.073	-0.073	0.000	0.000	0.000	0.000
23	C	55	SER	0	0.004	-0.001	18.658	0.015	0.015	0.000	0.000	0.000	0.000
24	C	56	ILE	0	-0.042	-0.019	15.760	-0.025	-0.025	0.000	0.000	0.000	0.000
25	C	57	ASN	0	-0.036	-0.025	14.810	-0.022	-0.022	0.000	0.000	0.000	0.000
26	C	58	THR	0	-0.017	-0.011	18.392	0.002	0.002	0.000	0.000	0.000	0.000
27	C	59	LYS	1	0.876	0.944	17.848	-0.184	-0.184	0.000	0.000	0.000	0.000
28	C	60	ILE	0	0.048	0.034	18.697	0.011	0.011	0.000	0.000	0.000	0.000
29	C	61	PRO	0	0.045	0.017	15.096	0.018	0.018	0.000	0.000	0.000	0.000
30	C	62	TYR	0	-0.052	-0.038	14.671	-0.046	-0.046	0.000	0.000	0.000	0.000
31	C	63	PHE	0	0.073	0.028	15.599	0.045	0.045	0.000	0.000	0.000	0.000
32	C	64	ASN	0	-0.043	-0.017	14.247	0.006	0.006	0.000	0.000	0.000	0.000
33	C	65	ALA	0	0.000	0.013	11.835	0.100	0.100	0.000	0.000	0.000	0.000
34	C	66	PRO	0	-0.005	-0.006	6.382	-0.116	-0.116	0.000	0.000	0.000	0.000
35	C	67	ILE	0	-0.005	0.003	8.276	0.040	0.040	0.000	0.000	0.000	0.000
36	C	68	TYR	0	-0.050	-0.030	2.375	-1.680	-0.350	0.968	-0.596	-1.702	0.003
37	C	69	LEU	0	0.065	0.034	6.921	-0.072	-0.072	0.000	0.000	0.000	0.000
38	C	70	GLU	-1	-0.839	-0.890	6.669	-0.273	-0.273	0.000	0.000	0.000	0.000
39	C	71	ASN	0	-0.015	0.013	7.466	-0.132	-0.132	0.000	0.000	0.000	0.000
40	C	72	LYS	1	0.806	0.890	1.940	0.553	1.248	2.030	-0.961	-1.764	0.007
41	C	73	THR	0	-0.010	-0.023	2.783	-3.563	-1.198	0.891	-1.355	-1.901	-0.017
42	C	74	GLN	0	-0.051	-0.034	3.349	0.281	0.710	0.013	-0.112	-0.330	0.000
43	C	75	VAL	0	-0.002	-0.004	4.924	-0.267	-0.218	-0.001	-0.004	-0.044	0.000
44	C	76	GLY	0	0.059	0.023	8.408	-0.094	-0.094	0.000	0.000	0.000	0.000
45	C	77	LYS	1	0.800	0.909	9.009	-0.142	-0.142	0.000	0.000	0.000	0.000
46	C	78	VAL	0	0.023	0.011	11.595	-0.100	-0.100	0.000	0.000	0.000	0.000
47	C	79	ASP	-1	-0.898	-0.947	14.573	0.292	0.292	0.000	0.000	0.000	0.000
48	C	80	GLU	-1	-0.826	-0.904	17.756	0.168	0.168	0.000	0.000	0.000	0.000
49	C	81	ILE	0	-0.064	-0.048	18.724	0.015	0.015	0.000	0.000	0.000	0.000
50	C	82	LEU	0	-0.003	0.012	22.018	-0.015	-0.015	0.000	0.000	0.000	0.000
51	C	83	GLY	0	0.047	0.022	24.973	0.002	0.002	0.000	0.000	0.000	0.000
52	C	84	PRO	0	-0.020	-0.002	27.680	0.002	0.002	0.000	0.000	0.000	0.000
53	C	85	LEU	0	0.033	-0.009	27.716	0.005	0.005	0.000	0.000	0.000	0.000
54	C	86	ASN	0	-0.035	-0.012	27.083	0.005	0.005	0.000	0.000	0.000	0.000
55	C	87	GLU	-1	-0.855	-0.918	25.799	0.072	0.072	0.000	0.000	0.000	0.000
56	C	88	VAL	0	-0.012	0.016	21.651	0.001	0.001	0.000	0.000	0.000	0.000
57	C	89	PHE	0	0.004	-0.012	21.747	-0.001	-0.001	0.000	0.000	0.000	0.000
58	C	90	PHE	0	-0.019	-0.010	14.683	0.014	0.014	0.000	0.000	0.000	0.000
59	C	91	THR	0	-0.028	-0.020	18.654	-0.015	-0.015	0.000	0.000	0.000	0.000
60	C	92	ILE	0	-0.010	-0.011	12.368	0.046	0.046	0.000	0.000	0.000	0.000
61	C	93	LYS	1	0.817	0.919	14.829	-0.272	-0.272	0.000	0.000	0.000	0.000
62	C	94	CYS	0	-0.039	-0.022	13.347	0.056	0.056	0.000	0.000	0.000	0.000
63	C	95	GLY	0	0.013	0.002	10.953	0.019	0.019	0.000	0.000	0.000	0.000
64	C	96	ASP	-1	-0.870	-0.946	12.003	0.043	0.043	0.000	0.000	0.000	0.000
65	C	97	GLY	0	-0.031	-0.014	12.353	-0.009	-0.009	0.000	0.000	0.000	0.000
66	C	98	VAL	0	-0.049	-0.006	10.937	-0.027	-0.027	0.000	0.000	0.000	0.000
67	C	99	GLN	0	-0.010	-0.012	14.261	0.003	0.003	0.000	0.000	0.000	0.000
68	C	100	ALA	0	0.055	0.023	17.385	-0.011	-0.011	0.000	0.000	0.000	0.000
69	C	101	THR	0	-0.026	-0.032	18.375	-0.003	-0.003	0.000	0.000	0.000	0.000
70	C	102	SER	0	-0.085	-0.037	16.762	-0.012	-0.012	0.000	0.000	0.000	0.000
71	C	103	PHE	0	0.001	0.008	12.759	-0.010	-0.010	0.000	0.000	0.000	0.000
72	C	104	LYS	1	0.852	0.906	18.868	0.023	0.023	0.000	0.000	0.000	0.000
73	C	105	GLU	-1	-0.884	-0.960	20.295	0.055	0.055	0.000	0.000	0.000	0.000
74	C	106	GLY	0	-0.048	-0.019	20.755	-0.012	-0.012	0.000	0.000	0.000	0.000
75	C	107	ASP	-1	-0.819	-0.880	16.102	-0.013	-0.013	0.000	0.000	0.000	0.000
76	C	108	LYS	1	0.828	0.898	14.063	0.011	0.011	0.000	0.000	0.000	0.000
77	C	109	PHE	0	0.009	0.002	11.466	-0.017	-0.017	0.000	0.000	0.000	0.000
78	C	110	TYR	0	-0.043	-0.060	8.024	-0.009	-0.009	0.000	0.000	0.000	0.000
79	C	111	ILE	0	0.010	0.004	8.536	0.209	0.209	0.000	0.000	0.000	0.000
80	C	112	ALA	0	0.046	0.026	6.814	-0.085	-0.085	0.000	0.000	0.000	0.000
81	C	113	ALA	0	0.021	-0.005	8.326	-0.163	-0.163	0.000	0.000	0.000	0.000
82	C	114	ASP	-1	-0.811	-0.884	10.016	0.811	0.811	0.000	0.000	0.000	0.000
83	C	115	LYS	1	0.793	0.890	9.143	-1.019	-1.019	0.000	0.000	0.000	0.000
84	C	116	LEU	0	0.019	0.011	13.312	-0.035	-0.035	0.000	0.000	0.000	0.000
85	C	117	LEU	0	0.007	0.005	16.190	-0.027	-0.027	0.000	0.000	0.000	0.000
86	C	118	PRO	0	-0.021	-0.005	20.014	-0.007	-0.007	0.000	0.000	0.000	0.000
87	C	119	ILE	0	0.100	0.026	22.658	0.000	0.000	0.000	0.000	0.000	0.000
88	C	120	GLU	-1	-0.826	-0.912	25.199	0.123	0.123	0.000	0.000	0.000	0.000
89	C	121	ARG	1	0.786	0.888	22.436	-0.169	-0.169	0.000	0.000	0.000	0.000
90	C	122	PHE	0	-0.014	-0.002	22.316	0.003	0.003	0.000	0.000	0.000	0.000
91	C	123	LEU	0	-0.025	-0.003	28.312	-0.007	-0.007	0.000	0.000	0.000	0.000
92	C	124	PRO	0	-0.002	0.011	31.491	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)