FMO DATABASE

FMODB ID: 1491Z

Calculation Name: 3U4Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U4Z

Chain ID: A

ChEMBL ID:

UniProt ID: D2CVN6

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:

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-905140.770939
FMO2-HF: Nuclear repulsion	859721.77438
FMO2-HF: Total energy	-45418.996559
FMO2-MP2: Total energy	-45552.189332

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:375:THR)

Summations of interaction energy for fragment #1(A:375:THR)

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.
-11.319	-2.684	2.237	-4.352	-6.523	-0.017

Interaction energy analysis for fragmet #1(A:375:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.031

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	377	LEU	0	0.040	0.021	3.104	-1.766	0.589	0.113	-1.147	-1.322	-0.004
4	A	378	ILE	0	0.044	0.010	4.944	0.731	0.782	-0.001	-0.002	-0.048	0.000
5	A	379	SER	0	0.002	-0.007	7.821	0.184	0.184	0.000	0.000	0.000	0.000
6	A	380	GLU	-1	-0.877	-0.955	6.699	-0.654	-0.654	0.000	0.000	0.000	0.000
7	A	381	VAL	0	0.005	0.019	6.779	0.335	0.335	0.000	0.000	0.000	0.000
8	A	382	LEU	0	0.025	0.011	9.329	0.141	0.141	0.000	0.000	0.000	0.000
9	A	383	LYS	1	0.909	0.939	12.111	0.117	0.117	0.000	0.000	0.000	0.000
10	A	384	THR	0	-0.068	-0.023	9.320	0.090	0.090	0.000	0.000	0.000	0.000
11	A	385	SER	0	0.010	0.000	12.039	0.022	0.022	0.000	0.000	0.000	0.000
12	A	386	LYS	1	0.938	0.983	6.608	-2.221	-2.221	0.000	0.000	0.000	0.000
13	A	387	GLN	0	0.034	0.022	11.600	-0.029	-0.029	0.000	0.000	0.000	0.000
14	A	388	TYR	0	0.039	0.012	9.242	-0.101	-0.101	0.000	0.000	0.000	0.000
15	A	389	LEU	0	-0.031	-0.024	5.703	0.057	0.057	0.000	0.000	0.000	0.000
16	A	390	SER	0	0.033	0.027	2.647	-2.283	-1.494	0.259	-0.342	-0.707	0.001
17	A	391	VAL	0	-0.001	0.013	2.638	-1.097	1.489	1.408	-1.967	-2.028	-0.011
18	A	392	LEU	0	-0.029	0.004	2.779	-3.165	-1.524	0.401	-0.520	-1.522	-0.004
19	A	393	ALA	0	0.021	0.002	3.843	-0.029	0.080	0.001	-0.022	-0.088	0.000
20	A	394	GLN	0	-0.018	-0.022	7.564	0.125	0.125	0.000	0.000	0.000	0.000
21	A	395	VAL	0	-0.009	0.008	11.167	0.100	0.100	0.000	0.000	0.000	0.000
22	A	396	VAL	0	0.013	0.007	13.673	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	397	ASP	-1	-0.902	-0.955	16.741	0.003	0.003	0.000	0.000	0.000	0.000
24	A	398	ILE	0	0.003	0.006	17.783	0.039	0.039	0.000	0.000	0.000	0.000
25	A	399	GLN	0	0.008	0.017	19.833	0.007	0.007	0.000	0.000	0.000	0.000
26	A	400	SER	0	-0.022	-0.029	21.995	0.032	0.032	0.000	0.000	0.000	0.000
27	A	401	SER	0	-0.005	-0.006	23.547	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	402	ASP	-1	-0.903	-0.952	26.054	0.134	0.134	0.000	0.000	0.000	0.000
29	A	403	LYS	1	0.900	0.947	25.619	-0.148	-0.148	0.000	0.000	0.000	0.000
30	A	404	ASN	0	0.044	0.004	21.891	0.053	0.053	0.000	0.000	0.000	0.000
31	A	405	ILE	0	0.001	0.031	17.828	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	406	ARG	1	0.882	0.934	18.464	-0.137	-0.137	0.000	0.000	0.000	0.000
33	A	407	LEU	0	0.029	0.014	13.600	-0.033	-0.033	0.000	0.000	0.000	0.000
34	A	408	LYS	1	0.936	0.982	15.668	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	409	ILE	0	-0.033	-0.022	8.814	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	410	CYS	0	0.075	0.028	11.608	0.043	0.043	0.000	0.000	0.000	0.000
37	A	411	ASP	-1	-0.750	-0.844	6.712	-1.870	-1.870	0.000	0.000	0.000	0.000
38	A	412	ASN	0	0.023	0.002	8.899	0.209	0.209	0.000	0.000	0.000	0.000
39	A	413	SER	0	-0.100	-0.073	7.743	0.162	0.162	0.000	0.000	0.000	0.000
40	A	414	CYS	0	-0.046	-0.023	10.090	0.147	0.147	0.000	0.000	0.000	0.000
41	A	415	ASN	0	0.008	0.012	12.551	-0.040	-0.040	0.000	0.000	0.000	0.000
42	A	416	GLN	0	-0.010	-0.006	14.249	0.061	0.061	0.000	0.000	0.000	0.000
43	A	417	GLU	-1	-0.887	-0.944	13.475	-0.205	-0.205	0.000	0.000	0.000	0.000
44	A	418	LEU	0	-0.023	0.000	9.918	0.059	0.059	0.000	0.000	0.000	0.000
45	A	419	LYN	0	0.026	0.026	13.593	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	420	VAL	0	0.012	0.014	11.360	0.092	0.092	0.000	0.000	0.000	0.000
47	A	421	VAL	0	-0.018	-0.013	14.553	-0.083	-0.083	0.000	0.000	0.000	0.000
48	A	422	ILE	0	0.008	0.005	13.843	0.097	0.097	0.000	0.000	0.000	0.000
49	A	423	PHE	0	0.007	-0.023	17.032	-0.049	-0.049	0.000	0.000	0.000	0.000
50	A	424	PRO	0	0.009	-0.035	19.692	0.025	0.025	0.000	0.000	0.000	0.000
51	A	425	ASP	-1	-0.868	-0.921	20.184	0.429	0.429	0.000	0.000	0.000	0.000
52	A	426	LEU	0	0.031	0.012	13.372	-0.038	-0.038	0.000	0.000	0.000	0.000
53	A	427	CYS	0	-0.092	-0.031	18.015	-0.045	-0.045	0.000	0.000	0.000	0.000
54	A	428	TYR	0	-0.014	-0.010	19.561	-0.042	-0.042	0.000	0.000	0.000	0.000
55	A	429	GLU	-1	-0.944	-0.960	17.475	0.341	0.341	0.000	0.000	0.000	0.000
56	A	430	TRP	0	0.006	-0.018	13.187	-0.065	-0.065	0.000	0.000	0.000	0.000
57	A	431	ARG	1	0.884	0.954	18.339	-0.167	-0.167	0.000	0.000	0.000	0.000
58	A	432	ASP	-1	-0.923	-0.966	21.512	0.077	0.077	0.000	0.000	0.000	0.000
59	A	433	LYS	1	0.918	0.984	15.905	-0.145	-0.145	0.000	0.000	0.000	0.000
60	A	434	PHE	0	-0.011	-0.012	12.315	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	435	SER	0	-0.025	-0.017	16.053	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	436	ILE	0	0.028	0.011	16.014	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	437	ASN	0	-0.028	-0.029	15.488	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	438	LYS	1	0.831	0.932	13.534	0.126	0.126	0.000	0.000	0.000	0.000
65	A	439	TRP	0	-0.028	-0.010	7.431	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	440	TYR	0	-0.002	-0.015	8.311	0.066	0.066	0.000	0.000	0.000	0.000
67	A	441	TYR	0	0.022	0.004	2.939	-1.908	-0.922	0.057	-0.350	-0.692	0.001
68	A	442	PHE	0	-0.022	-0.007	5.248	0.053	0.053	0.000	0.000	0.000	0.000
69	A	443	ASN	0	-0.021	-0.033	5.399	2.566	2.684	-0.001	-0.002	-0.116	0.000
70	A	444	GLU	-1	-0.898	-0.965	6.456	1.282	1.282	0.000	0.000	0.000	0.000
71	A	445	PHE	0	0.000	0.017	8.032	-0.709	-0.709	0.000	0.000	0.000	0.000
72	A	446	VAL	0	-0.034	-0.025	9.766	0.140	0.140	0.000	0.000	0.000	0.000
73	A	447	ARG	1	0.881	0.942	11.005	-0.619	-0.619	0.000	0.000	0.000	0.000
74	A	448	GLN	0	-0.003	-0.014	12.768	-0.067	-0.067	0.000	0.000	0.000	0.000
75	A	449	ILE	0	0.025	0.007	16.437	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	450	TYR	0	-0.074	-0.034	18.982	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	451	ASN	0	-0.017	-0.021	22.001	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	452	ASP	-1	-0.919	-0.939	22.694	0.089	0.089	0.000	0.000	0.000	0.000
79	A	453	GLU	-1	-0.944	-0.959	19.233	0.042	0.042	0.000	0.000	0.000	0.000
80	A	454	VAL	0	-0.057	-0.031	13.442	0.054	0.054	0.000	0.000	0.000	0.000
81	A	455	GLN	0	-0.018	-0.024	14.676	-0.083	-0.083	0.000	0.000	0.000	0.000
82	A	456	LEU	0	-0.020	-0.005	8.959	0.104	0.104	0.000	0.000	0.000	0.000
83	A	457	LYS	1	0.852	0.945	13.039	-0.727	-0.727	0.000	0.000	0.000	0.000
84	A	458	ASN	0	0.073	0.027	13.448	0.262	0.262	0.000	0.000	0.000	0.000
85	A	459	ASN	0	-0.026	-0.029	14.316	0.026	0.026	0.000	0.000	0.000	0.000
86	A	460	ILE	0	0.029	0.019	15.508	0.046	0.046	0.000	0.000	0.000	0.000
87	A	461	HIS	0	0.006	0.003	13.237	-0.054	-0.054	0.000	0.000	0.000	0.000
88	A	462	SER	0	-0.043	-0.009	11.495	0.085	0.085	0.000	0.000	0.000	0.000
89	A	463	SER	0	0.006	0.000	10.557	-0.241	-0.241	0.000	0.000	0.000	0.000
90	A	464	ILE	0	0.017	0.006	9.250	0.301	0.301	0.000	0.000	0.000	0.000
91	A	465	LYS	1	0.929	0.965	8.632	-0.718	-0.718	0.000	0.000	0.000	0.000
92	A	466	GLU	-1	-0.829	-0.893	8.655	-0.319	-0.319	0.000	0.000	0.000	0.000
93	A	467	SER	0	-0.043	-0.017	7.712	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	468	ASP	-1	-0.840	-0.928	9.415	-0.256	-0.256	0.000	0.000	0.000	0.000
95	A	469	ASP	-1	-0.983	-0.975	10.732	-0.721	-0.721	0.000	0.000	0.000	0.000
96	A	470	GLN	0	0.000	0.007	11.303	-0.143	-0.143	0.000	0.000	0.000	0.000
97	A	471	ARG	1	0.927	0.957	13.417	0.604	0.604	0.000	0.000	0.000	0.000
98	A	472	LYS	1	0.991	0.993	16.794	0.197	0.197	0.000	0.000	0.000	0.000
99	A	473	VAL	0	0.021	0.013	18.881	0.025	0.025	0.000	0.000	0.000	0.000
100	A	474	ILE	0	-0.026	-0.017	21.196	0.008	0.008	0.000	0.000	0.000	0.000
101	A	475	THR	0	0.003	0.007	24.396	0.001	0.001	0.000	0.000	0.000	0.000
102	A	476	TYR	0	-0.006	-0.004	26.394	0.012	0.012	0.000	0.000	0.000	0.000
103	A	477	ASN	0	-0.008	-0.006	27.031	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	478	GLN	0	-0.006	0.004	30.940	0.006	0.006	0.000	0.000	0.000	0.000
105	A	479	GLU	-1	-0.893	-0.946	34.722	-0.098	-0.098	0.000	0.000	0.000	0.000
106	A	480	GLN	0	0.024	-0.015	32.790	0.002	0.002	0.000	0.000	0.000	0.000
107	A	481	GLY	0	0.006	0.016	37.622	0.001	0.001	0.000	0.000	0.000	0.000
108	A	482	VAL	0	-0.062	-0.026	40.416	0.005	0.005	0.000	0.000	0.000	0.000
109	A	483	PHE	0	-0.041	-0.010	36.835	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:375:THR)