FMO DATABASE

FMODB ID: V5MY1

Calculation Name: 4U13-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U13

Chain ID: A

ChEMBL ID:

UniProt ID: Q92YJ1

Base Structure: X-ray

Registration Date: 2023-09-20

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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-824967.624763
FMO2-HF: Nuclear repulsion	783122.273468
FMO2-HF: Total energy	-41845.351295
FMO2-MP2: Total energy	-41967.466109

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:-2:PHE)

Summations of interaction energy for fragment #1(A:-2:PHE)

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.
-18.047	-6.158	15.123	-6.258	-20.756	-0.01

Interaction energy analysis for fragmet #1(A:-2:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / 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

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	0	SER	0	0.046	0.025	3.233	-1.711	1.372	0.650	-0.779	-2.954	0.005
4	A	1	MET	0	-0.060	-0.021	4.147	-0.745	-0.453	0.000	0.011	-0.304	0.000
5	A	2	ASP	-1	-0.890	-0.935	2.818	-3.134	0.271	0.552	-1.774	-2.184	-0.014
6	A	3	LEU	0	-0.095	-0.048	2.340	-1.867	-0.849	1.570	-0.432	-2.156	0.001
7	A	4	PRO	0	0.016	-0.004	4.948	0.294	0.329	-0.001	-0.005	-0.029	0.000
8	A	5	ASP	-1	-0.853	-0.929	8.390	-0.355	-0.355	0.000	0.000	0.000	0.000
9	A	6	ILE	0	-0.036	-0.022	10.156	-0.028	-0.028	0.000	0.000	0.000	0.000
10	A	7	VAL	0	-0.013	-0.004	6.022	0.027	0.027	0.000	0.000	0.000	0.000
11	A	8	ASN	0	-0.009	-0.021	5.406	-0.179	-0.179	0.000	0.000	0.000	0.000
12	A	9	MET	0	0.016	0.025	7.145	0.038	0.038	0.000	0.000	0.000	0.000
13	A	10	TYR	0	0.013	0.007	9.382	0.044	0.044	0.000	0.000	0.000	0.000
14	A	11	PHE	0	-0.001	-0.014	6.019	0.082	0.082	0.000	0.000	0.000	0.000
15	A	12	ASP	-1	-0.857	-0.921	8.631	-0.568	-0.568	0.000	0.000	0.000	0.000
16	A	13	ALA	0	0.016	0.008	10.366	0.049	0.049	0.000	0.000	0.000	0.000
17	A	14	ASP	-1	-0.831	-0.915	11.254	-0.228	-0.228	0.000	0.000	0.000	0.000
18	A	15	SER	0	-0.057	-0.031	10.511	0.054	0.054	0.000	0.000	0.000	0.000
19	A	16	CYS	0	-0.043	-0.006	12.615	0.024	0.024	0.000	0.000	0.000	0.000
20	A	17	ASN	0	-0.105	-0.056	15.487	0.027	0.027	0.000	0.000	0.000	0.000
21	A	18	ASP	-1	-0.846	-0.930	16.492	-0.179	-0.179	0.000	0.000	0.000	0.000
22	A	19	THR	0	0.009	-0.032	17.942	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	20	ASP	-1	-0.912	-0.933	20.392	-0.128	-0.128	0.000	0.000	0.000	0.000
24	A	21	ALA	0	0.087	0.062	16.004	0.000	0.000	0.000	0.000	0.000	0.000
25	A	22	LEU	0	-0.033	-0.025	14.569	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	23	SER	0	-0.097	-0.062	16.872	0.007	0.007	0.000	0.000	0.000	0.000
27	A	24	GLU	-1	-0.984	-0.984	18.470	-0.155	-0.155	0.000	0.000	0.000	0.000
28	A	25	THR	0	0.005	0.000	13.669	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	26	PHE	0	-0.049	-0.034	15.474	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	27	ALA	0	-0.005	0.006	18.435	0.010	0.010	0.000	0.000	0.000	0.000
31	A	28	PRO	0	0.023	-0.016	21.362	0.000	0.000	0.000	0.000	0.000	0.000
32	A	29	ASP	-1	-0.958	-0.983	24.431	-0.096	-0.096	0.000	0.000	0.000	0.000
33	A	30	ALA	0	-0.017	0.016	19.752	0.002	0.002	0.000	0.000	0.000	0.000
34	A	31	VAL	0	-0.073	-0.049	20.575	0.010	0.010	0.000	0.000	0.000	0.000
35	A	32	VAL	0	0.053	0.029	17.303	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	33	GLU	-1	-1.052	-1.030	18.853	-0.069	-0.069	0.000	0.000	0.000	0.000
37	A	34	ASP	-1	-0.739	-0.889	17.990	-0.119	-0.119	0.000	0.000	0.000	0.000
38	A	35	GLU	-1	-0.980	-0.976	19.906	-0.096	-0.096	0.000	0.000	0.000	0.000
39	A	36	GLY	0	-0.025	-0.001	22.155	0.004	0.004	0.000	0.000	0.000	0.000
40	A	37	ALA	0	-0.050	-0.023	23.678	0.005	0.005	0.000	0.000	0.000	0.000
41	A	38	ARG	1	0.935	0.960	23.171	0.069	0.069	0.000	0.000	0.000	0.000
42	A	39	HIS	0	0.004	0.004	21.672	0.007	0.007	0.000	0.000	0.000	0.000
43	A	40	GLN	0	0.027	0.006	23.153	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	41	GLY	0	0.013	0.018	24.487	0.005	0.005	0.000	0.000	0.000	0.000
45	A	42	VAL	0	0.068	0.021	21.767	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	43	VAL	0	-0.002	0.003	23.696	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	44	ALA	0	-0.024	-0.024	25.320	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	45	ILE	0	0.054	0.043	19.016	0.000	0.000	0.000	0.000	0.000	0.000
49	A	46	LEU	0	0.051	0.024	20.849	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	47	ARG	1	0.854	0.929	22.425	0.081	0.081	0.000	0.000	0.000	0.000
51	A	48	TRP	0	-0.024	-0.010	15.638	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	49	TRP	0	-0.013	0.004	15.421	0.012	0.012	0.000	0.000	0.000	0.000
53	A	50	VAL	0	-0.006	-0.010	19.812	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	51	ALA	0	-0.029	-0.029	22.568	0.001	0.001	0.000	0.000	0.000	0.000
55	A	52	ALA	0	0.096	0.061	19.325	0.004	0.004	0.000	0.000	0.000	0.000
56	A	53	LYS	1	0.848	0.945	15.136	0.229	0.229	0.000	0.000	0.000	0.000
57	A	54	LYS	1	0.874	0.934	20.574	0.109	0.109	0.000	0.000	0.000	0.000
58	A	55	ALA	0	-0.026	-0.005	23.069	0.004	0.004	0.000	0.000	0.000	0.000
59	A	56	ALA	0	0.006	-0.008	20.089	0.005	0.005	0.000	0.000	0.000	0.000
60	A	57	SER	0	-0.093	-0.048	19.836	0.001	0.001	0.000	0.000	0.000	0.000
61	A	58	TYR	0	-0.090	-0.043	13.657	0.007	0.007	0.000	0.000	0.000	0.000
62	A	59	VAL	0	0.024	0.012	11.016	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	60	ALA	0	0.012	0.001	9.763	0.028	0.028	0.000	0.000	0.000	0.000
64	A	61	GLU	-1	-0.921	-0.968	5.885	-0.866	-0.866	0.000	0.000	0.000	0.000
65	A	62	PRO	0	-0.014	-0.016	2.516	-1.162	-0.070	1.251	-0.703	-1.640	0.007
66	A	63	LEU	0	-0.056	-0.021	3.276	-2.292	-0.462	0.296	-0.694	-1.433	-0.001
67	A	64	GLU	-1	-0.936	-0.981	2.271	-4.067	-2.722	9.623	-4.711	-6.256	0.000
68	A	65	SER	0	-0.010	-0.016	2.522	-1.498	-2.194	1.181	2.880	-3.365	-0.008
69	A	66	THR	0	0.003	0.014	3.976	-0.165	0.049	0.001	-0.010	-0.205	0.000
70	A	67	VAL	0	-0.021	-0.014	7.020	-0.023	-0.023	0.000	0.000	0.000	0.000
71	A	68	ASP	-1	-0.932	-0.963	9.278	0.010	0.010	0.000	0.000	0.000	0.000
72	A	69	GLY	0	0.002	0.004	13.017	0.004	0.004	0.000	0.000	0.000	0.000
73	A	70	ASP	-1	-0.847	-0.917	13.968	-0.135	-0.135	0.000	0.000	0.000	0.000
74	A	71	LYS	1	0.888	0.945	13.002	0.117	0.117	0.000	0.000	0.000	0.000
75	A	72	ALA	0	0.045	0.028	7.420	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	73	LEU	0	-0.016	0.002	8.178	0.051	0.051	0.000	0.000	0.000	0.000
77	A	74	VAL	0	0.023	0.013	4.108	-0.409	-0.138	0.000	-0.041	-0.230	0.000
78	A	75	ARG	1	0.970	1.009	6.106	-0.201	-0.201	0.000	0.000	0.000	0.000
79	A	76	ALA	0	0.029	0.003	6.489	0.517	0.517	0.000	0.000	0.000	0.000
80	A	77	LYS	1	0.923	0.975	8.238	0.277	0.277	0.000	0.000	0.000	0.000
81	A	78	VAL	0	0.052	0.025	10.309	-0.053	-0.053	0.000	0.000	0.000	0.000
82	A	79	SER	0	-0.002	-0.005	12.976	0.014	0.014	0.000	0.000	0.000	0.000
83	A	80	GLY	0	0.019	-0.017	15.152	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	81	ARG	1	0.857	0.949	18.462	0.123	0.123	0.000	0.000	0.000	0.000
85	A	82	PHE	0	0.034	0.010	17.016	0.004	0.004	0.000	0.000	0.000	0.000
86	A	83	PRO	0	-0.013	-0.014	22.481	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	84	GLY	0	0.017	0.000	22.475	0.001	0.001	0.000	0.000	0.000	0.000
88	A	85	SER	0	-0.005	0.062	18.278	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	86	PRO	0	-0.052	-0.030	14.645	0.002	0.002	0.000	0.000	0.000	0.000
90	A	87	VAL	0	0.038	-0.001	15.466	0.012	0.012	0.000	0.000	0.000	0.000
91	A	88	THR	0	-0.057	-0.029	10.570	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	89	LEU	0	-0.009	0.003	11.984	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	90	THR	0	0.002	-0.002	10.269	0.072	0.072	0.000	0.000	0.000	0.000
94	A	91	TYR	0	0.037	0.016	9.011	-0.020	-0.020	0.000	0.000	0.000	0.000
95	A	92	SER	0	-0.007	-0.007	9.540	-0.049	-0.049	0.000	0.000	0.000	0.000
96	A	93	PHE	0	0.032	0.007	8.383	0.021	0.021	0.000	0.000	0.000	0.000
97	A	94	THR	0	-0.076	-0.049	12.185	0.006	0.006	0.000	0.000	0.000	0.000
98	A	95	ILE	0	0.030	0.026	11.471	0.004	0.004	0.000	0.000	0.000	0.000
99	A	96	LYS	1	0.848	0.907	15.296	0.119	0.119	0.000	0.000	0.000	0.000
100	A	97	ASP	-1	-0.900	-0.960	18.931	-0.101	-0.101	0.000	0.000	0.000	0.000
101	A	98	GLY	0	-0.023	-0.007	16.245	0.003	0.003	0.000	0.000	0.000	0.000
102	A	99	ARG	1	0.939	0.987	16.784	0.143	0.143	0.000	0.000	0.000	0.000
103	A	100	ILE	0	0.023	0.014	12.482	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	101	ALA	0	-0.016	-0.016	16.140	0.018	0.018	0.000	0.000	0.000	0.000
105	A	102	ARG	1	0.919	0.938	16.846	0.118	0.118	0.000	0.000	0.000	0.000
106	A	103	LEU	0	0.004	0.018	12.414	-0.023	-0.023	0.000	0.000	0.000	0.000
107	A	104	GLU	-1	-0.942	-0.953	14.873	-0.074	-0.074	0.000	0.000	0.000	0.000
108	A	105	ILE	0	-0.004	0.000	13.734	-0.010	-0.010	0.000	0.000	0.000	0.000
109	A	106	GLN	0	-0.040	-0.020	14.823	0.020	0.020	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-2:PHE)