FMO DATABASE

FMODB ID: 85VZY

Calculation Name: 4A8X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4A8X

Chain ID: A

ChEMBL ID:

UniProt ID: Q15287

Base Structure: X-ray

Registration Date: 2023-09-19

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	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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-610863.462358
FMO2-HF: Nuclear repulsion	574860.948605
FMO2-HF: Total energy	-36002.513753
FMO2-MP2: Total energy	-36104.474948

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:157:SER)

Summations of interaction energy for fragment #1(A:157:SER)

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.
-2.771	-1.269	0.016	-0.835	-0.682	0

Interaction energy analysis for fragmet #1(A:157:SER)

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

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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].
3	A	159	LYS	1	0.888	0.931	3.365	-2.060	-0.558	0.016	-0.835	-0.682
4	A	160	PRO	0	-0.002	-0.005	5.862	0.691	0.691	0.000	0.000	0.000
5	A	161	THR	0	0.052	0.015	8.110	0.019	0.019	0.000	0.000	0.000
6	A	162	LYS	1	0.841	0.945	11.497	0.149	0.149	0.000	0.000	0.000
7	A	163	VAL	0	0.029	0.008	12.811	-0.107	-0.107	0.000	0.000	0.000
8	A	164	HIS	0	-0.058	-0.027	15.431	0.070	0.070	0.000	0.000	0.000
9	A	165	ILE	0	0.012	0.005	18.010	-0.030	-0.030	0.000	0.000	0.000
10	A	166	GLY	0	0.050	0.017	21.292	0.024	0.024	0.000	0.000	0.000
11	A	167	ARG	1	0.906	0.944	23.649	0.159	0.159	0.000	0.000	0.000
12	A	168	LEU	0	0.037	0.044	25.423	0.006	0.006	0.000	0.000	0.000
13	A	169	THR	0	-0.015	-0.043	28.690	0.006	0.006	0.000	0.000	0.000
14	A	170	ARG	1	0.916	0.949	32.214	0.079	0.079	0.000	0.000	0.000
15	A	171	ASN	0	-0.035	-0.025	34.611	0.011	0.011	0.000	0.000	0.000
16	A	172	VAL	0	-0.057	-0.008	29.092	0.003	0.003	0.000	0.000	0.000
17	A	173	THR	0	0.022	-0.007	31.735	0.003	0.003	0.000	0.000	0.000
18	A	174	LYS	1	0.910	0.917	25.604	0.041	0.041	0.000	0.000	0.000
19	A	175	ASP	-1	-0.892	-0.949	28.452	-0.052	-0.052	0.000	0.000	0.000
20	A	176	HIS	0	0.066	0.059	30.383	-0.006	-0.006	0.000	0.000	0.000
21	A	177	ILE	0	-0.017	-0.001	24.341	-0.008	-0.008	0.000	0.000	0.000
22	A	178	MET	0	-0.009	-0.004	25.641	-0.012	-0.012	0.000	0.000	0.000
23	A	179	GLU	-1	-0.923	-0.946	26.596	-0.079	-0.079	0.000	0.000	0.000
24	A	180	ILE	0	0.001	0.002	25.777	-0.006	-0.006	0.000	0.000	0.000
25	A	181	PHE	0	0.005	-0.014	21.081	-0.011	-0.011	0.000	0.000	0.000
26	A	182	SER	0	0.011	-0.010	22.684	-0.009	-0.009	0.000	0.000	0.000
27	A	183	THR	0	-0.065	-0.021	24.765	0.010	0.010	0.000	0.000	0.000
28	A	184	TYR	0	-0.123	-0.097	20.377	-0.006	-0.006	0.000	0.000	0.000
29	A	185	GLY	0	0.040	0.011	20.061	-0.024	-0.024	0.000	0.000	0.000
30	A	186	LYS	1	0.929	0.974	20.636	0.013	0.013	0.000	0.000	0.000
31	A	187	ILE	0	-0.002	-0.009	19.759	-0.006	-0.006	0.000	0.000	0.000
32	A	188	LYS	1	0.846	0.916	15.698	-0.088	-0.088	0.000	0.000	0.000
33	A	189	MET	0	-0.034	-0.019	19.258	0.020	0.020	0.000	0.000	0.000
34	A	190	ILE	0	0.039	0.021	20.377	-0.025	-0.025	0.000	0.000	0.000
35	A	191	ASP	-1	-0.918	-0.954	21.440	-0.048	-0.048	0.000	0.000	0.000
36	A	192	MET	0	-0.008	0.005	23.110	-0.019	-0.019	0.000	0.000	0.000
37	A	193	PRO	0	-0.018	0.007	24.447	0.011	0.011	0.000	0.000	0.000
38	A	194	VAL	0	0.052	0.028	27.503	-0.007	-0.007	0.000	0.000	0.000
39	A	195	GLU	-1	-0.896	-0.953	31.222	-0.073	-0.073	0.000	0.000	0.000
40	A	196	ARG	1	0.909	0.948	30.060	0.043	0.043	0.000	0.000	0.000
41	A	197	MET	0	0.024	0.011	34.661	0.005	0.005	0.000	0.000	0.000
42	A	198	HIS	0	-0.061	-0.031	36.844	0.000	0.000	0.000	0.000	0.000
43	A	199	PRO	0	0.082	0.035	35.284	-0.004	-0.004	0.000	0.000	0.000
44	A	200	HIS	0	0.013	0.014	35.352	0.000	0.000	0.000	0.000	0.000
45	A	201	LEU	0	-0.023	-0.002	35.197	-0.004	-0.004	0.000	0.000	0.000
46	A	202	SER	0	0.058	0.032	29.597	0.001	0.001	0.000	0.000	0.000
47	A	203	LYS	1	0.842	0.906	27.859	0.072	0.072	0.000	0.000	0.000
48	A	204	GLY	0	0.025	0.020	28.665	-0.007	-0.007	0.000	0.000	0.000
49	A	205	TYR	0	-0.040	-0.022	22.675	-0.011	-0.011	0.000	0.000	0.000
50	A	206	ALA	0	0.002	-0.005	22.997	0.021	0.021	0.000	0.000	0.000
51	A	207	TYR	0	-0.043	-0.005	17.309	-0.035	-0.035	0.000	0.000	0.000
52	A	208	VAL	0	0.035	0.007	18.346	0.037	0.037	0.000	0.000	0.000
53	A	209	GLU	-1	-0.873	-0.933	14.484	-0.030	-0.030	0.000	0.000	0.000
54	A	210	PHE	0	0.019	0.009	15.454	0.030	0.030	0.000	0.000	0.000
55	A	211	GLU	-1	-0.942	-0.971	15.459	0.063	0.063	0.000	0.000	0.000
56	A	212	ASN	0	-0.023	-0.012	13.440	0.005	0.005	0.000	0.000	0.000
57	A	213	PRO	0	0.029	-0.010	9.310	-0.029	-0.029	0.000	0.000	0.000
58	A	214	ASP	-1	-0.896	-0.933	11.562	-0.476	-0.476	0.000	0.000	0.000
59	A	215	GLU	-1	-0.806	-0.897	14.128	-0.126	-0.126	0.000	0.000	0.000
60	A	216	ALA	0	-0.009	0.002	12.643	-0.005	-0.005	0.000	0.000	0.000
61	A	217	GLU	-1	-0.849	-0.906	10.893	-1.053	-1.053	0.000	0.000	0.000
62	A	218	LYS	1	0.894	0.963	14.236	0.217	0.217	0.000	0.000	0.000
63	A	219	ALA	0	0.028	0.012	17.618	0.026	0.026	0.000	0.000	0.000
64	A	220	LEU	0	-0.046	-0.021	13.178	0.010	0.010	0.000	0.000	0.000
65	A	221	LYS	1	0.944	0.974	17.406	0.373	0.373	0.000	0.000	0.000
66	A	222	HIS	0	-0.124	-0.076	19.022	0.037	0.037	0.000	0.000	0.000
67	A	223	MET	0	0.009	0.019	21.099	0.033	0.033	0.000	0.000	0.000
68	A	224	ASP	-1	-0.864	-0.908	19.029	-0.379	-0.379	0.000	0.000	0.000
69	A	225	GLY	0	0.031	0.022	21.198	-0.006	-0.006	0.000	0.000	0.000
70	A	226	GLY	0	-0.024	-0.003	24.471	0.019	0.019	0.000	0.000	0.000
71	A	227	GLN	0	-0.031	-0.032	26.374	0.012	0.012	0.000	0.000	0.000
72	A	228	ILE	0	-0.017	-0.013	26.083	0.005	0.005	0.000	0.000	0.000
73	A	229	ASP	-1	-0.815	-0.879	30.316	-0.094	-0.094	0.000	0.000	0.000
74	A	230	GLY	0	0.009	0.015	33.869	0.003	0.003	0.000	0.000	0.000
75	A	231	GLN	0	-0.040	-0.024	30.473	0.005	0.005	0.000	0.000	0.000
76	A	232	GLU	-1	-0.937	-0.964	27.155	-0.210	-0.210	0.000	0.000	0.000
77	A	233	ILE	0	-0.086	-0.035	23.458	0.007	0.007	0.000	0.000	0.000
78	A	234	THR	0	0.038	0.019	21.080	-0.003	-0.003	0.000	0.000	0.000
79	A	235	ALA	0	-0.042	-0.031	18.847	0.023	0.023	0.000	0.000	0.000
80	A	236	THR	0	0.054	0.023	15.150	-0.029	-0.029	0.000	0.000	0.000
81	A	237	ALA	0	-0.012	-0.002	10.266	0.053	0.053	0.000	0.000	0.000
82	A	238	VAL	0	-0.028	-0.017	11.866	0.007	0.007	0.000	0.000	0.000
83	A	239	LEU	0	0.001	0.002	5.389	0.038	0.038	0.000	0.000	0.000
84	A	240	ALA	0	0.027	0.007	9.633	0.057	0.057	0.000	0.000	0.000
85	A	241	PRO	0	-0.005	-0.001	12.517	0.007	0.007	0.000	0.000	0.000
86	A	242	TRP	0	0.013	-0.002	14.809	-0.046	-0.046	0.000	0.000	0.000
87	A	243	PRO	0	0.060	0.029	18.122	0.025	0.025	0.000	0.000	0.000
88	A	244	ARG	1	0.929	0.974	18.347	-0.097	-0.097	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:157:SER)