FMO DATABASE

FMODB ID: YVQ92

Calculation Name: 3KP8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KP8

Chain ID: A

ChEMBL ID:

UniProt ID: Q2JJF6

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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-623068.435325
FMO2-HF: Nuclear repulsion	587231.020381
FMO2-HF: Total energy	-35837.414943
FMO2-MP2: Total energy	-35939.798316

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:186:SER)

Summations of interaction energy for fragment #1(A:186: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.
-18.138	-15.2	9.444	-5.257	-7.123	0.031

Interaction energy analysis for fragmet #1(A:186:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.020

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	188	LEU	0	0.009	0.020	2.809	-3.677	-0.951	0.691	-1.350	-2.067	0.009
4	A	189	ALA	0	0.027	0.012	2.021	-8.055	-9.493	8.701	-3.432	-3.831	0.022
5	A	190	VAL	0	0.026	0.002	3.077	-1.528	-0.561	0.045	-0.328	-0.684	0.001
6	A	191	GLY	0	-0.013	0.002	5.498	-0.010	-0.010	0.000	0.000	0.000	0.000
7	A	192	LEU	0	0.003	0.005	6.777	-0.242	-0.242	0.000	0.000	0.000	0.000
8	A	193	ALA	0	0.013	0.009	7.614	-0.102	-0.102	0.000	0.000	0.000	0.000
9	A	194	ALA	0	-0.037	-0.016	9.303	0.018	0.018	0.000	0.000	0.000	0.000
10	A	195	HIS	0	-0.043	-0.036	11.342	0.019	0.019	0.000	0.000	0.000	0.000
11	A	196	LEU	0	0.031	0.005	10.761	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	197	ARG	1	0.906	0.957	13.139	0.053	0.053	0.000	0.000	0.000	0.000
13	A	198	GLN	0	-0.112	-0.056	15.383	0.031	0.031	0.000	0.000	0.000	0.000
14	A	199	ILE	0	-0.057	-0.018	16.478	0.006	0.006	0.000	0.000	0.000	0.000
15	A	200	GLY	0	0.010	0.018	18.371	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	201	GLY	0	-0.055	-0.022	16.677	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	202	THR	0	-0.025	-0.017	16.187	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	203	MET	0	-0.065	-0.013	14.731	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	204	TYR	0	0.035	0.003	17.267	0.012	0.012	0.000	0.000	0.000	0.000
20	A	205	GLY	0	0.035	-0.020	19.270	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	206	ALA	0	0.011	0.013	20.307	0.033	0.033	0.000	0.000	0.000	0.000
22	A	207	TYR	0	-0.047	-0.031	19.232	-0.041	-0.041	0.000	0.000	0.000	0.000
23	A	208	TRP	0	0.017	0.013	19.622	-0.035	-0.035	0.000	0.000	0.000	0.000
24	A	209	CYS	0	-0.050	-0.006	20.623	0.001	0.001	0.000	0.000	0.000	0.000
25	A	210	PRO	0	0.068	0.016	19.012	-0.045	-0.045	0.000	0.000	0.000	0.000
26	A	211	HIS	0	0.098	0.050	17.391	-0.085	-0.085	0.000	0.000	0.000	0.000
27	A	212	CYS	0	-0.069	-0.010	15.907	-0.054	-0.054	0.000	0.000	0.000	0.000
28	A	213	GLN	0	-0.006	-0.008	14.560	-0.031	-0.031	0.000	0.000	0.000	0.000
29	A	214	ASP	-1	-0.825	-0.908	13.041	-0.813	-0.813	0.000	0.000	0.000	0.000
30	A	215	GLN	0	-0.041	-0.029	10.554	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	216	LYS	1	0.901	0.952	10.043	0.388	0.388	0.000	0.000	0.000	0.000
32	A	217	GLU	-1	-0.901	-0.953	8.639	-1.290	-1.290	0.000	0.000	0.000	0.000
33	A	218	LEU	0	-0.082	-0.025	7.050	-0.446	-0.446	0.000	0.000	0.000	0.000
34	A	219	PHE	0	-0.054	-0.030	4.642	-1.457	-1.300	-0.001	-0.006	-0.149	0.000
35	A	220	GLY	0	0.027	0.018	4.298	-1.331	-1.189	-0.001	-0.028	-0.113	0.000
36	A	221	ALA	0	0.035	-0.003	5.834	0.341	0.341	0.000	0.000	0.000	0.000
37	A	222	ALA	0	-0.027	-0.002	3.750	0.297	0.406	0.000	-0.031	-0.077	0.000
38	A	223	PHE	0	0.005	-0.024	5.760	0.467	0.467	0.000	0.000	0.000	0.000
39	A	224	ASP	-1	-0.889	-0.924	9.053	-0.412	-0.412	0.000	0.000	0.000	0.000
40	A	225	GLN	0	-0.052	-0.031	8.581	0.244	0.244	0.000	0.000	0.000	0.000
41	A	226	VAL	0	-0.033	-0.012	9.830	0.094	0.094	0.000	0.000	0.000	0.000
42	A	227	PRO	0	-0.002	0.012	12.579	0.000	0.000	0.000	0.000	0.000	0.000
43	A	228	TYR	0	-0.017	-0.051	15.605	-0.054	-0.054	0.000	0.000	0.000	0.000
44	A	229	VAL	0	0.022	0.019	17.529	0.027	0.027	0.000	0.000	0.000	0.000
45	A	230	GLU	-1	-0.755	-0.872	21.024	-0.343	-0.343	0.000	0.000	0.000	0.000
46	A	231	CYS	0	-0.060	-0.016	22.359	0.019	0.019	0.000	0.000	0.000	0.000
47	A	232	SER	0	0.008	0.013	24.458	0.019	0.019	0.000	0.000	0.000	0.000
48	A	233	PRO	0	0.041	0.015	25.889	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	234	ASN	0	-0.025	-0.020	26.847	0.003	0.003	0.000	0.000	0.000	0.000
50	A	235	GLY	0	0.012	0.026	27.351	0.007	0.007	0.000	0.000	0.000	0.000
51	A	236	PRO	0	0.001	-0.010	27.216	0.009	0.009	0.000	0.000	0.000	0.000
52	A	237	GLY	0	-0.004	-0.002	29.359	0.010	0.010	0.000	0.000	0.000	0.000
53	A	238	THR	0	-0.073	-0.022	30.688	0.013	0.013	0.000	0.000	0.000	0.000
54	A	239	PRO	0	-0.007	-0.016	31.796	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	240	GLN	0	0.000	0.017	27.631	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	241	ALA	0	0.008	-0.006	27.561	0.013	0.013	0.000	0.000	0.000	0.000
57	A	242	GLN	0	0.002	-0.007	29.529	0.000	0.000	0.000	0.000	0.000	0.000
58	A	243	GLU	-1	-0.871	-0.949	26.733	-0.162	-0.162	0.000	0.000	0.000	0.000
59	A	245	THR	0	-0.011	-0.009	27.707	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	246	GLU	-1	-0.938	-0.972	31.181	-0.100	-0.100	0.000	0.000	0.000	0.000
61	A	247	ALA	0	-0.060	-0.008	26.747	0.006	0.006	0.000	0.000	0.000	0.000
62	A	248	GLY	0	-0.008	0.004	28.353	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	249	ILE	0	-0.059	-0.027	24.015	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	250	THR	0	0.009	-0.005	27.044	0.002	0.002	0.000	0.000	0.000	0.000
65	A	251	SER	0	-0.045	-0.024	24.248	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	252	TYR	0	-0.025	0.011	21.203	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	253	PRO	0	0.030	-0.007	16.405	0.002	0.002	0.000	0.000	0.000	0.000
68	A	254	THR	0	-0.026	-0.033	19.264	0.021	0.021	0.000	0.000	0.000	0.000
69	A	255	TRP	0	-0.014	-0.014	12.031	0.012	0.012	0.000	0.000	0.000	0.000
70	A	256	ILE	0	0.013	0.006	18.640	0.027	0.027	0.000	0.000	0.000	0.000
71	A	257	ILE	0	0.019	0.007	15.181	0.000	0.000	0.000	0.000	0.000	0.000
72	A	258	ASN	0	0.032	0.014	19.062	0.015	0.015	0.000	0.000	0.000	0.000
73	A	259	GLY	0	0.014	0.006	21.830	0.009	0.009	0.000	0.000	0.000	0.000
74	A	260	ARG	1	0.913	0.969	21.584	0.124	0.124	0.000	0.000	0.000	0.000
75	A	261	THR	0	0.042	0.018	21.697	-0.017	-0.017	0.000	0.000	0.000	0.000
76	A	262	TYR	0	-0.073	-0.038	18.254	0.011	0.011	0.000	0.000	0.000	0.000
77	A	263	THR	0	0.046	0.024	19.412	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	264	GLY	0	0.053	0.030	19.181	0.004	0.004	0.000	0.000	0.000	0.000
79	A	265	VAL	0	0.028	0.010	13.296	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	266	ARG	1	0.802	0.904	13.248	0.434	0.434	0.000	0.000	0.000	0.000
81	A	267	SER	0	0.073	0.043	9.572	-0.083	-0.083	0.000	0.000	0.000	0.000
82	A	268	LEU	0	0.058	0.014	3.511	-0.177	0.098	0.009	-0.082	-0.202	-0.001
83	A	269	GLU	-1	-0.881	-0.944	7.437	-0.640	-0.640	0.000	0.000	0.000	0.000
84	A	270	ALA	0	-0.037	-0.019	9.536	0.153	0.153	0.000	0.000	0.000	0.000
85	A	271	LEU	0	0.020	0.006	9.730	0.095	0.095	0.000	0.000	0.000	0.000
86	A	272	ALA	0	0.003	0.016	9.239	0.084	0.084	0.000	0.000	0.000	0.000
87	A	273	VAL	0	0.000	0.003	11.225	0.053	0.053	0.000	0.000	0.000	0.000
88	A	274	ALA	0	-0.051	-0.017	14.548	0.029	0.029	0.000	0.000	0.000	0.000
89	A	275	SER	0	-0.050	-0.043	12.892	0.043	0.043	0.000	0.000	0.000	0.000
90	A	276	GLY	0	0.000	0.022	15.551	0.028	0.028	0.000	0.000	0.000	0.000
91	A	277	TYR	0	-0.039	-0.012	8.172	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	278	PRO	0	0.002	-0.012	12.423	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	279	LEU	0	0.000	0.010	8.693	0.101	0.101	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:186:SER)