FMO DATABASE

FMODB ID: VQ2V1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-623008.57653
FMO2-HF: Nuclear repulsion	587170.901016
FMO2-HF: Total energy	-35837.675514
FMO2-MP2: Total energy	-35940.031637

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.
-15.712	-11.022	7.827	-5.358	-7.155	0.032

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 : 0.091 / q_NPA : 0.048

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	2.739	-4.069	-0.729	0.786	-1.770	-2.356	0.013
4	A	189	ALA	0	0.037	0.019	2.109	-8.048	-8.312	7.004	-3.094	-3.646	0.019
5	A	190	VAL	0	0.026	0.001	3.232	-1.338	-0.405	0.031	-0.352	-0.611	0.001
6	A	191	GLY	0	-0.012	0.003	5.572	0.222	0.222	0.000	0.000	0.000	0.000
7	A	192	LEU	0	0.004	0.003	6.857	-0.126	-0.126	0.000	0.000	0.000	0.000
8	A	193	ALA	0	0.014	0.009	7.635	-0.046	-0.046	0.000	0.000	0.000	0.000
9	A	194	ALA	0	-0.041	-0.017	9.332	0.064	0.064	0.000	0.000	0.000	0.000
10	A	195	HIS	0	-0.037	-0.028	11.432	0.042	0.042	0.000	0.000	0.000	0.000
11	A	196	LEU	0	0.026	0.003	10.677	0.015	0.015	0.000	0.000	0.000	0.000
12	A	197	ARG	1	0.863	0.928	13.058	0.379	0.379	0.000	0.000	0.000	0.000
13	A	198	GLN	0	-0.074	-0.036	15.325	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	199	ILE	0	-0.050	-0.016	16.422	0.019	0.019	0.000	0.000	0.000	0.000
15	A	200	GLY	0	0.009	0.017	18.398	0.013	0.013	0.000	0.000	0.000	0.000
16	A	201	GLY	0	-0.056	-0.023	16.707	0.011	0.011	0.000	0.000	0.000	0.000
17	A	202	THR	0	-0.025	-0.019	16.209	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	203	MET	0	-0.072	-0.012	14.590	0.000	0.000	0.000	0.000	0.000	0.000
19	A	204	TYR	0	0.039	0.001	17.288	0.000	0.000	0.000	0.000	0.000	0.000
20	A	205	GLY	0	0.042	-0.017	19.294	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	206	ALA	0	0.005	0.008	20.332	0.011	0.011	0.000	0.000	0.000	0.000
22	A	207	TYR	0	-0.031	-0.025	19.271	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	208	TRP	0	0.009	0.005	19.657	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	209	CYS	0	-0.059	-0.005	20.551	0.008	0.008	0.000	0.000	0.000	0.000
25	A	210	PRO	0	0.074	0.019	19.031	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	211	HIS	0	0.091	0.051	17.398	-0.028	-0.028	0.000	0.000	0.000	0.000
27	A	212	CYS	0	-0.065	-0.006	15.911	-0.032	-0.032	0.000	0.000	0.000	0.000
28	A	213	GLN	0	-0.009	-0.008	14.580	-0.038	-0.038	0.000	0.000	0.000	0.000
29	A	214	ASP	-1	-0.829	-0.913	13.059	-0.229	-0.229	0.000	0.000	0.000	0.000
30	A	215	GLN	0	-0.035	-0.026	10.552	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	216	LYS	1	0.885	0.943	10.051	0.151	0.151	0.000	0.000	0.000	0.000
32	A	217	GLU	-1	-0.902	-0.955	8.670	-0.326	-0.326	0.000	0.000	0.000	0.000
33	A	218	LEU	0	-0.082	-0.024	7.187	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	219	PHE	0	-0.055	-0.032	4.649	-1.010	-0.844	-0.001	-0.006	-0.158	0.000
35	A	220	GLY	0	0.032	0.021	4.352	-0.682	-0.555	-0.001	-0.023	-0.103	0.000
36	A	221	ALA	0	0.033	-0.004	5.774	-0.144	-0.144	0.000	0.000	0.000	0.000
37	A	222	ALA	0	-0.032	-0.005	3.715	-0.154	-0.043	0.000	-0.031	-0.079	0.000
38	A	223	PHE	0	0.012	-0.021	5.743	0.310	0.310	0.000	0.000	0.000	0.000
39	A	224	ASP	-1	-0.896	-0.927	9.023	-0.458	-0.458	0.000	0.000	0.000	0.000
40	A	225	GLN	0	-0.033	-0.017	8.583	0.263	0.263	0.000	0.000	0.000	0.000
41	A	226	VAL	0	-0.033	-0.010	9.856	0.082	0.082	0.000	0.000	0.000	0.000
42	A	227	PRO	0	0.002	0.014	12.621	0.018	0.018	0.000	0.000	0.000	0.000
43	A	228	TYR	0	-0.007	-0.042	15.625	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	229	VAL	0	0.018	0.016	17.569	0.011	0.011	0.000	0.000	0.000	0.000
45	A	230	GLU	-1	-0.760	-0.873	21.059	-0.167	-0.167	0.000	0.000	0.000	0.000
46	A	231	CYS	0	-0.048	-0.018	22.401	0.006	0.006	0.000	0.000	0.000	0.000
47	A	232	SER	0	0.003	0.010	24.498	0.013	0.013	0.000	0.000	0.000	0.000
48	A	233	PRO	0	0.046	0.019	25.936	0.000	0.000	0.000	0.000	0.000	0.000
49	A	234	ASN	0	-0.029	-0.023	26.892	0.002	0.002	0.000	0.000	0.000	0.000
50	A	235	GLY	0	0.019	0.031	27.388	0.006	0.006	0.000	0.000	0.000	0.000
51	A	236	PRO	0	0.001	-0.009	27.200	0.002	0.002	0.000	0.000	0.000	0.000
52	A	237	GLY	0	-0.009	-0.003	29.387	0.004	0.004	0.000	0.000	0.000	0.000
53	A	238	THR	0	-0.065	-0.024	30.777	0.003	0.003	0.000	0.000	0.000	0.000
54	A	239	PRO	0	-0.007	-0.015	31.824	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	240	GLN	0	-0.008	0.023	27.866	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	241	ALA	0	0.006	-0.006	27.558	0.005	0.005	0.000	0.000	0.000	0.000
57	A	242	GLN	0	0.018	0.000	29.565	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	243	GLU	-1	-0.896	-0.952	27.096	-0.118	-0.118	0.000	0.000	0.000	0.000
59	A	245	THR	0	-0.001	-0.009	27.733	0.000	0.000	0.000	0.000	0.000	0.000
60	A	246	GLU	-1	-0.929	-0.963	31.203	-0.064	-0.064	0.000	0.000	0.000	0.000
61	A	247	ALA	0	-0.063	-0.012	26.755	0.002	0.002	0.000	0.000	0.000	0.000
62	A	248	GLY	0	-0.012	0.003	28.365	0.000	0.000	0.000	0.000	0.000	0.000
63	A	249	ILE	0	-0.070	-0.035	23.902	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	250	THR	0	0.019	0.001	27.036	0.003	0.003	0.000	0.000	0.000	0.000
65	A	251	SER	0	-0.057	-0.025	24.409	0.001	0.001	0.000	0.000	0.000	0.000
66	A	252	TYR	0	-0.015	0.005	21.288	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	253	PRO	0	0.029	-0.007	16.375	0.007	0.007	0.000	0.000	0.000	0.000
68	A	254	THR	0	-0.042	-0.041	19.272	0.016	0.016	0.000	0.000	0.000	0.000
69	A	255	TRP	0	0.003	-0.011	11.797	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	256	ILE	0	0.011	0.008	18.745	0.020	0.020	0.000	0.000	0.000	0.000
71	A	257	ILE	0	0.013	0.006	15.178	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	258	ASN	0	0.025	0.009	18.877	0.008	0.008	0.000	0.000	0.000	0.000
73	A	259	GLY	0	0.013	0.006	21.936	0.009	0.009	0.000	0.000	0.000	0.000
74	A	260	ARG	1	0.920	0.975	21.813	0.063	0.063	0.000	0.000	0.000	0.000
75	A	261	THR	0	0.043	0.016	21.796	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	262	TYR	0	-0.065	-0.033	18.332	0.014	0.014	0.000	0.000	0.000	0.000
77	A	263	THR	0	0.041	0.031	19.497	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	264	GLY	0	0.048	0.033	19.244	0.007	0.007	0.000	0.000	0.000	0.000
79	A	265	VAL	0	0.023	0.006	13.330	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	266	ARG	1	0.805	0.893	13.421	0.190	0.190	0.000	0.000	0.000	0.000
81	A	267	SER	0	0.029	-0.006	9.644	-0.035	-0.035	0.000	0.000	0.000	0.000
82	A	268	LEU	0	0.054	0.017	3.551	-0.287	-0.010	0.008	-0.082	-0.202	-0.001
83	A	269	GLU	-1	-0.829	-0.897	7.164	-0.324	-0.324	0.000	0.000	0.000	0.000
84	A	270	ALA	0	-0.030	-0.015	9.548	0.080	0.080	0.000	0.000	0.000	0.000
85	A	271	LEU	0	0.021	0.009	9.987	0.045	0.045	0.000	0.000	0.000	0.000
86	A	272	ALA	0	0.003	0.026	9.252	0.028	0.028	0.000	0.000	0.000	0.000
87	A	273	VAL	0	0.000	0.003	11.288	0.012	0.012	0.000	0.000	0.000	0.000
88	A	274	ALA	0	-0.056	-0.018	14.593	0.005	0.005	0.000	0.000	0.000	0.000
89	A	275	SER	0	-0.048	-0.055	13.008	0.011	0.011	0.000	0.000	0.000	0.000
90	A	276	GLY	0	-0.006	0.017	15.633	0.001	0.001	0.000	0.000	0.000	0.000
91	A	277	TYR	0	-0.040	-0.011	8.302	-0.068	-0.068	0.000	0.000	0.000	0.000
92	A	278	PRO	0	-0.002	-0.014	12.467	0.010	0.010	0.000	0.000	0.000	0.000
93	A	279	LEU	0	0.000	0.010	8.549	0.087	0.087	0.000	0.000	0.000	0.000

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