FMO DATABASE

FMODB ID: 9GKL2

Calculation Name: 1KVE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KVE

Chain ID: A

ChEMBL ID:

UniProt ID: P19972

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-258072.463088
FMO2-HF: Nuclear repulsion	235512.681042
FMO2-HF: Total energy	-22559.782046
FMO2-MP2: Total energy	-22624.335901

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:19:TRP)

Summations of interaction energy for fragment #1(A:19:TRP)

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.
-6.178	-1.301	0.993	-2.015	-3.855	0.001

Interaction energy analysis for fragmet #1(A:19:TRP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.004

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	21	LEU	0	0.072	0.039	3.819	-1.454	0.898	-0.027	-1.201	-1.124	0.004
4	A	22	ARG	1	0.962	0.985	6.706	-0.851	-0.851	0.000	0.000	0.000	0.000
5	A	23	TRP	0	0.005	0.006	9.652	-0.026	-0.026	0.000	0.000	0.000	0.000
6	A	24	ARG	1	0.980	0.971	12.864	-0.273	-0.273	0.000	0.000	0.000	0.000
7	A	25	MET	0	0.006	0.013	16.615	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	26	GLN	0	-0.029	-0.009	19.310	0.019	0.019	0.000	0.000	0.000	0.000
9	A	27	LYS	1	0.989	0.981	21.103	-0.072	-0.072	0.000	0.000	0.000	0.000
10	A	28	SER	0	0.033	0.021	22.835	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	29	THR	0	-0.049	-0.029	24.527	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	30	THR	0	0.059	0.026	26.493	0.002	0.002	0.000	0.000	0.000	0.000
13	A	31	ILE	0	-0.006	0.001	28.525	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	32	ALA	0	0.046	0.021	27.488	0.000	0.000	0.000	0.000	0.000	0.000
15	A	33	ALA	0	-0.039	-0.013	28.880	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	34	ILE	0	-0.009	0.001	23.782	0.002	0.002	0.000	0.000	0.000	0.000
17	A	35	ALA	0	-0.011	-0.006	27.504	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	36	GLY	0	0.053	0.029	26.385	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	37	CYS	0	-0.099	-0.048	18.785	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	38	SER	0	0.024	-0.001	25.132	0.000	0.000	0.000	0.000	0.000	0.000
21	A	39	GLY	0	0.015	0.009	22.395	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	40	ALA	0	-0.014	0.003	20.670	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	41	ALA	0	-0.030	-0.017	16.441	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	42	THR	0	0.024	-0.001	18.500	0.007	0.007	0.000	0.000	0.000	0.000
25	A	43	PHE	0	0.022	0.021	12.849	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	44	GLY	0	0.019	-0.010	13.924	0.020	0.020	0.000	0.000	0.000	0.000
27	A	45	GLY	0	-0.002	0.002	14.607	0.029	0.029	0.000	0.000	0.000	0.000
28	A	46	LEU	0	-0.053	-0.010	15.789	0.028	0.028	0.000	0.000	0.000	0.000
29	A	47	ALA	0	0.018	0.007	19.371	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	48	GLY	0	0.039	0.027	21.431	0.007	0.007	0.000	0.000	0.000	0.000
31	A	49	GLY	0	0.003	-0.017	22.469	0.007	0.007	0.000	0.000	0.000	0.000
32	A	50	ILE	0	0.060	0.020	23.214	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	51	VAL	0	0.031	0.011	18.990	0.000	0.000	0.000	0.000	0.000	0.000
34	A	52	GLY	0	0.073	0.046	18.768	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	54	ILE	0	0.010	0.008	17.004	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	55	ALA	0	-0.002	0.000	14.539	0.004	0.004	0.000	0.000	0.000	0.000
37	A	56	ALA	0	-0.006	-0.011	14.195	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	57	GLY	0	0.024	0.017	15.762	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	58	ILE	0	-0.020	-0.022	10.958	0.007	0.007	0.000	0.000	0.000	0.000
40	A	59	LEU	0	-0.019	-0.003	9.840	0.020	0.020	0.000	0.000	0.000	0.000
41	A	60	ALA	0	0.027	0.022	11.445	0.030	0.030	0.000	0.000	0.000	0.000
42	A	61	ILE	0	-0.018	-0.001	11.782	0.002	0.002	0.000	0.000	0.000	0.000
43	A	62	LEU	0	-0.048	-0.042	6.634	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	63	GLN	0	0.034	0.018	8.113	0.068	0.068	0.000	0.000	0.000	0.000
45	A	64	GLY	0	-0.023	-0.002	10.146	-0.041	-0.041	0.000	0.000	0.000	0.000
46	A	65	PHE	0	-0.042	-0.047	8.089	-0.038	-0.038	0.000	0.000	0.000	0.000
47	A	66	GLU	-1	-0.875	-0.923	6.253	0.061	0.061	0.000	0.000	0.000	0.000
48	A	67	VAL	0	-0.024	-0.010	6.990	-0.239	-0.239	0.000	0.000	0.000	0.000
49	A	68	ASN	0	-0.013	-0.018	9.333	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	69	TRP	0	-0.009	0.012	2.748	-3.206	-0.681	1.020	-0.814	-2.731	-0.003
51	A	70	HIS	0	-0.041	-0.008	5.010	-0.351	-0.351	0.000	0.000	0.000	0.000
52	A	71	ASN	0	-0.064	-0.032	7.147	0.028	0.028	0.000	0.000	0.000	0.000
53	A	72	GLY	0	0.020	0.024	9.646	0.079	0.079	0.000	0.000	0.000	0.000
54	A	73	GLY	0	-0.028	-0.030	11.279	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	74	GLY	0	0.006	-0.003	11.820	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	75	GLY	0	-0.035	-0.024	13.884	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	76	ASP	-1	-0.901	-0.932	15.181	0.017	0.017	0.000	0.000	0.000	0.000
58	A	77	ARG	1	0.854	0.928	12.561	0.100	0.100	0.000	0.000	0.000	0.000
59	A	78	SER	0	-0.025	-0.017	16.545	0.011	0.011	0.000	0.000	0.000	0.000
60	A	79	ASN	0	0.034	0.002	17.702	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	80	PRO	0	-0.004	0.011	19.799	0.010	0.010	0.000	0.000	0.000	0.000
62	A	81	VAL	0	0.028	0.024	20.469	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:TRP)