FMO DATABASE

FMODB ID: 2KZGR

Calculation Name: 1KPT-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KPT

Chain ID: A

ChEMBL ID:

UniProt ID: Q90121

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	100
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-746738.930679
FMO2-HF: Nuclear repulsion	705246.027296
FMO2-HF: Total energy	-41492.903383
FMO2-MP2: Total energy	-41604.980843

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:1:LEU )

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

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.
-1.735	10.56	14.399	-11.857	-14.836	-0.135

Interaction energy analysis for fragmet #1(A:1:LEU )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.738 / q_NPA : 0.869

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	3	ILE	0	0.038	0.027	2.870	-4.743	-1.628	0.338	-1.674	-1.778	-0.010
4	A	4	ASN	0	-0.090	-0.045	2.497	1.475	3.403	1.425	-0.929	-2.424	-0.010
5	A	78	CYS	0	-0.026	-0.010	4.732	1.655	1.701	0.000	-0.007	-0.038	0.000
6	A	6	ARG	1	0.933	0.976	2.600	40.201	42.004	1.276	-0.579	-2.500	-0.003
7	A	7	GLY	0	0.060	0.018	6.383	-0.037	-0.037	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.004	0.005	9.079	0.519	0.519	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.074	0.019	12.167	-0.141	-0.141	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.021	0.019	14.600	0.837	0.837	0.000	0.000	0.000	0.000
11	A	81	CYS	0	-0.071	-0.031	10.604	1.059	1.059	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.020	-0.012	15.196	0.383	0.383	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.004	0.007	16.663	0.538	0.538	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.009	0.015	18.679	0.614	0.614	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.053	0.035	20.273	-0.256	-0.256	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.026	0.002	22.362	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	17	ASN	0	0.031	0.014	18.444	-0.949	-0.949	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.021	-0.003	18.176	0.233	0.233	0.000	0.000	0.000	0.000
19	A	19	MET	0	0.037	0.038	12.040	0.301	0.301	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.004	0.000	17.083	-0.048	-0.048	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.973	0.992	20.059	11.657	11.657	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.008	0.002	16.878	0.317	0.317	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.928	0.966	18.059	14.011	14.011	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.882	-0.952	19.436	-12.073	-12.073	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.059	-0.034	22.343	0.185	0.185	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.009	-0.007	19.747	0.263	0.263	0.000	0.000	0.000	0.000
27	A	67	CYS	0	-0.088	-0.035	16.573	-0.510	-0.510	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.042	0.041	23.260	0.382	0.382	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.031	-0.017	25.203	0.581	0.581	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.028	-0.036	23.443	-0.477	-0.477	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.025	0.028	25.119	-0.180	-0.180	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.028	-0.001	23.407	0.252	0.252	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.000	-0.012	22.264	-0.401	-0.401	0.000	0.000	0.000	0.000
34	A	34	TRP	0	-0.050	-0.034	16.980	-0.027	-0.027	0.000	0.000	0.000	0.000
35	A	60	CYS	0	0.021	0.016	17.468	-0.966	-0.966	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.006	-0.018	15.950	-0.245	-0.245	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.016	-0.005	15.885	0.793	0.793	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.841	-0.907	17.346	-12.766	-12.766	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.830	0.907	17.655	12.792	12.792	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.849	0.922	19.576	13.388	13.388	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.020	0.035	19.199	0.469	0.469	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.872	0.922	19.184	11.156	11.156	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.011	0.007	20.509	0.645	0.645	0.000	0.000	0.000	0.000
44	A	105	CYS	-1	-0.891	-0.937	21.549	-12.396	-12.396	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.053	0.039	24.027	0.208	0.208	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.030	-0.028	25.329	0.284	0.284	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.024	0.012	26.473	-0.038	-0.038	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.052	-0.012	21.129	-0.284	-0.284	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.021	0.002	20.324	0.132	0.132	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.029	0.040	15.387	-0.625	-0.625	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.015	-0.025	16.186	0.813	0.813	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.018	0.016	14.483	-1.112	-1.112	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.018	-0.016	11.803	1.193	1.193	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.054	0.047	12.941	-1.697	-1.697	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.013	-0.001	9.028	0.377	0.377	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.010	0.004	8.422	-1.790	-1.790	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.029	0.018	10.688	-0.517	-0.517	0.000	0.000	0.000	0.000
58	A	58	ASN	0	0.023	0.016	13.788	0.611	0.611	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.048	-0.022	15.953	1.809	1.809	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.005	0.003	15.212	-0.281	-0.281	0.000	0.000	0.000	0.000
61	A	62	SER	0	0.026	0.009	19.050	0.823	0.823	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.083	0.025	20.061	-0.698	-0.698	0.000	0.000	0.000	0.000
63	A	64	THR	0	0.010	0.005	21.090	-0.194	-0.194	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.878	-0.941	17.246	-16.941	-16.941	0.000	0.000	0.000	0.000
65	A	66	ALA	0	0.021	0.012	16.240	-1.109	-1.109	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.986	0.997	13.990	19.911	19.911	0.000	0.000	0.000	0.000
67	A	69	HIS	0	-0.058	-0.039	11.723	0.325	0.325	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.017	0.000	12.966	-0.857	-0.857	0.000	0.000	0.000	0.000
69	A	71	THR	0	-0.027	-0.018	14.986	0.511	0.511	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.059	-0.027	11.917	1.673	1.673	0.000	0.000	0.000	0.000
71	A	73	LEU	0	0.000	-0.003	8.652	-0.428	-0.428	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.051	-0.017	12.259	0.310	0.310	0.000	0.000	0.000	0.000
73	A	75	ASN	0	-0.029	-0.032	15.183	0.828	0.828	0.000	0.000	0.000	0.000
74	A	76	HIS	0	-0.008	0.005	7.252	0.853	0.853	0.000	0.000	0.000	0.000
75	A	77	GLY	0	0.020	0.019	11.889	-0.238	-0.238	0.000	0.000	0.000	0.000
76	A	79	ARG	1	0.875	0.926	12.174	14.834	14.834	0.000	0.000	0.000	0.000
77	A	80	VAL	0	-0.050	-0.032	14.002	0.741	0.741	0.000	0.000	0.000	0.000
78	A	82	GLY	0	0.048	0.026	7.669	-0.105	-0.105	0.000	0.000	0.000	0.000
79	A	83	SER	0	-0.024	-0.015	5.353	2.079	2.079	0.000	0.000	0.000	0.000
80	A	84	ASP	-1	-0.763	-0.890	6.208	-32.257	-32.257	0.000	0.000	0.000	0.000
81	A	85	PRO	0	-0.031	-0.007	5.302	0.921	0.921	0.000	0.000	0.000	0.000
82	A	86	LEU	0	-0.008	-0.001	7.652	2.686	2.686	0.000	0.000	0.000	0.000
83	A	87	TYR	0	-0.001	0.006	10.345	2.182	2.182	0.000	0.000	0.000	0.000
84	A	88	ALA	0	0.055	0.013	9.818	-3.124	-3.124	0.000	0.000	0.000	0.000
85	A	89	GLY	0	0.010	0.014	8.439	-0.295	-0.295	0.000	0.000	0.000	0.000
86	A	90	ASN	0	-0.053	-0.028	6.879	-2.079	-2.079	0.000	0.000	0.000	0.000
87	A	91	ASP	-1	-0.788	-0.886	1.867	-124.716	-121.078	9.678	-7.795	-5.522	-0.105
88	A	92	VAL	0	0.012	-0.014	2.258	11.419	12.978	1.682	-0.857	-2.384	-0.007
89	A	93	SER	0	-0.061	-0.026	4.393	12.170	12.376	0.000	-0.016	-0.190	0.000
90	A	94	ARG	1	0.917	0.943	6.141	39.287	39.287	0.000	0.000	0.000	0.000
91	A	95	GLY	0	0.022	0.022	8.328	3.712	3.712	0.000	0.000	0.000	0.000
92	A	96	GLN	0	-0.028	-0.033	5.583	-4.859	-4.859	0.000	0.000	0.000	0.000
93	A	97	LEU	0	-0.004	0.017	8.930	2.676	2.676	0.000	0.000	0.000	0.000
94	A	98	THR	0	-0.015	-0.019	8.472	-2.496	-2.496	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.044	0.025	10.222	2.101	2.101	0.000	0.000	0.000	0.000
96	A	100	ASN	0	0.058	0.003	10.575	-0.490	-0.490	0.000	0.000	0.000	0.000
97	A	101	TYR	0	0.017	-0.007	12.403	0.928	0.928	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.032	-0.009	14.946	-0.604	-0.604	0.000	0.000	0.000	0.000
99	A	103	ASN	0	-0.018	-0.021	17.644	0.791	0.791	0.000	0.000	0.000	0.000
100	A	104	SER	0	0.065	0.036	20.830	0.437	0.437	0.000	0.000	0.000	0.000

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