FMO DATABASE

FMODB ID: 824NY

Calculation Name: 1K78-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K78

Chain ID: A

ChEMBL ID:

UniProt ID: P27577

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-837411.40257
FMO2-HF: Nuclear repulsion	789205.59169
FMO2-HF: Total energy	-48205.810879
FMO2-MP2: Total energy	-48346.758247

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:GLY)

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

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.
-1.054	1.584	2.783	-2.417	-3.005	-0.022

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.001

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	21	ASN	0	-0.026	-0.004	3.806	1.226	2.084	-0.010	-0.320	-0.528	0.000
4	A	22	GLN	0	0.087	0.011	6.211	0.183	0.183	0.000	0.000	0.000	0.000
5	A	23	LEU	0	-0.068	-0.007	9.530	0.174	0.174	0.000	0.000	0.000	0.000
6	A	24	GLY	0	0.029	0.019	8.823	0.182	0.182	0.000	0.000	0.000	0.000
7	A	25	GLY	0	-0.022	-0.015	8.181	0.160	0.160	0.000	0.000	0.000	0.000
8	A	26	VAL	0	0.017	0.019	3.788	-1.261	-1.139	0.000	-0.058	-0.065	0.000
9	A	27	PHE	0	-0.062	-0.033	2.958	0.510	1.806	0.355	-0.687	-0.964	-0.004
10	A	28	VAL	0	0.055	0.024	2.202	-5.227	-4.938	2.439	-1.333	-1.395	-0.018
11	A	29	ASN	0	0.013	-0.008	4.155	0.551	0.624	-0.001	-0.019	-0.053	0.000
12	A	30	GLY	0	0.056	0.040	6.131	0.246	0.246	0.000	0.000	0.000	0.000
13	A	31	ARG	1	0.898	0.949	8.340	0.533	0.533	0.000	0.000	0.000	0.000
14	A	32	PRO	0	-0.038	-0.018	9.702	-0.127	-0.127	0.000	0.000	0.000	0.000
15	A	33	LEU	0	0.020	0.014	9.613	-0.053	-0.053	0.000	0.000	0.000	0.000
16	A	34	PRO	0	0.083	0.027	9.817	0.120	0.120	0.000	0.000	0.000	0.000
17	A	35	ASP	-1	-0.825	-0.932	12.975	-0.285	-0.285	0.000	0.000	0.000	0.000
18	A	36	VAL	0	0.043	0.028	14.860	0.002	0.002	0.000	0.000	0.000	0.000
19	A	37	VAL	0	0.010	0.005	11.982	0.012	0.012	0.000	0.000	0.000	0.000
20	A	38	ARG	1	0.812	0.898	14.344	0.443	0.443	0.000	0.000	0.000	0.000
21	A	39	GLN	0	0.029	0.005	17.115	0.020	0.020	0.000	0.000	0.000	0.000
22	A	40	ARG	1	0.973	0.996	17.931	0.252	0.252	0.000	0.000	0.000	0.000
23	A	41	ILE	0	-0.009	-0.002	15.181	0.004	0.004	0.000	0.000	0.000	0.000
24	A	42	VAL	0	0.013	-0.001	19.465	0.016	0.016	0.000	0.000	0.000	0.000
25	A	43	GLU	-1	-0.868	-0.915	22.642	-0.153	-0.153	0.000	0.000	0.000	0.000
26	A	44	LEU	0	0.007	-0.008	19.983	0.009	0.009	0.000	0.000	0.000	0.000
27	A	45	ALA	0	-0.020	-0.010	23.554	0.011	0.011	0.000	0.000	0.000	0.000
28	A	46	HIS	0	-0.042	-0.006	25.136	0.012	0.012	0.000	0.000	0.000	0.000
29	A	47	GLN	0	-0.076	-0.054	26.928	0.009	0.009	0.000	0.000	0.000	0.000
30	A	48	GLY	0	0.019	0.027	28.088	0.009	0.009	0.000	0.000	0.000	0.000
31	A	49	VAL	0	-0.070	-0.026	22.835	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	50	ARG	1	1.007	0.986	24.666	0.185	0.185	0.000	0.000	0.000	0.000
33	A	51	PRO	0	0.094	0.041	21.663	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	52	CYS	0	-0.046	-0.014	19.978	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	53	ASP	-1	-0.852	-0.942	19.508	-0.257	-0.257	0.000	0.000	0.000	0.000
36	A	54	ILE	0	0.023	0.029	17.907	-0.029	-0.029	0.000	0.000	0.000	0.000
37	A	55	SER	0	-0.093	-0.050	14.928	-0.031	-0.031	0.000	0.000	0.000	0.000
38	A	56	ARG	1	0.941	0.947	14.994	0.209	0.209	0.000	0.000	0.000	0.000
39	A	57	GLN	0	-0.020	-0.001	15.927	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	58	LEU	0	-0.009	-0.008	14.483	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	59	ARG	1	0.890	0.955	10.801	0.458	0.458	0.000	0.000	0.000	0.000
42	A	60	VAL	0	0.016	0.013	10.386	-0.298	-0.298	0.000	0.000	0.000	0.000
43	A	61	SER	0	0.038	0.021	11.019	0.131	0.131	0.000	0.000	0.000	0.000
44	A	62	HIS	0	0.116	0.030	12.613	0.020	0.020	0.000	0.000	0.000	0.000
45	A	63	GLY	0	0.045	0.034	15.364	0.039	0.039	0.000	0.000	0.000	0.000
46	A	64	CYS	0	-0.052	-0.021	12.165	0.062	0.062	0.000	0.000	0.000	0.000
47	A	65	VAL	0	0.055	0.023	15.050	0.040	0.040	0.000	0.000	0.000	0.000
48	A	66	SER	0	-0.010	0.001	17.453	0.046	0.046	0.000	0.000	0.000	0.000
49	A	67	LYS	1	0.927	0.962	17.189	0.321	0.321	0.000	0.000	0.000	0.000
50	A	68	ILE	0	-0.048	-0.029	14.992	0.027	0.027	0.000	0.000	0.000	0.000
51	A	69	LEU	0	0.025	0.020	19.390	0.026	0.026	0.000	0.000	0.000	0.000
52	A	70	GLY	0	0.025	0.022	22.474	0.022	0.022	0.000	0.000	0.000	0.000
53	A	71	ARG	1	0.930	0.956	19.523	0.275	0.275	0.000	0.000	0.000	0.000
54	A	72	TYR	0	0.001	0.001	23.410	0.015	0.015	0.000	0.000	0.000	0.000
55	A	73	TYR	0	0.017	-0.011	24.998	0.011	0.011	0.000	0.000	0.000	0.000
56	A	74	GLU	-1	-0.922	-0.937	27.338	-0.135	-0.135	0.000	0.000	0.000	0.000
57	A	75	THR	0	-0.098	-0.035	26.145	0.009	0.009	0.000	0.000	0.000	0.000
58	A	76	GLY	0	0.047	0.039	27.656	0.009	0.009	0.000	0.000	0.000	0.000
59	A	77	SER	0	-0.030	-0.023	24.185	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	78	ILE	0	0.072	0.029	20.161	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	79	LYS	1	0.876	0.935	19.538	0.174	0.174	0.000	0.000	0.000	0.000
62	A	80	PRO	0	-0.057	-0.014	16.346	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	81	GLY	0	0.017	0.003	18.496	0.028	0.028	0.000	0.000	0.000	0.000
64	A	82	VAL	0	0.011	0.000	19.088	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	83	ILE	0	0.001	-0.007	14.379	0.002	0.002	0.000	0.000	0.000	0.000
66	A	84	GLY	0	-0.003	0.002	18.671	0.017	0.017	0.000	0.000	0.000	0.000
67	A	85	GLY	0	0.012	0.013	19.979	0.000	0.000	0.000	0.000	0.000	0.000
68	A	86	SER	0	0.007	-0.004	23.274	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	87	LYS	1	0.941	0.981	26.094	0.066	0.066	0.000	0.000	0.000	0.000
70	A	88	PRO	0	-0.004	-0.020	29.720	0.003	0.003	0.000	0.000	0.000	0.000
71	A	89	LYS	1	0.999	1.007	29.449	0.022	0.022	0.000	0.000	0.000	0.000
72	A	90	VAL	0	0.120	0.060	34.075	0.000	0.000	0.000	0.000	0.000	0.000
73	A	91	ALA	0	-0.037	-0.005	35.826	0.000	0.000	0.000	0.000	0.000	0.000
74	A	92	THR	0	-0.037	-0.025	37.422	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	93	PRO	0	0.041	0.003	38.029	0.002	0.002	0.000	0.000	0.000	0.000
76	A	94	LYS	1	1.048	1.020	40.720	0.024	0.024	0.000	0.000	0.000	0.000
77	A	95	VAL	0	0.019	0.019	41.425	0.001	0.001	0.000	0.000	0.000	0.000
78	A	96	VAL	0	-0.030	-0.022	39.186	0.002	0.002	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.944	-0.970	42.477	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	98	LYS	1	0.933	0.972	45.629	0.017	0.017	0.000	0.000	0.000	0.000
81	A	99	ILE	0	-0.014	0.001	42.525	0.002	0.002	0.000	0.000	0.000	0.000
82	A	100	ALA	0	-0.026	-0.013	45.823	0.001	0.001	0.000	0.000	0.000	0.000
83	A	101	GLU	-1	-0.906	-0.956	47.469	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	102	TYR	0	-0.080	-0.106	49.168	0.001	0.001	0.000	0.000	0.000	0.000
85	A	103	LYS	1	0.917	0.968	47.597	0.006	0.006	0.000	0.000	0.000	0.000
86	A	104	ARG	1	0.948	0.967	50.783	0.016	0.016	0.000	0.000	0.000	0.000
87	A	105	GLN	0	0.006	0.025	52.973	0.001	0.001	0.000	0.000	0.000	0.000
88	A	106	ASN	0	-0.014	-0.004	54.250	0.000	0.000	0.000	0.000	0.000	0.000
89	A	107	PRO	0	0.031	0.019	52.492	0.001	0.001	0.000	0.000	0.000	0.000
90	A	108	THR	0	0.001	-0.015	52.124	0.000	0.000	0.000	0.000	0.000	0.000
91	A	109	MET	0	-0.032	0.023	51.421	0.000	0.000	0.000	0.000	0.000	0.000
92	A	110	PHE	0	-0.005	-0.025	49.789	0.000	0.000	0.000	0.000	0.000	0.000
93	A	111	ALA	0	-0.003	-0.018	44.770	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	112	TRP	0	-0.016	-0.017	46.879	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	113	GLU	-1	-0.767	-0.862	48.054	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	114	ILE	0	-0.019	-0.012	46.407	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	115	ARG	1	0.849	0.916	44.908	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	116	ASP	-1	-0.799	-0.911	47.110	0.000	0.000	0.000	0.000	0.000	0.000
99	A	117	ARG	1	0.844	0.929	50.507	0.008	0.008	0.000	0.000	0.000	0.000
100	A	118	LEU	0	-0.009	-0.013	44.693	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	119	LEU	0	-0.018	0.003	46.409	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	120	ALA	0	-0.011	-0.002	49.670	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	121	GLU	-1	-0.810	-0.856	51.868	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	122	ARG	1	0.903	0.951	49.971	0.008	0.008	0.000	0.000	0.000	0.000
105	A	123	VAL	0	-0.032	-0.005	45.613	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	124	CYS	0	-0.115	-0.070	43.945	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	125	ASP	-1	-0.763	-0.876	43.815	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	126	ASN	0	-0.026	-0.039	44.476	0.001	0.001	0.000	0.000	0.000	0.000
109	A	127	ASP	-1	-0.887	-0.932	40.019	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	128	THR	0	-0.114	-0.048	39.543	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	129	VAL	0	-0.028	-0.009	40.505	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	130	PRO	0	-0.025	-0.012	39.364	0.001	0.001	0.000	0.000	0.000	0.000
113	A	131	SER	0	0.068	0.032	37.348	0.001	0.001	0.000	0.000	0.000	0.000
114	A	132	VAL	0	0.126	0.038	40.145	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	133	SER	0	-0.008	-0.004	37.021	0.000	0.000	0.000	0.000	0.000	0.000
116	A	134	SER	0	-0.051	-0.034	36.520	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	135	ILE	0	0.063	0.051	37.973	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	136	ASN	0	0.073	0.029	41.223	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	137	ARG	1	0.881	0.953	33.584	0.010	0.010	0.000	0.000	0.000	0.000
120	A	138	ILE	0	-0.069	-0.042	38.233	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	139	ILE	0	-0.018	-0.003	39.469	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	140	ARG	1	0.944	0.956	36.125	0.002	0.002	0.000	0.000	0.000	0.000
123	A	141	THR	0	-0.060	-0.003	35.188	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	142	LYS	1	1.002	1.005	38.274	0.027	0.027	0.000	0.000	0.000	0.000

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