FMO DATABASE

FMODB ID: J3729

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	OptAll
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	-839602.268603
FMO2-HF: Nuclear repulsion	791395.499224
FMO2-HF: Total energy	-48206.769379
FMO2-MP2: Total energy	-48347.563433

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.
-4.32	-3.879	7.958	-4.661	-3.739	-0.033

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 : 0.041 / q_NPA : 0.024

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	-0.030	-0.014	3.868	0.915	2.482	-0.011	-0.832	-0.724	0.003
4	A	22	GLN	0	0.057	0.004	6.550	0.043	0.043	0.000	0.000	0.000	0.000
5	A	23	LEU	0	-0.031	0.009	10.055	0.145	0.145	0.000	0.000	0.000	0.000
6	A	24	GLY	0	0.023	0.018	9.149	0.141	0.141	0.000	0.000	0.000	0.000
7	A	25	GLY	0	-0.001	-0.005	8.419	-0.025	-0.025	0.000	0.000	0.000	0.000
8	A	26	VAL	0	0.005	0.003	3.825	-0.882	-0.734	0.000	-0.061	-0.087	0.000
9	A	27	PHE	0	-0.078	-0.035	3.144	1.012	2.488	0.308	-0.797	-0.988	-0.005
10	A	28	VAL	0	0.055	0.026	1.906	-6.001	-8.808	7.662	-2.948	-1.907	-0.031
11	A	29	ASN	0	0.041	0.013	4.053	-0.655	-0.598	-0.001	-0.023	-0.033	0.000
12	A	30	GLY	0	0.054	0.035	6.337	0.070	0.070	0.000	0.000	0.000	0.000
13	A	31	ARG	1	0.874	0.934	7.994	-0.217	-0.217	0.000	0.000	0.000	0.000
14	A	32	PRO	0	-0.014	-0.008	9.722	-0.126	-0.126	0.000	0.000	0.000	0.000
15	A	33	LEU	0	0.035	0.028	9.630	-0.089	-0.089	0.000	0.000	0.000	0.000
16	A	34	PRO	0	0.080	0.027	9.650	0.161	0.161	0.000	0.000	0.000	0.000
17	A	35	ASP	-1	-0.783	-0.890	12.769	-0.289	-0.289	0.000	0.000	0.000	0.000
18	A	36	VAL	0	0.054	0.038	15.007	0.009	0.009	0.000	0.000	0.000	0.000
19	A	37	VAL	0	0.014	0.005	11.970	0.008	0.008	0.000	0.000	0.000	0.000
20	A	38	ARG	1	0.810	0.896	14.334	0.383	0.383	0.000	0.000	0.000	0.000
21	A	39	GLN	0	0.030	0.010	17.209	0.021	0.021	0.000	0.000	0.000	0.000
22	A	40	ARG	1	0.966	0.995	17.783	0.441	0.441	0.000	0.000	0.000	0.000
23	A	41	ILE	0	0.003	-0.009	15.058	0.010	0.010	0.000	0.000	0.000	0.000
24	A	42	VAL	0	0.022	0.007	19.396	0.024	0.024	0.000	0.000	0.000	0.000
25	A	43	GLU	-1	-0.854	-0.909	22.636	-0.222	-0.222	0.000	0.000	0.000	0.000
26	A	44	LEU	0	-0.018	-0.018	20.029	0.007	0.007	0.000	0.000	0.000	0.000
27	A	45	ALA	0	-0.016	-0.012	23.550	0.015	0.015	0.000	0.000	0.000	0.000
28	A	46	HIS	0	-0.055	-0.013	25.177	0.021	0.021	0.000	0.000	0.000	0.000
29	A	47	GLN	0	-0.071	-0.053	26.740	0.003	0.003	0.000	0.000	0.000	0.000
30	A	48	GLY	0	0.027	0.028	28.165	0.005	0.005	0.000	0.000	0.000	0.000
31	A	49	VAL	0	-0.058	-0.023	23.174	0.001	0.001	0.000	0.000	0.000	0.000
32	A	50	ARG	1	0.929	0.929	24.962	0.241	0.241	0.000	0.000	0.000	0.000
33	A	51	PRO	0	0.093	0.032	21.619	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	52	CYS	0	-0.028	-0.017	19.937	-0.037	-0.037	0.000	0.000	0.000	0.000
35	A	53	ASP	-1	-0.789	-0.861	19.748	-0.339	-0.339	0.000	0.000	0.000	0.000
36	A	54	ILE	0	0.023	0.028	18.082	-0.054	-0.054	0.000	0.000	0.000	0.000
37	A	55	SER	0	-0.097	-0.059	15.042	-0.055	-0.055	0.000	0.000	0.000	0.000
38	A	56	ARG	1	0.890	0.916	15.099	0.258	0.258	0.000	0.000	0.000	0.000
39	A	57	GLN	0	-0.007	-0.001	16.189	-0.071	-0.071	0.000	0.000	0.000	0.000
40	A	58	LEU	0	-0.024	-0.012	14.522	-0.049	-0.049	0.000	0.000	0.000	0.000
41	A	59	ARG	1	0.910	0.969	11.152	0.796	0.796	0.000	0.000	0.000	0.000
42	A	60	VAL	0	0.030	0.031	10.587	-0.291	-0.291	0.000	0.000	0.000	0.000
43	A	61	SER	0	0.054	0.030	11.156	0.120	0.120	0.000	0.000	0.000	0.000
44	A	62	HIS	0	0.089	0.027	12.795	0.034	0.034	0.000	0.000	0.000	0.000
45	A	63	GLY	0	0.055	0.037	15.828	0.036	0.036	0.000	0.000	0.000	0.000
46	A	64	CYS	0	-0.057	-0.024	11.913	0.064	0.064	0.000	0.000	0.000	0.000
47	A	65	VAL	0	0.039	0.010	15.058	0.029	0.029	0.000	0.000	0.000	0.000
48	A	66	SER	0	0.000	0.010	17.442	0.041	0.041	0.000	0.000	0.000	0.000
49	A	67	LYS	1	0.943	0.964	17.615	0.141	0.141	0.000	0.000	0.000	0.000
50	A	68	ILE	0	-0.050	-0.020	14.894	0.023	0.023	0.000	0.000	0.000	0.000
51	A	69	LEU	0	0.011	0.009	19.347	0.021	0.021	0.000	0.000	0.000	0.000
52	A	70	GLY	0	0.029	0.018	22.491	0.019	0.019	0.000	0.000	0.000	0.000
53	A	71	ARG	1	0.877	0.937	20.761	0.141	0.141	0.000	0.000	0.000	0.000
54	A	72	TYR	0	-0.007	-0.008	23.347	0.012	0.012	0.000	0.000	0.000	0.000
55	A	73	TYR	0	0.004	-0.014	24.955	0.004	0.004	0.000	0.000	0.000	0.000
56	A	74	GLU	-1	-0.908	-0.935	27.338	-0.078	-0.078	0.000	0.000	0.000	0.000
57	A	75	THR	0	-0.106	-0.062	26.175	0.012	0.012	0.000	0.000	0.000	0.000
58	A	76	GLY	0	0.057	0.050	28.205	0.005	0.005	0.000	0.000	0.000	0.000
59	A	77	SER	0	-0.025	-0.021	24.491	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	78	ILE	0	0.068	0.028	19.806	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	79	LYS	1	0.840	0.921	18.924	0.171	0.171	0.000	0.000	0.000	0.000
62	A	80	PRO	0	-0.010	-0.004	16.088	0.007	0.007	0.000	0.000	0.000	0.000
63	A	81	GLY	0	0.001	-0.002	18.246	0.017	0.017	0.000	0.000	0.000	0.000
64	A	82	VAL	0	0.033	0.013	18.573	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	83	ILE	0	-0.025	-0.015	14.283	0.009	0.009	0.000	0.000	0.000	0.000
66	A	84	GLY	0	0.024	0.016	18.203	0.016	0.016	0.000	0.000	0.000	0.000
67	A	85	GLY	0	0.002	0.005	19.836	-0.025	-0.025	0.000	0.000	0.000	0.000
68	A	86	SER	0	-0.015	-0.011	23.367	0.014	0.014	0.000	0.000	0.000	0.000
69	A	87	LYS	1	0.956	0.970	26.139	-0.084	-0.084	0.000	0.000	0.000	0.000
70	A	88	PRO	0	0.003	-0.003	29.843	0.009	0.009	0.000	0.000	0.000	0.000
71	A	89	LYS	1	1.008	1.004	29.255	-0.146	-0.146	0.000	0.000	0.000	0.000
72	A	90	VAL	0	0.101	0.059	34.892	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	91	ALA	0	-0.047	-0.014	35.691	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	92	THR	0	0.010	0.000	37.520	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	93	PRO	0	0.028	0.001	37.899	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	94	LYS	1	0.975	0.985	40.685	-0.057	-0.057	0.000	0.000	0.000	0.000
77	A	95	VAL	0	0.009	0.012	41.618	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	96	VAL	0	-0.043	-0.023	39.016	0.000	0.000	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.937	-0.962	42.403	0.031	0.031	0.000	0.000	0.000	0.000
80	A	98	LYS	1	0.853	0.916	45.559	-0.039	-0.039	0.000	0.000	0.000	0.000
81	A	99	ILE	0	-0.015	-0.006	42.537	0.000	0.000	0.000	0.000	0.000	0.000
82	A	100	ALA	0	-0.002	-0.005	45.516	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	101	GLU	-1	-0.864	-0.921	47.274	0.029	0.029	0.000	0.000	0.000	0.000
84	A	102	TYR	0	-0.039	-0.059	49.662	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	103	LYS	1	0.837	0.908	48.058	-0.045	-0.045	0.000	0.000	0.000	0.000
86	A	104	ARG	1	0.858	0.926	50.212	-0.031	-0.031	0.000	0.000	0.000	0.000
87	A	105	GLN	0	0.032	0.033	52.978	0.000	0.000	0.000	0.000	0.000	0.000
88	A	106	ASN	0	-0.016	-0.012	54.278	0.000	0.000	0.000	0.000	0.000	0.000
89	A	107	PRO	0	0.068	0.037	52.617	0.002	0.002	0.000	0.000	0.000	0.000
90	A	108	THR	0	0.018	0.004	52.173	0.002	0.002	0.000	0.000	0.000	0.000
91	A	109	MET	0	-0.032	0.018	51.716	0.002	0.002	0.000	0.000	0.000	0.000
92	A	110	PHE	0	0.031	0.018	49.982	0.002	0.002	0.000	0.000	0.000	0.000
93	A	111	ALA	0	0.002	-0.017	44.884	0.000	0.000	0.000	0.000	0.000	0.000
94	A	112	TRP	0	0.001	-0.007	46.845	0.003	0.003	0.000	0.000	0.000	0.000
95	A	113	GLU	-1	-0.784	-0.882	48.496	0.045	0.045	0.000	0.000	0.000	0.000
96	A	114	ILE	0	-0.013	-0.009	46.442	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	115	ARG	1	0.820	0.871	45.334	-0.067	-0.067	0.000	0.000	0.000	0.000
98	A	116	ASP	-1	-0.757	-0.854	47.313	0.060	0.060	0.000	0.000	0.000	0.000
99	A	117	ARG	1	0.837	0.910	50.735	-0.040	-0.040	0.000	0.000	0.000	0.000
100	A	118	LEU	0	-0.023	-0.013	44.891	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	119	LEU	0	-0.026	0.000	46.823	0.000	0.000	0.000	0.000	0.000	0.000
102	A	120	ALA	0	-0.018	-0.008	50.016	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	121	GLU	-1	-0.784	-0.872	52.004	0.037	0.037	0.000	0.000	0.000	0.000
104	A	122	ARG	1	0.927	0.970	50.383	-0.046	-0.046	0.000	0.000	0.000	0.000
105	A	123	VAL	0	-0.003	0.016	45.986	0.000	0.000	0.000	0.000	0.000	0.000
106	A	124	CYS	0	-0.108	-0.065	42.781	0.001	0.001	0.000	0.000	0.000	0.000
107	A	125	ASP	-1	-0.732	-0.832	44.307	0.065	0.065	0.000	0.000	0.000	0.000
108	A	126	ASN	0	0.002	-0.028	44.801	0.001	0.001	0.000	0.000	0.000	0.000
109	A	127	ASP	-1	-0.900	-0.936	40.939	0.088	0.088	0.000	0.000	0.000	0.000
110	A	128	THR	0	-0.099	-0.079	39.948	0.007	0.007	0.000	0.000	0.000	0.000
111	A	129	VAL	0	-0.022	0.002	41.163	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	130	PRO	0	-0.057	-0.032	39.628	0.006	0.006	0.000	0.000	0.000	0.000
113	A	131	SER	0	0.081	0.043	37.541	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	132	VAL	0	0.108	0.035	40.582	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	133	SER	0	0.026	0.009	37.793	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	134	SER	0	-0.050	-0.029	36.766	0.002	0.002	0.000	0.000	0.000	0.000
117	A	135	ILE	0	0.030	0.038	38.216	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	136	ASN	0	0.041	0.007	41.126	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	137	ARG	1	0.894	0.956	33.419	-0.103	-0.103	0.000	0.000	0.000	0.000
120	A	138	ILE	0	-0.001	0.009	38.084	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	139	ILE	0	0.009	0.008	39.406	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	140	ARG	1	0.899	0.949	37.082	-0.076	-0.076	0.000	0.000	0.000	0.000
123	A	141	THR	0	-0.052	-0.020	34.747	0.000	0.000	0.000	0.000	0.000	0.000
124	A	142	LYS	1	0.950	0.977	38.086	-0.035	-0.035	0.000	0.000	0.000	0.000

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