FMO DATABASE

FMODB ID: N1J2Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-837679.887288
FMO2-HF: Nuclear repulsion	789473.452897
FMO2-HF: Total energy	-48206.43439
FMO2-MP2: Total energy	-48347.286423

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.
-3.14	0.174	2.989	-2.991	-3.312	-0.021

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 : 0.044 / q_NPA : 0.027

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	ASN	0	-0.045	-0.018	3.806	1.026	2.562	-0.012	-0.754	-0.769	0.004
4	A	22	GLN	0	0.083	0.014	6.222	0.038	0.038	0.000	0.000	0.000	0.000
5	A	23	LEU	0	-0.049	-0.002	9.576	0.159	0.159	0.000	0.000	0.000	0.000
6	A	24	GLY	0	0.019	0.013	8.828	0.162	0.162	0.000	0.000	0.000	0.000
7	A	25	GLY	0	-0.001	0.001	8.181	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	26	VAL	0	0.009	0.014	3.664	-1.106	-0.947	0.001	-0.074	-0.087	0.000
9	A	27	PHE	0	-0.062	-0.032	3.113	1.256	2.543	0.348	-0.682	-0.953	-0.004
10	A	28	VAL	0	0.056	0.021	2.163	-5.594	-5.328	2.653	-1.466	-1.453	-0.021
11	A	29	ASN	0	0.022	0.003	3.991	-0.468	-0.402	-0.001	-0.015	-0.050	0.000
12	A	30	GLY	0	0.055	0.037	6.023	0.210	0.210	0.000	0.000	0.000	0.000
13	A	31	ARG	1	0.893	0.946	8.214	-0.097	-0.097	0.000	0.000	0.000	0.000
14	A	32	PRO	0	-0.027	-0.014	9.555	-0.150	-0.150	0.000	0.000	0.000	0.000
15	A	33	LEU	0	0.015	0.017	9.686	-0.081	-0.081	0.000	0.000	0.000	0.000
16	A	34	PRO	0	0.093	0.028	9.873	0.156	0.156	0.000	0.000	0.000	0.000
17	A	35	ASP	-1	-0.770	-0.885	13.020	-0.293	-0.293	0.000	0.000	0.000	0.000
18	A	36	VAL	0	0.043	0.029	15.130	0.006	0.006	0.000	0.000	0.000	0.000
19	A	37	VAL	0	0.017	0.004	12.144	0.012	0.012	0.000	0.000	0.000	0.000
20	A	38	ARG	1	0.825	0.912	14.175	0.418	0.418	0.000	0.000	0.000	0.000
21	A	39	GLN	0	0.020	0.004	17.151	0.020	0.020	0.000	0.000	0.000	0.000
22	A	40	ARG	1	0.971	0.994	18.040	0.437	0.437	0.000	0.000	0.000	0.000
23	A	41	ILE	0	-0.007	-0.003	15.096	0.009	0.009	0.000	0.000	0.000	0.000
24	A	42	VAL	0	0.018	0.004	19.532	0.024	0.024	0.000	0.000	0.000	0.000
25	A	43	GLU	-1	-0.861	-0.911	22.709	-0.225	-0.225	0.000	0.000	0.000	0.000
26	A	44	LEU	0	0.002	-0.011	20.146	0.008	0.008	0.000	0.000	0.000	0.000
27	A	45	ALA	0	-0.015	-0.010	23.620	0.016	0.016	0.000	0.000	0.000	0.000
28	A	46	HIS	0	-0.060	-0.015	25.197	0.021	0.021	0.000	0.000	0.000	0.000
29	A	47	GLN	0	-0.066	-0.051	27.029	0.006	0.006	0.000	0.000	0.000	0.000
30	A	48	GLY	0	0.022	0.029	28.159	0.009	0.009	0.000	0.000	0.000	0.000
31	A	49	VAL	0	-0.072	-0.028	23.023	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	50	ARG	1	0.942	0.933	24.986	0.249	0.249	0.000	0.000	0.000	0.000
33	A	51	PRO	0	0.101	0.038	21.660	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	52	CYS	0	-0.045	-0.019	19.989	-0.038	-0.038	0.000	0.000	0.000	0.000
35	A	53	ASP	-1	-0.789	-0.865	19.522	-0.352	-0.352	0.000	0.000	0.000	0.000
36	A	54	ILE	0	0.026	0.031	18.043	-0.053	-0.053	0.000	0.000	0.000	0.000
37	A	55	SER	0	-0.093	-0.059	14.948	-0.056	-0.056	0.000	0.000	0.000	0.000
38	A	56	ARG	1	0.924	0.926	15.009	0.261	0.261	0.000	0.000	0.000	0.000
39	A	57	GLN	0	-0.017	0.000	15.927	-0.072	-0.072	0.000	0.000	0.000	0.000
40	A	58	LEU	0	-0.016	-0.011	14.624	-0.047	-0.047	0.000	0.000	0.000	0.000
41	A	59	ARG	1	0.893	0.958	10.915	0.835	0.835	0.000	0.000	0.000	0.000
42	A	60	VAL	0	0.013	0.013	10.487	-0.326	-0.326	0.000	0.000	0.000	0.000
43	A	61	SER	0	0.046	0.034	11.010	0.142	0.142	0.000	0.000	0.000	0.000
44	A	62	HIS	0	0.113	0.031	12.627	0.022	0.022	0.000	0.000	0.000	0.000
45	A	63	GLY	0	0.041	0.031	15.371	0.042	0.042	0.000	0.000	0.000	0.000
46	A	64	CYS	0	-0.056	-0.027	12.056	0.072	0.072	0.000	0.000	0.000	0.000
47	A	65	VAL	0	0.049	0.022	15.064	0.035	0.035	0.000	0.000	0.000	0.000
48	A	66	SER	0	-0.003	0.003	17.424	0.045	0.045	0.000	0.000	0.000	0.000
49	A	67	LYS	1	0.933	0.967	17.423	0.168	0.168	0.000	0.000	0.000	0.000
50	A	68	ILE	0	-0.048	-0.029	14.927	0.027	0.027	0.000	0.000	0.000	0.000
51	A	69	LEU	0	0.021	0.018	19.328	0.022	0.022	0.000	0.000	0.000	0.000
52	A	70	GLY	0	0.024	0.020	22.435	0.021	0.021	0.000	0.000	0.000	0.000
53	A	71	ARG	1	0.924	0.955	20.083	0.166	0.166	0.000	0.000	0.000	0.000
54	A	72	TYR	0	-0.002	-0.004	23.331	0.014	0.014	0.000	0.000	0.000	0.000
55	A	73	TYR	0	0.023	-0.009	24.949	0.003	0.003	0.000	0.000	0.000	0.000
56	A	74	GLU	-1	-0.923	-0.936	27.252	-0.089	-0.089	0.000	0.000	0.000	0.000
57	A	75	THR	0	-0.088	-0.043	26.238	0.012	0.012	0.000	0.000	0.000	0.000
58	A	76	GLY	0	0.039	0.037	27.575	0.008	0.008	0.000	0.000	0.000	0.000
59	A	77	SER	0	-0.037	-0.025	24.519	-0.015	-0.015	0.000	0.000	0.000	0.000
60	A	78	ILE	0	0.066	0.028	20.422	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	79	LYS	1	0.826	0.895	19.329	0.178	0.178	0.000	0.000	0.000	0.000
62	A	80	PRO	0	-0.051	-0.014	16.158	0.006	0.006	0.000	0.000	0.000	0.000
63	A	81	GLY	0	0.009	-0.006	18.385	0.021	0.021	0.000	0.000	0.000	0.000
64	A	82	VAL	0	0.009	0.004	18.930	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	83	ILE	0	-0.008	-0.010	14.217	0.013	0.013	0.000	0.000	0.000	0.000
66	A	84	GLY	0	0.004	0.007	18.464	0.005	0.005	0.000	0.000	0.000	0.000
67	A	85	GLY	0	0.015	0.014	19.921	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	86	SER	0	-0.025	-0.014	23.386	0.013	0.013	0.000	0.000	0.000	0.000
69	A	87	LYS	1	0.974	0.988	26.214	-0.062	-0.062	0.000	0.000	0.000	0.000
70	A	88	PRO	0	0.000	-0.013	29.796	0.009	0.009	0.000	0.000	0.000	0.000
71	A	89	LYS	1	0.983	0.998	29.333	-0.138	-0.138	0.000	0.000	0.000	0.000
72	A	90	VAL	0	0.130	0.064	34.373	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	91	ALA	0	-0.043	-0.005	35.981	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	92	THR	0	-0.017	-0.021	37.538	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	93	PRO	0	0.038	0.002	38.045	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	94	LYS	1	0.995	1.003	40.727	-0.051	-0.051	0.000	0.000	0.000	0.000
77	A	95	VAL	0	0.015	0.011	41.644	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	96	VAL	0	-0.031	-0.022	39.173	0.000	0.000	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.942	-0.965	42.573	0.024	0.024	0.000	0.000	0.000	0.000
80	A	98	LYS	1	0.849	0.915	45.654	-0.034	-0.034	0.000	0.000	0.000	0.000
81	A	99	ILE	0	-0.006	0.002	42.854	0.000	0.000	0.000	0.000	0.000	0.000
82	A	100	ALA	0	-0.017	-0.008	45.786	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	101	GLU	-1	-0.903	-0.952	47.531	0.026	0.026	0.000	0.000	0.000	0.000
84	A	102	TYR	0	-0.044	-0.063	49.791	0.000	0.000	0.000	0.000	0.000	0.000
85	A	103	LYS	1	0.855	0.912	48.082	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	104	ARG	1	0.914	0.963	50.379	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	105	GLN	0	0.017	0.028	53.025	0.000	0.000	0.000	0.000	0.000	0.000
88	A	106	ASN	0	-0.017	-0.008	54.404	0.000	0.000	0.000	0.000	0.000	0.000
89	A	107	PRO	0	0.064	0.034	52.645	0.002	0.002	0.000	0.000	0.000	0.000
90	A	108	THR	0	0.013	0.001	52.328	0.001	0.001	0.000	0.000	0.000	0.000
91	A	109	MET	0	-0.034	0.021	51.937	0.002	0.002	0.000	0.000	0.000	0.000
92	A	110	PHE	0	0.021	0.008	50.265	0.002	0.002	0.000	0.000	0.000	0.000
93	A	111	ALA	0	0.008	-0.013	45.165	0.000	0.000	0.000	0.000	0.000	0.000
94	A	112	TRP	0	-0.001	-0.010	47.275	0.002	0.002	0.000	0.000	0.000	0.000
95	A	113	GLU	-1	-0.777	-0.874	48.544	0.041	0.041	0.000	0.000	0.000	0.000
96	A	114	ILE	0	-0.015	-0.014	46.780	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	115	ARG	1	0.802	0.863	45.436	-0.061	-0.061	0.000	0.000	0.000	0.000
98	A	116	ASP	-1	-0.775	-0.867	47.548	0.055	0.055	0.000	0.000	0.000	0.000
99	A	117	ARG	1	0.863	0.928	50.977	-0.035	-0.035	0.000	0.000	0.000	0.000
100	A	118	LEU	0	-0.009	-0.007	45.020	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	119	LEU	0	-0.024	0.002	46.976	0.000	0.000	0.000	0.000	0.000	0.000
102	A	120	ALA	0	-0.010	-0.003	50.108	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	121	GLU	-1	-0.776	-0.852	52.132	0.033	0.033	0.000	0.000	0.000	0.000
104	A	122	ARG	1	0.906	0.952	50.324	-0.042	-0.042	0.000	0.000	0.000	0.000
105	A	123	VAL	0	-0.012	0.004	46.058	0.000	0.000	0.000	0.000	0.000	0.000
106	A	124	CYS	0	-0.105	-0.064	44.310	0.002	0.002	0.000	0.000	0.000	0.000
107	A	125	ASP	-1	-0.729	-0.835	44.322	0.059	0.059	0.000	0.000	0.000	0.000
108	A	126	ASN	0	-0.022	-0.031	44.978	0.001	0.001	0.000	0.000	0.000	0.000
109	A	127	ASP	-1	-0.892	-0.940	40.674	0.085	0.085	0.000	0.000	0.000	0.000
110	A	128	THR	0	-0.128	-0.081	40.070	0.005	0.005	0.000	0.000	0.000	0.000
111	A	129	VAL	0	-0.036	-0.009	40.919	0.000	0.000	0.000	0.000	0.000	0.000
112	A	130	PRO	0	-0.023	-0.013	39.664	0.005	0.005	0.000	0.000	0.000	0.000
113	A	131	SER	0	0.062	0.032	37.761	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	132	VAL	0	0.127	0.035	40.667	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	133	SER	0	0.015	0.007	37.736	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	134	SER	0	-0.035	-0.020	36.877	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	135	ILE	0	0.064	0.055	38.352	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	136	ASN	0	0.033	0.012	41.370	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	137	ARG	1	0.880	0.944	33.813	-0.090	-0.090	0.000	0.000	0.000	0.000
120	A	138	ILE	0	-0.056	-0.031	38.296	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	139	ILE	0	-0.013	-0.002	39.641	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	140	ARG	1	0.930	0.959	36.695	-0.068	-0.068	0.000	0.000	0.000	0.000
123	A	141	THR	0	-0.069	-0.018	35.045	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	142	LYS	1	1.011	1.007	38.244	-0.029	-0.029	0.000	0.000	0.000	0.000

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