FMO DATABASE

FMODB ID: 76ZGK

Calculation Name: 1KJN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KJN

Chain ID: A

ChEMBL ID:

UniProt ID: O26871

Base Structure: X-ray

Registration Date: 2023-09-23

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1448036.227128
FMO2-HF: Nuclear repulsion	1389175.566692
FMO2-HF: Total energy	-58860.660436
FMO2-MP2: Total energy	-59031.4302

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:6:THR)

Summations of interaction energy for fragment #1(A:6:THR)

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.
-6.951	-3.424	0.103	-1.874	-1.757	-0.008

Interaction energy analysis for fragmet #1(A:6:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.039

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	8	LYS	1	0.880	0.946	3.791	-0.483	1.325	-0.023	-0.972	-0.813	0.000
4	A	9	ALA	0	0.003	0.004	6.739	0.521	0.521	0.000	0.000	0.000	0.000
5	A	10	LEU	0	0.028	0.029	9.217	-0.068	-0.068	0.000	0.000	0.000	0.000
6	A	11	MET	0	-0.063	-0.030	12.910	0.112	0.112	0.000	0.000	0.000	0.000
7	A	12	VAL	0	0.053	0.020	15.307	0.000	0.000	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.081	-0.045	19.009	0.032	0.032	0.000	0.000	0.000	0.000
9	A	14	GLY	0	0.108	0.051	21.862	0.004	0.004	0.000	0.000	0.000	0.000
10	A	15	CYS	0	-0.070	-0.030	25.547	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	16	PRO	0	-0.047	-0.022	27.149	0.003	0.003	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.887	-0.943	28.659	-0.111	-0.111	0.000	0.000	0.000	0.000
13	A	18	SER	0	-0.013	-0.020	28.936	0.006	0.006	0.000	0.000	0.000	0.000
14	A	19	PRO	0	-0.006	-0.007	28.653	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	20	VAL	0	-0.019	-0.006	26.199	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	21	GLN	0	0.007	0.013	23.381	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	22	ILE	0	0.058	0.036	22.508	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	23	PRO	0	-0.008	-0.007	21.434	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	24	LEU	0	0.014	-0.002	20.793	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.037	0.051	18.344	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	26	ILE	0	0.033	0.011	16.632	-0.046	-0.046	0.000	0.000	0.000	0.000
22	A	27	TYR	0	-0.134	-0.100	16.190	-0.029	-0.029	0.000	0.000	0.000	0.000
23	A	28	THR	0	0.020	-0.026	13.957	0.007	0.007	0.000	0.000	0.000	0.000
24	A	29	SER	0	0.024	-0.014	12.272	-0.059	-0.059	0.000	0.000	0.000	0.000
25	A	30	HIS	0	0.022	0.012	11.177	-0.134	-0.134	0.000	0.000	0.000	0.000
26	A	31	LYS	1	0.857	0.929	11.579	0.128	0.128	0.000	0.000	0.000	0.000
27	A	32	LEU	0	0.029	0.014	8.409	0.045	0.045	0.000	0.000	0.000	0.000
28	A	33	LYS	1	0.895	0.943	6.984	0.908	0.908	0.000	0.000	0.000	0.000
29	A	34	LYS	1	0.836	0.930	7.521	0.204	0.204	0.000	0.000	0.000	0.000
30	A	35	LYS	1	0.837	0.917	6.671	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	36	GLY	0	-0.022	0.001	3.381	0.474	0.722	0.010	-0.056	-0.202	0.000
32	A	37	PHE	0	-0.032	0.000	3.038	-3.419	-2.064	0.117	-0.837	-0.636	-0.008
33	A	38	ARG	1	0.911	0.967	4.368	2.111	2.227	-0.001	-0.009	-0.106	0.000
34	A	39	VAL	0	-0.026	-0.035	6.812	0.058	0.058	0.000	0.000	0.000	0.000
35	A	40	THR	0	0.018	0.008	9.918	0.016	0.016	0.000	0.000	0.000	0.000
36	A	41	VAL	0	-0.026	-0.015	13.022	0.056	0.056	0.000	0.000	0.000	0.000
37	A	42	THR	0	0.002	-0.005	16.248	0.017	0.017	0.000	0.000	0.000	0.000
38	A	43	ALA	0	0.045	-0.017	19.216	0.023	0.023	0.000	0.000	0.000	0.000
39	A	44	ASN	0	0.078	0.056	22.752	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	45	PRO	0	0.074	0.014	25.823	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	46	ALA	0	-0.023	-0.012	27.295	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	47	ALA	0	0.052	0.022	24.102	0.000	0.000	0.000	0.000	0.000	0.000
43	A	48	LEU	0	0.042	0.022	20.927	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	49	ARG	1	0.915	0.955	23.504	0.183	0.183	0.000	0.000	0.000	0.000
45	A	50	LEU	0	-0.021	-0.011	25.746	0.007	0.007	0.000	0.000	0.000	0.000
46	A	51	VAL	0	0.031	0.012	19.085	0.009	0.009	0.000	0.000	0.000	0.000
47	A	52	GLN	0	0.001	-0.010	22.062	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	53	VAL	0	-0.066	-0.025	23.129	0.009	0.009	0.000	0.000	0.000	0.000
49	A	54	ALA	0	-0.049	-0.020	23.277	0.013	0.013	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.832	-0.905	17.877	-0.370	-0.370	0.000	0.000	0.000	0.000
51	A	56	PRO	0	-0.049	-0.019	21.161	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	57	GLU	-1	-0.944	-0.979	20.778	-0.218	-0.218	0.000	0.000	0.000	0.000
53	A	58	GLY	0	-0.045	-0.003	18.142	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	59	ILE	0	-0.042	-0.017	16.035	-0.052	-0.052	0.000	0.000	0.000	0.000
55	A	60	TYR	0	-0.078	-0.063	14.261	-0.036	-0.036	0.000	0.000	0.000	0.000
56	A	61	THR	0	-0.040	0.002	12.946	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	62	ASP	-1	-0.801	-0.866	9.560	-1.284	-1.284	0.000	0.000	0.000	0.000
58	A	63	GLU	-1	-0.920	-0.957	12.699	-0.831	-0.831	0.000	0.000	0.000	0.000
59	A	64	MET	0	-0.030	-0.012	14.949	0.021	0.021	0.000	0.000	0.000	0.000
60	A	65	VAL	0	0.021	0.023	17.375	0.024	0.024	0.000	0.000	0.000	0.000
61	A	66	ASP	-1	-0.849	-0.936	20.081	-0.254	-0.254	0.000	0.000	0.000	0.000
62	A	67	LEU	0	-0.032	0.005	22.144	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.811	-0.904	23.342	-0.222	-0.222	0.000	0.000	0.000	0.000
64	A	69	SER	0	-0.051	-0.030	23.235	0.001	0.001	0.000	0.000	0.000	0.000
65	A	70	CYS	0	-0.056	-0.014	18.202	-0.031	-0.031	0.000	0.000	0.000	0.000
66	A	71	ILE	0	0.010	-0.001	20.354	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	72	ASN	0	-0.091	-0.042	22.619	0.026	0.026	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.985	-0.996	18.721	-0.315	-0.315	0.000	0.000	0.000	0.000
69	A	74	LEU	0	-0.095	-0.023	15.396	-0.040	-0.040	0.000	0.000	0.000	0.000
70	A	75	ALA	0	0.000	0.002	16.251	0.074	0.074	0.000	0.000	0.000	0.000
71	A	76	GLU	-1	-0.886	-0.945	14.745	-0.297	-0.297	0.000	0.000	0.000	0.000
72	A	77	GLY	0	-0.043	-0.023	11.061	0.011	0.011	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.902	-0.943	9.827	-0.956	-0.956	0.000	0.000	0.000	0.000
74	A	79	TYR	0	-0.097	-0.078	9.106	-0.310	-0.310	0.000	0.000	0.000	0.000
75	A	80	GLU	-1	-0.826	-0.910	4.986	-2.325	-2.325	0.000	0.000	0.000	0.000
76	A	81	PHE	0	-0.053	-0.025	8.340	0.261	0.261	0.000	0.000	0.000	0.000
77	A	82	LEU	0	0.039	0.035	10.711	-0.170	-0.170	0.000	0.000	0.000	0.000
78	A	83	ALA	0	-0.010	-0.002	13.938	0.082	0.082	0.000	0.000	0.000	0.000
79	A	84	GLY	0	0.049	0.028	15.754	-0.042	-0.042	0.000	0.000	0.000	0.000
80	A	85	PHE	0	-0.101	-0.044	17.897	0.036	0.036	0.000	0.000	0.000	0.000
81	A	86	VAL	0	0.018	-0.011	21.914	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	87	PRO	0	-0.030	-0.022	25.298	0.012	0.012	0.000	0.000	0.000	0.000
83	A	88	ASN	0	0.024	-0.001	28.459	0.003	0.003	0.000	0.000	0.000	0.000
84	A	89	ASP	-1	-0.778	-0.886	29.162	-0.108	-0.108	0.000	0.000	0.000	0.000
85	A	90	ALA	0	-0.055	-0.021	30.002	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	91	ALA	0	-0.032	-0.020	25.373	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	92	ALA	0	0.040	0.016	25.192	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	93	ALA	0	0.038	0.022	25.911	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	94	TYR	0	-0.052	-0.044	23.731	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.022	-0.001	19.279	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	96	VAL	0	0.045	0.025	21.736	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	97	THR	0	-0.036	-0.020	23.090	0.001	0.001	0.000	0.000	0.000	0.000
93	A	98	PHE	0	-0.019	-0.041	18.753	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	99	ALA	0	0.015	0.003	18.420	-0.032	-0.032	0.000	0.000	0.000	0.000
95	A	100	GLY	0	-0.018	0.003	18.981	0.005	0.005	0.000	0.000	0.000	0.000
96	A	101	ILE	0	-0.051	-0.018	17.632	0.010	0.010	0.000	0.000	0.000	0.000
97	A	102	LEU	0	-0.028	-0.033	13.139	-0.029	-0.029	0.000	0.000	0.000	0.000
98	A	103	ASN	0	-0.065	-0.006	14.583	0.010	0.010	0.000	0.000	0.000	0.000
99	A	104	THR	0	0.025	0.013	10.914	0.056	0.056	0.000	0.000	0.000	0.000
100	A	105	GLU	-1	-0.929	-0.957	11.856	0.155	0.155	0.000	0.000	0.000	0.000
101	A	106	THR	0	0.016	-0.015	13.820	-0.087	-0.087	0.000	0.000	0.000	0.000
102	A	107	LEU	0	-0.083	-0.038	15.949	0.040	0.040	0.000	0.000	0.000	0.000
103	A	108	ALA	0	0.054	0.039	17.612	-0.036	-0.036	0.000	0.000	0.000	0.000
104	A	109	ILE	0	-0.062	-0.035	17.929	0.023	0.023	0.000	0.000	0.000	0.000
105	A	110	ILE	0	0.048	0.029	22.003	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	111	PHE	0	-0.092	-0.072	24.596	0.009	0.009	0.000	0.000	0.000	0.000
107	A	112	ASP	-1	-0.664	-0.834	28.189	-0.094	-0.094	0.000	0.000	0.000	0.000
108	A	113	ARG	1	0.757	0.859	31.824	0.075	0.075	0.000	0.000	0.000	0.000
109	A	114	ASP	-1	-0.881	-0.933	34.720	-0.056	-0.056	0.000	0.000	0.000	0.000
110	A	115	ALA	0	-0.051	-0.060	34.973	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	116	ASP	-1	-0.854	-0.903	35.413	-0.050	-0.050	0.000	0.000	0.000	0.000
112	A	117	VAL	0	0.012	0.022	33.314	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	118	LEU	0	-0.133	-0.067	30.119	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	119	GLU	-1	-0.952	-0.970	31.498	-0.049	-0.049	0.000	0.000	0.000	0.000
115	A	120	GLU	-1	-0.906	-0.951	33.174	-0.069	-0.069	0.000	0.000	0.000	0.000
116	A	121	LEU	0	-0.003	-0.003	29.119	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	122	VAL	0	-0.073	-0.044	28.344	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	123	ASN	0	-0.025	-0.020	29.146	0.003	0.003	0.000	0.000	0.000	0.000
119	A	124	GLU	-1	-0.847	-0.917	29.438	-0.093	-0.093	0.000	0.000	0.000	0.000
120	A	125	ILE	0	-0.039	-0.007	24.053	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	126	MET	0	-0.066	-0.035	26.455	0.002	0.002	0.000	0.000	0.000	0.000
122	A	127	GLU	-1	-0.959	-0.972	28.145	-0.052	-0.052	0.000	0.000	0.000	0.000
123	A	128	THR	0	-0.104	-0.065	27.662	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	129	LEU	0	-0.083	-0.053	21.771	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	130	ASP	-1	-0.950	-0.944	20.420	-0.024	-0.024	0.000	0.000	0.000	0.000
126	A	131	ALA	0	-0.008	-0.018	19.844	-0.011	-0.011	0.000	0.000	0.000	0.000
127	A	132	GLU	-1	-0.945	-0.958	18.447	0.021	0.021	0.000	0.000	0.000	0.000
128	A	133	ILE	0	0.037	0.009	20.392	-0.024	-0.024	0.000	0.000	0.000	0.000
129	A	134	ILE	0	-0.073	-0.027	19.075	0.015	0.015	0.000	0.000	0.000	0.000
130	A	135	ALA	0	0.077	0.042	23.060	-0.012	-0.012	0.000	0.000	0.000	0.000
131	A	136	ALA	0	-0.108	-0.083	26.485	0.011	0.011	0.000	0.000	0.000	0.000
132	A	137	ARG	1	1.014	1.033	28.731	0.048	0.048	0.000	0.000	0.000	0.000
133	A	138	ALA	0	-0.080	-0.048	28.600	0.005	0.005	0.000	0.000	0.000	0.000
134	A	139	HIS	0	0.065	0.024	30.414	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	140	HIS	0	0.067	0.018	30.766	-0.010	-0.010	0.000	0.000	0.000	0.000
136	A	141	ASN	0	-0.024	-0.003	30.137	-0.007	-0.007	0.000	0.000	0.000	0.000
137	A	142	PRO	0	0.086	0.037	25.061	0.003	0.003	0.000	0.000	0.000	0.000
138	A	143	ALA	0	-0.006	-0.005	25.741	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	144	PRO	0	-0.010	-0.003	26.007	0.003	0.003	0.000	0.000	0.000	0.000
140	A	145	LEU	0	0.070	0.029	23.331	0.007	0.007	0.000	0.000	0.000	0.000
141	A	146	ARG	1	0.911	0.960	21.087	0.113	0.113	0.000	0.000	0.000	0.000
142	A	147	VAL	0	-0.029	-0.017	21.191	0.001	0.001	0.000	0.000	0.000	0.000
143	A	148	ARG	1	0.922	0.951	22.061	0.071	0.071	0.000	0.000	0.000	0.000
144	A	149	ILE	0	0.061	0.046	16.782	0.011	0.011	0.000	0.000	0.000	0.000
145	A	150	ASP	-1	-0.827	-0.896	17.350	-0.110	-0.110	0.000	0.000	0.000	0.000
146	A	151	ARG	1	0.920	0.952	17.696	0.029	0.029	0.000	0.000	0.000	0.000
147	A	152	PHE	0	0.096	0.058	13.702	0.020	0.020	0.000	0.000	0.000	0.000
148	A	153	MET	0	0.013	-0.003	12.466	0.033	0.033	0.000	0.000	0.000	0.000
149	A	154	GLU	-1	-1.064	-1.028	13.439	0.042	0.042	0.000	0.000	0.000	0.000
150	A	155	GLU	-1	-1.000	-1.021	14.935	0.100	0.100	0.000	0.000	0.000	0.000
151	A	156	LYS	1	0.881	0.968	13.653	-0.019	-0.019	0.000	0.000	0.000	0.000
152	A	157	PRO	0	0.034	0.049	8.433	0.109	0.109	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:THR)