FMO DATABASE

FMODB ID: 2JLNR

Calculation Name: 3KHN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KHN

Chain ID: A

ChEMBL ID:

UniProt ID: Q729W9

Base Structure: X-ray

Registration Date: 2023-06-22

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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1680043.172469
FMO2-HF: Nuclear repulsion	1615207.41946
FMO2-HF: Total energy	-64835.753008
FMO2-MP2: Total energy	-65029.647995

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-83.112	-89.37	34.728	-16.209	-12.261	-0.171

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.826 / q_NPA : 0.858

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	9	GLN	0	0.073	0.039	3.642	2.533	4.039	0.011	-0.566	-0.950	0.000
4	A	10	ARG	1	0.986	1.002	3.556	32.664	33.335	0.010	-0.153	-0.528	0.000
5	A	11	GLU	-1	-0.786	-0.863	1.697	-143.585	-152.020	34.707	-15.490	-10.783	-0.171
6	A	12	LEU	0	-0.023	0.006	5.841	4.318	4.318	0.000	0.000	0.000	0.000
7	A	13	ILE	0	0.039	0.013	8.272	2.267	2.267	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.769	-0.833	8.657	-20.972	-20.972	0.000	0.000	0.000	0.000
9	A	15	ALA	0	-0.005	-0.005	9.269	2.299	2.299	0.000	0.000	0.000	0.000
10	A	16	GLN	0	0.007	0.036	11.153	1.632	1.632	0.000	0.000	0.000	0.000
11	A	17	ARG	1	0.870	0.902	13.173	21.739	21.739	0.000	0.000	0.000	0.000
12	A	18	GLN	0	-0.068	-0.051	12.685	2.015	2.015	0.000	0.000	0.000	0.000
13	A	19	THR	0	-0.021	-0.031	14.751	1.215	1.215	0.000	0.000	0.000	0.000
14	A	20	TYR	0	0.005	-0.015	17.280	1.134	1.134	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.009	-0.002	18.327	1.269	1.269	0.000	0.000	0.000	0.000
16	A	22	GLU	-1	-0.865	-0.912	18.520	-15.198	-15.198	0.000	0.000	0.000	0.000
17	A	23	MET	0	-0.058	-0.020	20.094	0.731	0.731	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.946	0.971	23.377	12.602	12.602	0.000	0.000	0.000	0.000
19	A	25	THR	0	0.012	0.004	24.373	0.566	0.566	0.000	0.000	0.000	0.000
20	A	26	TYR	0	-0.064	-0.059	25.830	0.525	0.525	0.000	0.000	0.000	0.000
21	A	27	PHE	0	0.061	0.006	25.566	0.343	0.343	0.000	0.000	0.000	0.000
22	A	28	THR	0	-0.037	-0.038	29.453	0.288	0.288	0.000	0.000	0.000	0.000
23	A	29	VAL	0	-0.036	-0.013	29.989	0.365	0.365	0.000	0.000	0.000	0.000
24	A	30	ASN	0	-0.058	-0.025	30.179	0.489	0.489	0.000	0.000	0.000	0.000
25	A	31	GLY	0	0.022	0.027	33.522	0.209	0.209	0.000	0.000	0.000	0.000
26	A	32	VAL	0	-0.041	-0.029	31.494	0.253	0.253	0.000	0.000	0.000	0.000
27	A	33	GLU	-1	-0.843	-0.907	30.440	-10.023	-10.023	0.000	0.000	0.000	0.000
28	A	34	GLY	0	-0.026	-0.013	32.359	-0.042	-0.042	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.087	-0.044	34.351	0.242	0.242	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.004	-0.001	28.531	-0.042	-0.042	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.032	0.042	29.497	-0.201	-0.201	0.000	0.000	0.000	0.000
32	A	38	ALA	0	-0.007	-0.010	24.435	-0.202	-0.202	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.009	0.004	22.708	0.030	0.030	0.000	0.000	0.000	0.000
34	A	40	PHE	0	-0.006	-0.020	13.244	-0.445	-0.445	0.000	0.000	0.000	0.000
35	A	41	ASP	-1	-0.899	-0.945	17.453	-14.051	-14.051	0.000	0.000	0.000	0.000
36	A	42	GLU	-1	-0.880	-0.945	11.339	-20.115	-20.115	0.000	0.000	0.000	0.000
37	A	43	GLY	0	-0.027	-0.018	12.197	-1.468	-1.468	0.000	0.000	0.000	0.000
38	A	44	VAL	0	-0.012	0.001	13.460	-0.136	-0.136	0.000	0.000	0.000	0.000
39	A	45	ILE	0	-0.012	-0.002	16.610	0.520	0.520	0.000	0.000	0.000	0.000
40	A	46	THR	0	-0.044	-0.026	19.355	0.314	0.314	0.000	0.000	0.000	0.000
41	A	47	LEU	0	-0.008	0.006	22.941	0.213	0.213	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.834	0.892	25.075	11.181	11.181	0.000	0.000	0.000	0.000
43	A	49	VAL	0	0.017	0.014	29.483	0.068	0.068	0.000	0.000	0.000	0.000
44	A	50	PRO	0	0.055	0.027	32.932	0.038	0.038	0.000	0.000	0.000	0.000
45	A	51	SER	0	0.045	0.001	36.374	0.087	0.087	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.876	-0.930	37.981	-7.391	-7.391	0.000	0.000	0.000	0.000
47	A	53	VAL	0	-0.046	-0.017	37.391	0.147	0.147	0.000	0.000	0.000	0.000
48	A	54	LEU	0	-0.026	-0.011	34.386	-0.080	-0.080	0.000	0.000	0.000	0.000
49	A	55	PHE	0	-0.001	-0.014	36.654	0.041	0.041	0.000	0.000	0.000	0.000
50	A	56	ALA	0	0.026	0.026	42.051	0.030	0.030	0.000	0.000	0.000	0.000
51	A	57	PRO	0	0.056	0.005	44.712	-0.106	-0.106	0.000	0.000	0.000	0.000
52	A	58	GLY	0	0.013	0.018	45.354	0.114	0.114	0.000	0.000	0.000	0.000
53	A	59	ALA	0	-0.032	0.001	45.161	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	60	VAL	0	0.031	0.014	41.579	-0.134	-0.134	0.000	0.000	0.000	0.000
55	A	61	GLU	-1	-0.845	-0.900	41.165	-7.615	-7.615	0.000	0.000	0.000	0.000
56	A	62	LEU	0	-0.011	-0.004	37.266	0.033	0.033	0.000	0.000	0.000	0.000
57	A	63	ALA	0	-0.003	0.000	41.475	0.197	0.197	0.000	0.000	0.000	0.000
58	A	64	PRO	0	0.016	-0.015	42.176	-0.172	-0.172	0.000	0.000	0.000	0.000
59	A	65	GLY	0	-0.002	0.014	42.257	-0.031	-0.031	0.000	0.000	0.000	0.000
60	A	66	ALA	0	0.027	0.018	37.986	-0.168	-0.168	0.000	0.000	0.000	0.000
61	A	67	ASP	-1	-0.815	-0.890	36.900	-8.603	-8.603	0.000	0.000	0.000	0.000
62	A	68	ARG	1	0.916	0.968	36.270	8.130	8.130	0.000	0.000	0.000	0.000
63	A	69	VAL	0	-0.002	0.007	32.772	-0.226	-0.226	0.000	0.000	0.000	0.000
64	A	70	LEU	0	0.013	-0.005	32.375	-0.377	-0.377	0.000	0.000	0.000	0.000
65	A	71	ALA	0	0.039	0.016	31.878	-0.336	-0.336	0.000	0.000	0.000	0.000
66	A	72	THR	0	-0.008	-0.016	30.197	-0.253	-0.253	0.000	0.000	0.000	0.000
67	A	73	LEU	0	-0.007	-0.005	27.349	-0.445	-0.445	0.000	0.000	0.000	0.000
68	A	74	LYS	1	0.923	0.983	27.154	8.992	8.992	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.787	-0.866	27.550	-11.633	-11.633	0.000	0.000	0.000	0.000
70	A	76	LEU	0	-0.002	0.011	22.338	-0.514	-0.514	0.000	0.000	0.000	0.000
71	A	77	PHE	0	0.016	-0.004	23.043	-0.763	-0.763	0.000	0.000	0.000	0.000
72	A	78	ILE	0	0.014	0.018	23.153	-0.499	-0.499	0.000	0.000	0.000	0.000
73	A	79	ARG	1	0.838	0.918	22.396	12.021	12.021	0.000	0.000	0.000	0.000
74	A	80	ARG	1	0.752	0.866	15.543	16.863	16.863	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.935	0.952	19.311	14.818	14.818	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.811	-0.888	13.690	-18.801	-18.801	0.000	0.000	0.000	0.000
77	A	83	GLN	0	-0.013	0.000	15.665	-0.837	-0.837	0.000	0.000	0.000	0.000
78	A	84	ASN	0	0.026	0.011	16.774	1.116	1.116	0.000	0.000	0.000	0.000
79	A	85	ILE	0	-0.022	-0.021	20.059	-0.048	-0.048	0.000	0.000	0.000	0.000
80	A	86	ASN	0	0.004	0.009	20.799	0.872	0.872	0.000	0.000	0.000	0.000
81	A	87	ILE	0	0.008	0.005	24.606	0.065	0.065	0.000	0.000	0.000	0.000
82	A	88	LYS	1	0.902	0.946	24.414	11.679	11.679	0.000	0.000	0.000	0.000
83	A	89	GLY	0	0.024	0.031	29.386	0.019	0.019	0.000	0.000	0.000	0.000
84	A	90	PHE	0	-0.008	-0.012	28.378	-0.074	-0.074	0.000	0.000	0.000	0.000
85	A	91	THR	0	-0.045	-0.043	34.417	0.040	0.040	0.000	0.000	0.000	0.000
86	A	92	ASP	-1	-0.768	-0.879	37.060	-7.447	-7.447	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.832	-0.921	39.711	-7.237	-7.237	0.000	0.000	0.000	0.000
88	A	94	VAL	0	-0.047	-0.017	41.556	0.169	0.169	0.000	0.000	0.000	0.000
89	A	95	GLN	0	-0.008	-0.010	42.150	-0.110	-0.110	0.000	0.000	0.000	0.000
90	A	96	PRO	0	-0.037	-0.005	44.083	0.087	0.087	0.000	0.000	0.000	0.000
91	A	97	SER	0	0.005	-0.001	46.874	0.128	0.128	0.000	0.000	0.000	0.000
92	A	98	ALA	0	0.049	0.013	50.594	-0.039	-0.039	0.000	0.000	0.000	0.000
93	A	99	ASN	0	-0.081	-0.030	51.994	0.132	0.132	0.000	0.000	0.000	0.000
94	A	100	ALA	0	0.014	0.002	49.775	0.015	0.015	0.000	0.000	0.000	0.000
95	A	101	ARG	1	0.910	0.959	45.275	6.808	6.808	0.000	0.000	0.000	0.000
96	A	102	PHE	0	-0.008	-0.016	44.695	-0.107	-0.107	0.000	0.000	0.000	0.000
97	A	103	LYS	1	0.833	0.900	43.958	6.997	6.997	0.000	0.000	0.000	0.000
98	A	104	ASP	-1	-0.788	-0.885	41.688	-7.170	-7.170	0.000	0.000	0.000	0.000
99	A	105	ASN	0	0.068	0.005	39.467	-0.032	-0.032	0.000	0.000	0.000	0.000
100	A	106	TRP	0	-0.015	0.027	33.554	-0.309	-0.309	0.000	0.000	0.000	0.000
101	A	107	GLU	-1	-0.800	-0.889	38.219	-7.108	-7.108	0.000	0.000	0.000	0.000
102	A	108	VAL	0	0.002	0.003	40.345	-0.105	-0.105	0.000	0.000	0.000	0.000
103	A	109	SER	0	-0.023	-0.024	35.458	-0.186	-0.186	0.000	0.000	0.000	0.000
104	A	110	ALA	0	0.014	0.018	35.457	-0.277	-0.277	0.000	0.000	0.000	0.000
105	A	111	LEU	0	-0.024	-0.014	36.489	-0.144	-0.144	0.000	0.000	0.000	0.000
106	A	112	ARG	1	0.849	0.923	37.248	7.583	7.583	0.000	0.000	0.000	0.000
107	A	113	SER	0	0.001	-0.017	32.517	-0.223	-0.223	0.000	0.000	0.000	0.000
108	A	114	VAL	0	-0.017	-0.013	33.848	-0.260	-0.260	0.000	0.000	0.000	0.000
109	A	115	ASN	0	-0.024	-0.023	35.636	-0.087	-0.087	0.000	0.000	0.000	0.000
110	A	116	VAL	0	0.010	0.008	32.000	-0.026	-0.026	0.000	0.000	0.000	0.000
111	A	117	LEU	0	-0.001	0.001	30.043	-0.169	-0.169	0.000	0.000	0.000	0.000
112	A	118	ARG	1	0.828	0.891	32.838	7.744	7.744	0.000	0.000	0.000	0.000
113	A	119	TYR	0	-0.050	-0.031	33.133	-0.091	-0.091	0.000	0.000	0.000	0.000
114	A	120	PHE	0	0.015	-0.011	29.425	-0.108	-0.108	0.000	0.000	0.000	0.000
115	A	121	LEU	0	-0.012	-0.009	30.357	-0.195	-0.195	0.000	0.000	0.000	0.000
116	A	122	GLY	0	0.006	0.009	32.324	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	123	ALA	0	-0.100	-0.043	31.700	0.099	0.099	0.000	0.000	0.000	0.000
118	A	124	GLY	0	0.031	0.013	30.960	-0.101	-0.101	0.000	0.000	0.000	0.000
119	A	125	ILE	0	-0.075	-0.032	25.490	-0.446	-0.446	0.000	0.000	0.000	0.000
120	A	126	GLU	-1	-0.775	-0.864	22.076	-14.178	-14.178	0.000	0.000	0.000	0.000
121	A	127	PRO	0	0.060	0.014	25.444	-0.351	-0.351	0.000	0.000	0.000	0.000
122	A	128	ALA	0	-0.001	0.014	23.305	-0.049	-0.049	0.000	0.000	0.000	0.000
123	A	129	ARG	1	0.786	0.899	20.688	13.654	13.654	0.000	0.000	0.000	0.000
124	A	130	LEU	0	-0.032	-0.001	22.761	-0.222	-0.222	0.000	0.000	0.000	0.000
125	A	131	THR	0	-0.031	-0.033	24.651	0.243	0.243	0.000	0.000	0.000	0.000
126	A	132	ALA	0	0.012	0.001	27.191	0.016	0.016	0.000	0.000	0.000	0.000
127	A	133	THR	0	-0.054	-0.033	28.292	-0.096	-0.096	0.000	0.000	0.000	0.000
128	A	134	GLY	0	0.041	0.030	30.665	-0.028	-0.028	0.000	0.000	0.000	0.000
129	A	135	LEU	0	-0.023	-0.013	28.378	-0.074	-0.074	0.000	0.000	0.000	0.000
130	A	136	GLY	0	0.033	0.014	33.092	0.098	0.098	0.000	0.000	0.000	0.000
131	A	137	GLU	-1	-0.838	-0.901	35.405	-7.549	-7.549	0.000	0.000	0.000	0.000
132	A	138	LEU	0	-0.020	-0.013	30.587	0.060	0.060	0.000	0.000	0.000	0.000
133	A	139	ASP	-1	-0.936	-0.974	28.481	-9.847	-9.847	0.000	0.000	0.000	0.000
134	A	140	PRO	0	-0.052	-0.023	31.183	-0.144	-0.144	0.000	0.000	0.000	0.000
135	A	141	LEU	0	-0.022	0.004	28.250	-0.108	-0.108	0.000	0.000	0.000	0.000
136	A	142	PHE	0	-0.012	-0.011	31.530	-0.090	-0.090	0.000	0.000	0.000	0.000
137	A	143	PRO	0	0.055	0.033	34.636	0.087	0.087	0.000	0.000	0.000	0.000
138	A	144	ASN	0	0.033	0.023	37.593	-0.010	-0.010	0.000	0.000	0.000	0.000
139	A	145	THR	0	-0.002	-0.012	40.321	0.114	0.114	0.000	0.000	0.000	0.000
140	A	146	SER	0	-0.051	-0.044	42.220	0.145	0.145	0.000	0.000	0.000	0.000
141	A	147	ASP	-1	-0.777	-0.876	42.312	-6.776	-6.776	0.000	0.000	0.000	0.000
142	A	148	GLU	-1	-0.861	-0.911	40.824	-7.076	-7.076	0.000	0.000	0.000	0.000
143	A	149	ASN	0	-0.053	-0.035	37.947	-0.333	-0.333	0.000	0.000	0.000	0.000
144	A	150	ARG	1	0.827	0.899	37.832	6.580	6.580	0.000	0.000	0.000	0.000
145	A	151	ALA	0	-0.004	-0.006	39.128	-0.125	-0.125	0.000	0.000	0.000	0.000
146	A	152	ARG	1	0.872	0.945	34.536	8.198	8.198	0.000	0.000	0.000	0.000
147	A	153	ASN	0	-0.030	-0.030	34.331	-0.538	-0.538	0.000	0.000	0.000	0.000
148	A	154	ARG	1	0.838	0.914	35.240	7.163	7.163	0.000	0.000	0.000	0.000
149	A	155	ARG	1	0.801	0.920	29.296	9.568	9.568	0.000	0.000	0.000	0.000
150	A	156	VAL	0	-0.016	-0.016	31.091	0.092	0.092	0.000	0.000	0.000	0.000
151	A	157	GLU	-1	-0.761	-0.841	26.583	-10.884	-10.884	0.000	0.000	0.000	0.000
152	A	158	PHE	0	0.005	-0.019	26.010	0.106	0.106	0.000	0.000	0.000	0.000
153	A	159	VAL	0	0.038	0.029	20.478	-0.280	-0.280	0.000	0.000	0.000	0.000
154	A	160	LEU	0	-0.043	-0.019	20.300	0.053	0.053	0.000	0.000	0.000	0.000
155	A	161	GLU	-1	-0.832	-0.903	16.263	-16.287	-16.287	0.000	0.000	0.000	0.000
156	A	162	ARG	1	0.850	0.913	10.444	23.658	23.658	0.000	0.000	0.000	0.000
157	A	163	ARG	1	0.778	0.851	14.272	16.384	16.384	0.000	0.000	0.000	0.000
158	A	164	VAL	0	0.013	0.014	11.971	-1.589	-1.589	0.000	0.000	0.000	0.000
159	A	165	VAL	0	0.002	-0.009	12.594	1.024	1.024	0.000	0.000	0.000	0.000
160	A	166	ARG	1	0.792	0.886	15.145	16.885	16.885	0.000	0.000	0.000	0.000
161	A	167	GLU	-1	-0.813	-0.896	18.879	-12.990	-12.990	0.000	0.000	0.000	0.000
162	A	168	GLY	0	0.012	0.012	21.326	-0.011	-0.011	0.000	0.000	0.000	0.000
163	A	169	HIS	0	0.003	-0.005	21.797	0.544	0.544	0.000	0.000	0.000	0.000
164	A	170	HIS	1	0.789	0.884	25.636	11.672	11.672	0.000	0.000	0.000	0.000
165	A	171	HIS	0	0.028	0.007	26.459	0.508	0.508	0.000	0.000	0.000	0.000
166	A	172	HIS	0	0.028	0.035	30.473	0.160	0.160	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)