FMO DATABASE

FMODB ID: 895ZY

Calculation Name: 3KHT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KHT

Chain ID: A

ChEMBL ID:

UniProt ID: Q2SI73

Base Structure: X-ray

Registration Date: 2023-09-21

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	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1175330.71562
FMO2-HF: Nuclear repulsion	1123428.604237
FMO2-HF: Total energy	-51902.111383
FMO2-MP2: Total energy	-52052.84833

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:14:SER)

Summations of interaction energy for fragment #1(A:14:SER)

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.
-1.773	2.711	0.393	-1.975	-2.902	0.01

Interaction energy analysis for fragmet #1(A:14:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.023

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	16	ARG	1	0.865	0.914	3.773	2.671	4.070	0.003	-0.624	-0.778	0.004
4	A	17	VAL	0	-0.018	-0.006	6.343	-0.072	-0.072	0.000	0.000	0.000	0.000
5	A	18	LEU	0	-0.030	0.001	9.529	-0.077	-0.077	0.000	0.000	0.000	0.000
6	A	19	VAL	0	-0.009	-0.020	12.680	0.048	0.048	0.000	0.000	0.000	0.000
7	A	20	VAL	0	-0.016	-0.017	15.415	-0.039	-0.039	0.000	0.000	0.000	0.000
8	A	21	GLU	-1	-0.817	-0.915	18.734	0.131	0.131	0.000	0.000	0.000	0.000
9	A	22	ASP	-1	-0.903	-0.968	20.155	0.017	0.017	0.000	0.000	0.000	0.000
10	A	23	ASN	0	0.033	0.040	22.843	-0.020	-0.020	0.000	0.000	0.000	0.000
11	A	24	PRO	0	0.025	-0.002	21.542	0.013	0.013	0.000	0.000	0.000	0.000
12	A	25	ASP	-1	-0.914	-0.956	21.501	0.067	0.067	0.000	0.000	0.000	0.000
13	A	26	ASP	-1	-0.824	-0.906	21.149	0.141	0.141	0.000	0.000	0.000	0.000
14	A	27	ILE	0	-0.034	-0.014	16.462	0.033	0.033	0.000	0.000	0.000	0.000
15	A	28	ALA	0	-0.033	-0.011	16.872	0.028	0.028	0.000	0.000	0.000	0.000
16	A	29	LEU	0	-0.035	-0.025	17.923	0.023	0.023	0.000	0.000	0.000	0.000
17	A	30	ILE	0	0.016	-0.002	13.828	0.044	0.044	0.000	0.000	0.000	0.000
18	A	31	ARG	1	0.922	0.959	11.953	0.020	0.020	0.000	0.000	0.000	0.000
19	A	32	ARG	1	0.951	0.980	13.419	-0.070	-0.070	0.000	0.000	0.000	0.000
20	A	33	VAL	0	-0.012	0.001	15.314	0.016	0.016	0.000	0.000	0.000	0.000
21	A	34	LEU	0	-0.036	-0.030	9.516	0.007	0.007	0.000	0.000	0.000	0.000
22	A	35	ASP	-1	-0.895	-0.929	11.830	0.328	0.328	0.000	0.000	0.000	0.000
23	A	36	ARG	1	0.938	0.971	12.989	-0.199	-0.199	0.000	0.000	0.000	0.000
24	A	37	LYS	1	0.819	0.924	14.222	-0.429	-0.429	0.000	0.000	0.000	0.000
25	A	38	ASP	-1	-0.855	-0.914	11.670	0.647	0.647	0.000	0.000	0.000	0.000
26	A	39	ILE	0	-0.074	-0.031	8.451	0.187	0.187	0.000	0.000	0.000	0.000
27	A	40	HIS	0	-0.025	-0.023	5.140	-0.082	-0.082	0.000	0.000	0.000	0.000
28	A	41	CYS	0	-0.091	-0.041	3.209	0.388	1.277	0.071	-0.385	-0.575	0.003
29	A	42	GLN	0	-0.069	-0.031	2.936	-6.092	-3.884	0.320	-0.963	-1.565	0.003
30	A	43	LEU	0	0.044	0.017	5.127	-0.083	-0.095	-0.001	-0.003	0.016	0.000
31	A	44	GLU	-1	-0.787	-0.852	8.771	-0.687	-0.687	0.000	0.000	0.000	0.000
32	A	45	PHE	0	0.028	0.009	11.675	0.052	0.052	0.000	0.000	0.000	0.000
33	A	46	VAL	0	-0.014	-0.012	15.291	-0.049	-0.049	0.000	0.000	0.000	0.000
34	A	47	ASP	-1	-0.748	-0.850	18.347	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	48	ASN	0	0.013	-0.016	21.628	0.000	0.000	0.000	0.000	0.000	0.000
36	A	49	GLY	0	0.112	0.061	21.900	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	50	ALA	0	-0.048	-0.012	22.728	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	51	LYS	1	0.807	0.871	19.839	0.061	0.061	0.000	0.000	0.000	0.000
39	A	52	ALA	0	0.036	0.024	18.203	-0.022	-0.022	0.000	0.000	0.000	0.000
40	A	53	LEU	0	-0.026	-0.019	18.300	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	54	TYR	0	-0.024	-0.003	17.656	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	55	GLN	0	0.047	0.007	12.916	-0.030	-0.030	0.000	0.000	0.000	0.000
43	A	56	VAL	0	-0.033	-0.004	14.530	-0.039	-0.039	0.000	0.000	0.000	0.000
44	A	57	GLN	0	-0.076	-0.037	15.912	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	58	GLN	0	-0.032	-0.004	13.926	-0.041	-0.041	0.000	0.000	0.000	0.000
46	A	59	ALA	0	-0.025	-0.004	9.502	-0.122	-0.122	0.000	0.000	0.000	0.000
47	A	60	LYS	1	0.853	0.952	9.366	0.035	0.035	0.000	0.000	0.000	0.000
48	A	61	TYR	0	-0.057	-0.068	8.728	-0.200	-0.200	0.000	0.000	0.000	0.000
49	A	62	ASP	-1	-0.868	-0.945	6.327	0.484	0.484	0.000	0.000	0.000	0.000
50	A	63	LEU	0	-0.025	-0.015	9.453	0.071	0.071	0.000	0.000	0.000	0.000
51	A	64	ILE	0	0.005	0.007	12.102	-0.039	-0.039	0.000	0.000	0.000	0.000
52	A	65	ILE	0	-0.033	-0.007	14.355	0.015	0.015	0.000	0.000	0.000	0.000
53	A	66	LEU	0	-0.015	-0.010	17.040	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	67	ASP	-1	-0.679	-0.827	20.271	0.111	0.111	0.000	0.000	0.000	0.000
55	A	68	ILE	0	-0.077	-0.039	23.209	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	69	GLY	0	0.022	0.015	26.294	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	70	LEU	0	0.018	0.013	23.730	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	71	PRO	0	-0.009	0.010	27.652	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	72	ILE	0	0.014	-0.005	27.567	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	73	ALA	0	0.012	0.006	23.949	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	74	ASN	0	-0.082	-0.037	24.861	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	75	GLY	0	0.103	0.048	24.917	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	76	PHE	0	0.016	-0.005	25.306	0.004	0.004	0.000	0.000	0.000	0.000
64	A	77	GLU	-1	-0.858	-0.933	27.180	0.021	0.021	0.000	0.000	0.000	0.000
65	A	78	VAL	0	-0.013	-0.007	20.851	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	79	MET	0	-0.024	0.001	22.617	0.003	0.003	0.000	0.000	0.000	0.000
67	A	80	SER	0	-0.008	-0.015	23.680	0.001	0.001	0.000	0.000	0.000	0.000
68	A	81	ALA	0	-0.073	-0.037	23.289	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	82	VAL	0	-0.016	-0.005	18.086	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	83	ARG	1	0.803	0.896	18.624	-0.133	-0.133	0.000	0.000	0.000	0.000
71	A	84	LYS	1	0.903	0.968	22.487	0.002	0.002	0.000	0.000	0.000	0.000
72	A	85	PRO	0	0.019	0.002	21.523	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	86	GLY	0	0.054	0.029	19.445	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	87	ALA	0	-0.002	0.000	13.714	0.024	0.024	0.000	0.000	0.000	0.000
75	A	88	ASN	0	-0.008	-0.014	13.340	0.063	0.063	0.000	0.000	0.000	0.000
76	A	89	GLN	0	0.019	0.045	15.660	0.029	0.029	0.000	0.000	0.000	0.000
77	A	90	HIS	0	-0.006	-0.019	17.175	0.022	0.022	0.000	0.000	0.000	0.000
78	A	91	THR	0	-0.044	-0.023	13.084	0.053	0.053	0.000	0.000	0.000	0.000
79	A	92	PRO	0	0.036	0.025	13.544	-0.031	-0.031	0.000	0.000	0.000	0.000
80	A	93	ILE	0	0.010	-0.001	15.686	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	94	VAL	0	-0.012	-0.001	17.041	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	95	ILE	0	-0.011	-0.020	19.329	-0.013	-0.013	0.000	0.000	0.000	0.000
83	A	96	LEU	0	-0.034	-0.016	18.946	0.017	0.017	0.000	0.000	0.000	0.000
84	A	97	THR	0	0.003	-0.033	22.162	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	98	ASP	-1	-0.807	-0.875	25.366	0.126	0.126	0.000	0.000	0.000	0.000
86	A	99	ASN	0	-0.039	-0.015	28.227	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	100	VAL	0	-0.036	0.003	27.313	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	101	SER	0	0.061	0.031	30.627	0.001	0.001	0.000	0.000	0.000	0.000
89	A	102	ASP	-1	-0.854	-0.947	32.482	0.105	0.105	0.000	0.000	0.000	0.000
90	A	103	ASP	-1	-0.950	-0.971	33.645	0.071	0.071	0.000	0.000	0.000	0.000
91	A	104	ARG	1	0.887	0.955	30.128	-0.066	-0.066	0.000	0.000	0.000	0.000
92	A	105	ALA	0	0.088	0.044	29.005	0.002	0.002	0.000	0.000	0.000	0.000
93	A	106	LYS	1	0.982	0.992	29.436	-0.073	-0.073	0.000	0.000	0.000	0.000
94	A	107	GLN	0	-0.009	-0.015	31.396	0.001	0.001	0.000	0.000	0.000	0.000
95	A	108	CYS	0	-0.044	-0.032	26.228	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	109	MET	0	-0.037	-0.008	24.886	0.004	0.004	0.000	0.000	0.000	0.000
97	A	110	ALA	0	-0.051	-0.019	27.894	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	111	ALA	0	-0.021	-0.006	27.679	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	112	GLY	0	0.022	0.019	24.892	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	113	ALA	0	0.009	-0.003	22.419	0.013	0.013	0.000	0.000	0.000	0.000
101	A	114	SER	0	-0.031	-0.015	19.431	0.001	0.001	0.000	0.000	0.000	0.000
102	A	115	SER	0	-0.014	-0.009	20.422	0.009	0.009	0.000	0.000	0.000	0.000
103	A	116	VAL	0	0.014	0.008	22.330	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	117	VAL	0	-0.039	-0.017	21.094	0.005	0.005	0.000	0.000	0.000	0.000
105	A	118	ASP	-1	-0.766	-0.873	24.117	0.127	0.127	0.000	0.000	0.000	0.000
106	A	119	LYS	1	0.788	0.870	22.318	-0.107	-0.107	0.000	0.000	0.000	0.000
107	A	120	SER	0	-0.017	-0.034	25.008	0.010	0.010	0.000	0.000	0.000	0.000
108	A	121	SER	0	-0.025	-0.037	26.152	0.001	0.001	0.000	0.000	0.000	0.000
109	A	122	ASN	0	-0.048	-0.014	27.448	0.001	0.001	0.000	0.000	0.000	0.000
110	A	123	ASN	0	-0.024	-0.025	29.269	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	124	VAL	0	0.069	0.027	25.060	0.014	0.014	0.000	0.000	0.000	0.000
112	A	125	THR	0	-0.022	-0.010	25.091	0.018	0.018	0.000	0.000	0.000	0.000
113	A	126	ASP	-1	-0.825	-0.898	25.271	0.187	0.187	0.000	0.000	0.000	0.000
114	A	127	PHE	0	-0.007	0.012	21.608	0.026	0.026	0.000	0.000	0.000	0.000
115	A	128	TYR	0	0.013	0.002	18.595	0.035	0.035	0.000	0.000	0.000	0.000
116	A	129	GLY	0	-0.025	-0.020	20.053	0.043	0.043	0.000	0.000	0.000	0.000
117	A	130	ARG	1	0.840	0.898	20.448	-0.149	-0.149	0.000	0.000	0.000	0.000
118	A	131	ILE	0	-0.005	0.015	15.952	0.038	0.038	0.000	0.000	0.000	0.000
119	A	132	TYR	0	0.026	-0.007	14.915	0.028	0.028	0.000	0.000	0.000	0.000
120	A	133	ALA	0	0.005	0.000	15.768	0.074	0.074	0.000	0.000	0.000	0.000
121	A	134	ILE	0	-0.011	0.011	14.994	0.048	0.048	0.000	0.000	0.000	0.000
122	A	135	PHE	0	0.051	-0.003	10.285	0.031	0.031	0.000	0.000	0.000	0.000
123	A	136	SER	0	0.014	0.019	11.508	0.179	0.179	0.000	0.000	0.000	0.000
124	A	137	TYR	0	0.025	0.018	13.028	0.078	0.078	0.000	0.000	0.000	0.000
125	A	138	TRP	0	-0.003	-0.010	13.010	0.035	0.035	0.000	0.000	0.000	0.000
126	A	139	LEU	0	-0.013	-0.006	7.147	0.094	0.094	0.000	0.000	0.000	0.000
127	A	140	THR	0	-0.090	-0.068	8.840	0.271	0.271	0.000	0.000	0.000	0.000
128	A	141	VAL	0	-0.034	0.000	10.942	-0.073	-0.073	0.000	0.000	0.000	0.000
129	A	142	ASN	0	-0.030	-0.005	12.942	-0.108	-0.108	0.000	0.000	0.000	0.000
130	A	143	HIS	0	0.034	0.019	12.323	0.113	0.113	0.000	0.000	0.000	0.000
131	A	144	CYS	0	-0.014	0.016	8.310	0.033	0.033	0.000	0.000	0.000	0.000
132	A	145	GLN	0	0.031	0.014	6.676	-0.055	-0.055	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:SER)