FMO DATABASE

FMODB ID: NN9MQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1177376.526974
FMO2-HF: Nuclear repulsion	1125473.875936
FMO2-HF: Total energy	-51902.651038
FMO2-MP2: Total energy	-52053.318239

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.
-2.663	1.365	1.314	-2.12	-3.22	0.005

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 : -0.030 / q_NPA : -0.026

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	0.839	0.907	3.867	2.187	3.356	-0.006	-0.536	-0.626	0.003
4	A	17	VAL	0	-0.005	0.002	6.480	-0.061	-0.061	0.000	0.000	0.000	0.000
5	A	18	LEU	0	-0.018	0.007	9.764	-0.069	-0.069	0.000	0.000	0.000	0.000
6	A	19	VAL	0	-0.008	-0.008	12.917	0.033	0.033	0.000	0.000	0.000	0.000
7	A	20	VAL	0	-0.039	-0.022	15.770	-0.039	-0.039	0.000	0.000	0.000	0.000
8	A	21	GLU	-1	-0.826	-0.917	19.028	0.165	0.165	0.000	0.000	0.000	0.000
9	A	22	ASP	-1	-0.901	-0.959	20.521	0.041	0.041	0.000	0.000	0.000	0.000
10	A	23	ASN	0	0.022	0.016	23.025	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	24	PRO	0	0.006	-0.002	21.699	0.017	0.017	0.000	0.000	0.000	0.000
12	A	25	ASP	-1	-0.896	-0.955	21.297	0.110	0.110	0.000	0.000	0.000	0.000
13	A	26	ASP	-1	-0.800	-0.886	21.304	0.167	0.167	0.000	0.000	0.000	0.000
14	A	27	ILE	0	-0.034	-0.015	16.589	0.040	0.040	0.000	0.000	0.000	0.000
15	A	28	ALA	0	-0.035	-0.023	16.905	0.039	0.039	0.000	0.000	0.000	0.000
16	A	29	LEU	0	-0.045	-0.019	18.125	0.029	0.029	0.000	0.000	0.000	0.000
17	A	30	ILE	0	0.032	0.003	14.045	0.044	0.044	0.000	0.000	0.000	0.000
18	A	31	ARG	1	0.928	0.967	11.549	-0.087	-0.087	0.000	0.000	0.000	0.000
19	A	32	ARG	1	0.958	0.976	13.892	-0.110	-0.110	0.000	0.000	0.000	0.000
20	A	33	VAL	0	-0.044	-0.016	15.402	0.005	0.005	0.000	0.000	0.000	0.000
21	A	34	LEU	0	-0.021	-0.017	9.971	0.014	0.014	0.000	0.000	0.000	0.000
22	A	35	ASP	-1	-0.906	-0.944	12.236	0.445	0.445	0.000	0.000	0.000	0.000
23	A	36	ARG	1	0.920	0.960	13.295	-0.242	-0.242	0.000	0.000	0.000	0.000
24	A	37	LYS	1	0.820	0.919	13.842	-0.502	-0.502	0.000	0.000	0.000	0.000
25	A	38	ASP	-1	-0.824	-0.883	10.986	0.753	0.753	0.000	0.000	0.000	0.000
26	A	39	ILE	0	-0.053	-0.018	8.452	0.238	0.238	0.000	0.000	0.000	0.000
27	A	40	HIS	0	-0.046	-0.038	5.483	0.102	0.102	0.000	0.000	0.000	0.000
28	A	41	CYS	0	-0.083	-0.038	3.745	0.651	1.087	0.007	-0.155	-0.288	0.000
29	A	42	GLN	0	-0.059	-0.027	2.625	-7.243	-4.813	1.314	-1.425	-2.318	0.002
30	A	43	LEU	0	0.029	0.011	5.108	-0.235	-0.242	-0.001	-0.004	0.012	0.000
31	A	44	GLU	-1	-0.784	-0.847	8.852	-0.531	-0.531	0.000	0.000	0.000	0.000
32	A	45	PHE	0	0.034	-0.001	11.602	0.064	0.064	0.000	0.000	0.000	0.000
33	A	46	VAL	0	-0.042	-0.025	15.293	-0.053	-0.053	0.000	0.000	0.000	0.000
34	A	47	ASP	-1	-0.723	-0.839	18.498	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	48	ASN	0	-0.011	-0.016	21.868	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	49	GLY	0	0.093	0.039	22.078	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	50	ALA	0	-0.030	-0.012	23.070	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	51	LYS	1	0.827	0.888	19.845	0.040	0.040	0.000	0.000	0.000	0.000
39	A	52	ALA	0	0.014	0.014	18.462	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	53	LEU	0	-0.017	-0.021	18.620	-0.015	-0.015	0.000	0.000	0.000	0.000
41	A	54	TYR	0	-0.032	-0.005	18.090	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	55	GLN	0	0.029	-0.002	13.323	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	56	VAL	0	-0.053	-0.018	14.814	-0.042	-0.042	0.000	0.000	0.000	0.000
44	A	57	GLN	0	-0.030	-0.011	16.301	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	58	GLN	0	-0.045	-0.010	13.983	-0.049	-0.049	0.000	0.000	0.000	0.000
46	A	59	ALA	0	-0.011	0.001	9.559	-0.114	-0.114	0.000	0.000	0.000	0.000
47	A	60	LYS	1	0.821	0.938	9.575	0.070	0.070	0.000	0.000	0.000	0.000
48	A	61	TYR	0	-0.052	-0.057	8.965	-0.191	-0.191	0.000	0.000	0.000	0.000
49	A	62	ASP	-1	-0.848	-0.936	6.551	0.535	0.535	0.000	0.000	0.000	0.000
50	A	63	LEU	0	-0.032	-0.013	9.742	0.055	0.055	0.000	0.000	0.000	0.000
51	A	64	ILE	0	-0.001	0.000	12.345	-0.038	-0.038	0.000	0.000	0.000	0.000
52	A	65	ILE	0	-0.003	0.003	14.554	0.020	0.020	0.000	0.000	0.000	0.000
53	A	66	LEU	0	-0.010	-0.005	17.417	-0.032	-0.032	0.000	0.000	0.000	0.000
54	A	67	ASP	-1	-0.679	-0.810	20.679	0.122	0.122	0.000	0.000	0.000	0.000
55	A	68	ILE	0	-0.038	-0.025	23.685	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	69	GLY	0	0.017	0.016	26.734	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	70	LEU	0	0.005	0.000	24.111	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	71	PRO	0	-0.019	-0.007	28.082	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	72	ILE	0	0.021	0.008	27.321	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	73	ALA	0	0.037	0.024	24.033	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	74	ASN	0	-0.056	-0.024	24.651	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	75	GLY	0	0.106	0.047	24.630	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	76	PHE	0	0.021	-0.001	25.327	0.006	0.006	0.000	0.000	0.000	0.000
64	A	77	GLU	-1	-0.877	-0.935	27.637	0.025	0.025	0.000	0.000	0.000	0.000
65	A	78	VAL	0	0.005	0.001	21.089	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	79	MET	0	-0.031	0.000	22.690	0.001	0.001	0.000	0.000	0.000	0.000
67	A	80	SER	0	0.014	-0.005	23.914	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	81	ALA	0	-0.064	-0.020	23.549	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	82	VAL	0	0.004	-0.003	18.710	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	83	ARG	1	0.799	0.884	18.932	-0.130	-0.130	0.000	0.000	0.000	0.000
71	A	84	LYS	1	0.855	0.934	23.136	0.006	0.006	0.000	0.000	0.000	0.000
72	A	85	PRO	0	-0.003	-0.010	22.367	0.000	0.000	0.000	0.000	0.000	0.000
73	A	86	GLY	0	0.067	0.032	20.118	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	87	ALA	0	-0.006	0.001	14.451	0.022	0.022	0.000	0.000	0.000	0.000
75	A	88	ASN	0	0.008	-0.026	13.767	0.051	0.051	0.000	0.000	0.000	0.000
76	A	89	GLN	0	-0.024	0.013	16.161	0.034	0.034	0.000	0.000	0.000	0.000
77	A	90	HIS	0	0.000	-0.010	17.268	0.031	0.031	0.000	0.000	0.000	0.000
78	A	91	THR	0	-0.039	-0.016	13.093	0.045	0.045	0.000	0.000	0.000	0.000
79	A	92	PRO	0	0.010	0.017	13.680	-0.032	-0.032	0.000	0.000	0.000	0.000
80	A	93	ILE	0	0.018	0.008	15.873	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	94	VAL	0	-0.013	-0.012	17.353	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	95	ILE	0	-0.019	-0.019	19.630	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	96	LEU	0	0.009	-0.004	19.274	0.019	0.019	0.000	0.000	0.000	0.000
84	A	97	THR	0	0.004	-0.020	22.522	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	98	ASP	-1	-0.790	-0.852	25.755	0.144	0.144	0.000	0.000	0.000	0.000
86	A	99	ASN	0	-0.058	-0.029	28.802	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	100	VAL	0	-0.029	-0.004	27.618	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	101	SER	0	0.057	0.031	31.012	0.002	0.002	0.000	0.000	0.000	0.000
89	A	102	ASP	-1	-0.853	-0.935	32.840	0.106	0.106	0.000	0.000	0.000	0.000
90	A	103	ASP	-1	-0.854	-0.931	33.645	0.074	0.074	0.000	0.000	0.000	0.000
91	A	104	ARG	1	0.846	0.929	30.386	-0.075	-0.075	0.000	0.000	0.000	0.000
92	A	105	ALA	0	0.074	0.028	29.129	0.002	0.002	0.000	0.000	0.000	0.000
93	A	106	LYS	1	0.877	0.929	29.533	-0.072	-0.072	0.000	0.000	0.000	0.000
94	A	107	GLN	0	0.002	-0.002	31.786	0.000	0.000	0.000	0.000	0.000	0.000
95	A	108	CYS	0	-0.028	-0.002	26.402	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	109	MET	0	-0.026	-0.006	25.023	0.004	0.004	0.000	0.000	0.000	0.000
97	A	110	ALA	0	-0.036	-0.010	28.016	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	111	ALA	0	-0.028	-0.008	28.031	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	112	GLY	0	0.013	0.019	25.453	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	113	ALA	0	0.019	-0.004	22.778	0.010	0.010	0.000	0.000	0.000	0.000
101	A	114	SER	0	-0.030	-0.016	19.600	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	115	SER	0	-0.028	-0.022	20.786	0.014	0.014	0.000	0.000	0.000	0.000
103	A	116	VAL	0	0.002	-0.003	22.556	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	117	VAL	0	-0.037	-0.008	21.376	0.004	0.004	0.000	0.000	0.000	0.000
105	A	118	ASP	-1	-0.747	-0.857	24.314	0.142	0.142	0.000	0.000	0.000	0.000
106	A	119	LYS	1	0.752	0.856	22.589	-0.129	-0.129	0.000	0.000	0.000	0.000
107	A	120	SER	0	0.016	-0.019	25.498	0.010	0.010	0.000	0.000	0.000	0.000
108	A	121	SER	0	-0.039	-0.046	26.527	0.002	0.002	0.000	0.000	0.000	0.000
109	A	122	ASN	0	-0.055	-0.026	27.678	0.002	0.002	0.000	0.000	0.000	0.000
110	A	123	ASN	0	-0.050	-0.037	29.570	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	124	VAL	0	0.083	0.033	25.127	0.014	0.014	0.000	0.000	0.000	0.000
112	A	125	THR	0	-0.009	-0.001	25.179	0.020	0.020	0.000	0.000	0.000	0.000
113	A	126	ASP	-1	-0.806	-0.886	25.066	0.207	0.207	0.000	0.000	0.000	0.000
114	A	127	PHE	0	0.006	0.017	21.828	0.027	0.027	0.000	0.000	0.000	0.000
115	A	128	TYR	0	-0.007	-0.010	18.373	0.033	0.033	0.000	0.000	0.000	0.000
116	A	129	GLY	0	0.001	-0.007	20.021	0.044	0.044	0.000	0.000	0.000	0.000
117	A	130	ARG	1	0.768	0.863	20.534	-0.158	-0.158	0.000	0.000	0.000	0.000
118	A	131	ILE	0	-0.003	0.008	16.184	0.032	0.032	0.000	0.000	0.000	0.000
119	A	132	TYR	0	0.030	0.003	14.881	0.027	0.027	0.000	0.000	0.000	0.000
120	A	133	ALA	0	-0.006	-0.004	15.853	0.072	0.072	0.000	0.000	0.000	0.000
121	A	134	ILE	0	-0.004	0.003	15.330	0.038	0.038	0.000	0.000	0.000	0.000
122	A	135	PHE	0	0.047	0.005	10.593	0.027	0.027	0.000	0.000	0.000	0.000
123	A	136	SER	0	0.006	0.012	11.746	0.163	0.163	0.000	0.000	0.000	0.000
124	A	137	TYR	0	0.044	0.034	13.031	0.082	0.082	0.000	0.000	0.000	0.000
125	A	138	TRP	0	0.001	-0.017	13.325	0.042	0.042	0.000	0.000	0.000	0.000
126	A	139	LEU	0	-0.017	0.000	7.326	0.052	0.052	0.000	0.000	0.000	0.000
127	A	140	THR	0	-0.095	-0.065	8.776	0.327	0.327	0.000	0.000	0.000	0.000
128	A	141	VAL	0	-0.017	0.010	11.194	-0.070	-0.070	0.000	0.000	0.000	0.000
129	A	142	ASN	0	-0.001	0.002	13.163	-0.125	-0.125	0.000	0.000	0.000	0.000
130	A	143	HIS	0	0.004	0.015	12.679	0.120	0.120	0.000	0.000	0.000	0.000
131	A	144	CYS	0	-0.016	0.005	8.664	0.029	0.029	0.000	0.000	0.000	0.000
132	A	145	GLN	0	0.036	0.019	6.579	-0.020	-0.020	0.000	0.000	0.000	0.000

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