FMO DATABASE

FMODB ID: G56K1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1174599.745168
FMO2-HF: Nuclear repulsion	1122698.572215
FMO2-HF: Total energy	-51901.172953
FMO2-MP2: Total energy	-52051.965106

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.
-0.563	3.444	0.222	-1.651	-2.579	0.012

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 : -0.010 / 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	0.962	0.980	3.790	3.200	4.501	-0.005	-0.561	-0.735	0.004
4	A	17	VAL	0	-0.021	-0.011	6.217	0.002	0.002	0.000	0.000	0.000	0.000
5	A	18	LEU	0	-0.021	0.010	9.636	-0.064	-0.064	0.000	0.000	0.000	0.000
6	A	19	VAL	0	-0.013	-0.021	12.747	0.058	0.058	0.000	0.000	0.000	0.000
7	A	20	VAL	0	-0.022	-0.022	15.523	-0.037	-0.037	0.000	0.000	0.000	0.000
8	A	21	GLU	-1	-0.799	-0.896	18.894	0.112	0.112	0.000	0.000	0.000	0.000
9	A	22	ASP	-1	-0.902	-0.968	20.261	0.002	0.002	0.000	0.000	0.000	0.000
10	A	23	ASN	0	0.049	0.047	22.944	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	24	PRO	0	0.027	-0.005	21.649	0.013	0.013	0.000	0.000	0.000	0.000
12	A	25	ASP	-1	-0.923	-0.961	21.571	0.065	0.065	0.000	0.000	0.000	0.000
13	A	26	ASP	-1	-0.844	-0.920	21.245	0.138	0.138	0.000	0.000	0.000	0.000
14	A	27	ILE	0	-0.034	-0.009	16.388	0.035	0.035	0.000	0.000	0.000	0.000
15	A	28	ALA	0	-0.040	-0.012	16.921	0.031	0.031	0.000	0.000	0.000	0.000
16	A	29	LEU	0	-0.040	-0.030	17.923	0.029	0.029	0.000	0.000	0.000	0.000
17	A	30	ILE	0	0.014	-0.004	13.900	0.050	0.050	0.000	0.000	0.000	0.000
18	A	31	ARG	1	0.938	0.964	11.868	0.009	0.009	0.000	0.000	0.000	0.000
19	A	32	ARG	1	0.961	0.978	13.369	-0.079	-0.079	0.000	0.000	0.000	0.000
20	A	33	VAL	0	-0.019	0.002	15.420	0.026	0.026	0.000	0.000	0.000	0.000
21	A	34	LEU	0	-0.037	-0.032	9.358	0.012	0.012	0.000	0.000	0.000	0.000
22	A	35	ASP	-1	-0.871	-0.923	11.722	0.414	0.414	0.000	0.000	0.000	0.000
23	A	36	ARG	1	0.896	0.957	12.857	-0.229	-0.229	0.000	0.000	0.000	0.000
24	A	37	LYS	1	0.828	0.927	14.143	-0.461	-0.461	0.000	0.000	0.000	0.000
25	A	38	ASP	-1	-0.874	-0.935	11.494	0.784	0.784	0.000	0.000	0.000	0.000
26	A	39	ILE	0	-0.080	-0.031	8.563	0.215	0.215	0.000	0.000	0.000	0.000
27	A	40	HIS	0	0.002	-0.001	5.000	-0.067	-0.067	0.000	0.000	0.000	0.000
28	A	41	CYS	0	-0.076	-0.031	3.175	0.645	1.586	0.083	-0.411	-0.613	0.003
29	A	42	GLN	0	-0.087	-0.034	3.074	-5.258	-3.479	0.145	-0.677	-1.248	0.005
30	A	43	LEU	0	0.052	0.021	5.287	-0.133	-0.147	-0.001	-0.002	0.017	0.000
31	A	44	GLU	-1	-0.858	-0.885	8.870	-0.766	-0.766	0.000	0.000	0.000	0.000
32	A	45	PHE	0	0.025	0.008	11.842	0.052	0.052	0.000	0.000	0.000	0.000
33	A	46	VAL	0	-0.032	-0.014	15.427	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	47	ASP	-1	-0.810	-0.903	18.488	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	48	ASN	0	0.035	0.003	21.645	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	49	GLY	0	0.111	0.060	21.762	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	50	ALA	0	-0.059	-0.015	22.607	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	51	LYS	1	0.858	0.898	19.816	0.086	0.086	0.000	0.000	0.000	0.000
39	A	52	ALA	0	0.031	0.027	18.086	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	53	LEU	0	-0.023	-0.023	18.192	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	54	TYR	0	-0.015	0.011	17.784	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	55	GLN	0	0.065	0.003	12.763	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	56	VAL	0	-0.035	-0.005	14.450	-0.054	-0.054	0.000	0.000	0.000	0.000
44	A	57	GLN	0	-0.075	-0.040	15.855	-0.032	-0.032	0.000	0.000	0.000	0.000
45	A	58	GLN	0	-0.050	-0.002	13.875	-0.055	-0.055	0.000	0.000	0.000	0.000
46	A	59	ALA	0	-0.033	-0.008	9.392	-0.144	-0.144	0.000	0.000	0.000	0.000
47	A	60	LYS	1	0.833	0.929	9.262	0.227	0.227	0.000	0.000	0.000	0.000
48	A	61	TYR	0	-0.062	-0.086	8.666	-0.268	-0.268	0.000	0.000	0.000	0.000
49	A	62	ASP	-1	-0.873	-0.948	6.231	-0.108	-0.108	0.000	0.000	0.000	0.000
50	A	63	LEU	0	-0.028	-0.012	9.453	0.117	0.117	0.000	0.000	0.000	0.000
51	A	64	ILE	0	0.010	0.011	12.102	-0.054	-0.054	0.000	0.000	0.000	0.000
52	A	65	ILE	0	-0.032	-0.011	14.164	0.029	0.029	0.000	0.000	0.000	0.000
53	A	66	LEU	0	-0.023	-0.013	17.122	-0.036	-0.036	0.000	0.000	0.000	0.000
54	A	67	ASP	-1	-0.696	-0.829	20.367	0.092	0.092	0.000	0.000	0.000	0.000
55	A	68	ILE	0	-0.094	-0.029	23.296	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	69	GLY	0	0.017	0.004	26.388	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	70	LEU	0	0.041	0.018	23.901	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	71	PRO	0	-0.021	0.006	27.760	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	72	ILE	0	0.022	0.000	27.669	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	73	ALA	0	0.015	0.004	24.079	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	74	ASN	0	-0.066	-0.046	24.743	0.000	0.000	0.000	0.000	0.000	0.000
62	A	75	GLY	0	0.099	0.029	24.852	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	76	PHE	0	0.013	-0.009	25.180	0.001	0.001	0.000	0.000	0.000	0.000
64	A	77	GLU	-1	-0.854	-0.902	27.069	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	78	VAL	0	-0.007	-0.002	20.654	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	79	MET	0	-0.030	-0.002	22.514	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	80	SER	0	-0.007	-0.028	23.598	0.000	0.000	0.000	0.000	0.000	0.000
68	A	81	ALA	0	-0.071	-0.033	23.152	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	82	VAL	0	-0.027	-0.007	17.955	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	83	ARG	1	0.801	0.888	18.455	-0.086	-0.086	0.000	0.000	0.000	0.000
71	A	84	LYS	1	0.892	0.967	22.397	0.039	0.039	0.000	0.000	0.000	0.000
72	A	85	PRO	0	0.004	-0.007	21.441	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	86	GLY	0	0.059	0.033	19.375	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	87	ALA	0	0.007	0.003	13.627	0.024	0.024	0.000	0.000	0.000	0.000
75	A	88	ASN	0	-0.002	-0.001	13.157	0.033	0.033	0.000	0.000	0.000	0.000
76	A	89	GLN	0	0.037	0.055	15.576	0.030	0.030	0.000	0.000	0.000	0.000
77	A	90	HIS	0	0.003	-0.016	17.081	0.024	0.024	0.000	0.000	0.000	0.000
78	A	91	THR	0	-0.049	-0.022	12.970	0.051	0.051	0.000	0.000	0.000	0.000
79	A	92	PRO	0	0.036	0.030	13.496	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	93	ILE	0	0.020	0.005	15.686	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	94	VAL	0	-0.007	-0.005	17.041	0.006	0.006	0.000	0.000	0.000	0.000
82	A	95	ILE	0	-0.011	-0.018	19.314	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	96	LEU	0	-0.043	-0.022	18.919	0.021	0.021	0.000	0.000	0.000	0.000
84	A	97	THR	0	-0.023	-0.036	22.209	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	98	ASP	-1	-0.774	-0.837	25.419	0.119	0.119	0.000	0.000	0.000	0.000
86	A	99	ASN	0	-0.025	-0.001	28.266	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	100	VAL	0	-0.061	-0.004	27.303	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	101	SER	0	0.069	0.038	30.669	0.002	0.002	0.000	0.000	0.000	0.000
89	A	102	ASP	-1	-0.842	-0.944	32.467	0.098	0.098	0.000	0.000	0.000	0.000
90	A	103	ASP	-1	-0.956	-0.971	33.631	0.062	0.062	0.000	0.000	0.000	0.000
91	A	104	ARG	1	0.901	0.954	30.214	-0.050	-0.050	0.000	0.000	0.000	0.000
92	A	105	ALA	0	0.080	0.046	28.982	0.000	0.000	0.000	0.000	0.000	0.000
93	A	106	LYS	1	0.978	0.986	29.422	-0.069	-0.069	0.000	0.000	0.000	0.000
94	A	107	GLN	0	-0.018	-0.022	31.396	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	108	CYS	0	-0.045	-0.025	26.152	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	109	MET	0	-0.037	-0.009	24.906	0.002	0.002	0.000	0.000	0.000	0.000
97	A	110	ALA	0	-0.047	-0.019	27.896	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	111	ALA	0	-0.025	-0.006	27.741	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	112	GLY	0	0.019	0.019	24.892	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	113	ALA	0	0.012	0.000	22.420	0.008	0.008	0.000	0.000	0.000	0.000
101	A	114	SER	0	-0.035	-0.023	19.436	0.001	0.001	0.000	0.000	0.000	0.000
102	A	115	SER	0	-0.017	-0.004	20.293	0.004	0.004	0.000	0.000	0.000	0.000
103	A	116	VAL	0	0.033	0.016	22.316	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	117	VAL	0	-0.070	-0.033	20.998	0.008	0.008	0.000	0.000	0.000	0.000
105	A	118	ASP	-1	-0.798	-0.917	24.102	0.119	0.119	0.000	0.000	0.000	0.000
106	A	119	LYS	1	0.802	0.864	22.417	-0.098	-0.098	0.000	0.000	0.000	0.000
107	A	120	SER	0	-0.012	-0.011	25.021	0.011	0.011	0.000	0.000	0.000	0.000
108	A	121	SER	0	-0.048	-0.083	26.079	0.004	0.004	0.000	0.000	0.000	0.000
109	A	122	ASN	0	-0.045	-0.011	27.452	0.003	0.003	0.000	0.000	0.000	0.000
110	A	123	ASN	0	0.008	0.002	29.275	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	124	VAL	0	0.068	0.023	25.036	0.014	0.014	0.000	0.000	0.000	0.000
112	A	125	THR	0	-0.023	-0.009	25.046	0.020	0.020	0.000	0.000	0.000	0.000
113	A	126	ASP	-1	-0.880	-0.945	25.210	0.189	0.189	0.000	0.000	0.000	0.000
114	A	127	PHE	0	-0.040	-0.007	21.238	0.028	0.028	0.000	0.000	0.000	0.000
115	A	128	TYR	0	0.025	0.006	19.305	0.033	0.033	0.000	0.000	0.000	0.000
116	A	129	GLY	0	-0.023	-0.023	19.997	0.046	0.046	0.000	0.000	0.000	0.000
117	A	130	ARG	1	0.974	0.989	20.434	-0.161	-0.161	0.000	0.000	0.000	0.000
118	A	131	ILE	0	-0.005	0.022	16.037	0.035	0.035	0.000	0.000	0.000	0.000
119	A	132	TYR	0	0.003	-0.021	14.889	0.030	0.030	0.000	0.000	0.000	0.000
120	A	133	ALA	0	0.005	-0.002	15.755	0.078	0.078	0.000	0.000	0.000	0.000
121	A	134	ILE	0	-0.009	0.014	14.918	0.046	0.046	0.000	0.000	0.000	0.000
122	A	135	PHE	0	0.050	-0.005	10.314	0.028	0.028	0.000	0.000	0.000	0.000
123	A	136	SER	0	0.008	0.022	11.496	0.187	0.187	0.000	0.000	0.000	0.000
124	A	137	TYR	0	0.020	0.022	13.020	0.084	0.084	0.000	0.000	0.000	0.000
125	A	138	TRP	0	-0.007	-0.010	13.010	0.031	0.031	0.000	0.000	0.000	0.000
126	A	139	LEU	0	-0.009	-0.007	7.074	0.073	0.073	0.000	0.000	0.000	0.000
127	A	140	THR	0	-0.109	-0.080	8.836	0.278	0.278	0.000	0.000	0.000	0.000
128	A	141	VAL	0	-0.041	-0.007	10.938	-0.071	-0.071	0.000	0.000	0.000	0.000
129	A	142	ASN	0	-0.029	-0.004	13.328	-0.097	-0.097	0.000	0.000	0.000	0.000
130	A	143	HIS	0	0.012	0.008	12.321	0.112	0.112	0.000	0.000	0.000	0.000
131	A	144	CYS	0	-0.021	-0.008	8.177	0.000	0.000	0.000	0.000	0.000	0.000
132	A	145	GLN	0	0.004	0.003	6.596	-0.070	-0.070	0.000	0.000	0.000	0.000

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