FMO DATABASE

FMODB ID: G6LN1

Calculation Name: 3K8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K8U

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DW05

Base Structure: X-ray

Registration Date: 2023-06-21

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1282368.441621
FMO2-HF: Nuclear repulsion	1228757.873457
FMO2-HF: Total energy	-53610.568164
FMO2-MP2: Total energy	-53769.022175

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:5:HIS)

Summations of interaction energy for fragment #1(A:5:HIS)

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.
-3.273	-1.684	-0.022	-0.697	-0.87	0.001

Interaction energy analysis for fragmet #1(A:5:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.004

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	7	LYS	1	0.878	0.949	3.800	-1.631	-0.042	-0.022	-0.697	-0.870	0.001
4	A	8	LEU	0	0.005	0.032	5.932	-0.338	-0.338	0.000	0.000	0.000	0.000
5	A	9	VAL	0	-0.049	-0.017	9.111	0.076	0.076	0.000	0.000	0.000	0.000
6	A	10	PRO	0	-0.025	-0.008	11.743	-0.077	-0.077	0.000	0.000	0.000	0.000
7	A	11	GLN	0	-0.029	-0.038	14.369	-0.045	-0.045	0.000	0.000	0.000	0.000
8	A	12	ILE	0	0.004	-0.004	18.134	0.020	0.020	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.849	-0.915	20.773	0.297	0.297	0.000	0.000	0.000	0.000
10	A	14	THR	0	0.009	-0.014	22.827	0.021	0.021	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.929	0.972	24.521	-0.248	-0.248	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.764	-0.878	20.954	0.358	0.358	0.000	0.000	0.000	0.000
13	A	17	CYS	0	0.002	0.049	19.254	0.033	0.033	0.000	0.000	0.000	0.000
14	A	18	GLY	0	0.079	0.033	18.920	0.032	0.032	0.000	0.000	0.000	0.000
15	A	19	PRO	0	-0.016	-0.011	19.571	0.023	0.023	0.000	0.000	0.000	0.000
16	A	20	ALA	0	0.001	0.013	15.943	0.026	0.026	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.043	0.035	14.783	0.087	0.087	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.006	0.012	14.801	0.027	0.027	0.000	0.000	0.000	0.000
19	A	23	ALA	0	0.016	0.002	15.150	0.011	0.011	0.000	0.000	0.000	0.000
20	A	24	SER	0	-0.059	-0.040	10.915	0.110	0.110	0.000	0.000	0.000	0.000
21	A	25	VAL	0	0.022	0.011	10.815	0.063	0.063	0.000	0.000	0.000	0.000
22	A	26	ALA	0	0.015	0.013	12.289	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.930	0.962	8.943	-1.090	-1.090	0.000	0.000	0.000	0.000
24	A	28	HIS	0	-0.081	-0.042	6.628	0.144	0.144	0.000	0.000	0.000	0.000
25	A	29	TYR	0	-0.008	-0.018	9.238	0.039	0.039	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.021	0.019	11.190	-0.055	-0.055	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.013	0.010	12.642	-0.050	-0.050	0.000	0.000	0.000	0.000
28	A	32	ASN	0	-0.025	-0.019	12.515	0.138	0.138	0.000	0.000	0.000	0.000
29	A	33	TYR	0	0.078	0.040	15.447	-0.050	-0.050	0.000	0.000	0.000	0.000
30	A	34	SER	0	0.019	0.005	17.120	0.040	0.040	0.000	0.000	0.000	0.000
31	A	35	ILE	0	0.071	0.027	16.906	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	36	ALA	0	-0.005	-0.004	20.060	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	37	TYR	0	0.032	0.018	21.883	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	38	LEU	0	0.033	0.007	18.341	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	39	ARG	1	0.770	0.859	22.565	-0.346	-0.346	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.922	-0.949	24.694	0.202	0.202	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.006	0.003	24.316	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	42	SER	0	-0.061	-0.025	24.232	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.841	0.914	26.384	-0.188	-0.188	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.012	0.024	25.117	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	45	ASN	0	0.058	0.023	27.925	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	46	LYS	1	0.955	0.968	29.182	-0.171	-0.171	0.000	0.000	0.000	0.000
43	A	47	GLN	0	-0.039	-0.029	30.003	0.006	0.006	0.000	0.000	0.000	0.000
44	A	48	GLY	0	0.027	0.031	26.793	0.006	0.006	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.019	-0.026	24.187	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	50	THR	0	0.021	0.015	26.152	0.003	0.003	0.000	0.000	0.000	0.000
47	A	51	ALA	0	0.101	0.034	24.913	0.013	0.013	0.000	0.000	0.000	0.000
48	A	52	LEU	0	0.014	0.002	25.578	0.007	0.007	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.054	0.039	27.185	0.001	0.001	0.000	0.000	0.000	0.000
50	A	54	ILE	0	-0.006	-0.008	20.659	0.010	0.010	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.005	-0.002	23.023	0.010	0.010	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.797	-0.890	24.657	0.184	0.184	0.000	0.000	0.000	0.000
53	A	57	ALA	0	-0.018	-0.009	23.469	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	58	ALA	0	0.031	0.004	20.939	0.007	0.007	0.000	0.000	0.000	0.000
55	A	59	LYS	1	0.909	0.951	22.211	-0.176	-0.176	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.818	0.912	25.140	-0.221	-0.221	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.082	-0.033	19.572	0.003	0.003	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.023	0.034	21.837	0.013	0.013	0.000	0.000	0.000	0.000
59	A	63	PHE	0	-0.056	-0.033	16.052	0.012	0.012	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.929	-0.963	21.453	0.129	0.129	0.000	0.000	0.000	0.000
61	A	65	THR	0	-0.042	-0.039	21.140	0.007	0.007	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.991	0.999	18.788	-0.152	-0.152	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.005	-0.003	22.342	0.022	0.022	0.000	0.000	0.000	0.000
64	A	68	ILE	0	0.009	0.008	21.773	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	69	LYS	1	0.839	0.901	24.509	-0.111	-0.111	0.000	0.000	0.000	0.000
66	A	70	ALA	0	-0.002	-0.010	22.543	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.759	-0.858	24.141	0.025	0.025	0.000	0.000	0.000	0.000
68	A	72	MET	0	-0.022	-0.022	19.268	0.014	0.014	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.016	-0.017	21.213	-0.014	-0.014	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.036	-0.005	18.440	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	75	PHE	0	-0.070	-0.066	15.430	0.003	0.003	0.000	0.000	0.000	0.000
72	A	76	ASP	-1	-0.897	-0.945	17.290	-0.147	-0.147	0.000	0.000	0.000	0.000
73	A	77	TYR	0	-0.085	-0.043	19.304	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	78	ASN	0	0.004	-0.027	16.847	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	79	ASP	-1	-0.861	-0.891	16.114	-0.126	-0.126	0.000	0.000	0.000	0.000
76	A	80	LEU	0	-0.086	-0.029	14.669	0.046	0.046	0.000	0.000	0.000	0.000
77	A	81	THR	0	-0.035	-0.015	13.468	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	82	TYR	0	0.008	0.029	9.527	0.039	0.039	0.000	0.000	0.000	0.000
79	A	83	PRO	0	-0.007	-0.016	8.992	0.012	0.012	0.000	0.000	0.000	0.000
80	A	84	PHE	0	-0.012	-0.013	10.828	-0.013	-0.013	0.000	0.000	0.000	0.000
81	A	85	ILE	0	-0.001	0.000	14.139	0.056	0.056	0.000	0.000	0.000	0.000
82	A	86	VAL	0	0.005	0.017	16.514	-0.053	-0.053	0.000	0.000	0.000	0.000
83	A	87	HIS	0	-0.033	-0.010	18.950	0.023	0.023	0.000	0.000	0.000	0.000
84	A	88	VAL	0	-0.002	-0.006	19.312	-0.022	-0.022	0.000	0.000	0.000	0.000
85	A	89	ILE	0	-0.004	-0.003	22.278	0.013	0.013	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.829	0.908	19.990	-0.324	-0.324	0.000	0.000	0.000	0.000
87	A	91	GLY	0	0.024	0.012	25.015	0.006	0.006	0.000	0.000	0.000	0.000
88	A	92	LYS	1	0.961	0.961	28.467	-0.147	-0.147	0.000	0.000	0.000	0.000
89	A	93	ARG	1	0.833	0.926	21.910	-0.341	-0.341	0.000	0.000	0.000	0.000
90	A	94	LEU	0	0.056	0.018	26.668	0.004	0.004	0.000	0.000	0.000	0.000
91	A	95	GLN	0	-0.016	0.003	25.926	0.002	0.002	0.000	0.000	0.000	0.000
92	A	96	HIS	0	-0.018	-0.023	18.799	-0.019	-0.019	0.000	0.000	0.000	0.000
93	A	97	TYR	0	-0.030	-0.041	19.026	-0.033	-0.033	0.000	0.000	0.000	0.000
94	A	98	TYR	0	-0.013	-0.026	14.577	0.053	0.053	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.002	0.005	10.797	-0.061	-0.061	0.000	0.000	0.000	0.000
96	A	100	VAL	0	0.004	-0.001	11.722	0.063	0.063	0.000	0.000	0.000	0.000
97	A	101	TYR	0	-0.001	-0.055	6.472	0.062	0.062	0.000	0.000	0.000	0.000
98	A	102	GLY	0	0.042	0.017	7.986	-0.131	-0.131	0.000	0.000	0.000	0.000
99	A	103	SER	0	-0.031	-0.007	9.727	0.080	0.080	0.000	0.000	0.000	0.000
100	A	104	GLN	0	0.031	0.023	8.750	-0.333	-0.333	0.000	0.000	0.000	0.000
101	A	105	ASN	0	0.017	0.011	11.950	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	106	ASN	0	0.051	0.031	15.401	0.040	0.040	0.000	0.000	0.000	0.000
103	A	107	GLN	0	-0.017	-0.022	13.496	0.007	0.007	0.000	0.000	0.000	0.000
104	A	108	LEU	0	0.040	0.029	12.625	-0.083	-0.083	0.000	0.000	0.000	0.000
105	A	109	ILE	0	-0.035	-0.009	6.175	0.063	0.063	0.000	0.000	0.000	0.000
106	A	110	ILE	0	0.007	-0.007	9.620	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.021	-0.004	10.254	0.250	0.250	0.000	0.000	0.000	0.000
108	A	112	ASP	-1	-0.781	-0.892	11.201	0.387	0.387	0.000	0.000	0.000	0.000
109	A	113	PRO	0	-0.007	-0.017	14.406	0.082	0.082	0.000	0.000	0.000	0.000
110	A	114	ASP	-1	-0.770	-0.857	15.519	0.459	0.459	0.000	0.000	0.000	0.000
111	A	115	PRO	0	0.002	-0.009	15.488	0.086	0.086	0.000	0.000	0.000	0.000
112	A	116	SER	0	-0.072	-0.044	15.981	0.047	0.047	0.000	0.000	0.000	0.000
113	A	117	VAL	0	-0.046	-0.016	14.612	-0.033	-0.033	0.000	0.000	0.000	0.000
114	A	118	LYS	1	0.912	0.955	10.785	-0.962	-0.962	0.000	0.000	0.000	0.000
115	A	119	VAL	0	0.001	0.000	6.049	-0.159	-0.159	0.000	0.000	0.000	0.000
116	A	120	THR	0	0.007	0.010	9.499	-0.021	-0.021	0.000	0.000	0.000	0.000
117	A	121	ARG	1	0.882	0.947	7.653	0.544	0.544	0.000	0.000	0.000	0.000
118	A	122	MET	0	-0.022	-0.004	11.951	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	123	SER	0	0.003	0.000	15.308	-0.040	-0.040	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.996	0.983	17.216	0.152	0.152	0.000	0.000	0.000	0.000
121	A	125	GLU	-1	-0.861	-0.924	19.186	0.015	0.015	0.000	0.000	0.000	0.000
122	A	126	ARG	1	0.929	0.967	19.803	-0.131	-0.131	0.000	0.000	0.000	0.000
123	A	127	PHE	0	0.035	-0.002	17.732	0.022	0.022	0.000	0.000	0.000	0.000
124	A	128	GLN	0	0.006	-0.003	19.838	0.011	0.011	0.000	0.000	0.000	0.000
125	A	129	SER	0	-0.074	-0.031	22.821	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	130	GLU	-1	-0.810	-0.868	20.590	0.270	0.270	0.000	0.000	0.000	0.000
127	A	131	TRP	0	-0.013	0.003	20.990	0.010	0.010	0.000	0.000	0.000	0.000
128	A	132	THR	0	0.027	0.003	22.857	-0.021	-0.021	0.000	0.000	0.000	0.000
129	A	133	GLY	0	0.076	0.046	23.772	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.095	-0.028	23.494	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	135	ALA	0	0.026	0.021	19.347	0.022	0.022	0.000	0.000	0.000	0.000
132	A	136	ILE	0	-0.022	-0.021	19.408	-0.017	-0.017	0.000	0.000	0.000	0.000
133	A	137	PHE	0	0.006	0.006	16.223	0.037	0.037	0.000	0.000	0.000	0.000
134	A	138	LEU	0	-0.001	-0.023	16.662	-0.010	-0.010	0.000	0.000	0.000	0.000
135	A	139	ALA	0	0.026	0.022	16.528	0.016	0.016	0.000	0.000	0.000	0.000
136	A	140	PRO	0	0.014	0.022	16.240	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	141	GLN	0	0.010	0.025	19.186	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:HIS)