FMO DATABASE

FMODB ID: YY4G2

Calculation Name: 3K29-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K29

Chain ID: A

ChEMBL ID:

UniProt ID: O84677

Base Structure: X-ray

Registration Date: 2023-06-19

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	162
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1306403.863408
FMO2-HF: Nuclear repulsion	1237656.641719
FMO2-HF: Total energy	-68747.221688
FMO2-MP2: Total energy	-68948.144187

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:1:MET)

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

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.
3.136	5.788	0.332	-0.989	-1.994	0.001

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.008

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	3	ARG	1	0.940	0.970	2.786	-0.640	2.012	0.332	-0.989	-1.994	0.001
4	A	4	TYR	0	0.038	0.019	6.012	0.236	0.236	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.041	0.022	9.820	-0.143	-0.143	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.007	0.000	11.042	-0.038	-0.038	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.817	-0.913	9.828	-0.377	-0.377	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.013	-0.002	11.375	0.069	0.069	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.000	0.008	14.305	0.053	0.053	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.007	-0.003	14.081	0.039	0.039	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.007	0.001	14.695	0.025	0.025	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.018	0.009	16.611	0.040	0.040	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.882	0.937	19.742	0.192	0.192	0.000	0.000	0.000	0.000
14	A	14	LYS	1	1.004	1.003	15.678	0.213	0.213	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.833	-0.899	20.590	-0.229	-0.229	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.801	0.893	22.689	0.160	0.160	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.023	0.006	24.592	0.015	0.015	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.826	-0.887	23.656	-0.135	-0.135	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.864	0.912	24.242	0.186	0.186	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.003	0.003	28.808	0.008	0.008	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.843	-0.927	28.292	-0.079	-0.079	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.933	0.972	30.903	0.117	0.117	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.028	-0.022	32.679	0.005	0.005	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.047	0.033	34.574	0.005	0.005	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.954	0.982	35.263	0.073	0.073	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.824	-0.904	36.926	-0.066	-0.066	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.927	0.955	38.689	0.074	0.074	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.956	0.979	38.663	0.051	0.051	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.840	0.930	41.519	0.064	0.064	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.033	-0.022	42.201	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.021	0.017	44.772	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.890	-0.947	46.043	-0.035	-0.035	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.006	-0.005	46.493	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.816	-0.884	49.207	-0.042	-0.042	0.000	0.000	0.000	0.000
35	A	35	GLN	0	0.026	-0.001	50.028	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.972	-0.980	51.828	-0.033	-0.033	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.920	0.948	52.775	0.043	0.043	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.044	-0.042	55.121	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.918	0.954	52.171	0.033	0.033	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.919	-0.951	57.924	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.878	0.943	59.490	0.032	0.032	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.891	-0.963	59.937	-0.025	-0.025	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.009	0.019	62.369	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.887	-0.968	63.982	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.864	0.929	64.083	0.023	0.023	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.887	-0.944	65.847	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.817	0.926	66.488	0.025	0.025	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.019	0.019	70.443	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.998	0.989	70.230	0.019	0.019	0.000	0.000	0.000	0.000
50	A	50	ASN	0	-0.021	-0.031	70.824	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	HIS	0	0.027	0.030	74.314	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.005	-0.002	76.015	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.023	-0.029	75.255	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.016	-0.004	76.915	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.881	0.947	80.362	0.016	0.016	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.006	-0.005	79.707	0.001	0.001	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.917	0.960	78.681	0.014	0.014	0.000	0.000	0.000	0.000
58	A	58	GLN	0	0.100	0.065	82.633	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.028	-0.014	86.276	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.934	0.945	84.043	0.012	0.012	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.874	-0.933	86.540	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	62	GLN	0	-0.023	-0.003	90.120	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.102	-0.063	90.089	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.956	-0.972	90.938	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.933	-0.957	94.131	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.039	0.010	96.306	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.007	-0.021	94.689	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.002	-0.006	97.352	0.000	0.000	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.061	0.008	96.977	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.873	-0.935	96.205	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.034	-0.001	94.363	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	ILE	0	0.042	0.018	91.884	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.024	-0.019	91.155	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.971	0.988	90.066	0.014	0.014	0.000	0.000	0.000	0.000
75	A	75	MET	0	0.004	0.005	88.085	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.939	0.962	86.557	0.013	0.013	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.042	-0.008	85.887	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	TYR	0	0.027	-0.001	84.064	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.014	0.011	81.825	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.933	0.960	80.979	0.014	0.014	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.019	0.023	79.554	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.005	0.007	76.803	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.005	-0.011	76.236	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.003	0.020	75.506	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	GLN	0	0.068	0.028	73.568	0.000	0.000	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.018	-0.011	70.735	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.046	-0.025	70.639	0.000	0.000	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.914	-0.965	69.732	-0.024	-0.024	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.883	-0.935	66.982	-0.027	-0.027	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.853	-0.940	65.867	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.860	-0.903	64.227	-0.028	-0.028	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.853	0.910	63.135	0.026	0.026	0.000	0.000	0.000	0.000
93	A	93	VAL	0	-0.019	-0.008	61.374	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.012	-0.021	60.335	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.894	0.942	59.519	0.029	0.029	0.000	0.000	0.000	0.000
96	A	96	GLN	0	-0.061	0.001	53.631	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.933	0.962	55.490	0.024	0.024	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.938	-0.960	55.001	-0.034	-0.034	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.046	-0.026	52.459	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.006	-0.001	50.901	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.009	0.009	50.195	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	102	ALA	0	-0.006	-0.005	49.149	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.022	0.010	46.394	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	104	SER	0	0.014	0.005	45.312	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.957	0.971	45.286	0.037	0.037	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.899	-0.938	41.997	-0.063	-0.063	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.010	-0.003	40.043	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.913	-0.950	40.300	-0.040	-0.040	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.853	0.906	40.123	0.050	0.050	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.001	0.003	36.773	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.901	-0.961	35.494	-0.052	-0.052	0.000	0.000	0.000	0.000
112	A	112	VAL	0	-0.008	0.009	35.494	0.000	0.000	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.873	-0.946	33.551	-0.080	-0.080	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.002	-0.001	29.900	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.012	-0.009	30.440	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.878	0.932	30.721	0.074	0.074	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.702	0.839	27.171	0.096	0.096	0.000	0.000	0.000	0.000
118	A	118	ARG	1	0.982	0.992	26.097	0.062	0.062	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.969	1.003	26.033	0.050	0.050	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.902	-0.936	25.338	-0.104	-0.104	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.915	-0.974	20.189	-0.128	-0.128	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.754	-0.869	21.300	-0.056	-0.056	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.880	0.947	22.399	0.067	0.067	0.000	0.000	0.000	0.000
124	A	124	THR	0	-0.026	-0.021	17.467	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.828	0.912	17.657	0.022	0.022	0.000	0.000	0.000	0.000
126	A	126	LEU	0	0.014	0.012	17.898	0.008	0.008	0.000	0.000	0.000	0.000
127	A	127	HIS	0	-0.030	-0.020	18.505	0.009	0.009	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.883	0.954	10.922	0.283	0.283	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.890	-0.955	13.904	0.055	0.055	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.928	-0.979	15.626	0.067	0.067	0.000	0.000	0.000	0.000
131	A	131	TRP	0	-0.006	0.007	7.321	-0.013	-0.013	0.000	0.000	0.000	0.000
132	A	132	MET	0	0.001	0.000	10.208	0.048	0.048	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.955	0.975	12.023	-0.052	-0.052	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.844	-0.934	14.704	0.325	0.325	0.000	0.000	0.000	0.000
135	A	135	ALA	0	-0.060	-0.018	9.172	0.054	0.054	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.002	-0.015	9.526	0.124	0.124	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.913	0.960	11.859	-0.217	-0.217	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.882	-0.935	12.597	0.473	0.473	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.900	-0.956	9.345	1.545	1.545	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.010	0.006	11.764	-0.028	-0.028	0.000	0.000	0.000	0.000
141	A	141	ARG	1	0.828	0.922	14.809	-0.405	-0.405	0.000	0.000	0.000	0.000
142	A	142	GLN	0	-0.063	-0.032	12.962	-0.063	-0.063	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.920	-0.967	11.637	0.903	0.903	0.000	0.000	0.000	0.000
144	A	144	GLU	-1	-0.970	-0.979	15.623	0.256	0.256	0.000	0.000	0.000	0.000
145	A	145	LYS	1	0.910	0.967	17.027	-0.512	-0.512	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.895	-0.968	15.636	0.444	0.444	0.000	0.000	0.000	0.000
147	A	147	GLN	0	-0.041	-0.019	18.486	-0.037	-0.037	0.000	0.000	0.000	0.000
148	A	148	ASP	-1	-0.927	-0.947	20.553	0.240	0.240	0.000	0.000	0.000	0.000
149	A	149	GLU	-1	-0.975	-0.990	21.243	0.300	0.300	0.000	0.000	0.000	0.000
150	A	150	MET	0	-0.028	-0.022	19.371	-0.037	-0.037	0.000	0.000	0.000	0.000
151	A	151	GLY	0	0.005	0.009	22.626	-0.025	-0.025	0.000	0.000	0.000	0.000
152	A	152	GLN	0	-0.030	-0.032	25.495	-0.038	-0.038	0.000	0.000	0.000	0.000
153	A	153	LEU	0	0.024	0.025	23.219	-0.022	-0.022	0.000	0.000	0.000	0.000
154	A	154	LEU	0	0.023	0.006	24.921	-0.021	-0.021	0.000	0.000	0.000	0.000
155	A	155	HIS	0	-0.010	-0.003	27.957	-0.015	-0.015	0.000	0.000	0.000	0.000
156	A	156	GLN	0	-0.038	-0.041	29.425	-0.012	-0.012	0.000	0.000	0.000	0.000
157	A	157	LEU	0	0.014	0.012	27.997	-0.013	-0.013	0.000	0.000	0.000	0.000
158	A	158	HIS	0	-0.076	-0.039	30.685	-0.016	-0.016	0.000	0.000	0.000	0.000
159	A	159	LYS	1	0.933	0.967	34.384	-0.129	-0.129	0.000	0.000	0.000	0.000
160	A	160	GLN	0	-0.028	0.004	34.077	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	161	LYS	1	0.926	0.961	35.824	-0.118	-0.118	0.000	0.000	0.000	0.000
162	A	162	GLN	0	-0.038	0.003	38.403	-0.005	-0.005	0.000	0.000	0.000	0.000

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