FMO DATABASE

FMODB ID: 9GNN2

Calculation Name: 3K29-A-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	164
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1311479.878494
FMO2-HF: Nuclear repulsion	1242561.759999
FMO2-HF: Total energy	-68918.118496
FMO2-MP2: Total energy	-69119.572122

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:0:ACE )

Summations of interaction energy for fragment #1(A:0:ACE )

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.
2.221	3.182	-0.005	-0.425	-0.53	-0.001

Interaction energy analysis for fragmet #1(A:0:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.017

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	2	VAL	0	0.074	0.046	3.816	0.943	1.904	-0.005	-0.425	-0.530	-0.001
4	A	3	ARG	1	0.934	0.966	6.603	1.210	1.210	0.000	0.000	0.000	0.000
5	A	4	TYR	0	0.038	0.020	9.708	0.103	0.103	0.000	0.000	0.000	0.000
6	A	5	PRO	0	0.044	0.024	12.969	0.018	0.018	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.010	-0.001	14.214	0.034	0.034	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.818	-0.914	14.126	-0.287	-0.287	0.000	0.000	0.000	0.000
9	A	8	PRO	0	0.010	-0.004	15.181	0.018	0.018	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.001	0.009	18.170	0.017	0.017	0.000	0.000	0.000	0.000
11	A	10	LEU	0	0.005	-0.004	18.646	0.009	0.009	0.000	0.000	0.000	0.000
12	A	11	SER	0	-0.006	-0.004	18.821	0.007	0.007	0.000	0.000	0.000	0.000
13	A	12	ILE	0	0.040	0.020	20.855	0.013	0.013	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.880	0.936	23.824	0.095	0.095	0.000	0.000	0.000	0.000
15	A	14	LYS	1	1.002	1.002	20.526	0.189	0.189	0.000	0.000	0.000	0.000
16	A	15	ASP	-1	-0.828	-0.897	24.699	-0.088	-0.088	0.000	0.000	0.000	0.000
17	A	16	ARG	1	0.799	0.892	26.979	0.068	0.068	0.000	0.000	0.000	0.000
18	A	17	VAL	0	0.022	0.005	29.108	0.008	0.008	0.000	0.000	0.000	0.000
19	A	18	ASP	-1	-0.825	-0.886	28.191	-0.085	-0.085	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.863	0.912	28.210	0.066	0.066	0.000	0.000	0.000	0.000
21	A	20	ALA	0	0.001	0.002	33.100	0.005	0.005	0.000	0.000	0.000	0.000
22	A	21	GLU	-1	-0.843	-0.928	33.034	-0.071	-0.071	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.934	0.972	35.262	0.050	0.050	0.000	0.000	0.000	0.000
24	A	23	VAL	0	-0.027	-0.022	37.140	0.004	0.004	0.000	0.000	0.000	0.000
25	A	24	VAL	0	0.044	0.032	39.071	0.003	0.003	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.958	0.984	39.813	0.046	0.046	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.824	-0.904	41.372	-0.029	-0.029	0.000	0.000	0.000	0.000
28	A	27	LYS	1	0.926	0.955	42.894	0.033	0.033	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.957	0.979	43.473	0.042	0.042	0.000	0.000	0.000	0.000
30	A	29	ARG	1	0.840	0.929	45.853	0.030	0.030	0.000	0.000	0.000	0.000
31	A	30	LEU	0	-0.035	-0.023	46.346	0.002	0.002	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.020	0.016	49.230	0.001	0.001	0.000	0.000	0.000	0.000
33	A	32	GLU	-1	-0.889	-0.946	50.573	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.008	-0.004	50.744	0.001	0.001	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.817	-0.884	53.528	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	35	GLN	0	0.025	-0.001	54.650	0.002	0.002	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.972	-0.980	56.332	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	37	LYS	1	0.920	0.948	57.018	0.019	0.019	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.045	-0.043	59.575	0.001	0.001	0.000	0.000	0.000	0.000
40	A	39	ARG	1	0.922	0.957	56.790	0.023	0.023	0.000	0.000	0.000	0.000
41	A	40	GLU	-1	-0.921	-0.952	62.234	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.876	0.942	63.832	0.016	0.016	0.000	0.000	0.000	0.000
43	A	42	GLU	-1	-0.890	-0.963	64.545	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	43	SER	0	-0.008	0.020	66.886	0.001	0.001	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.887	-0.968	68.356	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	45	ARG	1	0.864	0.929	68.679	0.015	0.015	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.886	-0.944	70.479	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	47	LYS	1	0.817	0.926	70.920	0.014	0.014	0.000	0.000	0.000	0.000
49	A	48	VAL	0	0.018	0.019	74.903	0.000	0.000	0.000	0.000	0.000	0.000
50	A	49	LYS	1	1.001	0.990	74.828	0.014	0.014	0.000	0.000	0.000	0.000
51	A	50	ASN	0	-0.024	-0.031	75.470	0.000	0.000	0.000	0.000	0.000	0.000
52	A	51	HIS	0	0.027	0.030	78.900	0.000	0.000	0.000	0.000	0.000	0.000
53	A	52	TYR	0	-0.007	-0.003	80.528	0.000	0.000	0.000	0.000	0.000	0.000
54	A	53	MET	0	-0.022	-0.029	80.192	0.000	0.000	0.000	0.000	0.000	0.000
55	A	54	GLN	0	-0.013	-0.003	81.472	0.000	0.000	0.000	0.000	0.000	0.000
56	A	55	LYS	1	0.881	0.947	84.916	0.009	0.009	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.011	-0.007	84.286	0.000	0.000	0.000	0.000	0.000	0.000
58	A	57	ARG	1	0.921	0.961	83.411	0.011	0.011	0.000	0.000	0.000	0.000
59	A	58	GLN	0	0.102	0.066	87.165	0.000	0.000	0.000	0.000	0.000	0.000
60	A	59	LEU	0	-0.032	-0.016	90.851	0.000	0.000	0.000	0.000	0.000	0.000
61	A	60	ARG	1	0.935	0.946	88.787	0.010	0.010	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.871	-0.932	91.232	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	62	GLN	0	-0.024	-0.003	94.789	0.000	0.000	0.000	0.000	0.000	0.000
64	A	63	LEU	0	-0.104	-0.064	94.707	0.000	0.000	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.957	-0.972	95.668	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	65	ASP	-1	-0.931	-0.956	98.829	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	66	GLY	0	-0.040	0.010	100.982	0.000	0.000	0.000	0.000	0.000	0.000
68	A	67	THR	0	-0.010	-0.022	99.244	0.000	0.000	0.000	0.000	0.000	0.000
69	A	68	THR	0	0.000	-0.006	101.863	0.000	0.000	0.000	0.000	0.000	0.000
70	A	69	SER	0	0.061	0.007	101.458	0.000	0.000	0.000	0.000	0.000	0.000
71	A	70	ASP	-1	-0.872	-0.935	100.618	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	71	ALA	0	-0.035	-0.002	98.793	0.000	0.000	0.000	0.000	0.000	0.000
73	A	72	ILE	0	0.042	0.018	96.376	0.000	0.000	0.000	0.000	0.000	0.000
74	A	73	LEU	0	-0.022	-0.019	95.585	0.000	0.000	0.000	0.000	0.000	0.000
75	A	74	LYS	1	0.973	0.989	94.403	0.007	0.007	0.000	0.000	0.000	0.000
76	A	75	MET	0	0.004	0.005	92.506	0.000	0.000	0.000	0.000	0.000	0.000
77	A	76	LYS	1	0.938	0.961	90.977	0.008	0.008	0.000	0.000	0.000	0.000
78	A	77	ALA	0	-0.043	-0.008	90.256	0.000	0.000	0.000	0.000	0.000	0.000
79	A	78	TYR	0	0.031	0.001	88.421	0.000	0.000	0.000	0.000	0.000	0.000
80	A	79	ILE	0	0.008	0.009	86.291	0.000	0.000	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.935	0.961	85.367	0.008	0.008	0.000	0.000	0.000	0.000
82	A	81	VAL	0	0.020	0.024	83.804	0.000	0.000	0.000	0.000	0.000	0.000
83	A	82	VAL	0	0.006	0.007	81.194	0.000	0.000	0.000	0.000	0.000	0.000
84	A	83	ALA	0	-0.005	-0.011	80.601	0.000	0.000	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.001	0.020	79.685	0.000	0.000	0.000	0.000	0.000	0.000
86	A	85	GLN	0	0.068	0.028	77.850	0.000	0.000	0.000	0.000	0.000	0.000
87	A	86	LEU	0	-0.018	-0.011	75.180	0.000	0.000	0.000	0.000	0.000	0.000
88	A	87	SER	0	-0.043	-0.023	75.015	0.000	0.000	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.915	-0.966	73.984	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	89	GLU	-1	-0.883	-0.935	71.304	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	90	GLU	-1	-0.854	-0.940	70.218	-0.014	-0.014	0.000	0.000	0.000	0.000
92	A	91	GLU	-1	-0.858	-0.902	68.404	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	92	LYS	1	0.852	0.910	67.350	0.012	0.012	0.000	0.000	0.000	0.000
94	A	93	VAL	0	-0.020	-0.009	65.660	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	94	ASN	0	-0.010	-0.019	64.722	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.892	0.940	63.682	0.013	0.013	0.000	0.000	0.000	0.000
97	A	96	GLN	0	-0.063	0.001	57.938	0.000	0.000	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.936	0.963	59.839	0.017	0.017	0.000	0.000	0.000	0.000
99	A	98	GLU	-1	-0.939	-0.960	59.385	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	99	ASN	0	-0.046	-0.026	56.674	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	100	VAL	0	-0.006	-0.002	55.203	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	101	LEU	0	0.009	0.010	54.629	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	102	ALA	0	-0.003	-0.004	53.292	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	103	ALA	0	0.020	0.010	50.694	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	104	SER	0	0.014	0.004	49.721	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	105	LYS	1	0.957	0.971	49.768	0.021	0.021	0.000	0.000	0.000	0.000
107	A	106	GLU	-1	-0.898	-0.938	46.104	-0.029	-0.029	0.000	0.000	0.000	0.000
108	A	107	LEU	0	-0.012	-0.004	44.610	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	108	GLU	-1	-0.912	-0.950	44.813	-0.031	-0.031	0.000	0.000	0.000	0.000
110	A	109	ARG	1	0.855	0.907	44.381	0.024	0.024	0.000	0.000	0.000	0.000
111	A	110	ALA	0	-0.004	0.002	41.192	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	111	GLU	-1	-0.900	-0.961	39.945	-0.045	-0.045	0.000	0.000	0.000	0.000
113	A	112	VAL	0	-0.005	0.010	40.047	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	113	GLU	-1	-0.874	-0.945	37.768	-0.045	-0.045	0.000	0.000	0.000	0.000
115	A	114	LEU	0	-0.005	-0.002	34.507	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	115	THR	0	-0.012	-0.009	34.993	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	116	LYS	1	0.880	0.932	35.193	0.039	0.039	0.000	0.000	0.000	0.000
118	A	117	ARG	1	0.701	0.839	31.548	0.052	0.052	0.000	0.000	0.000	0.000
119	A	118	ARG	1	0.980	0.991	30.502	0.064	0.064	0.000	0.000	0.000	0.000
120	A	119	LYS	1	0.968	1.003	30.520	0.053	0.053	0.000	0.000	0.000	0.000
121	A	120	GLU	-1	-0.900	-0.935	29.349	-0.065	-0.065	0.000	0.000	0.000	0.000
122	A	121	GLU	-1	-0.919	-0.976	24.832	-0.135	-0.135	0.000	0.000	0.000	0.000
123	A	122	GLU	-1	-0.749	-0.867	25.660	-0.129	-0.129	0.000	0.000	0.000	0.000
124	A	123	LYS	1	0.881	0.947	26.538	0.066	0.066	0.000	0.000	0.000	0.000
125	A	124	THR	0	-0.029	-0.022	21.552	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	125	ARG	1	0.833	0.914	21.941	0.131	0.131	0.000	0.000	0.000	0.000
127	A	126	LEU	0	0.010	0.011	21.935	-0.017	-0.017	0.000	0.000	0.000	0.000
128	A	127	HIS	0	-0.026	-0.019	21.681	0.002	0.002	0.000	0.000	0.000	0.000
129	A	128	LYS	1	0.879	0.952	15.204	0.321	0.321	0.000	0.000	0.000	0.000
130	A	129	GLU	-1	-0.891	-0.955	17.679	-0.201	-0.201	0.000	0.000	0.000	0.000
131	A	130	GLU	-1	-0.925	-0.977	19.328	-0.134	-0.134	0.000	0.000	0.000	0.000
132	A	131	TRP	0	-0.007	0.006	10.782	0.001	0.001	0.000	0.000	0.000	0.000
133	A	132	MET	0	-0.001	-0.002	14.131	-0.032	-0.032	0.000	0.000	0.000	0.000
134	A	133	LYS	1	0.957	0.976	15.313	0.126	0.126	0.000	0.000	0.000	0.000
135	A	134	GLU	-1	-0.842	-0.934	17.174	-0.134	-0.134	0.000	0.000	0.000	0.000
136	A	135	ALA	0	-0.059	-0.018	11.734	0.004	0.004	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.005	-0.016	12.774	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	137	LYS	1	0.914	0.960	14.438	0.148	0.148	0.000	0.000	0.000	0.000
139	A	138	GLU	-1	-0.882	-0.935	13.574	-0.064	-0.064	0.000	0.000	0.000	0.000
140	A	139	GLU	-1	-0.900	-0.956	10.038	-0.223	-0.223	0.000	0.000	0.000	0.000
141	A	140	ALA	0	0.010	0.006	12.680	0.034	0.034	0.000	0.000	0.000	0.000
142	A	141	ARG	1	0.830	0.922	15.872	0.132	0.132	0.000	0.000	0.000	0.000
143	A	142	GLN	0	-0.065	-0.033	12.886	0.051	0.051	0.000	0.000	0.000	0.000
144	A	143	GLU	-1	-0.921	-0.967	11.994	-0.204	-0.204	0.000	0.000	0.000	0.000
145	A	144	GLU	-1	-0.970	-0.978	15.418	-0.040	-0.040	0.000	0.000	0.000	0.000
146	A	145	LYS	1	0.911	0.967	16.214	-0.019	-0.019	0.000	0.000	0.000	0.000
147	A	146	GLU	-1	-0.897	-0.968	14.722	0.080	0.080	0.000	0.000	0.000	0.000
148	A	147	GLN	0	-0.040	-0.019	17.921	0.007	0.007	0.000	0.000	0.000	0.000
149	A	148	ASP	-1	-0.926	-0.946	20.028	-0.011	-0.011	0.000	0.000	0.000	0.000
150	A	149	GLU	-1	-0.976	-0.990	20.257	0.053	0.053	0.000	0.000	0.000	0.000
151	A	150	MET	0	-0.029	-0.023	18.409	0.011	0.011	0.000	0.000	0.000	0.000
152	A	151	GLY	0	0.007	0.010	21.657	0.000	0.000	0.000	0.000	0.000	0.000
153	A	152	GLN	0	-0.030	-0.033	24.731	0.003	0.003	0.000	0.000	0.000	0.000
154	A	153	LEU	0	0.023	0.025	21.943	0.001	0.001	0.000	0.000	0.000	0.000
155	A	154	LEU	0	0.023	0.006	24.075	0.000	0.000	0.000	0.000	0.000	0.000
156	A	155	HIS	0	-0.009	-0.002	26.928	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	156	GLN	0	-0.038	-0.042	28.205	0.003	0.003	0.000	0.000	0.000	0.000
158	A	157	LEU	0	0.012	0.012	26.664	0.001	0.001	0.000	0.000	0.000	0.000
159	A	158	HIS	0	-0.076	-0.040	29.734	-0.001	-0.001	0.000	0.000	0.000	0.000
160	A	159	LYS	1	0.932	0.965	33.310	-0.019	-0.019	0.000	0.000	0.000	0.000
161	A	160	GLN	0	-0.023	0.007	32.630	0.000	0.000	0.000	0.000	0.000	0.000
162	A	161	LYS	1	0.913	0.954	34.571	-0.025	-0.025	0.000	0.000	0.000	0.000
163	A	162	GLN	0	-0.015	0.029	37.183	0.000	0.000	0.000	0.000	0.000	0.000
164	A	163	NME	0	-0.017	-0.022	40.316	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ACE )