FMO DATABASE

FMODB ID: VR9G1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1307460.489671
FMO2-HF: Nuclear repulsion	1238711.565813
FMO2-HF: Total energy	-68748.923858
FMO2-MP2: Total energy	-68949.846199

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.
2.436	5.004	0.916	-1.182	-2.303	0.003

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 : 0.021 / 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	3	ARG	1	0.928	0.978	2.416	-1.532	1.036	0.916	-1.182	-2.303	0.003
4	A	4	TYR	0	0.027	0.014	6.188	0.303	0.303	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.045	0.022	9.857	-0.164	-0.164	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.014	0.002	11.027	-0.068	-0.068	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.785	-0.877	10.257	-0.277	-0.277	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.014	0.001	11.426	0.035	0.035	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.011	-0.001	14.332	0.036	0.036	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.001	-0.003	14.545	0.024	0.024	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.006	0.001	14.842	0.011	0.011	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.014	0.011	16.867	0.029	0.029	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.882	0.937	19.871	0.124	0.124	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.984	0.999	16.146	0.154	0.154	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.840	-0.909	20.763	-0.207	-0.207	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.764	0.865	23.014	0.116	0.116	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.027	0.012	24.849	0.012	0.012	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.850	-0.905	24.264	-0.118	-0.118	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.877	0.918	24.053	0.160	0.160	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.008	0.005	29.121	0.006	0.006	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.788	-0.868	28.916	-0.059	-0.059	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.932	0.970	31.170	0.106	0.106	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.022	-0.017	32.941	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.033	0.024	34.854	0.004	0.004	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.960	0.986	35.542	0.067	0.067	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.794	-0.859	37.200	-0.059	-0.059	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.854	0.907	39.045	0.058	0.058	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.838	0.895	38.901	0.040	0.040	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.816	0.885	41.649	0.058	0.058	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.034	-0.017	42.298	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.020	0.013	45.043	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.828	-0.907	46.291	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.012	-0.013	46.686	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.807	-0.858	49.541	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	35	GLN	0	0.041	0.007	50.428	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.856	-0.918	51.972	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.836	0.897	52.758	0.037	0.037	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.031	-0.034	55.381	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.777	0.866	52.135	0.030	0.030	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.799	-0.873	58.200	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.794	0.878	59.722	0.028	0.028	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.735	-0.866	60.422	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.003	0.010	62.617	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.851	-0.917	63.940	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.733	0.840	64.476	0.019	0.019	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.809	-0.892	66.230	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.790	0.899	66.096	0.023	0.023	0.000	0.000	0.000	0.000
48	A	48	VAL	0	0.021	0.019	70.691	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.907	0.942	69.250	0.016	0.016	0.000	0.000	0.000	0.000
50	A	50	ASN	0	-0.047	-0.051	71.287	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	HIS	0	0.021	0.027	74.536	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.011	-0.007	76.256	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.014	-0.021	75.228	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.018	-0.006	76.681	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.887	0.947	80.579	0.014	0.014	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.004	-0.003	80.044	0.000	0.000	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.914	0.964	78.975	0.011	0.011	0.000	0.000	0.000	0.000
58	A	58	GLN	0	0.098	0.063	82.998	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.037	-0.021	86.504	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.811	0.874	86.604	0.009	0.009	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.867	-0.939	86.178	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	62	GLN	0	-0.043	-0.010	90.325	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.084	-0.054	90.409	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.874	-0.916	90.972	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.905	-0.945	94.338	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.033	0.013	96.509	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.005	-0.021	94.845	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.012	0.000	97.601	0.000	0.000	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.058	0.009	97.234	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.906	-0.954	96.479	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.004	0.010	94.641	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	ILE	0	0.036	0.019	92.307	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.032	-0.018	91.426	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.972	0.985	90.550	0.012	0.012	0.000	0.000	0.000	0.000
75	A	75	MET	0	0.004	0.005	88.347	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.953	0.968	86.825	0.010	0.010	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.038	-0.006	86.172	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	TYR	0	0.030	-0.001	84.311	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.009	0.008	82.246	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.938	0.966	81.260	0.012	0.012	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.018	0.018	79.791	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.009	0.008	76.983	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.004	-0.002	76.519	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	ILE	0	0.007	0.014	75.780	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	GLN	0	0.058	0.026	73.882	0.000	0.000	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.011	-0.010	71.086	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.039	-0.023	70.929	0.000	0.000	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.927	-0.964	70.043	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.872	-0.923	67.472	-0.023	-0.023	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.781	-0.899	66.160	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.831	-0.894	64.633	-0.021	-0.021	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.817	0.890	63.436	0.022	0.022	0.000	0.000	0.000	0.000
93	A	93	VAL	0	-0.032	-0.016	61.680	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.048	-0.031	60.630	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.858	0.918	59.764	0.023	0.023	0.000	0.000	0.000	0.000
96	A	96	GLN	0	-0.063	-0.010	53.995	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.851	0.914	55.793	0.019	0.019	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.874	-0.917	55.307	-0.025	-0.025	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.043	-0.026	52.731	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.009	-0.004	51.216	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.006	0.009	50.492	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	102	ALA	0	-0.009	-0.005	49.422	0.000	0.000	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.014	0.005	46.715	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	104	SER	0	-0.001	0.003	45.615	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.954	0.975	45.581	0.024	0.024	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.859	-0.905	42.294	-0.049	-0.049	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.002	-0.003	40.402	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.852	-0.930	40.590	-0.028	-0.028	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.869	0.913	40.328	0.037	0.037	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.010	-0.001	37.170	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.790	-0.880	35.801	-0.038	-0.038	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.005	0.015	35.775	0.001	0.001	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.786	-0.876	33.751	-0.052	-0.052	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.011	0.006	30.227	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.014	-0.009	30.724	0.000	0.000	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.800	0.880	31.006	0.047	0.047	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.713	0.834	27.477	0.066	0.066	0.000	0.000	0.000	0.000
118	A	118	ARG	1	0.917	0.934	26.411	0.047	0.047	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.956	0.994	26.294	0.013	0.013	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.836	-0.895	25.489	-0.063	-0.063	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.877	-0.960	20.166	-0.081	-0.081	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.764	-0.845	21.582	0.003	0.003	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.919	0.966	22.573	0.012	0.012	0.000	0.000	0.000	0.000
124	A	124	THR	0	-0.044	-0.031	17.863	0.006	0.006	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.789	0.844	17.903	-0.019	-0.019	0.000	0.000	0.000	0.000
126	A	126	LEU	0	0.028	0.021	17.853	0.016	0.016	0.000	0.000	0.000	0.000
127	A	127	HIS	0	-0.049	-0.042	18.517	0.007	0.007	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.827	0.901	10.743	0.222	0.222	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.894	-0.934	13.761	0.136	0.136	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.892	-0.950	15.421	0.155	0.155	0.000	0.000	0.000	0.000
131	A	131	TRP	0	-0.002	-0.004	7.254	-0.041	-0.041	0.000	0.000	0.000	0.000
132	A	132	MET	0	0.007	0.005	9.825	0.067	0.067	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.963	0.980	11.779	-0.114	-0.114	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.782	-0.873	14.472	0.438	0.438	0.000	0.000	0.000	0.000
135	A	135	ALA	0	-0.046	-0.010	9.048	0.057	0.057	0.000	0.000	0.000	0.000
136	A	136	LEU	0	0.013	-0.004	9.200	0.134	0.134	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.834	0.911	11.596	-0.332	-0.332	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.844	-0.889	12.570	0.607	0.607	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.913	-0.963	8.854	1.989	1.989	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.010	0.006	11.596	-0.059	-0.059	0.000	0.000	0.000	0.000
141	A	141	ARG	1	0.794	0.864	14.571	-0.542	-0.542	0.000	0.000	0.000	0.000
142	A	142	GLN	0	-0.044	-0.035	12.852	-0.093	-0.093	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.934	-0.968	12.443	0.782	0.782	0.000	0.000	0.000	0.000
144	A	144	GLU	-1	-0.993	-0.992	15.044	0.296	0.296	0.000	0.000	0.000	0.000
145	A	145	LYS	1	0.834	0.906	17.275	-0.536	-0.536	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.887	-0.940	14.945	0.484	0.484	0.000	0.000	0.000	0.000
147	A	147	GLN	0	-0.041	-0.019	16.732	-0.086	-0.086	0.000	0.000	0.000	0.000
148	A	148	ASP	-1	-0.916	-0.946	20.034	0.244	0.244	0.000	0.000	0.000	0.000
149	A	149	GLU	-1	-0.920	-0.958	20.818	0.327	0.327	0.000	0.000	0.000	0.000
150	A	150	MET	0	-0.016	-0.016	18.953	-0.045	-0.045	0.000	0.000	0.000	0.000
151	A	151	GLY	0	0.010	0.011	22.211	-0.028	-0.028	0.000	0.000	0.000	0.000
152	A	152	GLN	0	-0.031	-0.030	25.033	-0.040	-0.040	0.000	0.000	0.000	0.000
153	A	153	LEU	0	0.008	0.019	22.825	-0.024	-0.024	0.000	0.000	0.000	0.000
154	A	154	LEU	0	0.029	0.005	24.121	-0.023	-0.023	0.000	0.000	0.000	0.000
155	A	155	HIS	0	0.006	0.013	27.583	-0.019	-0.019	0.000	0.000	0.000	0.000
156	A	156	GLN	0	-0.033	-0.036	29.216	-0.015	-0.015	0.000	0.000	0.000	0.000
157	A	157	LEU	0	0.009	0.010	27.701	-0.013	-0.013	0.000	0.000	0.000	0.000
158	A	158	HIS	0	-0.081	-0.053	30.223	-0.018	-0.018	0.000	0.000	0.000	0.000
159	A	159	LYS	1	0.929	0.967	34.027	-0.127	-0.127	0.000	0.000	0.000	0.000
160	A	160	GLN	0	-0.023	0.003	33.627	-0.002	-0.002	0.000	0.000	0.000	0.000
161	A	161	LYS	1	0.896	0.950	35.040	-0.109	-0.109	0.000	0.000	0.000	0.000
162	A	162	GLN	0	-0.020	0.011	38.095	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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