FMO DATABASE

FMODB ID: 729RK

Calculation Name: 3PGE-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PGE

Chain ID: B

ChEMBL ID:

UniProt ID: P15873

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptAll
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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1498817.933058
FMO2-HF: Nuclear repulsion	1433372.020464
FMO2-HF: Total energy	-65445.912595
FMO2-MP2: Total energy	-65633.152901

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-25.69	-23.374	32.809	-15.444	-19.679	-0.12

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.081 / q_NPA : -0.046

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	B	3	GLU	-1	-0.879	-0.942	2.668	-4.523	-0.947	0.282	-1.396	-2.462	-0.001
4	B	4	ALA	0	-0.006	0.006	4.635	0.210	0.274	-0.001	-0.014	-0.048	0.000
5	B	5	LYS	1	0.877	0.943	8.402	0.961	0.961	0.000	0.000	0.000	0.000
6	B	6	PHE	0	0.011	-0.007	10.688	0.033	0.033	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.868	-0.932	14.339	-0.407	-0.407	0.000	0.000	0.000	0.000
8	B	8	GLU	-1	-0.824	-0.882	16.938	-0.194	-0.194	0.000	0.000	0.000	0.000
9	B	9	ALA	0	0.011	0.009	17.324	-0.016	-0.016	0.000	0.000	0.000	0.000
10	B	10	SER	0	-0.051	-0.051	18.273	0.014	0.014	0.000	0.000	0.000	0.000
11	B	11	LEU	0	-0.041	-0.013	18.356	0.024	0.024	0.000	0.000	0.000	0.000
12	B	12	PHE	0	0.088	0.035	14.816	0.010	0.010	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.868	0.922	18.399	0.157	0.157	0.000	0.000	0.000	0.000
14	B	14	ARG	1	0.854	0.918	20.962	0.240	0.240	0.000	0.000	0.000	0.000
15	B	15	ILE	0	0.016	0.015	19.285	0.015	0.015	0.000	0.000	0.000	0.000
16	B	16	ILE	0	0.010	0.008	18.050	0.018	0.018	0.000	0.000	0.000	0.000
17	B	17	ASP	-1	-0.882	-0.966	22.047	-0.099	-0.099	0.000	0.000	0.000	0.000
18	B	18	GLY	0	-0.042	-0.007	25.127	0.016	0.016	0.000	0.000	0.000	0.000
19	B	19	PHE	0	0.008	-0.002	20.093	0.000	0.000	0.000	0.000	0.000	0.000
20	B	20	LYS	1	0.823	0.911	24.102	0.106	0.106	0.000	0.000	0.000	0.000
21	B	21	ASP	-1	-0.888	-0.918	25.556	-0.073	-0.073	0.000	0.000	0.000	0.000
22	B	22	CYS	0	-0.103	-0.041	27.955	0.003	0.003	0.000	0.000	0.000	0.000
23	B	23	VAL	0	0.052	0.016	24.733	0.006	0.006	0.000	0.000	0.000	0.000
24	B	24	GLN	0	-0.023	-0.006	24.697	-0.010	-0.010	0.000	0.000	0.000	0.000
25	B	25	LEU	0	-0.024	-0.016	21.465	0.010	0.010	0.000	0.000	0.000	0.000
26	B	26	VAL	0	0.025	0.014	18.221	-0.014	-0.014	0.000	0.000	0.000	0.000
27	B	27	ASN	0	0.012	-0.009	16.079	0.039	0.039	0.000	0.000	0.000	0.000
28	B	28	PHE	0	-0.005	-0.012	13.183	-0.030	-0.030	0.000	0.000	0.000	0.000
29	B	29	GLN	0	0.018	0.011	12.315	-0.121	-0.121	0.000	0.000	0.000	0.000
30	B	30	CYS	0	-0.030	0.010	8.560	0.066	0.066	0.000	0.000	0.000	0.000
31	B	31	LYS	1	0.920	0.951	9.942	1.105	1.105	0.000	0.000	0.000	0.000
32	B	32	GLU	-1	-0.846	-0.927	8.857	-1.863	-1.863	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.936	-0.965	10.502	-1.050	-1.050	0.000	0.000	0.000	0.000
34	B	34	GLY	0	0.024	0.008	12.596	0.165	0.165	0.000	0.000	0.000	0.000
35	B	35	ILE	0	-0.043	-0.024	10.754	-0.136	-0.136	0.000	0.000	0.000	0.000
36	B	36	ILE	0	0.001	0.007	13.783	0.123	0.123	0.000	0.000	0.000	0.000
37	B	37	ALA	0	-0.004	-0.011	15.845	-0.014	-0.014	0.000	0.000	0.000	0.000
38	B	38	GLN	0	-0.001	-0.012	18.341	0.008	0.008	0.000	0.000	0.000	0.000
39	B	39	ALA	0	0.002	0.007	21.247	0.011	0.011	0.000	0.000	0.000	0.000
40	B	40	VAL	0	0.009	0.005	23.967	-0.009	-0.009	0.000	0.000	0.000	0.000
41	B	41	ASP	-1	-0.717	-0.831	27.696	-0.081	-0.081	0.000	0.000	0.000	0.000
42	B	42	ASP	-1	-0.819	-0.919	29.737	-0.049	-0.049	0.000	0.000	0.000	0.000
43	B	43	SER	0	-0.110	-0.078	31.683	0.008	0.008	0.000	0.000	0.000	0.000
44	B	44	ARG	1	0.704	0.861	27.939	0.079	0.079	0.000	0.000	0.000	0.000
45	B	45	VAL	0	-0.034	-0.024	33.164	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	46	LEU	0	-0.056	-0.018	30.452	-0.005	-0.005	0.000	0.000	0.000	0.000
47	B	47	LEU	0	0.002	0.006	26.245	0.001	0.001	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.012	-0.010	24.140	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	49	SER	0	0.014	-0.006	23.132	-0.014	-0.014	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.057	-0.016	18.798	0.018	0.018	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.926	-0.968	18.992	-0.543	-0.543	0.000	0.000	0.000	0.000
52	B	52	ILE	0	-0.055	-0.026	15.953	0.063	0.063	0.000	0.000	0.000	0.000
53	B	53	GLY	0	0.096	0.051	15.722	-0.120	-0.120	0.000	0.000	0.000	0.000
54	B	54	VAL	0	0.033	0.005	13.067	0.014	0.014	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.942	-0.974	15.348	-0.660	-0.660	0.000	0.000	0.000	0.000
56	B	56	ALA	0	-0.081	-0.024	16.928	0.075	0.075	0.000	0.000	0.000	0.000
57	B	57	PHE	0	-0.074	-0.045	12.521	0.004	0.004	0.000	0.000	0.000	0.000
58	B	58	GLN	0	-0.056	-0.040	13.195	0.004	0.004	0.000	0.000	0.000	0.000
59	B	59	GLU	-1	-0.968	-0.988	9.100	-1.176	-1.176	0.000	0.000	0.000	0.000
60	B	60	TYR	0	-0.054	-0.051	9.142	-0.104	-0.104	0.000	0.000	0.000	0.000
61	B	61	ARG	1	0.780	0.878	1.944	4.153	4.106	5.178	-1.781	-3.351	-0.005
62	B	62	CYS	0	0.022	-0.001	4.928	-0.808	-0.691	-0.001	-0.039	-0.077	0.000
63	B	63	ASP	-1	-0.834	-0.890	1.880	-14.714	-15.321	11.142	-5.767	-4.768	-0.059
64	B	64	HIS	0	-0.033	-0.021	3.780	1.971	2.293	0.000	-0.048	-0.273	0.000
65	B	65	PRO	0	0.006	0.007	5.609	-0.619	-0.619	0.000	0.000	0.000	0.000
66	B	66	VAL	0	-0.028	-0.006	5.739	0.236	0.236	0.000	0.000	0.000	0.000
67	B	67	THR	0	0.002	-0.012	8.160	-0.050	-0.050	0.000	0.000	0.000	0.000
68	B	68	LEU	0	0.012	0.007	7.655	0.183	0.183	0.000	0.000	0.000	0.000
69	B	69	GLY	0	0.076	0.059	11.797	-0.050	-0.050	0.000	0.000	0.000	0.000
70	B	70	MET	0	-0.038	-0.025	13.370	0.124	0.124	0.000	0.000	0.000	0.000
71	B	71	ASP	-1	-0.681	-0.804	16.958	0.011	0.011	0.000	0.000	0.000	0.000
72	B	72	LEU	0	0.045	0.029	19.154	0.014	0.014	0.000	0.000	0.000	0.000
73	B	73	THR	0	-0.016	-0.006	21.381	-0.008	-0.008	0.000	0.000	0.000	0.000
74	B	74	SER	0	-0.070	-0.059	20.376	0.022	0.022	0.000	0.000	0.000	0.000
75	B	75	LEU	0	0.048	0.032	15.544	0.024	0.024	0.000	0.000	0.000	0.000
76	B	76	SER	0	-0.010	-0.027	18.771	-0.004	-0.004	0.000	0.000	0.000	0.000
77	B	77	LYS	1	0.736	0.858	21.448	-0.088	-0.088	0.000	0.000	0.000	0.000
78	B	78	ILE	0	0.053	0.025	15.049	-0.006	-0.006	0.000	0.000	0.000	0.000
79	B	79	LEU	0	0.037	0.016	16.064	-0.005	-0.005	0.000	0.000	0.000	0.000
80	B	80	ARG	1	0.846	0.928	18.952	-0.013	-0.013	0.000	0.000	0.000	0.000
81	B	81	CYS	0	-0.092	-0.022	18.137	0.015	0.015	0.000	0.000	0.000	0.000
82	B	82	GLY	0	0.033	0.023	18.439	0.011	0.011	0.000	0.000	0.000	0.000
83	B	83	ASN	0	0.021	0.014	19.486	-0.011	-0.011	0.000	0.000	0.000	0.000
84	B	84	ASN	0	-0.115	-0.076	20.724	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	85	THR	0	0.055	0.024	21.742	-0.008	-0.008	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.836	-0.877	16.643	-0.120	-0.120	0.000	0.000	0.000	0.000
87	B	87	THR	0	0.037	0.032	13.785	-0.047	-0.047	0.000	0.000	0.000	0.000
88	B	88	LEU	0	-0.034	-0.035	12.434	0.067	0.067	0.000	0.000	0.000	0.000
89	B	89	THR	0	0.036	0.014	6.852	-0.124	-0.124	0.000	0.000	0.000	0.000
90	B	90	LEU	0	-0.033	-0.009	8.529	0.274	0.274	0.000	0.000	0.000	0.000
91	B	91	ILE	0	0.018	0.000	2.519	-1.148	-0.925	1.612	-0.340	-1.495	-0.002
92	B	92	ALA	0	0.010	-0.004	4.246	-0.292	0.202	0.011	-0.145	-0.359	0.001
93	B	93	ASP	-1	-0.857	-0.913	2.154	0.606	3.536	5.374	-4.283	-4.022	-0.027
94	B	94	ASN	0	-0.002	-0.019	1.874	-7.773	-12.669	9.212	-1.605	-2.710	-0.027
95	B	95	THR	0	-0.087	-0.044	4.297	0.391	0.531	0.000	-0.026	-0.114	0.000
96	B	96	PRO	0	0.027	0.046	6.440	0.143	0.143	0.000	0.000	0.000	0.000
97	B	97	ASP	-1	-0.845	-0.931	8.307	0.640	0.640	0.000	0.000	0.000	0.000
98	B	98	SER	0	-0.093	-0.079	10.118	-0.316	-0.316	0.000	0.000	0.000	0.000
99	B	99	ILE	0	0.006	0.032	8.713	0.376	0.376	0.000	0.000	0.000	0.000
100	B	100	ILE	0	0.018	0.008	5.833	-0.041	-0.041	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.030	-0.019	8.500	-0.286	-0.286	0.000	0.000	0.000	0.000
102	B	102	LEU	0	0.041	0.016	7.893	0.101	0.101	0.000	0.000	0.000	0.000
103	B	103	PHE	0	-0.009	-0.004	10.407	-0.134	-0.134	0.000	0.000	0.000	0.000
104	B	104	GLU	-1	-0.880	-0.936	12.047	-0.291	-0.291	0.000	0.000	0.000	0.000
105	B	105	ASP	-1	-0.807	-0.887	14.903	-0.158	-0.158	0.000	0.000	0.000	0.000
106	B	106	THR	0	-0.050	-0.043	17.638	-0.006	-0.006	0.000	0.000	0.000	0.000
107	B	107	LYS	1	0.927	0.975	19.917	0.044	0.044	0.000	0.000	0.000	0.000
108	B	108	LYS	1	0.946	0.959	17.432	-0.037	-0.037	0.000	0.000	0.000	0.000
109	B	109	ASP	-1	-0.966	-0.986	18.434	0.004	0.004	0.000	0.000	0.000	0.000
110	B	110	ARG	1	0.771	0.859	17.407	0.077	0.077	0.000	0.000	0.000	0.000
111	B	111	ILE	0	0.005	0.003	12.591	-0.030	-0.030	0.000	0.000	0.000	0.000
112	B	112	ALA	0	-0.040	-0.020	14.272	0.046	0.046	0.000	0.000	0.000	0.000
113	B	113	GLU	-1	-0.912	-0.946	8.336	0.659	0.659	0.000	0.000	0.000	0.000
114	B	114	TYR	0	-0.035	-0.019	11.875	0.024	0.024	0.000	0.000	0.000	0.000
115	B	115	SER	0	-0.015	-0.014	10.947	0.081	0.081	0.000	0.000	0.000	0.000
116	B	116	LEU	0	-0.065	-0.029	12.525	-0.085	-0.085	0.000	0.000	0.000	0.000
117	B	117	LYS	1	0.966	0.978	13.494	-0.519	-0.519	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.026	-0.006	10.007	-0.118	-0.118	0.000	0.000	0.000	0.000
119	B	119	MET	0	-0.073	-0.036	14.622	0.033	0.033	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.890	-0.936	16.811	0.167	0.167	0.000	0.000	0.000	0.000
121	B	121	ILE	0	-0.069	-0.039	18.211	-0.006	-0.006	0.000	0.000	0.000	0.000
122	B	122	ASP	-1	-0.903	-0.939	19.565	-0.050	-0.050	0.000	0.000	0.000	0.000
123	B	123	ALA	0	-0.050	-0.038	20.035	-0.014	-0.014	0.000	0.000	0.000	0.000
124	B	124	ASP	-1	-0.838	-0.899	21.486	-0.140	-0.140	0.000	0.000	0.000	0.000
125	B	125	PHE	0	-0.066	-0.056	24.690	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	126	LEU	0	-0.049	-0.004	23.890	-0.004	-0.004	0.000	0.000	0.000	0.000
127	B	127	LYS	1	0.837	0.894	24.827	0.236	0.236	0.000	0.000	0.000	0.000
128	B	128	ILE	0	0.003	0.008	25.585	-0.017	-0.017	0.000	0.000	0.000	0.000
129	B	129	GLU	-1	-0.838	-0.911	28.170	-0.224	-0.224	0.000	0.000	0.000	0.000
130	B	130	GLU	-1	-0.959	-0.967	30.207	-0.244	-0.244	0.000	0.000	0.000	0.000
131	B	131	LEU	0	-0.018	-0.015	32.862	0.005	0.005	0.000	0.000	0.000	0.000
132	B	132	GLN	0	-0.061	-0.031	36.071	0.007	0.007	0.000	0.000	0.000	0.000
133	B	133	TYR	0	0.047	0.009	34.014	0.000	0.000	0.000	0.000	0.000	0.000
134	B	134	ASP	-1	-0.911	-0.942	40.171	-0.115	-0.115	0.000	0.000	0.000	0.000
135	B	135	SER	0	-0.063	-0.043	42.455	0.007	0.007	0.000	0.000	0.000	0.000
136	B	136	THR	0	-0.031	-0.017	37.667	-0.008	-0.008	0.000	0.000	0.000	0.000
137	B	137	LEU	0	-0.019	0.000	39.725	0.005	0.005	0.000	0.000	0.000	0.000
138	B	138	SER	0	0.013	0.006	37.669	-0.009	-0.009	0.000	0.000	0.000	0.000
139	B	139	LEU	0	-0.011	0.005	38.557	0.006	0.006	0.000	0.000	0.000	0.000
140	B	140	PRO	0	0.031	0.015	37.727	-0.010	-0.010	0.000	0.000	0.000	0.000
141	B	141	SER	0	0.060	0.029	33.359	0.009	0.009	0.000	0.000	0.000	0.000
142	B	142	SER	0	-0.005	-0.011	36.115	0.005	0.005	0.000	0.000	0.000	0.000
143	B	143	GLU	-1	-0.887	-0.951	37.995	-0.099	-0.099	0.000	0.000	0.000	0.000
144	B	144	PHE	0	0.065	0.024	36.751	0.006	0.006	0.000	0.000	0.000	0.000
145	B	145	SER	0	0.030	0.023	36.816	0.009	0.009	0.000	0.000	0.000	0.000
146	B	146	LYS	1	0.761	0.861	38.838	0.076	0.076	0.000	0.000	0.000	0.000
147	B	147	ILE	0	0.045	0.018	42.237	0.006	0.006	0.000	0.000	0.000	0.000
148	B	148	VAL	0	0.045	0.023	39.133	0.005	0.005	0.000	0.000	0.000	0.000
149	B	149	ARG	1	0.886	0.948	38.925	0.094	0.094	0.000	0.000	0.000	0.000
150	B	150	ASP	-1	-0.831	-0.891	42.577	-0.063	-0.063	0.000	0.000	0.000	0.000
151	B	151	LEU	0	-0.009	-0.018	45.582	0.004	0.004	0.000	0.000	0.000	0.000
152	B	152	SER	0	0.006	-0.015	42.653	0.002	0.002	0.000	0.000	0.000	0.000
153	B	153	GLN	0	-0.091	-0.031	45.022	0.005	0.005	0.000	0.000	0.000	0.000
154	B	154	LEU	0	-0.088	-0.040	47.795	0.004	0.004	0.000	0.000	0.000	0.000
155	B	155	SER	0	-0.030	-0.031	47.991	0.003	0.003	0.000	0.000	0.000	0.000
156	B	156	ASP	-1	-0.895	-0.923	44.772	-0.048	-0.048	0.000	0.000	0.000	0.000
157	B	157	SER	0	-0.068	-0.042	44.179	-0.004	-0.004	0.000	0.000	0.000	0.000
158	B	158	ILE	0	0.012	0.020	42.710	0.003	0.003	0.000	0.000	0.000	0.000
159	B	159	ASN	0	-0.035	-0.015	44.747	-0.003	-0.003	0.000	0.000	0.000	0.000
160	B	160	ILE	0	0.021	0.007	42.644	-0.001	-0.001	0.000	0.000	0.000	0.000
161	B	161	MET	0	-0.022	-0.009	46.082	0.001	0.001	0.000	0.000	0.000	0.000
162	B	162	ILE	0	0.031	0.014	44.346	-0.001	-0.001	0.000	0.000	0.000	0.000
163	B	163	THR	0	-0.017	0.001	48.986	0.003	0.003	0.000	0.000	0.000	0.000

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