FMO DATABASE

FMODB ID: 94362

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1499112.252352
FMO2-HF: Nuclear repulsion	1433668.874177
FMO2-HF: Total energy	-65443.378175
FMO2-MP2: Total energy	-65630.83602

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.
-13.184	-28.047	54.58	-21.182	-18.535	-0.097

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 : -0.056 / q_NPA : -0.028

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	-0.975	-1.009	3.281	-5.794	-1.790	0.080	-1.874	-2.210	0.001
4	B	4	ALA	0	-0.005	0.016	4.835	0.398	0.420	-0.001	-0.006	-0.014	0.000
5	B	5	LYS	1	0.964	0.996	8.565	0.842	0.842	0.000	0.000	0.000	0.000
6	B	6	PHE	0	-0.004	-0.024	10.822	0.030	0.030	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.948	-0.975	14.476	-0.378	-0.378	0.000	0.000	0.000	0.000
8	B	8	GLU	-1	-0.924	-0.958	17.343	-0.244	-0.244	0.000	0.000	0.000	0.000
9	B	9	ALA	0	0.002	-0.014	17.079	-0.026	-0.026	0.000	0.000	0.000	0.000
10	B	10	SER	0	-0.087	-0.048	18.063	-0.005	-0.005	0.000	0.000	0.000	0.000
11	B	11	LEU	0	-0.009	0.003	18.808	0.024	0.024	0.000	0.000	0.000	0.000
12	B	12	PHE	0	0.100	0.041	14.823	0.011	0.011	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.895	0.948	18.446	0.213	0.213	0.000	0.000	0.000	0.000
14	B	14	ARG	1	0.931	0.960	20.855	0.272	0.272	0.000	0.000	0.000	0.000
15	B	15	ILE	0	0.018	0.019	19.263	0.019	0.019	0.000	0.000	0.000	0.000
16	B	16	ILE	0	0.009	0.006	18.349	0.018	0.018	0.000	0.000	0.000	0.000
17	B	17	ASP	-1	-0.891	-0.974	22.034	-0.163	-0.163	0.000	0.000	0.000	0.000
18	B	18	GLY	0	-0.062	-0.021	25.113	0.019	0.019	0.000	0.000	0.000	0.000
19	B	19	PHE	0	-0.013	-0.026	20.201	0.004	0.004	0.000	0.000	0.000	0.000
20	B	20	LYS	1	0.886	0.965	24.295	0.149	0.149	0.000	0.000	0.000	0.000
21	B	21	ASP	-1	-0.949	-0.974	25.464	-0.112	-0.112	0.000	0.000	0.000	0.000
22	B	22	CYS	0	-0.082	-0.019	28.195	0.007	0.007	0.000	0.000	0.000	0.000
23	B	23	VAL	0	0.043	0.017	24.554	0.010	0.010	0.000	0.000	0.000	0.000
24	B	24	GLN	0	-0.013	-0.003	24.473	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	25	LEU	0	-0.001	-0.013	21.171	0.000	0.000	0.000	0.000	0.000	0.000
26	B	26	VAL	0	0.031	0.030	18.085	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	27	ASN	0	-0.015	-0.010	15.869	0.012	0.012	0.000	0.000	0.000	0.000
28	B	28	PHE	0	-0.023	-0.016	13.282	-0.011	-0.011	0.000	0.000	0.000	0.000
29	B	29	GLN	0	-0.015	-0.019	12.407	-0.100	-0.100	0.000	0.000	0.000	0.000
30	B	30	CYS	0	-0.024	0.001	8.383	0.070	0.070	0.000	0.000	0.000	0.000
31	B	31	LYS	1	0.952	0.979	9.538	1.012	1.012	0.000	0.000	0.000	0.000
32	B	32	GLU	-1	-0.831	-0.934	9.168	-1.994	-1.994	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.952	-0.977	10.572	-1.025	-1.025	0.000	0.000	0.000	0.000
34	B	34	GLY	0	0.018	0.015	12.395	0.151	0.151	0.000	0.000	0.000	0.000
35	B	35	ILE	0	-0.039	-0.021	11.362	-0.097	-0.097	0.000	0.000	0.000	0.000
36	B	36	ILE	0	0.002	0.012	14.181	0.126	0.126	0.000	0.000	0.000	0.000
37	B	37	ALA	0	-0.012	-0.018	16.211	-0.027	-0.027	0.000	0.000	0.000	0.000
38	B	38	GLN	0	0.002	0.017	18.730	0.030	0.030	0.000	0.000	0.000	0.000
39	B	39	ALA	0	-0.003	0.001	21.449	0.004	0.004	0.000	0.000	0.000	0.000
40	B	40	VAL	0	0.005	0.017	23.972	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	41	ASP	-1	-0.790	-0.910	27.439	-0.125	-0.125	0.000	0.000	0.000	0.000
42	B	42	ASP	-1	-0.908	-0.969	29.618	-0.092	-0.092	0.000	0.000	0.000	0.000
43	B	43	SER	0	-0.061	-0.037	31.801	0.010	0.010	0.000	0.000	0.000	0.000
44	B	44	ARG	1	0.859	0.934	28.497	0.119	0.119	0.000	0.000	0.000	0.000
45	B	45	VAL	0	-0.035	-0.005	33.166	0.000	0.000	0.000	0.000	0.000	0.000
46	B	46	LEU	0	-0.037	-0.008	30.477	-0.005	-0.005	0.000	0.000	0.000	0.000
47	B	47	LEU	0	0.002	0.005	26.074	0.000	0.000	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.034	-0.015	24.331	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	49	SER	0	0.015	-0.012	23.481	-0.019	-0.019	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.047	-0.024	18.291	0.014	0.014	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.926	-0.977	19.096	-0.582	-0.582	0.000	0.000	0.000	0.000
52	B	52	ILE	0	-0.074	-0.033	16.126	0.060	0.060	0.000	0.000	0.000	0.000
53	B	53	GLY	0	0.096	0.048	16.542	-0.100	-0.100	0.000	0.000	0.000	0.000
54	B	54	VAL	0	0.064	0.005	13.649	-0.028	-0.028	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-0.993	-0.993	16.092	-0.610	-0.610	0.000	0.000	0.000	0.000
56	B	56	ALA	0	-0.047	-0.011	17.609	0.077	0.077	0.000	0.000	0.000	0.000
57	B	57	PHE	0	-0.083	-0.034	12.407	-0.012	-0.012	0.000	0.000	0.000	0.000
58	B	58	GLN	0	-0.034	-0.018	14.004	0.052	0.052	0.000	0.000	0.000	0.000
59	B	59	GLU	-1	-0.981	-0.995	9.214	-1.254	-1.254	0.000	0.000	0.000	0.000
60	B	60	TYR	0	0.001	0.003	9.867	-0.168	-0.168	0.000	0.000	0.000	0.000
61	B	61	ARG	1	0.926	0.965	1.813	4.578	2.684	8.005	-2.372	-3.739	-0.001
62	B	62	CYS	0	-0.023	-0.018	5.296	-1.170	-1.170	0.000	0.000	0.000	0.000
63	B	63	ASP	-1	-0.894	-0.931	2.515	-11.109	-7.503	1.077	-2.314	-2.368	-0.027
64	B	64	HIS	0	0.000	-0.007	3.824	1.623	1.905	0.000	-0.033	-0.249	0.000
65	B	65	PRO	0	-0.033	-0.017	5.647	-0.473	-0.473	0.000	0.000	0.000	0.000
66	B	66	VAL	0	0.005	0.013	5.959	0.309	0.309	0.000	0.000	0.000	0.000
67	B	67	THR	0	-0.018	-0.020	8.058	-0.066	-0.066	0.000	0.000	0.000	0.000
68	B	68	LEU	0	0.024	0.014	8.182	0.171	0.171	0.000	0.000	0.000	0.000
69	B	69	GLY	0	0.078	0.054	11.690	-0.042	-0.042	0.000	0.000	0.000	0.000
70	B	70	MET	0	-0.036	-0.022	13.268	0.104	0.104	0.000	0.000	0.000	0.000
71	B	71	ASP	-1	-0.783	-0.884	16.903	-0.069	-0.069	0.000	0.000	0.000	0.000
72	B	72	LEU	0	0.036	0.003	19.305	0.002	0.002	0.000	0.000	0.000	0.000
73	B	73	THR	0	-0.008	0.008	21.421	-0.006	-0.006	0.000	0.000	0.000	0.000
74	B	74	SER	0	-0.080	-0.051	20.029	0.011	0.011	0.000	0.000	0.000	0.000
75	B	75	LEU	0	0.046	0.021	15.884	0.017	0.017	0.000	0.000	0.000	0.000
76	B	76	SER	0	0.017	-0.008	19.068	-0.006	-0.006	0.000	0.000	0.000	0.000
77	B	77	LYS	1	0.811	0.906	21.639	0.002	0.002	0.000	0.000	0.000	0.000
78	B	78	ILE	0	0.044	0.021	15.934	0.012	0.012	0.000	0.000	0.000	0.000
79	B	79	LEU	0	0.078	0.045	16.295	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	80	ARG	1	0.811	0.917	19.529	0.058	0.058	0.000	0.000	0.000	0.000
81	B	81	CYS	0	-0.059	0.000	18.116	0.029	0.029	0.000	0.000	0.000	0.000
82	B	82	GLY	0	0.045	0.011	19.818	0.019	0.019	0.000	0.000	0.000	0.000
83	B	83	ASN	0	0.037	0.027	20.564	-0.012	-0.012	0.000	0.000	0.000	0.000
84	B	84	ASN	0	-0.125	-0.084	21.091	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	85	THR	0	0.055	0.029	22.081	-0.003	-0.003	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.822	-0.890	17.663	-0.187	-0.187	0.000	0.000	0.000	0.000
87	B	87	THR	0	0.058	0.047	13.927	-0.057	-0.057	0.000	0.000	0.000	0.000
88	B	88	LEU	0	-0.034	-0.009	12.395	0.056	0.056	0.000	0.000	0.000	0.000
89	B	89	THR	0	0.043	0.016	7.031	-0.092	-0.092	0.000	0.000	0.000	0.000
90	B	90	LEU	0	-0.041	-0.018	8.305	0.263	0.263	0.000	0.000	0.000	0.000
91	B	91	ILE	0	0.042	0.022	2.577	-1.130	-0.482	0.309	-0.164	-0.794	-0.001
92	B	92	ALA	0	0.010	0.006	4.049	0.862	1.225	-0.001	-0.103	-0.259	0.000
93	B	93	ASP	-1	-0.881	-0.933	1.893	-0.215	0.612	9.554	-6.161	-4.221	-0.032
94	B	94	ASN	0	0.004	-0.019	1.595	2.675	-20.228	35.556	-8.112	-4.541	-0.037
95	B	95	THR	0	-0.055	-0.049	4.420	0.050	0.232	0.001	-0.043	-0.140	0.000
96	B	96	PRO	0	0.011	0.065	6.205	0.104	0.104	0.000	0.000	0.000	0.000
97	B	97	ASP	-1	-0.817	-0.922	8.037	0.484	0.484	0.000	0.000	0.000	0.000
98	B	98	SER	0	-0.063	-0.059	9.825	-0.193	-0.193	0.000	0.000	0.000	0.000
99	B	99	ILE	0	-0.017	0.013	8.648	0.137	0.137	0.000	0.000	0.000	0.000
100	B	100	ILE	0	0.004	-0.011	6.968	0.102	0.102	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.049	-0.021	8.738	-0.314	-0.314	0.000	0.000	0.000	0.000
102	B	102	LEU	0	0.026	0.012	8.019	0.149	0.149	0.000	0.000	0.000	0.000
103	B	103	PHE	0	-0.017	-0.027	11.331	-0.109	-0.109	0.000	0.000	0.000	0.000
104	B	104	GLU	-1	-0.963	-0.989	13.320	-0.222	-0.222	0.000	0.000	0.000	0.000
105	B	105	ASP	-1	-0.851	-0.925	15.592	-0.161	-0.161	0.000	0.000	0.000	0.000
106	B	106	THR	0	0.001	-0.006	18.247	0.003	0.003	0.000	0.000	0.000	0.000
107	B	107	LYS	1	0.884	0.974	19.470	0.028	0.028	0.000	0.000	0.000	0.000
108	B	108	LYS	1	0.992	0.992	17.755	-0.047	-0.047	0.000	0.000	0.000	0.000
109	B	109	ASP	-1	-0.942	-0.985	18.743	-0.024	-0.024	0.000	0.000	0.000	0.000
110	B	110	ARG	1	0.772	0.873	18.237	0.129	0.129	0.000	0.000	0.000	0.000
111	B	111	ILE	0	0.035	-0.001	13.749	-0.025	-0.025	0.000	0.000	0.000	0.000
112	B	112	ALA	0	-0.065	-0.005	15.575	0.054	0.054	0.000	0.000	0.000	0.000
113	B	113	GLU	-1	-0.885	-0.945	9.982	0.560	0.560	0.000	0.000	0.000	0.000
114	B	114	TYR	0	-0.065	-0.043	13.152	0.057	0.057	0.000	0.000	0.000	0.000
115	B	115	SER	0	0.058	0.029	12.064	0.030	0.030	0.000	0.000	0.000	0.000
116	B	116	LEU	0	-0.095	-0.044	12.955	-0.031	-0.031	0.000	0.000	0.000	0.000
117	B	117	LYS	1	0.952	0.971	13.402	-0.333	-0.333	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.003	-0.001	10.004	-0.104	-0.104	0.000	0.000	0.000	0.000
119	B	119	MET	0	-0.100	-0.041	14.432	0.055	0.055	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.877	-0.926	16.003	0.094	0.094	0.000	0.000	0.000	0.000
121	B	121	ILE	0	-0.059	-0.044	18.136	0.000	0.000	0.000	0.000	0.000	0.000
122	B	122	ASP	-1	-0.927	-0.962	19.399	-0.090	-0.090	0.000	0.000	0.000	0.000
123	B	123	ALA	0	-0.059	-0.041	19.758	-0.012	-0.012	0.000	0.000	0.000	0.000
124	B	124	ASP	-1	-0.876	-0.917	21.509	-0.169	-0.169	0.000	0.000	0.000	0.000
125	B	125	PHE	0	-0.067	-0.055	24.366	-0.003	-0.003	0.000	0.000	0.000	0.000
126	B	126	LEU	0	-0.050	-0.005	24.188	-0.007	-0.007	0.000	0.000	0.000	0.000
127	B	127	LYS	1	0.978	0.984	23.061	0.304	0.304	0.000	0.000	0.000	0.000
128	B	128	ILE	0	-0.021	0.014	25.604	-0.019	-0.019	0.000	0.000	0.000	0.000
129	B	129	GLU	-1	-0.922	-0.996	28.304	-0.204	-0.204	0.000	0.000	0.000	0.000
130	B	130	GLU	-1	-0.979	-0.956	29.591	-0.258	-0.258	0.000	0.000	0.000	0.000
131	B	131	LEU	0	-0.014	-0.024	32.533	0.006	0.006	0.000	0.000	0.000	0.000
132	B	132	GLN	0	-0.079	-0.041	36.005	0.005	0.005	0.000	0.000	0.000	0.000
133	B	133	TYR	0	0.039	0.013	33.821	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	134	ASP	-1	-0.895	-0.938	39.935	-0.121	-0.121	0.000	0.000	0.000	0.000
135	B	135	SER	0	-0.080	-0.054	42.339	0.005	0.005	0.000	0.000	0.000	0.000
136	B	136	THR	0	0.005	0.007	37.844	-0.008	-0.008	0.000	0.000	0.000	0.000
137	B	137	LEU	0	-0.031	-0.004	40.145	0.005	0.005	0.000	0.000	0.000	0.000
138	B	138	SER	0	0.011	0.003	37.540	-0.009	-0.009	0.000	0.000	0.000	0.000
139	B	139	LEU	0	-0.012	-0.007	38.438	0.008	0.008	0.000	0.000	0.000	0.000
140	B	140	PRO	0	0.055	0.028	37.857	-0.011	-0.011	0.000	0.000	0.000	0.000
141	B	141	SER	0	0.065	0.025	33.422	0.009	0.009	0.000	0.000	0.000	0.000
142	B	142	SER	0	-0.006	-0.018	36.404	0.005	0.005	0.000	0.000	0.000	0.000
143	B	143	GLU	-1	-0.919	-0.950	38.147	-0.109	-0.109	0.000	0.000	0.000	0.000
144	B	144	PHE	0	0.058	0.018	36.465	0.007	0.007	0.000	0.000	0.000	0.000
145	B	145	SER	0	0.012	0.008	36.914	0.008	0.008	0.000	0.000	0.000	0.000
146	B	146	LYS	1	0.843	0.926	38.951	0.092	0.092	0.000	0.000	0.000	0.000
147	B	147	ILE	0	0.042	0.022	42.326	0.005	0.005	0.000	0.000	0.000	0.000
148	B	148	VAL	0	0.024	0.020	39.321	0.006	0.006	0.000	0.000	0.000	0.000
149	B	149	ARG	1	0.918	0.958	38.841	0.112	0.112	0.000	0.000	0.000	0.000
150	B	150	ASP	-1	-0.882	-0.941	42.419	-0.079	-0.079	0.000	0.000	0.000	0.000
151	B	151	LEU	0	-0.026	-0.033	45.836	0.005	0.005	0.000	0.000	0.000	0.000
152	B	152	SER	0	-0.023	-0.018	42.497	0.002	0.002	0.000	0.000	0.000	0.000
153	B	153	GLN	0	-0.089	-0.028	44.915	0.004	0.004	0.000	0.000	0.000	0.000
154	B	154	LEU	0	-0.064	-0.026	47.758	0.004	0.004	0.000	0.000	0.000	0.000
155	B	155	SER	0	-0.031	-0.010	48.248	0.004	0.004	0.000	0.000	0.000	0.000
156	B	156	ASP	-1	-0.839	-0.904	45.143	-0.069	-0.069	0.000	0.000	0.000	0.000
157	B	157	SER	0	-0.106	-0.062	44.225	-0.003	-0.003	0.000	0.000	0.000	0.000
158	B	158	ILE	0	0.008	0.010	42.944	0.003	0.003	0.000	0.000	0.000	0.000
159	B	159	ASN	0	-0.032	-0.022	44.946	-0.003	-0.003	0.000	0.000	0.000	0.000
160	B	160	ILE	0	0.021	0.011	42.395	0.001	0.001	0.000	0.000	0.000	0.000
161	B	161	MET	0	-0.017	-0.005	46.301	0.002	0.002	0.000	0.000	0.000	0.000
162	B	162	ILE	0	0.017	0.006	44.603	0.000	0.000	0.000	0.000	0.000	0.000
163	B	163	THR	0	-0.020	-0.002	49.009	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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