FMO DATABASE

FMODB ID: MV57Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1499025.590966
FMO2-HF: Nuclear repulsion	1433580.445097
FMO2-HF: Total energy	-65445.145869
FMO2-MP2: Total energy	-65632.442744

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.
-24.662	-24.372	33.832	-15.544	-18.576	-0.104

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 : -0.075 / q_NPA : -0.044

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	-0.891	-0.948	3.093	-5.423	-1.469	0.089	-1.811	-2.232	0.002
4	B	4	ALA	0	-0.015	0.003	4.997	0.152	0.186	-0.001	-0.005	-0.028	0.000
5	B	5	LYS	1	0.903	0.957	8.719	0.906	0.906	0.000	0.000	0.000	0.000
6	B	6	PHE	0	-0.006	-0.025	10.857	0.003	0.003	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.886	-0.934	14.547	-0.408	-0.408	0.000	0.000	0.000	0.000
8	B	8	GLU	-1	-0.856	-0.898	17.334	-0.200	-0.200	0.000	0.000	0.000	0.000
9	B	9	ALA	0	0.007	-0.003	17.206	-0.019	-0.019	0.000	0.000	0.000	0.000
10	B	10	SER	0	-0.085	-0.073	18.181	0.006	0.006	0.000	0.000	0.000	0.000
11	B	11	LEU	0	-0.025	-0.010	18.643	0.024	0.024	0.000	0.000	0.000	0.000
12	B	12	PHE	0	0.095	0.039	15.088	0.009	0.009	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.886	0.924	18.704	0.158	0.158	0.000	0.000	0.000	0.000
14	B	14	ARG	1	0.878	0.927	21.124	0.243	0.243	0.000	0.000	0.000	0.000
15	B	15	ILE	0	0.002	0.011	19.792	0.013	0.013	0.000	0.000	0.000	0.000
16	B	16	ILE	0	0.020	0.010	18.131	0.015	0.015	0.000	0.000	0.000	0.000
17	B	17	ASP	-1	-0.866	-0.947	22.155	-0.105	-0.105	0.000	0.000	0.000	0.000
18	B	18	GLY	0	-0.051	-0.016	25.381	0.015	0.015	0.000	0.000	0.000	0.000
19	B	19	PHE	0	-0.015	-0.021	20.129	0.002	0.002	0.000	0.000	0.000	0.000
20	B	20	LYS	1	0.777	0.902	24.095	0.100	0.100	0.000	0.000	0.000	0.000
21	B	21	ASP	-1	-0.868	-0.922	25.479	-0.071	-0.071	0.000	0.000	0.000	0.000
22	B	22	CYS	0	-0.056	-0.007	28.170	0.003	0.003	0.000	0.000	0.000	0.000
23	B	23	VAL	0	0.031	0.014	24.653	0.010	0.010	0.000	0.000	0.000	0.000
24	B	24	GLN	0	-0.003	-0.005	24.570	-0.004	-0.004	0.000	0.000	0.000	0.000
25	B	25	LEU	0	-0.021	-0.016	21.242	0.012	0.012	0.000	0.000	0.000	0.000
26	B	26	VAL	0	0.031	0.026	18.458	-0.010	-0.010	0.000	0.000	0.000	0.000
27	B	27	ASN	0	0.004	-0.007	16.023	0.037	0.037	0.000	0.000	0.000	0.000
28	B	28	PHE	0	-0.014	-0.014	13.240	-0.021	-0.021	0.000	0.000	0.000	0.000
29	B	29	GLN	0	-0.012	-0.014	12.429	-0.105	-0.105	0.000	0.000	0.000	0.000
30	B	30	CYS	0	-0.026	0.000	8.459	0.089	0.089	0.000	0.000	0.000	0.000
31	B	31	LYS	1	0.967	0.982	9.629	1.090	1.090	0.000	0.000	0.000	0.000
32	B	32	GLU	-1	-0.840	-0.922	9.195	-1.951	-1.951	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.942	-0.975	10.780	-1.071	-1.071	0.000	0.000	0.000	0.000
34	B	34	GLY	0	0.013	0.014	12.603	0.164	0.164	0.000	0.000	0.000	0.000
35	B	35	ILE	0	-0.060	-0.032	11.110	-0.091	-0.091	0.000	0.000	0.000	0.000
36	B	36	ILE	0	0.016	0.023	14.252	0.118	0.118	0.000	0.000	0.000	0.000
37	B	37	ALA	0	-0.011	-0.017	16.232	-0.015	-0.015	0.000	0.000	0.000	0.000
38	B	38	GLN	0	0.019	0.017	18.751	0.010	0.010	0.000	0.000	0.000	0.000
39	B	39	ALA	0	0.003	-0.001	21.469	0.010	0.010	0.000	0.000	0.000	0.000
40	B	40	VAL	0	0.021	0.018	23.991	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	41	ASP	-1	-0.765	-0.872	27.457	-0.089	-0.089	0.000	0.000	0.000	0.000
42	B	42	ASP	-1	-0.828	-0.931	29.636	-0.052	-0.052	0.000	0.000	0.000	0.000
43	B	43	SER	0	-0.098	-0.077	31.818	0.007	0.007	0.000	0.000	0.000	0.000
44	B	44	ARG	1	0.771	0.903	28.105	0.084	0.084	0.000	0.000	0.000	0.000
45	B	45	VAL	0	-0.042	-0.016	33.185	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	46	LEU	0	-0.040	-0.008	30.381	-0.006	-0.006	0.000	0.000	0.000	0.000
47	B	47	LEU	0	0.001	0.008	25.778	0.001	0.001	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.038	-0.020	24.325	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	49	SER	0	0.024	-0.001	23.500	-0.015	-0.015	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.056	-0.025	18.599	0.012	0.012	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.919	-0.968	19.256	-0.557	-0.557	0.000	0.000	0.000	0.000
52	B	52	ILE	0	-0.090	-0.038	16.560	0.059	0.059	0.000	0.000	0.000	0.000
53	B	53	GLY	0	0.105	0.050	16.542	-0.099	-0.099	0.000	0.000	0.000	0.000
54	B	54	VAL	0	0.065	0.005	13.515	-0.020	-0.020	0.000	0.000	0.000	0.000
55	B	55	GLU	-1	-1.007	-0.998	15.918	-0.602	-0.602	0.000	0.000	0.000	0.000
56	B	56	ALA	0	-0.039	-0.009	17.468	0.079	0.079	0.000	0.000	0.000	0.000
57	B	57	PHE	0	-0.080	-0.034	12.768	0.005	0.005	0.000	0.000	0.000	0.000
58	B	58	GLN	0	-0.054	-0.039	13.557	0.013	0.013	0.000	0.000	0.000	0.000
59	B	59	GLU	-1	-0.972	-0.995	9.153	-1.286	-1.286	0.000	0.000	0.000	0.000
60	B	60	TYR	0	-0.053	-0.042	9.816	-0.094	-0.094	0.000	0.000	0.000	0.000
61	B	61	ARG	1	0.797	0.885	2.059	4.795	4.728	4.925	-1.711	-3.147	0.003
62	B	62	CYS	0	0.003	-0.005	5.398	-1.037	-1.037	0.000	0.000	0.000	0.000
63	B	63	ASP	-1	-0.845	-0.898	1.983	-15.710	-14.463	6.680	-4.259	-3.668	-0.049
64	B	64	HIS	0	-0.003	-0.009	3.690	2.010	2.318	0.000	-0.044	-0.264	0.000
65	B	65	PRO	0	-0.012	-0.007	5.724	-0.479	-0.479	0.000	0.000	0.000	0.000
66	B	66	VAL	0	-0.013	0.005	5.747	0.286	0.286	0.000	0.000	0.000	0.000
67	B	67	THR	0	-0.012	-0.016	8.005	-0.034	-0.034	0.000	0.000	0.000	0.000
68	B	68	LEU	0	0.033	0.013	7.867	0.192	0.192	0.000	0.000	0.000	0.000
69	B	69	GLY	0	0.058	0.048	11.706	-0.057	-0.057	0.000	0.000	0.000	0.000
70	B	70	MET	0	-0.035	-0.019	13.491	0.125	0.125	0.000	0.000	0.000	0.000
71	B	71	ASP	-1	-0.675	-0.813	16.916	0.011	0.011	0.000	0.000	0.000	0.000
72	B	72	LEU	0	0.002	-0.005	19.242	0.013	0.013	0.000	0.000	0.000	0.000
73	B	73	THR	0	-0.025	-0.007	21.434	-0.008	-0.008	0.000	0.000	0.000	0.000
74	B	74	SER	0	-0.130	-0.102	20.203	0.015	0.015	0.000	0.000	0.000	0.000
75	B	75	LEU	0	0.020	0.012	15.963	0.018	0.018	0.000	0.000	0.000	0.000
76	B	76	SER	0	0.014	0.005	19.267	-0.006	-0.006	0.000	0.000	0.000	0.000
77	B	77	LYS	1	0.822	0.901	21.983	-0.100	-0.100	0.000	0.000	0.000	0.000
78	B	78	ILE	0	0.036	0.018	15.816	0.002	0.002	0.000	0.000	0.000	0.000
79	B	79	LEU	0	0.060	0.044	16.585	-0.005	-0.005	0.000	0.000	0.000	0.000
80	B	80	ARG	1	0.828	0.926	19.681	-0.012	-0.012	0.000	0.000	0.000	0.000
81	B	81	CYS	0	-0.063	-0.011	18.452	0.020	0.020	0.000	0.000	0.000	0.000
82	B	82	GLY	0	0.060	0.024	19.559	0.011	0.011	0.000	0.000	0.000	0.000
83	B	83	ASN	0	0.009	0.016	20.282	-0.007	-0.007	0.000	0.000	0.000	0.000
84	B	84	ASN	0	-0.135	-0.082	21.125	-0.012	-0.012	0.000	0.000	0.000	0.000
85	B	85	THR	0	0.060	0.035	22.109	-0.004	-0.004	0.000	0.000	0.000	0.000
86	B	86	ASP	-1	-0.824	-0.897	17.311	-0.149	-0.149	0.000	0.000	0.000	0.000
87	B	87	THR	0	0.042	0.038	13.816	-0.053	-0.053	0.000	0.000	0.000	0.000
88	B	88	LEU	0	-0.021	-0.011	12.865	0.056	0.056	0.000	0.000	0.000	0.000
89	B	89	THR	0	0.038	0.016	7.101	-0.127	-0.127	0.000	0.000	0.000	0.000
90	B	90	LEU	0	-0.041	-0.014	8.591	0.278	0.278	0.000	0.000	0.000	0.000
91	B	91	ILE	0	0.045	0.015	2.764	-1.397	-0.715	0.799	-0.254	-1.226	-0.001
92	B	92	ALA	0	0.007	0.009	4.253	0.111	0.519	0.001	-0.124	-0.285	0.000
93	B	93	ASP	-1	-0.852	-0.921	1.901	2.478	3.111	10.060	-6.200	-4.493	-0.032
94	B	94	ASN	0	0.006	-0.014	1.832	-7.015	-14.095	11.278	-1.097	-3.100	-0.027
95	B	95	THR	0	-0.099	-0.052	4.191	0.249	0.420	0.001	-0.039	-0.133	0.000
96	B	96	PRO	0	0.031	0.055	6.284	0.109	0.109	0.000	0.000	0.000	0.000
97	B	97	ASP	-1	-0.838	-0.930	8.040	0.654	0.654	0.000	0.000	0.000	0.000
98	B	98	SER	0	-0.079	-0.076	9.830	-0.293	-0.293	0.000	0.000	0.000	0.000
99	B	99	ILE	0	-0.012	0.009	8.654	0.255	0.255	0.000	0.000	0.000	0.000
100	B	100	ILE	0	-0.009	-0.017	6.248	-0.048	-0.048	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.041	-0.015	8.881	-0.297	-0.297	0.000	0.000	0.000	0.000
102	B	102	LEU	0	0.018	0.006	7.733	0.107	0.107	0.000	0.000	0.000	0.000
103	B	103	PHE	0	-0.001	-0.014	10.805	-0.125	-0.125	0.000	0.000	0.000	0.000
104	B	104	GLU	-1	-0.886	-0.936	12.580	-0.299	-0.299	0.000	0.000	0.000	0.000
105	B	105	ASP	-1	-0.844	-0.917	15.206	-0.153	-0.153	0.000	0.000	0.000	0.000
106	B	106	THR	0	-0.012	-0.020	17.956	0.000	0.000	0.000	0.000	0.000	0.000
107	B	107	LYS	1	0.928	0.996	19.284	0.042	0.042	0.000	0.000	0.000	0.000
108	B	108	LYS	1	0.935	0.956	17.478	-0.022	-0.022	0.000	0.000	0.000	0.000
109	B	109	ASP	-1	-0.949	-0.995	18.450	-0.010	-0.010	0.000	0.000	0.000	0.000
110	B	110	ARG	1	0.780	0.886	17.600	0.083	0.083	0.000	0.000	0.000	0.000
111	B	111	ILE	0	0.013	-0.009	13.312	-0.031	-0.031	0.000	0.000	0.000	0.000
112	B	112	ALA	0	-0.051	-0.001	14.991	0.057	0.057	0.000	0.000	0.000	0.000
113	B	113	GLU	-1	-0.890	-0.948	8.829	0.698	0.698	0.000	0.000	0.000	0.000
114	B	114	TYR	0	-0.052	-0.033	12.536	0.043	0.043	0.000	0.000	0.000	0.000
115	B	115	SER	0	0.047	0.033	10.897	0.040	0.040	0.000	0.000	0.000	0.000
116	B	116	LEU	0	-0.071	-0.032	12.729	-0.094	-0.094	0.000	0.000	0.000	0.000
117	B	117	LYS	1	0.968	0.978	13.406	-0.481	-0.481	0.000	0.000	0.000	0.000
118	B	118	LEU	0	-0.018	-0.005	9.811	-0.115	-0.115	0.000	0.000	0.000	0.000
119	B	119	MET	0	-0.089	-0.037	14.439	0.034	0.034	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.875	-0.924	16.015	0.181	0.181	0.000	0.000	0.000	0.000
121	B	121	ILE	0	-0.075	-0.049	17.971	-0.005	-0.005	0.000	0.000	0.000	0.000
122	B	122	ASP	-1	-0.912	-0.952	19.414	-0.054	-0.054	0.000	0.000	0.000	0.000
123	B	123	ALA	0	-0.055	-0.040	19.842	-0.012	-0.012	0.000	0.000	0.000	0.000
124	B	124	ASP	-1	-0.842	-0.898	21.423	-0.150	-0.150	0.000	0.000	0.000	0.000
125	B	125	PHE	0	-0.081	-0.069	24.296	-0.004	-0.004	0.000	0.000	0.000	0.000
126	B	126	LEU	0	-0.075	-0.017	24.626	-0.011	-0.011	0.000	0.000	0.000	0.000
127	B	127	LYS	1	0.860	0.908	24.911	0.242	0.242	0.000	0.000	0.000	0.000
128	B	128	ILE	0	-0.001	0.022	25.625	-0.017	-0.017	0.000	0.000	0.000	0.000
129	B	129	GLU	-1	-0.819	-0.924	28.368	-0.224	-0.224	0.000	0.000	0.000	0.000
130	B	130	GLU	-1	-0.977	-0.958	29.985	-0.251	-0.251	0.000	0.000	0.000	0.000
131	B	131	LEU	0	-0.019	-0.022	32.648	0.006	0.006	0.000	0.000	0.000	0.000
132	B	132	GLN	0	-0.064	-0.033	36.132	0.006	0.006	0.000	0.000	0.000	0.000
133	B	133	TYR	0	0.034	0.008	33.911	-0.001	-0.001	0.000	0.000	0.000	0.000
134	B	134	ASP	-1	-0.889	-0.934	40.059	-0.115	-0.115	0.000	0.000	0.000	0.000
135	B	135	SER	0	-0.081	-0.054	42.478	0.005	0.005	0.000	0.000	0.000	0.000
136	B	136	THR	0	-0.014	-0.007	38.038	-0.007	-0.007	0.000	0.000	0.000	0.000
137	B	137	LEU	0	-0.022	0.002	40.237	0.004	0.004	0.000	0.000	0.000	0.000
138	B	138	SER	0	0.028	0.016	37.692	-0.008	-0.008	0.000	0.000	0.000	0.000
139	B	139	LEU	0	-0.023	-0.014	38.429	0.007	0.007	0.000	0.000	0.000	0.000
140	B	140	PRO	0	0.052	0.032	37.896	-0.010	-0.010	0.000	0.000	0.000	0.000
141	B	141	SER	0	0.064	0.026	33.661	0.009	0.009	0.000	0.000	0.000	0.000
142	B	142	SER	0	-0.002	-0.017	36.531	0.005	0.005	0.000	0.000	0.000	0.000
143	B	143	GLU	-1	-0.921	-0.961	38.399	-0.100	-0.100	0.000	0.000	0.000	0.000
144	B	144	PHE	0	0.073	0.029	36.872	0.006	0.006	0.000	0.000	0.000	0.000
145	B	145	SER	0	0.015	0.021	37.172	0.009	0.009	0.000	0.000	0.000	0.000
146	B	146	LYS	1	0.767	0.865	39.137	0.078	0.078	0.000	0.000	0.000	0.000
147	B	147	ILE	0	0.042	0.017	42.593	0.005	0.005	0.000	0.000	0.000	0.000
148	B	148	VAL	0	0.047	0.030	39.228	0.006	0.006	0.000	0.000	0.000	0.000
149	B	149	ARG	1	0.900	0.957	38.947	0.096	0.096	0.000	0.000	0.000	0.000
150	B	150	ASP	-1	-0.835	-0.893	42.478	-0.065	-0.065	0.000	0.000	0.000	0.000
151	B	151	LEU	0	-0.016	-0.027	45.815	0.005	0.005	0.000	0.000	0.000	0.000
152	B	152	SER	0	-0.022	-0.037	42.531	0.002	0.002	0.000	0.000	0.000	0.000
153	B	153	GLN	0	-0.093	-0.030	44.932	0.005	0.005	0.000	0.000	0.000	0.000
154	B	154	LEU	0	-0.065	-0.023	47.775	0.003	0.003	0.000	0.000	0.000	0.000
155	B	155	SER	0	-0.021	-0.005	48.282	0.004	0.004	0.000	0.000	0.000	0.000
156	B	156	ASP	-1	-0.853	-0.912	45.142	-0.050	-0.050	0.000	0.000	0.000	0.000
157	B	157	SER	0	-0.104	-0.057	44.243	-0.004	-0.004	0.000	0.000	0.000	0.000
158	B	158	ILE	0	0.006	0.004	42.812	0.002	0.002	0.000	0.000	0.000	0.000
159	B	159	ASN	0	-0.026	-0.017	44.965	-0.002	-0.002	0.000	0.000	0.000	0.000
160	B	160	ILE	0	-0.004	0.001	42.807	0.000	0.000	0.000	0.000	0.000	0.000
161	B	161	MET	0	0.001	-0.004	46.321	0.001	0.001	0.000	0.000	0.000	0.000
162	B	162	ILE	0	0.019	0.012	44.492	0.000	0.000	0.000	0.000	0.000	0.000
163	B	163	THR	0	-0.011	0.001	49.065	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)