FMO DATABASE

FMODB ID: 5372Z

Calculation Name: 4G7W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4G7W

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-20

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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DGL=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-674582.764567
FMO2-HF: Nuclear repulsion	634396.121413
FMO2-HF: Total energy	-40186.643154
FMO2-MP2: Total energy	-40296.242721

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:SER)

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

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.
-3.318	-0.301	0.033	-1.561	-1.488	0.005

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.012

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

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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	ILE	0	0.005	-0.001	3.368	0.352	2.956	0.032	-1.487	-1.148	0.005
4	A	4	ASN	0	-0.026	-0.011	6.065	-0.373	-0.373	0.000	0.000	0.000	0.000
5	A	5	CYS	0	-0.060	-0.011	8.611	0.238	0.238	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.871	-0.938	12.114	0.096	0.096	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.021	-0.005	14.056	0.071	0.071	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.079	-0.037	17.192	0.029	0.029	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.055	0.041	11.907	0.042	0.042	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.030	0.005	14.675	-0.026	-0.026	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.058	-0.031	9.129	-0.029	-0.029	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.018	0.020	11.650	0.022	0.022	0.000	0.000	0.000	0.000
13	A	13	HIS	1	0.888	0.950	7.176	-1.006	-1.006	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.036	0.017	10.529	-0.194	-0.194	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.051	-0.025	11.260	0.102	0.102	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.019	0.017	13.684	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.047	0.023	15.714	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.088	0.060	18.770	0.022	0.022	0.000	0.000	0.000	0.000
19	A	19	PHE	0	0.012	-0.001	21.830	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.024	-0.013	24.501	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.042	-0.033	23.332	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.060	-0.014	25.493	0.009	0.009	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.007	-0.011	23.541	0.010	0.010	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.010	0.020	19.679	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.007	0.017	21.241	0.029	0.029	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.041	-0.053	19.707	0.015	0.015	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.015	0.014	14.559	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.027	-0.011	14.991	0.012	0.012	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.015	-0.028	7.369	0.091	0.091	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.894	-0.952	8.248	-1.567	-1.567	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.029	0.024	10.977	-0.087	-0.087	0.000	0.000	0.000	0.000
32	A	33	MET	0	-0.029	-0.023	13.999	0.032	0.032	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.017	-0.018	11.664	0.040	0.040	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.773	-0.870	16.275	0.052	0.052	0.000	0.000	0.000	0.000
35	A	36	ILE	0	-0.036	-0.011	18.406	0.046	0.046	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.888	-0.965	17.668	0.410	0.410	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.860	0.912	20.421	-0.168	-0.168	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.891	-0.927	24.016	0.258	0.258	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.955	-0.980	25.741	0.175	0.175	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.034	-0.029	28.383	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.004	-0.002	27.947	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.016	0.001	23.762	0.003	0.003	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.033	0.020	19.654	0.003	0.003	0.000	0.000	0.000	0.000
44	A	45	TRP	0	-0.007	-0.021	20.044	0.041	0.041	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.017	-0.012	21.423	-0.031	-0.031	0.000	0.000	0.000	0.000
46	A	47	CYS	0	-0.060	0.018	20.512	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.009	-0.008	23.522	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	49	SER	0	0.053	-0.002	24.860	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.060	-0.026	26.106	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.886	-0.949	28.118	0.152	0.152	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.070	-0.036	25.233	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.003	0.008	23.446	0.005	0.005	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.942	-0.959	23.603	0.161	0.161	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.023	-0.005	19.538	0.023	0.023	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.906	0.947	14.326	-0.665	-0.665	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.072	0.043	16.995	-0.039	-0.039	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.043	-0.011	14.386	0.114	0.114	0.000	0.000	0.000	0.000
58	A	60	TYR	0	-0.020	-0.022	14.196	-0.074	-0.074	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.875	0.934	14.200	-0.335	-0.335	0.000	0.000	0.000	0.000
60	A	62	PRO	0	0.030	0.026	13.192	-0.047	-0.047	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.821	0.920	16.113	-0.028	-0.028	0.000	0.000	0.000	0.000
62	A	64	PHE	0	0.033	0.011	19.103	-0.023	-0.023	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.056	-0.026	20.745	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	66	GLN	0	0.043	0.002	16.796	-0.028	-0.028	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.016	0.014	19.103	0.001	0.001	0.000	0.000	0.000	0.000
66	A	68	VAL	0	-0.040	-0.020	20.480	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	69	SER	0	0.042	0.014	19.937	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	70	PRO	0	-0.048	-0.009	21.034	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	71	ASN	0	-0.039	-0.023	22.721	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	72	TRP	0	-0.003	0.000	20.520	0.023	0.023	0.000	0.000	0.000	0.000
71	A	73	PRO	0	0.067	0.030	22.884	-0.022	-0.022	0.000	0.000	0.000	0.000
72	A	74	MET	0	0.010	0.004	18.314	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	75	CYS	0	-0.073	-0.027	17.181	0.020	0.020	0.000	0.000	0.000	0.000
74	A	76	ASP	-1	-0.806	-0.893	18.892	0.019	0.019	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.024	-0.032	14.229	0.029	0.029	0.000	0.000	0.000	0.000
76	A	78	SER	0	0.002	-0.007	18.815	0.026	0.026	0.000	0.000	0.000	0.000
77	A	79	GLY	0	-0.022	0.008	22.139	0.000	0.000	0.000	0.000	0.000	0.000
78	A	80	ALA	0	0.017	-0.003	23.937	0.013	0.013	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.055	0.023	21.295	0.008	0.008	0.000	0.000	0.000	0.000
80	A	82	ALA	0	-0.041	-0.025	23.455	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.898	-0.965	23.435	0.074	0.074	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.897	0.950	22.208	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	86	ILE	0	0.002	0.010	16.167	0.010	0.010	0.000	0.000	0.000	0.000
84	A	87	TYR	0	-0.003	-0.043	11.661	0.064	0.064	0.000	0.000	0.000	0.000
85	A	88	PRO	0	-0.007	0.010	13.608	-0.091	-0.091	0.000	0.000	0.000	0.000
86	A	89	TYR	0	-0.015	-0.020	3.336	0.084	0.259	0.001	-0.052	-0.124	0.000
87	A	90	CYS	0	-0.057	-0.028	9.284	-0.213	-0.213	0.000	0.000	0.000	0.000
88	A	91	PRO	0	-0.005	0.001	6.164	-0.284	-0.284	0.000	0.000	0.000	0.000
89	A	92	GLU	-1	-0.986	-1.001	3.886	-0.071	0.167	0.000	-0.022	-0.216	0.000
90	A	93	GLY	0	0.010	0.029	6.066	0.031	0.031	0.000	0.000	0.000	0.000
91	A	94	DGL	-1	-0.966	-1.000	9.701	-0.531	-0.531	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.975	-0.984	12.387	-0.198	-0.198	0.000	0.000	0.000	0.000
93	A	97	VAL	0	0.045	0.031	14.574	0.055	0.055	0.000	0.000	0.000	0.000
94	A	98	PRO	0	-0.034	-0.015	17.318	-0.014	-0.014	0.000	0.000	0.000	0.000

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