FMO DATABASE

FMODB ID: VRMR1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-674437.515382
FMO2-HF: Nuclear repulsion	634250.132615
FMO2-HF: Total energy	-40187.382767
FMO2-MP2: Total energy	-40296.932799

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.
-4.959	-2.978	0.017	-0.867	-1.13	0.002

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 : -0.004 / q_NPA : -0.013

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	0.016	0.012	3.452	-0.932	0.723	0.019	-0.819	-0.855	0.002
4	A	4	ASN	0	-0.030	-0.020	5.787	-0.099	-0.099	0.000	0.000	0.000	0.000
5	A	5	CYS	0	-0.059	-0.023	8.366	0.096	0.096	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.798	-0.889	11.932	0.091	0.091	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.034	-0.019	14.166	0.026	0.026	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.105	-0.067	17.004	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.003	0.024	11.426	0.010	0.010	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.021	-0.008	14.431	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.056	-0.019	8.511	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.024	-0.036	10.817	0.048	0.048	0.000	0.000	0.000	0.000
13	A	13	HIS	1	0.806	0.908	8.383	-0.471	-0.471	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.058	0.027	10.735	-0.166	-0.166	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.052	0.003	10.915	0.096	0.096	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.008	-0.002	13.015	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	17	PHE	0	0.057	0.021	15.460	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.095	0.062	18.689	0.001	0.001	0.000	0.000	0.000	0.000
19	A	19	PHE	0	0.017	0.003	21.789	0.011	0.011	0.000	0.000	0.000	0.000
20	A	20	GLY	0	-0.020	-0.013	24.512	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.041	-0.027	22.986	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.050	-0.014	25.025	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.017	-0.008	23.510	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.026	0.014	19.405	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.007	0.010	20.841	0.012	0.012	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.033	-0.055	19.909	0.008	0.008	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.019	-0.011	14.726	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.005	0.015	15.145	0.011	0.011	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.039	0.005	7.205	0.045	0.045	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.873	-0.943	8.616	-0.334	-0.334	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.010	0.006	11.341	0.000	0.000	0.000	0.000	0.000	0.000
32	A	33	MET	0	-0.019	-0.002	14.140	0.008	0.008	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.002	-0.012	12.030	0.026	0.026	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.798	-0.850	16.539	0.046	0.046	0.000	0.000	0.000	0.000
35	A	36	ILE	0	-0.033	0.001	18.348	0.023	0.023	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.829	-0.907	17.052	0.192	0.192	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.881	0.923	20.579	-0.089	-0.089	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.864	-0.906	24.085	0.099	0.099	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.956	-0.993	25.835	0.057	0.057	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.027	-0.016	28.635	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	42	GLY	0	-0.013	-0.003	28.196	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.024	-0.020	23.602	0.005	0.005	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.017	0.021	19.709	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	45	TRP	0	0.008	-0.015	19.425	0.020	0.020	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.030	-0.017	21.500	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	47	CYS	0	-0.079	-0.002	20.457	0.006	0.006	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.024	-0.006	23.242	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	49	SER	0	0.045	0.005	24.630	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.006	0.004	25.148	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.885	-0.945	27.830	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.093	-0.050	24.953	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.004	0.008	23.390	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.974	-0.990	23.259	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	55	TYR	0	0.007	0.003	19.233	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.901	0.939	14.293	-0.171	-0.171	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.061	0.035	16.756	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.054	-0.010	14.500	0.049	0.049	0.000	0.000	0.000	0.000
58	A	60	TYR	0	0.019	-0.007	14.246	-0.035	-0.035	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.865	0.941	14.178	-0.143	-0.143	0.000	0.000	0.000	0.000
60	A	62	PRO	0	0.015	0.008	12.783	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.829	0.904	15.566	-0.058	-0.058	0.000	0.000	0.000	0.000
62	A	64	PHE	0	0.020	-0.001	18.720	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.036	-0.016	21.143	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	66	GLN	0	0.040	0.006	16.749	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.021	0.014	18.834	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	68	VAL	0	-0.056	-0.037	20.411	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	69	SER	0	0.060	0.030	20.317	0.002	0.002	0.000	0.000	0.000	0.000
68	A	70	PRO	0	-0.059	-0.019	21.329	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	71	ASN	0	-0.009	-0.008	22.863	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	72	TRP	0	-0.017	-0.013	20.544	0.007	0.007	0.000	0.000	0.000	0.000
71	A	73	PRO	0	0.047	0.019	22.871	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	74	MET	0	0.018	0.022	18.855	0.000	0.000	0.000	0.000	0.000	0.000
73	A	75	CYS	0	-0.091	-0.009	16.951	0.009	0.009	0.000	0.000	0.000	0.000
74	A	76	ASP	-1	-0.776	-0.883	18.547	-0.060	-0.060	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.022	-0.020	14.253	0.016	0.016	0.000	0.000	0.000	0.000
76	A	78	SER	0	-0.076	-0.042	18.291	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	79	GLY	0	0.035	0.018	21.763	0.003	0.003	0.000	0.000	0.000	0.000
78	A	80	ALA	0	0.011	-0.006	23.243	0.004	0.004	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.045	0.022	20.835	0.006	0.006	0.000	0.000	0.000	0.000
80	A	82	ALA	0	-0.040	-0.022	23.077	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.823	-0.903	23.536	0.026	0.026	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.824	0.886	22.051	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	86	ILE	0	0.023	0.002	16.487	0.014	0.014	0.000	0.000	0.000	0.000
84	A	87	TYR	0	0.008	-0.048	11.454	0.015	0.015	0.000	0.000	0.000	0.000
85	A	88	PRO	0	-0.014	0.006	13.690	-0.020	-0.020	0.000	0.000	0.000	0.000
86	A	89	TYR	0	-0.025	-0.021	3.640	0.265	0.405	-0.001	-0.034	-0.105	0.000
87	A	90	CYS	0	-0.069	-0.029	8.732	0.074	0.074	0.000	0.000	0.000	0.000
88	A	91	PRO	0	0.003	0.000	5.968	-0.423	-0.423	0.000	0.000	0.000	0.000
89	A	92	GLU	-1	-0.963	-0.994	4.272	-3.060	-2.874	-0.001	-0.014	-0.170	0.000
90	A	93	GLY	0	0.008	0.007	6.289	0.358	0.358	0.000	0.000	0.000	0.000
91	A	94	DGL	-1	-0.998	-1.001	10.152	-0.219	-0.219	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.935	-0.968	12.403	-0.291	-0.291	0.000	0.000	0.000	0.000
93	A	97	VAL	0	0.060	0.052	14.247	0.017	0.017	0.000	0.000	0.000	0.000
94	A	98	PRO	0	-0.079	-0.040	17.180	0.034	0.034	0.000	0.000	0.000	0.000

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