FMO DATABASE

FMODB ID: K3LV3

Calculation Name: 4EXW-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EXW

Chain ID: D

ChEMBL ID:

UniProt ID: Q1J1N6

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	119
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-971783.281153
FMO2-HF: Nuclear repulsion	924457.172699
FMO2-HF: Total energy	-47326.108454
FMO2-MP2: Total energy	-47466.271609

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(D:-1:PHE)

Summations of interaction energy for fragment #1(D:-1:PHE)

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.
-3.757	-0.448	0.098	-1.451	-1.956	0.003

Interaction energy analysis for fragmet #1(D:-1:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.022

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	D	1	MET	0	0.008	0.014	3.226	-3.696	-0.387	0.098	-1.451	-1.956	0.003
4	D	2	LEU	0	-0.012	-0.001	5.640	0.474	0.474	0.000	0.000	0.000	0.000
5	D	3	HIS	1	0.810	0.879	7.505	1.795	1.795	0.000	0.000	0.000	0.000
6	D	4	ILE	0	-0.003	0.018	12.102	0.079	0.079	0.000	0.000	0.000	0.000
7	D	5	GLU	-1	-0.825	-0.896	15.888	-0.362	-0.362	0.000	0.000	0.000	0.000
8	D	6	PHE	0	0.024	0.014	18.153	0.025	0.025	0.000	0.000	0.000	0.000
9	D	7	ILE	0	0.004	0.020	21.607	0.005	0.005	0.000	0.000	0.000	0.000
10	D	8	THR	0	0.012	-0.008	23.451	0.008	0.008	0.000	0.000	0.000	0.000
11	D	9	ASP	-1	-0.831	-0.918	25.908	-0.174	-0.174	0.000	0.000	0.000	0.000
12	D	10	LEU	0	-0.051	-0.024	28.143	0.012	0.012	0.000	0.000	0.000	0.000
13	D	11	GLY	0	-0.016	-0.003	28.919	0.007	0.007	0.000	0.000	0.000	0.000
14	D	12	ALA	0	-0.018	0.001	24.813	-0.002	-0.002	0.000	0.000	0.000	0.000
15	D	13	LYS	1	0.850	0.901	20.795	0.295	0.295	0.000	0.000	0.000	0.000
16	D	14	VAL	0	0.002	-0.003	18.708	0.001	0.001	0.000	0.000	0.000	0.000
17	D	15	THR	0	-0.010	-0.007	13.871	0.004	0.004	0.000	0.000	0.000	0.000
18	D	16	VAL	0	-0.015	-0.002	14.444	0.021	0.021	0.000	0.000	0.000	0.000
19	D	17	ASP	-1	-0.801	-0.893	8.075	-1.655	-1.655	0.000	0.000	0.000	0.000
20	D	18	VAL	0	-0.036	-0.028	9.961	0.176	0.176	0.000	0.000	0.000	0.000
21	D	19	GLU	-1	-0.868	-0.916	5.915	-1.344	-1.344	0.000	0.000	0.000	0.000
22	D	20	SER	0	0.029	-0.034	5.614	-0.576	-0.576	0.000	0.000	0.000	0.000
23	D	21	ALA	0	0.011	-0.006	7.795	0.199	0.199	0.000	0.000	0.000	0.000
24	D	22	ASP	-1	-0.866	-0.904	9.657	-0.826	-0.826	0.000	0.000	0.000	0.000
25	D	23	LYS	1	0.881	0.942	9.045	1.016	1.016	0.000	0.000	0.000	0.000
26	D	24	LEU	0	-0.027	-0.006	13.258	0.031	0.031	0.000	0.000	0.000	0.000
27	D	25	LEU	0	0.007	-0.009	14.467	0.058	0.058	0.000	0.000	0.000	0.000
28	D	26	ASP	-1	-0.883	-0.936	16.209	-0.370	-0.370	0.000	0.000	0.000	0.000
29	D	27	VAL	0	0.016	0.003	13.846	0.043	0.043	0.000	0.000	0.000	0.000
30	D	28	GLN	0	-0.010	-0.016	17.133	0.016	0.016	0.000	0.000	0.000	0.000
31	D	29	ARG	1	0.878	0.923	19.867	0.304	0.304	0.000	0.000	0.000	0.000
32	D	30	GLN	0	-0.073	-0.015	17.857	-0.001	-0.001	0.000	0.000	0.000	0.000
33	D	31	TYR	0	0.038	0.014	17.518	0.041	0.041	0.000	0.000	0.000	0.000
34	D	32	GLY	0	0.042	0.036	22.593	0.024	0.024	0.000	0.000	0.000	0.000
35	D	33	ARG	1	0.847	0.884	22.254	0.274	0.274	0.000	0.000	0.000	0.000
36	D	34	LEU	0	-0.054	-0.006	24.202	0.018	0.018	0.000	0.000	0.000	0.000
37	D	35	GLY	0	-0.031	-0.009	27.634	0.010	0.010	0.000	0.000	0.000	0.000
38	D	36	TRP	0	-0.055	-0.027	20.421	-0.006	-0.006	0.000	0.000	0.000	0.000
39	D	37	THR	0	-0.019	-0.006	25.443	0.000	0.000	0.000	0.000	0.000	0.000
40	D	38	SER	0	-0.028	-0.028	20.740	-0.016	-0.016	0.000	0.000	0.000	0.000
41	D	39	GLY	0	0.017	0.012	23.157	0.004	0.004	0.000	0.000	0.000	0.000
42	D	40	GLU	-1	-0.905	-0.956	25.222	-0.193	-0.193	0.000	0.000	0.000	0.000
43	D	41	VAL	0	-0.028	-0.004	28.781	-0.006	-0.006	0.000	0.000	0.000	0.000
44	D	42	PRO	0	-0.018	0.005	30.012	0.006	0.006	0.000	0.000	0.000	0.000
45	D	43	VAL	0	0.027	-0.005	32.438	0.007	0.007	0.000	0.000	0.000	0.000
46	D	44	GLY	0	0.024	0.015	36.153	0.003	0.003	0.000	0.000	0.000	0.000
47	D	45	GLY	0	-0.015	0.020	34.787	0.005	0.005	0.000	0.000	0.000	0.000
48	D	46	TYR	0	0.011	-0.019	27.911	0.000	0.000	0.000	0.000	0.000	0.000
49	D	47	GLN	0	-0.006	0.000	31.450	0.019	0.019	0.000	0.000	0.000	0.000
50	D	48	PHE	0	0.007	0.006	27.990	-0.011	-0.011	0.000	0.000	0.000	0.000
51	D	49	PRO	0	0.027	0.003	30.438	0.009	0.009	0.000	0.000	0.000	0.000
52	D	50	LEU	0	-0.016	0.001	33.455	-0.002	-0.002	0.000	0.000	0.000	0.000
53	D	51	GLU	-1	-0.879	-0.954	34.494	-0.117	-0.117	0.000	0.000	0.000	0.000
54	D	52	ASN	0	0.010	-0.007	29.487	-0.001	-0.001	0.000	0.000	0.000	0.000
55	D	53	GLU	-1	-0.779	-0.839	33.202	-0.117	-0.117	0.000	0.000	0.000	0.000
56	D	54	PRO	0	-0.023	-0.008	35.794	-0.002	-0.002	0.000	0.000	0.000	0.000
57	D	55	ASP	-1	-0.810	-0.899	32.354	-0.140	-0.140	0.000	0.000	0.000	0.000
58	D	56	PHE	0	0.005	0.009	28.406	-0.012	-0.012	0.000	0.000	0.000	0.000
59	D	57	ASP	-1	-0.780	-0.854	26.035	-0.216	-0.216	0.000	0.000	0.000	0.000
60	D	58	TRP	0	0.007	-0.020	27.861	-0.013	-0.013	0.000	0.000	0.000	0.000
61	D	59	SER	0	-0.022	-0.025	25.799	-0.010	-0.010	0.000	0.000	0.000	0.000
62	D	60	LEU	0	-0.031	-0.014	22.715	-0.020	-0.020	0.000	0.000	0.000	0.000
63	D	61	ILE	0	-0.057	-0.025	24.692	-0.013	-0.013	0.000	0.000	0.000	0.000
64	D	62	GLY	0	0.039	0.024	26.571	0.011	0.011	0.000	0.000	0.000	0.000
65	D	63	ALA	0	-0.110	-0.047	27.850	0.015	0.015	0.000	0.000	0.000	0.000
66	D	64	ARG	1	0.935	0.965	30.614	0.122	0.122	0.000	0.000	0.000	0.000
67	D	65	LYS	1	0.904	0.952	33.273	0.126	0.126	0.000	0.000	0.000	0.000
68	D	66	TRP	0	-0.011	-0.026	36.664	-0.003	-0.003	0.000	0.000	0.000	0.000
69	D	67	THR	0	0.011	0.030	39.845	0.000	0.000	0.000	0.000	0.000	0.000
70	D	68	ASN	0	-0.116	-0.036	43.449	0.002	0.002	0.000	0.000	0.000	0.000
71	D	69	PRO	0	0.045	0.017	46.167	0.002	0.002	0.000	0.000	0.000	0.000
72	D	70	GLU	-1	-0.901	-0.970	45.635	-0.067	-0.067	0.000	0.000	0.000	0.000
73	D	71	GLY	0	0.020	0.017	46.338	0.002	0.002	0.000	0.000	0.000	0.000
74	D	72	GLU	-1	-0.819	-0.891	46.211	-0.079	-0.079	0.000	0.000	0.000	0.000
75	D	73	GLU	-1	-0.798	-0.903	39.309	-0.112	-0.112	0.000	0.000	0.000	0.000
76	D	74	MET	0	-0.050	-0.018	41.382	0.002	0.002	0.000	0.000	0.000	0.000
77	D	75	ILE	0	-0.016	0.006	35.029	-0.003	-0.003	0.000	0.000	0.000	0.000
78	D	76	LEU	0	-0.018	-0.011	36.338	0.004	0.004	0.000	0.000	0.000	0.000
79	D	77	HIS	0	0.022	-0.010	30.112	-0.003	-0.003	0.000	0.000	0.000	0.000
80	D	78	ARG	1	0.922	0.953	27.351	0.213	0.213	0.000	0.000	0.000	0.000
81	D	79	GLY	0	0.048	0.041	34.080	0.005	0.005	0.000	0.000	0.000	0.000
82	D	80	HIS	0	-0.090	-0.046	37.317	0.007	0.007	0.000	0.000	0.000	0.000
83	D	81	ALA	0	0.059	0.029	38.108	-0.005	-0.005	0.000	0.000	0.000	0.000
84	D	82	TYR	0	-0.038	-0.031	36.442	0.005	0.005	0.000	0.000	0.000	0.000
85	D	83	ARG	1	0.842	0.890	40.551	0.081	0.081	0.000	0.000	0.000	0.000
86	D	84	ARG	1	0.800	0.851	40.518	0.097	0.097	0.000	0.000	0.000	0.000
87	D	85	ARG	1	0.910	0.949	42.520	0.093	0.093	0.000	0.000	0.000	0.000
88	D	86	GLU	-1	-0.794	-0.868	43.918	-0.093	-0.093	0.000	0.000	0.000	0.000
89	D	98	PRO	0	0.020	-0.014	42.682	0.001	0.001	0.000	0.000	0.000	0.000
90	D	99	ALA	0	-0.005	0.017	43.832	0.000	0.000	0.000	0.000	0.000	0.000
91	D	100	ALA	0	0.025	-0.001	41.246	-0.004	-0.004	0.000	0.000	0.000	0.000
92	D	101	VAL	0	-0.023	0.024	39.612	0.005	0.005	0.000	0.000	0.000	0.000
93	D	102	LYS	1	0.807	0.892	39.774	0.090	0.090	0.000	0.000	0.000	0.000
94	D	103	TYR	0	0.038	-0.006	37.566	0.003	0.003	0.000	0.000	0.000	0.000
95	D	104	SER	0	-0.053	-0.020	39.167	-0.003	-0.003	0.000	0.000	0.000	0.000
96	D	105	ARG	1	0.926	0.986	39.321	0.113	0.113	0.000	0.000	0.000	0.000
97	D	106	GLY	0	0.057	0.022	43.882	0.000	0.000	0.000	0.000	0.000	0.000
98	D	107	ALA	0	-0.048	-0.024	43.517	-0.001	-0.001	0.000	0.000	0.000	0.000
99	D	108	LYS	1	0.969	0.985	45.523	0.081	0.081	0.000	0.000	0.000	0.000
100	D	109	ASN	0	0.060	0.045	40.817	0.007	0.007	0.000	0.000	0.000	0.000
101	D	125	TYR	0	0.029	0.013	43.396	0.001	0.001	0.000	0.000	0.000	0.000
102	D	126	VAL	0	-0.036	-0.025	39.233	-0.001	-0.001	0.000	0.000	0.000	0.000
103	D	127	THR	0	-0.047	-0.061	38.405	0.004	0.004	0.000	0.000	0.000	0.000
104	D	128	LEU	0	0.006	0.028	32.670	-0.003	-0.003	0.000	0.000	0.000	0.000
105	D	129	ALA	0	0.002	-0.009	33.664	-0.010	-0.010	0.000	0.000	0.000	0.000
106	D	130	ILE	0	-0.042	-0.025	35.226	0.011	0.011	0.000	0.000	0.000	0.000
107	D	131	PHE	0	0.015	0.025	32.767	-0.006	-0.006	0.000	0.000	0.000	0.000
108	D	132	ARG	1	0.925	0.938	36.421	0.121	0.121	0.000	0.000	0.000	0.000
109	D	133	GLY	0	0.040	0.037	36.849	-0.003	-0.003	0.000	0.000	0.000	0.000
110	D	134	GLY	0	0.019	0.013	33.970	-0.006	-0.006	0.000	0.000	0.000	0.000
111	D	135	LYS	1	0.986	0.983	28.778	0.153	0.153	0.000	0.000	0.000	0.000
112	D	136	ARG	1	0.812	0.886	31.022	0.132	0.132	0.000	0.000	0.000	0.000
113	D	137	GLN	0	-0.037	-0.023	25.439	-0.022	-0.022	0.000	0.000	0.000	0.000
114	D	138	GLU	-1	-0.785	-0.887	25.894	-0.162	-0.162	0.000	0.000	0.000	0.000
115	D	139	ARG	1	0.886	0.945	21.658	0.253	0.253	0.000	0.000	0.000	0.000
116	D	140	TYR	0	-0.022	-0.025	23.926	-0.021	-0.021	0.000	0.000	0.000	0.000
117	D	141	ALA	0	0.033	0.036	26.545	0.006	0.006	0.000	0.000	0.000	0.000
118	D	142	VAL	0	-0.002	0.004	26.882	-0.018	-0.018	0.000	0.000	0.000	0.000
119	D	143	PRO	0	-0.021	0.003	24.660	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:-1:PHE)