FMO DATABASE

FMODB ID: 3JGVL

Calculation Name: 5FD7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FD7

Chain ID: A

ChEMBL ID:

UniProt ID: P39929

Base Structure: X-ray

Registration Date: 2023-09-23

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-764547.576788
FMO2-HF: Nuclear repulsion	714453.320465
FMO2-HF: Total energy	-50094.256323
FMO2-MP2: Total energy	-50236.662203

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:18:SER)

Summations of interaction energy for fragment #1(A:18: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.
-6.236	-1.019	2.977	-3.159	-5.035	0.015

Interaction energy analysis for fragmet #1(A:18:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.007

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	A	20	THR	0	0.065	0.036	3.095	-2.162	0.051	0.121	-0.993	-1.341	-0.003
4	A	21	LYS	1	0.964	0.981	2.344	-7.577	-4.804	2.856	-2.125	-3.504	0.018
5	A	22	ALA	0	-0.012	0.003	3.858	1.609	1.840	0.000	-0.041	-0.190	0.000
6	A	23	ILE	0	0.058	0.031	6.109	0.737	0.737	0.000	0.000	0.000	0.000
7	A	24	VAL	0	0.011	0.005	7.257	0.418	0.418	0.000	0.000	0.000	0.000
8	A	25	ARG	1	0.960	0.972	6.956	0.634	0.634	0.000	0.000	0.000	0.000
9	A	26	LEU	0	-0.002	0.010	9.627	0.213	0.213	0.000	0.000	0.000	0.000
10	A	27	ARG	1	0.895	0.929	11.561	0.865	0.865	0.000	0.000	0.000	0.000
11	A	28	GLU	-1	-0.945	-0.968	11.950	-0.220	-0.220	0.000	0.000	0.000	0.000
12	A	29	HIS	0	-0.020	-0.017	12.622	0.095	0.095	0.000	0.000	0.000	0.000
13	A	30	ILE	0	0.049	0.022	15.255	0.059	0.059	0.000	0.000	0.000	0.000
14	A	31	ASN	0	0.004	0.021	17.102	0.062	0.062	0.000	0.000	0.000	0.000
15	A	32	LEU	0	-0.021	-0.019	17.424	0.043	0.043	0.000	0.000	0.000	0.000
16	A	33	LEU	0	-0.045	-0.020	18.753	0.034	0.034	0.000	0.000	0.000	0.000
17	A	34	SER	0	0.055	0.015	21.387	0.023	0.023	0.000	0.000	0.000	0.000
18	A	35	LYS	1	0.974	0.996	22.765	0.128	0.128	0.000	0.000	0.000	0.000
19	A	36	LYS	1	0.934	0.976	23.822	0.099	0.099	0.000	0.000	0.000	0.000
20	A	37	GLN	0	0.010	-0.019	25.571	0.005	0.005	0.000	0.000	0.000	0.000
21	A	38	SER	0	-0.036	-0.021	27.409	0.011	0.011	0.000	0.000	0.000	0.000
22	A	39	HIS	0	0.049	0.022	29.023	0.006	0.006	0.000	0.000	0.000	0.000
23	A	40	LEU	0	-0.019	-0.002	28.692	0.008	0.008	0.000	0.000	0.000	0.000
24	A	41	ARG	1	0.872	0.907	30.305	0.105	0.105	0.000	0.000	0.000	0.000
25	A	42	THR	0	0.018	0.009	33.195	0.005	0.005	0.000	0.000	0.000	0.000
26	A	43	GLN	0	-0.058	-0.035	32.815	0.008	0.008	0.000	0.000	0.000	0.000
27	A	44	ILE	0	-0.023	-0.007	34.166	0.005	0.005	0.000	0.000	0.000	0.000
28	A	45	THR	0	0.047	0.019	37.890	0.002	0.002	0.000	0.000	0.000	0.000
29	A	46	ASN	0	-0.001	0.003	39.223	0.002	0.002	0.000	0.000	0.000	0.000
30	A	47	GLN	0	-0.047	-0.025	40.628	0.005	0.005	0.000	0.000	0.000	0.000
31	A	48	GLU	-1	-0.862	-0.931	42.447	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	49	ASN	0	0.018	0.002	43.699	0.004	0.004	0.000	0.000	0.000	0.000
33	A	50	GLU	-1	-0.808	-0.899	43.881	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	51	ALA	0	-0.022	-0.017	46.660	0.002	0.002	0.000	0.000	0.000	0.000
35	A	52	ARG	1	0.891	0.949	48.383	0.036	0.036	0.000	0.000	0.000	0.000
36	A	53	ILE	0	0.035	0.013	49.789	0.001	0.001	0.000	0.000	0.000	0.000
37	A	54	PHE	0	-0.025	-0.019	48.675	0.002	0.002	0.000	0.000	0.000	0.000
38	A	55	LEU	0	-0.090	-0.037	52.726	0.001	0.001	0.000	0.000	0.000	0.000
39	A	56	THR	0	-0.029	-0.013	54.575	0.001	0.001	0.000	0.000	0.000	0.000
40	A	57	LYS	1	0.956	0.983	54.058	0.022	0.022	0.000	0.000	0.000	0.000
41	A	58	GLY	0	0.018	0.004	56.293	0.001	0.001	0.000	0.000	0.000	0.000
42	A	59	ASN	0	0.036	0.032	56.515	0.000	0.000	0.000	0.000	0.000	0.000
43	A	60	LYS	1	1.037	0.993	54.788	0.019	0.019	0.000	0.000	0.000	0.000
44	A	61	VAL	0	0.005	0.009	53.156	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	62	MET	0	0.027	0.023	50.329	0.000	0.000	0.000	0.000	0.000	0.000
46	A	63	ALA	0	0.055	0.036	49.475	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	64	LYS	1	0.948	0.972	48.563	0.020	0.020	0.000	0.000	0.000	0.000
48	A	65	ASN	0	0.004	-0.015	47.352	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	66	ALA	0	0.044	0.046	45.112	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	67	LEU	0	0.023	-0.002	43.792	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	68	LYS	1	0.879	0.943	43.259	0.020	0.020	0.000	0.000	0.000	0.000
52	A	69	LYS	1	0.884	0.949	40.790	0.028	0.028	0.000	0.000	0.000	0.000
53	A	70	LYS	1	0.826	0.898	39.448	0.044	0.044	0.000	0.000	0.000	0.000
54	A	71	LYS	1	0.953	0.976	38.368	0.032	0.032	0.000	0.000	0.000	0.000
55	A	72	THR	0	-0.046	-0.033	37.438	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	73	ILE	0	0.004	0.007	34.147	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	74	GLU	-1	-0.779	-0.880	33.584	-0.055	-0.055	0.000	0.000	0.000	0.000
58	A	75	GLN	0	0.005	0.006	33.386	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	76	LEU	0	-0.023	-0.004	29.125	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	77	LEU	0	-0.001	-0.004	28.947	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	78	SER	0	-0.003	0.008	28.540	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	79	LYS	1	0.995	0.995	27.106	0.041	0.041	0.000	0.000	0.000	0.000
63	A	80	VAL	0	-0.030	0.005	24.052	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.751	-0.864	23.710	-0.121	-0.121	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.041	0.028	24.240	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	83	THR	0	-0.062	-0.038	19.679	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	84	MET	0	-0.065	-0.022	19.729	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	85	GLU	-1	-0.785	-0.866	19.533	-0.204	-0.204	0.000	0.000	0.000	0.000
69	A	86	SER	0	-0.022	-0.024	19.276	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	87	MET	0	-0.068	-0.040	15.413	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	88	GLU	-1	-0.891	-0.959	15.359	-0.332	-0.332	0.000	0.000	0.000	0.000
72	A	89	GLN	0	-0.035	-0.030	17.267	-0.027	-0.027	0.000	0.000	0.000	0.000
73	A	90	GLN	0	-0.035	-0.002	12.784	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	91	LEU	0	-0.042	-0.013	11.407	-0.095	-0.095	0.000	0.000	0.000	0.000
75	A	92	PHE	0	0.021	0.019	13.585	-0.052	-0.052	0.000	0.000	0.000	0.000
76	A	93	SER	0	-0.005	-0.016	14.242	0.018	0.018	0.000	0.000	0.000	0.000
77	A	94	ILE	0	-0.038	-0.026	8.136	-0.028	-0.028	0.000	0.000	0.000	0.000
78	A	95	GLU	-1	-0.831	-0.914	10.702	-0.847	-0.847	0.000	0.000	0.000	0.000
79	A	96	SER	0	0.000	0.010	12.426	0.037	0.037	0.000	0.000	0.000	0.000
80	A	97	ALA	0	0.019	0.002	11.034	0.038	0.038	0.000	0.000	0.000	0.000
81	A	98	ASN	0	-0.106	-0.049	8.382	-0.209	-0.209	0.000	0.000	0.000	0.000
82	A	99	LEU	0	0.075	0.041	10.785	0.062	0.062	0.000	0.000	0.000	0.000
83	A	100	ASN	0	-0.031	0.006	14.398	0.072	0.072	0.000	0.000	0.000	0.000
84	A	101	LEU	0	0.019	0.005	8.695	0.040	0.040	0.000	0.000	0.000	0.000
85	A	102	GLU	-1	-0.919	-0.972	12.192	-0.499	-0.499	0.000	0.000	0.000	0.000
86	A	103	THR	0	-0.013	-0.010	14.240	0.045	0.045	0.000	0.000	0.000	0.000
87	A	104	MET	0	0.009	-0.006	15.309	0.031	0.031	0.000	0.000	0.000	0.000
88	A	105	ARG	1	0.909	0.956	8.162	0.473	0.473	0.000	0.000	0.000	0.000
89	A	106	ALA	0	0.027	0.021	16.163	0.021	0.021	0.000	0.000	0.000	0.000
90	A	107	MET	0	-0.022	-0.007	19.234	0.014	0.014	0.000	0.000	0.000	0.000
91	A	108	GLN	0	0.026	0.009	17.999	0.014	0.014	0.000	0.000	0.000	0.000
92	A	109	GLU	-1	-0.843	-0.903	18.874	-0.095	-0.095	0.000	0.000	0.000	0.000
93	A	110	GLY	0	0.025	0.013	21.272	0.010	0.010	0.000	0.000	0.000	0.000
94	A	111	ALA	0	0.001	-0.002	23.647	0.009	0.009	0.000	0.000	0.000	0.000
95	A	112	LYS	1	0.777	0.868	18.487	0.093	0.093	0.000	0.000	0.000	0.000
96	A	113	ALA	0	0.034	0.026	25.090	0.007	0.007	0.000	0.000	0.000	0.000
97	A	114	MET	0	0.017	0.005	27.246	0.006	0.006	0.000	0.000	0.000	0.000
98	A	115	LYS	1	0.966	0.992	27.834	0.020	0.020	0.000	0.000	0.000	0.000
99	A	116	THR	0	-0.032	-0.030	28.771	0.003	0.003	0.000	0.000	0.000	0.000
100	A	117	ILE	0	-0.024	-0.003	30.971	0.003	0.003	0.000	0.000	0.000	0.000
101	A	118	HIS	0	-0.022	-0.013	33.039	0.000	0.000	0.000	0.000	0.000	0.000
102	A	119	SER	0	-0.060	-0.038	34.271	0.003	0.003	0.000	0.000	0.000	0.000
103	A	120	GLY	0	0.016	0.006	36.044	0.002	0.002	0.000	0.000	0.000	0.000
104	A	121	LEU	0	-0.017	-0.015	38.081	0.001	0.001	0.000	0.000	0.000	0.000
105	A	122	ASP	-1	-0.935	-0.969	40.680	-0.018	-0.018	0.000	0.000	0.000	0.000
106	A	123	ILE	0	-0.031	-0.012	36.468	0.002	0.002	0.000	0.000	0.000	0.000
107	A	124	ASP	-1	-0.946	-0.960	40.179	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	125	LYS	1	0.844	0.922	41.730	0.012	0.012	0.000	0.000	0.000	0.000
109	A	126	VAL	0	-0.001	-0.002	44.413	0.002	0.002	0.000	0.000	0.000	0.000
110	A	127	ASP	-1	-0.888	-0.918	46.331	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	128	GLU	-1	-0.790	-0.886	47.568	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	129	THR	0	0.025	0.000	43.269	0.001	0.001	0.000	0.000	0.000	0.000
113	A	130	MET	0	-0.035	-0.012	46.587	0.002	0.002	0.000	0.000	0.000	0.000
114	A	131	ASH	0	-0.082	-0.079	48.994	0.001	0.001	0.000	0.000	0.000	0.000
115	A	132	GLU	-1	-0.898	-0.937	46.078	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	133	ILE	0	-0.028	-0.025	44.674	0.001	0.001	0.000	0.000	0.000	0.000
117	A	134	ARG	1	0.905	0.952	48.940	0.001	0.001	0.000	0.000	0.000	0.000
118	A	135	GLU	-1	-0.917	-0.957	52.607	0.000	0.000	0.000	0.000	0.000	0.000
119	A	136	GLN	0	-0.045	-0.022	48.739	0.001	0.001	0.000	0.000	0.000	0.000
120	A	137	VAL	0	-0.072	-0.036	50.897	0.001	0.001	0.000	0.000	0.000	0.000
121	A	138	GLU	-1	-0.986	-0.988	53.243	0.004	0.004	0.000	0.000	0.000	0.000
122	A	139	LEU	0	-0.051	-0.005	53.657	0.000	0.000	0.000	0.000	0.000	0.000
123	A	140	GLY	0	-0.100	-0.050	54.467	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:SER)