FMO DATABASE

FMODB ID: 7JL9K

Calculation Name: 1GVP-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GVP

Chain ID: A

ChEMBL ID:

UniProt ID: P69543

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-541656.995743
FMO2-HF: Nuclear repulsion	507775.380243
FMO2-HF: Total energy	-33881.615501
FMO2-MP2: Total energy	-33980.293464

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:MET )

Summations of interaction energy for fragment #1(A: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.
-3.857	-0.688	0.225	-1.436	-1.958	-0.008

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.004

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	LYS	1	1.017	1.013	3.564	-0.827	0.334	0.008	-0.475	-0.695	0.002
4	A	4	VAL	0	0.000	-0.002	5.796	0.003	0.003	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.880	-0.945	8.703	0.229	0.229	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.012	0.024	11.772	-0.008	-0.008	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.919	0.937	14.991	-0.120	-0.120	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.034	-0.011	17.861	-0.005	-0.005	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.016	-0.003	21.147	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.014	0.008	17.136	0.001	0.001	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.017	0.019	19.970	0.002	0.002	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.016	0.031	21.092	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.023	-0.011	22.240	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.012	-0.002	23.745	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.001	-0.020	25.730	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.923	0.978	26.064	-0.085	-0.085	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.001	-0.015	29.108	0.001	0.001	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.001	-0.004	31.767	0.001	0.001	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.013	0.026	33.890	0.000	0.000	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.007	0.003	32.940	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.984	0.966	32.994	-0.049	-0.049	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.008	0.010	34.690	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.038	0.023	37.629	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.962	0.975	30.374	-0.056	-0.056	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.027	0.008	34.213	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.042	-0.009	28.980	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.021	-0.006	29.262	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.021	-0.011	23.955	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	ASN	0	0.083	0.056	23.081	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.835	-0.913	21.072	0.105	0.105	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.010	0.001	18.025	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.025	-0.013	18.382	0.010	0.010	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.035	0.003	13.437	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.012	0.001	13.832	0.004	0.004	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.013	0.000	8.157	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.878	-0.948	8.276	0.116	0.116	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.035	-0.027	7.353	-0.145	-0.145	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.010	0.016	9.018	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.071	-0.034	10.469	0.022	0.022	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.909	-0.958	13.974	0.029	0.029	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.018	-0.003	16.062	0.011	0.011	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.034	-0.029	12.719	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.032	0.034	12.098	0.006	0.006	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.045	-0.030	14.129	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.004	0.008	12.275	0.009	0.009	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.845	0.899	15.475	-0.104	-0.104	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.028	0.023	13.969	0.023	0.023	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.031	-0.018	16.730	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.012	-0.017	17.802	0.017	0.017	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.844	-0.915	17.691	0.152	0.152	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.970	-0.995	20.367	0.055	0.055	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.001	0.001	23.312	0.000	0.000	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.016	0.012	16.566	0.007	0.007	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.030	-0.027	20.596	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.020	0.010	19.769	0.005	0.005	0.000	0.000	0.000	0.000
56	A	56	TYR	0	0.010	0.014	13.922	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.056	0.032	17.018	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.026	-0.024	15.962	0.003	0.003	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.022	0.017	14.089	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.019	-0.004	8.913	0.006	0.006	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.037	-0.043	8.158	0.005	0.005	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.010	0.006	2.826	-3.035	-1.332	0.217	-0.942	-0.978	-0.010
63	A	63	VAL	0	-0.011	-0.010	4.573	0.279	0.470	0.000	-0.012	-0.178	0.000
64	A	64	HIS	0	0.068	0.080	5.641	0.292	0.292	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.077	0.021	6.769	0.199	0.199	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.037	-0.050	9.104	0.005	0.005	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.009	0.001	9.203	-0.109	-0.109	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.049	-0.011	5.255	-0.194	-0.080	0.000	-0.007	-0.107	0.000
69	A	69	LYS	1	0.885	0.951	10.931	-0.322	-0.322	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.007	0.007	13.270	0.025	0.025	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.008	-0.005	15.032	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.017	-0.018	17.423	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.017	-0.016	19.453	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.022	0.025	18.089	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.007	0.013	14.107	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.025	-0.016	7.679	0.003	0.003	0.000	0.000	0.000	0.000
77	A	77	MET	0	0.027	0.011	11.911	0.004	0.004	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.001	0.004	8.691	0.060	0.060	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.900	-0.955	11.958	0.122	0.122	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.959	0.969	13.956	-0.190	-0.190	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.023	-0.009	8.857	0.059	0.059	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.798	0.894	11.110	-0.308	-0.308	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.030	-0.010	8.985	0.044	0.044	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.021	0.010	7.551	0.023	0.023	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.019	-0.038	8.482	-0.062	-0.062	0.000	0.000	0.000	0.000
86	A	86	ALA	0	-0.001	-0.014	6.833	-0.055	-0.055	0.000	0.000	0.000	0.000
87	A	87	LYS	0	0.001	0.043	7.436	-0.004	-0.004	0.000	0.000	0.000	0.000

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