FMO DATABASE

FMODB ID: K96M3

Calculation Name: 3GHD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GHD

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZN4

Base Structure: X-ray

Registration Date: 2023-09-20

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-403457.241757
FMO2-HF: Nuclear repulsion	376840.460976
FMO2-HF: Total energy	-26616.780781
FMO2-MP2: Total energy	-26694.684727

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:14:LYS)

Summations of interaction energy for fragment #1(A:14:LYS)

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.
-40.408	-37.113	23.434	-13.19	-13.539	-0.134

Interaction energy analysis for fragmet #1(A:14:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.900 / q_NPA : 0.947

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	16	ILE	0	-0.028	-0.018	3.067	-7.787	-4.016	0.027	-1.870	-1.928	0.005
4	A	17	VAL	0	0.033	0.026	5.927	2.404	2.404	0.000	0.000	0.000	0.000
5	A	18	VAL	0	-0.044	-0.020	9.697	-0.680	-0.680	0.000	0.000	0.000	0.000
6	A	19	GLN	0	0.022	0.008	12.472	1.479	1.479	0.000	0.000	0.000	0.000
7	A	20	PRO	0	-0.035	-0.026	16.220	-0.440	-0.440	0.000	0.000	0.000	0.000
8	A	21	LYS	1	0.858	0.917	18.160	13.851	13.851	0.000	0.000	0.000	0.000
9	A	22	ASP	-1	-0.808	-0.875	15.668	-19.282	-19.282	0.000	0.000	0.000	0.000
10	A	23	THR	0	0.003	-0.018	17.667	-0.137	-0.137	0.000	0.000	0.000	0.000
11	A	24	VAL	0	0.039	0.019	16.036	-1.390	-1.390	0.000	0.000	0.000	0.000
12	A	25	ASP	-1	-0.794	-0.881	15.671	-17.936	-17.936	0.000	0.000	0.000	0.000
13	A	26	ARG	1	0.838	0.927	14.747	18.541	18.541	0.000	0.000	0.000	0.000
14	A	27	VAL	0	0.061	0.018	11.065	-1.742	-1.742	0.000	0.000	0.000	0.000
15	A	28	ALA	0	0.043	0.024	10.884	-2.807	-2.807	0.000	0.000	0.000	0.000
16	A	29	LYS	1	0.851	0.928	11.079	16.422	16.422	0.000	0.000	0.000	0.000
17	A	30	ILE	0	-0.023	-0.005	7.968	-2.159	-2.159	0.000	0.000	0.000	0.000
18	A	31	LEU	0	-0.017	0.000	6.307	-5.269	-5.269	0.000	0.000	0.000	0.000
19	A	32	SER	0	0.037	-0.002	6.029	-7.450	-7.450	0.000	0.000	0.000	0.000
20	A	33	ARG	1	0.890	0.943	6.862	29.694	29.694	0.000	0.000	0.000	0.000
21	A	34	ASN	0	-0.026	-0.006	3.701	0.573	1.142	0.000	-0.244	-0.325	-0.001
22	A	35	LYS	1	0.957	0.983	1.826	-2.080	-4.040	10.294	-4.391	-3.943	-0.056
23	A	36	ALA	0	-0.001	0.005	1.808	-42.063	-41.880	13.089	-6.679	-6.593	-0.081
24	A	37	GLY	0	0.116	0.072	3.464	7.936	8.468	0.025	0.013	-0.570	-0.001
25	A	38	SER	0	-0.067	-0.055	4.692	6.626	6.826	-0.001	-0.019	-0.180	0.000
26	A	39	ALA	0	0.014	0.013	6.055	-4.085	-4.085	0.000	0.000	0.000	0.000
27	A	40	VAL	0	0.011	-0.002	7.396	2.333	2.333	0.000	0.000	0.000	0.000
28	A	41	VAL	0	-0.004	0.005	10.117	0.020	0.020	0.000	0.000	0.000	0.000
29	A	42	MET	0	-0.032	-0.025	13.060	0.038	0.038	0.000	0.000	0.000	0.000
30	A	43	GLU	-1	-0.835	-0.937	15.739	-14.102	-14.102	0.000	0.000	0.000	0.000
31	A	44	GLY	0	0.000	0.003	19.471	0.617	0.617	0.000	0.000	0.000	0.000
32	A	45	ASP	-1	-0.872	-0.941	18.081	-15.071	-15.071	0.000	0.000	0.000	0.000
33	A	46	GLU	-1	-0.860	-0.912	17.505	-13.594	-13.594	0.000	0.000	0.000	0.000
34	A	47	ILE	0	0.006	-0.004	11.678	-0.463	-0.463	0.000	0.000	0.000	0.000
35	A	48	LEU	0	0.007	0.014	15.247	0.743	0.743	0.000	0.000	0.000	0.000
36	A	49	GLY	0	0.032	-0.004	14.003	1.041	1.041	0.000	0.000	0.000	0.000
37	A	50	VAL	0	-0.026	0.005	7.852	-1.234	-1.234	0.000	0.000	0.000	0.000
38	A	51	VAL	0	-0.001	0.019	10.724	1.560	1.560	0.000	0.000	0.000	0.000
39	A	52	THR	0	0.001	-0.028	7.983	-2.437	-2.437	0.000	0.000	0.000	0.000
40	A	53	GLU	-1	-0.881	-0.967	8.231	-32.028	-32.028	0.000	0.000	0.000	0.000
41	A	54	ARG	1	0.833	0.883	10.628	19.685	19.685	0.000	0.000	0.000	0.000
42	A	55	ASP	-1	-0.778	-0.837	12.252	-18.142	-18.142	0.000	0.000	0.000	0.000
43	A	56	ILE	0	0.009	0.002	12.226	1.141	1.141	0.000	0.000	0.000	0.000
44	A	57	LEU	0	-0.003	-0.004	14.130	1.203	1.203	0.000	0.000	0.000	0.000
45	A	58	ASP	-1	-0.775	-0.859	16.254	-15.291	-15.291	0.000	0.000	0.000	0.000
46	A	59	LYS	1	0.807	0.889	15.759	16.979	16.979	0.000	0.000	0.000	0.000
47	A	60	VAL	0	-0.015	0.003	18.722	0.479	0.479	0.000	0.000	0.000	0.000
48	A	61	VAL	0	0.039	0.023	18.866	0.630	0.630	0.000	0.000	0.000	0.000
49	A	62	ALA	0	-0.023	-0.007	20.727	0.694	0.694	0.000	0.000	0.000	0.000
50	A	63	LYS	1	0.799	0.882	22.072	13.142	13.142	0.000	0.000	0.000	0.000
51	A	64	GLY	0	0.014	0.023	24.799	0.410	0.410	0.000	0.000	0.000	0.000
52	A	65	LYS	1	0.894	0.957	23.911	12.668	12.668	0.000	0.000	0.000	0.000
53	A	66	ASN	0	0.035	0.004	23.936	-1.158	-1.158	0.000	0.000	0.000	0.000
54	A	67	PRO	0	0.011	-0.012	19.157	-0.092	-0.092	0.000	0.000	0.000	0.000
55	A	68	LYS	1	0.892	0.941	20.456	13.676	13.676	0.000	0.000	0.000	0.000
56	A	69	GLU	-1	-0.883	-0.914	22.608	-11.296	-11.296	0.000	0.000	0.000	0.000
57	A	70	VAL	0	-0.018	-0.010	19.997	0.362	0.362	0.000	0.000	0.000	0.000
58	A	71	LYS	1	0.801	0.893	19.842	12.238	12.238	0.000	0.000	0.000	0.000
59	A	72	VAL	0	0.033	0.007	14.145	0.264	0.264	0.000	0.000	0.000	0.000
60	A	73	GLU	-1	-0.756	-0.881	17.330	-13.539	-13.539	0.000	0.000	0.000	0.000
61	A	74	GLU	-1	-0.832	-0.910	19.514	-12.724	-12.724	0.000	0.000	0.000	0.000
62	A	75	ILE	0	-0.023	-0.013	16.050	0.312	0.312	0.000	0.000	0.000	0.000
63	A	76	MET	0	-0.068	-0.012	14.877	-0.585	-0.585	0.000	0.000	0.000	0.000
64	A	77	THR	0	0.006	0.013	13.125	1.442	1.442	0.000	0.000	0.000	0.000
65	A	78	LYS	1	0.881	0.924	14.238	13.297	13.297	0.000	0.000	0.000	0.000
66	A	79	ASN	0	0.002	-0.014	14.051	-0.333	-0.333	0.000	0.000	0.000	0.000
67	A	80	PRO	0	-0.003	0.007	12.845	0.737	0.737	0.000	0.000	0.000	0.000
68	A	81	VAL	0	-0.010	-0.006	13.062	0.444	0.444	0.000	0.000	0.000	0.000
69	A	82	LYS	1	0.811	0.908	16.021	12.895	12.895	0.000	0.000	0.000	0.000
70	A	83	ILE	0	0.009	0.011	18.721	0.412	0.412	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:LYS)