FMO DATABASE

FMODB ID: M3QVZ

Calculation Name: 3P04-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P04

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NNN6

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	OptHSide
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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-459234.339902
FMO2-HF: Nuclear repulsion	429536.463586
FMO2-HF: Total energy	-29697.876316
FMO2-MP2: Total energy	-29783.860558

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:64:SER)

Summations of interaction energy for fragment #1(A:64: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.
-12.892	-9.814	6.318	-4.481	-4.914	0.024

Interaction energy analysis for fragmet #1(A:64:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.001

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	66	GLN	0	0.038	0.019	3.781	-1.363	1.323	-0.016	-1.289	-1.380	0.004
4	A	67	SER	0	-0.074	-0.023	5.973	0.020	0.020	0.000	0.000	0.000	0.000
5	A	68	THR	0	-0.015	-0.008	9.431	-0.046	-0.046	0.000	0.000	0.000	0.000
6	A	69	ILE	0	-0.051	-0.031	12.038	0.047	0.047	0.000	0.000	0.000	0.000
7	A	70	VAL	0	0.050	0.031	12.379	0.067	0.067	0.000	0.000	0.000	0.000
8	A	71	PRO	0	-0.018	-0.008	14.977	0.088	0.088	0.000	0.000	0.000	0.000
9	A	72	VAL	0	-0.005	-0.009	18.044	0.008	0.008	0.000	0.000	0.000	0.000
10	A	73	GLH	0	-0.079	-0.069	20.793	0.017	0.017	0.000	0.000	0.000	0.000
11	A	74	LEU	0	-0.036	-0.019	22.221	0.008	0.008	0.000	0.000	0.000	0.000
12	A	75	HIS	0	-0.038	-0.030	25.936	0.001	0.001	0.000	0.000	0.000	0.000
13	A	76	SER	0	0.016	0.014	28.066	0.018	0.018	0.000	0.000	0.000	0.000
14	A	77	PHE	0	0.004	-0.021	25.862	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	78	GLU	-1	-0.911	-0.951	25.692	-0.038	-0.038	0.000	0.000	0.000	0.000
16	A	79	ASP	-1	-0.781	-0.895	23.749	-0.140	-0.140	0.000	0.000	0.000	0.000
17	A	80	ALA	0	-0.003	-0.002	21.747	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	81	GLN	0	-0.040	-0.019	19.770	0.010	0.010	0.000	0.000	0.000	0.000
19	A	82	VAL	0	-0.010	-0.002	18.258	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	83	ILE	0	-0.005	0.004	16.662	-0.050	-0.050	0.000	0.000	0.000	0.000
21	A	84	GLY	0	0.004	-0.018	15.138	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	85	GLY	0	-0.047	-0.017	14.124	0.052	0.052	0.000	0.000	0.000	0.000
23	A	86	ALA	0	0.058	0.027	11.972	0.005	0.005	0.000	0.000	0.000	0.000
24	A	87	PHE	0	0.004	-0.005	10.399	-0.077	-0.077	0.000	0.000	0.000	0.000
25	A	88	ARG	1	0.781	0.870	9.837	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	89	ASP	-1	-0.886	-0.921	8.086	0.270	0.270	0.000	0.000	0.000	0.000
27	A	90	GLY	0	0.011	0.014	5.405	-0.354	-0.354	0.000	0.000	0.000	0.000
28	A	91	ASP	-1	-0.836	-0.908	6.070	-2.625	-2.625	0.000	0.000	0.000	0.000
29	A	92	ALA	0	-0.030	-0.024	8.651	0.377	0.377	0.000	0.000	0.000	0.000
30	A	93	VAL	0	-0.024	-0.012	11.152	-0.071	-0.071	0.000	0.000	0.000	0.000
31	A	94	VAL	0	-0.027	-0.012	14.640	0.078	0.078	0.000	0.000	0.000	0.000
32	A	95	PHE	0	0.019	-0.013	18.054	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	96	ASP	-1	-0.738	-0.813	21.070	-0.165	-0.165	0.000	0.000	0.000	0.000
34	A	97	MET	0	-0.073	-0.042	24.812	0.017	0.017	0.000	0.000	0.000	0.000
35	A	98	SER	0	-0.030	-0.052	27.489	0.020	0.020	0.000	0.000	0.000	0.000
36	A	99	LEU	0	-0.060	-0.020	30.038	0.012	0.012	0.000	0.000	0.000	0.000
37	A	100	LEU	0	-0.020	0.022	27.006	0.009	0.009	0.000	0.000	0.000	0.000
38	A	101	SER	0	-0.034	-0.044	31.594	0.006	0.006	0.000	0.000	0.000	0.000
39	A	102	ARG	1	0.969	0.958	32.482	0.017	0.017	0.000	0.000	0.000	0.000
40	A	103	GLU	-1	-0.923	-0.978	32.525	0.008	0.008	0.000	0.000	0.000	0.000
41	A	104	GLU	-1	-0.774	-0.864	30.128	-0.051	-0.051	0.000	0.000	0.000	0.000
42	A	105	ALA	0	0.032	0.018	28.174	0.003	0.003	0.000	0.000	0.000	0.000
43	A	106	ARG	1	0.793	0.866	27.344	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	107	ARG	1	0.932	0.976	27.715	0.001	0.001	0.000	0.000	0.000	0.000
45	A	108	ILE	0	0.006	0.016	22.971	0.017	0.017	0.000	0.000	0.000	0.000
46	A	109	VAL	0	0.006	-0.005	23.055	0.009	0.009	0.000	0.000	0.000	0.000
47	A	110	ASP	-1	-0.813	-0.878	23.163	0.075	0.075	0.000	0.000	0.000	0.000
48	A	111	PHE	0	-0.025	-0.011	19.526	0.033	0.033	0.000	0.000	0.000	0.000
49	A	112	ALA	0	0.021	0.001	19.151	0.030	0.030	0.000	0.000	0.000	0.000
50	A	113	ALA	0	0.008	-0.002	18.577	0.028	0.028	0.000	0.000	0.000	0.000
51	A	114	GLY	0	-0.005	0.005	19.907	0.044	0.044	0.000	0.000	0.000	0.000
52	A	115	LEU	0	-0.043	-0.013	15.653	0.057	0.057	0.000	0.000	0.000	0.000
53	A	116	CYS	0	-0.058	-0.030	15.084	0.059	0.059	0.000	0.000	0.000	0.000
54	A	117	PHE	0	-0.012	0.005	15.725	0.084	0.084	0.000	0.000	0.000	0.000
55	A	118	ALA	0	-0.030	-0.018	16.497	0.062	0.062	0.000	0.000	0.000	0.000
56	A	119	LEU	0	-0.040	-0.012	10.734	0.086	0.086	0.000	0.000	0.000	0.000
57	A	120	HIS	0	-0.006	0.015	11.767	0.007	0.007	0.000	0.000	0.000	0.000
58	A	121	GLY	0	0.014	0.017	12.330	0.019	0.019	0.000	0.000	0.000	0.000
59	A	122	LYS	1	0.840	0.903	13.252	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	123	MET	0	0.025	0.020	15.505	-0.082	-0.082	0.000	0.000	0.000	0.000
61	A	124	GLN	0	-0.044	-0.022	17.404	0.049	0.049	0.000	0.000	0.000	0.000
62	A	125	LYS	1	0.940	0.992	20.160	0.062	0.062	0.000	0.000	0.000	0.000
63	A	126	ILE	0	-0.045	-0.019	19.834	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	127	ASP	-1	-0.771	-0.887	23.897	-0.170	-0.170	0.000	0.000	0.000	0.000
65	A	128	SER	0	-0.108	-0.067	26.928	0.011	0.011	0.000	0.000	0.000	0.000
66	A	129	VAL	0	-0.028	-0.007	28.040	0.018	0.018	0.000	0.000	0.000	0.000
67	A	130	THR	0	0.031	0.023	22.425	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	131	PHE	0	-0.013	-0.017	21.257	0.023	0.023	0.000	0.000	0.000	0.000
69	A	132	ALA	0	0.020	0.006	16.543	-0.042	-0.042	0.000	0.000	0.000	0.000
70	A	133	VAL	0	-0.020	0.003	14.218	0.065	0.065	0.000	0.000	0.000	0.000
71	A	134	VAL	0	-0.017	-0.026	10.757	-0.137	-0.137	0.000	0.000	0.000	0.000
72	A	135	PRO	0	0.046	0.029	7.200	0.177	0.177	0.000	0.000	0.000	0.000
73	A	136	GLU	-1	-0.913	-0.941	8.890	1.321	1.321	0.000	0.000	0.000	0.000
74	A	137	LEU	0	-0.038	-0.024	6.353	0.161	0.161	0.000	0.000	0.000	0.000
75	A	138	SER	0	0.034	0.010	2.005	-9.132	-8.867	6.335	-3.175	-3.425	0.020
76	A	139	ASN	0	-0.095	-0.054	4.558	-1.638	-1.511	-0.001	-0.017	-0.109	0.000
77	A	140	ILE	0	0.032	0.028	5.122	-0.243	-0.243	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:64:SER)