FMO DATABASE

FMODB ID: G51V1

Calculation Name: 2P04-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P04

Chain ID: A

ChEMBL ID:

UniProt ID: D0VWX5

Base Structure: X-ray

Registration Date: 2023-09-24

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-871889.169356
FMO2-HF: Nuclear repulsion	828711.463665
FMO2-HF: Total energy	-43177.705691
FMO2-MP2: Total energy	-43304.277547

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.
-2.712	0.011	2.477	-0.721	-4.479	0

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 : 0.029 / q_NPA : 0.019

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].
3	A	3	PRO	0	0.010	0.013	2.319	-1.465	1.622	2.407	-1.303	-4.192
4	A	4	PRO	0	-0.011	-0.003	4.043	-1.195	-1.559	0.070	0.582	-0.287
5	A	5	HIS	0	0.033	0.007	7.667	0.020	0.020	0.000	0.000	0.000
6	A	6	LEU	0	-0.027	-0.010	10.250	-0.107	-0.107	0.000	0.000	0.000
7	A	7	THR	0	0.016	0.002	12.805	0.030	0.030	0.000	0.000	0.000
8	A	8	LEU	0	-0.017	0.000	15.417	-0.012	-0.012	0.000	0.000	0.000
9	A	9	SER	0	0.046	0.026	19.085	-0.002	-0.002	0.000	0.000	0.000
10	A	10	PRO	0	0.083	0.020	21.641	0.001	0.001	0.000	0.000	0.000
11	A	11	GLU	-1	-0.883	-0.936	23.727	-0.008	-0.008	0.000	0.000	0.000
12	A	12	LEU	0	0.009	0.003	21.307	0.001	0.001	0.000	0.000	0.000
13	A	13	LEU	0	0.000	-0.001	20.003	0.002	0.002	0.000	0.000	0.000
14	A	14	ALA	0	0.011	0.003	23.209	-0.001	-0.001	0.000	0.000	0.000
15	A	15	LYS	1	0.783	0.883	26.724	0.005	0.005	0.000	0.000	0.000
16	A	16	ALA	0	-0.024	-0.006	23.329	0.000	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.006	-0.004	20.649	0.000	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.032	0.028	26.059	-0.002	-0.002	0.000	0.000	0.000
19	A	19	PHE	0	-0.013	-0.047	28.876	-0.001	-0.001	0.000	0.000	0.000
20	A	20	HIS	0	-0.001	0.015	24.926	-0.001	-0.001	0.000	0.000	0.000
21	A	21	PHE	0	0.000	-0.005	26.629	0.000	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.006	0.010	23.931	-0.001	-0.001	0.000	0.000	0.000
23	A	23	PHE	0	0.017	0.000	25.227	0.001	0.001	0.000	0.000	0.000
24	A	24	SER	0	0.097	0.043	25.023	-0.002	-0.002	0.000	0.000	0.000
25	A	25	ARG	1	0.823	0.863	21.551	0.038	0.038	0.000	0.000	0.000
26	A	26	ASN	0	-0.052	-0.023	26.767	0.000	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.780	0.858	29.252	0.016	0.016	0.000	0.000	0.000
28	A	28	GLU	-1	-0.865	-0.907	30.587	-0.015	-0.015	0.000	0.000	0.000
29	A	29	ILE	0	-0.030	-0.020	29.547	-0.001	-0.001	0.000	0.000	0.000
30	A	30	VAL	0	0.008	-0.008	26.255	0.000	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.040	-0.020	23.860	-0.001	-0.001	0.000	0.000	0.000
32	A	32	THR	0	-0.030	-0.054	28.362	0.000	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.011	0.030	29.201	0.000	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.799	-0.902	29.808	-0.006	-0.006	0.000	0.000	0.000
35	A	35	VAL	0	-0.102	-0.048	32.671	0.000	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.000	0.002	31.129	0.000	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.863	-0.912	32.906	-0.010	-0.010	0.000	0.000	0.000
38	A	38	ARG	1	0.921	0.970	35.724	0.006	0.006	0.000	0.000	0.000
39	A	39	ILE	0	-0.063	-0.028	36.843	0.000	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.019	-0.025	37.982	0.000	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.034	-0.017	40.040	0.000	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.863	-0.930	40.810	-0.010	-0.010	0.000	0.000	0.000
43	A	43	PRO	0	0.020	0.019	38.411	0.000	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.031	0.005	34.373	0.000	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.016	0.017	31.868	0.000	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.002	0.008	33.415	0.000	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.798	0.921	34.780	0.011	0.011	0.000	0.000	0.000
48	A	48	LEU	0	0.012	0.013	34.044	-0.001	-0.001	0.000	0.000	0.000
49	A	49	ILE	0	0.031	0.010	29.335	0.001	0.001	0.000	0.000	0.000
50	A	50	GLU	-1	-0.778	-0.866	33.517	-0.012	-0.012	0.000	0.000	0.000
51	A	51	GLN	0	-0.038	-0.008	36.487	0.000	0.000	0.000	0.000	0.000
52	A	52	HIS	1	0.828	0.903	36.023	0.010	0.010	0.000	0.000	0.000
53	A	53	PHE	0	0.007	0.009	32.739	0.001	0.001	0.000	0.000	0.000
54	A	54	GLN	0	-0.016	-0.009	35.455	-0.001	-0.001	0.000	0.000	0.000
55	A	55	ILE	0	0.017	0.009	29.909	0.000	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.076	-0.048	33.264	0.001	0.001	0.000	0.000	0.000
57	A	57	ARG	1	0.863	0.925	30.740	0.007	0.007	0.000	0.000	0.000
58	A	58	PRO	0	0.121	0.066	27.249	0.000	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.914	0.947	30.304	0.008	0.008	0.000	0.000	0.000
60	A	60	ILE	0	0.004	0.012	28.188	0.000	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.044	0.017	32.504	0.001	0.001	0.000	0.000	0.000
62	A	62	ILE	0	-0.006	0.004	31.154	-0.001	-0.001	0.000	0.000	0.000
63	A	63	ASP	-1	-0.806	-0.918	29.063	-0.020	-0.020	0.000	0.000	0.000
64	A	64	PHE	0	0.048	0.035	22.301	-0.001	-0.001	0.000	0.000	0.000
65	A	65	ASP	-1	-0.767	-0.852	24.692	-0.035	-0.035	0.000	0.000	0.000
66	A	66	ALA	0	-0.040	-0.031	24.600	-0.003	-0.003	0.000	0.000	0.000
67	A	67	ILE	0	-0.016	-0.005	23.569	-0.001	-0.001	0.000	0.000	0.000
68	A	68	SER	0	-0.031	-0.014	20.619	-0.003	-0.003	0.000	0.000	0.000
69	A	69	LYS	1	0.797	0.887	19.870	0.025	0.025	0.000	0.000	0.000
70	A	70	GLN	0	-0.039	-0.025	21.678	0.003	0.003	0.000	0.000	0.000
71	A	71	PRO	0	0.048	0.012	16.944	0.004	0.004	0.000	0.000	0.000
72	A	72	ARG	1	0.918	0.958	13.188	0.099	0.099	0.000	0.000	0.000
73	A	73	ALA	0	-0.014	0.014	19.858	0.005	0.005	0.000	0.000	0.000
74	A	74	LEU	0	-0.023	-0.011	23.340	0.000	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.016	0.008	23.776	0.002	0.002	0.000	0.000	0.000
76	A	76	ILE	0	-0.036	-0.016	27.063	0.001	0.001	0.000	0.000	0.000
77	A	77	LEU	0	0.010	0.001	28.830	-0.001	-0.001	0.000	0.000	0.000
78	A	78	GLU	-1	-0.833	-0.883	32.178	-0.005	-0.005	0.000	0.000	0.000
79	A	79	PHE	0	0.029	0.003	35.495	0.000	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.000	-0.013	36.802	0.001	0.001	0.000	0.000	0.000
81	A	81	HIS	0	-0.041	0.001	39.828	0.000	0.000	0.000	0.000	0.000
82	A	82	ASN	0	0.011	-0.023	39.342	0.000	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.047	0.040	40.301	0.000	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.063	-0.004	35.558	0.000	0.000	0.000	0.000	0.000
85	A	85	GLN	0	0.010	0.005	34.731	0.000	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.034	-0.016	30.456	0.001	0.001	0.000	0.000	0.000
87	A	87	LYS	1	0.957	0.977	27.648	0.001	0.001	0.000	0.000	0.000
88	A	88	GLY	0	0.028	-0.004	24.701	0.002	0.002	0.000	0.000	0.000
89	A	89	GLN	0	-0.053	-0.013	18.559	-0.005	-0.005	0.000	0.000	0.000
90	A	90	MET	0	-0.011	0.015	21.796	0.002	0.002	0.000	0.000	0.000
91	A	91	MET	0	-0.033	-0.020	15.622	-0.005	-0.005	0.000	0.000	0.000
92	A	92	TYR	0	-0.058	-0.056	17.400	0.003	0.003	0.000	0.000	0.000
93	A	93	GLN	0	-0.039	-0.034	14.771	-0.017	-0.017	0.000	0.000	0.000
94	A	94	PRO	0	-0.015	-0.011	14.210	0.004	0.004	0.000	0.000	0.000
95	A	95	GLU	-1	-0.920	-0.948	13.847	-0.023	-0.023	0.000	0.000	0.000
96	A	96	GLU	-1	-0.905	-0.947	16.880	-0.016	-0.016	0.000	0.000	0.000
97	A	97	GLU	-1	-0.824	-0.868	19.735	-0.038	-0.038	0.000	0.000	0.000
98	A	98	VAL	0	-0.005	-0.005	20.612	0.004	0.004	0.000	0.000	0.000
99	A	99	ILE	0	-0.045	-0.021	20.369	-0.005	-0.005	0.000	0.000	0.000
100	A	100	PHE	0	0.045	0.018	19.645	0.004	0.004	0.000	0.000	0.000
101	A	101	PHE	0	0.020	-0.004	21.823	-0.002	-0.002	0.000	0.000	0.000
102	A	102	LEU	0	0.006	0.002	19.120	0.002	0.002	0.000	0.000	0.000
103	A	103	GLY	0	0.025	-0.003	23.080	-0.001	-0.001	0.000	0.000	0.000
104	A	104	SER	0	-0.065	-0.020	26.133	0.001	0.001	0.000	0.000	0.000
105	A	105	PRO	0	0.040	0.015	29.107	-0.001	-0.001	0.000	0.000	0.000
106	A	106	TRP	0	-0.092	-0.046	31.690	0.001	0.001	0.000	0.000	0.000
107	A	107	ILE	0	0.029	0.020	33.312	0.000	0.000	0.000	0.000	0.000

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