FMO DATABASE

FMODB ID: YY822

Calculation Name: 3MAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MAY

Chain ID: A

ChEMBL ID:

UniProt ID: I6X8R5

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	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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-470008.522449
FMO2-HF: Nuclear repulsion	438299.209434
FMO2-HF: Total energy	-31709.313015
FMO2-MP2: Total energy	-31799.779155

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:40:CYS)

Summations of interaction energy for fragment #1(A:40:CYS)

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.
-30.85	-21.42	12.003	-8.213	-13.222	-0.056

Interaction energy analysis for fragmet #1(A:40:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.039

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	42	ALA	0	0.043	0.010	3.848	-1.809	-0.652	-0.004	-0.559	-0.594	0.002
4	A	43	SER	0	0.002	-0.028	5.999	-0.132	-0.132	0.000	0.000	0.000	0.000
5	A	44	GLU	-1	-0.802	-0.866	2.329	1.364	2.175	0.591	-0.434	-0.969	-0.002
6	A	45	VAL	0	0.011	0.021	3.382	-0.416	0.041	0.019	-0.089	-0.386	0.000
7	A	46	ALA	0	0.029	0.025	5.592	-0.108	-0.108	0.000	0.000	0.000	0.000
8	A	47	ARG	1	0.866	0.913	7.145	-1.474	-1.474	0.000	0.000	0.000	0.000
9	A	48	THR	0	-0.027	-0.006	6.243	0.037	0.037	0.000	0.000	0.000	0.000
10	A	49	VAL	0	0.012	0.004	8.914	-0.124	-0.124	0.000	0.000	0.000	0.000
11	A	50	GLY	0	0.010	0.011	11.238	0.037	0.037	0.000	0.000	0.000	0.000
12	A	51	SER	0	-0.040	-0.034	11.222	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	52	VAL	0	0.022	0.021	11.787	0.012	0.012	0.000	0.000	0.000	0.000
14	A	53	ALA	0	-0.003	-0.001	14.759	0.036	0.036	0.000	0.000	0.000	0.000
15	A	54	LYS	1	0.795	0.879	16.761	0.285	0.285	0.000	0.000	0.000	0.000
16	A	55	SER	0	-0.001	-0.008	16.944	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	56	MET	0	0.001	0.001	16.588	0.031	0.031	0.000	0.000	0.000	0.000
18	A	57	GLY	0	0.025	0.011	20.114	0.027	0.027	0.000	0.000	0.000	0.000
19	A	58	ASP	-1	-0.792	-0.877	21.887	-0.244	-0.244	0.000	0.000	0.000	0.000
20	A	59	TYR	0	-0.052	-0.052	23.074	0.034	0.034	0.000	0.000	0.000	0.000
21	A	60	LEU	0	-0.011	-0.014	22.978	0.019	0.019	0.000	0.000	0.000	0.000
22	A	61	ASP	-1	-0.944	-0.962	26.061	-0.249	-0.249	0.000	0.000	0.000	0.000
23	A	62	SER	0	-0.035	-0.033	27.561	0.014	0.014	0.000	0.000	0.000	0.000
24	A	63	HIS	1	0.802	0.905	27.785	0.402	0.402	0.000	0.000	0.000	0.000
25	A	64	PRO	0	0.077	0.026	30.156	-0.028	-0.028	0.000	0.000	0.000	0.000
26	A	65	GLU	-1	-0.845	-0.902	32.414	-0.396	-0.396	0.000	0.000	0.000	0.000
27	A	66	THR	0	0.059	-0.002	26.187	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	67	ASN	0	-0.010	0.007	28.023	-0.058	-0.058	0.000	0.000	0.000	0.000
29	A	68	GLN	0	0.003	0.022	29.085	0.004	0.004	0.000	0.000	0.000	0.000
30	A	69	VAL	0	-0.003	0.001	28.556	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	70	MET	0	0.014	-0.003	23.248	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	71	THR	0	-0.028	-0.017	26.989	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	72	ALA	0	-0.010	-0.003	29.243	0.004	0.004	0.000	0.000	0.000	0.000
34	A	73	VAL	0	-0.001	-0.017	24.887	0.000	0.000	0.000	0.000	0.000	0.000
35	A	74	LEU	0	-0.021	-0.003	23.223	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	75	GLN	0	-0.013	-0.009	27.107	0.008	0.008	0.000	0.000	0.000	0.000
37	A	76	GLN	0	-0.031	-0.019	30.545	0.007	0.007	0.000	0.000	0.000	0.000
38	A	77	GLN	0	-0.050	-0.021	27.449	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	78	VAL	0	-0.005	-0.003	23.185	-0.036	-0.036	0.000	0.000	0.000	0.000
40	A	79	GLY	0	0.040	0.032	26.576	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	80	PRO	0	-0.006	-0.024	29.890	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	81	GLY	0	0.017	0.017	31.154	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	82	SER	0	0.011	0.008	29.232	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	83	VAL	0	0.023	0.010	26.096	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	84	ALA	0	-0.054	-0.028	28.398	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	85	SER	0	0.023	0.007	31.166	0.014	0.014	0.000	0.000	0.000	0.000
47	A	86	LEU	0	-0.018	-0.011	24.009	0.007	0.007	0.000	0.000	0.000	0.000
48	A	87	LYS	1	0.901	0.971	26.633	0.637	0.637	0.000	0.000	0.000	0.000
49	A	88	ALA	0	0.090	0.050	28.183	0.005	0.005	0.000	0.000	0.000	0.000
50	A	89	HIS	0	-0.054	-0.018	27.707	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	90	PHE	0	0.016	-0.018	22.185	0.002	0.002	0.000	0.000	0.000	0.000
52	A	91	GLU	-1	-0.941	-0.982	27.619	-0.575	-0.575	0.000	0.000	0.000	0.000
53	A	92	ALA	0	-0.028	-0.004	29.891	0.023	0.023	0.000	0.000	0.000	0.000
54	A	93	ASN	0	-0.061	-0.014	29.418	0.045	0.045	0.000	0.000	0.000	0.000
55	A	94	PRO	0	0.064	0.022	26.987	-0.035	-0.035	0.000	0.000	0.000	0.000
56	A	95	LYS	1	0.830	0.909	25.438	0.393	0.393	0.000	0.000	0.000	0.000
57	A	96	VAL	0	0.017	0.015	24.825	-0.031	-0.031	0.000	0.000	0.000	0.000
58	A	97	ALA	0	0.023	0.026	23.077	-0.051	-0.051	0.000	0.000	0.000	0.000
59	A	98	SER	0	-0.027	-0.032	20.886	-0.079	-0.079	0.000	0.000	0.000	0.000
60	A	99	ASP	-1	-0.786	-0.851	20.014	-0.562	-0.562	0.000	0.000	0.000	0.000
61	A	100	LEU	0	0.003	-0.007	19.884	-0.040	-0.040	0.000	0.000	0.000	0.000
62	A	101	HIS	0	-0.020	0.000	14.329	0.002	0.002	0.000	0.000	0.000	0.000
63	A	102	ALA	0	-0.012	-0.007	15.586	-0.195	-0.195	0.000	0.000	0.000	0.000
64	A	103	LEU	0	-0.021	-0.016	15.358	-0.044	-0.044	0.000	0.000	0.000	0.000
65	A	104	SER	0	-0.042	-0.032	13.972	-0.096	-0.096	0.000	0.000	0.000	0.000
66	A	105	GLN	0	-0.001	0.007	10.161	-0.115	-0.115	0.000	0.000	0.000	0.000
67	A	106	PRO	0	0.041	0.023	9.157	-0.724	-0.724	0.000	0.000	0.000	0.000
68	A	107	LEU	0	0.000	-0.002	7.220	-0.516	-0.516	0.000	0.000	0.000	0.000
69	A	108	THR	0	0.040	0.016	6.802	-1.131	-1.131	0.000	0.000	0.000	0.000
70	A	109	ASP	-1	-0.862	-0.927	5.729	-5.029	-5.029	0.000	0.000	0.000	0.000
71	A	110	LEU	0	-0.041	-0.017	2.957	-7.427	-6.122	2.559	-0.804	-3.061	-0.004
72	A	111	SER	0	-0.017	-0.020	1.959	-14.106	-14.832	7.545	-3.401	-3.417	-0.046
73	A	112	THR	0	-0.031	-0.013	3.308	-0.083	2.940	0.014	-1.489	-1.548	-0.005
76	A	116	LEU	0	0.021	0.026	2.384	0.240	3.494	1.281	-1.432	-3.104	-0.001
77	A	117	PRO	0	-0.044	-0.009	5.266	1.131	1.280	-0.002	-0.005	-0.143	0.000
78	A	118	ILE	0	0.038	0.006	7.157	-0.735	-0.735	0.000	0.000	0.000	0.000
79	A	119	SER	0	0.015	-0.016	7.673	0.207	0.207	0.000	0.000	0.000	0.000
80	A	120	GLY	0	0.017	0.024	9.158	0.341	0.341	0.000	0.000	0.000	0.000
81	A	121	LEU	0	0.027	0.005	12.537	0.098	0.098	0.000	0.000	0.000	0.000
82	A	122	GLN	0	-0.025	-0.024	7.538	0.128	0.128	0.000	0.000	0.000	0.000
83	A	123	ALA	0	-0.012	0.001	10.361	0.157	0.157	0.000	0.000	0.000	0.000
84	A	124	ILE	0	-0.047	-0.015	12.793	0.157	0.157	0.000	0.000	0.000	0.000
85	A	125	GLY	0	-0.014	0.001	13.240	0.078	0.078	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:40:CYS)