FMO DATABASE

FMODB ID: GYNR1

Calculation Name: 3DA7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DA7

Chain ID: A

ChEMBL ID:

UniProt ID: P11540

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-864857.278588
FMO2-HF: Nuclear repulsion	822171.514504
FMO2-HF: Total energy	-42685.764084
FMO2-MP2: Total energy	-42812.890226

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:4:ARG)

Summations of interaction energy for fragment #1(A:4:ARG)

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.
-93.02	-82.139	39.342	-21.942	-28.281	-0.22

Interaction energy analysis for fragmet #1(A:4:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.806 / q_NPA : 0.895

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	6	TRP	0	0.036	0.005	3.043	-6.589	-2.701	0.253	-1.501	-2.640	-0.001
4	A	7	ARG	1	0.906	0.956	6.107	24.857	24.857	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.796	-0.859	9.535	-19.779	-19.779	0.000	0.000	0.000	0.000
6	A	9	ALA	0	0.016	0.003	12.261	0.996	0.996	0.000	0.000	0.000	0.000
7	A	10	ASP	-1	-0.739	-0.815	15.523	-15.027	-15.027	0.000	0.000	0.000	0.000
8	A	11	ILE	0	-0.008	-0.004	16.933	-0.021	-0.021	0.000	0.000	0.000	0.000
9	A	12	ASN	0	0.006	0.023	19.749	0.544	0.544	0.000	0.000	0.000	0.000
10	A	13	TYR	0	-0.038	-0.023	23.220	0.356	0.356	0.000	0.000	0.000	0.000
11	A	14	THR	0	-0.011	-0.001	24.815	0.103	0.103	0.000	0.000	0.000	0.000
12	A	15	SER	0	0.001	-0.014	28.396	0.243	0.243	0.000	0.000	0.000	0.000
13	A	16	GLY	0	0.050	0.050	30.009	-0.085	-0.085	0.000	0.000	0.000	0.000
14	A	17	PHE	0	-0.006	-0.005	28.883	-0.256	-0.256	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.791	0.862	18.820	13.979	13.979	0.000	0.000	0.000	0.000
16	A	19	ASN	0	0.036	0.008	22.193	-0.116	-0.116	0.000	0.000	0.000	0.000
17	A	20	SER	0	0.011	0.006	21.248	-0.200	-0.200	0.000	0.000	0.000	0.000
18	A	21	ASP	-1	-0.852	-0.911	18.939	-14.550	-14.550	0.000	0.000	0.000	0.000
19	A	22	ARG	1	0.777	0.876	14.571	15.514	15.514	0.000	0.000	0.000	0.000
20	A	23	ILE	0	-0.012	0.005	12.120	-0.549	-0.549	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.038	-0.024	8.342	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	25	TYR	0	0.041	0.013	7.400	-1.029	-1.029	0.000	0.000	0.000	0.000
23	A	26	SER	0	-0.002	-0.032	2.338	3.627	4.590	1.039	-0.624	-1.378	0.001
24	A	27	SER	0	0.017	0.003	2.500	0.486	2.577	1.622	-1.657	-2.055	-0.014
25	A	28	ASP	-1	-0.827	-0.875	1.764	-111.848	-113.038	18.063	-8.314	-8.559	-0.116
26	A	29	TRP	0	-0.013	0.000	4.598	1.588	1.678	-0.001	-0.010	-0.079	0.000
27	A	30	LEU	0	0.020	0.025	2.281	3.421	4.302	0.809	-0.392	-1.299	0.001
28	A	31	ILE	0	0.022	-0.001	5.554	1.087	1.087	0.000	0.000	0.000	0.000
29	A	32	TYR	0	-0.030	-0.023	6.416	1.654	1.654	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.976	1.009	10.220	17.163	17.163	0.000	0.000	0.000	0.000
31	A	34	THR	0	-0.019	0.004	13.519	-0.248	-0.248	0.000	0.000	0.000	0.000
32	A	35	THR	0	0.079	0.026	15.615	0.087	0.087	0.000	0.000	0.000	0.000
33	A	36	ASP	-1	-0.823	-0.869	18.072	-15.556	-15.556	0.000	0.000	0.000	0.000
34	A	37	HIS	0	0.033	0.007	18.510	-0.137	-0.137	0.000	0.000	0.000	0.000
35	A	38	TYR	0	-0.099	-0.092	13.526	0.362	0.362	0.000	0.000	0.000	0.000
36	A	39	GLN	0	-0.002	0.019	15.474	-0.993	-0.993	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.043	-0.051	15.556	-0.855	-0.855	0.000	0.000	0.000	0.000
38	A	41	PHE	0	0.030	-0.001	11.233	-0.499	-0.499	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.062	-0.026	13.261	0.087	0.087	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.922	0.962	9.944	24.439	24.439	0.000	0.000	0.000	0.000
41	A	44	ILE	0	0.021	-0.006	11.395	1.788	1.788	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.854	0.913	12.308	19.623	19.623	0.000	0.000	0.000	0.000
43	A	46	CYM	-1	-0.772	-0.859	14.610	-15.782	-15.782	0.000	0.000	0.000	0.000
44	A	47	ALA	0	-0.062	-0.045	17.105	0.043	0.043	0.000	0.000	0.000	0.000
45	A	48	GLN	0	-0.003	0.007	20.552	0.352	0.352	0.000	0.000	0.000	0.000
46	A	49	VAL	0	0.046	0.019	20.278	-0.166	-0.166	0.000	0.000	0.000	0.000
47	A	50	ILE	0	-0.046	-0.004	22.503	0.587	0.587	0.000	0.000	0.000	0.000
48	A	51	ASN	0	-0.046	-0.047	20.101	0.328	0.328	0.000	0.000	0.000	0.000
49	A	52	THR	0	0.029	-0.008	21.576	-0.606	-0.606	0.000	0.000	0.000	0.000
50	A	53	PHE	0	-0.022	-0.023	16.156	-0.673	-0.673	0.000	0.000	0.000	0.000
51	A	54	ASP	-1	-0.778	-0.889	16.792	-16.069	-16.069	0.000	0.000	0.000	0.000
52	A	55	GLY	0	0.012	0.007	18.046	-0.357	-0.357	0.000	0.000	0.000	0.000
53	A	56	VAL	0	-0.010	-0.013	15.587	-0.198	-0.198	0.000	0.000	0.000	0.000
54	A	57	ALA	0	-0.003	-0.010	13.458	-0.857	-0.857	0.000	0.000	0.000	0.000
55	A	58	ASP	-1	-0.868	-0.930	14.016	-17.201	-17.201	0.000	0.000	0.000	0.000
56	A	59	TYR	0	0.010	0.020	16.591	0.132	0.132	0.000	0.000	0.000	0.000
57	A	60	LEU	0	-0.037	-0.022	11.577	-0.321	-0.321	0.000	0.000	0.000	0.000
58	A	61	GLN	0	-0.030	-0.019	9.223	-0.795	-0.795	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.032	0.003	13.405	-0.065	-0.065	0.000	0.000	0.000	0.000
60	A	63	TYR	0	-0.021	-0.023	16.210	0.519	0.519	0.000	0.000	0.000	0.000
61	A	64	HIS	1	0.772	0.888	11.779	22.766	22.766	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.868	0.937	13.045	13.683	13.683	0.000	0.000	0.000	0.000
63	A	66	LEU	0	-0.014	0.001	14.167	-0.213	-0.213	0.000	0.000	0.000	0.000
64	A	67	PRO	0	0.042	0.016	16.176	0.470	0.470	0.000	0.000	0.000	0.000
65	A	68	ASP	-1	-0.781	-0.893	19.781	-13.064	-13.064	0.000	0.000	0.000	0.000
66	A	69	ASN	0	-0.033	0.000	21.854	0.185	0.185	0.000	0.000	0.000	0.000
67	A	70	TYR	0	-0.025	-0.037	18.870	0.017	0.017	0.000	0.000	0.000	0.000
68	A	71	ILE	0	-0.006	0.011	20.945	0.208	0.208	0.000	0.000	0.000	0.000
69	A	72	THR	0	-0.023	-0.036	17.285	-0.210	-0.210	0.000	0.000	0.000	0.000
70	A	73	LYS	1	0.836	0.891	16.912	16.640	16.640	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.008	0.000	20.927	0.599	0.599	0.000	0.000	0.000	0.000
72	A	75	GLU	-1	-0.789	-0.869	20.468	-12.956	-12.956	0.000	0.000	0.000	0.000
73	A	76	ALA	0	0.025	0.012	24.042	0.488	0.488	0.000	0.000	0.000	0.000
74	A	77	GLN	0	-0.045	-0.037	24.168	0.035	0.035	0.000	0.000	0.000	0.000
75	A	78	ALA	0	-0.012	0.015	26.853	0.418	0.418	0.000	0.000	0.000	0.000
76	A	79	LEU	0	-0.016	0.002	28.018	0.330	0.330	0.000	0.000	0.000	0.000
77	A	80	GLY	0	0.019	0.006	30.743	0.250	0.250	0.000	0.000	0.000	0.000
78	A	81	TRP	0	-0.031	-0.016	23.513	-0.099	-0.099	0.000	0.000	0.000	0.000
79	A	82	VAL	0	-0.030	-0.033	29.669	-0.046	-0.046	0.000	0.000	0.000	0.000
80	A	83	ALA	0	0.027	0.004	26.647	0.121	0.121	0.000	0.000	0.000	0.000
81	A	84	SER	0	-0.004	-0.016	28.647	-0.045	-0.045	0.000	0.000	0.000	0.000
82	A	85	LYS	1	0.964	0.986	31.448	8.571	8.571	0.000	0.000	0.000	0.000
83	A	86	GLY	0	-0.002	0.013	30.188	0.114	0.114	0.000	0.000	0.000	0.000
84	A	87	ASN	0	-0.005	-0.001	31.269	-0.181	-0.181	0.000	0.000	0.000	0.000
85	A	88	LEU	0	0.009	0.016	25.028	0.069	0.069	0.000	0.000	0.000	0.000
86	A	89	ALA	0	-0.015	-0.013	29.555	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	90	ASP	-1	-0.911	-0.960	31.353	-8.446	-8.446	0.000	0.000	0.000	0.000
88	A	91	VAL	0	-0.051	-0.025	30.099	0.149	0.149	0.000	0.000	0.000	0.000
89	A	92	ALA	0	-0.028	-0.015	27.991	-0.051	-0.051	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.036	0.016	29.085	-0.319	-0.319	0.000	0.000	0.000	0.000
91	A	94	GLY	0	-0.007	0.005	29.049	-0.075	-0.075	0.000	0.000	0.000	0.000
92	A	95	LYS	1	0.834	0.917	24.333	11.272	11.272	0.000	0.000	0.000	0.000
93	A	96	SER	0	0.001	0.002	21.759	0.336	0.336	0.000	0.000	0.000	0.000
94	A	97	ILE	0	0.019	0.013	19.072	-0.142	-0.142	0.000	0.000	0.000	0.000
95	A	98	GLY	0	-0.026	-0.032	16.837	-0.475	-0.475	0.000	0.000	0.000	0.000
96	A	99	GLY	0	0.025	0.012	13.845	0.473	0.473	0.000	0.000	0.000	0.000
97	A	100	ASP	-1	-0.832	-0.900	13.807	-16.294	-16.294	0.000	0.000	0.000	0.000
98	A	101	ILE	0	-0.012	-0.016	9.350	-1.495	-1.495	0.000	0.000	0.000	0.000
99	A	102	PHE	0	0.032	0.019	8.279	0.964	0.964	0.000	0.000	0.000	0.000
100	A	103	SER	0	-0.055	-0.049	8.035	-1.973	-1.973	0.000	0.000	0.000	0.000
101	A	104	ASN	0	-0.021	-0.004	6.211	2.635	2.635	0.000	0.000	0.000	0.000
102	A	105	ARG	1	0.990	0.981	9.082	18.031	18.031	0.000	0.000	0.000	0.000
103	A	106	GLU	-1	-0.863	-0.920	12.125	-17.354	-17.354	0.000	0.000	0.000	0.000
104	A	107	GLY	0	-0.021	-0.002	9.058	0.445	0.445	0.000	0.000	0.000	0.000
105	A	108	LYS	1	0.800	0.910	9.430	17.827	17.827	0.000	0.000	0.000	0.000
106	A	109	LEU	0	-0.039	-0.003	5.660	-0.384	-0.384	0.000	0.000	0.000	0.000
107	A	110	PRO	0	0.019	0.005	3.079	-2.035	-0.795	0.401	-0.427	-1.215	0.003
108	A	111	GLY	0	0.046	0.030	2.844	-9.975	-7.329	0.296	-1.378	-1.563	-0.014
109	A	112	LYS	1	0.992	1.009	1.901	-16.792	-16.520	16.860	-7.639	-9.493	-0.080

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ARG)