FMO DATABASE

FMODB ID: Q1LGY

Calculation Name: 3N3F-A-Xray372

Preferred Name: Collagen

Target Type: PROTEIN COMPLEX GROUP

Ligand Name:

ligand 3-letter code:

PDB ID: 3N3F

Chain ID: A

ChEMBL ID: CHEMBL2364188

UniProt ID: P39059

Base Structure: X-ray

Registration Date: 2023-03-14

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-278322.869635
FMO2-HF: Nuclear repulsion	256507.546876
FMO2-HF: Total energy	-21815.322759
FMO2-MP2: Total energy	-21879.016797

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:ASN)

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

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.
-14.442	-18.421	19.152	-7.709	-7.466	0.028

Interaction energy analysis for fragmet #1(A:1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.018

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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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	3	VAL	0	-0.026	0.007	3.860	0.774	2.297	-0.017	-0.739	-0.767	0.001
4	A	4	THR	0	0.007	0.007	6.016	-0.518	-0.518	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.000	-0.007	7.676	0.196	0.196	0.000	0.000	0.000	0.000
6	A	6	PHE	0	-0.005	0.013	10.015	-0.078	-0.078	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.058	-0.046	14.266	0.005	0.005	0.000	0.000	0.000	0.000
8	A	8	ASN	0	0.009	-0.001	17.980	0.017	0.017	0.000	0.000	0.000	0.000
9	A	9	MET	0	0.070	0.020	17.460	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.857	-0.924	17.823	-0.078	-0.078	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.838	-0.904	16.327	-0.285	-0.285	0.000	0.000	0.000	0.000
12	A	12	MET	0	0.032	0.018	12.544	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.021	-0.009	13.934	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.057	-0.027	16.107	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.807	0.891	11.865	0.252	0.252	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.038	0.026	10.940	-0.078	-0.078	0.000	0.000	0.000	0.000
17	A	17	HIS	0	-0.024	-0.016	10.046	0.030	0.030	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.028	-0.003	8.372	-0.095	-0.095	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.016	-0.003	5.302	-0.545	-0.545	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.010	0.018	2.156	-1.442	-0.375	1.765	-0.765	-2.068	0.002
21	A	21	GLU	-1	-0.836	-0.924	4.613	1.319	1.421	-0.001	-0.012	-0.089	0.000
22	A	22	GLY	0	0.000	-0.005	3.732	-0.858	-0.308	0.008	-0.191	-0.366	-0.001
23	A	23	THR	0	-0.103	-0.060	1.822	-10.053	-17.576	17.287	-5.984	-3.781	0.022
24	A	24	PHE	0	0.013	-0.002	3.520	-2.452	-2.150	0.110	-0.018	-0.395	0.004
25	A	25	ILE	0	-0.030	-0.028	6.937	0.076	0.076	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.010	0.012	9.870	-0.042	-0.042	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.026	-0.017	12.993	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.914	0.944	14.538	0.313	0.313	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.812	-0.891	18.069	-0.157	-0.157	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.037	-0.041	20.239	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.073	-0.031	18.855	0.009	0.009	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.799	-0.857	17.740	-0.052	-0.052	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.024	-0.009	10.944	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	34	PHE	0	0.016	0.005	12.077	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.014	0.008	8.124	0.046	0.046	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.858	0.919	6.458	-0.433	-0.433	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.049	-0.026	7.180	0.065	0.065	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.898	0.925	9.562	-0.268	-0.268	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.888	-0.932	11.780	0.169	0.169	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.013	0.002	12.804	-0.044	-0.044	0.000	0.000	0.000	0.000
41	A	41	TRP	0	0.029	0.010	10.982	0.066	0.066	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.931	0.968	12.105	-0.174	-0.174	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.909	0.956	12.899	0.050	0.050	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.031	-0.015	11.989	0.004	0.004	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.011	-0.011	14.774	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.010	-0.006	16.127	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.014	-0.007	19.790	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.880	-0.944	23.142	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.025	-0.010	23.808	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.013	-0.006	24.896	0.004	0.004	0.000	0.000	0.000	0.000
51	A	51	PRO	0	-0.029	-0.011	26.494	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.008	0.003	25.014	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.028	-0.014	28.691	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.008	0.014	31.917	-0.003	-0.003	0.000	0.000	0.000	0.000

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