Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: K9Z83

Calculation Name: 4RIS-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RIS

Chain ID: H

ChEMBL ID:

UniProt ID: Q70966

Base Structure: X-ray

Registration Date: 2023-06-26

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

DOI:


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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2303011.251239
FMO2-HF: Nuclear repulsion 2216554.854931
FMO2-HF: Total energy -86456.396308
FMO2-MP2: Total energy -86708.177956


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(H:1:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
-69.388-66.6340.363-1.178-1.9410
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.939 / q_NPA : -0.978
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   
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].
3H3GLN0-0.050-0.0232.679-9.341-7.0060.350-1.010-1.6760.000
4H4LEU0-0.0020.0095.978-1.367-1.3670.0000.0000.0000.000
5H5VAL00.000-0.0068.382-0.654-0.6540.0000.0000.0000.000
6H6GLN00.015-0.02211.080-0.354-0.3540.0000.0000.0000.000
7H7SER00.0200.03114.8710.1310.1310.0000.0000.0000.000
8H8GLY00.0120.00317.441-0.093-0.0930.0000.0000.0000.000
9H9ALA0-0.032-0.01519.522-0.199-0.1990.0000.0000.0000.000
10H10GLU-1-0.886-0.94822.56311.30611.3060.0000.0000.0000.000
11H11VAL0-0.056-0.03625.681-0.188-0.1880.0000.0000.0000.000
12H12LYS10.8800.94228.852-9.883-9.8830.0000.0000.0000.000
13H13LYS10.8910.94131.809-8.214-8.2140.0000.0000.0000.000
14H14PRO0-0.043-0.03835.0720.1160.1160.0000.0000.0000.000
15H15GLY00.0050.01636.528-0.194-0.1940.0000.0000.0000.000
16H16GLU-1-0.835-0.89133.0189.0669.0660.0000.0000.0000.000
17H17SER0-0.0110.00331.6950.1230.1230.0000.0000.0000.000
18H18LEU0-0.017-0.01525.3470.0270.0270.0000.0000.0000.000
19H19LYS10.8690.93723.197-12.133-12.1330.0000.0000.0000.000
20H20ILE00.0240.03620.8910.1540.1540.0000.0000.0000.000
21H21SER00.007-0.02017.6240.2130.2130.0000.0000.0000.000
22H22CYS0-0.0250.00414.5660.1880.1880.0000.0000.0000.000
23H23LYS10.9300.98610.190-23.498-23.4980.0000.0000.0000.000
24H24GLY00.0420.0229.5430.9750.9750.0000.0000.0000.000
25H25SER0-0.080-0.0485.661-0.369-0.3690.0000.0000.0000.000
26H26GLY00.1130.0493.4951.3601.5360.014-0.145-0.0460.000
27H27TYR0-0.016-0.0104.1652.1802.423-0.001-0.023-0.2190.000
28H28SER00.0240.0187.510-2.493-2.4930.0000.0000.0000.000
29H29PHE00.0700.02411.212-1.174-1.1740.0000.0000.0000.000
30H30THR0-0.007-0.01812.755-0.832-0.8320.0000.0000.0000.000
31H31SER0-0.057-0.02113.972-1.338-1.3380.0000.0000.0000.000
32H32TYR0-0.023-0.01111.3430.9410.9410.0000.0000.0000.000
33H33TRP0-0.030-0.01315.458-0.174-0.1740.0000.0000.0000.000
34H34ILE0-0.0060.00313.6631.1401.1400.0000.0000.0000.000
35H35GLY0-0.026-0.00817.160-1.067-1.0670.0000.0000.0000.000
36H36TRP00.010-0.00618.2540.7370.7370.0000.0000.0000.000
37H37VAL0-0.019-0.01920.338-0.639-0.6390.0000.0000.0000.000
38H38ARG10.8430.88821.936-9.744-9.7440.0000.0000.0000.000
39H39GLN00.0140.01023.1060.3110.3110.0000.0000.0000.000
40H40MET00.0470.04225.478-0.146-0.1460.0000.0000.0000.000
41H41PRO00.0210.00128.3510.0940.0940.0000.0000.0000.000
42H42GLY00.0080.01128.710-0.329-0.3290.0000.0000.0000.000
43H43LYS10.8530.92029.180-9.086-9.0860.0000.0000.0000.000
44H44GLY00.0360.02027.3560.3160.3160.0000.0000.0000.000
45H45LEU0-0.004-0.00521.592-0.016-0.0160.0000.0000.0000.000
46H46GLU-1-0.766-0.84625.4359.6499.6490.0000.0000.0000.000
47H47TRP00.0170.00422.7600.1490.1490.0000.0000.0000.000
48H48MET0-0.0360.00224.476-0.307-0.3070.0000.0000.0000.000
49H49GLY00.0660.01124.206-0.531-0.5310.0000.0000.0000.000
50H50ILE0-0.104-0.04120.1260.5470.5470.0000.0000.0000.000
51H51ILE00.0140.00920.010-0.555-0.5550.0000.0000.0000.000
52H52TYR00.0550.04418.2591.3171.3170.0000.0000.0000.000
53H52PRO00.010-0.00516.209-0.691-0.6910.0000.0000.0000.000
54H53GLY0-0.0070.00219.178-0.155-0.1550.0000.0000.0000.000
55H54ASP-1-0.868-0.94320.42912.76912.7690.0000.0000.0000.000
56H55SER0-0.059-0.01922.707-0.460-0.4600.0000.0000.0000.000
57H56ASP-1-0.753-0.83224.11810.90310.9030.0000.0000.0000.000
58H57THR0-0.034-0.03724.4580.6770.6770.0000.0000.0000.000
59H58ARG10.7980.88425.905-11.761-11.7610.0000.0000.0000.000
60H59TYR00.0540.02226.6190.4380.4380.0000.0000.0000.000
61H60SER00.0050.01328.538-0.389-0.3890.0000.0000.0000.000
62H61PRO00.0320.00130.180-0.052-0.0520.0000.0000.0000.000
63H62SER0-0.0100.00331.974-0.226-0.2260.0000.0000.0000.000
64H63PHE0-0.006-0.01329.079-0.050-0.0500.0000.0000.0000.000
65H64GLN00.0080.00631.6040.1800.1800.0000.0000.0000.000
66H65GLY00.0140.00632.925-0.277-0.2770.0000.0000.0000.000
67H66GLN0-0.078-0.02632.365-0.239-0.2390.0000.0000.0000.000
68H67VAL0-0.058-0.02627.3810.0650.0650.0000.0000.0000.000
69H68THR0-0.042-0.02127.862-0.141-0.1410.0000.0000.0000.000
70H69ILE00.0060.00522.6470.2930.2930.0000.0000.0000.000
71H70SER0-0.013-0.01023.309-0.234-0.2340.0000.0000.0000.000
72H71ALA00.029-0.00518.9980.5840.5840.0000.0000.0000.000
73H72ASP-1-0.831-0.89318.79013.97413.9740.0000.0000.0000.000
74H73LYS10.9200.94216.865-13.528-13.5280.0000.0000.0000.000
75H74SER0-0.067-0.03416.0390.9720.9720.0000.0000.0000.000
76H75ILE00.0120.00315.4370.8580.8580.0000.0000.0000.000
77H76SER0-0.072-0.04211.5711.7081.7080.0000.0000.0000.000
78H77THR0-0.023-0.00612.9421.2151.2150.0000.0000.0000.000
79H78ALA00.0260.02715.607-0.812-0.8120.0000.0000.0000.000
80H79TYR0-0.025-0.04718.0430.2200.2200.0000.0000.0000.000
81H80LEU00.0160.02821.105-0.222-0.2220.0000.0000.0000.000
82H81GLN00.0270.00923.8120.3130.3130.0000.0000.0000.000
83H82TRP00.0810.03925.336-0.136-0.1360.0000.0000.0000.000
84H82SER00.004-0.01130.4950.0650.0650.0000.0000.0000.000
85H82SER00.0220.00133.653-0.222-0.2220.0000.0000.0000.000
86H82LEU0-0.0090.01629.639-0.046-0.0460.0000.0000.0000.000
87H83LYS10.8790.92733.826-9.033-9.0330.0000.0000.0000.000
88H84ALA00.0620.02033.9080.2280.2280.0000.0000.0000.000
89H85SER0-0.024-0.01334.1660.0540.0540.0000.0000.0000.000
90H86ASP-1-0.846-0.91830.4389.2709.2700.0000.0000.0000.000
91H87THR00.0040.01829.2690.4270.4270.0000.0000.0000.000
92H88ALA0-0.045-0.02926.537-0.172-0.1720.0000.0000.0000.000
93H89MET0-0.0040.02620.9040.2220.2220.0000.0000.0000.000
94H90TYR0-0.020-0.04621.564-0.175-0.1750.0000.0000.0000.000
95H91TYR00.0230.01616.9450.6300.6300.0000.0000.0000.000
96H93ALA00.0450.01313.6790.7710.7710.0000.0000.0000.000
97H94ARG10.8280.9107.898-30.908-30.9080.0000.0000.0000.000
98H95LEU0-0.036-0.00813.6310.0200.0200.0000.0000.0000.000
99H96GLY00.0570.04813.1710.2900.2900.0000.0000.0000.000
100H97GLY00.008-0.00413.691-1.568-1.5680.0000.0000.0000.000
101H98ARG10.8820.95414.820-14.021-14.0210.0000.0000.0000.000
102H99TYR00.013-0.02416.559-1.135-1.1350.0000.0000.0000.000
103H100TYR00.0170.00118.3900.0490.0490.0000.0000.0000.000
104H100TYR0-0.0120.00122.509-0.092-0.0920.0000.0000.0000.000
105H100ASP-1-0.817-0.89924.42912.02812.0280.0000.0000.0000.000
106H100SER00.0250.01725.908-0.003-0.0030.0000.0000.0000.000
107H100SER0-0.124-0.08922.9000.4200.4200.0000.0000.0000.000
108H100GLY0-0.0150.00621.1930.7740.7740.0000.0000.0000.000
109H100TYR0-0.012-0.00816.2270.1110.1110.0000.0000.0000.000
110H100TYR0-0.003-0.01118.4420.7590.7590.0000.0000.0000.000
111H100TYR00.0040.00313.599-0.984-0.9840.0000.0000.0000.000
112H100PHE0-0.024-0.01615.3490.6850.6850.0000.0000.0000.000
113H101ASP-1-0.765-0.86410.97425.47225.4720.0000.0000.0000.000
114H102TYR0-0.0030.0065.3211.7181.7180.0000.0000.0000.000
115H103TRP00.003-0.01010.252-1.931-1.9310.0000.0000.0000.000
116H104GLY00.0320.01710.6851.4991.4990.0000.0000.0000.000
117H105GLN0-0.036-0.02412.5430.3560.3560.0000.0000.0000.000
118H106GLY00.0070.01213.971-0.903-0.9030.0000.0000.0000.000
119H107THR0-0.053-0.03217.4180.3380.3380.0000.0000.0000.000
120H108LEU00.004-0.00820.008-0.354-0.3540.0000.0000.0000.000
121H109VAL00.0090.01423.383-0.081-0.0810.0000.0000.0000.000
122H110THR0-0.007-0.00626.265-0.248-0.2480.0000.0000.0000.000
123H111VAL0-0.008-0.00229.579-0.079-0.0790.0000.0000.0000.000
124H112SER0-0.003-0.01832.635-0.275-0.2750.0000.0000.0000.000
125H113SER00.0590.01935.9050.0670.0670.0000.0000.0000.000
126H114ALA0-0.0290.00837.407-0.172-0.1720.0000.0000.0000.000
127H115SER00.005-0.00437.1340.2540.2540.0000.0000.0000.000
128H116THR0-0.013-0.00534.8080.0000.0000.0000.0000.0000.000
129H117LYS10.8200.89737.046-7.209-7.2090.0000.0000.0000.000
130H118GLY00.0800.05138.8880.1490.1490.0000.0000.0000.000
131H119PRO0-0.043-0.00639.249-0.142-0.1420.0000.0000.0000.000
132H120SER0-0.0190.00242.044-0.149-0.1490.0000.0000.0000.000
133H121VAL00.020-0.01843.4120.1160.1160.0000.0000.0000.000
134H122PHE0-0.0040.00346.073-0.181-0.1810.0000.0000.0000.000
135H123PRO0-0.042-0.01347.8320.1050.1050.0000.0000.0000.000
136H124LEU0-0.015-0.00345.849-0.071-0.0710.0000.0000.0000.000
137H125ALA00.0060.00449.8820.0500.0500.0000.0000.0000.000
138H126PRO00.0560.05952.419-0.031-0.0310.0000.0000.0000.000
139H127SER0-0.004-0.03654.294-0.083-0.0830.0000.0000.0000.000
140H128SER0-0.012-0.04657.9770.0110.0110.0000.0000.0000.000
141H129LYS10.9150.95060.362-4.858-4.8580.0000.0000.0000.000
142H130SER0-0.0350.01257.541-0.012-0.0120.0000.0000.0000.000
143H131THR00.0690.03159.017-0.013-0.0130.0000.0000.0000.000
144H132SER00.0250.00559.0170.0700.0700.0000.0000.0000.000
145H133GLY0-0.001-0.00258.456-0.053-0.0530.0000.0000.0000.000
146H134GLY00.0250.02456.0350.0400.0400.0000.0000.0000.000
147H135THR0-0.032-0.00550.7710.0570.0570.0000.0000.0000.000
148H136ALA0-0.029-0.01852.253-0.070-0.0700.0000.0000.0000.000
149H137ALA00.0140.01748.1500.1060.1060.0000.0000.0000.000
150H138LEU0-0.023-0.00847.915-0.135-0.1350.0000.0000.0000.000
151H139GLY00.0740.00445.8950.1620.1620.0000.0000.0000.000
152H140CYS0-0.086-0.00743.238-0.063-0.0630.0000.0000.0000.000
153H141LEU00.0270.01743.6770.1300.1300.0000.0000.0000.000
154H142VAL0-0.018-0.01739.636-0.123-0.1230.0000.0000.0000.000
155H143LYS10.9270.94441.443-6.447-6.4470.0000.0000.0000.000
156H144ASP-1-0.814-0.89041.8266.7476.7470.0000.0000.0000.000
157H145TYR00.0490.03834.863-0.132-0.1320.0000.0000.0000.000
158H146PHE00.0330.02333.5100.1150.1150.0000.0000.0000.000
159H147PRO00.0350.02331.163-0.171-0.1710.0000.0000.0000.000
160H148GLU-1-0.841-0.92530.5819.2689.2680.0000.0000.0000.000
161H149PRO00.000-0.00528.6320.1350.1350.0000.0000.0000.000
162H150VAL0-0.009-0.02431.556-0.135-0.1350.0000.0000.0000.000
163H151THR0-0.033-0.01032.7800.2190.2190.0000.0000.0000.000
164H152VAL0-0.020-0.01834.697-0.215-0.2150.0000.0000.0000.000
165H153SER0-0.014-0.00437.1360.2010.2010.0000.0000.0000.000
166H154TRP00.0030.00539.418-0.243-0.2430.0000.0000.0000.000
167H155ASN00.020-0.00442.9260.0700.0700.0000.0000.0000.000
168H156SER0-0.013-0.01742.079-0.022-0.0220.0000.0000.0000.000
169H157GLY00.0080.01140.0500.0850.0850.0000.0000.0000.000
170H158ALA0-0.033-0.00440.8220.0650.0650.0000.0000.0000.000
171H159LEU0-0.019-0.00343.029-0.129-0.1290.0000.0000.0000.000
172H160THR00.014-0.00538.9180.0620.0620.0000.0000.0000.000
173H161SER00.0140.00140.1970.1820.1820.0000.0000.0000.000
174H162GLY00.0340.01841.145-0.137-0.1370.0000.0000.0000.000
175H163VAL0-0.023-0.00339.133-0.129-0.1290.0000.0000.0000.000
176H164HIS0-0.0090.00435.3950.3700.3700.0000.0000.0000.000
177H165THR0-0.005-0.01035.783-0.306-0.3060.0000.0000.0000.000
178H166PHE0-0.025-0.00235.3150.2150.2150.0000.0000.0000.000
179H167PRO00.0520.01732.3980.0250.0250.0000.0000.0000.000
180H168ALA0-0.0170.00033.756-0.261-0.2610.0000.0000.0000.000
181H169VAL0-0.0070.00535.2180.1070.1070.0000.0000.0000.000
182H170LEU0-0.010-0.00134.737-0.036-0.0360.0000.0000.0000.000
183H171GLN0-0.0060.00137.570-0.222-0.2220.0000.0000.0000.000
184H172SER00.0390.01540.2740.1250.1250.0000.0000.0000.000
185H173SER0-0.009-0.00242.2480.0500.0500.0000.0000.0000.000
186H174GLY0-0.003-0.00738.3220.0390.0390.0000.0000.0000.000
187H175LEU0-0.064-0.02537.4640.1820.1820.0000.0000.0000.000
188H176TYR0-0.004-0.01231.601-0.082-0.0820.0000.0000.0000.000
189H177SER0-0.025-0.03538.179-0.178-0.1780.0000.0000.0000.000
190H178LEU0-0.0010.01735.5770.1100.1100.0000.0000.0000.000
191H179SER00.0250.00939.438-0.270-0.2700.0000.0000.0000.000
192H180SER0-0.018-0.00839.4720.1470.1470.0000.0000.0000.000
193H181VAL00.000-0.00741.105-0.201-0.2010.0000.0000.0000.000
194H182VAL00.0350.01642.4300.1600.1600.0000.0000.0000.000
195H183THR0-0.014-0.00344.811-0.174-0.1740.0000.0000.0000.000
196H184VAL00.0090.00947.2820.0670.0670.0000.0000.0000.000
197H185PRO00.0510.03049.969-0.075-0.0750.0000.0000.0000.000
198H186SER00.052-0.00753.2280.0040.0040.0000.0000.0000.000
199H187SER0-0.037-0.02256.153-0.018-0.0180.0000.0000.0000.000
200H188SER0-0.0140.00554.464-0.043-0.0430.0000.0000.0000.000
201H189LEU00.015-0.00653.7660.0260.0260.0000.0000.0000.000
202H190GLY0-0.031-0.00756.6320.0040.0040.0000.0000.0000.000
203H191THR0-0.051-0.02757.919-0.045-0.0450.0000.0000.0000.000
204H192GLN0-0.0090.00852.6740.0880.0880.0000.0000.0000.000
205H193THR00.0030.01651.478-0.048-0.0480.0000.0000.0000.000
206H194TYR00.0380.01648.5620.1350.1350.0000.0000.0000.000
207H195ILE0-0.003-0.01646.419-0.082-0.0820.0000.0000.0000.000
208H197ASN00.004-0.01740.723-0.036-0.0360.0000.0000.0000.000
209H198VAL00.0120.00139.3360.1970.1970.0000.0000.0000.000
210H199ASN00.004-0.00934.272-0.149-0.1490.0000.0000.0000.000
211H200HIS00.0350.03434.6060.0210.0210.0000.0000.0000.000
212H201LYS11.0261.00328.323-10.052-10.0520.0000.0000.0000.000
213H202PRO0-0.021-0.00331.285-0.061-0.0610.0000.0000.0000.000
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