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: N947Q

Calculation Name: 5CHL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CHL

Chain ID: B

ChEMBL ID:

UniProt ID: P0C0S5

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptH
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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1757860.487929
FMO2-HF: Nuclear repulsion 1691143.590642
FMO2-HF: Total energy -66716.897288
FMO2-MP2: Total energy -66915.307224


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(B:4:GLU)


Summations of interaction energy for fragment #1(B:4: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.
-190.657-183.9872.262-4.024-4.907-0.018
Interaction energy analysis for fragmet #1(B:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.892 / q_NPA : -0.934
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].
3B6TYR0-0.013-0.0433.239-6.906-4.7300.024-0.995-1.2050.002
4B7SER00.0660.0226.338-2.680-2.6800.0000.0000.0000.000
5B8ILE0-0.0090.0039.318-2.158-2.1580.0000.0000.0000.000
6B9TYR0-0.032-0.0377.418-1.047-1.0470.0000.0000.0000.000
7B10VAL00.0670.0379.684-1.373-1.3730.0000.0000.0000.000
8B11TYR0-0.010-0.00312.331-1.448-1.4480.0000.0000.0000.000
9B12LYS10.9300.96314.114-18.413-18.4130.0000.0000.0000.000
10B13VAL00.0630.03714.741-0.737-0.7370.0000.0000.0000.000
11B14LEU0-0.020-0.00816.651-0.654-0.6540.0000.0000.0000.000
12B15LYS10.7690.88518.608-14.202-14.2020.0000.0000.0000.000
13B16GLN0-0.012-0.00219.128-0.129-0.1290.0000.0000.0000.000
14B17VAL00.0270.02020.444-0.455-0.4550.0000.0000.0000.000
15B18HIS0-0.077-0.02922.541-0.640-0.6400.0000.0000.0000.000
16B19PRO00.0270.01723.6240.3810.3810.0000.0000.0000.000
17B20ASP-1-0.894-0.93424.81710.90710.9070.0000.0000.0000.000
18B21THR0-0.043-0.01122.319-0.259-0.2590.0000.0000.0000.000
19B22GLY0-0.014-0.00520.8500.4840.4840.0000.0000.0000.000
20B23ILE00.010-0.00714.487-0.138-0.1380.0000.0000.0000.000
21B24SER0-0.017-0.00817.5970.4130.4130.0000.0000.0000.000
22B25SER00.0840.02014.2480.5810.5810.0000.0000.0000.000
23B26LYS10.9850.99712.798-16.541-16.5410.0000.0000.0000.000
24B27ALA00.0050.00213.0551.0111.0110.0000.0000.0000.000
25B28MET00.0310.02510.1560.9270.9270.0000.0000.0000.000
26B29GLY00.0010.0038.5321.9511.9510.0000.0000.0000.000
27B30ILE00.008-0.0018.3272.5632.5630.0000.0000.0000.000
28B31MET00.0240.01510.0600.7030.7030.0000.0000.0000.000
29B32ASN00.0140.0163.108-2.718-2.2000.015-0.242-0.2910.002
30B33SER00.0220.0175.7174.9034.9030.0000.0000.0000.000
31B34PHE00.0510.0336.6860.3070.3070.0000.0000.0000.000
32B35VAL00.011-0.0056.827-0.549-0.5490.0000.0000.0000.000
33B36ASN0-0.076-0.0722.572-4.249-0.5362.219-2.690-3.242-0.023
34B37ASP-1-0.837-0.9075.45034.51934.5190.0000.0000.0000.000
35B38ILE0-0.020-0.0098.006-2.329-2.3290.0000.0000.0000.000
36B39PHE0-0.054-0.0385.664-2.124-2.1240.0000.0000.0000.000
37B40GLU-1-0.797-0.9046.05534.66034.6600.0000.0000.0000.000
38B41ARG10.9460.9839.178-20.993-20.9930.0000.0000.0000.000
39B42ILE00.0080.01012.268-1.534-1.5340.0000.0000.0000.000
40B43ALA0-0.032-0.02010.682-1.358-1.3580.0000.0000.0000.000
41B44GLY00.0330.01812.610-0.942-0.9420.0000.0000.0000.000
42B45GLU-1-0.804-0.88914.58513.54413.5440.0000.0000.0000.000
43B46ALA0-0.024-0.02715.842-1.022-1.0220.0000.0000.0000.000
44B47SER0-0.075-0.04115.896-0.940-0.9400.0000.0000.0000.000
45B48ARG10.8940.94617.863-14.018-14.0180.0000.0000.0000.000
46B49LEU00.009-0.00620.444-0.781-0.7810.0000.0000.0000.000
47B50ALA00.0150.01120.355-0.625-0.6250.0000.0000.0000.000
48B51HIS10.8120.89621.315-13.884-13.8840.0000.0000.0000.000
49B52TYR00.0360.03324.974-0.427-0.4270.0000.0000.0000.000
50B53ASN0-0.056-0.01223.471-0.610-0.6100.0000.0000.0000.000
51B54LYS11.0010.97927.667-8.643-8.6430.0000.0000.0000.000
52B55ARG10.9440.97525.248-10.714-10.7140.0000.0000.0000.000
53B56SER00.0170.03123.6560.3330.3330.0000.0000.0000.000
54B57THR0-0.080-0.04021.3660.2920.2920.0000.0000.0000.000
55B58ILE00.0830.05015.992-0.178-0.1780.0000.0000.0000.000
56B59THR0-0.125-0.08018.721-0.049-0.0490.0000.0000.0000.000
57B60SER00.0440.00119.3510.3100.3100.0000.0000.0000.000
58B61ARG10.9520.98720.357-11.051-11.0510.0000.0000.0000.000
59B62GLU-1-0.775-0.89819.79612.40812.4080.0000.0000.0000.000
60B63ILE0-0.0010.00614.8130.1790.1790.0000.0000.0000.000
61B64GLN00.0390.02718.3320.2640.2640.0000.0000.0000.000
62B65THR0-0.038-0.02021.233-0.328-0.3280.0000.0000.0000.000
63B66ALA00.0410.01617.504-0.124-0.1240.0000.0000.0000.000
64B67VAL0-0.008-0.00817.0410.1910.1910.0000.0000.0000.000
65B68ARG10.9370.96019.173-11.190-11.1900.0000.0000.0000.000
66B69LEU0-0.050-0.01321.098-0.349-0.3490.0000.0000.0000.000
67B70LEU0-0.047-0.01215.7220.1670.1670.0000.0000.0000.000
68B71LEU0-0.036-0.01016.5860.4310.4310.0000.0000.0000.000
69B72PRO00.0420.03220.422-0.517-0.5170.0000.0000.0000.000
70B73GLY00.0330.00323.6640.0800.0800.0000.0000.0000.000
71B74GLU-1-0.834-0.91726.06410.04210.0420.0000.0000.0000.000
72B75LEU00.0260.02119.8260.2180.2180.0000.0000.0000.000
73B76ALA0-0.0070.00721.7990.3030.3030.0000.0000.0000.000
74B77LYS10.8130.88722.848-10.031-10.0310.0000.0000.0000.000
75B78HIS00.0120.01723.501-0.323-0.3230.0000.0000.0000.000
76B79ALA00.0360.01919.2390.1230.1230.0000.0000.0000.000
77B80VAL0-0.036-0.01820.8610.1500.1500.0000.0000.0000.000
78B81SER0-0.0140.00722.967-0.217-0.2170.0000.0000.0000.000
79B82GLU-1-0.833-0.92420.41311.96411.9640.0000.0000.0000.000
80B83GLY0-0.007-0.00819.6610.1670.1670.0000.0000.0000.000
81B84THR0-0.042-0.02920.542-0.121-0.1210.0000.0000.0000.000
82B85LYS10.9140.95923.628-11.544-11.5440.0000.0000.0000.000
83B86ALA00.0000.00819.410-0.209-0.2090.0000.0000.0000.000
84B87VAL0-0.032-0.03220.103-0.071-0.0710.0000.0000.0000.000
85B88THR00.0240.01622.208-0.311-0.3110.0000.0000.0000.000
86B89LYS10.9781.00023.574-11.440-11.4400.0000.0000.0000.000
87B90TYR0-0.012-0.00320.721-0.106-0.1060.0000.0000.0000.000
88B91THR0-0.087-0.06023.322-0.274-0.2740.0000.0000.0000.000
89B92SER0-0.0010.01025.860-0.268-0.2680.0000.0000.0000.000
90B93SER00.0180.00827.028-0.206-0.2060.0000.0000.0000.000
91B94LYS10.8960.95123.809-10.492-10.4920.0000.0000.0000.000
92B95GLN00.0160.02123.3450.4650.4650.0000.0000.0000.000
93B96ARG10.9480.94715.771-14.247-14.2470.0000.0000.0000.000
94B97ALA0-0.012-0.00818.3510.5820.5820.0000.0000.0000.000
95B98GLY0-0.0050.00619.3130.1650.1650.0000.0000.0000.000
96B99LEU0-0.0260.00315.1180.0560.0560.0000.0000.0000.000
97B100GLN00.0250.01614.8590.5760.5760.0000.0000.0000.000
98B101PHE00.0110.0088.4101.3361.3360.0000.0000.0000.000
99B102PRO0-0.028-0.0027.320-1.243-1.2430.0000.0000.0000.000
100B103VAL00.0770.0169.1441.0031.0030.0000.0000.0000.000
101B104GLY0-0.018-0.00411.2830.0240.0240.0000.0000.0000.000
102B105ARG10.9280.9543.525-36.325-36.0620.004-0.097-0.1690.001
103B106ILE00.0740.0527.0190.9390.9390.0000.0000.0000.000
104B107HIS0-0.034-0.0298.1360.2940.2940.0000.0000.0000.000
105B108ARG10.9220.9508.228-22.655-22.6550.0000.0000.0000.000
106B109HIS00.0210.0175.103-0.640-0.6400.0000.0000.0000.000
107B110LEU00.0490.0257.576-0.261-0.2610.0000.0000.0000.000
108B111LYS10.8660.93210.884-18.107-18.1070.0000.0000.0000.000
109B112SER0-0.060-0.0259.036-0.103-0.1030.0000.0000.0000.000
110B113ARG10.9350.9587.071-33.352-33.3520.0000.0000.0000.000
111B114THR0-0.058-0.00412.547-1.120-1.1200.0000.0000.0000.000
112B115THR00.0760.04715.918-0.313-0.3130.0000.0000.0000.000
113B116SER0-0.045-0.03118.898-0.895-0.8950.0000.0000.0000.000
114B117HIS00.0750.03720.2890.7210.7210.0000.0000.0000.000
115B118GLY0-0.0010.02822.094-0.360-0.3600.0000.0000.0000.000
116B119ARG10.9160.94919.610-10.980-10.9800.0000.0000.0000.000
117B120VAL00.0790.04014.116-0.184-0.1840.0000.0000.0000.000
118B121GLY0-0.039-0.02117.365-0.184-0.1840.0000.0000.0000.000
119B122ALA00.036-0.00116.8380.5550.5550.0000.0000.0000.000
120B123THR00.0190.00017.0050.5820.5820.0000.0000.0000.000
121B124ALA00.0660.04815.8290.0250.0250.0000.0000.0000.000
122B125ALA00.0060.00212.5720.6700.6700.0000.0000.0000.000
123B126VAL0-0.052-0.02213.4430.5650.5650.0000.0000.0000.000
124B127TYR00.0440.00716.0840.2120.2120.0000.0000.0000.000
125B128SER00.0230.00411.7160.1890.1890.0000.0000.0000.000
126B129ALA0-0.035-0.01911.7820.7140.7140.0000.0000.0000.000
127B130ALA00.0130.00812.7410.1800.1800.0000.0000.0000.000
128B131ILE00.0020.01414.257-0.185-0.1850.0000.0000.0000.000
129B132LEU00.000-0.0068.3710.1400.1400.0000.0000.0000.000
130B133GLU-1-0.886-0.94112.43315.95215.9520.0000.0000.0000.000
131B134TYR00.0260.01014.611-0.065-0.0650.0000.0000.0000.000
132B135LEU00.0580.02214.115-0.220-0.2200.0000.0000.0000.000
133B136THR0-0.057-0.03312.4380.5860.5860.0000.0000.0000.000
134B137ALA0-0.007-0.01614.732-0.266-0.2660.0000.0000.0000.000
135B138GLU-1-0.871-0.92418.29112.38212.3820.0000.0000.0000.000
136B139VAL0-0.016-0.00116.118-0.298-0.2980.0000.0000.0000.000
137B140LEU0-0.069-0.05815.407-0.347-0.3470.0000.0000.0000.000
138B141GLU-1-0.916-0.94919.23911.29611.2960.0000.0000.0000.000
139B142LEU00.0870.04822.425-0.500-0.5000.0000.0000.0000.000
140B143ALA0-0.031-0.01920.228-0.297-0.2970.0000.0000.0000.000
141B144GLY0-0.046-0.03622.209-0.302-0.3020.0000.0000.0000.000
142B145ASN0-0.0030.00124.021-0.609-0.6090.0000.0000.0000.000
143B146ALA0-0.0090.01325.077-0.372-0.3720.0000.0000.0000.000
144B147SER0-0.111-0.10626.9800.0340.0340.0000.0000.0000.000
145B148LYS10.9550.97130.272-8.588-8.5880.0000.0000.0000.000
146B149ASP-1-0.903-0.93433.6818.0438.0430.0000.0000.0000.000
147B150LEU00.0120.02132.8620.0860.0860.0000.0000.0000.000
148B151LYS11.0281.02928.733-10.115-10.1150.0000.0000.0000.000
149B152VAL0-0.0020.00324.4080.0100.0100.0000.0000.0000.000
150B153LYS10.9780.98026.705-9.596-9.5960.0000.0000.0000.000
151B154ARG10.9330.96220.957-12.851-12.8510.0000.0000.0000.000
152B155ILE00.0610.05118.342-0.204-0.2040.0000.0000.0000.000
153B156THR0-0.045-0.04019.1890.7100.7100.0000.0000.0000.000
154B157PRO00.025-0.01616.584-0.022-0.0220.0000.0000.0000.000
155B158ARG10.9831.00718.489-11.418-11.4180.0000.0000.0000.000
156B159HIS00.0450.02121.3490.2160.2160.0000.0000.0000.000
157B160LEU00.0290.01614.809-0.168-0.1680.0000.0000.0000.000
158B161GLN0-0.0020.00519.033-0.378-0.3780.0000.0000.0000.000
159B162LEU0-0.040-0.02520.894-0.270-0.2700.0000.0000.0000.000
160B163ALA00.0250.02220.508-0.319-0.3190.0000.0000.0000.000
161B164ILE00.0040.00316.419-0.062-0.0620.0000.0000.0000.000
162B165ARG10.9110.94720.828-12.329-12.3290.0000.0000.0000.000
163B166GLY0-0.053-0.02123.525-0.426-0.4260.0000.0000.0000.000
164B167ASP-1-0.820-0.90023.16511.97811.9780.0000.0000.0000.000
165B168GLU-1-0.916-0.96124.06410.63810.6380.0000.0000.0000.000
166B169GLU-1-0.794-0.90823.39911.88611.8860.0000.0000.0000.000
167B170LEU0-0.021-0.01918.3320.8610.8610.0000.0000.0000.000
168B171ASP-1-0.842-0.90219.31514.03414.0340.0000.0000.0000.000
169B172SER0-0.025-0.01720.6510.4800.4800.0000.0000.0000.000
170B173LEU00.0100.00715.8740.4000.4000.0000.0000.0000.000
171B174ILE0-0.026-0.01714.5961.0701.0700.0000.0000.0000.000
172B175LYS10.8330.90316.140-12.241-12.2410.0000.0000.0000.000
173B176ALA00.0030.00618.3320.2040.2040.0000.0000.0000.000
174B177THR0-0.112-0.05711.7670.5330.5330.0000.0000.0000.000
175B178ILE0-0.021-0.00712.3091.2131.2130.0000.0000.0000.000
176B179ALA0-0.050-0.00414.4930.3180.3180.0000.0000.0000.000