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: NN3YQ

Calculation Name: 4IV1-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IV1

Chain ID: B

ChEMBL ID:

UniProt ID: Q6PN23

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2367619.498672
FMO2-HF: Nuclear repulsion 2286409.166622
FMO2-HF: Total energy -81210.33205
FMO2-MP2: Total energy -81449.589338


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:12:ASP)


Summations of interaction energy for fragment #1(B:12:ASP)
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.
-63.828-56.9521.605-3.953-4.5260.03
Interaction energy analysis for fragmet #1(B:12:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.918 / q_NPA : -0.970
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].
3B14ILE0-0.026-0.0092.696-22.484-16.7021.475-3.573-3.6830.030
4B15LEU00.0550.0453.42310.90111.9720.131-0.380-0.8210.000
5B16THR00.0140.0005.649-7.834-7.811-0.0010.000-0.0220.000
6B17THR0-0.0230.0018.5190.1590.1590.0000.0000.0000.000
7B18ARG10.9160.94611.178-19.606-19.6060.0000.0000.0000.000
8B19ASN0-0.0180.00014.201-0.523-0.5230.0000.0000.0000.000
9B20GLY00.0690.04917.639-0.593-0.5930.0000.0000.0000.000
10B21HIS0-0.028-0.02618.9991.2351.2350.0000.0000.0000.000
11B22THR0-0.048-0.03018.823-0.280-0.2800.0000.0000.0000.000
12B23THR00.025-0.00713.5060.0690.0690.0000.0000.0000.000
13B24SER0-0.064-0.03713.191-1.182-1.1820.0000.0000.0000.000
14B25THR00.0400.0158.8310.7880.7880.0000.0000.0000.000
15B26THR0-0.010-0.0018.550-1.746-1.7460.0000.0000.0000.000
16B27GLN00.0530.0137.2945.9845.9840.0000.0000.0000.000
17B28SER00.0060.0097.7160.4110.4110.0000.0000.0000.000
18B29SER0-0.0150.0056.574-4.779-4.7790.0000.0000.0000.000
19B30VAL00.0310.0027.1232.9622.9620.0000.0000.0000.000
20B31GLY00.0390.0347.042-1.371-1.3710.0000.0000.0000.000
21B32VAL0-0.023-0.0087.866-1.696-1.6960.0000.0000.0000.000
22B33THR00.0010.00710.7940.2420.2420.0000.0000.0000.000
23B34TYR00.0060.00412.0530.1600.1600.0000.0000.0000.000
24B35GLY00.009-0.00916.457-0.364-0.3640.0000.0000.0000.000
25B36TYR0-0.004-0.02119.996-0.221-0.2210.0000.0000.0000.000
26B37SER00.0300.01221.076-0.383-0.3830.0000.0000.0000.000
27B38THR0-0.016-0.00516.8860.2960.2960.0000.0000.0000.000
28B39GLN0-0.038-0.01719.0980.2890.2890.0000.0000.0000.000
29B40GLU-1-0.813-0.92221.82212.62612.6260.0000.0000.0000.000
30B41ASP-1-0.841-0.87624.94610.39910.3990.0000.0000.0000.000
31B42HIS00.0200.00728.4930.2430.2430.0000.0000.0000.000
32B43VAL00.0150.01328.227-0.154-0.1540.0000.0000.0000.000
33B44SER0-0.023-0.02031.237-0.091-0.0910.0000.0000.0000.000
34B45GLY0-0.008-0.01234.656-0.039-0.0390.0000.0000.0000.000
35B46PRO00.005-0.02037.163-0.065-0.0650.0000.0000.0000.000
36B47ASN0-0.032-0.01837.421-0.046-0.0460.0000.0000.0000.000
37B48THR00.009-0.01336.960-0.083-0.0830.0000.0000.0000.000
38B49SER0-0.058-0.02439.983-0.104-0.1040.0000.0000.0000.000
39B50GLY00.0040.00738.624-0.135-0.1350.0000.0000.0000.000
40B51LEU0-0.016-0.00439.3970.0090.0090.0000.0000.0000.000
41B52GLU-1-0.839-0.87034.1268.7458.7450.0000.0000.0000.000
42B53THR0-0.015-0.00433.7550.1080.1080.0000.0000.0000.000
43B54ARG10.8310.87722.556-12.574-12.5740.0000.0000.0000.000
44B55VAL00.0050.00529.219-0.126-0.1260.0000.0000.0000.000
45B56VAL00.0480.00824.7640.2730.2730.0000.0000.0000.000
46B57GLN0-0.012-0.00625.1110.4740.4740.0000.0000.0000.000
47B58ALA0-0.006-0.00926.8710.0350.0350.0000.0000.0000.000
48B59GLU-1-0.812-0.85121.98613.27213.2720.0000.0000.0000.000
49B60ARG10.9080.94920.643-12.581-12.5810.0000.0000.0000.000
50B61PHE0-0.006-0.01214.893-0.408-0.4080.0000.0000.0000.000
51B62PHE0-0.055-0.01820.815-0.576-0.5760.0000.0000.0000.000
52B63LYS10.8990.92919.603-15.215-15.2150.0000.0000.0000.000
53B64LYS10.9630.98123.973-11.472-11.4720.0000.0000.0000.000
54B65HIS0-0.0320.00324.7710.4090.4090.0000.0000.0000.000
55B66LEU0-0.062-0.03023.497-0.295-0.2950.0000.0000.0000.000
56B67PHE00.0800.01725.275-0.412-0.4120.0000.0000.0000.000
57B68ASP-1-0.845-0.91727.08611.46511.4650.0000.0000.0000.000
58B69TRP00.0080.00521.263-0.221-0.2210.0000.0000.0000.000
59B70THR0-0.040-0.07127.4220.2820.2820.0000.0000.0000.000
60B71PRO00.011-0.01129.7030.0220.0220.0000.0000.0000.000
61B72ASP-1-0.862-0.88630.8959.3779.3770.0000.0000.0000.000
62B73LYS10.8620.95630.216-10.277-10.2770.0000.0000.0000.000
63B74ALA00.0500.01530.6680.2590.2590.0000.0000.0000.000
64B75PHE00.003-0.00328.1570.1830.1830.0000.0000.0000.000
65B76GLY0-0.0020.00129.301-0.346-0.3460.0000.0000.0000.000
66B77HIS0-0.046-0.01729.819-0.304-0.3040.0000.0000.0000.000
67B78LEU0-0.023-0.01929.1650.4290.4290.0000.0000.0000.000
68B79GLU-1-0.852-0.90828.2029.9229.9220.0000.0000.0000.000
69B80LYS10.8950.93628.277-9.169-9.1690.0000.0000.0000.000
70B81LEU0-0.034-0.02125.910-0.241-0.2410.0000.0000.0000.000
71B82GLU-1-0.885-0.93428.2899.5629.5620.0000.0000.0000.000
72B83LEU0-0.070-0.00824.7610.0600.0600.0000.0000.0000.000
73B84PRO00.017-0.00428.866-0.133-0.1330.0000.0000.0000.000
74B85THR00.0240.00128.437-0.299-0.2990.0000.0000.0000.000
75B86ASP-1-0.926-0.96431.0039.0119.0110.0000.0000.0000.000
76B87HIS0-0.0100.01326.6180.0150.0150.0000.0000.0000.000
77B88LYS10.9550.96831.283-9.215-9.2150.0000.0000.0000.000
78B89GLY00.0230.00630.002-0.049-0.0490.0000.0000.0000.000
79B90VAL00.014-0.00729.130-0.192-0.1920.0000.0000.0000.000
80B91TYR0-0.017-0.04227.902-0.262-0.2620.0000.0000.0000.000
81B92GLY00.0250.01130.036-0.199-0.1990.0000.0000.0000.000
82B93HIS00.0450.02932.853-0.206-0.2060.0000.0000.0000.000
83B94LEU0-0.025-0.00830.679-0.228-0.2280.0000.0000.0000.000
84B95VAL00.008-0.00433.010-0.222-0.2220.0000.0000.0000.000
85B96ASP-1-0.920-0.95735.6168.0048.0040.0000.0000.0000.000
86B97SER0-0.055-0.02437.877-0.281-0.2810.0000.0000.0000.000
87B98PHE0-0.0060.00136.544-0.092-0.0920.0000.0000.0000.000
88B99ALA0-0.030-0.00238.6240.0640.0640.0000.0000.0000.000
89B100TYR0-0.055-0.03037.324-0.017-0.0170.0000.0000.0000.000
90B101MET0-0.016-0.01230.9840.0600.0600.0000.0000.0000.000
91B102ARG10.8130.90627.735-10.747-10.7470.0000.0000.0000.000
92B103ASN00.0020.01925.400-0.518-0.5180.0000.0000.0000.000
93B104GLY00.0880.06423.242-0.270-0.2700.0000.0000.0000.000
94B105TRP0-0.020-0.02121.619-0.191-0.1910.0000.0000.0000.000
95B106ASP-1-0.754-0.83915.33620.97220.9720.0000.0000.0000.000
96B107VAL0-0.004-0.02117.516-0.432-0.4320.0000.0000.0000.000
97B108GLU-1-0.822-0.90212.46324.67224.6720.0000.0000.0000.000
98B109VAL0-0.018-0.00816.279-1.194-1.1940.0000.0000.0000.000
99B110SER0-0.042-0.02516.8400.8840.8840.0000.0000.0000.000
100B111ALA00.033-0.00117.735-1.170-1.1700.0000.0000.0000.000
101B112VAL0-0.006-0.01217.4290.5560.5560.0000.0000.0000.000
102B113GLY00.0520.02719.281-0.915-0.9150.0000.0000.0000.000
103B114ASN0-0.034-0.02318.8050.4080.4080.0000.0000.0000.000
104B115GLN00.0540.00816.488-0.361-0.3610.0000.0000.0000.000
105B116PHE0-0.047-0.02218.428-0.076-0.0760.0000.0000.0000.000
106B117ASN0-0.028-0.00521.368-0.286-0.2860.0000.0000.0000.000
107B118GLY00.0300.01321.3700.6200.6200.0000.0000.0000.000
108B119GLY00.0450.02422.407-0.308-0.3080.0000.0000.0000.000
109B120CYS0-0.114-0.07220.3970.9700.9700.0000.0000.0000.000
110B121LEU00.0480.03820.312-0.719-0.7190.0000.0000.0000.000
111B122LEU00.0120.00919.9270.8070.8070.0000.0000.0000.000
112B123VAL0-0.009-0.01018.782-0.487-0.4870.0000.0000.0000.000
113B124ALA00.0410.00220.0570.5230.5230.0000.0000.0000.000
114B125MET0-0.0280.01321.081-0.265-0.2650.0000.0000.0000.000
115B126VAL0-0.003-0.01823.522-0.019-0.0190.0000.0000.0000.000
116B127PRO0-0.0030.00526.675-0.085-0.0850.0000.0000.0000.000
117B128GLU-1-0.841-0.91029.1999.0759.0750.0000.0000.0000.000
118B129TRP0-0.011-0.00430.4630.0640.0640.0000.0000.0000.000
119B130LYS10.8920.93632.864-8.855-8.8550.0000.0000.0000.000
120B131GLU-1-0.928-0.96234.4759.0479.0470.0000.0000.0000.000
121B132PHE0-0.019-0.00130.592-0.171-0.1710.0000.0000.0000.000
122B133THR00.006-0.00834.950-0.081-0.0810.0000.0000.0000.000
123B134PRO00.033-0.01435.0290.2450.2450.0000.0000.0000.000
124B135ARG10.9820.98034.238-7.741-7.7410.0000.0000.0000.000
125B136GLU-1-0.777-0.87933.3558.8208.8200.0000.0000.0000.000
126B137LYS10.8950.95230.401-9.124-9.1240.0000.0000.0000.000
127B138TYR0-0.046-0.02328.8490.3030.3030.0000.0000.0000.000
128B139GLN0-0.027-0.01728.0860.2280.2280.0000.0000.0000.000
129B140LEU00.0300.01926.1460.0960.0960.0000.0000.0000.000
130B141THR0-0.021-0.00821.9110.1320.1320.0000.0000.0000.000
131B142LEU0-0.0080.00723.0390.3380.3380.0000.0000.0000.000
132B143PHE0-0.034-0.00324.423-0.026-0.0260.0000.0000.0000.000
133B144PRO00.0120.01419.9500.5560.5560.0000.0000.0000.000
134B145HIS0-0.040-0.03418.9320.0440.0440.0000.0000.0000.000
135B146GLN00.0120.00511.3820.8520.8520.0000.0000.0000.000
136B147PHE00.0400.01815.452-1.003-1.0030.0000.0000.0000.000
137B148ILE0-0.0190.00615.1961.2881.2880.0000.0000.0000.000
138B149SER0-0.007-0.01015.771-1.168-1.1680.0000.0000.0000.000
139B150PRO00.0380.03115.8301.2191.2190.0000.0000.0000.000
140B151ARG10.9540.98915.720-15.866-15.8660.0000.0000.0000.000
141B152THR0-0.057-0.03310.8420.5650.5650.0000.0000.0000.000
142B153ASN0-0.022-0.02911.1561.7001.7000.0000.0000.0000.000
143B154MET00.0220.03512.663-1.990-1.9900.0000.0000.0000.000
144B155THR0-0.005-0.00512.097-0.955-0.9550.0000.0000.0000.000
145B156ALA00.0060.02612.9721.0671.0670.0000.0000.0000.000
146B157HIS10.7990.85111.161-24.428-24.4280.0000.0000.0000.000
147B158ILE0-0.0160.00913.7440.5080.5080.0000.0000.0000.000
148B159VAL0-0.0090.00414.594-0.267-0.2670.0000.0000.0000.000
149B160VAL0-0.028-0.00917.395-0.128-0.1280.0000.0000.0000.000
150B161PRO00.0330.03320.9720.0740.0740.0000.0000.0000.000
151B162TYR0-0.021-0.02823.519-0.184-0.1840.0000.0000.0000.000
152B163LEU0-0.024-0.01126.9930.0270.0270.0000.0000.0000.000
153B164GLY00.0570.01629.609-0.075-0.0750.0000.0000.0000.000
154B165VAL0-0.037-0.01633.175-0.026-0.0260.0000.0000.0000.000
155B166ASN0-0.0040.01336.133-0.273-0.2730.0000.0000.0000.000
156B167ARG10.9760.99733.776-8.569-8.5690.0000.0000.0000.000
157B168TYR0-0.016-0.02933.2580.3070.3070.0000.0000.0000.000
158B169ASP-1-0.742-0.84734.0318.7708.7700.0000.0000.0000.000
159B170GLN00.0220.00535.922-0.100-0.1000.0000.0000.0000.000
160B171TYR00.043-0.00529.559-0.184-0.1840.0000.0000.0000.000
161B172LYS10.7990.89635.593-7.962-7.9620.0000.0000.0000.000
162B173LYS10.8830.93638.565-7.553-7.5530.0000.0000.0000.000
163B174HIS10.7480.83034.078-9.169-9.1690.0000.0000.0000.000
164B175LYS10.9210.96732.317-9.195-9.1950.0000.0000.0000.000
165B176PRO00.0320.03129.9060.0110.0110.0000.0000.0000.000
166B177TRP00.0290.01224.4150.2010.2010.0000.0000.0000.000
167B178THR0-0.019-0.00827.846-0.289-0.2890.0000.0000.0000.000
168B179LEU00.0030.00721.9530.3030.3030.0000.0000.0000.000
169B180VAL0-0.007-0.01124.653-0.495-0.4950.0000.0000.0000.000
170B181VAL0-0.013-0.00822.8720.6990.6990.0000.0000.0000.000
171B182MET0-0.0100.00524.470-0.680-0.6800.0000.0000.0000.000
172B183VAL0-0.0120.00624.6790.5910.5910.0000.0000.0000.000
173B184VAL0-0.035-0.01222.857-0.413-0.4130.0000.0000.0000.000
174B185SER00.003-0.01824.333-0.547-0.5470.0000.0000.0000.000
175B186PRO00.0360.01125.3360.4690.4690.0000.0000.0000.000
176B187LEU0-0.0170.01224.2210.2520.2520.0000.0000.0000.000
177B188THR00.0120.00425.619-0.310-0.3100.0000.0000.0000.000
178B189THR0-0.015-0.01826.1280.4090.4090.0000.0000.0000.000
179B190ASN0-0.020-0.00825.8970.1800.1800.0000.0000.0000.000
180B191THR00.0330.00028.8790.0910.0910.0000.0000.0000.000
181B192VAL00.0380.02125.173-0.065-0.0650.0000.0000.0000.000
182B193SER0-0.0260.00924.2970.3660.3660.0000.0000.0000.000
183B194ALA00.0230.03023.827-0.369-0.3690.0000.0000.0000.000
184B195GLY00.0220.00525.663-0.138-0.1380.0000.0000.0000.000
185B196GLN0-0.027-0.02727.334-0.158-0.1580.0000.0000.0000.000
186B197ILE0-0.0150.01321.2350.3000.3000.0000.0000.0000.000
187B198LYS10.9050.97224.620-11.416-11.4160.0000.0000.0000.000
188B199VAL0-0.0070.00421.8630.7320.7320.0000.0000.0000.000
189B200TYR00.000-0.00121.432-0.825-0.8250.0000.0000.0000.000
190B201ALA00.0360.01720.6030.7580.7580.0000.0000.0000.000
191B202ASN0-0.0080.00716.340-1.734-1.7340.0000.0000.0000.000
192B203ILE00.0290.00418.5680.7370.7370.0000.0000.0000.000
193B204ALA00.0090.01618.941-0.433-0.4330.0000.0000.0000.000
194B205PRO0-0.0250.00920.8610.1840.1840.0000.0000.0000.000
195B206THR00.013-0.00619.1920.0980.0980.0000.0000.0000.000
196B207HIS0-0.015-0.01520.471-0.371-0.3710.0000.0000.0000.000
197B208VAL0-0.007-0.00124.647-0.378-0.3780.0000.0000.0000.000
198B209HIS0-0.007-0.00927.275-0.105-0.1050.0000.0000.0000.000
199B210VAL0-0.020-0.00230.894-0.001-0.0010.0000.0000.0000.000
200B211ALA00.0610.01234.315-0.036-0.0360.0000.0000.0000.000
201B212GLY00.0140.00937.865-0.012-0.0120.0000.0000.0000.000
202B213GLU-1-0.909-0.94340.9507.7527.7520.0000.0000.0000.000
203B214LEU0-0.048-0.02541.464-0.218-0.2180.0000.0000.0000.000
204B215PRO0-0.0200.00043.9940.0170.0170.0000.0000.0000.000
205B216SER00.014-0.00445.6200.1180.1180.0000.0000.0000.000
206B217LYS10.9100.93542.252-7.589-7.5890.0000.0000.0000.000
207B218GLU-1-0.950-0.94747.8956.4726.4720.0000.0000.0000.000